Related papers: Enhanced molecular dynamics performance with a pro…
There is growing interest in engineering unconventional computing devices that leverage the intrinsic dynamics of physical substrates to perform fast and energy-efficient computations. Granular metamaterials are one such substrate that has…
We accelerated an ab-initio molecular QMC calculation by using GPGPU. Only the bottle-neck part of the calculation is replaced by CUDA subroutine and performed on GPU. The performance on a (single core CPU + GPU) is compared with that on a…
The present level of development of molecular force field methods is assessed from the point of view of simulation-based engineering, outlining the immediate perspective for further development and highlighting the newly emerging discipline…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
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…
The evolution of computer architecture has led to a paradigm shift from traditional single-core processors to multi-core and domain-specific architectures that address the increasing demands of modern computational workloads. This paper…
The exponential growth of data-intensive machine learning workloads has exposed significant limitations in conventional GPU-accelerated systems, especially when processing datasets exceeding GPU DRAM capacity. We propose MQMS, an augmented…
The design of embedded systems is a complex activity that involves a lot of decisions. With high performance demands of present day usage scenarios and software, they often involve energy hungry state-of-the-art computing units. While…
As quantum computers continue to improve and support larger, more complex computations, smart control hardware and compilers are needed to efficiently leverage the capabilities of these systems. This paper introduces a novel approach to…
With heterogeneous systems, the number of GPUs per chip increases to provide computational capabilities for solving science at a nanoscopic scale. However, low utilization for single GPUs defies the need to invest more money for expensive…
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models…
Recent researches on robotics have shown significant improvement, spanning from algorithms, mechanics to hardware architectures. Robotics, including manipulators, legged robots, drones, and autonomous vehicles, are now widely applied in…
The Graphics Processing Unit (GPU) is a powerful tool for parallel computing. In the past years the performance and capabilities of GPUs have increased, and the Compute Unified Device Architecture (CUDA) - a parallel computing architecture…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
To prepare images for better segmentation, we need preprocessing applications, such as smoothing, to reduce noise. In this paper, we present an enhanced computation method for smoothing 2D object in binary case. Unlike existing approaches,…
We propose an optimization approach for determining both hardware and software parameters for the efficient implementation of a (family of) applications called dense stencil computations on programmable GPGPUs. We first introduce a simple,…
The use of quantum processing units (QPUs) promises speed-ups for solving computational problems, but the quantum devices currently available possess only a very limited number of qubits and suffer from considerable imperfections. One…