Related papers: Computing reaction rates in bio-molecular systems …
Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
Studies of fixation dynamics in Markov processes predominantly focus on the mean time to absorption. This may be inadequate if the distribution is broad and skewed. We compute the distribution of fixation times in one-step birth-death…
Adaptive multilevel splitting algorithms have been introduced rather recently for estimating tail distributions in a fast and efficient way. In particular, they can be used for computing the so-called reactive trajectories corresponding to…
The quantum normal form approach to quantum transition state theory is used to compute the cumulative reaction probability for collinear exchange reactions. It is shown that for heavy atom systems like the nitrogen exchange reaction the…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Rigorous statistical methods for estimating thermonuclear reaction rates and nucleosynthesis are becoming increasingly established in nuclear astrophysics. The main challenge being faced is that experimental reaction rates are highly…
Radical recombination has been proposed to lead to the formation of complex organic molecules (COMs) in CO-rich ices in the early stages of star formation. These COMs can then undergo hydrogen addition and abstraction reactions leading to a…
We present a general expression for the association rate for partially diffusion-controlled reactions between spherical molecules with an asymmetric reactive patch on each surface. Reaction can occur only if the two patches are in contact…
While most chemical reactions in the interstellar medium take place in the gas phase, those occurring on the surfaces of dust grains play an essential role. Chemical models based on rate equations including both gas phase and grain surface…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
Model-based prediction of stochastic noise in biomolecular reactions often resorts to approximation with unknown precision. As a result, unexpected stochastic fluctuation causes a headache for the designers of biomolecular circuits. This…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
Machine learning-based models to predict product state distributions from a distribution of reactant conditions for atom-diatom collisions are presented and quantitatively tested. The models are based on function-, kernel- and grid-based…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
Modeling of dynamic processes in nuclear reactors is carried out, mainly, on the basis of the multigroup diffusion approximation for the neutron flux. The basic model includes a multidimensional set of coupled parabolic equations and…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
In a molecular communication network, transmitters and receivers communicate by using signalling molecules. At the receivers, the signalling molecules react, via a chain of chemical reactions, to produce output molecules. The counts of…