Related papers: Spatially Resolved Thermodynamic Integration: An E…
The correct evaluation of gradients is at the cornerstone of the smoothed particle hydrodynamics (SPH) technique. Using an integral approach to estimate gradients has proven to enhance accuracy substantially. Such approach retains the…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
An ideal Maxwell-Boltzmann gas confined in various rectangular nano domains is considered under quantum size effects. Thermodynamic quantities are calculated from their relations with partition function which consists of triple infinite…
We present a simple modification of the direct-forcing immersed boundary method (IBM) proposed by Uhlmann [J. Comput. Phys, 2005] in order to enable it to be applied to particulate flows with solid-to-fluid density ratios around unity. The…
This study proposes a generalized coordinates based smoothed particle hydrodynamics (GSPH) method with overset methods using a Total Lagrangian (TL) formulation for large deformation and crack propagation problems. In the proposed GSPH, the…
A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic…
Stokesian Dynamics (SD) is a numerical framework used for simulating hydrodynamic interactions in particle suspensions at low Reynolds number. It combines far-field approximations with near-field lubrication corrections, offering a balance…
Smoothed Particle Hydrodynamics is a multidimensional Lagrangian method of numerical hydrodynamics that has been used to tackle a wide variety of problems in astrophysics. Here we develop the basic equations of the SPH scheme, and we…
Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to…
This paper proposes a novel numerical method based on Godunov Smoothed Particle Hydrodynamics for special relativistic fluid dynamics. Our method utilizes a Riemann solver to describe shock, enhancing accuracy in strong shock waves. The…
The insertion of solvent particles in molecular dynamics simulations of complex fluids is required in many situations involving open systems, but this challenging task has been scarcely explored in the literature. We propose a simple and…
A variety of simulation methodologies have been used for modeling reaction-diffusion dynamics -- including approaches based on Differential Equations (DE), the Stochastic Simulation Algorithm (SSA), Brownian Dynamics (BD), Green's Function…
An improved version of a recently developed stochastic cluster dynamics (SCD) method {[}Marian, J. and Bulatov, V. V., {\it J. Nucl. Mater.} \textbf{415} (2014) 84-95{]} is introduced as an alternative to rate theory (RT) methods for…
Eyring theory provides a convenient approximation to the rate of a chemical reaction, as it uses only local information evaluated near extremal points of a given potential energy surface. However, in cases of pronounced anharmonicity and…
A variety of problems in acoustic and electromagnetic scattering require the evaluation of impedance or layered media Green's functions. Given a point source located in an unbounded half-space or an infinitely extended layer, Sommerfeld and…
We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving…
The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of…
We present an efficient and robust semi-analytical formulation to compute the electric potential due to arbitrary-located point electrodes in three-dimensional cylindrically stratified media, where the radial thickness and the medium…
We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…