Bin Zhang

Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model Implicit 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...

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

Excited to see our IGME models applied to unravel the free energy landscape of the tetra-nucleosome. Wonderful collaboration with @binzmit.bsky.social! Congrats to all the authors!

Join us for the summer!

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!

We welcome 1st-year graduate student Chenxi Ye to join the group!

NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations DNA'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...

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....

First post on bluesky.