Related papers: From Metadynamics to Dynamics
We study a zero-range process with system-size dependent jump rates, which is known to exhibit a discontinuous condensation transition. Metastable homogeneous phases and condensed phases coexist in extended phase regions around the…
We consider a novel model of stochastic replicator dynamics for potential games that converts to a Langevin equation on a sphere after a change of variables. This is distinct from the models studied earlier. In particular, it is ill-posed…
We propose a model that describes phase transition including meta\-stable states present in the van der Waals Equation of State. From a convex optimization problem on the Helmoltz free energy of a mixture, we deduce a dynamical system that…
High-dimensional metastable molecular system can often be characterised by a few features of the system, i.e. collective variables (CVs). Thanks to the rapid advance in the area of machine learning and deep learning, various deep…
We propose the powerful integration of the Hybrid Monte Carlo (hybridMC) algorithm and Well-Tempered Metadynamics. This new algorithm, hybridMC-MetaD, enhances the flexibility and applicability of metadynamics by allowing for the…
The use of accelerated sampling methods such as metadynamics has shown significant advantage in calculations that involve infrequent events, which would otherwise require sampling a prohibitive number of configurations to determine, e.g.,…
We propose two metadynamics (MetaD)-based methodologies for efficiently mapping free energy surfaces (FESs) of multiple interacting carriers diffusing in crystalline solids. Our approaches circumvent the challenges of high-dimensional…
We introduce a method for elucidating and modifying the functionality of systems dominated by rare events that relies on the automated tuning of their underlying free energy surface. The proposed approach seeks to construct collective…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
An approach for the description of stochastic systems is derived. Some of the variables in the system are studied forward in time, others backward in time. The approach is based on a perturbation expansion in the strength of the coupling…
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…
The problem of metastability for a stochastic dynamics with a parallel updating rule is addressed in the Freidlin--Wentzel regime, namely, finite volume, small magnetic field, and small temperature. The model is characterized by the…
We propose a new geometric approach to describe the qualitative dynamics of chemical reactions networks. By this method we identify metastable regimes, defined as low dimensional regions of the phase space close to which the dynamics is…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
Glass-forming systems, which are characterized by a highly disordered energy landscape, have been studied in physics by a simulation-based state space aggregation. The purpose of this article is to develop a path-independent approach within…
The dynamics in a confined turbulent convection flow is dominated by multiple long-lived macroscopic circulation states, which are visited subsequently by the system in a Markov-type hopping process. In the present work, we analyze the…
In this paper, we use the cell dynamics method to study the dynamics of phase transformation when three phases exist. The system we study is a two-dimensional system. The system is able to achieve three phases coexistence, which for…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
Consider a droplet of liquid on top of a grooved substrate. The wetting or not of a groove implies the crossing of a potential barrier as the interface has to distort, to hit the bottom of the groove. We start with computing the free…
Many problems in physics, material sciences, chemistry and biology can be abstractly formulated as a system that navigates over a complex energy landscape of high or infinite dimensions. Well-known examples include phase transitions of…