Related papers: Metadynamics of paths
Atomistic simulations provide valuable insights into the physical processes governing material behavior. However, their applicability is fundamentally constrained by the limited time scales accessible to brute-force simulations. This…
Searching for reaction pathways describing rare events in large systems presents a long-standing challenge in chemistry and physics. Incorrectly computed reaction pathways result in the degeneracy of microscopic configurations and inability…
The histogram reweighting technique, widely used to analyze Monte Carlo data, is shown to be applicable to dynamic properties obtained from Molecular Dynamics simulations. The theory presented here is based on the fact that the correlation…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…
Constraint-based modeling has been widely used on metabolic networks analysis, such as biosynthetic prediction and flux optimization. The linear constraints, like mass conservation constraint, reversibility constraint, biological capacity…
This paper introduces a framework for simulating finite dimensional representations of (jump) diffusion sample paths over finite intervals, without discretisation error (exactly), in such a way that the sample path can be restored at any…
Transition interface sampling (TIS) and replica exchange TIS (RETIS) are powerful methods for computing rates of rare events inaccessible to straightforward molecular dynamics (MD) simulations. Path reweighting extends their output,…
Traditional stochastic modeling of reactive systems limits the domain of applicability of the associated path thermodynamics to systems involving a single elementary reaction at the origin of each observed change in composition. An…
Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of…
A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…
We describe a new, surprisingly simple algorithm, that simulates exact sample paths of a class of stochastic differential equations. It involves rejection sampling and, when applicable, returns the location of the path at a random…
The identification of trajectories that contribute to the reaction rate is the crucial dynamical ingredient in any classical chemical reactivity calculation. This problem often requires a full scale numerical simulation of the dynamics, in…
Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…
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…
This chapter discusses the way in which dimensionality reduction algorithms such as diffusion maps and sketch-map can be used to analyze molecular dynamics trajectories. The first part discusses how these various algorithms function, as…
Estimating the heat loads on re-entry vehicles is a crucial part of preparing for atmospheric re-entry manoeuvres. Re-entry flows at high altitudes are in the rarefied regime and are governed by high enthalpies and thermodynamic…
Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is…
Water molecules, confined in a carbon nanotube, were monitored using molecular dynamics simulation. Spontaneous directional transportation during a long timescale was observed in the symmetrical nanochannel by a ratchet-like mechanism. This…