Related papers: A hybrid moment equation approach to gas-grain che…
Cellular reactions have multi-scale nature in the sense that the abundance of molecular species and the magnitude of reaction rates can vary in a wide range. This diversity leads to hybrid models that combine deterministic and stochastic…
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…
A widely used approach to describe the dynamics of gene regulatory networks is based on the chemical master equation, which considers probability distributions over all possible combinations of molecular counts. The analysis of such models…
In the past few decades, the development of fluorescent technologies and microscopic techniques has greatly improved scientists' ability to observe real-time single-cell activities. In this paper, we consider the filtering problem associate…
Results are presented from numerical experiments aiming at the computation of stochastic phase-field models for phase transformations by coarse-graining molecular dynamics. The studied phase transformations occur between a solid crystal and…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian…
We demonstrate an approach to solving the coagulation equation that involves using a finite number of moments of the particle size distribution. This approach is particularly useful when only general properties of the distribution, and…
These are lecture notes of a course that I gave to people doing research for their Ph.D. thesis in theoretical chemistry or spectroscopy. The course was given on December 9-13, 2002, in Han-sur-Lesse, Belgium. The lecture notes start with…
In this work we propose a hierarchy of Monte Carlo methods for sampling equilibrium properties of stochastic lattice systems with competing short and long range interactions. Each Monte Carlo step is composed by two or more sub - steps…
The recent discovery of methyl formate and dimethyl ether in the gas phase of cold cores with temperatures as cold as 10 K challenges our previous astrochemical models concerning the formation of complex organic molecules. The strong…
Since Pearson [Philosophical Transactions of the Royal Society of London. A, 185 (1894), pp. 71-110] first applied the method of moments (MM) for modeling data as a mixture of one-dimensional Gaussians, moment-based estimation methods have…
We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, some molecules in the system will live on a fine-grained mesh,…
We investigate the roles of stochastic grain heating in the formation of complex organic molecules (COMs) in cold cores, where COMs have been detected. Two different types of grain-size distributions are used in the chemical models. The…
A macroscopic mesoscopic, deterministic stochastic coupling strategy is proposed to accelerate the direct simulation Monte Carlo (DSMC) method for chemical reaction. First, a macroscopic synthetic equation is formulated by integrating…
Reaction networks are often used to model interacting species in fields such as biochemistry and ecology. When the counts of the species are sufficiently large, the dynamics of their concentrations are typically modeled via a system of…
A combination of first principle molecular dynamics (MD) simulations with a rate equation model (MD-RE approach) is presented to study the trapping and the scattering of rare gas atoms from metal surfaces. The temporal evolution of the atom…
A generalized method of moments (GMM) estimator is unreliable for a large number of moment conditions, that is, it is comparable, or larger than the sample size. While classical GMM literature proposes several provisions to this problem,…
We have designed an improved algorithm that enables us to simulate the chemistry of cold dense interstellar clouds with a full gas-grain reaction network. The chemistry is treated by a unified microscopic-macroscopic Monte Carlo approach…
The temperatures of dust grains play important roles in the chemical evolution of molecular clouds. Unlike large grains, the temperature fluctuations of small grains induced by photons may be significant. Therefore, if the grain size…