Related papers: Parallelization of Cellular Automata for Surface R…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
Computational systems biology has provided plenty of insights into cell biology. Early on, the focus was on reaction networks between molecular species. Spatial distribution only began to be considered mostly within the last decade.…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
We develop a rather elaborate computer program to investigate the jointly periodic points of one-dimensional cellular automata. The experimental results and mathematical context lead to questions, conjectures and a contextual theorem.
The number of parameters in large-scale language models based on transformers is gradually increasing, and the scale of computing clusters is also growing. The technology of quickly mobilizing large amounts of computing resources for…
Parallel tempering, also known as replica exchange sampling, is an important method for simulating complex systems. In this algorithm simulations are conducted in parallel at a series of temperatures, and the key feature of the algorithm is…
This paper is centered on using chemical reaction as a computational metaphor for simultaneously solving problems. An artificial chemical reactor that can simultaneously solve instances of three unrelated problems was created. The reactor…
This paper presents a classification of Cellular Automata rules based on its properties at the nth iteration. Elaborate computer program has been designed to get the nth iteration for arbitrary 1-D or 2-D CA rules. Studies indicate that the…
A parallel reservoir simulator has been developed, which is designed for large-scale black oil simulations. It handles three phases, including water, oil and gas, and three components, including water, oil and gas. This simulator can…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
A fully parallel version of the contact dynamics (CD) method is presented in this paper. For large enough systems, 100% efficiency has been demonstrated for up to 256 processors using a hierarchical domain decomposition with dynamic load…
Design of next generation computer systems should be supported by simulation infrastructure that must achieve a few contradictory goals such as fast execution time, high accuracy, and enough flexibility to allow comparison between large…
We present and analyse a model for cell signalling processes in biological tissues. The model includes diffusion and nonlinear reactions on the cell surfaces, and both inter- and intracellular signalling. Using techniques from the theory of…
Task-based programming models have demonstrated their efficiency in the development of scientific applications on modern high-performance platforms. They allow delegation of the management of parallelization to the runtime system (RS),…
We have investigated plasma-surface interactions with molecular dynamics (MD) simulations. It, however, is high cost computation and is limited to simulations for materials of nanometer order. In order to overcome the limitation, a…
We implement in a reactive programming framework a simulation of three aspects of quantum mechanics: self-interference, state superposition, and entanglement. The simulation basically consists in a cellular automaton embedded in a…
New computational tools for solid-state synthesis recipe design are needed in order to accelerate the experimental realization of novel functional materials proposed by high-throughput materials discovery workflows. This work contributes a…
We report the results of intensive numerical calculations for four atomic H2+H2 energy transfer collision. A parallel computing technique based on LAM/MPI functions is used. In this algorithm, the data is distributed to the processors…
We present applications of a cellular automaton approach to pedestrian dynamics introduced in [1,2]. It is shown that the model is able to reproduce collective effects and self-organization phenomena encountered in pedestrian traffic, e.g.…