Related papers: High-productivity, high-performance workflow for v…
The accurate simulation of complex biochemical phenomena has historically been hampered by the computational requirements of high-fidelity molecular-modeling techniques. Quantum mechanical methods, such as ab initio wave-function (WF)…
Computing the solution of linear systems of equations is invariably the most time consuming task in the numerical solutions of PDEs in many fields of computational science. In this study, we focus on the numerical simulation of…
Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics which has been applied to numerous problems of physical chemistry and biophysics. Its essential limitations are the neglect of correlation effects and of…
Outstanding advances in solid-state laser technology, employing the optical parametric chirped-pulse-amplification (OPCPA) technique, have led physicists to focus laser pulses to highly-relativistic intensities which led to novel schemes…
There exists an increasing interest for using immersed boundary methods (IBMs) (Peskin 2000) to model moving objects in computational fluid dynamics. Indeed, this approach is particularly efficient, because the fluid mesh does not require…
In this paper, a highly efficient fast boundary element method (BEM) for solving large-scale engineering acoustic problems in a broad frequency range is developed and implemented. The acoustic problems are modeled by the Burton-Miller…
Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the…
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…
Background: Understanding electronic interactions in protein active sites is fundamental to drug discovery and enzyme engineering, but remains computationally challenging due to exponential scaling of quantum mechanical calculations.…
The current work presents a novel COllaborative Open-source Lattice Boltzmann Method framework, so-called CooLBM. The computational framework is developed for the simulation of single and multi-component multi-phase problems, along with a…
When the molecules of a gaseous system are far apart, say in microscale gas flows where the surface to volume ratio is high and hence the surface forces dominant, the molecule-surface interactions lead to the formation of a local…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…
This paper presents an improved immersed moving boundary model (IBM) for solving complex fluid-particle interactions in a coupled lattice Boltzmann method (LBM) and an adhesive discrete element method (DEM), using the "partially saturated…
We present and discuss a framework for computer-aided multiscale analysis, which enables models at a "fine" (microscopic/stochastic) level of description to perform modeling tasks at a "coarse" (macroscopic, systems) level. These…
Current GPU-accelerated supercomputers promise to enable large-scale simulations of turbulent flows. Lattice Boltzmann Methods (LBM) are particularly well-suited to fulfilling this promise due to their intrinsic compatibility with highly…
A GPU-accelerated version of the lattice Boltzmann method for efficient simulation of soft materials is introduced. Unlike standard approaches, this method reconstructs the distribution functions from available hydrodynamic variables…
We derive the partial differential equation (PDE) to which the pseudo-potential lattice Boltzmann method (P-LBM) converges under diffusive scaling, providing a rigorous basis for its consistency analysis. By establishing a direct link…
Kinetic equations model the position-velocity distribution of particles subject to transport and collision effects. Under a diffusive scaling, these combined effects converge to a diffusion equation for the position density in the limit of…
Accurate prediction of protein active-site structures remains a central challenge in structural biology, particularly for short and flexible peptide fragments where conventional and simulation-based methods often fail. Here, we present a…
The boundary element method (BEM) provides an efficient numerical framework for solving multiple scattering problems in unbounded homogeneous domains, since it reduces the discretization to the domain boundaries, thereby condensing the…