Communication: Introducing prescribed biases in out-of-equilibrium Markov models

Perspective: Maximum caliber is a general variational principle for dynamical systems

(2018) Purushottam D. Dixit et al.   JOURNAL OF CHEMICAL PHYSICS

Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models

(2018) Purushottam D. Dixit et al.   Journal of Chemical Theory and Computation

Combining experimental and simulation data of molecular processes via augmented Markov models

(2017) Simon Olsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamics of Computational Copying in Biochemical Systems

(2017) Thomas E. Ouldridge et al.   Physical Review X

Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement

(2016) Andrea Cesari et al.   Journal of Chemical Theory and Computation

A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations

(2016) Hongbin Wan et al.   Journal of Chemical Theory and Computation

Convergence of Molecular Dynamics Simulation of Protein Native States: Feasibility vs Self-Consistency Dilemma

(2016) Lucas Sawle et al.   Journal of Chemical Theory and Computation

Molecular Motors: Power Strokes Outperform Brownian Ratchets

(2016) Jason A. Wagoner et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

(2016) Tujin Shi et al.   Science Signaling

Efficient Estimation of Rare-Event Kinetics

(2016) Benjamin Trendelkamp-Schroer et al.   Physical Review X

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

(2016) Tujin Shi et al.   Science Signaling

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes

(2015) Purushottam D. Dixit et al.   Journal of Chemical Theory and Computation

Stationary properties of maximum-entropy random walks

(2015) Purushottam D. Dixit   PHYSICAL REVIEW E

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Inferring Microscopic Kinetic Rates from Stationary State Distributions

(2014) Purushottam D. Dixit et al.   Journal of Chemical Theory and Computation

Principles of maximum entropy and maximum caliber in statistical physics

(2013) Steve Pressé et al.   REVIEWS OF MODERN PHYSICS

Rapid Phospho-Turnover by Receptor Tyrosine Kinases Impacts Downstream Signaling and Drug Binding

(2011) Laura B. Kleiman et al.   MOLECULAR CELL

Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data

(2009) William W Chen et al.   Molecular Systems Biology

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE