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Implicit time integration is key to robustly simulating stiff materials and large deformations, but its performance is often dominated by repeatedly solving large linear systems. Adaptive coarsening can reduce this cost by concentrating…
We present the numerical methods, programming methodology, verification, and performance assessment of a non-equilibrium plasma fluid solver that can effectively utilize current and upcoming central processing and graphics processing unit…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Energy system optimization models are increasing in scope and resolution, yielding large and challenging linear programs. For a long time, the standard way to address such problems has relied on shared-memory interior-point methods (IPM),…
We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability density function of particles as a function of position and…
Simulations of physical phenomena are essential to the expedient design of precision components in aerospace and other high-tech industries. These phenomena are often described by mathematical models involving partial differential equations…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
This study presents an advanced sharp-interface immersed boundary method (IBM) integrated with the blastFOAM library on the OpenFOAM platform for high-speed compressible flow simulations. The developed solver extends the existing IBM…
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller…
This paper characterizes sharp solute-solvent interfaces in hydrophobic environments, and there are three major ingredients. The first is the variational implicit solvent model (VISM) which establishes the free energy functional of…
A new flow solver scalable on multiple Graphics Processing Units (GPUs) for direct numerical simulation of wall-bounded incompressible flow is presented. This solver utilizes a previously reported work (J. Comp. Physics, vol. 352 (2018),…
Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful…
The immersed boundary (IB) method has become a leading approach in cardiac fluid-structure interaction (FSI) modeling due to its ability to handle large deformations and complex geometries without requiring mesh regeneration. However, the…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
Solvent can occupy up to ~70% of macromolecular crystals and hence having models that predict solvent distributions in periodic systems could improve in the interpretation of crystallographic data. Yet there are few implicit solvent models…
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…
The phase-field method has become a useful tool for the simulation of classical metallurgical phase transformations as well as other phenomena related to materials science. The thermodynamic consistency that forms the basis of these…
One of the current challenges in physically-based simulations, and, more specifically, fluid simulations, is to produce visually appealing results at interactive rates, capable of being used in multiple forms of media. In recent times, a…
A number of recent studies have focused on developing surgical simulation platforms to train machine learning (ML) agents or models with synthetic data for surgical assistance. While existing platforms excel at tasks such as rigid body…