Related papers: On Designing Multicore-aware Simulators for Biolog…
Microprocessor roadmaps clearly show a trend towards multiple core CPUs. Modern operating systems already make use of these CPU architectures by distributing tasks between processing cores thereby increasing system performance. This review…
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 Calculus of Wrapped Compartments (CWC) is a recently proposed modelling language for the representation and simulation of biological systems behaviour. Although CWC has no explicit structure modelling a spatial geometry, its compartment…
It is essential to find new ways of enabling experts in different disciplines to collaborate more efficient in the development of ever more complex systems, under increasing market pressures. One possible solution for this challenge is to…
With the increasing interest in neuromorphic computing, designers of embedded systems face the challenge of efficiently simulating such platforms to enable architecture design exploration early in the development cycle. Executing artificial…
Stochastic computing (SC) is an emerging computing technique that promises high density, low power, and error tolerant solutions. In SC, values are encoded as unary bitstreams and SC arithmetic circuits operate on one or more bitstreams. In…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
In branching simulation, a novel approach to simulation presented in this paper, a multiplicity of plausible scenarios are concurrently developed and implemented. In conventional simulations of complex systems, there arise from time to time…
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…
The role of scalable high-performance workflows and flexible workflow management systems that can support multiple simulations will continue to increase in importance. For example, with the end of Dennard scaling, there is a need to…
The computer revolution has been driven by a sustained increase of computational speed of approximately one order of magnitude (a factor of ten) every five years since about 1950. In natural sciences this has led to a continuous increase of…
As the demand of real time computing increases day by day, there is a major paradigm shift in processing platform of real time system from single core to multi-core platform which provides advantages like higher throughput, linear power…
Cardiovascular disease affects millions of people worldwide and its social and economic cost clearly motivates scientific research. Computer simulation can lead to a better understanding of cardiac physiology, and for pathology presents…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modelling of biological systems. In the usual semantics of process algebras for modelling biological systems actions are instantaneous. When…
This paper studies parallelization schemes for stochastic Vector Quantization algorithms in order to obtain time speed-ups using distributed resources. We show that the most intuitive parallelization scheme does not lead to better…
Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulations must model networks of millions of molecular species and…
Simulating large-scale microswimmer dynamics in viscous fluid poses significant challenges due to the coupled high spatial and temporal complexity. Conventional high-performance computing (HPC) methods often address these two dimensions in…
FastFlow is a structured parallel programming framework targeting shared memory multicores. Its layered design and the optimized implementation of the communication mechanisms used to implement the FastFlow streaming networks provided to…
This paper proposes an efficient parallelised computation of field/circuit coupled systems co-simulated with the Waveform Relaxation (WR) technique. The main idea of the introduced approach lies in application of the parallel-in-time method…