Related papers: Parallelization of Gillespie algorithm based on bi…
In this study, we have developed a parallel version of the random time simulation algorithm. Firstly, we gave a rigorous basis of the random time description of the stochastic process of chemical reaction network time evolution. And then we…
Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed,…
Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration of all reactions and all chemical species that may arise in…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate…
The stochastic simulation algorithm commonly known as Gillespie's algorithm is now used ubiquitously in the modelling of biological processes in which stochastic effects play an important role. In well-mixed scenarios at the sub-cellular…
BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in…
We present a new notion of probabilistic duality for random variables involving mixture distributions. Using this notion, we show how to implement a highly-parallelizable Gibbs sampler for weakly coupled discrete pairwise graphical models…
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…
In this paper we survey recent work on the use of statistical model checking techniques for biological applications. We begin with an overview of the basic modelling techniques for biochemical reactions and their corresponding stochastic…
The M{\O}D computational framework implements rule-based generative chemistries as explicit transformations of graphs representing chemical structural formulae. Here, we expand M{\O}D by a stochastic simulation module that simulates the…
Many physical and biological processes are stochastic in nature. Computational models and simulations of such processes are a mathematical and computational challenge. The basic stochastic simulation algorithm was published by D. Gillespie…
At the cellular scale, biochemical processes are governed by random interactions between reactant molecules with small copy counts, leading to behavior that is inherently stochastic. Such systems are often modeled as continuous-time Markov…
The Gillespie algorithm and its extensions are commonly used for the simulation of chemical reaction networks. A limitation of these algorithms is that they have to process and update the system after every reaction, requiring significant…
We present a new approach to sample from generic binary distributions, based on an exact Hamiltonian Monte Carlo algorithm applied to a piecewise continuous augmentation of the binary distribution of interest. An extension of this idea to…
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…
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…
In the context of self-assembly, where complex structures can be assembled from smaller units, it is desirable to devise strategies towards disassembly and reassembly processes that reuse the constituent parts. A non-reciprocal multifarious…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
In the present paper we propose an improvement of the Gillespie algorithm allowing us to study the time evolution of an ensemble of chemical reactions occurring in a varying volume, whose growth is directly related to the amount of some…