Related papers: BioSimulator.jl: Stochastic simulation in Julia
Gaussian processes are a class of flexible nonparametric Bayesian tools that are widely used across the sciences, and in industry, to model complex data sources. Key to applying Gaussian process models is the availability of well-developed…
In biochemical systems some of the chemical species are present with only small numbers of molecules. In this situation discrete and stochastic simulation approaches are more relevant than continuous and deterministic ones. The fundamental…
Many biological systems exhibit multiscale dynamics, where some species occur in high copy numbers while others remain rare. This heterogeneity necessitates hybrid modelling approaches: deterministic models are computationally efficient but…
We propose a faster algorithm for individual based simulations for adaptive dynamics based on a simple modification to the standard Gillespie Algorithm for simulating stochastic birth-death processes. We provide an analytical explanation…
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…
We present a simple and general framework to simulate statistically correct realizations of a system of non-Markovian discrete stochastic processes. We give the exact analytical solution and a practical an efficient algorithm alike the…
Point processes model the occurrence of a countable number of random points over some support. They can model diverse phenomena, such as chemical reactions, stock market transactions and social interactions. We show that JumpProcesses.jl is…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Accurate and efficient methods to simulate nonadiabatic and quantum nuclear effects in high-dimensional and dissipative systems are crucial for the prediction of chemical dynamics in condensed phase. To facilitate effective development,…
MomentClosure.jl is a Julia package providing automated derivation of the time-evolution equations of the moments of molecule numbers for virtually any chemical reaction network using a wide range of moment closure approximations. It…
Classical methods to simulate quantum systems are not only a key element of the physicist's toolkit for studying many-body models but are also increasingly important for verifying and challenging upcoming quantum computers. Pauli…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
The Gillespie algorithm provides statistically exact methods for simulating stochastic dynamics modelled as interacting sequences of discrete events including systems of biochemical reactions or earthquake occurrences, networks of queuing…
Connectivity across landscapes influences a wide range of conservation-relevant ecological processes, including species movements, gene flow, and the spread of wildfire, pests, and diseases. Recent improvements in remote sensing data…
Simulation of non-adiabatic dynamics of a quantum system coupled to dissipative environments poses significant challenges. New sophisticated methods are regularly being developed with an eye towards moving to larger systems and more…
A practical introduction to stochastic modelling of reaction-diffusion processes is presented. No prior knowledge of stochastic simulations is assumed. The methods are explained using illustrative examples. The article starts with the…
This article presents an algorithm that allows modeling of biological networks in a qualitative framework with continuous time. Mathematical modeling is used as a systems biology tool to answer biological questions, and more precisely, to…
PowerSimulations.jl is a Julia-based BSD-licensed power system operations simulation tool developed as a flexible and open source software for quasi-static power systems simulations including Production Cost Models. PowerSimulations.jl…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Single-cell data reveal the presence of biological stochasticity between cells of identical genome and environment, in particular highlighting the transcriptional bursting phenomenon. To account for this property, gene expression may be…