Biophysical Journal

Article	Citations
A multiscale coarse-grained model of the SARS-CoV-2 virion	146
Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure	140
Physical phenotype of blood cells is altered in COVID-19	126
The emergence of phase separation as an organizing principle in bacteria	122
Encapsulation state of messenger RNA inside lipid nanoparticles	119
The flexibility of ACE2 in the context of SARS-CoV-2 infection	100
Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction	91
The key role of solvent in condensation: Mapping water in liquid-liquid phase-separated FUS	82
Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model	67
Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates	66
Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein	62
The Relative Densities of Cytoplasm and Nuclear Compartments Are Robust against Strong Perturbation	61
Mechanics of Bacterial Interaction and Death on Nanopatterned Surfaces	58
A predictive coarse-grained model for position-specific effects of post-translational modifications	57
Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide	56
Coupled membrane lipid miscibility and phosphotyrosine-driven protein condensation phase transitions	55
Determination of bacterial surface charge density via saturation of adsorbed ions	54
SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential	53
Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization	52
Chemotactic migration of bacteria in porous media	50
Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2	48
Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication	46
Phase separation of DNA: From past to present	46
EPA and DHA differentially modulate membrane elasticity in the presence of cholesterol	44
Phosphofructokinase relocalizes into subcellular compartments with liquid-like properties in vivo	42

Force-dependent stimulation of RNA unwinding by SARS-CoV-2 nsp13 helicase	41
A vesicle microrheometer for high-throughput viscosity measurements of lipid and polymer membranes	41
DNA length tunes the fluidity of DNA-based condensates	40
A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors	40
‘RNA modulation of transport properties and stability in phase-separated condensates	39
Real-time observation of structure and dynamics during the liquid-to-solid transition of FUS LC	39
Troponin Revealed: Uncovering the Structure of the Thin Filament On-Off Switch in Striated Muscle	38
Migration of Cytotoxic T Lymphocytes in 3D Collagen Matrices	38
Hydrating the respiratory tract: An alternative explanation why masks lower severity of COVID-19	37
Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain	37
Holding it together: when cadherin meets cadherin	36
Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element	35
Molecular dynamics simulations of Piezo1 channel opening by increases in membrane tension	34
Macromolecular crowding modulates α-synuclein amyloid fiber growth	34
Multivalent binding of the partially disordered SARS-CoV-2 nucleocapsid phosphoprotein dimer to RNA	33
Clathrin senses membrane curvature	33
Dynamic self-reinforcement of gene expression determines acquisition of cellular mechanical memory	32
On the stability and layered organization of protein-DNA condensates	32
Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane	31
Local actin dynamics couple speed and persistence in a cellular Potts model of cell migration	31
Low-frequency component of photoplethysmogram reflects the autonomic control of blood pressure	31
2.5 Å-resolution structure of human CDK-activating kinase bound to the clinical inhibitor ICEC0942	30
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies	30
Following the tracks: How transcription factor binding dynamics control transcription	30
RNA at the surface of phase-separated condensates impacts their size and number	30
Modeling of full-length Piezo1 suggests importance of the proximal N-terminus for dome structure	29
Origin of gradients in lipid density and surface tension between connected lipid droplet and bilayer	29
The interplay of chromatin phase separation and lamina interactions in nuclear organization	29
The Surface and Hydration Properties of Lipid Droplets	29
Quantifying charge state heterogeneity for proteins with multiple ionizable residues	28
Distribution of cholesterol in asymmetric membranes driven by composition and differential stress	28
Matrix-driven changes in metabolism support cytoskeletal activity to promote cell migration	28
Red blood cell shape transitions and dynamics in time-dependent capillary flows	27
Synergistic Allostery in Multiligand-Protein Interactions	27
The substrate import mechanism of the human serotonin transporter	27
Assembly of model postsynaptic densities involves interactions auxiliary to stoichiometric binding	27
Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data	27
mRNA lipid nanoparticle phase transition	26
Generalizing HMMs to Continuous Time for Fast Kinetics: Hidden Markov Jump Processes	26
Membrane-Mediated Ligand Unbinding of the PK-11195 Ligand from TSPO	26
The physics of liquid-to-solid transitions in multi-domain protein condensates	26
Folding@home: Achievements from over 20 years of citizen science herald the exascale era	26
Fat inclusions strongly alter membrane mechanics	26
Crowding-induced phase separation and gelling by co-condensation of PEG in NPM1-rRNA condensates	25
Unraveling the mechanism of octenidine and chlorhexidine on membranes: Does electrostatics matter?	25
Vast heterogeneity in cytoplasmic diffusion rates revealed by nanorheology and Doppelgänger simulations	25
Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition	25
Modeling bursty transcription and splicing with the chemical master equation	24
Intestinal villus structure contributes to even shedding of epithelial cells	24
Modeling Thrombus Shell: Linking Adhesion Receptor Properties and Macroscopic Dynamics	24

Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries	24
Image-derived modeling of nucleus strain amplification associated with chromatin heterogeneity	24
Collective motion enhances chemotaxis in a two-dimensional bacterial swarm	24
rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation	24
Conformational Ensembles of Antibodies Determine Their Hydrophobicity	24
Clot Permeability, Agonist Transport, and Platelet Binding Kinetics in Arterial Thrombosis	24
Sarcomere Length Nonuniformity and Force Regulation in Myofibrils and Sarcomeres	24
Manipulation of the Endocochlear Potential Reveals Two Distinct Types of Cochlear Nonlinearity	24
The Biased Ligands NGF and NT-3 Differentially Stabilize Trk-A Dimers	23
Extracting Transition Rates in Particle Tracking Using Analytical Diffusion Distribution Analysis	23
Improving SARS-CoV-2 structures: Peer review by early coordinate release	23
Influence of membrane-cortex linkers on the extrusion of membrane tubes	23
DeepTracer-ID: De novo protein identification from cryo-EM maps	23
Protein Dynamics Enables Phosphorylation of Buried Residues in Cdk2/Cyclin-A-Bound p27	23
Dedifferentiation alters chondrocyte nuclear mechanics during in vitro culture and expansion	23
Intrachain interaction topology can identify functionally similar intrinsically disordered proteins	23
Oscillations in K(ATP) conductance drive slow calcium oscillations in pancreatic β-cells	23
Actin bundle architecture and mechanics regulate myosin II force generation	23
CRISPR-based DNA and RNA detection with liquid-liquid phase separation	23
Neuronal oscillator robustness to multiple global perturbations	22
Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins	22
Time-Resolved Fluorescence Anisotropy and Molecular Dynamics Analysis of a Novel GFP Homo-FRET Dimer	22
ECM Stiffness Controls the Activation and Contractility of Corneal Keratocytes in Response to TGF-β1	22
Regulation of epithelial sodium channel activity by SARS-CoV-1 and SARS-CoV-2 proteins	22
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2	22
Regeneration of PEG slide for multiple rounds of single-molecule measurements	22
SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction	22
Single-virus content-mixing assay reveals cholesterol-enhanced influenza membrane fusion efficiency	21
Endocytosis and exocytosis protect cells against severe membrane tension variations	21
Spontaneous local membrane curvature induced by transmembrane proteins	21
Differentiating cancer cells reveal early large-scale genome regulation by pericentric domains	21
Dye Transport through Bilayers Agrees with Lipid Electropore Molecular Dynamics	21
EMT changes actin cortex rheology in a cell-cycle-dependent manner	21
Principles and practice for SARS-CoV-2 decontamination of N95 masks with UV-C	21
Integrin-based mechanosensing through conformational deformation	21
FiberSim: A flexible open-source model of myofilament-level contraction	21
Backstepping Mechanism of Kinesin-1	21
Developing initial conditions for simulations of asymmetric membranes: a practical recommendation	20
Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins	20
Membrane hydrophobicity determines the activation free energy of passive lipid transport	20
Cellular mechanics of wound formation in single cell layer under cyclic stretching	20
Simulating the chromatin-mediated phase separation of model proteins with multiple domains	20
Phase separation in amino acid mixtures is governed by composition	20
The development of nucleic acids force fields: From an unchallenged past to a competitive future	20
The N-terminal domain of the A12.2 subunit stimulates RNA polymerase I transcription elongation	20
Cardiomyopathy mutations impact the actin-activated power stroke of human cardiac myosin	19
Myofibril orientation as a metric for characterizing heart disease	19
Biochemical and rheological analysis of human colonic culture mucus reveals similarity to gut mucus	19
Multiscale mechanobiology: Coupling models of adhesion kinetics and nonlinear tissue mechanics	19
Endocytosis against high turgor pressure is made easier by partial coating and freely rotating base	19
Mechanisms of Premature Ventricular Complexes Caused by QT Prolongation	19
Facile tethering of stable and unstable proteins for optical tweezers experiments	19
Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging	19
Glass-like characteristics of intracellular motion in human cells	19
Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics	19
Branched actin cortices reconstituted in vesicles sense membrane curvature	18
Rapid viscoelastic changes are a hallmark of early leukocyte activation	18
Infrared Excitation Induces Heating and Calcium Microdomain Hyperactivity in Cortical Astrocytes	18
The origin and impact of bound water around intrinsically disordered proteins	18
Protein-induced membrane curvature in coarse-grained simulations	18
Novel elasticity measurements reveal C. elegans cuticle stiffens with age and in a long-lived mutant	18
Stability and conformation of the dimeric HIV-1 genomic RNA 5′UTR	18
Multimodal microscale mechanical mapping of cancer cells in complex microenvironments	18
ATP:Mg2+ shapes material properties of protein-RNA condensates and their partitioning of clients	17
Active chemo-mechanical feedbacks dictate the collective migration of cells on patterned surfaces	17
Compartmentalization with nuclear landmarks yields random, yet precise, genome organization	17
Modeling insights into SARS-CoV-2 respiratory tract infections prior to immune protection	17
Topological polymorphism of nucleosome fibers and folding of chromatin	17
Cholesterol stabilizes recombinant exocytic fusion pores by altering membrane bending rigidity	17
Using optogenetics to link myosin patterns to contractile cell behaviors during convergent extension	17
Predicting Genetic Variation Severity Using Machine Learning to Interpret Molecular Simulations	17
Comparative evaluation of spin-label modeling methods for protein structural studies	17
Small molecule therapeutics to destabilize the ACE2-RBD complex: A molecular dynamics study	17
Predicting YAP/TAZ nuclear translocation in response to ECM mechanosensing	17
Modeling coronavirus spike protein dynamics: implications for immunogenicity and immune escape	17
Enhanced persistence and collective migration in cooperatively aligning cell clusters	17
Induction of ciliary orientation by matrix patterning and characterization of mucociliary transport	16
Nanopore fingerprinting of supramolecular DNA nanostructures	16
Effects of polycationic drug carriers on the electromechanical and swelling properties of cartilage	16
Remodeling of yeast vacuole membrane lipidomes from the log (one phase) to stationary stage (two phases)	16

Short peptides as predictors for the structure of polyarginine sequences in disordered proteins	16
Zinc determines dynamical properties and aggregation kinetics of human insulin	16
Myofiber stretch induces tensile and shear deformation of muscle stem cells in their native niche	16
Influence of the extracellular domain size on the dynamic behavior of membrane proteins	16
Water Loss in Aging Erythrocytes Provides a Clue to a General Mechanism of Cellular Senescence	16
Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump	16
Characterizing fenestration size in sodium channel subtypes and their accessibility to inhibitors	16
Rotational decoupling between the hydrophilic and hydrophobic regions in lipid membranes	15
Protein orientation in time-dependent electric fields: orientation before destruction	15
Modeling Fibrillogenesis of Collagen-Mimetic Molecules	15
Functional characteristics of hub and wave-initiator cells in β cell networks	15
Response to Perspectives on the Classical Enzyme Carbonic Anhydrase and the Search for Inhibitors	15
Physical modeling of multivalent interactions in the nuclear pore complex	15
Computational modeling of biomechanics and biorheology of heated red blood cells	15
Membrane-dependent heterogeneity of LHCII characterized using single-molecule spectroscopy	15
Cancer as a biophysical disease: Targeting the mechanical-adaptability program	15
Adhesion strength between cells regulate nonmonotonic growth by a biomechanical feedback mechanism	15
Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions	15
Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy	15
Structural determinants of cholesterol recognition in helical integral membrane proteins	15
Controlling composition of coexisting phases via molecular transitions	15
Charge and redox states modulate granulin—TDP-43 coacervation toward phase separation or aggregation	15
Chromatin dynamics controls epigenetic domain formation	15
Mechanical Activation of MscL Revealed by a Locally Distributed Tension Molecular Dynamics Approach	15
Development of Nascent Focal Adhesions in Spreading Cells	15
Converging experimental and computational views of the knotting mechanism of a small knotted protein	15
Melatonin Alters Fluid Phase Coexistence in POPC/DPPC/Cholesterol Membranes	15
Mechanical memory stored through epigenetic remodeling reduces cell therapeutic potential	15
Molecular mechanisms of spontaneous curvature and softening in complex lipid bilayer mixtures	15
Cooperative Function of LL-37 and HNP1 Protects Mammalian Cell Membranes from Lysis	15
SNARE complex alters the interactions of the Ca2+ sensor synaptotagmin 1 with lipid bilayers	14
Muscle active force-length curve explained by an electrophysical model of interfilament spacing	14
Ion permeation, selectivity, and electronic polarization in fluoride channels	14
Oncogenic mutations on Rac1 affect global intrinsic dynamics underlying GTP and PAK1 binding	14
Dynamic allostery highlights the evolutionary differences between the CoV-1 and CoV-2 main proteases	14
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization	14
Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase	14
Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration	14
Three-dimensional loop extrusion	14
Membrane Curvature Revisited—the Archetype of Rhodopsin Studied by Time-Resolved Electronic Spectroscopy	14
Predicting pathological von Willebrand factor unraveling in elongational flow	14
Lingering Dynamics in Microvascular Blood Flow	14
Single-molecule micromanipulation studies of methylated DNA	14
Desmoglein 2 can undergo Ca2+-dependent interactions with both desmosomal and classical cadherins including E-cadherin and N-cadherin	14
Effects of Ligand Binding on the Energy Landscape of Acyl-CoA-Binding Protein	14
A hard-sphere model of protein corona formation on spherical and cylindrical nanoparticles	14
Influenza A M2 recruits M1 to the plasma membrane: A fluorescence fluctuation microscopy study	14
Effects of vimentin on the migration, search efficiency, and mechanical resilience of dendritic cells	14
Proton coupling and the multiscale kinetic mechanism of a peptide transporter	14
Spatiotemporal dynamics of growth and death within spherical bacterial colonies	14
Different membrane order measurement techniques are not mutually consistent	14
Systematic measurements of interleaflet friction in supported bilayers	14
Mechanosensitive axon outgrowth mediated by L1-laminin clutch interface	14
The G-Protein Rab5A Activates VPS34 Complex II, a Class III PI3K, by a Dual Regulatory Mechanism	14
Effects of H2A.B incorporation on nucleosome structures and dynamics	14
In silico and in vitro study of the adhesion dynamics of erythrophagocytosis in sickle cell disease	14
Lipid packing is disrupted in copolymeric nanodiscs compared with intact membranes	14
Differential regulation of GUV mechanics via actin network architectures	14
Curvature-based sorting of eight lipid types in asymmetric buckled plasma membrane models	14
In silico biophysics and hemorheology of blood hyperviscosity syndrome	14
Particle Diffusivity and Free-Energy Profiles in Hydrogels from Time-Resolved Penetration Data	14
Fibrillation of Human Calcitonin and Its Analogs: Effects of Phosphorylation and Disulfide Reduction	14
Stable polymer bilayers for protein channel recordings at high guanidinium chloride concentrations	14
Internalization of α-synuclein oligomers into SH-SY5Y cells	14
The contribution of electrostatics to hydrogen exchange in the unfolded protein state	13
Computational model of E-cadherin clustering under force	13
Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation	13
An NMR look at an engineered PET depolymerase	13
Mesoscale simulations: An indispensable approach to understand biomembranes	13
Soft Polydimethylsiloxane-Supported Lipid Bilayers for Studying T Cell Interactions	13
Reaction intermediate rotation during the decarboxylation of coproheme to heme b in C. diphtheriae	13
The structural basis of Akt PH domain interaction with calmodulin	13
Long-range DNA-water interactions	13
Nucleation limits the lengths of actin filaments assembled by formin	13
Fluorescence lifetime-based pH mapping of tumors in vivo using genetically encoded sensor SypHerRed	13
Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics	13
Prosecco: polarization reintroduced by optimal scaling of electronic continuum correction origin in MD simulations	13
The structural basis of BCR-ABL recruitment of GRB2 in chronic myelogenous leukemia	13
Activation of G-protein-coupled receptors is thermodynamically linked to lipid solvation	13
Multiscale computational study of ligand binding pathways: Case of p38 MAP kinase and its inhibitors	13
Negatively charged residues in the membrane ordering activity of SARS-CoV-1 and -2 fusion peptides	13
Chemical potential measurements constrain models of cholesterol-phosphatidylcholine interactions	13
Conformational Dynamics of Light-Harvesting Complex II in a Native Membrane Environment	13
Slow oscillations persist in pancreatic beta cells lacking phosphofructokinase M	13
Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif	13
Asymmetric glycerophospholipids impart distinctive biophysical properties to lipid bilayers	13
pH-triggered pore-forming peptides with strong composition-dependent membrane selectivity	12
Precision in iterative modulation enhanced single-molecule localization microscopy	12
Polarized interfacial tension induces collective migration of cells, as a cluster, in a 3D tissue	12
Vinculin transmits high-level integrin tensions that are dispensable for focal adhesion formation	12
Cross talk between endothelial and red blood cell glycocalyces via near-field flow	12
MDAnalysis 2.0 and beyond: fast and interoperable, community driven simulation analysis	12
Protein unfolded states populated at high and ambient pressure are similarly compact	12
Distinct allosteric pathways in imidazole glycerol phosphate synthase from yeast and bacteria	12
Bacterial cell shape control by nutrient-dependent synthesis of cell division inhibitors	12