Modeling Biomolecular Systems

The Zuckerman group develops and applies computer simulation methods for studying  biological systems. A primary focus is the deployment of sampling algorithms based on statistical physics that can be used to study (i) large-scale, potentially allosteric motions in proteins, (ii) signaling processes encoded in interaction networks, (iii) protein binding, and (iv) protein folding. Among the strategies used in the group are approaches that can yield super-linear parallel performance – estimation of observables using N processors that is more than N times faster than an estimate based on a single-processor simulation. Prof. Zuckerman also has a strong interest in biophysics education, which has led to a textbook and a new online book.


Recent Work:

Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein–Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide, Matthew C. Zwier, Adam J. Pratt, Joshua L. Adelman, Joseph W. Kaus, Daniel M. Zuckerman, and Lillian T. Chong, J. Phys. Chem. Lett., 7:3440–3445 (2016).

Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process, Ramu Anandakrishnan, Zining Zhang, Rory M. Donovan, and Daniel M. Zuckerman, Proceedings of the National Academy of Sciences, 113: 11220–11225 (2016).

Accurate estimation of protein folding and unfolding times: Beyond Markov state models, Suárez, Ernesto; Adelman, Joshua; Zuckerman, Daniel, Journal of Chemical Theory and Computation, 12:3473–3481 (2016).

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories, Rory M. Donovan, Jose-Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman, PLoS Computational Biology, 12(2):e1004611, 2016.

Estimating First Passage Time Distributions from Weighted Ensemble Simulations and non-Markovian Analyses, Ernesto Suarez, Adam J. Pratt, Lillian T. Chong, and Daniel M. Zuckerman, Protein Science, 25(1):67-78, 2016.

Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits, Justin Spiriti and Daniel M. Zuckerman, Journal of Chemical Physics, 143, 243159, 2015.

WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis, Zwier, Matthew; Adelman, Joshua; Kaus, Joseph; Pratt, Adam; Wong, Kim; Rego, Nicholas; Suárez, Ernesto; Lettieri, Steven; Wang, David; Grabe, Michael; Zuckerman, Daniel; Chong, Lillian, J. Chem. Theory Comput., 11, 800–809, 2015.

Structural Integrity of the Ribonuclease H domain in HIV-1 Reverse Transcriptase, Slack, Ryan L, Spiriti, Justin M, Ahn, Jinwoo. Parniak, Michael A Zuckerman, Daniel M., Ishima, Rieko, Proteins: Structure, function, and bioinformatics, 83(8):1526-38, 2015.