Related papers: A parallel implementation of a new fast algorithm …
We present a novel discontinuous Galerkin algorithm for the solution of a class of Fokker-Planck collision operators. These operators arise in many fields of physics, and our particular application is for kinetic plasma simulations. In…
In this work, we consider alternative discretizations for PDEs which use expansions involving integral operators to approximate spatial derivatives. These constructions use explicit information within the integral terms, but treat boundary…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
We present a new set of dissipationless N-body simulations to examine the feasibility of creating bright ellipticals (following the Kormendy relation) by hierarchically merging present-day early-type dwarf galaxies, and to study how the…
This paper presents a quantum algorithm for solving the fractional Poisson equation \((-\Delta)^s u = f\) with \(s \in (0,1)\) on bounded domains. The proposed approach combines rational approximation techniques with quantum linear system…
In this note we approach the classical, Newtonian, gravitational $N$-body problem by mean of a new, original numerical integration method. After a short summary of the fundamental characteristics of the problem, including a sketch of some…
We describe a computational framework for simulating suspensions of rigid particles in Newtonian Stokes flow. One central building block is a collision-resolution algorithm that overcomes the numerical constraints arising from particle…
The present work attempts to integrate the independent efforts in the fast N-body community to create the fastest N-body library for many-core and heterogenous architectures. Focus is placed on low accuracy optimizations, in response to the…
Simulation speed depends on code structures, hence it is crucial how to build a fast algorithm. We solve the Allen-Cahn equation by an explicit finite difference method, so it requires grid calculations implemented by many for-loops in the…
A parallel code has been written in FORTRAN90, C, and MPI for the analysis of biological simulation data. Using a master/slave algorithm, the software operates on AMBER generated trajectory data using either UNIX or MPI file IO, and it…
We have newly developed a Parallelized Particle-Particle Particle-tree code for Planet formation, PENTACLE, which is a parallelized hybrid $N$-body integrator executed on a CPU-based (super)computer. PENTACLE uses a 4th-order Hermite…
We describe source code level parallelization for the {\tt kira} direct gravitational $N$-body integrator, the workhorse of the {\tt starlab} production environment for simulating dense stellar systems. The parallelization strategy, called…
We propose a fast temporal decomposition procedure for solving long-horizon nonlinear dynamic programs. The core of the procedure is sequential quadratic programming (SQP) that utilizes a differentiable exact augmented Lagrangian as the…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
We present an efficient and accurate method for simulating massive neutrinos in cosmological structure formation simulations, together with an easy to use public implementation. Our method builds on our earlier implementation of the linear…
In this paper, we describe the implementation and performance of GreeM, a massively parallel TreePM code for large-scale cosmological N-body simulations. GreeM uses a recursive multi-section algorithm for domain decomposition. The size of…
The analysis of cosmological galaxy surveys requires realistic simulations for their interpretation. Forward modelling is a powerful method to simulate galaxy clustering without the need for an underlying complex model. This approach…
This work focuses on accelerating the multiplication of a dense random matrix with a (fixed) sparse matrix, which is frequently used in sketching algorithms. We develop a novel scheme that takes advantage of blocking and recomputation…
The Poisson-Boltzmann equation is widely used to model molecular electrostatics; however, it is usually solved in linearised form because the sinh nonlinearity is challenging, limiting its applicability in highly charged systems such as…
We consider the demixing problem of two (or more) high-dimensional vectors from nonlinear observations when the number of such observations is far less than the ambient dimension of the underlying vectors. Specifically, we demonstrate an…