相关论文: Glucans monomer-exchange dynamics as an open chemi…
All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory which accounts for interactions between chemical species within a…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
Chemical reaction networks with generalized mass-action kinetics lead to power-law dynamical systems. As a simple example, we consider the Lotka reactions with two chemical species and arbitrary power-law kinetics. We study existence,…
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…
Reaction-diffusion (RD) mechanisms in chemical and biological systems can yield a variety of patterns that may be functionally important. We show that diffusive coupling through the inactivating component in a generic model of coupled…
We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their…
We propose a coarse-grained model for polymer chains and polymer networks based on the meso-scale dynamics. The model takes the internal degrees of freedom of the constituent polymer chains into account using memory functions and colored…
Motivated by observations of the dynamics of {\it Myxococcus xanthus}, we present a self-interacting random walk model that describes the competition between chemokinesis and chemotaxis. Cells are constrained to move in one dimension, but…
Virtually every biological function emerges through the organization of molecules in time and space. Consequently, a major challenge in statistical physics is to uncover the universal principles governing macromolecular self-organization…
Within a mathematical model, the process of interaction of the metabolic processes such as glycolysis and gluconeogenesis is studied. As a result of the running of two opposite processes in a cell, the conditions for their interaction and…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
We explore the possibility to interpret as a 'gas' the dynamical self-organized scale-free network recently introduced by Kim et al (2005). The role of 'momentum' of individual nodes is played by the degree of the node, the 'configuration…
The functions of many networked systems in physics, biology or engineering rely on a coordinated or synchronized dynamics of its constituents. In power grids for example, all generators must synchronize and run at the same frequency and…
Using molecular simulations and theory, we develop an explicit mapping of the contribution of molecular relaxation modes in glassy thermosets to the shear modulus, where the relaxations were tuned by altering the polarity of side groups.…
Stochastic reaction-diffusion processes may be presented in terms of integrable quantum chains and can be used to describe various biological and chemical systems. Exploiting the integrability of the models one finds in some cases good…
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,…
We present a Generalized Langevin Equation for the dynamics of interacting semiflexible polymer chains, undergoing slow cooperative dynamics. The calculated Gaussian intermolecular center-of-mass and monomer potentials, wich enter the GLE,…
We report results of molecular-dynamics simulations for a glassy polymer melt consisting of short, linear bead-spring chains. It was shown in previous work that this onset of the glassy slowing down is compatible with the predictions of the…
We review the physical properties of macromolecular networks, consisting of semiflexible polymers such as actin. We start by giving a theoretical analysis of the conformational statistics and mechanical response of single filaments.…
We identify an intriguing feature of the electron-vibrational dynamics of molecular systems via a computational examination of \emph{trans}-polyacetylene oligomers. Here, via the vibronic interactions, the decay of an electron in the…