Related papers: GPU-powered Simulation Methodologies for Biologica…
Understanding how people view and interact with autonomous vehicles is important to guide future directions of research. One such way of aiding understanding is through simulations of virtual environments involving people and autonomous…
The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD,…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
Future computing systems, from handhelds to supercomputers, will undoubtedly be more parallel and heterogeneous than todays systems to provide more performance and energy efficiency. Thus, GPUs are increasingly being used to accelerate…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
A goal of systems biology is to understand the dynamics of intracellular systems. Stochastic chemical kinetic models are often utilized to accurately capture the stochastic nature of these systems due to low numbers of molecules. Collecting…
Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed,…
Pedestrian movement, although ubiquitous and well-studied, is still not that well understood due to the complicating nature of the embedded social dynamics. Interest among researchers in simulating pedestrian movement and interactions has…
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…
In this work, we present an extension of Gaussian process (GP) models with sophisticated parallelization and GPU acceleration. The parallelization scheme arises naturally from the modular computational structure w.r.t. datapoints in the…
The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems.…
We introduce a particle-based simulation method for granular material in interactive frame rates. We divide the simulation into two decoupled steps. In the first step, a relatively small number of particles is accurately simulated with a…
Commercial graphics processors (GPUs) have high compute capacity at very low cost, which makes them attractive for general purpose scientific computing. In this paper we show how graphics processors can be used for N-body simulations to…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
The problem of solving a system of polynomial equations is one of the most fundamental problems in applied mathematics. Among them, the problem of solving a system of binomial equations form a important subclass for which specialized…
Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…
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…
The ability of Gaussian processes (GPs) to predict the behavior of dynamical systems as a more sample-efficient alternative to parametric models seems promising for real-world robotics research. However, the computational complexity of GPs…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
The latest Graphics Processing Units (GPUs) are reported to reach up to 200 billion floating point operations per second (200 Gflops) and to have price performance of 0.1 cents per M flop. These facts raise great interest in the…