Related papers: pSpatiocyte: A Parallel Stochastic Method for Part…
In this paper we study from a numerical analysis perspective the Fractional Step Kinetic Monte Carlo (FS-KMC) algorithms proposed in [1] for the parallel simulation of spatially distributed particle systems on a lattice. FS-KMC are…
The role of dimensionality (Euclidean versus fractal), spatial extent, boundary effects and system topology on the efficiency of diffusion-reaction processes involving two simultaneously-diffusing reactants is analyzed. We present…
The paper introduces PDSP-Bench, a novel benchmarking system designed for a systematic understanding of performance of parallel stream processing in a distributed environment. Such an understanding is essential for determining how Stream…
"Leaping" methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address…
Diffusion models have achieved remarkable progress in high-fidelity image, video, and audio generation, yet inference remains computationally expensive. Nevertheless, current diffusion acceleration methods based on distributed parallelism…
The quantum computer offers significant advantages in simulating physical systems, particularly those with exponentially large state spaces, such as quantum systems. Stochastic reaction-diffusion systems, characterized by their stochastic…
Due to rapid data growth, statistical analysis of massive datasets often has to be carried out in a distributed fashion, either because several datasets stored in separate physical locations are all relevant to a given problem, or simply to…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
Reconstruction of the tridimensional geometry of a visual scene using the binocular disparity information is an important issue in computer vision and mobile robotics, which can be formulated as a Bayesian inference problem. However,…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
Stochastic kinetic models (SKMs) are increasingly used to account for the inherent stochasticity exhibited by interacting populations of species in areas such as epidemiology, population ecology and systems biology. Species numbers are…
We initiate the study of probabilistic parallel programs with dynamic process creation and synchronisation. To this end, we introduce probabilistic split-join systems (pSJSs), a model for parallel programs, generalising both probabilistic…
The reaction-diffusion master equation is a stochastic model often utilized in the study of biochemical reaction networks in living cells. It is applied when the spatial distribution of molecules is important to the dynamics of the system.…
We describe a new algorithm for simulating complex Markoff-processes. We have used a reaction-cell method in order to simulate arbitrary reactions. It can be used for any kind of RDS on arbitrary topologies, including fractal dimensions or…
In synaptic molecular communication (MC), the activation of postsynaptic receptors by neurotransmitters (NTs) is governed by a stochastic reaction-diffusion process. This randomness of synaptic MC contributes to the randomness of the…
In this paper, an algorithm is presented to calculate the transition rates between adjacent mesoscopic subvolumes in the presence of flow and diffusion. These rates can be integrated in stochastic simulations of reaction-diffusion systems…
State-of-the-art numerical simulations of laser plasma by means of the Particle-in-Cell method are often extremely computationally intensive. Therefore there is a growing need for development of approaches for efficient utilization of…
The development of cost-effective highperformance parallel computing on multi-processor supercomputers makes it attractive to port excessively time consuming simulation software from personal computers (PC) to super computes. The power…
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…
Diffusion models have achieved great success in synthesizing high-quality images. However, generating high-resolution images with diffusion models is still challenging due to the enormous computational costs, resulting in a prohibitive…