Related papers: Molecular Dynamics Simulation of Macromolecules Us…
Stochastic simulation techniques employed for the analysis of portfolios of insurance/reinsurance risk, often referred to as `Aggregate Risk Analysis', can benefit from exploiting state-of-the-art high-performance computing platforms. In…
Much of the current focus in high performance computing (HPC) for computational fluid dynamics (CFD) deals with grid based methods. However, parallel implementations for new meshfree particle methods such as Smoothed Particle Hydrodynamics…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…
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…
As in various fields like scientific research and industrial application, the computation time optimization is becoming a task that is of increasing importance because of its highly parallel architecture. The graphics processing unit is…
This work develops a parallelized algorithm to compute the dynamic mode decomposition (DMD) on a graphics processing unit using the streaming method of snapshots singular value decomposition. This allows the algorithm to operate efficiently…
The reliability of cardiovascular computational models depends on the accurate solution of the hemodynamics, the realistic characterization of the hyperelastic and electric properties of the tissues along with the correct description of…
Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Hydrodynamics calculations have been successfully used in studies of the bulk properties of the Quark-Gluon Plasma, particularly of elliptic flow and shear viscosity. However, there are areas (for instance event-by-event simulations for…
Particle accelerator modeling is an important field of research and development, essential to investigating, designing and operating some of the most complex scientific devices ever built. Kinetic simulations of relativistic, charged…
Starting from the single graphics processing unit (GPU) version of the Smoothed Particle Hydrodynamics (SPH) code DualSPHysics, a multi-GPU SPH program is developed for free-surface flows. The approach is based on a spatial decomposition…
We consider differential Lyapunov and Riccati equations, and generalized versions thereof. Such equations arise in many different areas and are especially important within the field of optimal control. In order to approximate their…
In this paper, we show the effectiveness of a pipeline implementation of Dynamic Programming (DP) on GPU. As an example, we explain how to solve a matrix-chain multiplication (MCM) problem by DP on GPU. This problem can be sequentially…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
Due to their highly parallel multi-cores architecture, GPUs are being increasingly used in a wide range of computationally intensive applications. Compared to CPUs, GPUs can achieve higher performances at accelerating the programs'…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…