Related papers: Graphical Conditions ensuring Equality between Dif…
We begin by reviewing a technique to approximate the dynamics of stochastic programs --written in a stochastic process algebra-- by a hybrid system, suitable to capture a mixed discrete/continuous evolution. In a nutshell, the discrete…
Chemical reaction networks are often used to model and understand biological processes such as cell signaling. Under the framework of chemical reaction network theory, a process is modeled with a directed graph and a choice of kinetics,…
Chemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a…
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…
This study address the computational determination of catalytic reaction rates by moving beyond traditional Transition State Theory (TST), addressing its limitations in complex systems. The Hill relation framework, integrated with Adaptive…
In this work we developed a RAFT polymerization model taking into account the main reactions of the experimental RAFT process and implemented that model in dissipative particle dynamics (DPD). With a help of a kinetic model based on the…
In chemical reaction network theory, ordinary differential equations are used to model the temporal change of chemical species concentration. As the functional form of these ordinary differential equations systems is derived from an…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
We consider nonlinear reaction systems satisfying mass-action kinetics with slow and fast reactions. It is known that the fast-reaction-rate limit can be described by an ODE with Lagrange multipliers and a set of nonlinear constraints that…
Why reaction rate constants for enzymatic reactions are typically inversely proportional to fractional power exponents of solvent viscosity remains to be already a thirty years old puzzle. Available interpretations of the phenomenon invoke…
Dynamical electronic- and vibrational-structure theories have received a growing interest in the last years due to their ability to simulate spectra recorded with ultrafast experimental techniques. The exact time evolution of a molecular…
Discrete-state, continuous-time Markov models are becoming commonplace in the modelling of biochemical processes. The mathematical formulations that such models lead to are opaque, and, due to their complexity, are often considered…
We consider the problem of estimating parameter sensitivities for stochastic models of multiscale reaction networks. These sensitivity values are important for model analysis, and, the methods that currently exist for sensitivity estimation…
We propose a statistical-stochastic surrogate modeling approach to predict the response of the mean and variance statistics under various initial conditions and external forcing perturbations. The proposed modeling framework extends the…
As computational chemistry methods evolve, dynamic effects have been increasingly recognized to govern chemical reaction pathways in both organic and inorganic systems. Here, we introduce a committor-based workflow that integrates a…
We critically explore the applicability of a recently proposed framework to sample the quantum dynamics of a many-body quantum system interacting with light by stochastic trajectories, applying it to the closed and open Tavis-Cummings model…
Polymers near the glass transition temperature Tg often exhibit a breakdown of time-temperature-superposition (TTS), with chain relaxation times and viscosity exhibiting a weaker temperature dependence than segmental relaxation times. The…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
Simulation of stochastic spatially-extended systems is a challenging problem. The fundamental quantities in these models are individual entities such as molecules, cells, or animals, which move and react in a random manner. In big systems,…
We introduce a unifying and generalizing framework for complex and detailed balanced steady states in chemical reaction network theory. To this end, we generalize the graph commonly used to represent a reaction network. Specifically, we…