127 citations · 139 across the 8 of their papers we have counts for
8 papers
Biomolecular transitions: efficient computation of pathways, free energies, and rates
Divesh Bhatt, Ivet Bahar
We present an efficient method to compute transition rates between states for a two-state system. The method utilizes the equivalence between steady-state flux and mean first passa…
Stochastic modeling of p53-regulated apoptosis upon radiation damage
Divesh Bhatt, Zoltan Oltvai, Ivet Bahar
We develop and study the evolution of a model of radiation induced apoptosis in cells using stochastic simulations, and identified key protein targets for effective mitigation of r…
Automated sampling assessment for molecular simulations using the effective sample size
Xin Zhang, Divesh Bhatt, Daniel M. Zuckerman
To quantify the progress in development of algorithms and forcefields used in molecular simulations, a method for the assessment of the sampling quality is needed. We propose a gen…
Symmetry of forward and reverse path populations
Divesh Bhatt, Daniel M. Zuckerman
In this note, we address formally the issue of symmetry for probabilities of different dynamical pathways in the forward and reverse directions of a conformational transition. Our…
Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Studied Using Well-Sampled Semi-Atomistic Simulations
Derek J. Cashman, Artem B. Mamonov, Divesh Bhatt +1
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the prot…
Steady-state simulations using weighted ensemble path sampling
Divesh Bhatt, Bin W. Zhang, Daniel M. Zuckerman
We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. The straightforward steady-state implementation of W…