Bin Zhang

The paper develops a simulation framework to infer nucleosome-resolution chromatin structures from RCMC data, revealing euchromatin as condensed domains with accessible promoter/enhancer regions.

The paper introduces MOFF2, a transferable coarse-grained protein force field that improves simulation accuracy for various protein types and predicts condensate behavior.

This study uses molecular dynamics simulations to show that spacer heterogeneity in stickers-and-spacers polymers promotes condensation but reduces condensate organization and compositional robustness.

This paper introduces Free Energy Spectroscopy (FES) to characterize chromatin compaction by analyzing end-to-end distance and nucleosome stacking interactions, revealing three mechanisms by which linker histones reshape compaction energetics.

This study shows that the lipid composition of the membrane actively regulates EGFR conformation and signaling, independent of ligand binding, with implications for cancer and normal cell function.

NEAT-DNA is a coarse-grained DNA model that improves physical realism and sequence specificity for large-scale simulations of genome structure.

This study maps chromatin folding pathways and rates using a coarse-grained model, showing that linker DNA length and nucleosome condensate affect stability and structure.

The paper uses atomistic simulations to study sequence-dependent conformational landscapes of IDPs, identifying a new metric that captures directional structural differences.

This study shows that single nucleosomes encode A/B compartment information through biophysical properties, specifically condensability, which correlates with gene expression and is electrostatic in nature.

This study reports the formation of symmetrical core-shell biomolecular condensates through programmed tetra-peptide libraries and identifies tryptophan's role in structuring these condensates.

The paper uses a protein language model to identify conserved, disordered motifs in IDRs that are implicated in phase separation and MLO formation.

This paper extends the stickers and spacers model to show that specific sticker-sticker interactions drive structured condensates, while non-specific spacer interactions lead to disorganized condensates, suggesting evolutionary pressure for low complexity domains in IDPs.

This study reanalyzes Brd2 depletion effects on chromatin compartments using Micro-C data and cooltools, showing persistent but reduced compartment strength changes.

OpenNucleome enables GPU-accelerated molecular dynamics simulations of the human nucleus to model structural organization and dynamic processes, revealing mechanisms of genomic anchoring and nuclear zoning.

The paper develops a transferable coarse-grained force field using graph neural networks trained on atomistic simulation data, achieving accurate solvation free energy estimations and reasonable transferability.

This study uses super-resolution imaging to reveal the 3D structure and organizing mechanism of accessible chromatin domains.

This study uses an information-theoretic model to infer the mechanism of chromatin domain formation from epigenetic data, revealing distinct domain types and their formation dynamics.