Biophysical Journal

Article	Citations
A multiscale coarse-grained model of the SARS-CoV-2 virion	134
The emergence of phase separation as an organizing principle in bacteria	111
Physical phenotype of blood cells is altered in COVID-19	110
Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure	102
The flexibility of ACE2 in the context of SARS-CoV-2 infection	98
Encapsulation state of messenger RNA inside lipid nanoparticles	88
Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction	87
Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins	84
The key role of solvent in condensation: Mapping water in liquid-liquid phase-separated FUS	74
Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol	63
Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model	59
Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein	58
The Relative Densities of Cytoplasm and Nuclear Compartments Are Robust against Strong Perturbation	55
Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates	55
A predictive coarse-grained model for position-specific effects of post-translational modifications	53
Mechanics of Bacterial Interaction and Death on Nanopatterned Surfaces	51
SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential	50
Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide	50
Coupled membrane lipid miscibility and phosphotyrosine-driven protein condensation phase transitions	49
Chemotactic migration of bacteria in porous media	46
Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization	44
Liquid Phase Separation Controlled by pH	44
Effect of DMSO on the Mechanical and Structural Properties of Model and Biological Membranes	44
Pulsed Electric Fields Can Create Pores in the Voltage Sensors of Voltage-Gated Ion Channels	44
Present and Emerging Methodologies in Cryo-EM Single-Particle Analysis	43

Determination of bacterial surface charge density via saturation of adsorbed ions	43
Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2	41
Cryo-EM and Molecular Docking Shows Myosin Loop 4 Contacts Actin and Tropomyosin on Thin Filaments	41
All-Optical Electrophysiology Refines Populations of In Silico Human iPSC-CMs for Drug Evaluation	41
Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication	39
Phosphofructokinase relocalizes into subcellular compartments with liquid-like properties in vivo	39
A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors	38
Force-dependent stimulation of RNA unwinding by SARS-CoV-2 nsp13 helicase	37
Improving the Accuracy of Protein Thermostability Predictions for Single Point Mutations	37
DNA length tunes the fluidity of DNA-based condensates	37
‘RNA modulation of transport properties and stability in phase-separated condensates	36
Migration of Cytotoxic T Lymphocytes in 3D Collagen Matrices	36
Phase separation of DNA: From past to present	36
A Stochastic Model of Gene Expression with Polymerase Recruitment and Pause Release	36
A vesicle microrheometer for high-throughput viscosity measurements of lipid and polymer membranes	36
EPA and DHA differentially modulate membrane elasticity in the presence of cholesterol	36
Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding	36
Troponin Revealed: Uncovering the Structure of the Thin Filament On-Off Switch in Striated Muscle	35
Molecular dynamics simulations of Piezo1 channel opening by increases in membrane tension	34
Target Membrane Cholesterol Modulates Single Influenza Virus Membrane Fusion Efficiency but Not Rate	34
Real-time observation of structure and dynamics during the liquid-to-solid transition of FUS LC	34
Hydrating the respiratory tract: An alternative explanation why masks lower severity of COVID-19	33
Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis	33
Mechanical Heterogeneity in the Bone Microenvironment as Characterized by Atomic Force Microscopy	33
Holding it together: when cadherin meets cadherin	33
Imaging ATP Consumption in Resting Skeletal Muscle: One Molecule at a Time	33
Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element	32
Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain	32
Quantifying Fibrinogen-Dependent Aggregation of Red Blood Cells in Type 2 Diabetes Mellitus	31
Multiscale Coarse-Grained Approach to Investigate Self-Association of Antibodies	31
Local actin dynamics couple speed and persistence in a cellular Potts model of cell migration	29
NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale	29
Phase Separation of Toxic Dipeptide Repeat Proteins Related to C9orf72 ALS/FTD	29
Induction of Ordered Lipid Raft Domain Formation by Loss of Lipid Asymmetry	29
Atomic Force Microscopy Imaging of Adsorbed Pulmonary Surfactant Films	29
Mesoscale Liquid Model of Chromatin Recapitulates Nuclear Order of Eukaryotes	29
Clathrin senses membrane curvature	28
Macromolecular crowding modulates α-synuclein amyloid fiber growth	28
Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling	28
Low-frequency component of photoplethysmogram reflects the autonomic control of blood pressure	28
Multivalent binding of the partially disordered SARS-CoV-2 nucleocapsid phosphoprotein dimer to RNA	27
Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane	27
Structural Description of the Nipah Virus Phosphoprotein and Its Interaction with STAT1	27
Increased Stiffness Inhibits Invadopodia Formation and Cell Migration in 3D	26
Amoeboid Swimming Is Propelled by Molecular Paddling in Lymphocytes	26
RNA at the surface of phase-separated condensates impacts their size and number	26
Assembly of model postsynaptic densities involves interactions auxiliary to stoichiometric binding	25
Dynamic self-reinforcement of gene expression determines acquisition of cellular mechanical memory	25
Membrane-Mediated Ligand Unbinding of the PK-11195 Ligand from TSPO	25
Following the tracks: How transcription factor binding dynamics control transcription	25

Protein-Protein Docking Reveals Dynamic Interactions of Tropomyosin on Actin Filaments	25
Chromatin Is Frequently Unknotted at the Megabase Scale	25
2.5 Å-resolution structure of human CDK-activating kinase bound to the clinical inhibitor ICEC0942	25
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies	25
Matrix-driven changes in metabolism support cytoskeletal activity to promote cell migration	24
Amyloid Evolution: Antiparallel Replaced by Parallel	24
Distribution of cholesterol in asymmetric membranes driven by composition and differential stress	24
Generalizing HMMs to Continuous Time for Fast Kinetics: Hidden Markov Jump Processes	24
On the stability and layered organization of protein-DNA condensates	24
Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data	24
Structural and Dynamical Signatures of Local DNA Damage in Live Cells	23
Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition	23
Intercellular Sodium Regulates Repolarization in Cardiac Tissue with Sodium Channel Gain of Function	23
The Surface and Hydration Properties of Lipid Droplets	23
Modeling of full-length Piezo1 suggests importance of the proximal N-terminus for dome structure	23
Fat inclusions strongly alter membrane mechanics	23
Origin of gradients in lipid density and surface tension between connected lipid droplet and bilayer	23
Manipulation of the Endocochlear Potential Reveals Two Distinct Types of Cochlear Nonlinearity	23
Synergistic Allostery in Multiligand-Protein Interactions	23
The Glycosphingolipid GM3 Modulates Conformational Dynamics of the Glucagon Receptor	23
Microtubule Simulations Provide Insight into the Molecular Mechanism Underlying Dynamic Instability	22
Conformational Ensembles of Antibodies Determine Their Hydrophobicity	22
The physics of liquid-to-solid transitions in multi-domain protein condensates	22
Nonequilibrium Biophysical Processes Influence the Large-Scale Architecture of the Cell Nucleus	22
Red blood cell shape transitions and dynamics in time-dependent capillary flows	22
The substrate import mechanism of the human serotonin transporter	22
Quantifying charge state heterogeneity for proteins with multiple ionizable residues	22
The interplay of chromatin phase separation and lamina interactions in nuclear organization	22
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2	22
z-STED Imaging and Spectroscopy to Investigate Nanoscale Membrane Structure and Dynamics	22
ECM Stiffness Controls the Activation and Contractility of Corneal Keratocytes in Response to TGF-β1	22
Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin	22
Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries	21
Neuronal oscillator robustness to multiple global perturbations	21
A Lamin-Associated Chromatin Model for Chromosome Organization	21
Backstepping Mechanism of Kinesin-1	21
A Unified Model for Treadmilling and Nucleation of Single-Stranded FtsZ Protofilaments	21
Improving SARS-CoV-2 structures: Peer review by early coordinate release	21
Modeling bursty transcription and splicing with the chemical master equation	21
SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction	21
Time-Resolved Fluorescence Anisotropy and Molecular Dynamics Analysis of a Novel GFP Homo-FRET Dimer	21
Protein Dynamics Enables Phosphorylation of Buried Residues in Cdk2/Cyclin-A-Bound p27	21
CRISPR-based DNA and RNA detection with liquid-liquid phase separation	21
Image-derived modeling of nucleus strain amplification associated with chromatin heterogeneity	21
Sarcomere Length Nonuniformity and Force Regulation in Myofibrils and Sarcomeres	21
Unraveling the mechanism of octenidine and chlorhexidine on membranes: Does electrostatics matter?	20
Influence of membrane-cortex linkers on the extrusion of membrane tubes	20
CompuCell3D Simulations Reproduce Mesenchymal Cell Migration on Flat Substrates	20
Principles and practice for SARS-CoV-2 decontamination of N95 masks with UV-C	20
Coarse-Grained Modeling of Pore Dynamics on the Red Blood Cell Membrane under Large Deformations	20
Regulation of Gene Activation by Competitive Cross Talking Pathways	20
Extracting Transition Rates in Particle Tracking Using Analytical Diffusion Distribution Analysis	20
Differentiating cancer cells reveal early large-scale genome regulation by pericentric domains	20
Regeneration of PEG slide for multiple rounds of single-molecule measurements	20
Regulation of epithelial sodium channel activity by SARS-CoV-1 and SARS-CoV-2 proteins	20
Single-virus content-mixing assay reveals cholesterol-enhanced influenza membrane fusion efficiency	19
Dye Transport through Bilayers Agrees with Lipid Electropore Molecular Dynamics	19
The Biased Ligands NGF and NT-3 Differentially Stabilize Trk-A Dimers	19
Mechanics of Multicentrosomal Clustering in Bipolar Mitotic Spindles	19
Spatiotemporal Dynamics of Dilute Red Blood Cell Suspensions in Low-Inertia Microchannel Flow	19
Effect of Divalent Cations on the Structure and Mechanics of Vimentin Intermediate Filaments	19
β Cells Operate Collectively to Help Maintain Glucose Homeostasis	19
Membrane Association Transforms an Inert Anti-TCRβ Fab’ Ligand into a Potent T Cell Receptor Agonist	19
Sequence-Based Prediction of Metamorphic Behavior in Proteins	19
DeepTracer-ID: De novo protein identification from cryo-EM maps	19
Intrachain interaction topology can identify functionally similar intrinsically disordered proteins	18
Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins	18
Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins	18
Chromatin Viscoelasticity Measured by Local Dynamic Analysis	18
Modeling Thrombus Shell: Linking Adhesion Receptor Properties and Macroscopic Dynamics	18
Modeling coronavirus spike protein dynamics: implications for immunogenicity and immune escape	18
mRNA lipid nanoparticle phase transition	18
Non-Langmuir Kinetics of DNA Surface Hybridization	18
The Effect of (−)-Epigallocatechin-3-Gallate on the Amyloid-β Secondary Structure	18
Intestinal villus structure contributes to even shedding of epithelial cells	18
rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation	18
Computing 3D Chromatin Configurations from Contact Probability Maps by Inverse Brownian Dynamics	18
Chromatin and Cytoskeletal Tethering Determine Nuclear Morphology in Progerin-Expressing Cells	18
Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging	18
Binding Dynamics of α-Actinin-4 in Dependence of Actin Cortex Tension	18

Mechanisms of Light-Induced Deformations in Photoreceptors	18
Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics	18
Effect of Protein Structure on Evolution of Cotranslational Folding	18
A Mechanical Instability in Planar Epithelial Monolayers Leads to Cell Extrusion	18
Dedifferentiation alters chondrocyte nuclear mechanics during in vitro culture and expansion	18
Endocytosis against high turgor pressure is made easier by partial coating and freely rotating base	17
Endocytosis and exocytosis protect cells against severe membrane tension variations	17
Rapid viscoelastic changes are a hallmark of early leukocyte activation	17
Collective motion enhances chemotaxis in a two-dimensional bacterial swarm	17
Protein-Folding Analysis Using Features Obtained by Persistent Homology	17
Chemical Exchange at the Trinuclear Copper Center of Small Laccase from Streptomyces coelicolor	17
Clot Permeability, Agonist Transport, and Platelet Binding Kinetics in Arterial Thrombosis	17
Anomalous Diffusion Characterization by Fourier Transform-FRAP with Patterned Illumination	17
EMT changes actin cortex rheology in a cell-cycle-dependent manner	17
Actin bundle architecture and mechanics regulate myosin II force generation	17
Myofibril orientation as a metric for characterizing heart disease	17
Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins	17
TENSCell: Imaging of Stretch-Activated Cells Reveals Divergent Nuclear Behavior and Tension	17
Facile tethering of stable and unstable proteins for optical tweezers experiments	17
Folding@home: Achievements from over 20 years of citizen science herald the exascale era	16
Oscillations in K(ATP) conductance drive slow calcium oscillations in pancreatic β-cells	16
Perspectives on the Classical Enzyme Carbonic Anhydrase and the Search for Inhibitors	16
Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization	16
Membrane Tension Can Enhance Adaptation to Maintain Polarity of Migrating Cells	16
Modeling insights into SARS-CoV-2 respiratory tract infections prior to immune protection	16
Simulating the chromatin-mediated phase separation of model proteins with multiple domains	16
Small molecule therapeutics to destabilize the ACE2-RBD complex: A molecular dynamics study	16
Tuning Cell Motility via Cell Tension with a Mechanochemical Cell Migration Model	16
Control of Platelet CLEC-2-Mediated Activation by Receptor Clustering and Tyrosine Kinase Signaling	16
Spontaneous local membrane curvature induced by transmembrane proteins	16
Cellular mechanics of wound formation in single cell layer under cyclic stretching	16
Queuing Models of Gene Expression: Analytical Distributions and Beyond	16
The N-terminal domain of the A12.2 subunit stimulates RNA polymerase I transcription elongation	16
Protein-induced membrane curvature in coarse-grained simulations	16
Induction of ciliary orientation by matrix patterning and characterization of mucociliary transport	16
Cardiomyopathy mutations impact the actin-activated power stroke of human cardiac myosin	15
Mechanisms of Premature Ventricular Complexes Caused by QT Prolongation	15
Cholesterol stabilizes recombinant exocytic fusion pores by altering membrane bending rigidity	15
Myofiber stretch induces tensile and shear deformation of muscle stem cells in their native niche	15
Membrane hydrophobicity determines the activation free energy of passive lipid transport	15
Structural Studies of Overlapping Dinucleosomes in Solution	15
Zinc determines dynamical properties and aggregation kinetics of human insulin	15
Redistribution of TPA Fluxes in the Presence of PAI-1 Regulates Spatial Thrombolysis	15
Developing initial conditions for simulations of asymmetric membranes: a practical recommendation	15
Multiscale mechanobiology: Coupling models of adhesion kinetics and nonlinear tissue mechanics	15
Biophysical Parameters of GEVIs: Considerations for Imaging Voltage	15
Durotaxis Index of 3T3 Fibroblast Cells Scales with Stiff-to-Soft Membrane Tension Polarity	15
Water Loss in Aging Erythrocytes Provides a Clue to a General Mechanism of Cellular Senescence	15
Zinc Fingers in HIV-1 Gag Precursor Are Not Equivalent for gRNA Recruitment at the Plasma Membrane	15
Dynamics of Cell Membrane Permeabilization by Saponins Using Terahertz Attenuated Total Reflection	15
Novel elasticity measurements reveal C. elegans cuticle stiffens with age and in a long-lived mutant	14
Sphingomyelin Acyl Chains Influence the Formation of Sphingomyelin- and Cholesterol-Enriched Domains	14
Comparative evaluation of spin-label modeling methods for protein structural studies	14
Sphingomyelins and ent-Sphingomyelins Form Homophilic Nano-Subdomains within Liquid Ordered Domains	14
Influence of the extracellular domain size on the dynamic behavior of membrane proteins	14
Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase	14
Membrane Curvature Revisited—the Archetype of Rhodopsin Studied by Time-Resolved Electronic Spectroscopy	14
Cooperative Function of LL-37 and HNP1 Protects Mammalian Cell Membranes from Lysis	14
Predicting Genetic Variation Severity Using Machine Learning to Interpret Molecular Simulations	14
ATP:Mg2+ shapes material properties of protein-RNA condensates and their partitioning of clients	14
Development of Nascent Focal Adhesions in Spreading Cells	14
Multimodal microscale mechanical mapping of cancer cells in complex microenvironments	14
Crowding-induced phase separation and gelling by co-condensation of PEG in NPM1-rRNA condensates	14
Infrared Excitation Induces Heating and Calcium Microdomain Hyperactivity in Cortical Astrocytes	14
Physical modeling of multivalent interactions in the nuclear pore complex	14
Glass-like characteristics of intracellular motion in human cells	14
Mechanical Activation of MscL Revealed by a Locally Distributed Tension Molecular Dynamics Approach	14
Dynamic Crowding Regulates Transcription	14
Short peptides as predictors for the structure of polyarginine sequences in disordered proteins	14
Ca2+ Release via IP3 Receptors Shapes the Cardiac Ca2+ Transient for Hypertrophic Signaling	13
Single-molecule micromanipulation studies of methylated DNA	13
Rotational decoupling between the hydrophilic and hydrophobic regions in lipid membranes	13
Exploration of Insulin Amyloid Polymorphism Using Raman Spectroscopy and Imaging	13
Fusion Pore Formation Observed during SNARE-Mediated Vesicle Fusion with Pore-Spanning Membranes	13
Phase separation in amino acid mixtures is governed by composition	13
Spatiotemporal dynamics of growth and death within spherical bacterial colonies	13
Melatonin Alters Fluid Phase Coexistence in POPC/DPPC/Cholesterol Membranes	13
Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association	13
Topological polymorphism of nucleosome fibers and folding of chromatin	13
Membrane Interactions of Cy3 and Cy5 Fluorophores and Their Effects on Membrane-Protein Dynamics	13
Effects of Ligand Binding on the Energy Landscape of Acyl-CoA-Binding Protein	13
A hard-sphere model of protein corona formation on spherical and cylindrical nanoparticles	13
Spatially Discordant Repolarization Alternans in the Absence of Conduction Velocity Restitution	13
Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics	13
Remodeling of yeast vacuole membrane lipidomes from the log (one phase) to stationary stage (two phases)	13
In silico biophysics and hemorheology of blood hyperviscosity syndrome	13
The G-Protein Rab5A Activates VPS34 Complex II, a Class III PI3K, by a Dual Regulatory Mechanism	13
Enhanced persistence and collective migration in cooperatively aligning cell clusters	13
Thermodynamics of Huntingtin Aggregation	13
Cancer as a biophysical disease: Targeting the mechanical-adaptability program	13
Nanopore fingerprinting of supramolecular DNA nanostructures	13
Fibrous Flagellar Hairs of Chlamydomonas reinhardtii Do Not Enhance Swimming	13
Influenza A M2 recruits M1 to the plasma membrane: A fluorescence fluctuation microscopy study	13
Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy	13
Heating-Induced DMPC/Glycyrrhizin Bicelle-to-Vesicle Transition: A X-Ray Contrast Variation Study	13