Deciphering the intrinsically disordered characteristics of the FG-Nups through the lens of polymer physics
Perspective article connecting polymer physics and intrinsically disordered FG-Nups in the nuclear pore complex.
Publications
Research outputs from the Molecular Cell Biomechanics Laboratory. Browse by type or search the full archive.
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SIMBA-GNN: mechanistic graph learning for microbiome prediction
Predicting how gut microbial communities assemble and change requires models that capture the underlying mechanisms driving interspecies ...
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Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory
The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transp...
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Identification of acrylamide-based covalent inhibitors of SARS-CoV-2 (SCoV-2) Nsp15 using high-throughput screening and machine learning
Non-structural protein 15 (Nsp15) is a SARS-CoV-2 (SCoV-2) endoribonuclease and is a promising target for drug development because of its...
Browse
2025
SIMBA-GNN: mechanistic graph learning for microbiome prediction
Authors: Javad Aminian-Dehkordi, Mohammad S. Parsa, Andrew Dickson, Mohammad R. K. Mofrad
Predicting how gut microbial communities assemble and change requires models that capture the underlying mechanisms driving interspecies interactions, not just taxonomic correlations. We present SIMBA, a simulation-augmented graph neural...
Keywords: Pairwise comparison, Microbiome, Graph, Metagenomics, Human microbiome, ENCODE, Human Microbiome Project
Semi-supervised Retrieval of Functional Residues Through the Integration of Protein Language Models and Gene Ontology Data
Authors: Andrew Dickson, Salma Mouline, Ali Tamadon, Mohammad R. K. Mofrad
Abstract Motivation Experimental studies of protein function often focus on mechanistic descriptions, characterizing how specific sites and residues contribute to activity. Abstractions such as domains and active sites enable quantitativ...
Keywords: Interpretability, Annotation, Function (biology), Gene ontology, Benchmark (surveying), Protein function prediction, Protein sequencing, Protein function, Generative grammar
Systems biology and microbiome innovations for personalized diabetic retinopathy management
Authors: Javad Aminian-Dehkordi, Fateme Montazeri, Ali Tamadon, Mohammad R. K. Mofrad
Keywords: Systems biology, Microbiome, Gut microbiome, Personalized medicine, Diabetic retinopathy, Modelling biological systems, Synthetic biology
Expanding the HP1a-binding consensus and molecular grammar for heterochromatin assembly
Authors: Serafin U. Colmenares, Shingo Tsukamoto, Collin Hickmann, Lucy D. Brennan, Mohammad Khavani, Mohammad R. K. Mofrad, Gary H. Karpen
The recruitment of Heterochromatin Protein 1 (HP1) partners is essential for heterochromatin assembly and function, yet our knowledge regarding their organization in heterochromatin remains limited. Here, we show that interactors engage ...
Keywords: Heterochromatin, Heterochromatin protein 1, Euchromatin, Grammar, Scaffold protein, Protein family
Computational drug design in the artificial intelligence era: A systematic review of molecular representations, generative architectures, and performance assessment
Authors: Karim Abbasi, Parvin Razzaghi, Ali Gharizadeh, Amin Ghareyazi, Abbas Dehnad, Hamid R. Rabiee, Mohammad R. K. Mofrad
Generative drug design has emerged as a transformative approach in pharmaceutical research, leveraging deep learning models to create novel molecules with targeted properties. This systematic review analyzes the current landscape of comp...
Keywords: Generative grammar, Generative Design, Categorization, Representation (politics), Field (mathematics), Transformative learning, Generative model, Benchmark (surveying)
Demographic drivers of gut microbiome diversity
Authors: Hannaneh Kabir, Matilda Holtz, Justine Choueiri, Mohammad R. K. Mofrad
Keywords: Microbiome, Biology, Diversity (politics), Phylogenetic diversity, Gut microbiome, Gut flora, Metagenomics, Disease, Ecology, Evolutionary biology, Bioinformatics, Immunology, Phylogenetics, Medicine, Genetics, Gene
Emerging mechanomedicines informed by mechanotransduction along the integrin–cytoskeleton–nucleus axis
Authors: Yuka Yokoyama, Nya Domkam, Hannaneh Kabir, Abdullah Mansour, Shingo Tsukamoto, Ghafar Yerima, Taiji ADACHI, Mohammad R. K. Mofrad
Mechanical forces are fundamental to the formation of normal biological tissues and the maintenance of physiological health. These forces are transmitted from the extracellular environment to the cell interior through cell-cell and cell-...
Keywords: Mechanotransduction, Integrin, Cytoskeleton, Cell biology, Nucleus, Chemistry, Biology, Cell, Biochemistry
Block ratio optimized cationic polyacrylamides for enhanced nitrate rejection under applied potential
Authors: Hossein Vahid, Arsalan Hashemi, Mohammad Khavani, Abhinav Sharma, Mohammad R. K. Mofrad, Tapio Ala-Nissilä
Nitrate contamination in water sources is a growing environmental concern, threatening both human health and ecosystems. However, its combination with sodium forms NaNO 3 , a compound essential for various industrial applications. The in...
Keywords: Cationic polymerization, Block (permutation group theory), Nitrate, Chemistry, Pulp and paper industry, Chromatography, Chemical engineering, Polymer chemistry, Organic chemistry, Mathematics, Engineering
Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory
Authors: Atsushi Matsuda, Mohammad R. K. Mofrad
The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent studies have highlighted the NPC...
Keywords: Nuclear pore, Brownian dynamics, Nuclear transport, Nucleoporin, Scaling, Chemical physics, Molecular dynamics, Statistical physics, Biophysics, Materials science, Physics, Chemistry, Biological system, Cytoplasm, Brownian motion, Cell nucleus, Computational chemistry, Biology, Mathematics
Meta Biome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities
Authors: Javad Aminian-Dehkordi, Andrew Dickson, Amin Valiei, Mohammad R. K. Mofrad
Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies ...
Keywords: In silico, Biome, Computer science, Biochemical engineering, Multiscale modeling, Systems biology, Representation (politics), Computational biology, Ecology, Biology, Biological system, Ecosystem, Bioinformatics, Engineering
Unravelling the Glycan Code: Molecular Dynamics and Quantum Chemistry Reveal How O‐Glycan Functional Groups Govern OgpA Selectivity in Mucin Degradation by Akkermansia muciniphila
Authors: Mohammad Khavani, Aliyeh Mehranfar, Mohammad R. K. Mofrad
Mucins, heavily O-glycosylated glycoproteins, are a key component of mucus, and certain gut microbiota, including Akkermansia muciniphila, can utilise mucin glycans as a carbon source. Akkermansia muciniphila produces the O-glycopeptidas...
Keywords: Chemistry, Akkermansia muciniphila, Glycan, Mucin, Peptide, Biochemistry, Threonine, Stereochemistry, Enzyme, Serine, Glycoprotein, Gut flora
Multiscale Kinematic Growth Coupled With Mechanosensitive Systems Biology in Open-Source Software
Authors: Steven A. LaBelle, Mohammadreza Soltany Sadrabadi, Seungik Baek, Mohammad R. K. Mofrad, Jeffrey A. Weiss, Amirhossein Arzani
Multiscale coupling between cell-scale biology and tissue-scale mechanics is a promising approach for modeling disease growth. In such models, tissue-level growth and remodeling (G&R) are driven by cell-level signaling pathways and syste...
Keywords: Multiscale modeling, Systems biology, Ode, Kinematics, Ordinary differential equation, Biological system, Computer science, Coupling (piping), Differential equation, Physics, Mathematics, Applied mathematics, Biology, Bioinformatics, Classical mechanics, Mathematical analysis, Engineering, Mechanical engineering
Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function
Authors: Shingo Tsukamoto, Mohammad R. K. Mofrad
Chromatin loop formation plays a crucial role in 3D genome interactions, with misfolding potentially leading to irregular gene expression and various diseases. While experimental tools such as Hi-C have advanced our understanding of geno...
Keywords: Chromatin, Chromosome conformation capture, Computational biology, Genome, Bridging (networking), Scaffold/matrix attachment region, Folding (DSP implementation), Biology, Function (biology), Computer science, Chromatin remodeling, Genetics, Gene, Gene expression, Engineering
Correction: Identification of acrylamide-based covalent inhibitors of SARS-CoV-2 (SCoV-2) Nsp15 using high-throughput screening and machine learning
Authors: Teena Bajaj, Babak Mosavati, Lydia H. Zhang, Mohammad S. Parsa, Huanchen Wang, Evan Kerek, Xueying Liang, Seyed Amir Tabatabaei Dakhili, Eddie Wehri, Silin Guo, Rushil Desai, Lauren M. Orr, Mohammad R. K. Mofrad, Julia Schaletzky, John R. Ussher, Xufang Deng, Robin E. Stanley, Basil P. Hubbard, Daniel K. Nomura, Niren Murthy
[This corrects the article DOI: 10.1039/D4RA06955B.].
Keywords: Identification (biology), Acrylamide, High-throughput screening, Chemistry, Throughput, Computational biology, Covalent bond, Combinatorial chemistry, Computer science, Biochemistry, Biology, Organic chemistry
Identification of acrylamide-based covalent inhibitors of SARS-CoV-2 (SCoV-2) Nsp15 using high-throughput screening and machine learning
Authors: Teena Bajaj, Babak Mosavati, Lydia H. Zhang, Mohammad S. Parsa, Huanchen Wang, Evan Kerek, Xueying Liang, Seyed Amir Tabatabaei Dakhili, Eddie Wehri, Silin Guo, R Desai, Lauren M. Orr, Mohammad R. K. Mofrad, Julia Schaletzky, John R. Ussher, Xufang Deng, Robin E. Stanley, Basil P. Hubbard, Daniel K. Nomura, Niren Murthy
Non-structural protein 15 (Nsp15) is a SARS-CoV-2 (SCoV-2) endoribonuclease and is a promising target for drug development because of its essential role in evading the host immune system. However, developing inhibitors against Nsp15 has ...
Keywords: High-throughput screening, Identification (biology), Acrylamide, Computational biology, Chemistry, Drug discovery, Combinatorial chemistry, Computer science, Biochemistry, Biology, Organic chemistry
2024
Nanoscale in silico and in vitro modeling of lipid bilayers for curvature induction and sensing
Authors: Ghafar Yerima, Ching‐Ting Tsai, Chih‐Hao Lu, Bianxiao Cui, Zeinab Jahed, Mohammad R. K. Mofrad
Cellular functions like motility, differentiation, or protein trafficking often require a change in membrane curvature and protein distribution. Defects associated with curvature sensitive proteins can cause several diseases. However, th...
Keywords: In silico, Nanoscopic scale, Curvature, In vitro, Membrane curvature, Lipid bilayer, Nanotechnology, Biological system, Materials science, Biophysics, Cell biology, Chemistry, Computational biology, Biology, Membrane, Biochemistry, Mathematics, Gene, Geometry
Small molecule modulation of protein corona for deep plasma proteome profiling
Authors: Ali Akbar Ashkarran, Hassan Gharibi, Seyed Amirhossein Sadeghi, Seyed Majed Modaresi, Qianyi Wang, Teng-Jui Lin, Ghafar Yerima, Ali Tamadon, Maryam Sayadi, Maryam Jafari, Zijin Lin, Danilo Ritz, David Kakhniashvili, Avirup Guha, Mohammad R. K. Mofrad, Liangliang Sun, Markita P. Landry, Amir Ata Saei, Morteza Mahmoudi
Keywords: Proteome, Plasma, Chemistry, Computational biology, Small molecule, Biophysics, Cell biology, Biology, Biochemistry, Physics
Regulating transport efficiency through the nuclear pore complex: The role of binding affinity with FG-Nups
Authors: Atsushi Matsuda, Mohammad R. K. Mofrad
Macromolecules are transported through the nuclear pore complex (NPC) via a series of transient binding and unbinding events with FG-Nups, which are intrinsically disordered proteins anchored to the pore's inner wall. Prior studies sugge...
Keywords: Nuclear pore, Nuclear transport, Receptor–ligand kinetics, Molecular dynamics, Biophysics, Biology, Kinetics, Plasma protein binding, Brownian dynamics, Intrinsically disordered proteins, Diffusion, Nucleoporin, Binding site, Transport protein, Nucleus, Brownian motion, Receptor, Cell biology, Physics, Biochemistry, Cell nucleus, Chemistry, Thermodynamics, Computational chemistry
Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche
Authors: Amin Valiei, Andrew Dickson, Javad Aminian-Dehkordi, Mohammad R. K. Mofrad
Keywords: Biology, Commensalism, Mutualism (biology), Niche, Ecosystem, Ecology, Microbiome, Microbial ecology, Bacteria, Niche differentiation, Microbial population biology, Food web, Bacterial growth, Biofilm, Bioinformatics
Mechanistic understanding of enhancing bioactivity via bio-ionic liquid functionalization of biomaterials
Authors: Aihik Banerjee, Mohammad Khavani, Kevin Dalsania, Prince David Okoro, Mohammad R. K. Mofrad, Iman Noshadi
• The role of bio-ionic liquids (BILs) as cell adhesion molecules for enhancing the bioactivity of bio-inert biomaterials has been investigated. • A bio-inert polyethylene glycol diacrylate (PEGDA) was bio-activated with an acrylated cho...
Keywords: Surface modification, Ionic liquid, Nanotechnology, Materials science, Chemistry, Chemical engineering, Engineering, Organic chemistry
Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities
Authors: Amin Valiei, Andrew Dickson, Javad Aminian-Dehkordi, Mohammad R. K. Mofrad
Keywords: Commensalism, Mutualism (biology), Biology, Microbiome, Biofilm, Competition (biology), In silico, Ecology, Microbiology, Bacteria, Genetics, Gene
Deciphering the intrinsically disordered characteristics of the FG-Nups through the lens of polymer physics
Matsuda A, Mansour A, Mofrad MRK. Deciphering the Intrinsically Disordered Characteristics of the FG-Nups through the Lens of Polymer Physics. Nucleus. 2024;15(1):2399247. doi:10.1080/19491034.2024.2399247
Authors: Atsushi Matsuda, Abdullah Mansour, Mohammad R. K. Mofrad
Perspective article connecting polymer physics and intrinsically disordered FG-Nups in the nuclear pore complex.
Keywords: Nucleoporin, Nuclear pore, Intrinsically disordered proteins, Nuclear transport, Biophysics, Polymer physics, Structural biology, Nucleus, Nanotechnology, Polymer, Physics, Materials science, Biology, Cell nucleus, Cell biology, Nuclear magnetic resonance
Fine-tuning protein embeddings for functional similarity evaluation
Authors: Andrew Dickson, Mohammad R. K. Mofrad
github.com/mofradlab/go_metric.
Keywords: Interpretability, Computer science, Similarity (geometry), Cluster analysis, Embedding, Annotation, Metric (unit), Artificial intelligence, Protein sequencing, Sequence (biology), Machine learning, Pattern recognition (psychology), Data mining, Peptide sequence, Biology, Gene, Genetics
HGTDR: Advancing drug repurposing with heterogeneous graph transformers
Authors: Ali Gharizadeh, Karim Abbasi, Amin Ghareyazi, Mohammad R. K. Mofrad, Hamid R. Rabiee
The source code and data are available at https://github.com/bcb-sut/HGTDR and http://git.dml.ir/BCB/HGTDR.
Keywords: Repurposing, Computer science, Drug repositioning, Transformer, Graph, Drug, Pharmacology, Theoretical computer science, Medicine, Engineering, Electrical engineering, Voltage
An in-silico study on the mechanical behavior of colorectal cancer cell lines in the micropipette aspiration process
Authors: Ibrahim Ghoytasi, Omid Bavi, Mohammad R. K. Mofrad, R. Naghdabadi
Keywords: In silico, Colorectal cancer, Process (computing), Pipette, Cancer, Medicine, Computer science, Biology, Chemistry, Internal medicine, Genetics
Integrin mechanosensing relies on a pivot-clip mechanism to reinforce cell adhesion
Authors: Andre R. Montes, Anahi Barroso, Wei Wang, Grace D. O’Connell, Adrián Buganza Tepole, Mohammad R. K. Mofrad
Keywords: Mechanism (biology), Integrin, Cell biology, Cell adhesion, Adhesion, Cell adhesion molecule, Chemistry, Cell, Biology, Physics, Biochemistry
Editorial overview: Biomechanics and mechanobiology: Mechano-genomics
Authors: Deborah Leckband, Mohammad R. K. Mofrad
Keywords: Mechanobiology, Biomechanics, Computer science, Medicine, Physiology, Anatomy
Deep Learning for Perfusion Cerebral Blood Flow (CBF) and Volume (CBV) Predictions and Diagnostics
Authors: Salmonn Talebi, Siyu Gai, Aaron Sossin, Vivian Zhu, Elizabeth Tong, Mohammad R. K. Mofrad
Dynamic susceptibility contrast magnetic resonance perfusion (DSC-MRP) is a non-invasive imaging technique for hemodynamic measurements. Various perfusion parameters, such as cerebral blood volume (CBV) and cerebral blood flow (CBF), can...
Keywords: Cerebral blood flow, Perfusion, Cerebral blood volume, Cardiology, Volume (thermodynamics), Medicine, Blood flow, Blood volume, Anesthesia, Physics, Thermodynamics
Exploring the performance and explainability of fine-tuned BERT models for neuroradiology protocol assignment
Authors: Salmonn Talebi, Elizabeth Tong, Anna Li, Ghiam Yamin, Greg Zaharchuk, Mohammad R. K. Mofrad
Keywords: Computer science, Protocol (science), Artificial intelligence, Context (archaeology), Encoder, Process (computing), Machine learning, Task (project management), Natural language processing, Medicine
Exploring sialic acid derivative inhibitors targeting influenza virus hemagglutinin (HA) protein
Authors: S. Erfan Ghazimirsaeed, Mohammad Khavani, Mohammad R. K. Mofrad
Keywords: Sialic acid, Neuraminidase, Hemagglutinin (influenza), Virology, Pandemic, Influenza A virus, Virus, Biology, Chemistry, Biochemistry, Medicine, Coronavirus disease 2019 (COVID-19), Infectious disease (medical specialty)
Force-induced salt bridge formation enhances HP1 homodimer interaction, implying augmented chromatin crosslinking and phase separation
Authors: Shingo Tsukamoto, Mohammad Khavani, Nya Domkam, Mohammad R. K. Mofrad
Keywords: Heterochromatin, Salt bridge, Biophysics, Chromatin, Heterochromatin protein 1, Chemistry, Molecular mechanics, Molecular dynamics, Helix (gastropod), Static electricity, Chemical physics, Physics, Biology, Biochemistry, DNA, Computational chemistry
Antimicrobial peptide interactions with bacterial cell membranes
Authors: Mohammad Khavani, Aliyeh Mehranfar, Mohammad R. K. Mofrad
Antimicrobial peptides (AMPs) are potential alternatives for common antibiotics because of their greater activity and efficiency against a broad range of viruses, bacteria, fungi, and parasites. In this project, two antimicrobial peptide...
Keywords: Antimicrobial, Peptide, Antimicrobial peptides, Membrane, Chemistry, Bacterial cell structure, Bacteria, Biology, Biochemistry, Microbiology, Genetics
Enhanced HP1α homodimer interaction via force-induced salt bridge formation: implications for chromatin crosslinking and phase separation
Authors: Shingo Tsukamoto, Mohammad Khavani, Nya Domkam, Mohammad R. K. Mofrad
Unlocking chromatin dyanamics: force-driven salt bridges may spearhead compaction and phase transition.
Keywords: Salt bridge, Chromatin, Bridge (graph theory), Biophysics, Chemistry, Phase (matter), Salt (chemistry), Heterochromatin protein 1, Cell biology, Materials science, Heterochromatin, Biology, DNA, Biochemistry, Anatomy
2023
Force transmission and SUN-KASH higher-order assembly in the LINC complex models
Authors: Ghafar Yerima, Nya Domkam, Jessica Ornowski, Zeinab Jahed, Mohammad R. K. Mofrad
Keywords: Order (exchange), Transmission (telecommunications), Physics, Telecommunications, Computer science, Business
Multiscale computational framework to investigate integrin mechanosensing and cell adhesion
Authors: Andre R. Montes, Gabriela Gutiérrez, Adrián Buganza Tepole, Mohammad R. K. Mofrad
Integrin mechanosensing plays an instrumental role in cell behavior, phenotype, and fate by transmitting mechanical signals that trigger downstream molecular and cellular changes. For instance, force transfer along key amino acid residue...
Keywords: Integrin, Cell adhesion, Fibronectin, Biophysics, Molecular dynamics, Adhesion, Chemistry, Cell adhesion molecule, Molecular mechanics, Cell, Cell biology, Nanotechnology, Materials science, Biochemistry, Biology
On the interactions of peptides with gold nanoparticles: effects of sequence and size
Authors: Mohammad Khavani, Aliyeh Mehranfar, Mohammad R. K. Mofrad
Peptide-based self-assembly and synthesis techniques have emerged as a viable approach to designing active and stable inorganic nanostructures in aqueous media. In the present study, we use all-atom molecular dynamic (MD) simulations to ...
Keywords: Colloidal gold, Peptide, Nanoparticle, van der Waals force, Chemistry, Amino acid, Molecular dynamics, Peptide sequence, Nanotechnology, Metal, Combinatorial chemistry, Crystallography, Molecule, Materials science, Computational chemistry, Organic chemistry, Biochemistry
Adsorption Process of Various Antimicrobial Peptides on Different Surfaces of Cellulose
Authors: Aliyeh Mehranfar, Mohammad Khavani, Mohammad R. K. Mofrad
Current antimicrobial challenges in hospitals, pharmaceutical production units, and food packaging have motivated the development of antimicrobial agents, among them the antimicrobial compounds based on cellulose and peptides. Herein, we...
Keywords: Magainin, Cellulose, Adsorption, Antimicrobial peptides, van der Waals force, Peptide, Bacterial cellulose, Chemistry, Molecular dynamics, Antimicrobial, Combinatorial chemistry, Hydrogen bond, Organic chemistry, Chemical engineering, Molecule, Stereochemistry, Computational chemistry, Biochemistry
Gut-on-a-chip models for dissecting the gut microbiology and physiology
Authors: Amin Valiei, Javad Aminian-Dehkordi, Mohammad R. K. Mofrad
Microfluidic technologies have been extensively investigated in recent years for developing organ-on-a-chip-devices as robust in vitro models aiming to recapitulate organ 3D topography and its physicochemical cues. Among these attempts, ...
Keywords: Gut microbiome, Gut flora, Organ-on-a-chip, Microbiome, Biology, Model organism, Human physiology, Model system, Computational biology, Neuroscience, Cell biology, Bioinformatics, Microfluidics, Immunology, Nanotechnology, Genetics
Smartphone-assisted lab-in-a-tube device using gold nanocluster-based aptasensor for detection of MUC1-overexpressed tumor cells
Authors: Alireza Sanati, Yasaman Esmaeili, Mohammad Khavani, Elham Bidram, Azadeh Rahimi, Arezou Dabiri, Mohammad Rafienia, Nafise Arbab Jolfaie, Mohammad R. K. Mofrad, Shaghayegh Haghjooy Javanmard, Laleh Shariati, Ali Zarrabi
Keywords: Aptamer, Biosensor, Detection limit, Chemistry, Nanoclusters, Nanotechnology, Circulating tumor cell, MUC1, Graphene, Biomedical engineering, Chromatography, Materials science, Molecular biology, Mucin, Cancer, Biochemistry
On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study
Authors: Mohammad Khavani, Aliyeh Mehranfar, Mohammad R. K. Mofrad
The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research ar...
Keywords: Platinum, Metal, Chemistry, Molecular dynamics, Crystallography, Biophysics, Nanotechnology, Materials science, Biochemistry, Computational chemistry, Biology, Organic chemistry
GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations
Authors: Andrew Dickson, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad
Supplementary data are available at Bioinformatics online.
Keywords: Benchmarking, Computer science, Annotation, Preprocessor, Code (set theory), Source code, Interface (matter), Data mining, Data pre-processing, Class (philosophy), Information retrieval, Machine learning, Artificial intelligence, Programming language
Membrane curvature sensed and induced by formin binding Protein 17
Authors: Abdel-Ghafar Yerima, Zeinab Jahed, Mohammad R. K. Mofrad
Keywords: Membrane curvature, Lipid bilayer, Curvature, Biophysics, Membrane protein, Context (archaeology), Elasticity of cell membranes, Membrane, Amphiphysin, Molecular dynamics, Bilayer, Chemistry, Cell biology, Biology, Integral membrane protein, Biochemistry, Receptor, Geometry, Computational chemistry
Spatial dimension and binding kinetics between FG-repeats characterize the free/bound diffusion of molecules inside the nuclear pore complex
Authors: Atsushi Matsuda, Mohammad R. K. Mofrad
Keywords: Diffusion, Kinetics, Dimension (graph theory), Receptor–ligand kinetics, Molecule, Chemistry, Biophysics, Nuclear pore, Chemical physics, Crystallography, Physics, Thermodynamics, Biology, Mathematics, Biochemistry, Classical mechanics, Combinatorics
On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation
Authors: Mohammad Khavani, Aliyeh Mehranfar, Mohammad R. K. Mofrad
Mumps virus is an infectious pathogen causing major health problems for humans such as encephalitis, orchitis, and parotitis. Therefore, designing an inhibitor for this virus is of great medical and public health importance. With this go...
Keywords: Sialic acid, Hydrogen bond, Mumps virus, Neuraminidase, Chemistry, Stereochemistry, Computational chemistry, Virus, Virology, Biology, Molecule, Biochemistry, Organic chemistry
A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication
Authors: Hesong Han, Albert Vallejo Gracia, Joachim Justad Røise, Lydia Boike, Kristoffer E. Leon, Ursula Schulze‐Gahmen, Michael R. Stentzel, Teena Bajaj, Dake Chen, I-Che Li, Maomao He, Kamyar Behrouzi, Zahra Khodabakhshi, Daniel K. Nomura, Mohammad R. K. Mofrad, G. Renuka Kumar, Mélanie Ott, Niren Murthy
Covalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 have great potential as antivirals, but their non-specific reactivity with thiols has limited their development. In this report, we performed an 8000 molecule electr...
Keywords: Papain, Covalent bond, Chemistry, Electrophile, Cysteine, Protease, IC50, Amide, Biochemistry, Reactivity (psychology), Viral replication, Small molecule, Stereochemistry, Enzyme, In vitro, Virology, Virus, Biology, Organic chemistry
Mercapto-pyrimidines are reversible covalent inhibitors of the papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication
Authors: Teena Bajaj, Eddie Wehri, Rahul K. Suryawanshi, Elizabeth A. King, Kundansingh A. Pardeshi, Kamyar Behrouzi, Zahra Khodabakhshi, Ursula Schulze‐Gahmen, G. Renuka Kumar, Mohammad R. K. Mofrad, Daniel K. Nomura, Mélanie Ott, Julia Schaletzky, Niren Murthy
The papain-like protease (PLpro) plays a critical role in SARS-CoV-2 (SCoV-2) pathogenesis and is essential for viral replication and for allowing the virus to evade the host immune response. Inhibitors of PLpro have great therapeutic po...
Keywords: Chemistry, Papain, Protease, Biochemistry, Covalent bond, Pyrimidine, Stereochemistry, Enzyme
2022
Effects of Ionic Liquids on the Stabilization Process of Gold Nanoparticles
Authors: Mohammad Khavani, Aliyeh Mehranfar, Mohammad R. K. Mofrad
Improving the stability of the gold nanoparticles (AuNPs) is an important challenge in nanoscience, given that the activity and ubiquitous application of the AuNPs in different fields depend largely on their stability in the solution pha...
Keywords: Ionic liquid, Colloidal gold, Chemistry, Nanoparticle, Dispersion (optics), Solvation, Molecular dynamics, Dispersion stability, Metal, Ion, Phase (matter), Chemical physics, Chemical engineering, Computational chemistry, Nanotechnology, Materials science, Organic chemistry, Catalysis
Emerging computational paradigms to address the complex role of gut microbial metabolism in cardiovascular diseases
Authors: Javad Aminian-Dehkordi, Amin Valiei, Mohammad R. K. Mofrad
The human gut microbiota and its associated perturbations are implicated in a variety of cardiovascular diseases (CVDs). There is evidence that the structure and metabolic composition of the gut microbiome and some of its metabolites hav...
Keywords: Microbiome, Gut microbiome, Computational biology, Gut flora, Variety (cybernetics), Computer science, Computational model, Systems biology, Bioinformatics, Biology, Data science, Artificial intelligence, Immunology
Design of a flexing organ-chip to model in situ loading of the intervertebral disc
Authors: Jonathan P. McKinley, Andre R. Montes, Maple N. Wang, Anuya R. Kamath, Gissell Jimenez, Jianhua Lim, Siddharth Marathe, Mohammad R. K. Mofrad, Grace D. O’Connell
The leading cause of disability of all ages worldwide is severe lower back pain. To address this untreated epidemic, further investigation is needed into the leading cause of back pain, intervertebral disc degeneration. In particular, mi...
Keywords: Annulus (botany), Intervertebral disc, Population, Biomedical engineering, Degeneration (medical), Organ-on-a-chip, Materials science, Strain (injury), Computer science, Nanotechnology, Anatomy, Biology, Medicine, Pathology, Composite material
On modeling the multiscale mechanobiology of soft tissues: Challenges and progress
Authors: Yifan Guo, Mohammad R. K. Mofrad, Adrián Buganza Tepole
Tissues grow and remodel in response to mechanical cues, extracellular and intracellular signals experienced through various biological events, from the developing embryo to disease and aging. The macroscale response of soft tissues is t...
Keywords: Mechanobiology, Microscale chemistry, Multiscale modeling, Adaptation (eye), Computer science, Neuroscience, Biological system, Nanotechnology, Biology, Materials science, Bioinformatics, Cell biology
Decoding the Effect of Hydrostatic Pressure on TRPV1 Lower-Gate Conformation by Molecular-Dynamics Simulation
Authors: Muhammad Harith Bin Zamri, Yoshihiro Ujihara, Masanori Nakamura, Mohammad R. K. Mofrad, Shukei Sugita
In response to hydrostatic pressure, the cation channel transient receptor potential vanilloid 1 (TRPV1) is essential in signaling pathways linked to glaucoma. When activated, TRPV1 undergoes a gating transition from a closed to an open ...
Keywords: Hydrostatic pressure, TRPV1, Gating, Molecular dynamics, Transient receptor potential channel, Chemistry, Biophysics, Membrane, Mechanics, Receptor, Biochemistry, Physics, Biology, Computational chemistry
On the nuclear pore complex and its emerging role in cellular mechanotransduction
Authors: Atsushi Matsuda, Mohammad R. K. Mofrad
The nuclear pore complex (NPC) is a large protein assembly that perforates the nuclear envelope and provides a sole gateway for traffic between the cytoplasm and the nucleus. The NPC controls the nucleocytoplasmic transport by selectivel...
Keywords: Nuclear pore, Mechanotransduction, Nucleoporin, Nuclear transport, Cell biology, Scaffold protein, Cytoplasm, Nuclear protein, Nucleus, NLS, Biology, Chemistry, Nuclear localization sequence, Biophysics, Neuroscience, Cell nucleus, Signal transduction, Transcription factor, Gene, Genetics
Methylation at a conserved lysine residue modulates tau assembly and cellular functions
Authors: Hengameh Shams, Atsuko Matsunaga, Qin Ma, Mohammad R. K. Mofrad, Alessandro Didonna
Keywords: Biology, Methylation, Microtubule, Lysine, In silico, Cell biology, Tau protein, Phosphorylation, Protein methylation, Computational biology, Biochemistry, Disease, Alzheimer's disease, Amino acid, Methyltransferase, Gene
A short HLA-DRA isoform binds the HLA-DR2 heterodimer on the outer domain of the peptide-binding site
Authors: Hengameh Shams, Jill A. Hollenbach, Atsuko Matsunaga, Mohammad R. K. Mofrad, Jorge R. Oksenberg, Alessandro Didonna
Keywords: Human leukocyte antigen, Gene isoform, Peptide, Biology, T-cell receptor, Chemistry, Cell biology, Antigen, T cell, Immune system, Biochemistry, Genetics, Gene
2021
Acid-Sensitive Surfactants Enhance the Delivery of Nucleic Acids
Authors: Joachim Justad Røise, Hesong Han, Jie Li, D. Lucas Kerr, Chung Taing, Kamyar Behrouzi, Maomao He, Emily Ruan, Lienna Y. Chan, Eli M. Espinoza, Sören Reinhard, Kanav Thakker, Justin Kwon, Mohammad R. K. Mofrad, Niren Murthy
The development of endosomal disruptive agents is a major challenge in the field of drug delivery and pharmaceutical chemistry. Current endosomal disruptive agents are composed of polymers, peptides, and nanoparticles and have had limite...
Keywords: Endosome, Chemistry, PEGylation, Drug delivery, Cationic polymerization, Nucleic acid, Nanotechnology, Combinatorial chemistry, Biochemistry, Organic chemistry, Cell, Materials science
Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex
Authors: Kathleen M. Lennon, Mohammad Soheilypour, Mohaddeseh Peyro, Devin L. Wakefield, Grace E. Choo, Mohammad R. K. Mofrad, Tijana Jovanović‐Talisman
Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitated when nuclear transport receptors (NTRs) weakly and transiently bind to intrins...
Keywords: Nuclear pore, Nuclear transport, Avidity, Biophysics, Intrinsically disordered proteins, Nucleoporin, Chemistry, Binding site, Molecular dynamics, Phase (matter), Cell biology, Cytoplasm, Biology, Biochemistry, Cell nucleus, Computational chemistry, Genetics
A Coupled Multiscale Approach to Modeling Aortic Valve Mechanics in Health and Disease
Authors: Ahmed A. Bakhaty, Sanjay Govindjee, Mohammad R. K. Mofrad
Mechano-biological processes in the aortic valve span multiple length scales ranging from the molecular and cell to tissue and organ levels. The valvular interstitial cells residing within the valve cusps sense and actively respond to le...
Keywords: Aortic valve, Calcification, Stenosis, Interstitial cell, Cardiology, valvular heart disease, Internal medicine, Medicine, Materials science
Nucleoporins’ exclusive amino acid sequence features regulate their transient interaction with and selectivity of cargo complexes in the nuclear pore
Authors: Mohaddeseh Peyro, Andrew Dickson, Mohammad R. K. Mofrad
Nucleocytoplasmic traffic of nucleic acids and proteins across the nuclear envelop via the nuclear pore complexes (NPCs) is vital for eukaryotic cells. NPCs screen transported macromolecules based on their morphology and surface chemistr...
Keywords: Nuclear pore, Nucleoporin, Biology, Cell biology, Nuclear transport, Peptide sequence, Nuclear protein, Sequence (biology), Biophysics, Amino acid, Cell nucleus, Biochemistry, Genetics, Cytoplasm, Gene, Transcription factor
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks
Authors: Esmaeil Nouranı, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad
Pretrained representations have recently gained attention in various machine learning applications. Nonetheless, the high computational costs associated with training these models have motivated alternative approaches for representation ...
Keywords: Computer science, Artificial intelligence, Machine learning, Representation (politics), Class (philosophy), Annotation, Feature learning, Deep learning, Artificial neural network, Sequence (biology), Biology
Free energy calculations shed light on the nuclear pore complex’s selective barrier nature
Authors: Atsushi Matsuda, Mohammad R. K. Mofrad
Keywords: Nuclear pore, Nucleoporin, Conformational entropy, Biophysics, Chemistry, Entropy (arrow of time), Chemical physics, Molecular dynamics, Nuclear transport, Physics, Biology, Thermodynamics, Computational chemistry, Molecule, Gene, Cytoplasm, Biochemistry, Cell nucleus
FG nucleoporins feature unique patterns that distinguish them from other IDPs
Authors: Mohaddeseh Peyro, Mohammad Soheilypour, Vikrum S. Nibber, Andrew Dickson, Mohammad R. K. Mofrad
Keywords: Nucleoporin, Intrinsically disordered proteins, UniProt, Nuclear pore, Function (biology), Biology, Biophysics, Chemistry, Computational biology, Nuclear transport, Evolutionary biology, Cell biology, Biochemistry, Cytoplasm, Cell nucleus, Gene
EpitopeVec: linear epitope prediction using deep protein sequence embeddings
Authors: Akash Bahai, Ehsaneddin Asgari, Mohammad R. K. Mofrad, Andreas Kloetgen, Alice C. McHardy
Supplementary data are available at Bioinformatics online.
Keywords: Generalizability theory, Computer science, Epitope, Artificial intelligence, Antigenicity, Linear epitope, Computational biology, Identification (biology), Benchmarking, Machine learning, Antigen, Biology, Mathematics, Statistics, Immunology
Molecular models of LINC complex assembly at the nuclear envelope
Authors: Zeinab Jahed, Nya Domkam, Jessica Ornowski, Ghafar Yerima, Mohammad R. K. Mofrad
Large protein complexes assemble at the nuclear envelope to transmit mechanical signals between the cytoskeleton and nucleoskeleton. These protein complexes are known as the linkers of the nucleoskeleton and cytoskeleton complexes (LINC ...
Keywords: Biology, Envelope (radar), Cytoskeleton, Cell biology, Biophysics, Lamin, Nucleus, Biochemistry, Cell
Hydrodynamic interactions significantly alter the dynamics of actin networks and result in a length scale dependent loss modulus
Authors: Reza Karimi, Mohammad‐Reza Alam, Mohammad R. K. Mofrad
Keywords: Protein filament, Cytoskeleton, Length scale, Actin, Dynamics (music), Physics, Modulus, Mechanics, Scale (ratio), Bending, Biophysics, Statistical physics, Materials science, Chemistry, Biology, Thermodynamics, Cell, Composite material
PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks
Authors: Seyyede Fatemeh Seyyedsalehi, Mahdieh Soleymani, Hamid R. Rabiee, Mohammad R. K. Mofrad
Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction a...
Keywords: Protein function prediction, Gene ontology, Computer science, Ontology, Function (biology), Construct (python library), Generative grammar, Term (time), Annotation, Artificial intelligence, Machine learning, Computational biology, Data mining, Protein function, Gene, Biology, Genetics
Intranuclear strain in living cells subjected to substrate stretching: A combined experimental and computational study
Authors: Shingo Tsukamoto, Takumi Asakawa, Shun Kimura, Naoyuki Takesue, Mohammad R. K. Mofrad, Naoya Sakamoto
Keywords: Nucleus, Strain (injury), Mechanotransduction, Biophysics, Cytochalasin D, Cell nucleus, Materials science, Chromatin, Cytoskeleton, Cell, Chemistry, Anatomy, Cell biology, Biology, Biochemistry
[Retracted] Atomic Scale Interactions between RNA and DNA Aptamers with the TNF‐α Protein
Authors: Homayoun Asadzadeh, Ali Moosavi, Georgios Alexandrakis, Mohammad R. K. Mofrad
Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these ap...
Keywords: Aptamer, RNA, Biosensor, Computational biology, DNA, Chemistry, Riboswitch, Docking (animal), Molecular recognition, Biophysics, Biology, Biochemistry, Molecular biology, Gene, Non-coding RNA, Molecule, Medicine
Drug delivery and adhesion of magnetic nanoparticles coated nanoliposomes and microbubbles to atherosclerotic plaques under magnetic and ultrasound fields
Authors: Mojgan Alishiri, Sina Ebrahimi, Amir Shamloo, Ahmad Boroumand, Mohammad R. K. Mofrad
The use of external fields such as magnet and ultrasound to enhance the targeted drug delivery (TDD) by nano-microcarriers could be a potential method. In this research, the drug delivery of magnetic nanoparticles (NPs) coated nanoliposo...
Keywords: Microbubbles, Drug delivery, Ultrasound, Materials science, Biomedical engineering, Targeted drug delivery, Magnetic nanoparticles, Magnetic field, Transducer, Nanoparticle, Nanotechnology, Medicine, Radiology, Acoustics
2020
Machine learning for endoleak detection after endovascular aortic repair
Authors: Salmonn Talebi, Mohammad Hamidi Madani, Ali Madani, Ashley Chien, Jody Shen, Domenico Mastrodicasa, Dominik Fleischmann, Frandics P. Chan, Mohammad R. K. Mofrad
Keywords: Medicine, Radiology, Gold standard (test), Segmentation, Diagnostic accuracy, Computer science, Artificial intelligence
Quantification of human sperm concentration using machine learning-based spectrophotometry
Authors: Ali Lesani, Somaieh Kazemnejad, Mahdi Moghimi Zand, Mojtaba Azadi, Hassan Jafari, Mohammad R. K. Mofrad, Reza Nosrati
Keywords: Spectrophotometry, Sperm, Semen, Artificial neural network, Computer science, Biological system, Artificial intelligence, Chromatography, Chemistry, Medicine, Andrology, Biology
A splice acceptor variant in HLA‐DRA affects the conformation and cellular localization of the class II DR alpha‐chain
Authors: Alessandro Didonna, Vincent Damotte, Hengameh Shams, Atsuko Matsunaga, Stacy J. Caillier, Ravi Dandekar, Maneesh Kumar Misra, Mohammad R. K. Mofrad, Jorge R. Oksenberg, Jill A. Hollenbach
Class II human leucocyte antigen (HLA) proteins are involved in the immune response by presenting pathogen-derived peptides to CD4+ T lymphocytes. At the molecular level, they are constituted by α/β-heterodimers on the surface of profess...
Keywords: Gene isoform, Human leukocyte antigen, Endoplasmic reticulum, Alternative splicing, Biology, Cell biology, Peptide, Antigen, Alpha chain, Gene, Biochemistry, Genetics
Killer Cell Immunoglobulin-like Receptor Variants Are Associated with Protection from Symptoms Associated with More Severe Course in Parkinson Disease
Authors: Kirsten M. Anderson, Danillo G. Augusto, Ravi Dandekar, Hengameh Shams, Chao Zhao, Tasneem Yusufali, Gonzalo Montero-Martín, Wesley M. Marin, Neda Nemat‐Gorgani, Lisa E. Creary, Stacy J. Caillier, Mohammad R. K. Mofrad, Peter Parham, Marcelo Fernández-Viña, Jorge R. Oksenberg, Paul J. Norman, Jill A. Hollenbach
Immune dysfunction plays a role in the development of Parkinson disease (PD). NK cells regulate immune functions and are modulated by killer cell immunoglobulin-like receptors (KIR). KIR are expressed on the surface of NK cells and inter...
Keywords: Human leukocyte antigen, Immunology, Allele, Receptor, Odds ratio, Immune system, Antibody, Disease, Biology, Gene, Medicine, Genetics, Internal medicine, Antigen
Nanoscale integrin cluster dynamics controls cellular mechanosensing via FAKY397 phosphorylation
Authors: Bo Cheng, Wanting Wan, Guoyou Huang, Yuhui Li, Guy M. Genin, Mohammad R. K. Mofrad, Tian Jian Lu, Feng Xu, Min Lin
Transduction of extracellular matrix mechanics affects cell migration, proliferation, and differentiation. While this mechanotransduction is known to depend on the regulation of focal adhesion kinase phosphorylation on Y397 (FAKpY397), t...
Keywords: Integrin, Mechanotransduction, Focal adhesion, Phosphorylation, Extracellular matrix, Cell biology, Cell adhesion, Signal transduction, Adhesion, Chemistry, Biophysics, Biology, Cell, Biochemistry
Kindlin Assists Talin to Promote Integrin Activation
Authors: Zainab Haydari, Hengameh Shams, Zeinab Jahed, Mohammad R. K. Mofrad
Keywords: Integrin, Cell biology, Chemistry, Computational biology, Biology, Biochemistry, Receptor
Characterization of Kindlin-2 Variants’ Molecular Behavior Under Applied Tension
Authors: Fayyaz Ahamed, Brian Jeffers, Zeinab Jahed, Mohammad R. K. Mofrad
Keywords: Dimer, Molecular dynamics, Biophysics, Integrin, Tension (geology), Chemistry, Adhesion, Focal adhesion, Monomer, Actin, Cell adhesion, Crystallography, Cell, Materials science, Biochemistry, Polymer, Biology, Computational chemistry
Kindlin Cooperates with Talin for Integrin Activation, a Molecular Dynamics Approach
Authors: Zainab Haydari, Hengameh Shams, Zeinab Jahed, Mohammad R. K. Mofrad
Keywords: Integrin, Cell biology, CD49c, Integrin, beta 6, Chemistry, Cell adhesion, Transmembrane protein, Platelet Glycoprotein GPIIb-IIIa Complex, Collagen receptor, Integrin alpha M, Cell, Biology, Biochemistry, Receptor
Mapping the Distribution of Mechanical Stresses in the LINC Complex
Authors: Kamyar Behrouzi, Zeinab Jahed, Mohammad R. K. Mofrad
Keywords: Mechanotransduction, Nucleus, Biophysics, Cytoskeleton, Integrin, Membrane, Chemistry, Molecular dynamics, Cell biology, Biology, Cell, Biochemistry
Specific Sequence Features Regulate the Transient Binding between FG Nucleoporins and Cargo Complexes
Authors: Mohaddeseh Peyro, Mohammad R. K. Mofrad
Keywords: Nuclear pore, Nucleoporin, Intrinsically disordered proteins, Nuclear transport, Sequence (biology), Function (biology), Biophysics, Molecular dynamics, Cytoplasm, Process (computing), Chemistry, Cell biology, Biology, Computer science, Biochemistry, Cell nucleus
Viscoelastic Mechanical Models of the LINC Complex
Authors: Kamyar Behrouzi, Zeinab Jahed, Mohammad R. K. Mofrad
Keywords: Viscoelasticity, Mechanotransduction, Context (archaeology), Physics, Cytoskeleton, Integrin, Biophysics, Biological system, Biology, Cell biology, Cell, Genetics
Strain-stiffening and strain-softening responses in random viscoelastic fibrous networks: interplay between fiber orientation and viscoelastic softening
Authors: Naeem Zolfaghari, Mahdi Moghimi Zand, Mohammad R. K. Mofrad
Collagen networks are usually modeled as an inelastic material that accentuates the role of bond dynamics in their viscoelastic response. However, permanent cross-links can be used to fix these fibers to a large degree. Here, we model a ...
Keywords: Viscoelasticity, Materials science, Softening, Composite material, Strain (injury), Stiffening, Fiber, Orientation (vector space), Anatomy, Geometry, Mathematics, Medicine
2019
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Authors: Naihui Zhou, Yuxiang Jiang, Timothy Bergquist, Alexandra Lee, Balint Z Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George P. Georghiou, Huy Nguyen, Md-Nafiz Hamid, L. Taylor Davis, Tunca Doğan, Volkan Atalay, Ahmet Süreyya Rifaioğlu, Alperen Dalkıran, Rengül Çetin-Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemović, Vladimir Perović, Radoslav Davidović, Neven Šumonja, Nevena Veljković, Ehsaneddin Asgari, Mohammad R. K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fábio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan Medlar, Elaine Zosa, Itamar Borukhov, Ilya B. Novikov, Angela D. Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Sašo Džeroski, Ian Sillitoe, Sayoni Das, Jonathan Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, José Manuel Rodrı́guez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Ré, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie‐Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo
Keywords: Biology, Annotation, Computational biology, Genome, Function (biology), Functional genomics, Drosophila melanogaster, Gene, Genomics, Genetics
Talin is required to increase stiffness of focal molecular complex in its early formation process
Authors: N. Nakao, Koichiro Maki, Mohammad R. K. Mofrad, Taiji ADACHI
Keywords: Vinculin, Stiffness, Focal adhesion, Actin, Cytoskeleton, Fibronectin, Cellular adaptation, Integrin, Biophysics, Chemistry, Atomic force microscopy, Extracellular matrix, Cell biology, Nanotechnology, Materials science, Biology, Signal transduction, Cell, Composite material, Biochemistry
Structural Basis of the Differential Binding of Engineered Knottins to Integrins αVβ3 and α5β1
Authors: Johannes F. Van Agthoven, Hengameh Shams, Frank V. Cochran, José Luís Izquierdo Alonso, James R. Kintzing, Kiavash Garakani, Brian D. Adair, Jian-Ping Xiong, Mohammad R. K. Mofrad, Jennifer R. Cochran, M. Amin Arnaout
Keywords: Integrin, Chemistry, Biophysics, Binding site, Stereochemistry, Biochemistry, Computational biology, Biology, Receptor
Sex-specific Tau methylation patterns and synaptic transcriptional alterations are associated with neural vulnerability during chronic neuroinflammation
Authors: Alessandro Didonna, Ester Cantó, Hengameh Shams, Noriko Isobe, Chao Zhao, Stacy J. Caillier, Carlo Condello, Hana Yamate-Morgan, Seema K. Tiwari‐Woodruff, Mohammad R. K. Mofrad, Stephen L. Hauser, Jorge R. Oksenberg
Keywords: Experimental autoimmune encephalomyelitis, Neuroinflammation, Neurodegeneration, Multiple sclerosis, Neuroscience, Central nervous system, Biology, Epigenetics, Transcriptome, Immunology, Inflammation, Disease, Medicine, Genetics, Internal medicine, Gene expression
Role of KASH domain lengths in the regulation of LINC complexes
Authors: Zeinab Jahed, Hongyan Hao, Vyom Thakkar, Uyen T. Vu, Venecia A. Valdez, Akshay Rathish, Chris Tolentino, Samuel C. J. Kim, Darya Fadavi, Daniel A. Starr, Mohammad R. K. Mofrad
The linker of the nucleoskeleton and cytoskeleton (LINC) complex is formed by the conserved interactions between Sad-1 and UNC-84 (SUN) and Klarsicht, ANC-1, SYNE homology (KASH) domain proteins, providing a physical coupling between the...
Keywords: Biology, Cell biology, Caenorhabditis elegans, Cytoplasm, Cytoskeleton, Protein domain, C2 domain, Biophysics, Membrane, Biochemistry, Gene, Cell
Bridging Finite Element and Machine Learning Modeling: Stress Prediction of Arterial Walls in Atherosclerosis
Authors: Ali Madani, Ahmed A. Bakhaty, Jiwon Kim, Yara Mubarak, Mohammad R. K. Mofrad
Finite element and machine learning modeling are two predictive paradigms that have rarely been bridged. In this study, we develop a parametric model to generate arterial geometries and accumulate a database of 12,172 2D finite element s...
Keywords: von Mises yield criterion, Finite element method, Artificial neural network, Parametric statistics, Artificial intelligence, Hyperelastic material, Computer science, Parametric model, Machine learning, Structural engineering, Engineering, Mathematics, Statistics
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)
Authors: Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad
Keywords: Computer science, Artificial intelligence, Pattern recognition (psychology), Segmentation, Protein sequencing, Structural motif, Probabilistic logic, Discriminative model, Sequence motif, Embedding, Computational biology, Peptide sequence, Biology, Genetics, Gene
Kindlin Is Mechanosensitive: Force-Induced Conformational Switch Mediates Cross-Talk among Integrins
Authors: Zeinab Jahed, Zainab Haydari, Akshay Rathish, Mohammad R. K. Mofrad
Keywords: Integrin, Mechanosensitive channels, Focal adhesion, Mechanotransduction, Dimer, Chemistry, Biophysics, Cell biology, Adhesion, Cytoskeleton, Biology, Signal transduction, Biochemistry, Receptor, Ion channel, Cell
Kindlin Dimer Strengthens Focal Adhesions under Force by Relieving and Mediating Intracellular Crosstalk Among Integrins
Authors: Zeinab Jahed, Zainab Haydari, Akshay Rathish, Mohammad R. K. Mofrad
Keywords: Integrin, Crosstalk, Focal adhesion, Dimer, Mechanotransduction, Chemistry, Biophysics, Cell biology, Cell adhesion, Cytoskeleton, Adhesion, Biology, Signal transduction, Cell, Biochemistry, Physics
Length of KASH Domains Affect Linc Complex Functions
Authors: Zeinab Jahed, Hongyan Hao, Vyom Thakkar, Uyen T. Vu, Venecia A. Valdez, Akshay Rathish, Darya Fadavi, Daniel A. Starr, Mohammad R. K. Mofrad
Keywords: Biology, Cell biology, Cytoplasm, Caenorhabditis elegans, Cytoskeleton, Inner membrane, Protein domain, Nuclear protein, Genetics, Transcription factor, Gene, Cell
Molecular Mechanisms of the Interaction between the RNA-Binding Protein Nab2 and the Nuclear Basket Protein Mlp1 in mRNA Quality Control
Authors: Mohammad Soheilypour, Mohaddeseh Peyro, Hengameh Shams, Stephanie Rider, Ali R. Kaazempur-Mofrad, Mohammad R. K. Mofrad
Keywords: Biology, RNA, Nuclear export signal, Cell biology, RNA-binding protein, Messenger RNA, Messenger RNP, Computational biology, Ribonucleoprotein, Biochemistry, Cytoplasm, Cell nucleus, Gene
The Amino Acid Sequence Features of the FG Nucleoporins Affect the Movement of Cargo Complex Inside the NPC
Authors: Mohaddeseh Peyro, Mohammad R. K. Mofrad
Keywords: Nuclear pore, Nucleoporin, Nuclear transport, Biophysics, Biology, Cell biology, Chemistry, Cytoplasm, Cell nucleus
Mechanobiology of the Nuclear Pore Complex Machinery
Authors: Mohammad R. K. Mofrad
Cite This Article R., M. (2019). Mechanobiology of the Nuclear Pore Complex Machinery. Molecular & Cellular Biomechanics, 16(Suppl.2), 19–20.
Keywords: Mechanobiology, Biomechanics, Chemistry, Biophysics, Biology, Anatomy
2018
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection
Authors: Ehsaneddin Asgari, Philipp C. Münch, Till Robin Lesker, Alice C. McHardy, Mohammad R. K. Mofrad
Supplementary data are available at Bioinformatics online.
Keywords: Computational biology, Cluster analysis, Computer science, Benchmark (surveying), Biomarker, Biome, Biomarker discovery, Biology, Data mining, Artificial intelligence, Genetics, Cartography, Gene, Geography, Ecology
Deep echocardiography: data-efficient supervised and semi-supervised deep learning towards automated diagnosis of cardiac disease
Authors: Ali Madani, Jia Rui Ong, Anshul Tibrewal, Mohammad R. K. Mofrad
Keywords: Artificial intelligence, Deep learning, Computer science, Machine learning, Pipeline (software), Binary classification, Medical imaging, Supervised learning, Big data, Data mining, Artificial neural network, Support vector machine
Conserved SUN-KASH Interfaces Mediate LINC Complex-Dependent Nuclear Movement and Positioning
Authors: Natalie E. Cain, Zeinab Jahed, Amy Schoenhofen, Venecia A. Valdez, Baila Elkin, Hongyan Hao, Nathan Harris, Leslie A. Herrera, Brian M. Woolums, Mohammad R. K. Mofrad, G. W. Gant Luxton, Daniel A. Starr
Keywords: Biology, Movement (music), Evolutionary biology, Physics
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples
Authors: Ehsaneddin Asgari, Kiavash Garakani, Alice C. McHardy, Mohammad R. K. Mofrad
The author wishes to inform readers that the affiliations for the authors were incorrect in the original paper. They appear correctly above. The paper has been corrected online.
Keywords: Representation (politics), 16S ribosomal RNA, Host (biology), Phenotype, Gene, Genetics, Computational biology, Biology, Ribosomal RNA
A molecular model for LINC complex regulation: activation of SUN2 for KASH binding
Authors: Zeinab Jahed, Uyen T. Vu, Darya Fadavi, Huimin Ke, Akshay Rathish, Samuel C. J. Kim, Wei Feng, Mohammad R. K. Mofrad
Linkers of the nucleoskeleton and cytoskeleton are key molecular complexes that span the nuclear envelope (NE) and provide a direct linkage between the nucleoskeleton and cytoskeleton. Two major components of these complexes are members ...
Keywords: Biology, Cell biology, Biophysics, Computational biology
Agent‐Based Modeling in Molecular Systems Biology
Authors: Mohammad Soheilypour, Mohammad R. K. Mofrad
Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding ...
Keywords: Computational biology, Biology, Systems biology, Evolutionary biology
Molecular Insights into the Mechanisms of SUN1 Oligomerization in the Nuclear Envelope
Authors: Zeinab Jahed, Darya Fadavi, Uyen T. Vu, Ehsaneddin Asgari, G. W. Gant Luxton, Mohammad R. K. Mofrad
Keywords: Envelope (radar), Computational biology, Chemistry, Neuroscience, Biophysics, Biology, Computer science
Quality control of mRNAs at the entry of the nuclear pore: Cooperation in a complex molecular system
Authors: Mohammad Soheilypour, Mohammad R. K. Mofrad
Despite extensive research on how mRNAs are quality controlled prior to export into the cytoplasm, the exact underlying mechanisms are still under debate. Specifically, it is unclear how quality control proteins at the entry of the nucle...
Keywords: Cytoplasm, Nuclear pore, Quality (philosophy), Messenger RNA, Cell biology, Control (management), Nuclear export signal, Biology, Computational biology, Cell nucleus, Genetics, Computer science, Gene, Physics, Artificial intelligence
Enhancing Enzymatic Activity for Cellulose Degradation
Authors: Hengameh Shams, Mohammad R. K. Mofrad
Keywords: Cellulose, Mutagenesis, Enzyme, Chemistry, Molecular dynamics, Carbohydrate-binding module, Cellulase, Biophysics, Biochemistry, Chemical engineering, Materials science, Mutation, Computational chemistry, Biology
STIM1-Induced Conformational Transition of ORAI-1 Leads to Channel Activation
Authors: Zainab Haydari, Hengameh Shams, Mohammad R. K. Mofrad
Keywords: STIM1, ORAI1, Chemistry, Endoplasmic reticulum, Biophysics, Calcium signaling, Gating, Voltage-dependent calcium channel, Cell biology, Calcium channel, Protein subunit, Signal transduction, Calcium, Biochemistry, Biology
The Nature's Superviscous Nano-channel: Insight from Big Data-Driven Biophysical Modeling
Authors: Ruhollah Moussavi-Baygi, Mohammad R. K. Mofrad
Keywords: Intrinsically disordered proteins, Nuclear pore, Fluorescence recovery after photobleaching, Rheology, Chemical physics, Biophysics, Nanotechnology, Materials science, Chemistry, Cytoplasm, Membrane, Biology, Composite material
Mechanical LINCs of the nuclear envelope: Where SUN meets KASH
Authors: Zeinab Jahed, Mohammad R. K. Mofrad
Keywords: Cytoskeleton, Envelope (radar), Lamin, Inner membrane, Membrane, Biophysics, Physics, Nucleus, Cell biology, Biology, Engineering, Biochemistry, Cell, Telecommunications
Fast and accurate view classification of echocardiograms using deep learning
Authors: Ali Madani, Ramy Arnaout, Mohammad R. K. Mofrad, Rima Arnaout
Keywords: Overfitting, Artificial intelligence, Convolutional neural network, Deep learning, Computer science, Visualization, Artificial neural network, Interpretation (philosophy), Pattern recognition (psychology), Machine learning
ProtDataTherm: A database for thermostability analysis and engineering of proteins
Authors: Hassan Pezeshgi Modarres, Mohammad R. K. Mofrad, Amir Sanati‐Nezhad
Protein thermostability engineering is a powerful tool to improve resistance of proteins against high temperatures and thereafter broaden their applications. For efficient protein thermostability engineering, different thermostability-cl...
Keywords: Thermostability, Protein engineering, Database, Thermophile, Computational biology, Psychrophile, Mesophile, Biology, Protein family, Bioinformatics, Chemistry, Computer science, Biochemistry, Genetics, Enzyme, Gene
2017
The “Stressful” Life of Cell Adhesion Molecules: On the Mechanosensitivity of Integrin Adhesome
Authors: Hengameh Shams, Brenton D. Hoffman, Mohammad R. K. Mofrad
Cells have evolved into complex sensory machines that communicate with their microenvironment via mechanochemical signaling. Extracellular mechanical cues trigger complex biochemical pathways in the cell, which regulate various cellular ...
Keywords: Mechanotransduction, Extracellular matrix, Focal adhesion, Integrin, Cell biology, Cell adhesion, Cytoskeleton, Cell adhesion molecule, Intracellular, Cell signaling, Actin cytoskeleton, Actin, Signal transduction, Biology, Extracellular, Chemistry, Cell, Biochemistry
Abstract 18074: Fast and Accurate View Classification of Cardiac Echocardiograms Using Deep Learning
Authors: Ali Madani, Ramy Arnaout, Mohammad R. K. Mofrad, Rima Arnaout
Background: Echocardiography is essential to modern cardiology. However, human interpretation limits accurate and standardized high-throughput analysis, limiting echocardiography from reaching its ...
Keywords: Medicine, Deep learning, Artificial intelligence, Cardiology, Internal medicine
A strain-based finite element model for calcification progression in aortic valves
Authors: Amirhossein Arzani, Mohammad R. K. Mofrad
Keywords: Calcification, Finite element method, Strain (injury), Aortic valve, Population, Cardiology, Medicine, Structural engineering, Anatomy, Internal medicine, Engineering
Mechanical Contact Characteristics of PC3 Human Prostate Cancer Cells on Complex-Shaped Silicon Micropillars
Authors: Brandon B. Seo, Zeinab Jahed, Jennifer A. Coggan, Yeung Yeung Chau, Jacob L. Rogowski, Frank Gu, Weijia Wen, Mohammad R. K. Mofrad, Ting Y. Tsui
In this study we investigated the contact characteristics of human prostate cancer cells (PC3) on silicon micropillar arrays with complex shapes by using high-resolution confocal fluorescence microscopy techniques. These arrays consist o...
Keywords: Nanometre, Materials science, DAPI, Silicon, Fluorescence, Pillar, Fluorescence microscope, Nanoscopic scale, Confocal, Nanotechnology, Resolution (logic), Biophysics, Atomic force microscopy, Confocal microscopy, Optics, Chemistry, Optoelectronics, Composite material, Biology, Biochemistry
Consistent trilayer biomechanical modeling of aortic valve leaflet tissue
Authors: Ahmed A. Bakhaty, Sanjay Govindjee, Mohammad R. K. Mofrad
Keywords: Multiphysics, Aortic valve, Peridynamics, Multiscale modeling, Nonlinear system, Microstructure, Continuum mechanics, Materials science, Collagen fiber, Biomedical engineering, Mechanics, Computer science, Structural engineering, Finite element method, Anatomy, Physics, Engineering, Composite material, Cardiology, Medicine, Bioinformatics
α-Actinin Induces a Kink in the Transmembrane Domain of β3-Integrin and Impairs Activation via Talin
Authors: Hengameh Shams, Mohammad R. K. Mofrad
Keywords: Integrin, Filamin, Cell biology, Cytoplasm, Chemistry, Transmembrane protein, Integrin, beta 6, Transmembrane domain, Focal adhesion, Collagen receptor, Biophysics, Signal transduction, Cell, Biology, Membrane, Receptor, Cytoskeleton, Biochemistry
Molecular mechanics of Staphylococcus aureus adhesin, CNA, and the inhibition of bacterial adhesion by stretching collagen
Authors: Ali Madani, Kiavash Garakani, Mohammad R. K. Mofrad
Bacterial adhesion to collagen, the most abundant protein in humans, is a critical step in the initiation and persistence of numerous bacterial infections. In this study, we explore the collagen binding mechanism of the multi-modular cel...
Keywords: Bacterial adhesin, Biophysics, Chemistry, Adhesion, Staphylococcus aureus, Molecular dynamics, Linker, Biochemistry, Biology, Bacteria, Escherichia coli, Genetics
Multiscale Systems Biology Model of Calcific Aortic Valve Disease Progression
Authors: Amirhossein Arzani, Kristyn S. Masters, Mohammad R. K. Mofrad
Calcific aortic valve disease is a common cause of aortic stenosis, a life threatening condition. In this study, a mathematical model is developed to simulate the cascade of mechanosensitive biochemical events that occur upon damage to t...
Keywords: Calcification, Fibrous cap, Stenosis, Medicine, Cardiology, Pathology, Internal medicine
Looking “Under the Hood” of Cellular Mechanotransduction with Computational Tools: A Systems Biomechanics Approach across Multiple Scales
Authors: Hengameh Shams, Mohammad Soheilypour, Mohaddeseh Peyro, Ruhollah Moussavi-Baygi, Mohammad R. K. Mofrad
Signal modulation has been developed in living cells throughout evolution to promote utilizing the same machinery for multiple cellular functions. Chemical and mechanical modules of signal transmission and transduction are interconnected...
Keywords: Mechanotransduction, Mechanobiology, Extracellular matrix, Computational model, In silico, Neuroscience, Biology, Computer science, Nanotechnology, Cell biology, Materials science, Simulation
Mechanosensitive Conformation of Vinculin Regulates Its Binding to MAPK1
Authors: Kiavash Garakani, Hengameh Shams, Mohammad R. K. Mofrad
Keywords: Vinculin, Cell biology, Chemistry, Focal adhesion, Biophysics, Protein–protein interaction, Extracellular matrix, Computational biology, Biochemistry, Signal transduction, Biology
Allosteric Regulation of Vinculin Activation by Alpha-Actinin
Authors: Hengameh Shams, Mohammad R. K. Mofrad
Keywords: Vinculin, Allosteric regulation, Mechanotransduction, Biophysics, Molecular dynamics, Chemistry, Focal adhesion, Cell biology, Biochemistry, Biology, Cell, Enzyme
Exploring the Interaction between MLP1 and NAB2 for mRNA Quality Control Purposes
Authors: Mohammad Soheilypour, Mohaddeseh Peyro, Hengameh Shams, Mohammad R. K. Mofrad
Keywords: Biology, Cell biology, Docking (animal), Transcription factor, RNA, Plasma protein binding, Computational biology, Biochemistry, Biophysics, Gene, Medicine
Like Charge Regions (LCRs) are One of the Key Regulators of Nucleocytoplasmic Transport
Authors: Mohaddeseh Peyro, Mohammad Soheilypour, Mohammad R. K. Mofrad
Keywords: Nuclear pore, Nucleoporin, Intrinsically disordered proteins, Nuclear transport, Molecular dynamics, Biophysics, Computational biology, Biology, Chemistry, Nucleus, Cell biology, Cell nucleus
Mechanical Response of Nesprin-2G to Cytoskeletal Forces Regulates Linc Complex-Dependent Mechanotransduction
Authors: Hengameh Shams, Gant Luxton, Mohammad R. K. Mofrad
Keywords: Cytoskeleton, Mechanotransduction, Spectrin, Nucleus, Actin, Actin cytoskeleton, Biophysics, Cell biology, Chemistry, Biology, Biochemistry, Cell
Bacterial Networks on Hydrophobic Micropillars
Authors: Zeinab Jahed, Hamed Shahsavan, Mohit S. Verma, Jacob L. Rogowski, Brandon B. Seo, Boxin Zhao, Ting Y. Tsui, Frank Gu, Mohammad R. K. Mofrad
Bacteria have evolved as intelligent microorganisms that can colonize and form highly structured and cooperative multicellular communities with sophisticated singular and collective behaviors. The initial stages of colony formation and i...
Keywords: Nanotechnology, Materials science
2016
Regulation of RNA-binding proteins affinity to export receptors enables the nuclear basket proteins to distinguish and retain aberrant mRNAs
Authors: Mohammad Soheilypour, Mohammad R. K. Mofrad
Keywords: Messenger RNA, Cytoplasm, RNA-binding protein, RNA, Nuclear export signal, Nucleus, Cell biology, Nuclear pore, Cell nucleus, Biology, Gene expression, Nuclear transport, Precursor mRNA, Gene, Chemistry, Biochemistry, RNA splicing
Gelatin/chondroitin sulfate nanofibrous scaffolds for stimulation of wound healing: In‐vitro and in‐vivo study
Authors: Mohamad Pezeshki‐Modaress, Hamid Mirzadeh, Mojgan Zandi, Sareh Rajabi‐Zeleti, Niloofar Sodeifi, Nasser Aghdami, Mohammad R. K. Mofrad
In this research, fabrication of gelatin/chondroitin sulfate (GAG) nanofibrous scaffolds using electrospinning technique for skin tissue engineering was studied. The influence of GAG content on chemical, physical, mechanical and biologic...
Keywords: Gelatin, Materials science, Electrospinning, Chondroitin sulfate, Tissue engineering, Biomedical engineering, Wound healing, In vivo, Glycosaminoglycan, Fibroblast, Hyaluronic acid, Nanofiber, In vitro, Nanotechnology, Chemistry, Composite material, Polymer, Anatomy, Biochemistry, Medicine, Surgery, Biology
Differential Collective- and Single-Cell Behaviors on Silicon Micropillar Arrays
Authors: Zeinab Jahed, Ramin Zareian, Yeung Yeung Chau, Brandon B. Seo, Mary West, Ting Y. Tsui, Weijia Wen, Mohammad R. K. Mofrad
Three-dimensional vertically aligned nano- and micropillars have emerged as promising tools for a variety of biological applications. Despite their increasing usage, the interaction mechanisms of cells with these rigid structures and the...
Keywords: Materials science, Filopodia, Nanotechnology, Silicon, Actin, Optoelectronics, Biology, Cell biology
The LINC and NPC relationship – it's complicated!
Authors: Zeinab Jahed, Mohammad Soheilypour, Mohaddeseh Peyro, Mohammad R. K. Mofrad
The genetic information of eukaryotic cells is enclosed within a double-layered nuclear envelope, which comprises an inner and outer nuclear membrane. Several transmembrane proteins locate to the nuclear envelope; however, only two integ...
Keywords: Biology, Nuclear pore, Inner membrane, Cytoplasm, Cell biology, Nucleoporin, Envelope (radar), Nucleus, Nuclear protein, Transmembrane protein, Cytoskeleton, Gateway (web page), NLS, Nuclear lamina, Nuclear transport, Cell nucleus, Nuclear localization sequence, Genetics, Cell, Gene, Transcription factor
Rapid Brownian Motion Primes Ultrafast Reconstruction of Intrinsically Disordered Phe-Gly Repeats Inside the Nuclear Pore Complex
Authors: Ruhollah Moussavi-Baygi, Mohammad R. K. Mofrad
Keywords: Macromolecule, Nanopore, Nuclear pore, Biophysics, Brownian dynamics, Brownian motion, Excluded volume, Chemistry, Chemical physics, Cytoplasm, Nanotechnology, Materials science, Physics, Polymer, Biology, Biochemistry
Micro and nanotechnologies in heart valve tissue engineering
Authors: Anwarul Hasan, John Saliba, Hassan Pezeshgi Modarres, Ahmed A. Bakhaty, Amir Nasajpour, Mohammad R. K. Mofrad, Amir Sanati‐Nezhad
Keywords: Heart valve, Biomedical engineering, Tissue engineering, Flexibility (engineering), Microscale chemistry, Microfluidics, Materials science, Decellularization, Nanotechnology, Systems engineering, Medicine, Engineering, Surgery
On the Nuclear Pore Complex and Its Roles in Nucleo-Cytoskeletal Coupling and Mechanobiology
Authors: Mohammad Soheilypour, Mohaddeseh Peyro, Zeinab Jahed, Mohammad R. K. Mofrad
Keywords: Cytoskeleton, Nuclear lamina, Cell biology, Mechanobiology, Cytoplasm, Nuclear pore, Intermediate filament, Biology, Lamin, Nucleoplasm, Nucleus, Nuclear protein, Nucleolus, Genetics, Transcription factor, Cell
Dynamic Regulation of α-Actinin’s Calponin Homology Domains on F-Actin
Authors: Hengameh Shams, Javad Golji, Kiavash Garakani, Mohammad R. K. Mofrad
Keywords: Actinin, Actin, Cytoskeleton, Actin-binding protein, Binding domain, Mutant, Cell biology, Actin cytoskeleton, Point mutation, Chemistry, Mutation, Biology, Biophysics, Binding site, Biochemistry, Gene, Cell
Agent-Based Modeling of Biological Pathways - A Case-Study on mRNA Export and Quality Control Mechanism
Authors: Mohammad Soheilypour, Mohammad R. K. Mofrad
Keywords: Mechanism (biology), Quality (philosophy), Computer science, Computational biology, Process (computing), Messenger RNA, Biological system, Biochemical engineering, Biology, Chemistry, Gene, Physics, Engineering, Genetics
Distinct Roles of α-Actinin in Regulating Talin-Induced Activation of αIIbβ3 versus α5β1 Integrins
Authors: Hengameh Shams, Mohammad R. K. Mofrad
Keywords: Integrin, Cell biology, Adhesion, Chemistry, Cell adhesion, Focal adhesion, Actin, Actin cytoskeleton, Signal transduction, Receptor, Cytoskeleton, Cell, Biology, Biochemistry
Like-Charge Regions (LCRs) and other Evolutionarily Conserved Features Regulate FG Network Formation at the Center of the NPC
Authors: Mohaddeseh Peyro, Mohammad Soheilypour, Briana Lynne Lee, Ali Ghavami, Mohammad R. K. Mofrad
Keywords: Center (category theory), Charge (physics), Evolutionary biology, Biology, Computational biology, Physics, Chemistry, Crystallography
Molecular Mechanism of α-Actinin Binding to F-Actin: Effect of K255E Mutation
Authors: Hengameh Shams, Kiavash Garakani, Javad Golji, Mohammad R. K. Mofrad
Keywords: Actin, Cytoskeleton, Actinin, Actin cytoskeleton, Chemistry, Actin-binding protein, Biophysics, Cell biology, Actin remodeling, Biology, Biochemistry, Cell
Molecular Mechanisms of Mechanotransduction through LINC Complexes
Authors: Zeinab Jahed, Hengameh Shams, Mohammad R. K. Mofrad
Keywords: Mechanotransduction, Biophysics, Cytoskeleton, Covalent bond, Chemistry, Molecular dynamics, Cysteine, Biology, Cell biology, Biochemistry, Enzyme, Computational chemistry
Molecular Mechanisms of STIM1-Mediated Orai-1 Channel Activation
Authors: Zainab Haydari, Hengameh Shams, Mohammad R. K. Mofrad
Keywords: STIM1, Chemistry, Endoplasmic reticulum, Cell biology, Calcium signaling, Intracellular, Signal transduction, Biophysics, Ion channel, Biochemistry, Biology, Receptor
Comparing Fifty Natural Languages and Twelve Genetic Languages Using Word Embedding Language Divergence (WELD) as a Quantitative Measure of Language Distance
Authors: Ehsaneddin Asgari, Mohammad R. K. Mofrad
We introduce a new measure of distance between languages based on word embedding, called word embedding language divergence (WELD). WELD is defined as divergence between unified similarity distribution of words between languages. Using s...
Keywords: Computer science, Natural language processing, Language family, Artificial intelligence, Word embedding, Natural language, Word (group theory), Language identification, Sentence, Divergence (linguistics), Coding (social sciences), Identification (biology), Linguistics, Embedding, Similarity (geometry), Mathematics, Biology, Statistics
Enhanced intracellular delivery of small molecules and drugs via non-covalent ternary dispersions of single-wall carbon nanotubes
Authors: Patrick D. Boyer, Hengameh Shams, Stefanie L. Baker, Mohammad R. K. Mofrad, Mohammad F. Islam, Kris Noel Dahl
Albumins are used biologically and pharmacologically as transport proteins to deliver molecules to cells. Albumins also efficiently coat single-wall carbon nanotubes (SWCNTs) and promote their entry into mammalian and immune cells by the...
Keywords: Bovine serum albumin, HeLa, Carbon nanotube, Rhodamine B, Fluorescence, Drug delivery, Molecule, Rhodamine, Biophysics, Materials science, Ternary operation, Small molecule, Covalent bond, Intracellular, Nanotechnology, Chemistry, Cell, Biochemistry, Organic chemistry, Biology
Interferon Beta: From Molecular Level to Therapeutic Effects
Authors: Mohadeseh Haji Abdolvahab, Mohammad R. K. Mofrad, Huub Schellekens
Keywords: Immunogenicity, Biology, Interferon, Immune system, Epitope, Cytokine, Immunology, Mechanism (biology), Cell, Signal transduction, Antibody, Computational biology, Cell biology, Genetics
Text Analysis and Automatic Triage of Posts in a Mental Health Forum
Authors: Ehsaneddin Asgari, Soroush Nasiriany, Mohammad R. K. Mofrad
We present an approach for automatic triage of message posts in ReachOut.com mental health forum, which was a shared task in the 2016 Computational Linguistics and Clinical Psychology (CLPsych). This effort is aimed at providing the trai...
Keywords: Triage, Mental health, Support vector machine, Random forest, Computer science, Identification (biology), Classifier (UML), Task (project management), Artificial intelligence, Machine learning, Psychology, Psychiatry, Engineering
2015
Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex
Authors: Mohaddeseh Peyro, Mohammad Soheilypour, Ali Ghavami, Mohammad R. K. Mofrad
Nucleocytoplasmic transport has been the subject of a large body of research in the past few decades. Recently, the focus of investigations in this field has shifted from studies of the overall function of the nuclear pore complex (NPC) ...
Keywords: Nucleoporin, Nuclear pore, Molecular dynamics, Homogeneous, Nuclear transport, Biophysics, Physics, Chemistry, Biology, Nucleus, Statistical physics, Cell biology, Cell nucleus
Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics
Authors: Ehsaneddin Asgari, Mohammad R. K. Mofrad
We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-...
Keywords: Structural genomics, Computational biology, Protein sequencing, Proteomics, Structural Classification of Proteins database, Genomics, Protein methods, Protein family, Support vector machine, Computer science, Feature vector, Representation (politics), Protein function prediction, Protein Data Bank, Artificial intelligence, Pattern recognition (psychology), Biology, Protein structure, Sequence analysis, Genome, Peptide sequence, Genetics, Gene
Evolutionarily Conserved Sequence Features Regulate the Formation of the FG Network at the Center of the Nuclear Pore Complex
Authors: Mohaddeseh Peyro, Mohammad Soheilypour, Bertrand Lee, Mohammad R. K. Mofrad
Keywords: Nuclear pore, Nucleoporin, Nuclear transport, Cytoplasm, Biophysics, Intrinsically disordered proteins, Sequence (biology), Chemistry, Nucleus, Center (category theory), Polar, Cell nucleus, Crystallography, Physics, Biology, Cell biology, Biochemistry
Adhesion characteristics ofStaphylococcus aureusbacterial cells on funnel-shaped palladium–cobalt alloy nanostructures
Authors: Junhua Gu, Paul Chen, Brandon B. Seo, Joanna M. Jardin, Mohit S. Verma, Zeinab Jahed, Mohammad R. K. Mofrad, Frank Gu, Ting Y. Tsui
The adhesion properties of Staphylococcus aureus on palladium–cobalt (Pd–Co) alloy nanostructures with various cross-sectional geometries have been characterised. They include solid core, hollow, c-shaped, and x-shaped pillars. These pil...
Keywords: Materials science, Adhesion, Alloy, Staphylococcus aureus, Nanostructure, Cobalt, Palladium, Funnel, Core (optical fiber), Composite material, Nanotechnology, Metallurgy, Chemistry, Bacteria, Biology
A Disulfide Bond Is Required for the Transmission of Forces through SUN-KASH Complexes
Authors: Zeinab Jahed, Hengameh Shams, Mohammad R. K. Mofrad
Keywords: Cytoskeleton, Mechanosensitive channels, Biophysics, Mechanotransduction, Chemistry, Nucleus, Cell biology, Biology, Cell, Biochemistry, Receptor
Cooperation within von Willebrand factors enhances adsorption mechanism
Authors: Maziar Heidari, Mehrdad Mehrbod, Mohammad Reza Ejtehadi, Mohammad R. K. Mofrad
von Willebrand factor (VWF) is a naturally collapsed protein that participates in primary haemostasis and coagulation events. The clotting process is triggered by the adsorption and conformational changes of the plasma VWFs localized to ...
Keywords: Cooperativity, Adsorption, Von Willebrand factor, van der Waals force, Chemistry, Biophysics, Coagulation, Chemical physics, Molecule, Platelet, Biochemistry, Physical chemistry, Immunology, Organic chemistry
Torsional Behavior of Axonal Microtubule Bundles
Authors: Carole Lazarus, Mohammad Soheilypour, Mohammad R. K. Mofrad
Keywords: Microtubule, Bundle, Torsion (gastropod), Axon, Ultimate tensile strength, Materials science, Cytoskeleton, Biophysics, Tension (geology), Composite material, Anatomy, Chemistry, Biology
Trapping polystyrene and latex nanospheres inside hollow nanostructures usingStaphylococcus aureuscells
Authors: Brandon B. Seo, Paul Chen, Zeinab Jahed, Mohammad R. K. Mofrad, Frank Gu, Ting Y. Tsui
A new methodology was developed to trap polystyrene or latex nanospheres in nanocrystalline nickel columnar nanostructures with various cross-sectional geometries. After filling the column interiors with polystyrene or latex nanospheres ...
Keywords: Materials science, Polystyrene, Nanopillar, Nanostructure, Nanocrystalline material, Scanning electron microscope, Staphylococcus aureus, Adhesive, Nickel, Trapping, Nanoparticle, Nanotechnology, Composite material, Polymer, Layer (electronics), Bacteria, Metallurgy
Coupled Simulation of Heart Valves: Applications to Clinical Practice
Authors: Ahmed A. Bakhaty, Mohammad R. K. Mofrad
Keywords: Modalities, Computer science, Heart valve, Clinical Practice, Heart disease, Disease, Intensive care medicine, Medicine, Risk analysis (engineering), Cardiology, Pathology
Buckling Behavior of Individual and Bundled Microtubules
Authors: Mohammad Soheilypour, Mohaddeseh Peyro, Stephen J. Peter, Mohammad R. K. Mofrad
Keywords: Buckling, Microtubule, Cytoskeleton, Compression (physics), Protein filament, Tension (geology), Stiffness, Bending, Biophysics, Bundle, Intermediate filament, Organelle, Buckle, Materials science, Nanotechnology, Chemistry, Biology, Composite material, Cell, Cell biology
The Interaction of RNA Helicase DDX3 with HIV-1 Rev-CRM1-RanGTP Complex during the HIV Replication Cycle
Authors: Seyed Hanif Mahboobi, Alex A. Javanpour, Mohammad R. K. Mofrad
Molecular traffic between the nucleus and the cytoplasm is regulated by the nuclear pore complex (NPC), which acts as a highly selective channel perforating the nuclear envelope in eukaryotic cells. The human immunodeficiency virus (HIV)...
Keywords: Ran, Nuclear export signal, Cell biology, Helicase, Biology, Nuclear transport, RNA Helicase A, RNA, Genetics, Cell nucleus, Cytoplasm, Gene
Directional migration and differentiation of neural stem cells within three-dimensional microenvironments
Authors: Amir Shamloo, Motahare Heibatollahi, Mohammad R. K. Mofrad
Harnessing neural stem cells to repair neuronal damage is a promising potential treatment for neuronal diseases. To enable future therapeutic efficacy, the survival, proliferation, migration and differentiation of neural stem/progenitor ...
Keywords: Neural stem cell, Stem cell, Cell biology, Neuroscience, Biology, Cellular differentiation, Biochemistry, Gene
Mechanisms of integrin and filamin binding and their interplay with talin during early focal adhesion formation
Authors: Tiffany Truong, Hengameh Shams, Mohammad R. K. Mofrad
Filamin plays a key role in cellular biomechanics as an actin cross-linker and as a versatile focal adhesion binding partner. It binds directly to integrins, a family of mechanosensitive transmembrane receptors that mediate attachment to...
Keywords: Filamin, Focal adhesion, Integrin, Adhesion, Cell biology, Chemistry, Biology, Cytoskeleton, Biochemistry, Signal transduction, Receptor, Cell
2014
Emerging Trends in Heart Valve Engineering: Part I. Solutions for Future
Authors: Arash Kheradvar, Elliott M. Groves, Lakshmi Prasad Dasi, S. Hamed Alavi, Robert T. Tranquillo, K. Jane Grande‐Allen, Craig A. Simmons, Boyce E. Griffith, Ahmad Falahatpisheh, Craig J. Goergen, Mohammad R. K. Mofrad, Frank Frank Baaijens, Stephen H. Little, Sunčica Čanić
Keywords: Heart valve, Tissue engineering, Heart valve replacement, Biomedical engineering, Process (computing), Biocompatible material, Nanotechnology, Computer science, Materials science, Biochemical engineering, Engineering, Cardiology, Medicine
Emerging Trends in Heart Valve Engineering: Part II. Novel and Standard Technologies for Aortic Valve Replacement
Authors: Arash Kheradvar, Elliott M. Groves, Craig J. Goergen, S. Hamed Alavi, Robert T. Tranquillo, Craig A. Simmons, Lakshmi Prasad Dasi, K. Jane Grande‐Allen, Mohammad R. K. Mofrad, Ahmad Falahatpisheh, Boyce E. Griffith, Frank Frank Baaijens, Stephen H. Little, Sunčica Čanić
Keywords: LEAPS, Heart valve, Valve replacement, The Renaissance, Aortic valve replacement, Heart valve replacement, Medicine, Cardiology, Internal medicine, valvular heart disease, Engineering, Business, Stenosis
Emerging Trends in Heart Valve Engineering: Part III. Novel Technologies for Mitral Valve Repair and Replacement
Authors: Arash Kheradvar, Elliott M. Groves, Craig A. Simmons, Boyce E. Griffith, S. Hamed Alavi, Robert T. Tranquillo, Lakshmi Prasad Dasi, Ahmad Falahatpisheh, K. Jane Grande‐Allen, Craig J. Goergen, Mohammad R. K. Mofrad, Frank Frank Baaijens, Sunčica Čanić, Stephen H. Little
Keywords: Mitral valve, Mitral valve replacement, Catheter, Mitral valve repair, Cardiology, Internal medicine, Medicine, Heart valve, Prosthesis design, Biomedical engineering, Surgery, Aortic valve
The Talin Dimer Structure Orientation Is Mechanically Regulated
Authors: Javad Golji, Mohammad R. K. Mofrad
Keywords: Vinculin, Focal adhesion, Dimer, Biophysics, Integrin, Chemistry, Cell, Biochemistry, Biology
An agent-based model for mRNA export through the nuclear pore complex
Authors: Mohammad Daud Azimi, Evgeny Bulat, Karsten Weis, Mohammad R. K. Mofrad
mRNA export from the nucleus is an essential step in the expression of every protein- coding gene in eukaryotes, but many aspects of this process remain poorly understood. The density of export receptors that must bind an mRNA to ensure ...
Keywords: Nuclear pore, Biology, Messenger RNA, Nuclear export signal, Cell biology, Limiting, Nuclear transport, Cytoplasm, Cell nucleus, Biophysics, Gene, Genetics
Cell responses to metallic nanostructure arrays with complex geometries
Authors: Zeinab Jahed, Sara Molladavoodi, Brandon B. Seo, Maud Gorbet, Ting Y. Tsui, Mohammad R. K. Mofrad
Keywords: Nanopillar, Materials science, Nanotechnology, Nanostructure, Nanowire
The α-Subunit Regulates Stability of the Metal Ion at the Ligand-associated Metal Ion-binding Site in β3 Integrins
Authors: Xianliang Rui, Mehrdad Mehrbod, Johannes F. Van Agthoven, Saurabh Anand, Jian-Ping Xiong, Mohammad R. K. Mofrad, M. Amin Arnaout
Keywords: Integrin, Ligand (biochemistry), Chemistry, Metal, Protein subunit, Biophysics, Crystallography, Stereochemistry, Metal ions in aqueous solution, Binding site, Divalent, Biochemistry, Receptor, Biology, Organic chemistry
The Interaction of CRM1 and the Nuclear Pore Protein Tpr
Authors: Charles Zhao, Seyed Hanif Mahboobi, Ruhollah Moussavi-Baygi, Mohammad R. K. Mofrad
While much has been devoted to the study of transport mechanisms through the nuclear pore complex (NPC), the specifics of interactions and binding between export transport receptors and the NPC periphery have remained elusive. Recent wor...
Keywords: Ran, Nuclear transport, Nuclear pore, Binding site, Biophysics, Nuclear export signal, Plasma protein binding, Chemistry, Computational biology, Biology, Cell nucleus, Nucleus, Cell biology, Biochemistry
Atomic Basis for the Species-specific Inhibition of αV Integrins by Monoclonal Antibody 17E6 Is Revealed by the Crystal Structure of αVβ3 Ectodomain-17E6 Fab Complex
Authors: Bhuvaneshwari Mahalingam, Johannes F. Van Agthoven, Jian-Ping Xiong, José Luís Izquierdo Alonso, Brian D. Adair, Xianliang Rui, Saurabh Anand, Mehrdad Mehrbod, Mohammad R. K. Mofrad, Christa Burger, Simon L. Goodman, M. Amin Arnaout
Keywords: Ectodomain, Integrin, Chemistry, Immunoglobulin Fab Fragments, Monoclonal antibody, Allosteric regulation, Stereochemistry, Biochemistry, Biology, Antibody, Receptor, Complementarity determining region
Responses of Staphylococcus aureus bacterial cells to nanocrystalline nickel nanostructures
Authors: Zeinab Jahed, Peter H. Lin, Brandon B. Seo, Mohit S. Verma, Frank Gu, Ting Y. Tsui, Mohammad R. K. Mofrad
Keywords: Staphylococcus aureus, Nanocrystalline material, Materials science, Nanostructure, Adhesion, Bacteria, Nickel, Microbiology, Nanotechnology, Biology, Metallurgy, Composite material
Conformational Behavior of the Confined Fg-Repeat Domains in the Nuclear Pore
Authors: Ruhollah Moussavi-Baygi, Mohammad R. K. Mofrad
Keywords: Nuclear pore, Nucleoporin, Biophysics, Nucleus, Nuclear transport, Channel (broadcasting), Chemistry, Function (biology), Chemical physics, Physics, Nanotechnology, Materials science, Cell nucleus, Biology, Computer science, Evolutionary biology, Cell biology
How Talin Head Domain and Soluble Ligand Contribute to Integrin αIIbβ3 Activation
Authors: Mehrdad Mehrbod, Stephen L. Trisno, Mohammad R. K. Mofrad
Keywords: Integrin, Transmembrane domain, Salt bridge, Chemistry, Transmembrane protein, Biophysics, Cytoplasm, CD49c, Membrane, Cell biology, Integrin, beta 6, Biochemistry, Biology, Receptor, Mutant
Mechanotransduction Pathways Linking the Extracellular Matrix to the Nucleus
Authors: Zeinab Jahed, Hengameh Shams, Mehrdad Mehrbod, Mohammad R. K. Mofrad
Keywords: Extracellular matrix, Mechanotransduction, Cell biology, Cytoskeleton, Biology, Cell adhesion molecule, Cell adhesion, Focal adhesion, Integrin, Nuclear matrix, Signal transduction, Cell, Biochemistry, Chromatin
Molecular Mechanisms Underlying the Inside-Out Signaling through Focal Adhesions
Authors: Hengameh Shams, Mohammad R. K. Mofrad
Keywords: Focal adhesion, Filamin, Integrin, Cell biology, Extracellular matrix, Actin, Actin cytoskeleton, Cell adhesion molecule, Signal transduction, Cell adhesion, Cytoskeleton, Adhesion, Chemistry, Biology, Receptor, Cell, Biochemistry
2013
Actin Reorganization through Dynamic Interactions with Single-Wall Carbon Nanotubes
Authors: Hengameh Shams, Brian D. Holt, Seyed Hanif Mahboobi, Zeinab Jahed, Mohammad F. Islam, Kris Noel Dahl, Mohammad R. K. Mofrad
Single-wall carbon nanotubes (SWCNTs) have been widely used for biological applications in recent years, and thus, it is critical to understand how these inert nanomaterials influence cell behavior. Recently, it has been observed that ce...
Keywords: Carbon nanotube, Actin, Materials science, Nanomaterials, Nanotechnology, Actin cytoskeleton, Biophysics, Nanoscopic scale, Cytoskeleton, Molecular dynamics, Chemistry, Cell, Biology
Higher Nucleoporin-Importinβ Affinity at the Nuclear Basket Increases Nucleocytoplasmic Import
Authors: Mohammad Daud Azimi, Mohammad R. K. Mofrad
Several in vitro studies have shown the presence of an affinity gradient in nuclear pore complex proteins for the import receptor Importinβ, at least partially contributing to nucleocytoplasmic transport, while others have historically a...
Keywords: Nuclear pore, Nucleoporin, Nuclear transport, Importin, Biophysics, Chemistry, Cytoplasm, Biochemistry, Biology, Cell nucleus
Quantifying intracellular protein binding thermodynamics during mechanotransduction based on FRET spectroscopy
Authors: Nur Aida Abdul Rahim, Serge Pelet, Mohammad R. K. Mofrad, Peter T. C. So, Roger D. Kamm
Keywords: Förster resonance energy transfer, Biophysics, Mechanotransduction, Focal adhesion, Chemistry, Force spectroscopy, Paxillin, Allosteric regulation, Phosphorylation, Cytosol, Dissociation constant, Cell biology, Biochemistry, Fluorescence, Biology, Enzyme, Receptor, Molecule
Biomechanical properties of native and tissue engineered heart valve constructs
Authors: Anwarul Hasan, Kim Ragaert, Wojciech Święszkowski, Šeila Selimović, Arghya Paul, Gulden Camci‐Unal, Mohammad R. K. Mofrad, Ali Khademhosseini
Keywords: Heart valve, Biomedical engineering, Mechanical heart, Human heart, Medicine, Cardiology
On the Activation of Integrin αIIbβ3: Outside-in and Inside-out Pathways
Authors: Mehrdad Mehrbod, Stephen L. Trisno, Mohammad R. K. Mofrad
Keywords: Integrin, Transmembrane protein, Transmembrane domain, Salt bridge, Protein subunit, CD49c, Integrin, beta 6, Cytoplasm, Cell biology, Chemistry, FERM domain, Membrane, Collagen receptor, Membrane protein, Biophysics, Biology, Biochemistry, Integral membrane protein, Receptor, Mutant
The Interaction of Vinculin with Actin
Authors: Javad Golji, Mohammad R. K. Mofrad
Vinculin can interact with F-actin both in recruitment of actin filaments to the growing focal adhesions and also in capping of actin filaments to regulate actin dynamics. Using molecular dynamics, both interactions are simulated using d...
Keywords: Vinculin, Actin, Biophysics, Protein filament, Chemistry, Molecular dynamics, Cell biology, Focal adhesion, Biochemistry, Biology, Signal transduction, Computational chemistry
IEEE Transactions on Biomedical Engineering Associate Editors
Authors: Fabio Babiloni, James A. Bankson, S. Cerutti, Todd P. Coleman, Stuart Crozier, Aniruddha Datta, Igor R. Efimov, Dario Louis, Georg-August Farina, Ilko K. Ilev, U Food, Drug Admin, Partal Pedro, P.C.M. van de Kerkhof, Zong‐Ming Li, Paul M. Meaney, Silvestro Micera, Mohammad R. K. Mofrad, Ramakrishna Mukkamala, Klaus‐Robert Müller, Konstantina S. Nikita, Xiaochuan Pan, Stephen D. Patek, Stephen Patek
Keywords: Computer science, Engineering
Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering
Authors: Mehrdad Mehrbod, Mohammad R. K. Mofrad
Integrin clustering plays a pivotal role in a host of cell functions. Hetero-dimeric integrin adhesion receptors regulate cell migration, survival, and differentiation by communicating signals bidirectionally across the plasma membrane. ...
Keywords: Ectodomain, Integrin, CD49c, Integrin, beta 6, Transmembrane protein, Cell biology, Collagen receptor, Transmembrane domain, Protein subunit, Integrin alpha M, Biology, Cytoplasm, Cell, Membrane, Receptor, Biochemistry, Gene
2012
A Molecular Trajectory of α-Actinin Activation
Authors: Hengameh Shams, Javad Golji, Mohammad R. K. Mofrad
Keywords: Mechanotransduction, Vinculin, Biophysics, Chemistry, Umbrella sampling, Focal adhesion, Cell biology, Actin, Adhesion, Linker, Actinin, Cytoskeleton, Biochemistry, Signal transduction, Molecular dynamics, Biology
An agent based model of integrin clustering: Exploring the role of ligand clustering, integrin homo-oligomerization, integrin–ligand affinity, membrane crowdedness and ligand mobility
Authors: Yousef Jamali, Tahereh Jamali, Mohammad R. K. Mofrad
Keywords: Integrin, Ligand (biochemistry), Cluster analysis, Integrin, beta 6, Cell biology, CD49c, Cell adhesion, Signal transduction, Adhesion, Chemistry, Biology, Cell, Receptor, Biochemistry, Computer science, Artificial intelligence
Altered Cell Mechanics from the Inside: Dispersed Single Wall Carbon Nanotubes Integrate with and Restructure Actin
Authors: Brian D. Holt, Hengameh Shams, Travis A. Horst, Saurav Basu, Andrew D. Rape, Yuli Wang, Gustavo K. Rohde, Mohammad R. K. Mofrad, Mohammad F. Islam, Kris Noel Dahl
With a range of desirable mechanical and optical properties, single wall carbon nanotubes (SWCNTs) are a promising material for nanobiotechnologies. SWCNTs also have potential as biomaterials for modulation of cellular structures. Previo...
Keywords: Actin, Materials science, Cytokinesis, Carbon nanotube, Biophysics, Nanotechnology, Myosin, Cytoskeleton, Actin remodeling, Actin cytoskeleton, Cell, Cell biology, Chemistry, Cell division, Biology, Biochemistry
Phosphorylation Primes Vinculin for Activation
Authors: Javad Golji, Timothy J. Wendorff, Mohammad R. K. Mofrad
Keywords: Vinculin, Phosphorylation, Focal adhesion, Cell biology, Molecular dynamics, Chemistry, Actin, Adhesion, Kinase, Biophysics, Biology
Computational Modeling of Axonal Microtubule Bundles under Tension
Authors: Stephen J. Peter, Mohammad R. K. Mofrad
Keywords: Microtubule, Bundle, Materials science, Axon, Tension (geology), Structural integrity, Ultimate tensile strength, Biophysics, Composite material, Neuroscience, Structural engineering, Biology, Cell biology, Engineering
Passive control of cell locomotion using micropatterns: the effect of micropattern geometry on the migratory behavior of adherent cells
Authors: Sang‐Hee Yoon, Young Kyun Kim, Eui Don Han, Young-Ho Seo, Byeong Hee Kim, Mohammad R. K. Mofrad
Directed cell migration is critical to a variety of biological and physiological processes. Although simple topographical patterns such as parallel grooves and three-dimensional post arrays have been studied to guide cell migration, the ...
Keywords: Cell migration, Divergence (linguistics), Characterization (materials science), Materials science, Pseudopodia, Biophysics, Biological system, Cell, Nanotechnology, Geometry, Chemistry, Biology, Mathematics
2011
On the Significance of Microtubule Flexural Behavior in Cytoskeletal Mechanics
Authors: Mehrdad Mehrbod, Mohammad R. K. Mofrad
Quantitative description of cell mechanics has challenged biological scientists for the past two decades. Various structural models have been attempted to analyze the structure of the cytoskeleton. One important aspect that has been larg...
Keywords: Cytoskeleton, Microtubule, Buckling, Mechanics, Tensegrity, Physics, Materials science, Structural engineering, Chemistry, Biology, Cell biology, Engineering, Cell, Composite material
Accounting for Diffusion in Agent Based Models of Reaction-Diffusion Systems with Application to Cytoskeletal Diffusion
Authors: Mohammad Daud Azimi, Yousef Jamali, Mohammad R. K. Mofrad
Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between p...
Keywords: Diffusion, Biological system, Discretization, Anomalous diffusion, Computer science, Viscosity, Statistical physics, Physics, Mathematics, Thermodynamics
Cell adhesion and detachment on gold surfaces modified with a thiol-functionalized RGD peptide
Authors: Sang-Hee Yoon, Mohammad R. K. Mofrad
Keywords: Adhesion, Cell adhesion, Biophysics, Materials science, Cell, Monolayer, Nanotechnology, Chemistry, Cell biology, Biochemistry, Biology, Composite material
Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex
Authors: Ruhollah Moussavi-Baygi, Yousef Jamali, Reza Karimi, Mohammad R. K. Mofrad
The nuclear pore complex (NPC) regulates molecular traffic across the nuclear envelope (NE). Selective transport happens on the order of milliseconds and the length scale of tens of nanometers; however, the transport mechanism remains el...
Keywords: Nuclear pore, Nuclear transport, Biophysics, Brownian dynamics, Molecular dynamics, Cytoplasm, Chemistry, Chemical physics, Physics, Brownian motion, Biology, Cell nucleus, Computational chemistry, Biochemistry
MEMS-based dynamic cell-to-cell culture platforms using electrochemical surface modifications
Authors: Jiyoung Chang, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Liwei Lin
MEMS-based biological platforms with the capability of both spatial placements and time releases of living cells for cell-to-cell culture experiments have been designed and demonstrated utilizing electrochemical surface modification effe...
Keywords: Electrode, Materials science, Microelectromechanical systems, Indium tin oxide, Nanotechnology, Electrochemical cell, Substrate (aquarium), Electrochemistry, Optoelectronics, Biomedical engineering, Chemistry, Engineering
Viscoelastic characterization of the retracting cytoskeleton using subcellular detachment
Authors: Sang-Hee Yoon, Chan Lee, Mohammad R. K. Mofrad
Characterization of the cytoskeleton’s viscoelastic properties is essential for understanding cellular dynamics in many biological functions of the cell, especially cell migration. The viscoelastic properties of the retracting NIH 3T3 fi...
Keywords: Viscoelasticity, Cytoskeleton, Characterization (materials science), Biophysics, Materials science, Chemistry, Cell, Nanotechnology, Biology, Composite material, Biochemistry
Biophysical Coarse-Grained Modeling Provides Insights into Transport through the Nuclear Pore Complex
Authors: Ruhollah Moussavi-Baygi, Yousef Jamali, Reza Karimi, Mohammad R. K. Mofrad
Keywords: Nuclear transport, Biophysics, Nuclear pore, Channel (broadcasting), Water transport, Chemistry, Nucleus, Biological system, Nanotechnology, Chemical physics, Physics, Mechanics, Materials science, Computer science, Cell nucleus, Biology, Environmental science, Telecommunications
Exploring Cellular Mechanotransduction at the Focal Adhesions, One Molecule at a Time
Authors: Mohammad R. K. Mofrad
Keywords: Mechanotransduction, Focal adhesion, Vinculin, Filamin, Cytoskeleton, Chemistry, Function (biology), Cell biology, Biophysics, Cell adhesion molecule, Molecular dynamics, Cell adhesion, Adhesion, Nanotechnology, Biology, Signal transduction, Cell, Materials science, Biochemistry
A biological breadboard platform for cell adhesion and detachment studies
Authors: Sang‐Hee Yoon, Jiyoung Chang, Liwei Lin, Mohammad R. K. Mofrad
The dynamic nature of cell adhesion and detachment, which plays a critical role in a variety of physiological and pathological phenomena, still remains unclear. This motivates the pursuit of controllable manipulation of cell adhesion and...
Keywords: Adhesion, Cell adhesion, Nanotechnology, Biophysics, Chemistry, Substrate (aquarium), Polyethylene glycol, Monolayer, PEG ratio, Cell, Materials science, Biochemistry, Organic chemistry, Biology
Vinculin Activation Is Necessary for Complete Talin Binding
Authors: Javad Golji, Johnny Lam, Mohammad R. K. Mofrad
Keywords: Vinculin, Chemistry, Focal adhesion, Biophysics, Conformational change, Plasma protein binding, Biochemistry, Biology, Signal transduction
2010
A Sub-Cellular Viscoelastic Model for Cell Population Mechanics
Authors: Yousef Jamali, Mohammad Daud Azimi, Mohammad R. K. Mofrad
Understanding the biomechanical properties and the effect of biomechanical force on epithelial cells is key to understanding how epithelial cells form uniquely shaped structures in two or three-dimensional space. Nevertheless, with the l...
Keywords: Extracellular matrix, Cell, Viscoelasticity, Population, Cell biology, Biological system, Chemistry, Biology, Physics
A Molecular Dynamics Investigation of Vinculin Activation
Authors: Javad Golji, Mohammad R. K. Mofrad
Keywords: Vinculin, Actin, Molecular dynamics, Biophysics, Chemistry, Cytoskeleton, Actin cytoskeleton, Focal adhesion, Cell biology, Biochemistry, Biology, Signal transduction, Computational chemistry
Liver-Assist Device With a Microfluidics-Based Vascular Bed in an Animal Model
Authors: Wen‐Ming Hsu, Amedeo Carraro, Katherine M. Kulig, Mark L. Miller, Mohammad R. K. Mofrad, Eli J. Weinberg, Fateh Entabi, Hassan Albadawi, Michael T. Watkins, Jeffrey T. Borenstein, Joseph P. Vacanti, Craig M. Neville
This device is the first to incorporate a microfluidics network in the systemic circulatory system. The microvascular network supported viability and function of liver cells in a short-term ex vivo model. Parenchymal chamber pressure gen...
Keywords: Microfluidics, Biomedical engineering, Medicine, Shunt (medical), Parenchyma, Pathology, Cardiology, Materials science, Nanotechnology
Analysis of Circular PDMS Microballoons With Ultralarge Deflection for MEMS Design
Authors: Sang‐Hee Yoon, Vimalier Reyes-Ortiz, Kwangho Kim, Young Ho Seo, Mohammad R. K. Mofrad
This paper presents the simplified analytical and numerical analyses of the ultralarge deflection of circular polydimethylsiloxane (PDMS) microballoons (MBs) under pressure for microelectromechanical systems design. The analytical model ...
Keywords: Polydimethylsiloxane, Materials science, Deflection (physics), Membrane, Glass microsphere, Composite material, Microelectromechanical systems, Polymer, Modulus, Elastic modulus, Curing (chemistry), Microsphere, Nanotechnology, Optics, Chemical engineering, Chemistry
Averaged implicit hydrodynamic model of semiflexible filaments
Authors: Preethi L. Chandran, Mohammad R. K. Mofrad
We introduce a method to incorporate hydrodynamic interaction in a model of semiflexible filament dynamics. Hydrodynamic screening and other hydrodynamic interaction effects lead to nonuniform drag along even a rigid filament, and cause ...
Keywords: Drag, Protein filament, Superposition principle, Brownian dynamics, Physics, Mechanics, String (physics), Classical mechanics, Brownian motion, Materials science, Theoretical physics
Mechanotransduction: a major regulator of homeostasis and development
Authors: Kevin S. Kolahi, Mohammad R. K. Mofrad
In nearly all aspects of biology, forces are a relevant regulator of life's form and function. More recently, science has established that cells are exquisitely sensitive to forces of varying magnitudes and time scales, and they convert ...
Keywords: Mechanotransduction, Organism, Regulator, Biology, Cell biology, Mechanobiology, Homeostasis, Neuroscience, Genetics
Carotid Atheroma Rupture Observed In Vivo and FSI-Predicted Stress Distribution Based on Pre-rupture Imaging
Authors: Joseph Leach, Vitaliy L. Rayz, Bruno P. Soares, Max Wintermark, Mohammad R. K. Mofrad, David Saloner
Keywords: Atheroma, Lesion, Fibrous cap, In vivo, Stroke (engine), Medicine, Radiology, Pathology, Cardiology, Physics, Biology
Molecular Biomechanics: The Molecular Basis of How Forces Regulate Cellular Function
Authors: Gang Bao, Roger D. Kamm, Wendy E. Thomas, Wonmuk Hwang, Daniel A. Fletcher, Alan J. Grodzinsky, Cheng Zhu, Mohammad R. K. Mofrad
Keywords: Mechanotransduction, Biomechanics, Mechanobiology, Neuroscience, Nanotechnology, Computer science, Biology, Physiology, Anatomy, Materials science
Hemodynamic Environments from Opposing Sides of Human Aortic Valve Leaflets Evoke Distinct Endothelial Phenotypes In Vitro
Authors: Eli J. Weinberg, Peter J. Mack, Frederick J. Schoen, Guillermo García‐Cardeña, Mohammad R. K. Mofrad
The regulation of valvular endothelial phenotypes by the hemodynamic environments of the human aortic valve is poorly understood. The nodular lesions of calcific aortic stenosis (CAS) develop predominantly beneath the aortic surface of t...
Keywords: Aortic valve, Aortic valve stenosis, Shear stress, Hemodynamics, Pulsatile flow, Bicuspid aortic valve, Cardiac cycle, Internal medicine, Aorta, Heart valve, Cardiology, Medicine, Mechanics, Physics
On the multiscale modeling of heart valve biomechanics in health and disease
Authors: Eli J. Weinberg, Danial Shahmirzadi, Mohammad R. K. Mofrad
Theoretical models of the human heart valves are useful tools for understanding and characterizing the dynamics of healthy and diseased valves. Enabled by advances in numerical modeling and in a range of disciplines within experimental b...
Keywords: Biomechanics, Heart valve, Multiscale modeling, Computer science, valvular heart disease, Management science, Engineering, Medicine, Cardiology, Bioinformatics, Anatomy
MEMS-based biological platform for dynamic cell-to-cell interaction characterization
Authors: Jiyoung Chang, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Liwei Lin
MEMS-based biological platforms with the capability of spatiotemporal control of living cells have been demonstrated. The space control is accomplished by microfabrication to have targeted gaps between two adjacent culture areas. The tim...
Keywords: Microfabrication, Microelectromechanical systems, Cell culture, Living cell, Computer science, Microfluidics, Fibroblast, Nanotechnology, Materials science, Biological system, Biology
2009
Phosphorylation Facilitates the Integrin Binding of Filamin under Force
Authors: Harvey S. Chen, Kevin S. Kolahi, Mohammad R. K. Mofrad
Keywords: Filamin, Phosphorylation, Chemistry, Cell biology, Integrin, Biophysics, Biology, Biochemistry, Cytoskeleton, Receptor
Pulmonary Tissue Engineering using Dual-Compartment Polymer Scaffolds with Integrated Vascular Tree
Authors: C. Fritsche, Oliver Simsch, Eli J. Weinberg, Brian K. Orrick, Christof Stamm, Mohammad R. K. Mofrad, Jeffrey T. Borenstein, Roland Hetzer, Joseph P. Vacanti
We conclude that functional hybrid microsystems mimicking the basic building plan of alveolar tissue can be engineered in vitro.
Keywords: Microcarrier, Tissue engineering, Biomedical engineering, Parenchyma, Transplantation, Cell biology, Pathology, Chemistry, Cell, Biology, Medicine, Surgery
An efficient two-stage approach for image-based FSI analysis of atherosclerotic arteries
Authors: Joseph Leach, Vitaliy L. Rayz, Mohammad R. K. Mofrad, David Saloner
Patient-specific biomechanical modeling of atherosclerotic arteries has the potential to aid clinicians in characterizing lesions and determining optimal treatment plans. To attain high levels of accuracy, recent models use medical imagi...
Keywords: Polygon mesh, Computer science, Computation, Domain (mathematical analysis), Construct (python library), Computational fluid dynamics, Simulation, Algorithm, Mathematics, Engineering, Computer graphics (images)
A Computational Model of Aging and Calcification in the Aortic Heart Valve
Authors: Eli J. Weinberg, Frederick J. Schöen, Mohammad R. K. Mofrad
The aortic heart valve undergoes geometric and mechanical changes over time. The cusps of a normal, healthy valve thicken and become less extensible over time. In the disease calcific aortic stenosis (CAS), calcified nodules progressivel...
Keywords: Calcification, Aortic valve, Cardiology, Internal medicine, Stenosis, Aortic valve stenosis, Medicine, Pathological
Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior
Authors: Javad Golji, Robert C. Collins, Mohammad R. K. Mofrad
alpha-Actinin is an actin crosslinking molecule that can serve as a scaffold and maintain dynamic actin filament networks. As a crosslinker in the stressed cytoskeleton, alpha-actinin can retain conformation, function, and strength. alph...
Keywords: Spectrin, Actinin, Biophysics, Actin, Molecular dynamics, Twist, Molecular motor, Cytoskeleton, Materials science, Chemistry, Biochemistry, Biology, Geometry, Computational chemistry
Quantitative analysis of epithelial morphogenesis in Drosophila oogenesis: New insights based on morphometric analysis and mechanical modeling
Authors: Kevin S. Kolahi, Phoebe White, D.M. Shreter, Anne-Kathrin Classen, David Bilder, Mohammad R. K. Mofrad
Keywords: Morphogenesis, Biology, Epithelium, Cell biology, Germline, Flattening, Live cell imaging, Developmental biology, Anatomy, Cell, Genetics
Band-like Stress Fiber Propagation in a Continuum and Implications for Myosin Contractile Stresses
Authors: Preethi L. Chandran, Christopher B. Wolf, Mohammad R. K. Mofrad
Stress fibers are band-like features that form with sarcomere-like actin and myosin arrangement between cell regions, resisting myosin contractility. We consider three aspects of stress fiber formation: (1) they form by cytoskeletal acti...
Keywords: Myosin, Cytoskeleton, Actin, Stress fiber, Sarcomere, Physics, Biophysics, Myosin light-chain kinase, Myosin head, Mechanics, Chemistry, Biology, Cell biology, Myocyte, Cell
Coupling Atomistic Simulation to a Continuum Based Model to Compute the Mechanical Properties of Focal Adhesions
Authors: Robert Metzke, Mohammad R. K. Mofrad, Wolfgang A. Wall
Keywords: Finite element method, Focal adhesion, Molecular dynamics, Computation, Coupling (piping), Mechanics, Integrin, Biological system, Physics, Materials science, Chemistry, Classical mechanics, Biophysics, Computer science, Cell, Computational chemistry, Composite material, Thermodynamics, Biology, Algorithm
Straining the Laws of Attraction: Mechanotransduction Studied Through Changes in Intracellular Binding Energy
Authors: Nur Aida Abdul Rahim, Mohammad R. K. Mofrad, Peter T. C. So, Roger D. Kamm
Keywords: Biophysics, Mechanotransduction, Focal adhesion, Paxillin, Allosteric regulation, Chemistry, Dissociation constant, Phosphorylation, Cytosol, Force spectroscopy, Cell biology, Biochemistry, Biology, Receptor, Molecule, Enzyme
Rods-on-string idealization captures semiflexible filament dynamics
Authors: Preethi L. Chandran, Mohammad R. K. Mofrad
We present an approach to modeling the two-dimensional Brownian dynamics of semiflexible filaments in the worm-model description as uniform, isotropic, and continuously flexible. Experimental observations increasingly show that the mecha...
Keywords: Brownian dynamics, Classical mechanics, Physics, Brownian motion, Protein filament, Rod, Isotropy, Statistical physics, String (physics), Mechanics, Theoretical physics, Materials science, Quantum mechanics
2008
Estimation of Nonlinear Mechanical Properties of Vascular Tissues via Elastography
Authors: Reza Karimi, Ting Zhu, Brett E. Bouma, Mohammad R. K. Mofrad
Keywords: Optical coherence tomography, Nonlinear system, Elastography, Computer science, Finite element method, Sensitivity (control systems), Algorithm, Noise (video), Image (mathematics), Artificial intelligence, Computer vision, Acoustics, Physics, Electronic engineering, Engineering, Optics, Structural engineering
A multiscale computational comparison of the bicuspid and tricuspid aortic valves in relation to calcific aortic stenosis
Authors: Eli J. Weinberg, Mohammad R. K. Mofrad
Keywords: Bicuspid valve, Stenosis, Cardiology, Aortic valve, Bicuspid aortic valve, Internal medicine, Calcification, Medicine, Tricuspid valve
Rheology of the Cytoskeleton
Authors: Mohammad R. K. Mofrad
The cytoskeleton is the primary internal structure of the cell, providing its structural integrity. The rheology and mechanics of the cytoskeleton, therefore, are key to the cell's ability to accomplish its diverse functions in health an...
Keywords: Cytoskeleton, Rheology, Mechanics, Materials science, Physics, Biology, Cell, Genetics
In vitro analysis of a hepatic device with intrinsic microvascular-based channels
Authors: Amedeo Carraro, Wen‐Ming Hsu, Katherine M. Kulig, Wing S. Cheung, Mark L. Miller, Eli J. Weinberg, Eric F. Swart, Mohammad R. K. Mofrad, Jeffrey T. Borenstein, Joseph P. Vacanti, Craig M. Neville
Keywords: Microfluidics, Soft lithography, Nanotechnology, Wafer, Materials science, Biomedical engineering, Fabrication, Engineering, Pathology
MODELING THE EQUILIBRIUM STATE OF ADHERENT CELLS
Authors: Robert Metzke, Mohammad R. K. Mofrad, Wolfgang A. Wall
Keywords: Carcinogenesis, Cell culture, Cell growth, Cell, Immortalised cell line, Transfection, Biology, Cancer research, In vitro, Western blot, Molecular biology, Cell biology, Cancer, Chemistry, Gene, Genetics
Concept and Computational Design for a Bioartificial Nephron-On-A-Chip
Authors: Eli J. Weinberg, Mohammad R. K. Mofrad, Jeffrey T. Borenstein
A MEMS-based, (Micro Electro Mechanical System) bioartificial device is proposed for replicating the function of a single nephron. Consistent with the anatomy and physiology of humans, our device has 3 distinct sections, replicating the ...
Keywords: Nephron, Glomerulus, Computer science, Microfabrication, Organ-on-a-chip, Nanotechnology, Microfluidics, Materials science, Chemistry, Renal function, Kidney, Internal medicine, Medicine
On the Octagonal Structure of the Nuclear Pore Complex: Insights from Coarse-Grained Models
Authors: Christopher B. Wolf, Mohammad R. K. Mofrad
Keywords: Nuclear pore, Nucleoporin, Symmetry (geometry), Deformation (meteorology), Physics, Stiffness, Bending, Nuclear transport, Biology, Nucleus, Cell nucleus, Geometry, Mathematics, Cell biology, Thermodynamics
Molecular Dynamics Study of Talin-Vinculin Binding
Authors: S.E. Lee, Surasak Chunsrivirot, Roger D. Kamm, Mohammad R. K. Mofrad
Keywords: Vinculin, Dynamics (music), Molecular dynamics, Computational biology, Biophysics, Chemistry, Cell biology, Focal adhesion, Biology, Physics, Signal transduction, Computational chemistry
Master Proof Molecular Dynamics Study of Talin-Vinculin Binding
Authors: S. E. Lee, Surasak Chunsrivirot, Roger D. Kamm, Mohammad R. K. Mofrad
Cells can sense mechanical force in regulating focal adhesion assembly. One vivid example is the force-induced recruitment of vinculin to reinforce initial contacts between a cell and the extracellular matrix. Crystal structures of the u...
Keywords: Vinculin, Biophysics, Chemistry, Molecular dynamics, Binding site, Helix (gastropod), Plasma protein binding, Conformational change, Focal adhesion, Crystallography, Stereochemistry, Biochemistry, Biology, Signal transduction, Computational chemistry
On the cytoskeleton and soft glassy rheology
Authors: Kranthi K. Mandadapu, Sanjay Govindjee, Mohammad R. K. Mofrad
Keywords: Microrheology, Rheology, Cytoskeleton, Soft matter, Polymer science, Materials science, Mechanics, Nanotechnology, Physics, Chemistry, Composite material, Cell, Physical chemistry
2007
Transient, Three-dimensional, Multiscale Simulations of the Human Aortic Valve
Authors: Eli J. Weinberg, Mohammad R. K. Mofrad
Keywords: Scale (ratio), Transient (computer programming), Aortic valve, Cusp (singularity), Mechanics, Closing (real estate), Nonlinear system, Anisotropy, Biological system, Materials science, Computer science, Geometry, Physics, Mathematics, Optics, Biology
Molecular Mechanics of Filamin's Rod Domain
Authors: Kevin S. Kolahi, Mohammad R. K. Mofrad
Keywords: Filamin, Cytoskeleton, Actin, Actin cytoskeleton, FLNA, Biophysics, Function (biology), Molecular dynamics, Molecular mechanics, Chemistry, Domain (mathematical analysis), Cell biology, Biology, Biochemistry, Cell, Computational chemistry
Liver assist device as bridge for liver transplant in hepatic failure: A first in vivo step of tissue engineering development
Authors: Amedeo Carraro, Wen‐Ming Hsu, Mark L. Miller, Katherine M. Kulig, Craig M. Neville, Jeffrey T. Borenstein, Keisha Bonner, B. Orrick, Eli J. Weinberg, Eric F. Swart, Kelly Morgan, Mohammad R. K. Mofrad, Umberto Cillo, Joseph P. Vacanti
Keywords: Bridge (graph theory), Medicine, Liver tissue, In vivo, Liver failure, Liver transplantation, Biomedical engineering, Internal medicine, Transplantation, Biotechnology, Biology
Microfabrication of Three-Dimensional Engineered Scaffolds
Authors: Jeffrey T. Borenstein, Eli J. Weinberg, Brian K. Orrick, Cathryn A. Sundback, Mohammad R. K. Mofrad, Joseph P. Vacanti
One of the principal challenges facing the field of tissue engineering over the past 2 decades has been the requirement for large-scale engineered constructs comprising precisely organized cellular microenvironments. For vital organ assi...
Keywords: Microfabrication, Scaffold, Tissue engineering, Microfluidics, Nanotechnology, Biofabrication, Biocompatible material, Materials science, Biomedical engineering, Computer science, Fabrication, Engineering
A computational study on power-law rheology of soft glassy materials with application to cell mechanics
Authors: A. Vaziri, Zhenyu Xue, Roger D. Kamm, Mohammad R. K. Mofrad
Keywords: Microrheology, Rheology, Power law, Cytoskeleton, Mechanics, Materials science, Physics, Classical mechanics, Nanotechnology, Chemistry, Mathematics, Cell, Thermodynamics
Special Issue on Computational Bioengineering
Authors: Suvranu De, Farshid Guilak, Mohammad R. K. Mofrad
Keywords: Postcrania, Taxon, Pleistocene, Cladistics, Evolutionary biology, Range (aeronautics), Geography, Biology, Paleontology, Zoology, Phylogenetic tree
Force-induced activation of Talin and its possible role in focal adhesion mechanotransduction
Authors: Seung E. Lee, Roger D. Kamm, Mohammad R. K. Mofrad
Keywords: Vinculin, Focal adhesion, Biophysics, Chemistry, Mechanotransduction, Molecular dynamics, Integrin, Conformational change, Cell biology, Stereochemistry, Biochemistry, Signal transduction, Biology, Receptor, Computational chemistry
2006
Mechanics and deformation of the nucleus in micropipette aspiration experiment
Authors: Ashkan Vaziri, Mohammad R. K. Mofrad
Keywords: Viscoelasticity, Lamin, Nucleoplasm, Nucleus, Nuclear lamina, Pipette, Mechanics, Deformation (meteorology), Envelope (radar), Physics, Materials science, Biophysics, Chemistry, Biology, Composite material, Engineering, Neuroscience, Nuclear protein
A Combined FEM/Genetic Algorithm for Vascular Soft tissue Elasticity Estimation
Authors: Ahmad S. Khalil, Brett E. Bouma, Mohammad R. K. Mofrad
Keywords: Elasticity (physics), Finite element method, Computer science, Algorithm, Inverse problem, Elastography, Mathematical optimization, Linear elasticity, Mathematics, Materials science, Structural engineering, Mathematical analysis, Engineering, Physics
Endothelialized Networks with a Vascular Geometry in Microfabricated Poly(dimethyl siloxane), Biomedical Microdevices 6:4, 269–278, 2004
Authors: Michael Shin, Kevin R. King, Kant Matsuda, Osamu Ishii, Hidetomi Terai, Eli J. Weinberg, Mohammad R. K. Mofrad, Jeffrey T. Borenstein, Michael Detmar, Joseph P. Vacanti
Keywords: Materials science, Siloxane, Biomedical engineering, Composite material, Polymer, Engineering
Deformation of the cell nucleus under indentation: Mechanics and mechanisms
Authors: A. Vaziri, Hohyun Lee, Mohammad R. K. Mofrad
Keywords: Nucleoplasm, Indentation, Nucleus, Lamin, Nuclear lamina, Materials science, Deformation (meteorology), Envelope (radar), Lamina, Nuclear membrane, Inner membrane, Cell nucleus, Biophysics, Membrane, Anatomy, Composite material, Nuclear protein, Chemistry, Biology, Nucleolus, Cell biology
A Novel Framework for Elastography and Modulus Estimation: Integration of Tissue Mechanics with Imaging
Authors: Reza Karimi, Raymond C. Chan, Stuart L. Houser, Brett E. Bouma, Mohammad R. K. Mofrad
The feasibility of optical coherence elastography is examined and the steps necessary for registration of optical coherence tomography (OCT) images are developed. We address the drawbacks of conventional techniques for solving the "image...
Keywords: Elastography, Optical coherence tomography, Inverse problem, Elasticity (physics), Computer science, Finite element method, Elastic modulus, Maxima and minima, Image registration, Medical imaging, Compressibility, Algorithm, Computer vision, Artificial intelligence, Mathematics, Image (mathematics), Acoustics, Optics, Physics, Mathematical analysis, Ultrasound
A finite shell element for heart mitral valve leaflet mechanics, with large deformations and 3D constitutive material model
Authors: Eli J. Weinberg, Mohammad R. K. Mofrad
Keywords: Shell (structure), Finite element method, Constitutive equation, Node (physics), Interpolation (computer graphics), Stress (linguistics), Deformation (meteorology), Mechanics, Structural engineering, Mathematical analysis, Classical mechanics, Physics, Mathematics, Engineering, Materials science, Mechanical engineering, Composite material
A Coarse-Grained Model for Force-Induced Protein Deformation and Kinetics
Authors: Hélène Karcher, Seung E. Lee, Mohammad R. K. Mofrad, Roger D. Kamm
Keywords: Energy landscape, Chemistry, Kinetics, Context (archaeology), Thermodynamics, Stiffness, Chemical physics, Biophysics, Physics, Classical mechanics, Biology
Force-induced activation of talin: its role in focal adhesion development
Authors: S.E. Lee, Mohammad R. K. Mofrad, Roger D. Kamm
Keywords: Arterial wall, Artery, Residual stress, Stress (linguistics), Materials science, RADIUS, Blood pressure, Mechanics, Cardiology, Internal medicine, Medicine, Composite material, Physics
Mechanics and mechanisms of nuclear deformation
Authors: A. Vaziri, H. Lee, R.D. Kamm, Mohammad R. K. Mofrad
Keywords: Deformation (meteorology), Mechanics, Classical mechanics, Physics, Materials science, Composite material
2005
Tissue Elasticity Estimation with Optical Coherence Elastography: Toward Mechanical Characterization of In Vivo Soft Tissue
Authors: Ahmad S. Khalil, Raymond C. Chan, Alexandra H. Chau, Brett E. Bouma, Mohammad R. K. Mofrad
Keywords: Optical coherence tomography, Elastography, Biomedical engineering, Elasticity (physics), Soft tissue, Materials science, Intravascular ultrasound, Elastic modulus, Image resolution, Optics, Ultrasound, Radiology, Physics, Medicine
Mass transport and fluid flow in stenotic arteries: Axisymmetric and asymmetric models
Authors: Mohammad R. K. Mofrad, Susumu Wada, Jerry G. Myers, C. Ross Ethier
Keywords: Stenosis, Rotational symmetry, Mass transport, Mass transfer, Mechanics, Flow (mathematics), Blood flow, Advection, Cardiology, Artery, Internal medicine, Medicine, Materials science, Physics, Thermodynamics
A large-strain finite element formulation for biological tissues with application to mitral valve leaflet tissue mechanics
Authors: Eli J. Weinberg, Mohammad R. K. Mofrad
Keywords: Finite element method, Positive definiteness, Mitral valve, Stiffness, Stiffness matrix, Displacement (psychology), Peridynamics, Function (biology), Mixed finite element method, Mechanics, Mathematics, Computer science, Applied mathematics, Structural engineering, Engineering, Continuum mechanics, Physics, Medicine, Surgery, Positive-definite matrix
Exploring the molecular basis for mechanosensation, signal transduction, and cytoskeletal remodeling
Authors: Mohammad R. K. Mofrad, N.A. Abdul-Rahim, Hélène Karcher, Peter J. Mack, Belinda Yap, Roger D. Kamm
Keywords: Mechanosensation, Mechanotransduction, Cytoskeleton, Signal transduction, Cell biology, Cell signaling, Cell adhesion, Integrin, Focal adhesion, Biology, Biophysics, Cell, Neuroscience, Chemistry, Biochemistry, Receptor
A viscoelastic model for nucleus deformation and mechanics in atomic force microscopy indentation
Authors: Ashkan Vaziri, Hyungsuk Lee, Roger D. Kamm, Mohammad R. K. Mofrad
Keywords: Indentation, Viscoelasticity, Atomic force microscopy, Deformation (meteorology), Nanoindentation, Classical mechanics, Microscopy, Materials science, Mechanics, Physics, Composite material, Nanotechnology, Optics
Endothelialized Microvasculature Based on a Biodegradable Elastomer
Authors: Christina W. Fidkowski, Mohammad R. K. Mofrad, Jeffrey T. Borenstein, Joseph P. Vacanti, Róbert Langer, Yadong Wang
Vital organs maintain dense microvasculature to sustain the proper function of their cells. For tissue- engineered organs to function properly, artificial capillary networks must be developed. We have microfabricated capillary networks w...
Keywords: Capillary action, Elastomer, Wafer, Biomedical engineering, Syringe driver, Materials science, Tissue engineering, Biocompatible material, Microelectromechanical systems, Nanotechnology, Syringe, Composite material, Mechanical engineering, Engineering
On the Constitutive Models for Heart Valve Leaflet Mechanics
Authors: Eli J. Weinberg, Mohammad R. K. Mofrad
Keywords: Constitutive equation, Heart valve, Leaflet (botany), Variety (cybernetics), Field (mathematics), Mechanics, Computer science, Physics, Engineering, Structural engineering, Mathematics, Finite element method, Artificial intelligence, Biology, Medicine, Cardiology
2004
Endothelialized Networks with a Vascular Geometry in Microfabricated Poly(dimethyl siloxane)
Authors: Michael Shin, Kant Matsuda, Osamu Ishii, Hidetomi Terai, Mohammad R. K. Mofrad, Jeffrey T. Borenstein, Michael Detmar, Joseph P. Vacanti
Keywords: Microfabrication, Materials science, Wafer, Polydimethylsiloxane, CD31, Tissue engineering, Nanotechnology, Template, Biomedical engineering, Chemistry, In vitro, Biochemistry
Mechanical Analysis of Atherosclerotic Plaques Based on Optical Coherence Tomography
Authors: Alexandra H. Chau, Raymond C. K. Chan, Milen Shishkov, Briain D. MacNeill, Nicusor Iftimia, Guillermo J. Tearney, Roger D. Kamm, Brett E. Bouma, Mohammad R. K. Mofrad
Keywords: Optical coherence tomography, Finite element method, Histology, Biomechanics, Biomedical engineering, Myocardial infarction, Medicine, Pathology, Radiology, Anatomy, Cardiology, Structural engineering, Engineering
OCT-based arterial elastography: robust estimation exploiting tissue biomechanics
Authors: Raymond C. Chan, Alexandra H. Chau, W.C. Karl, Seemantini K. Nadkarni, Ahmad S. Khalil, Nicusor Iftimia, Milen Shishkov, Guillermo J. Tearney, Mohammad R. K. Mofrad, Brett E. Bouma
We present a novel multi-resolution variational framework for vascular optical coherence elastography (OCE). This method exploits prior information about arterial wall biomechanics to produce robust estimates of tissue velocity and strai...
Keywords: Elastography, Decorrelation, Biomechanics, Optical coherence tomography, Biomedical engineering, Pulsatile flow, Estimator, Sensitivity (control systems), Materials science, Computer science, Optics, Acoustics, Computer vision, Mathematics, Physics, Medicine, Ultrasound, Anatomy, Statistics, Engineering
Hemodynamics and wall mechanics in human carotid bifurcation and its consequences for atherogenesis: investigation of inter-individual variation
Authors: Hamza Younis, Mohammad R. K. Mofrad, Raymond C. K. Chan, A. G. Isasi, Denise P. Hinton, Alexandra H. Chau, Li-jin Kim, Roger D. Kamm
Keywords: Common carotid artery, Carotid bifurcation, Shear stress, Bifurcation, Anatomy, Hemodynamics, Apex (geometry), External carotid artery, Mechanics, Materials science, Internal carotid artery, Geometry, Physics, Carotid arteries, Mathematics, Medicine, Cardiology, Internal medicine
Characterization of the Atherosclerotic Carotid Bifurcation Using MRI, Finite Element Modeling, and Histology
Authors: Mohammad R. K. Mofrad, A. G. Isasi, Hamza Younis, Raymond C. K. Chan, Denise P. Hinton, Galina K. Sukhova, Glenn M. LaMuraglia, Richard T. Lee, Roger D. Kamm
Keywords: Carotid bifurcation, Carotid endarterectomy, Ex vivo, Shear stress, Pathology, Bifurcation, Fibrous cap, Histology, In vivo, Arterial wall, Medicine, Biomedical engineering, Cardiology, Biology, Mechanics, Physics, Stenosis
Force-induced focal adhesion translocation: effects of force amplitude and frequency
Authors: Peter J. Mack, Mohammad R. K. Mofrad, Hélène Karcher, Richard Lee, Roger D. Kamm
Vascular endothelial cells rapidly transduce local mechanical forces into biological signals through numerous processes including the activation of focal adhesion sites. To examine the mechanosensing capabilities of these adhesion sites,...
Keywords: Amplitude, Adhesion, Focal adhesion, Physics, Materials science, Chemistry, Optics, Composite material
Living three-dimensional micro fabricated constructs for the replacement of vital organ function
Authors: Jeffrey T. Borenstein, Wang L. Cheung, L.M. Hartman, Mohammad R. K. Mofrad, Kevin R. King, Alexander Sevy, M. Shin, Eli J. Weinberg, Joseph P. Vacanti
We report the first demonstration of high-resolution three-dimensional constructs of living tissue suitable for transplantation for vital organ replacement devices. This work invokes a microfluidic approach, in which the blood supply of ...
Keywords: Capillary action, Biomedical engineering, Materials science, Microfluidics, Membrane, Replica, Polymer, Self-healing hydrogels, Nanoporous, Nanotechnology, Computer science, Chemistry, Composite material, Medicine, Polymer chemistry
DISTINCT ENDOTHELIAL PHENOTYPES EVOKED BY ARTERIAL WAVEFORMS DERIVED FROM ATHEROSCLEROSIS-PRONE AND ATHEROSCLEROSIS-PROTECTED REGIONS OF THE HUMAN VASCULATURE
Authors: Guohao Dai, Mohammad R. K. Mofrad, Roger D. Kamm, Yuzhi Zhang, Saran Vaughn, Guillermo García‐Cardeña, Michael A. Gimbrone
Keywords: Phenotype, Medicine, Cardiology, Internal medicine, Biology, Genetics, Gene
Vascular Optical Coherence Elastography: Assessment of Conventional Velocimetry Applied to OCT
Authors: Alexandra H. Chau, Raymond C. Chan, Mohammad R. K. Mofrad, Nicusor Iftimia, Milen Shishkov, Guillermo J. Tearney, Brett E. Bouma
Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text A. Chau, R. Chan, M. Kaazempur-Mofrad, N. Iftimia, M. Shishkov, G. Te...
Keywords: Citation, Computer science, Coherence (philosophical gambling strategy), Velocimetry, Optical coherence tomography, Optics, Physics, World Wide Web
2003
Cyclic strain in human carotid bifurcation and its potential correlation to atherogenesis: Idealized and anatomically-realistic models
Authors: Mohammad R. K. Mofrad, Hamza Younis, Shantanu Patel, A. G. Isasi, C. Chung, Raymond C. K. Chan, Denise P. Hinton, R.T. Lee, Roger D. Kamm
Keywords: Carotid bifurcation, Bifurcation, Strain (injury), Anatomy, Apex (geometry), Pathogenesis, Arterial wall, Carotid arteries, Geometry, Mechanics, Medicine, Cardiology, Pathology, Mathematics, Physics
Vascularized tissue engineering of vital organs: design, modeling and functional testing
Authors: Mohammad R. K. Mofrad, Jeffrey T. Borenstein, L.M. Hartman, Wing S. Cheung, Eli J. Weinberg, M. Shin, Alexander Sevy, Joseph P. Vacanti
We report engineering of vascularized tissue constructs for the replacement of vital organ function. A computational algorithm for simulation of blood flow and rheology in microcirculation is developed and utilized to design fractal micr...
Keywords: Tissue engineering, Microcirculation, Microfabrication, Computer science, Biomedical engineering, Replica, Blood flow, Materials science, Medicine, Pathology
A Three-Dimensional Viscoelastic Model for Cell Deformation with Experimental Verification
Authors: Hélène Karcher, Jan Lammerding, Hayden Huang, Richard Lee, Roger D. Kamm, Mohammad R. K. Mofrad
Keywords: Viscoelasticity, Deformation (meteorology), Materials science, Mechanics, Composite material, Physics
Computational Analysis of the Effects of Exercise on Hemodynamics in the Carotid Bifurcation
Authors: Hamza Younis, Mohammad R. K. Mofrad, C. Chung, Raymond C. K. Chan, Roger D. Kamm
Keywords: Hemodynamics, Shear stress, Cardiology, Common carotid artery, Internal medicine, Mean arterial pressure, Heart rate, Medicine, Blood flow, Mean flow, Vascular resistance, Blood pressure, Mechanics, Carotid arteries, Physics
Design of a single capillary-parenchymal co-culture bioreactor
Authors: E.S. Kim, Mohammad R. K. Mofrad, Jeffrey T. Borenstein, Joseph P. Vacanti, Roger D. Kamm
A bioreactor is designed and fabricated for the co-culture of endothelial and hepatic parenchymal cells. The device provides a structured environment mimicking the in vivo characteristics of a single capillary and the adjacent tissue. Th...
Keywords: Bioreactor, Capillary action, Tissue engineering, Parenchyma, Biomedical engineering, Membrane, Materials science, Mass transfer, Chemistry, Chromatography, Engineering, Biology, Composite material, Biochemistry
Single cell micromanipulation using magnetic beads: a computational model
Authors: Hélène Karcher, Mohammad R. K. Mofrad, Roger D. Kamm
A computational finite element model (FEM) model is developed for cell micromanipulation by magnetocytometry. The model provides a robust tool for analysis of detailed strain/stress fields induced in the cell monolayer. Correlation of th...
Keywords: Finite element method, Computational model, Stress (linguistics), Biological system, Computer science, Materials science, Artificial intelligence, Structural engineering, Engineering, Biology
Role of simulation in understanding biological systems
Authors: Mohammad R. K. Mofrad, Mark Bathe, Hélène Karcher, Hamza Younis, Hyeon-young Seong, Eun Bo Shim, Raymond C. Chan, Denise P. Hinton, A. G. Isasi, Arpita Upadhyaya, Mark J. Powers, Linda G. Griffith, Roger D. Kamm
Keywords: Computer science, Management science, Computational model, Computational simulation, Biological sciences, Data science, Engineering, Computational science, Simulation, Computational biology, Biology
Dynamic Rotational Seeding and Cell Culture System for Vascular Tube Formation
Authors: Boris Nasseri, Irina Pomerantseva, Mohammad R. K. Mofrad, Fraser Sutherland, Tjörvi E. Perry, Erin R. Ochoa, Craig A. Thompson, John E. Mayer, Stephen N. Oesterle, Joseph P. Vacanti
Optimization of cell seeding and culturing is an important step for the successful tissue engineering of vascular conduits. We evaluated the effectiveness of using a hybridization oven for rotational seeding and culturing of ovine vascul...
Keywords: Seeding, Biomedical engineering, Myofibroblast, Materials science, Scanning electron microscope, Tissue engineering, Tube (container), Polymer, Chemistry, Anatomy, Composite material, Pathology, Biology
A characteristic/finite element algorithm for time-dependent 3-D advection-dominated transport using unstructured grids
Authors: Mohammad R. K. Mofrad, P Minev, C. Ross Ethier
Keywords: Advection, Convection–diffusion equation, Mathematics, Finite element method, Péclet number, Galerkin method, Algorithm, Operator (biology), Applied mathematics, Discontinuous Galerkin method, Mathematical analysis, Mechanics, Physics, Thermodynamics
Stress-Induced Mechanotransduction: Some Preliminaries
Authors: Mohammad R. K. Mofrad, Peter J. Mack, Hélène Karcher, Javad Golji, Roger G. Kamm
Mechanical stimuli affect nearly every aspect of cellular function, yet the underlying mechanisms of transduction of force into biochemical signals are not clearly understood. One hypothesis is that forces transmitted via individual prot...
Keywords: Mechanotransduction, Cytoskeleton, Biophysics, Signaling proteins, Intracellular, Signal transduction, Cell biology, Cell adhesion, Viscoelasticity, Chemistry, Function (biology), Cell, Physics, Biology, Biochemistry
2002
An efficient characteristic Galerkin scheme for the advection equation in 3-D
Authors: Mohammad R. K. Mofrad, C. Ross Ethier
Keywords: Galerkin method, Advection, Mathematics, Quadrature (astronomy), Eulerian path, Convection–diffusion equation, Applied mathematics, Grid, Adaptive quadrature, Finite element method, Numerical diffusion, Discontinuous Galerkin method, Stability (learning theory), Scheme (mathematics), Gaussian, Mathematical analysis, Lagrangian, Computer science, Geometry, Mechanics, Control theory (sociology), Physics
Microfabrication Technology for Vascularized Tissue Engineering
Authors: Jeffrey T. Borenstein, Hidetomi Terai, Kevin R. King, Eli J. Weinberg, Mohammad R. K. Mofrad, Joseph P. Vacanti
Keywords: Microfabrication, Materials science, Tissue engineering, Biomedical engineering, Surface micromachining, Micropatterning, Nanotechnology, Wafer, Replica, Molding (decorative), Biocompatible material, Composite material, Fabrication, Pathology, Engineering
A microfabricated array bioreactor for perfused 3D liver culture
Authors: Mark J. Powers, Karel Domanský, Mohammad R. K. Mofrad, Artemis Kalezi, Adam T. Capitano, Arpita Upadhyaya, Petra Kurzawski, Kathryn E. Wack, Donna B. Stolz, Roger D. Kamm, Linda G. Griffith
We describe the design, fabrication, and performance of a bioreactor that enables both morphogenesis of 3D tissue structures under continuous perfusion and repeated in situ observation by light microscopy. Three-dimensional scaffolds wer...
Keywords: Bioreactor, Wafer, Biomedical engineering, Materials science, In situ, Shear stress, Biophysics, Seeding, Tissue engineering, Microscopy, Chemistry, Nanotechnology, Composite material, Biology, Optics
Atherosclerotic human carotid bifurcations: mechanical and histological factors
Authors: Mohammad R. K. Mofrad, A. G. Isasi, Hamza Younis, Raymond C. K. Chan, Denise P. Hinton, Galina K. Sukhova, Roger D. Kamm
3D finite element analyses were conducted of the diseased carotid bifurcation using reconstructed models based on in vivo MRI geometries and ultrasound velocity measurements. The resulting wall shear stress (WSS) and oscillatory shear in...
Keywords: Carotid bifurcation, Finite element method, Bifurcation, Shear stress, Shear (geology), Ultrasound, Materials science, Biomedical engineering, Physics, Carotid arteries, Structural engineering, Medicine, Composite material, Acoustics, Engineering, Cardiology
Optical Elastography for Determining Strain in Coronary Vessels
Authors: Nicusor Iftimia, Raymond C. Chan, Milen Shishkov, Christopher R. Kauffman, Stuart L. Houser, Mohammad R. K. Mofrad, Roger D. Kamm, Gary J. Tearney, Brett E. Bouma
The disruption of structurally compromised coronary plaque is thought to be the primary event causing heart attack. We have developed a new method for characterizing these vulnerable plaques using OCT and elastography.
Keywords: Elastography, Strain (injury), Cardiology, Medicine, Radiology, Internal medicine, Biomedical engineering, Ultrasound
2001
Mass Transport in an Anatomically Realistic Human Right Coronary Artery
Authors: Mohammad R. K. Mofrad, C. Ross Ethier
Keywords: Mass transfer, Shear stress, Blood flow, Hemodynamics, Artery, Right coronary artery, Finite element method, Mechanics, Cardiology, Advection, Anatomy, Materials science, Biomedical engineering, Geometry, Physics, Medicine, Mathematics, Structural engineering, Engineering, Coronary angiography
1996
Oxygen Mass Transfer in a Stenosis: Effects of Blood-Wall Coupling
Authors: J. A. Moore, C. Ross Ethier, Mohammad R. K. Mofrad
Abstract Motivation: Arterial transport of blood-borne materials is essential for maintenance of normal arterial wall physiology. Disturbed transport of such materials, due for example to altered hemodynamic patterns caused by local geom...
Keywords: Oxygen transport, Oxygen, Hemoglobin, Intimal hyperplasia, Hemodynamics, Artery, Oxygen tension, Cardiology, Pathogenesis, Stenosis, Internal medicine, Arterial wall, Arterial blood, Chemistry, Medicine, Smooth muscle
2018
Deep Genomics and Proteomics: Language Model-Based Embedding of Biological Sequences and Their Applications in Bioinformatics
Authors: Ehsaneddin Asgari, Mohammad R. K. Mofrad
Keywords: Computer science, Natural language processing, Artificial intelligence, UniProt, Word embedding, Machine translation, Word (group theory), Representation (politics), Connectionism, Language model, Embedding, Artificial neural network, Biology, Linguistics
Proteomics and Protein Interaction in Molecular Cell Signaling Pathways
Authors: Hassan Pezeshgi Modarres, Mohammad R. K. Mofrad
Keywords: Proteomics, Computational biology, Function (biology), Protein function, Biology, Cell function, Data science, Bioinformatics, Computer science, Cell, Cell biology, Genetics, Gene
Is SUN2 Autoinhibited?
Authors: Zeinab Jahed, Uyen T. Vu, Darya Fadavi, Samuel C. J. Kim, Mohammad R. K. Mofrad
Keywords: Trimer, Chemistry, Biophysics, Inner membrane, Crystallography, Biochemistry, Biology, Membrane, Dimer
Computational Modeling of Heart Valves: Understanding and Predicting Disease
Authors: Ahmed A. Bakhaty, Ali Hamidi Madani, Mohammad R. K. Mofrad
Keywords: Computer science, Heart valve, Computational model, Mechanical heart, Heart disease, Cardiac valve, Computational simulation, Medicine, Simulation, Cardiology, Computational science
2017
Cellular Nanomechanics
Authors: Roger D. Kamm, Jan Lammerding, Mohammad R. K. Mofrad
Keywords: Nanomechanics, Mechanobiology, Context (archaeology), Cell mechanics, Nanotechnology, Computer science, Engineering, Cytoskeleton, Chemistry, Cell, Materials science, Biology, Atomic force microscopy, Cell biology
2016
Protein thermostability engineering
Authors: Hassan Pezeshgi Modarres, Mohammad R. K. Mofrad, Amir Sanati‐Nezhad
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
Keywords: Thermostability, Protein stability, Protein engineering, Thermal stability, Sequence (biology), Chemistry, Biochemical engineering, Stability (learning theory), Computer science, Engineering, Biochemistry, Organic chemistry, Enzyme, Machine learning
Biological Breadboard Platform for Studies of Cellular Dynamics
Authors: Sang-Hee Yoon, Mohammad R. K. Mofrad
Keywords: Breadboard, Dynamics (music), Computer science, Biological system, Biology, Engineering, Psychology, Electronic engineering
2014
Rheology and Mechanics of the Cytoskeleton
Authors: Hamed Hatami-Marbini, Mohammad R. K. Mofrad
Keywords: Rheology, Mechanics, Materials science, Classical mechanics, Physics, Composite material
2012
Mechanobiological Approaches for the Control of Cell Motility
Authors: Sang‐Hee Yoon, Young Kyun Kim, Mohammad R. K. Mofrad
Keywords: Motility, Materials science, Biophysics, Nanotechnology, Cell, Chemistry, Cell biology, Biology, Biochemistry
Bacterial Electrical Conduction
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Electrical conduction, Thermal conduction, Materials science, Environmental science, Composite material
Band Alignment
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Basic MEMS Actuators
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Microelectromechanical systems, Actuator, Computer science, Engineering, Materials science, Artificial intelligence, Nanotechnology
Batteries
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Bendable Electronics
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Electronics, Electrical engineering, Engineering
Bending Strength
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, J R Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, P Von Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, Jose A. Sanz‐Herrera, Esther Reina-Romo, Bharat Bhushan
Keywords: Materials science, Bending, Composite material, Structural engineering, Engineering
Bilayer Graphene
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Bilayer graphene, Materials science, Graphene, Nanotechnology
Bio-FET
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Bio-inspired CMOS Cochlea
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, J. M. Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Cochlea, CMOS, Materials science, Neuroscience, Biology, Optoelectronics
Bio-optics
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Optics, Physics, Computer science
Bio-photonics
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Photonics, Computer science, Physics, Optoelectronics
Bioaccessibility/Bioavailability
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Bioavailability, Business, Chemistry, Environmental science, Environmental chemistry, Pharmacology, Biology
Bioadhesion
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Materials science
Bioadhesives
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science, Medicine
Biocalorimetry
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Bioderived Smart Materials
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Biofilms in Microfluidic Devices
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Biofilm, Microfluidics, Nanotechnology, Materials science, Biology, Bacteria
Biognosis
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Bioinspired Microneedles
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Materials science
Bioinspired Synthesis of Nanomaterials
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Nanomaterials, Nanotechnology, Materials science
Biological Nano-crystallization
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Crystallization, Nano-, Materials science, Nanotechnology, Chemical engineering, Engineering, Composite material
Biological Photonic Structures
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Photonics, Computer science, Materials science, Optoelectronics
Biological Platform
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science, Geology
Biological Sensors
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Biological Structural Color
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
BioMEMS/NEMS
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Nanoelectromechanical systems, Nanotechnology, Materials science
Biomimetic Antireflective Surfaces Arrays
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Anti-reflective coating, Materials science, Computer graphics (images), Art, Computer science, Nanotechnology
Biomimetic Energy Conversion Devices
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Energy transformation, Energy (signal processing), Materials science, Nanotechnology, Physics
Biomimetic Flow Sensors
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Flow sensor, Flow (mathematics), Computer science, Acoustics, Mechanics, Physics
Biomimetic Infrared Detector
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Infrared, Detector, Materials science, Optics, Physics
Biomimetic Mosquito-Like Microneedles
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Materials science, Nanotechnology
Biomimetic Muscles and Actuators
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Actuator, Computer science, Artificial intelligence
Biomimetic Synthesis
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Materials science
Biomimetic Synthesis of Nanomaterials
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Nanomaterials, Nanotechnology, Biomimetic synthesis, Materials science, Chemistry, Organic chemistry
Biomimetics
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, Esther Reina-Romo, Bharat Bhushan
Keywords: Biomimetics, Nanotechnology, Materials science
Biomimetics of Marine Adhesives
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, Esther Reina-Romo, Bharat Bhushan
Keywords: Biomimetics, Adhesive, Engineering, Nanotechnology, Materials science
Biomimetics of Optical Nanostructures
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Biomimetics, Nanotechnology, Nanostructure, Materials science
Biomimicked Microneedles
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Materials science
Biomimicry
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Biomimetics, Psychology, Computer science, Artificial intelligence
Biomolecular Mechanics
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Mechanics, Computer science, Physics
Bionic Ear
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Bionic Eye
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Bionic Microneedles
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Materials science
Bionics
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang-Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Bionics, Computer science, Artificial intelligence
BioPatterning
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Biopolymer
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Biopolymer, Materials science, Composite material, Polymer
Bioprobes
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Environmental science
Biosensing
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang-Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Biosensors
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Computer science
Bond-Order Potential
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, J. M. Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Bond, Order (exchange), Business, Finance
Bone Remodeling
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, Jose A. Sanz‐Herrera, Esther Reina-Romo, Bharat Bhushan
Keywords: Bone remodeling, Medicine, Internal medicine
Bone Turnover
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Bone remodeling, Business, Medicine, Internal medicine
Boron Nitride Nanotubes (BNNTs)
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Boron nitride, Materials science, Nanotechnology, Nitride
Boron- and/or Nitrogen-Doped Carbon Nanotubes
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Boron, Materials science, Nitrogen, Carbon nanotube, Carbon fibers, Doping, Nanotechnology, Chemical engineering, Chemistry, Composite material, Organic chemistry, Optoelectronics, Engineering
Bottom-Up Nanofabrication
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Nanolithography, Nanotechnology, Materials science, Medicine, Fabrication
Boundary Lubrication
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Lubrication, Boundary (topology), Materials science, Geology, Composite material, Mathematics, Mathematical analysis
Brain Implants
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Neuroscience, Medicine, Psychology
Buckminsterfullerene
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang-Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Buckminsterfullerene, Physics, Fullerene
Bulk Acoustic Wave MEMS Resonators
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Resonator, Microelectromechanical systems, Acoustics, Materials science, Physics, Optoelectronics
Biomimetic Muscles and Actuators Using Electroactive Polymers (EAP)
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Electroactive polymers, Actuator, Materials science, Polymer, Polymer science, Computer science, Composite material, Artificial intelligence
Biornametics – Architecture Defined by Natural Patterns
Authors: Arash Kheyraddini Mousavi, Zayd C. Leseman, Manuel L. B. Palacio, Bharat Bhushan, Scott R. Schricker, Vishnu-Baba Sundaresan, Stephen A. Sarles, Donald J. Leo, Suresh Neethirajan, David Karig, Aloke Kumar, Partha P. Mukherjee, Scott T. Retterer, Mitchel J. Doktycz, Andreas G. Katsiamis, Emmanuel M. Drakakis, Richard F. Lyon, Roberto Rica, Sang‐Hee Yoon, Mohammad R. K. Mofrad, Jérôme Casas, Chang Liu, Gijs Krijnen, Melur K. Ramasubramanian, Ranjeet Agarwala, Yoseph Bar‐Cohen, Bharat Bhushan, Pierre Becker, Elise Hennebert, Patrick Flammang, Andrew R. Parker, Remigio Picone, Ille C. Gebeshuber, Petra Gruber, Barbara Imhof, Henry O. Fatoyinbo, Michael P. Hughes, J. A. Sanz-Herrera, E. Reina-Romo, Bharat Bhushan
Keywords: Architecture, Natural (archaeology), Computer science, Geography, Archaeology
2011
Cytoskeletal Mechanics and Rheology
Authors: Hamed Hatami-Marbini, Mohammad R. K. Mofrad
Keywords: Multiphysics, Rheology, Cell mechanics, Cytoskeleton, Mechanics, Computational model, Nanotechnology, Materials science, Computer science, Engineering, Chemistry, Physics, Finite element method, Structural engineering, Simulation, Cell
Nuclear Pore Complex
Authors: Tahereh Jamali, Yousef Jamali, Mehrdad Mehrbod, Mohammad R. K. Mofrad
Keywords: Nuclear pore, Nucleoplasm, Nucleoporin, Nuclear transport, Biology, Cytoplasm, Cell biology, Chromosomal translocation, Biophysics, Nucleus, Intrinsically disordered proteins, Function (biology), Cell nucleus, Biochemistry, Gene, Nucleolus
2010
Library
Authors: John Norton Moore, Christopher Davis, Mohammad R. K. Mofrad, Roger D. Kamm, Peter J. Halley, Graeme A. George, Michael I. Friswell, John Penny, Seamus D. Garvey, Arthur W. Lees, Hsueh-Chia Nanofluidics, Leslie Chang, Yeo
Keywords: Materials science
Intracellular Fluid Dynamics.
Authors: Mohammad R. K. Mofrad
Keywords: Intracellular Fluid, Intracellular, Dynamics (music), Chemistry, Physics, Biochemistry, Acoustics
Cytoskeletal Mechanics and Cellular Mechanotransduction: A Molecular Perspective
Authors: Hamed Hatami-Marbini, Mohammad R. K. Mofrad
Keywords: Mechanobiology, Mechanotransduction, Cell mechanics, Cytoskeleton, Multiphysics, Cell function, Computational model, Nanotechnology, Computer science, Mechanics, Neuroscience, Physics, Chemistry, Materials science, Biology, Engineering, Cell, Cell biology, Finite element method, Simulation, Structural engineering
Computational Modeling in Biomechanics
De S, Guilak F, Mofrad MRK (eds). Computational Modeling in Biomechanics. Springer Dordrecht; April 1, 2010. ISBN 978-90-481-3574-5.
Authors: Suvranu De, Farshid Guilak, Mohammad R. K. Mofrad
Keywords: Biomechanics, Computational model, Computer science, Field (mathematics), Management science, Engineering, Simulation, Medicine, Anatomy, Mathematics
2009
Introduction
Authors: Roger D. Kamm, Mohammad R. K. Mofrad
Julius Wolff, a nineteenth-century anatomist, first observed that bone will adapt to the stresses it experiences and is capable of remodeling if the state of stress changes. This became known as Wolff’s Law and stands today as perhaps th...
Keywords: Computer science
Mechanotransduction
Authors: Christopher B. Wolf, Mohammad R. K. Mofrad
Cells, especially in multicellular organisms during development, are subject to a wide range of forces that help shape their overall fate and response to a variety of physiologically important stimuli. During such environmental interacti...
Keywords: Mechanotransduction, Multicellular organism, Biology, Neuroscience, Cell biology, Cell fate determination, Organism, Cell type, Cell, Genetics, Transcription factor
Plate Section
Authors: Mohammad R. K. Mofrad, Roger D. Kamm
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Keywords: Section (typography), Geology, Computer science, Operating system
A Molecular Perspective on Mechanotransduction in Focal Adhesions
Authors: Seung E. Lee, Roger D. Kamm, Mohammad R. K. Mofrad
Keywords: Mechanotransduction, Perspective (graphical), Focal adhesion, Cell biology, Biology, Art, Visual arts, Signal transduction
Cellular Mechanotransduction: Diverse Perspectives from Molecules to Tissues
Mofrad MRK, Kamm RD (eds). Cellular Mechanotransduction: Diverse Perspectives from Molecules to Tissues. Cambridge University Press; November 23, 2009.
Authors: Mohammad R. K. Mofrad, Roger D. Kamm
Keywords: mechanotransduction, cell biology, biomechanics
Computational Modeling of Aortic Heart Valve Mechanics Across Multiple Scales
Authors: Laura R. Croft, Mohammad R. K. Mofrad
Keywords: Heart valve, Aortic valve, Computer science, Cardiology, Mechanical heart-valve, Biomedical engineering, Engineering, Medicine
Computational Models of Vascular Mechanics
Authors: Joseph Leach, Mohammad R. K. Mofrad, David Saloner
Keywords: Computational mechanics, Disease, Arterial wall, Fluid mechanics, Medicine, Pathology, Mechanics, Cardiology, Physics, Engineering, Finite element method, Structural engineering
Computational Modeling of Aortic Heart Valves
Authors: Laura R. Croft, Mohammad R. K. Mofrad
Keywords: Cardiac cycle, Heart valve, Aortic valve, Computer science, Computational model, Cardiac valve, Biomedical engineering, Engineering, Cardiology, Medicine, Simulation
Editorial
Authors: Muhammad H. Zaman, Mohammad R. K. Mofrad, Gang Bao, Roger D. Kamm
Keywords: Computer science, Data science
Mechanotransduction and Its Role in Stem Cell Biology
Authors: Christopher B. Wolf, Mohammad R. K. Mofrad
Most cells can sense and actively respond to mechanical stimuli. Yet the exact processes that convert mechanical signals into a cascade of biochemical signals that affect the phenotype of the cell (a process called cellular mechanotrans...
Keywords: Mechanotransduction, Stem cell, Cell biology, Embryonic stem cell, Biology, Cell type, Neuroscience, Mechanobiology, Cell, Genetics
2008
Tissue Engineering of Microvascular Networks
Authors: Jeffrey T. Borenstein, Eli J. Weinberg, Mohammad R. K. Mofrad, Joseph P. Vacanti
Keywords: Tissue engineering, Computer science, Engineering, Biomedical engineering
2007
Tissue Engineering: Multiscaled Representation of Tissue Architecture and Function
Authors: Mohammad R. K. Mofrad, Eli J. Weinberg, Jeffrey T. Borenstein, Joseph P. Vacanti
Keywords: Tissue engineering, Function (biology), Architecture, Computer science, Field (mathematics), Representation (politics), Biomedical engineering, Engineering, Biology, Mathematics
2006
Cytoskeletal Mechanics : Models and Measurements in Cell Mechanics
Mofrad MRK, Kamm RD (eds). Cytoskeletal Mechanics: Models and Measurements in Cell Mechanics. Cambridge University Press; November 2009. ISBN 9780511607318.
Authors: Mohammad R. K. Mofrad, Roger D. Kamm
1. Introduction and the biological basis for cell mechanics Mohammad R. K. Mofrad and Roger Kamm 2. Experimental measurements of intracellular mechanics Paul Janmey and Christoph Schmidt 3. The cytoskeleton as a soft glassy material Jeff...
Keywords: Cytoskeleton, Continuum mechanics, Cell mechanics, Mechanics, Physics, Chemistry, Cell
2004
Biodegradable Microfluidics
Authors: Kevin R. King, Chiaochun Wang, Mohammad R. K. Mofrad, Joseph P. Vacanti, Jeffrey T. Borenstein
A biodegradable microfabrication platform for constructing 3D high- resolution devices for tissue engineering and drug delivery is presented. Biodegradable polymer films with built-in micrometer-scale features are stacked and fusion bond...
Keywords: Microfabrication, Materials science, Microfluidics, Nanotechnology, PLGA, Biodegradable polymer, Drug delivery, Polymer, Nanoparticle, Fabrication, Composite material
2003
Biological simulations at all scales
Authors: Mohammad R. K. Mofrad, Hamza Younis, Hélène Karcher, J.W. Lin, Javad Golji, A. G. Isasi, Jonathan S. Tan, Raymond C. Chan, Roger D. Kamm
Keywords: Environmental science, Statistical physics, Computer science, Physics
Biological simulations at all scales: From cardiovascular hemodynamics to protein molecular mechanics
Authors: Mohammad R. K. Mofrad, Hamza Younis, Hélène Karcher, J.W. Lin, Javad Golji, A. G. Isasi, Jonathan S. Tan, Raymond C. Chan, Roger D. Kamm
Publisher Summary This chapter provides a wide range of examples that show the extensive role of computational simulation in the development of biological sciences. Computational simulations provide a powerful tool for understanding the...
Keywords: Computer science, Process (computing), Complex system, Function (biology), Scale (ratio), Statistical physics, Physics, Artificial intelligence, Biology
Design of a single capillary-parenchymal co-culture bioreactor using a self-assembling peptide membrane
Authors: E.S. Kim, Mohammad R. K. Mofrad, Jeffrey T. Borenstein, Joseph P. Vacanti, Roger D. Kamm
Keywords: Peptide, Capillary action, Membrane, Bioreactor, Self-assembling peptide, Mass transfer, Materials science, Chromatography, Chemistry, Biophysics, Chemical engineering, Biochemistry, Engineering, Biology, Composite material
Numerical model of flow in distensible microfluidic network
Authors: Eli J. Weinberg, Mohammad R. K. Mofrad, Jeffrey T. Borenstein
Keywords: Laminar flow, Mechanics, Compressibility, Microfluidics, Flow (mathematics), Resistor, Deformation (meteorology), Fluidics, Internal flow, Materials science, Internal pressure, Pressure drop, Physics, Engineering, Composite material, Nanotechnology, Electrical engineering
2001
Computational modeling of blood flow and rheology in fractal microvascular networks
Authors: Mohammad R. K. Mofrad, Joseph P. Vacanti, R.D. Kamm
Keywords: Fractal, Rheology, Flow (mathematics), Blood flow, Fractal analysis, Computer science, Mechanics, Statistical physics, Materials science, Mathematics, Physics, Fractal dimension, Medicine, Cardiology, Mathematical analysis, Composite material
Introduction, with the biological basis for cell mechanics
Authors: Roger D. Kamm, Mohammad R. K. Mofrad
All living things, despite their profound diversity, share a common architectural building block: the cell. Cells are the basic functional units of life, yet are themselves comprised of numerous components with distinct mechanical charac...
Keywords: Cell mechanics, Cell, Mechanics, Physics, Biology, Cytoskeleton
2025
KODA: An Agentic Framework for KEGG Orthology-Driven Discovery of Antimicrobial Drug Targets in Gut Microbiome
Authors: Javad Aminian-Dehkordi, Mohammad S. Parsa, Mohsen Naghipourfar, Mohammad R. K. Mofrad
Abstract The gut microbiome plays a crucial role in human health and disease, influencing diverse biological processes such as immune regulation and nutrient metabolism. However, the complexity of micro-bial interactions and their metabo...
Keywords: Drug discovery, Microbiome, Drug, Computational biology, Data science, Computer science, Biology, Pharmacology, Bioinformatics
SIMBA-GNN: Simulation-augmented Microbiome Abundance Graph Neural Network
Authors: Mohammad S. Parsa, Javad Aminian-Dehkordi, Mohammad R. K. Mofrad
Abstract Understanding gut microbiome dynamics gut requires deciphering complex, metabolically driven interactions beyond taxonomic profiles. We present SIMBA , a novel framework that integrates mechanistic metabolic simulations with a g...
Keywords: Abundance (ecology), Microbiome, Graph, Computer science, Artificial neural network, Biology, Artificial intelligence, Bioinformatics, Ecology, Theoretical computer science
Genome modeling and design across all domains of life with Evo 2
Authors: Garyk Brixi, Matthew G. Durrant, Ja‐Lok Ku, Michael Poli, Greg Brockman, Daniel Chang, Gabriel González, S. B. King, David Li, S. B. King, Mohsen Naghipourfar, Eric Nguyen, Chiara Ricci-Tam, David W. Romero, Gwanggyu Sun, Ali Taghibakshi, A. A. Vorontsov, B. S. Yang, Mengjiao Deng, Liv Gorton, Nam C. Nguyen, Nicholas K. Wang, Emily R. Adams, Stephen A. Baccus, Steven Dillmann, Stefano Ermon, Deyin Guo, Rajesh Ilango, Ken Janik, Amy X. Lu, Rajendra G. Mehta, Mohammad R. K. Mofrad, Madelena Y. Ng, Jaspreet Pannu, Christopher Ré, Jonathan C. Schmok, John St. John, Jeremy A. Sullivan, Kevin Zhu, Greg Zynda, Daniel Balsam, Patrick Collison, Anthony Costa, Tina Hernandez‐Boussard, Eric Ho, Mingyu Liu, Thomas McGrath, Kimberly Powell, Donald S. Burke, Hani Goodarzi, Patrick D. Hsu, Brian Hie
Abstract All of life encodes information with DNA. While tools for sequencing, synthesis, and editing of genomic code have transformed biological research, intelligently composing new biological systems would also require a deep understa...
Keywords: Evolutionary biology, Computational biology, Biology
2024
Meta Biome: A Multiscale Model Integrating Agent-Based Modeling and Metabolic Networks Reveals Spatial Regulation in Mucosal Microbial Communities
Authors: Javad Aminian-Dehkordi, Andrew Dickson, Amin Valiei, Mohammad R. K. Mofrad
Abstract Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut, essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current meth...
Keywords: In silico, Biome, Computer science, Multiscale modeling, Biochemical engineering, Representation (politics), Systems biology, Computational biology, Biological system, Ecology, Biology, Ecosystem, Bioinformatics, Engineering
Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules
Authors: Ali Akbar Ashkarran, Hassan Gharibi, Seyed Amirhossein Sadeghi, Seyed Majed Modaresi, Qianyi Wang, Zijin Lin, Ghafar Yerima, Ali Tamadon, Maryam Sayadi, Maryam Jafari, Zijin Lin, Danilo Ritz, David Kakhniashvili, Avirup Guha, Mohammad R. K. Mofrad, Liangliang Sun, Markita P. Landry, Amir Ata Saei, Morteza Mahmoudi
The protein corona, a dynamic biomolecular layer that forms on nanoparticle (NP) surfaces upon exposure to biological fluids is emerging as a valuable diagnostic tool for improving plasma proteome coverage analyzed by liquid chromatograp...
Keywords: Profiling (computer programming), Proteome, Nanoparticle, Plasma, Nanotechnology, Small molecule, Corona (planetary geology), Chemistry, Computational biology, Materials science, Biophysics, Computer science, Physics, Biology, Biochemistry, Astrobiology
2023
Integrin Mechanosensing relies on Pivot-clip Mechanism to Reinforce Cell Adhesion
Authors: Andre R. Montes, Anahi Barroso, Wei Wang, Grace D. O’Connell, Adrián Buganza Tepole, Mohammad R. K. Mofrad
ABSTRACT Cells intricately sense mechanical forces from their surroundings, driving biophysical and biochemical activities. This mechanosensing phenomenon occurs at the cell-matrix interface, where mechanical forces resulting from cellul...
Keywords: Integrin, Fibronectin, Cell adhesion, Chemistry, Biophysics, Cell biology, Adhesion, Mechanism (biology), Extracellular matrix, Nanotechnology, Cell, Biology, Materials science, Biochemistry, Physics
Beyond the Hype: Assessing the Performance, Trustworthiness, and Clinical Suitability of GPT3.5
Authors: Salmonn Talebi, Elizabeth Tong, Mohammad R. K. Mofrad
The use of large language models (LLMs) in healthcare is gaining popularity, but their practicality and safety in clinical settings have not been thoroughly assessed. In high-stakes environments like medical settings, trust and safety ar...
Keywords: Popularity, Trustworthiness, Protocol (science), Computer science, Process (computing), Data science, Psychology, Computer security, Medicine, Alternative medicine, Pathology, Social psychology
Fine-tuning Protein Embeddings for Generalizable Annotation Propagation
Authors: Andrew Dickson, Mohammad R. K. Mofrad
A central goal of bioinformatics research is to understand proteins on a functional level, typically by extrapolating from experimental results with the protein sequence information. One strategy is to assume that proteins with similar s...
Keywords: Computer science, Similarity (geometry), Artificial intelligence, Function (biology), Machine learning, Annotation, Generalization, Embedding, Protein function prediction, Protein sequencing, Sequence (biology), Protein function, Pattern recognition (psychology), Mathematics, Biology, Peptide sequence
Exploring the Performance and Explainability of BERT for Medical Image Protocol Assignment
Authors: Salmonn Talebi, Elizabeth Tong, Mohammad R. K. Mofrad
Abstract Although deep learning has become state of the art for numerous tasks, it remains untouched for many specialized domains. High stake environments such as medical settings pose more challenges due to trust and safety issues for d...
Keywords: Computer science, Protocol (science), Encoder, Task (project management), Artificial intelligence, Transformer, Deep learning, Machine learning, Word (group theory), Image (mathematics), Natural language processing, Medicine
2020
The intriguing dynamics of chromatin folding and assembly
Authors: Zhihua Yang, Wenjun Miao, Mohammad R. K. Mofrad
ABSTRACT We investigate the dynamics of chromatin folding based on the “strings and binders” (SBS) model with molecular dynamics simulation. SBS model is a coarse-grained model considering a self-avoiding chain interacting with diffusive...
Keywords: Chromatin, Folding (DSP implementation), Physics, Dynamics (music), Biological system, Biophysics, Chemical physics, Chemistry, DNA, Biology, Engineering
2019
ProDyn0: Inferring calponin homology domain stretching behavior using\n graph neural networks
Authors: Ali Madani, Cyna Shirazinejad, Jia Rui Ong, Hengameh Shams, Mohammad R. K. Mofrad
Graph neural networks are a quickly emerging field for non-Euclidean data\nthat leverage the inherent graphical structure to predict node, edge, and\nglobal-level properties of a system. Protein properties can not easily be\nunderstood a...
Keywords: Computer science, Leverage (statistics), Artificial neural network, Graph, Theoretical computer science, Artificial intelligence, Algorithm
DeepPrime2Sec: Deep Learning for Protein Secondary Structure Prediction from the Primary Sequences
Authors: Ehsaneddin Asgari, Nina Poerner, Alice C. McHardy, Mohammad R. K. Mofrad
Abstract Motivation Here we investigate deep learning-based prediction of protein secondary structure from the protein primary sequence. We study the function of different features in this task, including one-hot vectors, biophysical fea...
Keywords: Protein secondary structure, Artificial intelligence, Computer science, Deep learning, Recurrent neural network, Convolutional neural network, Artificial neural network, Pattern recognition (psychology), Machine learning, Sequence (biology), Embedding, Task (project management), Biology
Fighting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics
Authors: Ariane Khaledi, Aaron Weimann, Monika Schniederjans, Ehsaneddin Asgari, Tzu‐Hao Kuo, Antonio Oliver, Gabriel Cabot, Axel Kola, Petra Gastmeier, Michael Hogardt, Daniel E Jonas, Mohammad R. K. Mofrad, Andreas Bremges, Alice C. McHardy, Susanne Häußler
Abstract The growing importance of antibiotic resistance on clinical outcomes and cost of care underscores the need for optimization of current diagnostics. For a number of bacterial species antimicrobial resistance can be unambiguously ...
Keywords: Pseudomonas aeruginosa, Antibiotic resistance, Ciprofloxacin, Biology, Antimicrobial, Drug resistance, Transcriptome, Computational biology, Molecular diagnostics, Gene, Microbiology, Genome, Antibiotics, Bacteria, Genetics, Gene expression
UniSent: Universal Adaptable Sentiment Lexica for 1000+ Languages
Authors: Ehsaneddin Asgari, Fabienne Braune, Benjamin Roth, Christoph Ringlstetter, Mohammad R. K. Mofrad
In this paper, we introduce UniSent universal sentiment lexica for $1000+$ languages. Sentiment lexica are vital for sentiment analysis in absence of document-level annotations, a very common scenario for low-resource languages. To the b...
Keywords: Sentiment analysis, Computer science, Domain (mathematical analysis), Natural language processing, German, Artificial intelligence, Word (group theory), Resource (disambiguation), Task (project management), Czech, Word embedding, Information retrieval, Embedding, Linguistics, Mathematics
2018
Nucleotide-pair encoding of 16S rRNA sequences for host phenotype and biomarker detection
Authors: Ehsaneddin Asgari, Philipp C. Münch, Till Robin Lesker, Alice C. McHardy, Mohammad R. K. Mofrad
ABSTRACT Identifying combinations of taxa distinctive for microbiome-associated diseases is considered key to the establishment of diagnosis and therapy options in precision medicine and imposes high demands on accuracy of microbiome ana...
Keywords: Biomarker, Computational biology, Microbiome, Biomarker discovery, Biology, Cluster analysis, Artificial intelligence, Pattern recognition (psychology), Computer science, Genetics, Gene
2017
Fast and accurate classification of echocardiograms using deep learning
Authors: Ali Madani, Ramy Arnaout, Mohammad R. K. Mofrad, Rima Arnaout
Echocardiography is essential to modern cardiology. However, human interpretation limits high throughput analysis, limiting echocardiography from reaching its full clinical and research potential for precision medicine. Deep learning is ...
Keywords: Artificial intelligence, Overfitting, Convolutional neural network, Deep learning, Computer science, Generalizability theory, Artificial neural network, Modality (human–computer interaction), Gold standard (test), Machine learning, Pattern recognition (psychology), Medicine, Radiology, Mathematics, Statistics
2016
Comparing Fifty Natural Languages and Twelve Genetic Languages Using\n Word Embedding Language Divergence (WELD) as a Quantitative Measure of\n Language Distance
Authors: Ehsaneddin Asgari, Mohammad R. K. Mofrad
We introduce a new measure of distance between languages based on word\nembedding, called word embedding language divergence (WELD). WELD is defined as\ndivergence between unified similarity distribution of words between languages.\nUsin...
Keywords: Computer science, Natural language processing, Language family, Artificial intelligence, Word embedding, Word (group theory), Natural language, Sentence, Divergence (linguistics), Language identification, Coding (social sciences), Identification (biology), Similarity (geometry), Embedding, Linguistics, Measure (data warehouse), Mathematics, Biology, Statistics
2015
A New Approach for Scalable Analysis of Microbial Communities
Authors: Ehsaneddin Asgari, Kiavash Garakani, Mohammad R. K. Mofrad
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic phylogen...
Keywords: Metagenomics, Microbiome, Microbial population biology, Phylogenetic tree, Dimensionality reduction, Scalability, Biology, Human Microbiome Project, Computer science, Computational biology, Function (biology), Artificial intelligence, Data mining, Machine learning, Human microbiome, Bioinformatics, Evolutionary biology, Genetics, Gene
2019
Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics
Authors: Ariane Khaledi§, Aaron Weinmann§, Monika Schniederjans, Ehsaneddin Asgari, Tzu‐Hao Kuo, Antonioa Oliver, Gabriel Cabot, Axel Kola, Petra Gastmeier, Michael Hogardt, Daniel E Jonas, Mohammad R. K. Mofrad, Andreas Bremges, Alice C. McHardy, Susanne Häußler
Datasets for manuscript "Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics" Metadata.zip phenotypes.txt: tabular file containing binary resistance phenotypes based on CLSI g...
Keywords: Pseudomonas aeruginosa, Antimicrobial, Microbiology, Antibiotic resistance, Biology, Computational biology, Bacteria, Antibiotics, Genetics
2011
On the Mechanics of Microtubule Filaments
Authors: Mehrdad Mehrbod, Mohammad R. K. Mofrad
Quantitative understanding of cell mechanics has challenged biological scientists during the past couple of decades. one of the promising attempts towards mechanical modeling of the cytoskeleton has been the “tensegrity” cytoskeletal mod...
Keywords: Tensegrity, Microtubule, Buckling, Cell mechanics, Cytoskeleton, Buckle, Bridging (networking), Mechanics, Structural engineering, Bending, Materials science, Physics, Computer science, Engineering, Chemistry, Biology, Cell, Cell biology
2010
Focal Adhesion Mechanotransduction: Molecular Events Leading to Vinculin Activation
Authors: Javad Golji, Mohammad R. K. Mofrad
Focal adhesions are formed as a molecular glue linking cytoskeletal actin filaments to the extracellular matrix (ECM). They are formed at the site of mechanical stimulation (1) and involve and initial recruitment of talin and vinculin to...
Keywords: Vinculin, Focal adhesion, Actin, Mechanotransduction, Actin cytoskeleton, Cytoskeleton, Integrin, Extracellular matrix, Cell biology, Chemistry, Biophysics, Biology, Biochemistry, Signal transduction, Cell
Molecular Mechanosensors and Focal Adhesion Mechanotransduction
Authors: Mohammad R. K. Mofrad
Cellular response to mechanical stimulation is mediated by both biochemical mechanisms via changes in gene expression and by biophysical mechanisms via mechanically induced changes in specific molecules’ structure and function. These mec...
Keywords: Mechanotransduction, Focal adhesion, Cell adhesion molecule, Cell biology, Cytoskeleton, Chemistry, Function (biology), Cell adhesion, Adhesion, Biophysics, Biology, Cell, Signal transduction, Biochemistry
Use of a Social Networking Recommendation Engine in Science and Engineering Education for Accessible Discovery, Organization and Collaboration of Research Knowledge
Authors: Mohammad Daud Azimi, Mohammad R. K. Mofrad
The World Wide Web is the primary tool used by researchers in the field of science and engineering to share knowledge. Whether students or researchers are trying to share their own discoveries or learn from the discoveries of others, the...
Keywords: Computer science, Resource (disambiguation), Field (mathematics), Task (project management), The Internet, World Wide Web, Search engine indexing, Quality (philosophy), Economic shortage, Data science, Engineering
2009
Hydrodynamics and Semi-Flexible Filament Behavior
Authors: Preethi L. Chandran, Mohammad R. K. Mofrad
In this paper we simulate the effect of hydrodynamic interaction on the Brownian dynamics of semiflexible filaments. Semiflexible filaments are those whose entropy-driven bending fluctuations are resisted by the elastic bending stiffness...
Keywords: Protein filament, Drag, Mechanics, Stiffness, Brownian dynamics, Brownian motion, Bending stiffness, Bending, Materials science, Physics, Classical mechanics, Composite material
MEMS-Based Microballoons Achieving Multidirectional Large-Strain for Cell Mechanics Studies
Authors: Sang‐Hee Yoon, Vimalier Reyes-Ortiz, Mohammad R. K. Mofrad
The influence of mechanical stresses on cells has been a topic of special interest [1]. Attention is being focused on the cell-to-cell and cell-to-surrounding interactions and the mechanical stimuli that could be directly linked with fun...
Keywords: Cell, Cell mechanics, Strain (injury), Microelectromechanical systems, Substrate (aquarium), Materials science, Nanotechnology, Cell biology, Computer science, Chemistry, Biology, Anatomy, Cytoskeleton
Patient Specific FEM Analysis of the Atherosclerotic Carotid Bifurcation
Authors: Joseph Leach, Vitaliy L. Rayz, Mohammad R. K. Mofrad, Max Wintermark, David Saloner
Atherosclerosis in the carotid bifurcation is a highly variable disease that, in its stable form, can cause a dangerous reduction of blood flow to the brain. If the plaque ruptures or ulcerates, the patient is likely to experience a thro...
Keywords: Carotid bifurcation, Stroke (engine), Medicine, Cardiology, Bifurcation, Disease, Carotid arteries, Internal medicine, Vascular disease, Blood flow, Cause of death, Pathology
2008
Multiscale Simulations of the Healthy and Calcific Human Aortic Valve
Authors: Eli J. Weinberg, Mohammad R. K. Mofrad
In the heart’s aortic valve, maintenance of a healthy state and transition to disease states are modulated by the cells in the valve. The cells found within the valve leaflets are valvular interstitial cells (VICs) and those found on the...
Keywords: Aortic valve, Closing (real estate), Heart valve, Multiscale modeling, Materials science, Biomedical engineering, Mechanics, Computer science, Physics, Engineering, Cardiology, Chemistry, Medicine
2007
Development of a Discrete Finite Element Cell Model
Authors: Karen M. Coghlan, Patrick McGarry, Mohammad R. K. Mofrad, P.E. McHugh
Computational models have proven useful in the study of cell mechanics and mechanotransduction. While most finite element (FE) models of cells are commonly described in terms of the laws of continuum mechanics, a model that can accuratel...
Keywords: Microscale chemistry, Cell mechanics, Finite element method, Cytoskeleton, Mechanotransduction, Continuum mechanics, Computational mechanics, Structural mechanics, Classical mechanics, Mechanics, Physics, Computer science, Cell, Mathematics, Chemistry, Neuroscience, Biology
Multiscale Fluid-Structure Simulations of the Aortic Valve
Authors: Eli J. Weinberg, Mohammad R. K. Mofrad
In the heart aortic valve, maintenance of healthy conditions and transition to diseased conditions are modulated by the cells in the valve. The cells found within the valve leaflets and walls are the valvular interstitial cells (VICs), a...
Keywords: Aortic valve, Closing (real estate), Materials science, Heart valve, Mechanics, Cardiology, Physics
2006
Non-rigid registration for fusion of carotid vascular ultrasound and MRI volumetric datasets
Authors: Raymond C. K. Chan, Sham Sokka, Denise P. Hinton, Stuart L. Houser, Robert Manzke, Annemarie Hanekamp, Vivek Y. Reddy, Mohammad R. K. Mofrad, Volker Rasche
In carotid plaque imaging, MRI provides exquisite soft-tissue characterization, but lacks the temporal resolution for tissue strain imaging that real-time 3D ultrasound (3DUS) can provide. On the other hand, real-time 3DUS currently lack...
Keywords: Fiducial marker, Ultrasound, 3D ultrasound, Image registration, Voxel, Modality (human–computer interaction), Image fusion, Biomedical engineering, Medicine, Computer science, Computer vision, Radiology, Artificial intelligence
2004
Force-induced unfolding of the focal adhesion targeting domain and the influence of paxillin binding.
Authors: Mohammad R. K. Mofrad, Javad Golji, Nur Aida Abdul Rahim, Roger D. Kamm
Membrane-bound integrin receptors are linked to intracellular signaling pathways through focal adhesion kinase (FAK). FAK tends to colocalize with integrin receptors at focal adhesions through its C-terminal focal adhesion targeting (FAT...
Keywords: Focal adhesion, Paxillin, Cell biology, PTK2, Intracellular, Integrin, Extracellular matrix, Signal transduction, Extracellular, Cell adhesion, Chemistry, Mechanotransduction, Biology, Receptor, Biochemistry, Cell, Protein kinase C
How flexible is alpha-actinin's rod domain?
Authors: Muhammad H. Zaman, Mohammad R. K. Mofrad
Alpha-actinin, an actin binding protein, plays a key role in cell migration, cross-links actin filaments in the Z-disk, and is a major component of contractile muscle apparatus. The flexibility of the molecule is critical to its function...
Keywords: Linker, Flexibility (engineering), Molecule, Biophysics, Chemistry, Crystallography, Actin, Protein structure, Actinin, Stereochemistry, Biochemistry, Cytoskeleton, Biology, Computer science, Cell, Mathematics
Distinct endothelial phenotypes evoked by arterial waveforms derived from atherosclerosis-susceptible and -resistant regions of human vasculature
Authors: Guohao Dai, Mohammad R. K. Mofrad, Sripriya Natarajan, Yuzhi Zhang, Saran Vaughn, Brett R. Blackman, Roger D. Kamm, Guillermo García‐Cardeña, Michael A. Gimbrone
Atherosclerotic lesion localization to regions of disturbed flow within certain arterial geometries, in humans and experimental animals, suggests an important role for local hemodynamic forces in atherogenesis. To explore how endothelial...
Keywords: Gene expression profiling, Biology, Gene expression, Phenotype, Cell biology, Proinflammatory cytokine, Gene, Pathology, Inflammation, Medicine, Genetics, Immunology
On the molecular basis for mechanotransduction.
Authors: Roger D. Kamm, Mohammad R. K. Mofrad
Much is currently known about the signaling pathways that are excited when cells are subjected to a mechanical stimulus, yet we understand little of the process by which the mechanical perturbation is transformed into a biochemical signa...
Keywords: Mechanotransduction, Focal adhesion, Transmembrane protein, Cell biology, Intracellular, Receptor, Signal transduction, Chemistry, Biophysics, Signaling proteins, Stimulus (psychology), Affinities, Biology, Biochemistry
A MEMS-BASED RENAL REPLACEMENT SYSTEM
Authors: Jeffrey T. Borenstein, Mohammad R. K. Mofrad, Nicholas Krebs, Joseph P. Vacanti
Over the last decade, medicine and the biological sciences have benefited from advances in microfabrication technologies and microdevices originally developed for consumer and industrial electronics, automotives and aerospace, and nation...
Keywords: Microfabrication, Nanotechnology, Biocompatible material, Biomedical engineering, Regenerative medicine, Microelectromechanical systems, Microfluidics, Computer science, Medicine, Materials science, Stem cell, Pathology, Fabrication
Design and Fabrication of a Constant Shear Microfluidic Network for Tissue Engineering
Authors: Eli J. Weinberg, Jeffrey T. Borenstein, Mohammad R. K. Mofrad, Brian K. Orrick, Joseph P. Vacanti
Keywords: Microfluidics, Materials science, Microfabrication, Shear stress, Tissue engineering, Fluidics, Pulsatile flow, Nanotechnology, Scaffold, Biomedical engineering, Mechanotransduction, Mechanical engineering, Fabrication, Composite material, Engineering