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We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…
We consider the numerical integration of Langevin equations for particles in a channel, in the presence of boundary conditions fixing the concentration values at the ends. This kind of boundary condition appears for instance when…
A numerical tool relying on sharp Immersed Boundary Method (IBM) is developed for the analysis of aerospace applications. The method, which is conceived for application using segregated solvers relying on implicit time discretization, uses…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
The distant dipolar field (DDF) is a long-range, nonlocal contribution to liquid-state spin dynamics that arises from intermolecular dipolar couplings and can generate multiple-quantum coherences and novel MRI contrast. Its sign-changing…
This paper tests a dielectric model for variation of hydration free energy with geometry of complex solutes in water. It works out some basic aspects of the theory of boundary integral methods for these problems. One aspect of the…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
This study investigates the flow field induced by a surface dielectric barrier discharge (SDBD) system, known for its efficient pollution remediation of volatile organic compounds (VOCs). We aim to understand the flow dynamics that…
We show that the standard boundary integral operators, defined on the unit sphere, for the Stokes equations diagonalize on a specific set of vector spherical harmonics and provide formulas for their spectra. We also derive analytical…
In the immersed boundary (IB) approach to fluid-structure interaction modeling, the coupling between the fluid and structure variables is mediated using a regularized version of Dirac delta function. In the IB literature, the regularized…
A new type of absorbing boundary conditions for molecular dynamics simulations are presented. The exact boundary conditions for crystalline solids with harmonic approximation are expressed as a dynamic Dirichlet- to-Neumann (DtN) map. It…
An adiabatic approach is developed for the problem of boundary friction between two atomically smooth and incommensurate solid surfaces, separated by a monolayer of lubricant atoms. This method permits to consider very slow macroscopic…
The Immersed Boundary method has evolved into one of the most useful computational methods in studying fluid structure interaction. On the other hand, the Immersed Boundary method is also known to suffer from a severe timestep stability…
Direct and large-eddy simulations of turbulence are often solved using explicit temporal schemes. However, this imposes very small time-steps because the eigenvalues of the (linearized) dynamical system, re-scaled by the time-step, must lie…
We investigate the interplay between electronic screening inside a metal and screening by a polar molecular solvent, focusing on their impact on the charge induced by an ion and the solvent structure at the interface. To that end, we…
In condensed matter physics, particularly in perovskite materials, the rotational motion of molecules and ions is associated with important issues such as ion conduction mechanism. Constrained Molecular Dynamics (MD) simulations offer a…
Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting…
We present a robust immersed boundary (IB) method for high density ratio multiphase flows that is capable of modeling complex wave-structure interaction (WSI) problems arising in marine and coastal engineering applications. The IB/WSI…