Related papers: Equilibrium Sampling From Nonequilibrium Dynamics
First-principles particle-in-cell (PIC) simulation is a powerful tool for understanding plasma behavior, but this power often comes at great computational expense. Artificially reducing the ion/electron mass ratio is a time-honored practice…
This short review covers a wide selection of topics from a multidisciplinary area of dynamics of nonequilibrium systems in physics, chemistry, biology. Theoretical models of colloid particle and protein deposition and adhesion at surfaces,…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
Non-equilibrium critical phenomena generally exist in many dynamic systems, like chemical reactions and some driven-dissipative {reactive} particle systems. Here, by using computer simulation and theoretical analysis, we demonstrate the…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
Event sequences can be modeled by temporal point processes (TPPs) to capture their asynchronous and probabilistic nature. We propose an intensity-free framework that directly models the point process distribution by utilizing normalizing…
Nonparametric mixture models based on the Pitman-Yor process represent a flexible tool for density estimation and clustering. Natural generalization of the popular class of Dirichlet process mixture models, they allow for more robust…
We introduce the implicit processes (IPs), a stochastic process that places implicitly defined multivariate distributions over any finite collections of random variables. IPs are therefore highly flexible implicit priors over functions,…
This chapter is devoted to the computation of equilibrium (thermodynamic) properties of quantum systems. In particular, we will be interested in the situation where the interaction between particles is so strong that it cannot be treated as…
Particle-in-cell (PIC) simulations are widely used as a tool to investigate instabilities that develop between a collisionless plasma and beams of charged particles. However, even on contemporary supercomputers, it is not always possible to…
The use of random sampling in decision-making and control has become popular with the ease of access to graphic processing units that can generate and calculate multiple random trajectories for real-time robotic applications. In contrast to…
In immune system simulation there are two competing simulation approaches: System Dynamics Simulation (SDS) and Agent-Based Simulation (ABS). In the literature there is little guidance on how to choose the best approach for a specific…
A number of problems arise when long-range forces, such as those governed by Bessel functions, are used in particle-particle simulations. If a simple cut-off for the interaction is used, the system may find an equilibrium configuration at…
In this study we explore a new simulation scheme for partial differential equations known as Information Field Dynamics (IFD). Information field dynamics attempts to improve on existing simulation schemes by incorporating Bayesian field…
Non-equilibrium steady states (NESS) of Markov processes give rise to non-trivial cyclic probability fluxes. Cycle decompositions of the steady state offer an effective description of such fluxes. Here, we present an iterative cycle…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
The efficient importance sampling (EIS) method is a general principle for the numerical evaluation of high-dimensional integrals that uses the sequential structure of target integrands to build variance minimising importance samplers.…
We propose a hybrid process calculus for modelling and reasoning on cyber-physical systems (CPS{s}). The dynamics of the calculus is expressed in terms of a labelled transition system in the SOS style of Plotkin. This is used to define a…
We study the dynamics of weakly deformed interfaces separating two stable phases, starting from the fluctuating hydrodynamics of the phase-separating fields. Using a well-chosen definition for the interface and the dynamical-action…
We establish a correspondence between two very general paradigms for systems that persist away from thermal equilibrium. In the first paradigm, a nonequilibrium steady state (NESS) is maintained by applying fixed thermodynamic forces that…