Related papers: Stochastic boundary conditions for molecular dynam…
Statistical mechanics has grown without bounds in space. Statistical mechanics of point particles in an unbounded perfect gas is commonly accepted as a foundation for understanding many systems, including liquids like the concentrated salt…
The exact dynamics of a system coupled to an environment can be described by an integro-differential stochastic equation of its reduced density. The influence of the environment is incorporated through a mean-field which is both stochastic…
This paper reviews the state of the art of periodic boundary conditions (PBCs) in Finite-Difference Time-Domain (FDTD) simulations. The mathematical principles and 3D FDTD implementation details are systematically outlined. Techniques for…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
We study thermodynamic processes in contact with a heat bath that may have an arbitrary time-varying periodic temperature profile. Within the framework of stochastic thermodynamics, and for models of thermo-dynamic engines in the idealized…
The dynamics of many systems nowadays follow not only physical laws but also man-made rules. These systems are known as discrete event dynamic systems and their performances can be accurately evaluated only through simulations. Existing…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
We consider a generic class of stochastic particle-based models whose state at an instant in time is described by a set of continuous degrees of freedom (e.g. positions), and the length of this set changes stochastically in time due to…
In this paper, we study Stochastic Control Barrier Functions (SCBFs) to enable the design of probabilistic safe real-time controllers in presence of uncertainties and based on noisy measurements. Our goal is to design controllers that bound…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
Multi-color Stochastic Rotation Dynamics (SRDmc) has been introduced by Inoue et al. as a particle based simulation method to study the flow of emulsion droplets in non-wetting microchannels. In this work, we extend the multi-color method…
It is well known that in the computational fluid dynamics simulations related to the cardiovascular system the enforcement of outflow boundary conditions is a crucial point. In fact, they highly affect the computed flow and a wrong setup…
Stochastic parabolic equations are widely used to model many random phenomena in natural sciences, such as the temperature distribution in a noisy medium, the dynamics of a chemical reaction in a noisy environment, or the evolution of the…
In this paper, we compute finite sample bounds for data-driven approximations of the solution to stochastic reachability problems. Our approach uses a nonparametric technique known as kernel distribution embeddings, and provides…
A stochastic representation of the dynamics of open quantum systems, suitable for non-perturbative system-reservoir interaction, non-Markovian effects and arbitrarily driven systems is presented. It includes the case of driving on…
Quantum-Induced Stochastic Dynamics arises from the coupling between a classical system and a quantum environment. Unlike standard thermal reservoirs, this environment acts as a dynamic bath, capable of simultaneously exchanging heat and…
Simulating stochastic differential equations (SDEs) in bounded domains, presents significant computational challenges due to particle exit phenomena, which requires accurate modeling of interior stochastic dynamics and boundary…
In this work, we study in the framework of the so-called driven tight-binding chain (TBC) the issue of quantum unitary dynamics interspersed at random times with stochastic resets mimicking non-unitary evolution due to interactions with the…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
Many practical applications of control require that constraints on the inputs and states of the system be respected, while optimizing some performance criterion. In the presence of model uncertainties or disturbances, for many control…