Bin Zhang

Bin Zhang

@binzmit.bsky.social

Associate Professor at MIT Chemistry; Enthusiastic about chromatin, biophysics, molecular dynamics, and AI.

52 followers21 following10 posts

Bin Zhang
@binzmit.bsky.social

New preprint: CV-SVGD combines Stein variational gradient descent with parallel restrained MD for multidimensional sampling. In peptide tests, it recovered free-energy surfaces with less aggregate MD sampling than umbrella-sampling references. arxiv.org/abs/2610.27429

arxiv.orgCollective-Variable Stein Variational Gradient Descent for Free Energy Surface ExplorationEnhanced-sampling methods enable molecular simulations to access configurational regions that are difficult to explore with conventional dynamics, but their efficiency often deteriorates as the number...
Bin Zhang
@binzmit.bsky.social

Our new model simulates limited-valency sticker interactions in biomolecular condensates. Simulations reveal a trade-off: heterogeneous spacer interactions promote condensation but can disrupt sticker-mediated organization and robust molecular recruitment. doi.org/10.1021/acs....

doi.orgValency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Trade-Off between Condensation and OrganizationAbstract. Biomolecular condensates formed by intrinsically disordered proteins (IDPs) are often described using stickers-and-spacers models, in which speci
Bin Zhang
@binzmit.bsky.social

How open is “open” chromatin? Our new Nature Genetics paper uses nucleosome-resolution modeling to reveal condensed euchromatin domains with short, accessible regulatory regions at the surface. www.nature.com/articles/s41...

nature.comEuchromatin forms condensed domains with short active regions on the surface - Nature GeneticsSimulations integrating micro-C and imaging data provide a coherent view of chromatin organization from nucleosomes to clutches to domains, revealing that most regions form compact domains but short regulatory elements are highly exposed.
Bin Zhang
@binzmit.bsky.social

Pretraining implicit solvent, or coarse grained, models is difficult, limiting the transferability of the resulting ML force fields. However, Justin just figured out a novel method for pretraining using protein language models. More can be found at: arxiv.org/abs/2601.05388

arxiv.orgKnowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent ModelImplicit solvent models (ISMs) promise to deliver the accuracy of explicit solvent simulations at a fraction of the computational cost. However, despite decades of development, their accuracy has rema...
Bin Zhang
@binzmit.bsky.social

Thrilled to share our new JCP editorial (shorturl.at/6mKdY), co-authored with @tamar_schlick, introducing the special collection “Chromatin Structure and Dynamics: Recent Advancements.” Huge thanks to all the outstanding contributors!

shorturl.atChromatin structure and dynamics: Recent advancementsChromatin structure and dynamics are central to nearly every aspect of eukaryotic gene regulation. The spatial organization of the genome influences how genes a
Bin Zhang
@binzmit.bsky.social

Our preprint on a single-bead-per-nucleotide DNA model is live! This model reproduces both atomistic simulations and persistent length for a variety of sequences. It's compatible with openMM, allowing for highly efficient GPU simulations. www.biorxiv.org/content/10.1....

biorxiv.orgNEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA SimulationsDNA's physical properties play a central role in genome organization and regulation, but simulating its behavior across biologically relevant scales remains a major computational challenge. Coarse gra...

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