Related papers: Force field optimization by imposing kinetic const…
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
We propose a new sensitivity analysis methodology for complex stochastic dynamics based on the Relative Entropy Rate. The method becomes computationally feasible at the stationary regime of the process and involves the calculation of…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
We introduce a path sampling method for obtaining statistical properties of an arbitrary stochastic dynamics. The method works by decomposing a trajectory in time, estimating the probability of satisfying a progress constraint, modifying…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Parameterizing mathematical models of biological systems often requires fitting to stable periodic data. In cardiac electrophysiology this typically requires converging to a stable action potential through long simulations. We explore this…
Modern optimal control theory involves adjoining the already known equations of motion of a dynamic system to the objective function using dynamic costates; this is done in order to constrain the optimal control solutions to satisfy the…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
Many proteins in cells are capable of sensing and responding to piconewton scale forces, a regime in which conformational changes are small but significant for biological processes. In order to efficiently and effectively sample the…
Although instantaneous interactions are unphysical, a large variety of maximum entropy statistical inference methods match the model-inferred and the empirically-measured equal-time correlation functions. Focusing on collective motion of…
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…
Markov State Models (MSM) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations, for example…
The hybrid particle-field molecular dynamics method is an efficient alternative to standard particle-based coarse grained approaches. In this work, we propose an automated protocol for optimisation of the effective parameters that define…
A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…
We report a computational strategy to obtain the charges of individual dielectric particles from experimental observation of their interactions as a function of time. This strategy uses evolutionary optimization to minimize the difference…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
The influence of microscopic force fields on the motion of Brownian particles plays a fundamental role in a broad range of fields, including soft matter, biophysics, and active matter. Often, the experimental calibration of these force…