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We investigate the physical properties of steady flows in a holographic first-order phase transition model, extending from the thermodynamics at equilibrium to the real-time dynamics far from equilibrium. Through spinodal decomposition or…
The kinetics of carbon condensation, or carbon clustering, in detonation of carbon-rich high explosives is modeled by solving a system of rate equations for concentrations of carbon particles. Unlike previous efforts, the rate equations…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…
By observing reconstituted chromatin by fluorescence microscopy (FM) and atomic force microscopy (AFM), we found that the density of nucleosomes exhibits a bimodal profile, i.e., there is a large transition between the dense and dispersed…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
Diffusion models generate high-resolution images through iterative stochastic processes. In particular, the denoising method is one of the most popular approaches that predicts the noise in samples and denoises it at each time step. It has…
Using Brownian Dynamics, we study the dynamical behavior of a polymer grafted onto an adhesive surface close to the mechanically induced adsorption-stretching transition. Even though the transition is first order, (in the infinite chain…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
For some centuries, first order chemical rate constants were determined mainly by a linear logarithmic plot of reagent concentration terms against time where the initial concentration was required, which is experimentally often a…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
Theory of fast binary chemical reaction, ${\cal A}+{\cal B}\to{\cal C}$, in a statistically stationary chaotic flow at large Schmidt number ${Sc}$ and large Damk\"ohler number ${Da}$ is developed. For stoichiometric condition we identify…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
The first step in the construction of a regression model or a data-driven analysis, aiming to predict or elucidate the relationship between the atomic scale structure of matter and its properties, involves transforming the Cartesian…
In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid-liquid phase separation and a further transition into a…
The structural relaxation of amorphous materials is described as arising from the superposition of elementary processes with varying activation energies. We show that it is possible to obtain the kinetic parameters of these processes from…
There is current interest in developing photoactive materials that deform on illumination and can thus be used for photomechanical actuation. This is attractive since it can be affected at a distance, different frequencies can be used to…
We derive the nonequilibrium conductance matrix for open stationary Chemical Reaction Networks (CRNs) described by a deterministic mass action kinetic equation. As an illustration, we determine the nonequilibrium conductance matrix of a CRN…
We investigate the formation and evolution of Au-CO single-molecule break junctions. The conductance histogram exhibits two distinct molecular configurations, which are further investigated by a combined statistical analysis. According to…