Related papers: Accurate Chemical Master Equation Solution Using M…
We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe networks of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is…
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…
We present an adaptive Finite State Projection (FSP) method for efficiently solving the Chemical Master Equation (CME) with rigorous error control. Our approach integrates time-stepping with dynamic state-space truncation, balancing…
The chemical diffusion master equation (CDME) describes the probabilistic dynamics of reaction--diffusion systems at the molecular level [del Razo et al., Lett. Math. Phys. 112:49, 2022]; it can be considered the master equation for…
The reaction-diffusion master equation (RDME) is commonly used to model processes where both the spatial and stochastic nature of chemical reactions need to be considered. We show that the RDME in many cases is inconsistent with a…
We consider a Markov process in continuous time with a finite number of discrete states. The time-dependent probabilities of being in any state of the Markov chain are governed by a set of ordinary differential equations, whose dimension…
The modeling and simulation of stochastic reaction-diffusion processes is a topic of steady interest that is approached with a wide range of methods. \rev{At the level of particle-resolved descriptions, where chemical reactions are coupled…
Accurate thermochemical data with sub-chemical accuracy (within 1 kcal mol$^{-1}$ of the empirical ground truth) are essential for advancing computational chemistry methods. However, existing datasets that reach this level of accuracy…
Stochastic reaction networks are a fundamental model to describe interactions between species where random fluctuations are relevant. The master equation provides the evolution of the probability distribution across the discrete state space…
We show that discrete distributions on the $d$-dimensional non-negative integer lattice can be approximated arbitrarily well via the marginals of stationary distributions for various classes of stochastic chemical reaction networks. We…
In recent years dynamical modelling has been provided with a range of breakthrough methods to perform exact Bayesian inference. However it is often computationally unfeasible to apply exact statistical methodologies in the context of large…
The study and prediction of chemical reactivity is one of the most important application areas of molecular quantum chemistry. Large-scale, fully error-tolerant quantum computers could provide exact or near-exact solutions to the underlying…
We propose a probabilistic derivation of the so-called chemical diffusion master equation (CDME) and describe an infinite dimensional moment generating function method for finding its analytical solution. CDMEs model by means of an infinite…
Models defined by stochastic differential equations (SDEs) allow for the representation of random variability in dynamical systems. The relevance of this class of models is growing in many applied research areas and is already a standard…
This work introduces a novel probabilistic deep learning technique called deep Gaussian mixture ensembles (DGMEs), which enables accurate quantification of both epistemic and aleatoric uncertainty. By assuming the data generating process…
The Finite State Projection (FSP) method approximates the Chemical Master Equation (CME) by restricting the dynamics to a finite subset of the (typically infinite) state space, enabling direct numerical solution with computable error…
In the presence of renewable resources, distribution networks have become extremely complex to monitor, operate and control. Furthermore, for the real time applications, active distribution networks require fast real time distribution state…
In this work, we consider the problem of estimating summary statistics to characterise biochemical reaction networks of interest. Such networks are often described using the framework of the Chemical Master Equation (CME). For…
Stochastic master equations are often used to describe conditional spin squeezing of atomic ensemble, but are limited so far to the systems with few atoms due to the exponentially increased Hilbert space. In this article, we present an…
A machine learning (ML) based equivariant neural network for constructing distributed charge models (DCMs) of arbitrary resolution, DCM-net, is presented. DCMs efficiently and accurately model the anisotropy of the molecular electrostatic…