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Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
Well-conditioned boundary integral methods for the solution of elliptic boundary value problems (BVPs) are powerful tools for static and dynamic physical simulations. When there are many close-to-touching boundaries (eg, in complex fluids)…
The effective electrostatic interaction between a pair of colloids, both of them located close to each other at an electrolyte interface, is studied by employing the full, nonlinear Poisson-Boltzmann (PB) theory within classical density…
In this article, we apply the binary level set method to the Variational Implicit Solvent Model (VISM), which is a theoretical and computational tool to study biomolecular systems with complex topology. Central in VISM is an effective free…
Accurately predicting protein structures from amino acid sequences remains a fundamental challenge in computational biology, with profound implications for understanding biological functions and enabling structure-based drug discovery.…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
An explicit solution of the stationary one dimensional half-space boundary value problem for the linear Boltzmann equation is presented in the presence of an arbitrarily high constant external field. The collision kernel is assumed to be…
We utilize the Open Accelerator (OpenACC) approach for graphics processing unit (GPU) accelerated particle-resolved thermal lattice Boltzmann (LB) simulation. We adopt the momentum-exchange method to calculate fluid-particle interactions to…
We propose a highly versatile computational framework for the simulation of cellular blood flow focusing on extreme performance without compromising accuracy or complexity. The tool couples the lattice Boltzmann solver Palabos for the…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
A novel boundary element method (BEM) removes the classical dependence on explicit fundamental solutions and extends quasi-optimal BEM discretisations to strongly elliptic operators with variable coefficients. The approach constructs a…
The non-orthogonal local submatrix method applied to electronic-structure based molecular dynamics simulations is shown to exceed 1.1 EFLOP/s in FP16/FP32 mixed floating-point arithmetic when using 4,400 NVIDIA A100 GPUs of the Perlmutter…
Phase diagrams (PDs) illustrate the relative stability of competing phases under varying conditions, serving as critical tools for synthesizing complex materials. Reliable phase diagrams rely on precise free energy calculations, which are…
In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is…
The Bethe-Salpeter equation (BSE) is currently the state of the art in the description of neutral electron excitations in both solids and large finite systems. It is capable of accurately treating charge-transfer excitations that present…
Advanced ab initio materials simulations face growing challenges as increasing systems and phenomena complexity requires higher accuracy, driving up computational demands. Quantum many-body GW methods are state-of-the-art for treating…
The achievement of sustained nuclear fusion in magnetically confined plasma relies on efficient confinement of high-energy ions produced by the fusion reaction. Such particles can excite Alfven Eigenmodes (AEs), which significantly degrade…
For multispecies ions, we study boundary layer solutions of charge conserving Poisson-Boltzmann (CCPB) equations [50] (with a small parameter \k{o}) over a finite one-dimensional (1D) spatial domain, subjected to Robin type boundary…
We present a computational framework for the simulation of blood flow with fully resolved red blood cells (RBCs) using a modular approach that consists of a lattice Boltzmann solver for the blood plasma, a novel finite element based solver…
A simple, yet efficient procedure to solve quasistatic problems of special linear visco-elastic solids at small strains with equal rheological response in all tensorial components, utilizing boundary element method (BEM), is introduced.…