Related papers: Parallelization of Cellular Automata for Surface R…
In this work we propose a highly optimized version of a simulated annealing (SA) algorithm adapted to the more recently developed Graphic Processor Units (GPUs). The programming has been carried out with CUDA toolkit, specially designed for…
We consider the problem of efficiently simulating population protocols. In the population model, we are given a distributed system of $n$ agents modeled as identical finite-state machines. In each time step, a pair of agents is selected…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
We introduce a new update scheme to systematically improve the efficiency of parallel tempering simulations. We show that by adapting the number of sweeps between replica exchanges to the canonical autocorrelation time, the average…
With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
Generation of pseudo random sequences by cellular automata, as well as by hybrid cellular automata is surveyed. An application to the fast evaluation and FPGA implementation of some classes of boolean functions is sketched out.
The numerical simulation of atherosclerotic plaque growth is computationally prohibitive, since it involves a complex cardiovascular fluid-structure interaction (FSI) problem with a characteristic time scale of milliseconds to seconds, as…
We discuss the scalable parallel solution of the Poisson equation within a Particle-In-Cell (PIC) code for the simulation of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences.…
Microstructures forming during ternary eutectic directional solidification processes have significant influence on the macroscopic mechanical properties of metal alloys. For a realistic simulation, we use the well established…
We develop a novel parallel resampling algorithm for fully parallelized particle filters, which is designed with GPUs (graphics processing units) or similar parallel computing devices in mind. With our new algorithm, a full cycle of…
This paper is about partitioning in parallel and distributed simulation. That means decomposing the simulation model into a numberof components and to properly allocate them on the execution units. An adaptive solution based on…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
Skin modeling is an ongoing research area that highly benefits from modern parallel algorithms. This article aims at applying shape optimization to compute cell size and arrangement for elastic energy minimization of a cellular composite…
High fidelity Computational Fluid Dynamics simulations are generally associated with large computing requirements, which are progressively acute with each new generation of supercomputers. However, significant research efforts are required…
The present paper describes a parallel unstructured-mesh Plasma simulation code based on Finite Volume method. The code dynamically refines and coarses mesh for accurate resolution of the different features regarding the electron density.…
Paints and coatings undergo a variety of physical and chemical changes under environmental exposures. Accurate prediction of these changes is important for the applications of coatings. This work presents a novel approach to modeling…
We introduce a novel method of quantum emulation of a classical reversible cellular automaton. By applying this method to a chaotic cellular automaton, the obtained quantum many-body system thermalizes while all the energy eigenstates and…
We propose a method to directly couple molecular dynamics, finite element method and particle-in-cell techniques to simulate metal surface response to high electric fields. We use this method to simulate the evolution of a field emitting…
The Kernel Polynomial Method (KPM) is one of the fast diagonalization methods used for simulations of quantum systems in research fields of condensed matter physics and chemistry. The algorithm has a difficulty to be parallelized on a…