Related papers: Microscopic Models for Chemical Thermodynamics
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
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…
In the first part of this paper we give a short review of the hierarchy of stochastic models, related to physical chemistry. In the basement of this hierarchy there are two models --- stochastic chemical kinetics and the Kac model for…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
Abstact: We introduce new models of energy redistribution in stochastic chemical kinetics with several molecule types and energy parameters. The main results concern the situations when there are product form measures. Using a probabilistic…
In this paper we consider the stochastic dynamics of a finite system of particles in a finite volume (Kac-like particle system) which annihilate with probability $\alpha \in (0,1)$ or collide elastically with probability $1-\alpha$. We…
Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…
We present the energetic aspect of open systems which may exchange particles with their environments. Our attention shall be paid to the scale that the motion of the particles is described by the classical Langevin dynamics. Along a…
This article analyzes the formulation of space-time continuous hyperbolic hydrodynamic models for systems of interacting particles moving on a lattice, by connecting their local stochastic lattice dynamics to the formulation of an…
We present a mechanism for thermalizing a moving particle by microscopic deterministic scattering. As an example, we consider the periodic Lorentz gas. We modify the collision rules by including energy transfer between particle and…
We formulate thermodynamics of economic systems in terms of an arbitrary probability distribution for a conserved economic quantity. As in statistical physics, thermodynamic macroeconomic variables emerge as the mean value of microeconomic…
We introduce mesoscopic and macroscopic model equations of chemotaxis with anomalous subdiffusion for modelling chemically directed transport of biological organisms in changing chemical environments with diffusion hindered by traps or…
Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics like work, heat and entropy production to the level of individual trajectories of well-defined…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
Concepts of everyday use like energy, heat, and temperature have acquired a precise meaning after the development of thermodynamics. Thermodynamics provides the basis for understanding how heat and work are related and with the general…
Chemical waves constitute a known class of dissipative structures emerging in reaction-diffusion systems. They play a crucial role in biology, spreading information rapidly to synchronize and coordinate biological events. We develop a…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
The thermodynamics with medium effects expressed by the dispersion relation of the temperature and density dependent particle mass is studied. Many previous treatments have been reviewed. A new thermodynamical treatment based on the…
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…
In this paper we study a model of randomly colliding particles interacting with a thermal bath. Collisions between particles are modeled via the Kac master equation while the thermostat is seen as an infinite gas at thermal equilibrium at…