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Laboratory experiments play a key role in deciphering the chemistry of the interstellar medium (ISM) and the role that product complex organic molecules (COMs) may play in the origins of life. However, to date, most studies in experimental…
Numerical heating in particle-in-cell (PIC) codes currently precludes the accurate simulation of cold, relativistic plasma over long periods, severely limiting their applications in astrophysical environments. We present a spatially…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
Based on a rate equation model for single-mode two-level lasers, two algorithms for stochastically simulating the dynamics and steady-state behaviour of micro- and nanolasers are described in detail. Both methods lead to steady-state photon…
We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, some molecules in the system will live on a fine-grained mesh,…
Spatially-coupled (SC) codes, known for their threshold saturation phenomenon and low-latency windowed decoding algorithms, are ideal for streaming applications. They also find application in various data storage systems because of their…
Polynomial Chaos Expansions represent a powerful tool to simulate stochastic models of dynamical systems. Yet, deriving the expansion's coefficients for complex systems might require a significant and non-trivial manipulation of the model,…
Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing…
A fast algorithm for the approximate multiplication of matrices with decay is introduced; the Sparse Approximate Matrix Multiply (SpAMM) reduces complexity in the product space, a different approach from current methods that economize…
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…
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
This study considers using Metropolis-Hastings algorithm for stochastic simulation of chemical reactions. The proposed method uses SSA (Stochastic Simulation Algorithm) distribution which is a standard method for solving well-stirred…
Finite element methods require the composition of the global stiffness matrix from local finite element contributions. The composition process combines the computation of element stiffness matrices and their assembly into the global…
The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can only be applied to small systems. By contrast, we demonstrate that quantum…
We study matrix-matrix multiplication of two matrices, $A$ and $B$, each of size $n \times n$. This operation results in a matrix $C$ of size $n\times n$. Our goal is to produce $C$ as efficiently as possible given a cache: a 1-D limited…
For the calculation of complex neutral/ionized gas phase chemical equilibria, we present a semi-analytical versatile and efficient computer program, called FastChem. The applied method is based on the solution of a system of coupled…
In studies of the interstellar medium in galaxies, radiative transfer models of molecular emission are useful for relating molecular line observations back to the physical conditions of the gas they trace. However, doing this requires…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
Because of the vast volume of data being produced by today's scientific simulations, lossy compression allowing user-controlled information loss can significantly reduce the data size and the I/O burden. However, for large-scale cosmology…