相关论文: Kinetics of Barrier Crossing Events from Temperatu…
Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective…
Temperature Accelerated Sliced Sampling (TASS) is an efficient method to compute high dimensional free energy landscapes. The original TASS method employs the Weighted Histogram Analysis Method (WHAM) which is an iterative post-processing…
Biased sampling methods such as the Temperature Accelerated Sliced Sampling (TASS), which can explore high dimensional collective variable (CV) space, is of great interest in free energy calculations. Such methods can efficiently sample…
Enhanced sampling techniques have become an essential tool in computational chemistry and physics, where they are applied to sample activated processes that occur on a time scale that is inaccessible to conventional simulations. Despite…
We review two recently developed efficient methods for calculating rate constants of processes dominated by rare events in high-dimensional complex systems. The first is transition interface sampling (TIS), based on the measurement of…
Transient absorption spectroscopy (TAS) is among the most common ultrafast photochemical experiments, but its interpretation remains challenging. In this work, we present an efficient and robust method for simulating TAS signals from first…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
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,…
Action chunking is a widely adopted approach in Learning from Demonstration (LfD). By modeling multi-step action chunks rather than single-step actions, action chunking significantly enhances modeling capabilities for human expert policies.…
Transition path sampling is a method for estimating the rates of rare events in molecular systems based on the gradual transformation of a path distribution containing a small fraction of reactive trajectories into a biased distribution in…
Computing accurate rate constants for catalytic events occurring at the surface of a given material represents a challenging task with multiple potential applications in chemistry. To address this question, we propose an approach based on a…
Stochastic nonlinear dynamical systems can undergo rapid transitions relative to the change in their forcing, for example due to the occurrence of multiple equilibrium solutions for a specific interval of parameters. In this paper, we…
Attosecond transient-absorption spectroscopy (ATAS) is an established method for exploring electron dynamics on the subfemtosecond time-scale. ATAS spectra contain certain ubiquitous features, such as oscillating fringes, light-induced…
We introduce a path sampling method for the computation of rate constants for systems with a highly diffusive character. Based on the recently developed algorithm of transition interface sampling (TIS) this procedure increases the…
In comparison to numerous enhanced sampling methods for equilbrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here we derive a time-reversal path sampling…
The dynamics of complex systems often involve thermally activated barrier crossing events that allow these systems to move from one basin of attraction on the high dimensional energy surface to another. Such events are ubiquitous, but…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
Climate science needs more efficient ways to study high-impact, low-probability extreme events, which are rare by definition and costly to simulate in large numbers. Rare event sampling (RES) and ensemble boosting use small perturbations to…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
We present an accelerated algorithm that samples correctly the thermodynamic ensemble in complex systems where the dynamics is controlled by activation barriers. The efficiency of the thermodynamically-weighted activation-relaxation…