Related papers: pSpatiocyte: A Parallel Stochastic Method for Part…
A random-batch method for multi-species interacting particle systems is proposed, extending the method of S. Jin, L. Li, and J.-G. Liu [J. Comput. Phys. 400 (2020), 108877]. The idea of the algorithmus is to randomly divide, at each time…
This article describes a geometric partitioning software that can be used for quick computation of data partitions on many-core HPC machines. It is most suited for dynamic applications with load distributions that vary with time.…
In this work we propose an accelerated stochastic learning system for very large-scale applications. Acceleration is achieved by mapping the training algorithm onto massively parallel processors: we demonstrate a parallel, asynchronous GPU…
We present a computational modeling framework for data-driven simulations and analysis of infectious disease spread in large populations. For the purpose of efficient simulations, we devise a parallel solution algorithm targeting…
Particle-based stochastic reaction-diffusion (PBSRD) models are a popular approach for studying biological systems involving both noise in the reaction process and diffusive transport. In this work we derive coarse-grained deterministic…
Many-body simulations of quantum systems is an active field of research that involves many different methods targeting various computing platforms. Many methods commonly employed, particularly coupled cluster methods, have been adapted to…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
We present a parallel hierarchical solver for general sparse linear systems on distributed-memory machines. For large-scale problems, this fully algebraic algorithm is faster and more memory-efficient than sparse direct solvers because it…
In this paper we present a high-order kernel method for numerically solving diffusion and reaction-diffusion partial differential equations (PDEs) on smooth, closed surfaces embedded in $\mathbb{R}^d$. For two-dimensional surfaces embedded…
Inspired by the recent developments in modeling and analysis of reaction networks, we provide a geometric formulation of the reversible reaction networks under the influence of diffusion. Using the graph knowledge of the underlying reaction…
Solving multiscale diffusion problems is often computationally expensive due to the spatial and temporal discretization challenges arising from high-contrast coefficients. To address this issue, a partially explicit temporal splitting…
We study a stochastic system of $N$ interacting particles which models bimolecular chemical reaction-diffusion. In this model, each particle $i$ carries two attributes: the spatial location $X_t^i\in \mathbb{T}^d$, and the type $\Xi_t^i\in…
Biochemical reaction networks frequently consist of species evolving on multiple timescales. Stochastic simulations of such networks are often computationally challenging and therefore various methods have been developed to obtain sensible…
We present algorithmic improvements for fast and memory-efficient use of discrete spatial symmetries in Exact Diagonalization computations of quantum many-body systems. These techniques allow us to work flexibly in the reduced basis of…
Developments in dynamical systems theory provides new support for the macroscale modelling of pdes and other microscale systems such as Lattice Boltzmann, Monte Carlo or Molecular Dynamics simulators. By systematically resolving subgrid…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
This paper discusses temporally continuous and discrete forms of the speed-limited particle-in-cell (SLPIC) method first treated by Werner et al. [Phys. Plasmas 25, 123512 (2018)]. The dispersion relation for a 1D1V electrostatic plasma…
To extend prevailing scaling limits when solving time-dependent partial differential equations, the parallel full approximation scheme in space and time (PFASST) has been shown to be a promising parallel-in-time integrator. Similar to a…
Distributed Computation has been a recent trend in engineering research. Parallel Computation is widely used in different areas of Data Mining, Image Processing, Simulating Models, Aerodynamics and so forth. One of the major usage of…