相关论文: Nonlinear Stochastic Dynamics of Complex Systems, …
We briefly review the recently developed, Markov process based isothermal chemical thermodynamics for nonlinear, driven mesoscopic kinetic systems. Both the instantaneous Shannon entropy {\boldmath $S[p_{\alpha}(t)]$} and relative entropy…
From a mathematical model that describes a complex chemical kinetic system of $N$ species and $M$ elementrary reactions in a rapidly stirred vessel of size $V$ as a Markov process, we show that a macroscopic chemical thermodynamics emerges…
This paper studies a mathematical formalism of nonequilibrium thermodynamics for chemical reaction models with $N$ species, $M$ reactions, and general rate law. We establish a mathematical basis for J. W. Gibbs' macroscopic chemical…
Multistability of mesoscopic, driven biochemical reaction systems has implications to a wide range of cellular processes. Using several simple models, we show that one class of bistable chemical systems has a deterministic counterpart in…
We study long-range interacting systems driven by external stochastic forces that act collectively on all the particles constituting the system. Such a scenario is frequently encountered in the context of plasmas, self-gravitating systems,…
The consistency across scales of a recently developed mathematical thermodynamic structure, between a continuous stochastic nonlinear dynamical system (diffusion process with Langevin or Fokker-Planck equations) and its emergent discrete,…
We give an introduction to phase transitions in the steady states of systems that evolve stochastically with equilibrium and nonequilibrium dynamics, the latter defined as those that do not possess a time-reversal symmetry. We try as much…
The main subject of the thesis is the study of stationary nonequilibrium states trough the use of microscopic stochastic models that encode the physical interaction in the rules of Markovian dynamics for particles configurations. These…
Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport,…
Stochastic thermodynamics provides a framework for describing small systems like colloids or biomolecules driven out of equilibrium but still in contact with a heat bath. Both, a first-law like energy balance involving exchanged heat and…
To describe the nonequilibrium states of a system we introduce a new thermodynamic parameter - the lifetime of a system. The statistical distributions which can be obtained out of the mesoscopic description characterizing the behaviour of a…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
The general theory of a complex system of nonlinear chemical reactions is a primary language of chemistry that includes chemical engineering and cellular biochemistry. Its significance as an analytical framework, however, has not been fully…
A rigorous mathematical framework for analyzing the chemical master equation (CME) with bistability, based on the theory of large deviation, is proposed. Using a simple phosphorylation-dephosphorylation cycle with feedback as an example, we…
We study long-range interacting systems perturbed by external stochastic forces. Unlike the case of short-range systems, where stochastic forces usually act locally on each particle, here we consider perturbations by external stochastic…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
The developing field of stochastic thermodynamics extends concepts of macroscopic thermodynamics such as entropy production and work to the microscopic level of individual trajectories taken by a system through phase space. The scheme…
A Markov evolution of a system of point particles in $\mathbb{R}^d$ is described at micro-and mesoscopic levels. The particles reproduce themselves at distant points (dispersal) and die, independently and under the influence of each other…
We develop the stochastic approach to thermodynamics based on the stochastic dynamics, which can be discrete (master equation) continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of…