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Numerous applications of Eikonal equations prompted the development of many efficient numerical algorithms. The Heap-Cell Method (HCM) is a recent serial two-scale technique that has been shown to have advantages over other serial…
This paper presents advancements in automated early-stage prediction of the success of reprogramming human induced pluripotent stem cells (iPSCs) as a potential source for regenerative cell therapies.The minuscule success rate of…
In this paper, we describe the algorithms we implemented in FDPS to make efficient use of accelerator hardware such as GPGPUs. We have developed FDPS to make it possible for many researchers to develop their own high-performance parallel…
In this paper we sum up our works on multiscale programs, mainly simulations. We first start with describing what multiscaling is about, how it helps perceiving signal from a background noise in a ?ow of data for example, for a direct…
Three dimensional particle-in-cell laser-plasma simulation is an important area of computational physics. Solving state-of-the-art problems requires large-scale simulation on a supercomputer using specialized codes. A growing demand in…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
Last level cache management and core interconnection network play important roles in performance and power consumption in multicore system. Large scale chip multicore uses mesh interconnect widely due to scalability and simplicity of the…
Scientific applications often contain large, computationally-intensive, and irregular parallel loops or tasks that exhibit stochastic characteristics. Applications may suffer from load imbalance during their execution on high-performance…
For computational fluid dynamics (CFD) applications with a large number of grid points/cells, parallel computing is a common efficient strategy to reduce the computational time. How to achieve the best performance in the modern…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
Large-scale HPC simulations of plasma dynamics in fusion devices require efficient parallel I/O to avoid slowing down the simulation and to enable the post-processing of critical information. Such complex simulations lacking parallel I/O…
Optimization via simulation has been well established to find optimal solutions and designs in complex systems. However, it still faces modeling and computational challenges when extended to the multi-stage setting. This survey reviews the…
The latest trends in high-performance computing systems show an increasing demand on the use of a large scale multicore systems in a efficient way, so that high compute-intensive applications can be executed reasonably well. However, the…
In decision support systems, it is essential to get a candidate solution fast, even if it means resorting to an approximation. This constraint introduces a scalability requirement with regard to the kind of heuristics which can be used in…
We explore the use of the Cell Broadband Engine (Cell/BE for short) for combinatorial optimization applications: we present a parallel version of a constraint-based local search algorithm that has been implemented on a multiprocessor…
A modular, maintainable and extensible particle beam simulation architecture is presented. Design considerations for single particle, multi particle, and rms envelope simulations (in two and three dimensions) are outlined. Envelope…
We present a parallel implementation of cellular automata to simulate chemical reactions on surfaces. The scaling of the computer time with the number of processors for this parallel implementation is quite close to the ideal T/P, where T…
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…
This article presents new hexagonal and pentagonal PEM fuel cell models. The models have been optimized after achieving improved cell performance. The input parameters of the multi-objective optimization algorithm were pressure and…
Dose-finding trials are a key component of the drug development process and rely on a statistical design to help inform dosing decisions. Triallists wishing to choose a design require knowledge of operating characteristics of competing…