Bin Zhang
@binzmit.bsky.social
Associate Professor at MIT Chemistry; Enthusiastic about chromatin, biophysics, molecular dynamics, and AI.
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
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...
arxiv.org
January 12, 2026 at 9:30 AM
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
Reposted by Bin Zhang
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!
December 14, 2025 at 3:54 AM
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!
December 8, 2025 at 8:09 PM
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!
Huge thanks to all the outstanding contributors!
Chromatin structure and dynamics: Recent advancements
Chromatin structure and dynamics are central to nearly every aspect of eukaryotic gene regulation. The spatial organization of the genome influences how genes a
shorturl.at
December 5, 2025 at 4:45 PM
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!
Huge thanks to all the outstanding contributors!
We welcome 1st-year graduate student Chenxi Ye to join the group!
November 15, 2025 at 3:44 PM
We welcome 1st-year graduate student Chenxi Ye to join the group!
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....
www.biorxiv.org/content/10.1....
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...
www.biorxiv.org
November 9, 2025 at 12:26 PM
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....
www.biorxiv.org/content/10.1....
First post on bluesky.
November 9, 2025 at 12:10 PM
First post on bluesky.