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Efficient hybrid DFT simulations of solid state materials would be extremely beneficial for computational chemistry and materials science, but is presently bottlenecked by difficulties in computing Hartree-Fock (HF) exchange with plane wave…
Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally…
This paper reviews Irradiation Driven Molecular Dynamics (IDMD) - a novel computational methodology for atomistic simulations of the irradiation driven transformations of complex molecular systems implemented in the MBN Explorer software…
We develop numerical methods for reaction-diffusion systems based on the equations of fluctuating hydrodynamics (FHD). While the FHD formulation is formally described by stochastic partial differential equations (SPDEs), it becomes similar…
Electronic structure theory calculations offer an understanding of matter at the quantum level, complementing experimental studies in materials science and chemistry. One of the most widely used methods, density functional theory (DFT),…
Point multipole expansions are widely used to gain physical insight into complex distributions of charges and to reduce the cost of computing interactions between such distributions. However, practical applications that typically retain…
We propose to use a new platform - ultracold polar molecules - for quantum computing with switchable interactions. The on/off switch is accomplished by selective excitation of one of the "0" or "1" qubits - long-lived molecular states - to…
In this paper, a fast multipole method (FMM) is proposed to compute long-range interactions of wave sources embedded in 3-D layered media. The layered media Green's function for the Helmholtz equation, which satisfies the transmission…
Micromagnetics has made significant strides, particularly due to its wide-ranging applications in magnetic storage design. Numerical simulation is a cornerstone of micromagnetics research, relying on first-principle rules to compute the…
In this paper, we use multithreaded fast Fourier transforms provided in three highly optimized packages, FFTW-2.1.5, FFTW-3.3.7, and Intel MKL FFT, to present a novel model-based parallel computing technique as a very effective and portable…
Understanding complex chemical systems -- such as biomolecules, catalysts, and novel materials -- is a central goal of quantum simulations. Near-term strategies hinge on the use of variational quantum eigensolver (VQE) algorithms combined…
Variable charge models (e.g., EEM, QEq, ES+) in reactive molecular dynamics simulations often inherently impose a global charge transfer between atoms (approximating each system as ideal metal). Consequently, most surface processes (e.g.,…
In this paper, we propose a general framework to accelerate significantly the algorithms for nonnegative matrix factorization (NMF). This framework is inspired from the extrapolation scheme used to accelerate gradient methods in convex…
Tumor angiogenesis involves a collection of tumor cells moving towards blood vessels for nutrients to grow. Angiogenesis, and in general chemotaxis systems have been modeled using partial differential equations (PDEs) and as such require…
Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…
The Fast Multipole Method (FMM) provides a highly efficient computational tool for solving constant coefficient partial differential equations (e.g. the Poisson equation) on infinite domains. The solution to such an equation is given as the…
We present an implementation of Pagh's compressed matrix multiplication algorithm, a randomized algorithm that constructs sketches of matrices to compute an unbiased estimate of their product. By leveraging fast polynomial multiplication…
Mean-Field Ring Polymer Molecular Dynamics (MF-RPMD) is a powerful, efficient, and accurate method for approximate quantum dynamic simulations of multi-level system dynamics. Initial efforts to compute nonadiabatic reaction rates using…
The energetic electrons (EEs) generated through auxiliary heating have been found to destabilize various Alfven eigenmodes (AEs) in recent experiments, which in turn lead to the EE transport and degrade the plasma energy confinement. In…
To investigate the effect and ability of FACTS devices using the Fast and Flexible Holomorphic Embedding technique (FFHE), it is necessary to develop an embedded system for these devices. Therefore, this paper presents FFHE based embedded…