Publications

 

* indicates co-corresponding authors.

Submitted

Contrastive Learning of Coarse-Grained Force Fields
Xinqiang Ding, Bin Zhang
arXiv

Phase separation and correlated motions in motorized genome
Zhongling Jiang, Yifeng Qi, Kartik Kamat, Bin Zhang
bioRxiv

Chromatin fiber breaks into clutches under tension and crowding
Shuming Liu, Xingcheng Lin, Bin Zhang
bioRxiv

Genome Compartmentalization with Nuclear Landmarks: Random yet Precise
Kartik Kamat, Yifeng Qi, Yuchuan Wang, Jian Ma, Bin Zhang
bioRxiv

2022

Ligand-induced transmembrane conformational coupling in monomeric EGFR
Shwetha Srinivasan, Raju Regmi, Xingcheng Lin, Steven D. Quinn, Wei He, Kermit L. Carraway, III, Matthew A. Coleman, Bin Zhang*, Gabriela S. Schlau-Cohen*
Nat Commun, in press

On the stability and layered organization of protein-DNA condensates
Andrew Latham, Bin Zhang
Biophy J, 2022

Single-stranded nucleic acid sensing and coacervation by linker histone H1
Rachel Leicher, Adewola Osunsade, Andrew Latham, Gabriella N.L. Chua, John W. Watters, Sophia Christodoulou-Rubalcava, Bin Zhang, Yael David, Shixin Liu
Nat. Struct. Mol. Biol., 2022

BRD2 Compartmentalizes the Accessible Genome
Liangqi Xie, Peng Dong, Yifeng Qi, Margherita De Marzio, Xingqi Chen, Sambashiva Banala, Wesley R Legant, Brian P English, Anders S Hansen, Anton Schulmann, Luke D Lavis, Eric Betzig, Rafael Casellas, Howard Y Chang, Bin Zhang*, Robert Tjian*, Zhe Liu*
Nat. Genet, 2022

Unifying Coarse-grained Force Fields for Folded and Disordered Proteins
Andrew P. Latham, Bin Zhang
Curr Opin Struct Bio, 2022

2021

Chromatin Network Retards Droplet Coalescence
Yifeng Qi, Bin Zhang
Nat Comm, 2021

Multiscale Modeling of Genome Organization with Maximum Entropy Optimization
Xingcheng Lin, Yifeng Qi, Andrew Latham, Bin Zhang
JCP Perspective, 2021
Featured as cover article

Cooperative DNA Looping by PRC2 Complexes
Xingcheng Lin, Rachel Leicher, Shixin Liu, Bin Zhang
Nucleic Acids Research, 2021

Consistent Force Field Captures Homolog Resolved HP1 Phase Separation
Andrew P. Latham, Bin Zhang
JCTC, in press, 2021
Gromacs Implementation

Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface
Xinqiang Ding, Xingcheng Lin, and Bin Zhang
Nat Comm, 12:1091, 2021

DeepBAR: A Fast and Exact Method for Binding Free Energy Computation
Xinqiang Ding, Bin Zhang
J Phys Chem Lett, 12:2509-2515, 2021
See MIT News Release; Online Presentation

Quantifying the stability of coupled genetic and epigenetic switch with variational methods
Amogh Sood, Bin Zhang
Frontiers in Genetics, 11:1-9, 2021

On the role of transcription in positioning nucleosomes
Zhongling Jiang, Bin Zhang
PLoS Comp Bio, 17:1-22, 2021

2020

Phosphorylation-Dependent Conformations of the Disordered Carboxyl-Terminus Domain in the Epidermal Growth Factor Receptor
Raju Regmi, Shwetha Srinivasan, Vandna Kukshal, Andrew P. Latham, Weidong Cui, Bin Zhang, Ron Bose, Gabriela S. Schlau-Cohen
J Phy Chem Lett, 11:10037-10044 (2020)

Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin
Rachel Leicher, J Ge Eva, Xingcheng Lin, Matthew J Reynolds, Thomas Walz, Bin Zhang*, Tom W Muir, Shixin Liu*
PNAS, 117:30465-30475 (2020)

Computing Absolute Free Energy with Deep Generative Models
Xinqiang Ding, Bin Zhang
J Phys Chem B, 124:10166–10172 (2020)

Data-driven polymer model for mechanistic exploration of diploid genome organization
Yifeng Qi, Alejandro Reyes, Sarah E Johnstone, Martin J Aryee, Bradley E Bernstein, Bin Zhang
Biophys J, 119:1905-1916 (2020)
Highlighted as New and Notable

Characterizing chromatin folding coordinate and landscape with deep learning
Wen Jun Xie, Yifeng Qi, Bin Zhang
PLoS Comp Bio, 16, e1008262 (2020)

Structural and Dynamic Features of N-glycosylated Human RNase1
Henry Kilgore, Andrew Latham, Valerie Ressler, Bin Zhang*, Ronald T. Raines*
Biochemistry, 59:3148–3156 (2020)

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer
Sarah E. Johnstone, Alejandro Reyes, Yifeng Qi, Esmat Hegazi, Karin Pelka, Jonathan Chen, Luli Zou, Yotam Drier, Vivian Hecht, Noam Shoresh, Caleb Lareau, Sowmya Iyer, Nir Hacohen, Rafael Irizarry, Bin Zhang, Martin J. Aryee, Bradley E. Bernstein
Cell, 182:1474-1489.e23 (2020)

3D ATAC-PALM: super-resolution imaging of the accessible genome
Xie, Liangqi, Dong, Peng, Chen, Xingqi, Hsieh, Tsung-Han S., Banala, Sambashiva, De Marzio, Margherita, English, Brian P., Qi, Yifeng, Jung, Seol Kyoung, Kieffer-Kwon, Kyong-Rim, Legant, Wesley R., Hansen, Anders S., Schulmann, Anton, Casellas, Rafael, Zhang, Bin, Betzig, Eric, Lavis, Luke D., Chang, Howard Y., Tjian, Robert, Liu, Zhe
Nat Met, 17, 430 (2020)

Quantifying Epigenetic Stability with Minimum Action Paths
Amogh Sood, Bin Zhang
Phys. Rev. E, 101, 062409 (2020)

2019

Theory of active chromatin remodeling
Zhongling Jiang, Bin Zhang
PRL, 123, 208102 (2019)

Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins
Andrew P Latham, Bin Zhang
JCTC, 16, 773 (2019)

Predicting three-dimensional genome organization with chromatin states
Yifeng Qi, Bin Zhang
PLoS Comp Bio, 15, e1007024 (2019)

Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals
Jorge L Rosa-Raíces, Bin Zhang, Thomas F Miller III
JCP, 151, 164120 (2019)

Learning the formation mechanism of domain-Level chromatin states with epigenomics data
Wen Jun Xie, Bin Zhang
Biophys J, 116, 2047 (2019)

Critical role of histone tail entropy in nucleosome unwinding
Thomas Parsons, Bin Zhang
JCP, 150, 185103 (2019)
Highlighted as Editors’ Choice

Learning genomic energy landscapes from experiments
MICHELE Di Pierro, RYAN R Cheng, B Zhang, JOSÉ N Onuchic, PETER G Wolynes
Book Chapter, CRC Press, 305 (2019)

Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data
Andrew P Latham, Bin Zhang
JPCB, 123, 1026 (2019)

Before MIT

Genomic energy landscapes
Bin Zhang, Peter G Wolynes
Biophys J, 112, 427 (2017)

Transferable model for chromosome architecture
Michele Di Pierro, Bin Zhang, Erez Lieberman Aiden, Peter G Wolynes, José N Onuchic
PNAS, 113, 12168 (2016)

Molecular mechanism of facilitated dissociation of Fis protein from DNA
Min-Yeh Tsai, Bin Zhang, Weihua Zheng, Peter G Wolynes
JACS, 138, 13497 (2016)

A link between integral membrane protein expression and simulated integration efficiency
Stephen S Marshall, Michiel JM Niesen, Axel Müller, Katrin Tiemann, Shyam M Saladi, Rachel P Galimidi, Bin Zhang, William M Clemons Jr, Thomas F Miller III
Cell Rep, 16, 2169 (2016)

Exploring the free energy landscape of nucleosomes
Bin Zhang, Weihua Zheng, Garegin A Papoian, Peter G Wolynes
JACS, 138, 8126 (2016)

Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome
Bin Zhang, Peter G Wolynes
PRL, 116, 248101 (2016)

Regulation of multispanning membrane protein topology via post-translational annealing
Reid C Van Lehn, Bin Zhang, Thomas F Miller
Elife, 4, (2015)

Topology, structures, and energy landscapes of human chromosomes
Bin Zhang, Peter G Wolynes
PNAS, 112, 6062, (2015)

Stem cell differentiation as a many-body problem
Bin Zhang, Peter G Wolynes
PNAS, 111, 10185, (2014)

Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation
Bin Zhang, Thomas F Miller
Cell Rep, 2, 924, (2012)

Direct simulation of early-stage Sec-facilitated protein translocation
Bin Zhang, Thomas F Miller
JACS, 134, 13700 (2012)

Hydrophobically stabilized open state for the lateral gate of the Sec translocon
Bin Zhang, Thomas F Miller
PNAS, 107, 5399 (2010)