Related papers: From Metadynamics to Dynamics
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
The element of metastability is incorporated in the fluctuating nonlinear hydrodynamic description of the mode coupling theory (MCT) of the liquid-glass transition. This is achieved through the introduction of the defect density variable…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the…
We apply a recently developed theory for metastability in open quantum systems to a one-dimensional dissipative quantum Ising model. Earlier results suggest this model features either a non-equilibrium phase transition or a smooth but sharp…
In this paper, we consider some hyperbolic variants of the mass conserving Allen-Cahn equation, which is a nonlocal reaction-diffusion equation, introduced (as a simpler alternative to the Cahn-Hilliard equation) to describe phase…
We investigate the dynamics of a gas of non-interacting particle-like soliton waves, demonstrating that phase transitions originate from their collective behavior. This is predicted by solving exactly the nonlinear equations and by…
Enhanced sampling methods are indispensable in computational physics and chemistry, where atomistic simulations cannot exhaustively sample the high-dimensional configuration space of dynamical systems due to the sampling problem. A class of…
Neural ODE Processes approach the problem of meta-learning for dynamics using a latent variable model, which permits a flexible aggregation of contextual information. This flexibility is inherited from the Neural Process framework and…
We investigate the kinetics and the free energy landscape of the crystallization of hard spheres from a supersaturated metastable liquid though direct simulations and forward flux sampling. In this first paper, we describe and test two…
Causal phenomena associated with rare events occur across a wide range of engineering problems, such as risk-sensitive safety analysis, accident analysis and prevention, and extreme value theory. However, current methods for causal…
The long-time behavior of many complex molecular systems is often governed by slow relaxation dynamics that can be described by a few reaction coordinates referred to as collective variables (CVs). However, identifying CVs hidden in a…
We analyse the dynamics of metastable Markovian open quantum systems by unravelling their average dynamics into stochastic trajectories. We use quantum reset processes as examples to illustrate metastable phenomenology, including a simple…
Flux sampling is an analysis that, based on a distribution, picks randomly an efficient number of points from the solution space of a metabolic model. Unlike most constraint-based analyses, flux sampling does not require an objective…
A novel and powerful method is presented for the study of rare switching events in complex systems with multiscale energy landscapes. The method performs an umbrella sampling of the equilibrium distribution of the system in hyperplanes…
We present a method to study rare nonadiabatic dynamics in open quantum systems using transition path sampling and quantum jump trajectories. As with applications of transition path sampling to classical dynamics, the method does not rely…
A method is proposed to identify target states that optimize a metastability index amongst a set of trial states and use these target states as milestones (or core sets) to build Markov State Models (MSMs). If the optimized metastability…
Sampling from high-dimensional Gibbs measures poses a challenge when the energy landscape consists of multiple metastable states. Enhanced-sampling methods mitigate this difficulty by introducing adaptive biasing potentials to facilitate…
The physics of activated escape of objects out of a metastable state plays a key role in diverse scientific areas involving chemical kinetics, diffusion and dislocation motion in solids, nucleation, electrical transport, motion of flux…
We present an efficient method to compute transition rates between states for a two-state system. The method utilizes the equivalence between steady-state flux and mean first passage rate for such systems. More specifically, the procedure…