Related papers: Stochastic boundary conditions for molecular dynam…
Stochastic boundary conditions for interactions with a particle reservoir are discussed in many-particle systems. We introduce the boundary conditions with the injection rate and the momentum distribution of particles coming from a particle…
Periodic Boundary Conditions (PBC) introduce well-known lattice artifacts. We present a novel Pseudoperiodic Spherical Boundary Condition (SBC) that is perfectly isotropic. Through detailed comparative simulations, we demonstrate that SBC…
We develop an algorithm for bosonic path integral molecular dynamics (PIMD) simulations with periodic boundary conditions (PBC) that scales quadratically with the number of particles. Path integral methods are a powerful tool to simulate…
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
Stochastic hydrodynamics is a central tool in the study of first order phase transitions at a fundamental level. Combined with sophisticated free energy models, e.g. as developed in classical Density Functional Theory, complex processes…
Applying the method of moments to the chemical master equation (CME) appearing in stochastic chemical kinetics often leads to the so-called closure problem. Recently, several authors showed that this problem can be partially overcome using…
In this work, we explore various relevant aspects of the Smoothed Particle Hydrodynamics regarding Burger's equation. The stability, precision, and efficiency of the algorithm are investigated in terms of different implementations. In…
Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NpT) ensembles. In their simplest application, a biological system of interest is…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…
This work presents a comprehensive framework for enhanced diffusion modeling in fluid-structure interactions by combining the Immersed Boundary Method (IBM) with stochastic trajectories and high-order spectral boundary conditions. Using…
Stochastic thermodynamics is the field of study relating fluctuations in stochastic systems to thermodynamic quantities. The total entropy production (EP), is central to the thermodynamic classification of systems. Non-equilibrium systems…
It is very common with molecular dynamics and other simulation techniques to apply Lees-Edwards periodic boundary conditions (PBCs) for the simulation of shear flow. However the behavior of a complex liquid can be quite different under…
Dealing with boundary conditions in Smoothed Particle Hydrodynamics (SPH) poses significant difficulties, indeed being one of the SPHERIC Grand Challenges. In particular, wall boundary conditions have been pivotal in SPH model development…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
We present rotating periodic boundary conditions (PBCs) for the simulation of nonequilibrium molecular dynamics (NEMD) under uniaxial stretching flow (USF) or biaxial stretching flow (BSF). Such nonequilibrium flows need specialized PBCs…
Small systems in a thermodynamic medium --- like colloids in a suspension or the molecular machinery in living cells --- are strongly affected by the thermal fluctuations of their environment. Physicists model such systems by means of…
We provide a framework to build periodic boundary conditions on the pseudosphere (or hyperbolic plane), the infinite two-dimensional Riemannian space of constant negative curvature. Starting from the common case of periodic boundary…
Lees Edwards boundary conditions (LEbc) for Molecular Dynamics simulations are an extension of the well known periodic boundary conditions and allow the simulation of bulk systems in a simple shear flow. We show how the idea of LEbc can be…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
In this letter, by writing the volume as a function of coordinates of atoms, we present a new constant-pressure molecular dynamics method with parameters free. This method is specially appropriate for the finite system in which the periodic…