Related papers: BioSimulator.jl: Stochastic simulation in Julia
Microstructure.jl is a Julia package designed for probabilistic estimation of tissue microstructural parameters from diffusion or combined diffusion-relaxometry MRI data. It provides a flexible and extensible framework for defining…
We present an efficient numerical implementation of the quasi-classical doorway-window approximation, specifically designed for on-the-fly simulations of time-resolved nonlinear spectroscopic signals in the Julia package WaveMixings.jl. The…
The demand for high-performance computing (HPC) is ever-increasing for everyday statistical computing purposes. The downside is that we need to write specialized code for each HPC environment. CPU-level parallelization needs to be…
In the infectious disease literature, significant effort has been devoted to studying dynamics at a single scale. For example, compartmental models describing population-level dynamics are often formulated using differential equations. In…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
We apply the "weighted ensemble" (WE) simulation strategy, previously employed in the context of molecular dynamics simulations, to a series of systems-biology models that range in complexity from one-dimensional to a system with 354…
Biochemical reaction networks are often modelled using discrete-state, continuous-time Markov chains. System statistics of these Markov chains usually cannot be calculated analytically and therefore estimates must be generated via…
We describe a package realized in the Julia programming language which performs symbolic manipulations applied to nonlinear evolution equations, their flows, and commutators of such objects. This tool was employed to perform contrived…
Stochastic evolution underpins several approaches to the dynamics of open quantum systems, such as random modulation of Hamiltonian parameters, the stochastic Schrodinger equation (SSE), and the stochastic Liouville equation (SLE). These…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
We take up the challenge of designing realistic computational models of large interacting cell populations. The goal is essentially to bring Gillespie's celebrated stochastic methodology to the level of an interacting population of cells.…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Approximating partial differential equations for extensive industrial and scientific applications requires leveraging the power of modern high-performance computing. In large-scale parallel computations, the geometrical discretisation…
We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian…
Tau-leaping is a family of algorithms for the approximate simulation of the discrete state continuous time Markov chains. Motivation for the development of such methods can be found, for instance, in the fields of chemical kinetics and…
The MPSDynamics.jl package provides an easy to use interface for performing open quantum systems simulations at zero and finite temperatures. The package has been developed with the aim of studying non-Markovian open system dynamics using…
The existing literature on stochastic simulation of chemical reaction networks has a tendency to move as quickly as possible to the abstract formulation of the stochastic dynamics in terms of probabilities based on the concept of the…
We present the preliminary high-level design and features of DynamicPPL.jl, a modular library providing a lightning-fast infrastructure for probabilistic programming. Besides a computational performance that is often close to or better than…
BlockSystems.jl and NetworkDynamics.jl are two novel software packages which facilitate highly efficient transient stability simulations of power networks. Users may specify inputs and power system design in a convenient modular and…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…