503 papers
This study introduces amyAMP, a generative deep-learning framework combined with molecular dynamics simulations, to successfully design and validate novel peptides that integrate antimicrobial activity with amyloid-like self-assembly through shared physicochemical principles.
This paper introduces the Self-Returning Excluded Volume (SR-EV) model, a minimal polymer framework demonstrating that complex chromatin features like TADs and Hi-C loops emerge as statistical enrichments of heterogeneous single-cell conformations rather than as invariant 3D structures, thereby providing a unified reference for interpreting multimodal experimental data.
By combining high-resolution tracking, genetic experiments, and polymer modeling, this study reveals that the gradual decrease in chromatin motion during the cell cycle is driven globally by DNA content doubling rather than cohesin-mediated sister chromatid entrapment.
This paper introduces a systematic reparameterization strategy that successfully replaces external hydrogen-bond correction potentials (gHBfix19) with equivalent, native Lennard-Jones NBfix modifications in RNA force fields, thereby simplifying deployment and reducing computational overhead while maintaining the accuracy of RNA structural dynamics simulations.
This paper establishes an explicit analytical theory for fitness landscape design (FLD) and validates it against a large-scale experimental dataset of antibody-antigen binding affinities, demonstrating the feasibility of engineering quantitatively programmable biophysical fitness landscapes for protein evolution.
This paper introduces CASPULE, an efficient computational pipeline utilizing a novel force field and LAMMPS engine to simulate and analyze sticker-spacer polymer condensates, thereby providing critical insights into the kinetic and thermodynamic mechanisms governing their formation and function.
This paper presents a theoretical framework demonstrating that macromolecular crowding exerts an osmotic pressure on stretched DNA that typically induces compression and potential collapse at a critical force, though fluctuation-dependent corrections for large crowders can alternatively drive polymer expansion.
The paper introduces OpenFPM, an open-source, low-cost Fourier ptychographic microscopy platform built with 3D-printed components and controlled via a Raspberry Pi, which successfully achieves high-resolution amplitude and phase imaging over a 1 mm field-of-view to make advanced LED-array microscopy accessible for biomedical research.
This paper presents optimized experimental workflows that overcome key challenges in cryo-volume electron microscopy (cvEM), such as sample preparation and beam damage, to achieve high-resolution 3D imaging of whole unicellular and multicellular organisms in their near-native state.
This study demonstrates that visible light Optical Coherence Tomography can non-invasively detect and quantify sub-clinical age-related thickening and structural changes at the RPE-Bruch's membrane interface in living human eyes, revealing early biomarkers that resemble the deposits found in age-related macular degeneration.
This study utilizes molecular dynamics simulations to demonstrate that GTP hydrolysis in RhoA is driven by a dissociative mechanism facilitated by the tautomerization of Gln63, which protonates the leaving group and enables solvent-mediated restoration of the active site.
This paper introduces a physics-based inversion framework that converts nanoscale dynamic AFM measurements of living plant cell walls into spatially resolved mechanical fields, revealing how local relaxation times are encoded in the coupling between storage and dissipation to bridge molecular activity with continuum growth laws.
This study utilizes coarse-grained molecular dynamics and experimental validation to elucidate the multistep assembly pathway and structural determinants of 4F peptide nanodiscs, revealing how lipid composition and temperature govern their stability while demonstrating that their peptide-rimmed architecture effectively inhibits amyloid fibrillization comparable to MSP-based scaffolds.
This study reveals that bacterial cell volume growth exhibits subdiffusive dynamics driven by the viscoelastic mechanical properties of the peptidoglycan cell wall rather than biological regulatory programs, challenging standard white-noise growth models.
This paper presents a nucleosome-resolution maximum entropy framework that infers effective pairwise interaction parameters from Micro-C data to reconstruct accurate, physically interpretable 3D chromatin structures and interaction landscapes.
Using vertex models and zebrafish mesendoderm data, this study demonstrates that optimal collective migration in heterogeneous tissues occurs at an intermediate adhesion strength that balances cluster cohesion with the interfacial remodeling necessary for forward motion.
This study demonstrates that -Synuclein remodels cellular membranes through a synergistic mechanism where the structured N-terminal domain induces curvature via helix insertion, while the disordered C-terminal domain provides an electrostatic repulsive force that cooperatively lowers the energy barrier for membrane bending and fission.
This study utilizes molecular dynamics simulations, enhanced sampling, and machine learning to reveal that coupled protein and solvent dynamics distinguish EGFR Exon-19 deletion mutants into two profiles, where localized motions correlate with high ATP affinity and TKI resistance, while delocalized motions between kinase lobes reduce ATP binding and increase drug sensitivity.
The paper introduces mdBIRCH, a fast, scalable, and online clustering algorithm for molecular dynamics trajectories that adapts the BIRCH CF-tree with an RMSD-calibrated merge test to avoid pairwise distance calculations while offering interpretable, user-controlled resolution through novel threshold selection protocols.
This study resolves the paradox of glassy dynamics in active epithelial cells by demonstrating, through combined experiments and an active vertex model, that a mechanochemical feedback loop mediated by cell shape changes is essential to drive glass transitions and collective oscillations in dense tissues, overcoming the fluidizing effects of cell division.