Related papers: Constraint methods for determining pathways and fr…
An activated process consists of energy activation and barrier crossing; the former is a prerequisite for the latter. Barrier crossing has been studied extensively, but energy activation has been overlooked due to a lack of means to gauge…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We show how additional constraints, restricting the spectrum of the optimized pulse or confining the system dynamics, can be used to steer optimization in quantum control towards distinct solutions. Our examples are multi-photon excitation…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
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…
We propose an approach for estimating the probability that a given small target, among many, will be the first to be reached in a molecular dynamics simulation. Reaching small targets out of a vast number of possible configurations…
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
Autocatalytic chemical networks play a predominant role in a large number of natural systems such as in metabolic pathways and in ecological networks. Despite recent efforts, the precise impact of thermodynamic constraints on these networks…
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical…
We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…
We introduce a method of exploring potential energy contours in complex dynamical systems based on potentiostatic kinematics wherein the systems are evolved with minimal changes to their potential energy. We construct a simple iterative…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
In this work we compare previously measured energy barriers over the course of temperature with the results of simulations of the behaviour of the energy barriers. For the measurements the temperature dependent magnetorelaxation method…
The classical theory of chemical reactions can be understood in terms of diffusive barrier crossing, where the rate of a reaction is determined by the inverse of the mean first passage time (FPT) to cross a free energy barrier. Whenever a…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…
Molecular modeling of thermally activated chemistry in condensed phases is essential to understand polymerization, depolymerization, and other processing steps of molecular materials. Current methods typically combine molecular dynamics…
Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability…
We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the…
The efficiency of atomic simulations of materials and molecules can rapidly deteriorate when large free energy barriers exist between local minima. We propose smooth basin classification, a universal method to define reaction coordinates…
Many processes in chemistry, physics, and biology depend on thermally activated events in which the system changes its state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation…