相关论文: A spatial measure-valued model for chemical reacti…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
We introduce Markov Random Geometric Graphs (MRGGs), a growth model for temporal dynamic networks. It is based on a Markovian latent space dynamic: consecutive latent points are sampled on the Euclidean Sphere using an unknown Markov…
The paper deals with the asymptotic properties of a random jump process in a high contrast periodic medium in $\mathbb R^d$, $d\geq 1$. We show that if the coordinates of the random jump process in $\mathbb R^d$ are equipped with an extra…
This paper studies birth and death processes in interactive random environments where the birth and death rates and the dynamics of the state of the environment are dependent on each other. Two models of a random environment are considered:…
We describe spatio-temporal random processes using linear mixed models. We show how many commonly used models can be viewed as special cases of this general framework and pay close attention to models with separable or product-sum…
In this article we focus on dynamic network data which describe interactions among a fixed population through time. We model this data using the latent space framework, in which the probability of a connection forming is expressed as a…
In the first part of this paper, we propose new optimization-based methods for the computation of preferred (dense, sparse, reversible, detailed and complex balanced) linearly conjugate reaction network structures with mass action dynamics.…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
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…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
The physical interpretation of the functioning of the adaptive immune system, which has been thoroughly characterized on genetic and molecular levels, provides a unique opportunity to define an adaptive self-organizing biological system in…
This article is dedicated to the study and comparison of two chemostat-like competition models in a heterogeneous environment. The first model is a probabilistic model where we build a PDMP simulating the effect of the temporal…
We consider the stochastic ranking process with space-time dependent jump rates for the particles. The process is a simplified model of the time evolution of the rankings such as sales ranks at online bookstores. We prove that the joint…
Large multidimensionality of high-throughput datasets pertaining to cell signaling and gene regulation renders it difficult to extract mechanisms underlying the complex kinetics involving various biochemical compounds (e.g., proteins,…
We determine filtering and master equations for a quantum system interacting with wave packet of light in a continuous-mode squeezed number state. We formulate the problem of conditional evolution of a quantum system making use of model of…
Stereoselective reactions (both chemical and enzymatic reactions) have been essential for origin of life, evolution, human biology and medicine. Since late 1960s, there have been numerous successes in the exciting new frontier of asymmetric…
Continuous-time Markov chains are frequently used as stochastic models for chemical reaction networks, especially in the growing field of systems biology. A fundamental problem for these Stochastic Chemical Reaction Networks (SCRNs) is to…
Detailed balance of a chemical reaction network can be defined in several different ways. Here we investigate the relationship among four types of detailed balance conditions: deterministic, stochastic, local, and zero-order local detailed…
We consider a model for which every site of $\mathbb{N}$ is assigned a fitness in $[0,1]$. At every discrete time all the sites are updated and each site samples a uniform on $[0,1]$, independently of everything else. At every discrete time…
This paper is motivated by examples from stochastic reaction network theory. The $Q$-matrix of a stochastic reaction network can be derived from the reaction graph, an edge-labelled directed graph encoding the jump vectors of an associated…