Related papers: GALAMOST: GPU-accelerated large-scale molecular si…
This paper introduces novel method of simulation of lipid biomembranes based on Metropolis Hastings algorithm and Graphic Processing Unit computational power. Method gives up to 55 times computational boost in comparison to classical…
This work concerns the numerical simulation of the Vlasov-Poisson set of equations using semi- Lagrangian methods on Graphical Processing Units (GPU). To accomplish this goal, modifications to traditional methods had to be implemented.…
One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…
Due to its flexible architecture, FPGAs support unique, deep hardware pipeline implementations for accelerating HPC applications. However, these devices are quite new in the HPC space, and thus, have been scarcely explored outside some…
Quantum computing is an emerging technology, promising a paradigm shift in computing, and allowing for speedups in many different problems. However, quantum devices are still in their early stages, most with only a small number qubits. This…
Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging…
Crystallization processes at the mesoscopic scale, where faceted, dendritic growth, and multigrain formation can be observed, are of particular interest within materials science and metallurgy. These processes are highly nonlinear,…
Bosonic quantum devices offer a novel approach to realize quantum computations, where the quantum two-level system (qubit) is replaced with the quantum (an)harmonic oscillator (qumode) as the fundamental building block of the quantum…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
Deep learning in molecular and materials sciences is limited by the lack of integration between applied science, artificial intelligence, and high-performance computing. Bottlenecks with respect to the amount of training data, the size and…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
A strategy is developed for generating equilibrated high molecular-weight polymer melts described with microscopic detail by sequentially backmapping coarse-grained (CG) configurations. The microscopic test model is generic but retains…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM…
A previous study of MD algorithms designed for GPU use is extended to cover more recent developments in GPU architecture. Algorithm modifications are described, together with extensions to more complex systems. New measurements include the…
A novel approach is presented for fast generation of synthetic seismograms due to microseismic events, using heterogeneous marine velocity models. The partial differential equations (PDEs) for the 3D elastic wave equation have been…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
The geometric multigrid method (GMG) is one of the most efficient solving techniques for discrete algebraic systems arising from elliptic partial differential equations. GMG utilizes a hierarchy of grids or discretizations and reduces the…
Amorphous solids form an enormous and underutilized class of materials. In order to drive the discovery of new useful amorphous materials further we need to achieve a closer convergence between computational and experimental methods. In…