Related papers: Chemical Thermodynamics for Growing Systems
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…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
Living systems are maintained out-of-equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break equilibrium symmetries and originate from the expansion of the accessible chemical space due…
We investigate the thermodynamic implications of two control mechanisms of open chemical reaction networks. The first controls the concentrations of the species that are exchanged with the surroundings, while the other controls the exchange…
Complexity Theory is highly interdisciplinary, therefore any regularities must hold on all levels of organization, independent on the nature of the system. An open question in science is how complex systems self-organize to produce emergent…
Cell growth, division and death are defining features of biological tissues that contribute to morphogenesis. In hydrodynamic descriptions of cohesive tissues, their occurrence implies a non-zero rate of variation of cell density. We show…
The population dynamics and stability of ecosystems of interacting species is studied from the perspective of non-equilibrium thermodynamics by assuming that species, through their biotic and abiotic interactions, are units of entropy…
In this work, we study the crystalline nuclei growth in glassy systems focusing primarily on the early stages of the process, at which the size of a growing nucleus is still comparable with the critical size. On the basis of molecular…
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…
Previous studies have primarily focused on the nonequilibrium thermodynamics of chemical reaction networks (CRNs) occurring in closed systems. In contrast, CRNs in open systems exhibit much richer nonequilibrium phenomena due to sustained…
We establish a Hessian geometric structure in chemical thermodynamics which describes chemical reaction networks (CRNs) with equilibrium states. In our setup, the ideal gas assumption and mass action kinetics are not required. The existence…
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…
Temperature gradients represent energy sources that can be harvested to generate steady reaction or transport fluxes. Technological developments could lead to the transfer of free energy from heat sources and sinks to chemical systems for…
The catalytic reaction system (CRS) formalism by Hordijk and Steel is a versatile method to model autocatalytic biochemical reaction networks. It is particularly suited, and has been widely used, to study self-sustainment and…
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…
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 living organism is considered as an open system, whereas Prigogine's approach to the thermodynamics of such systems is used. The approach allows one to formulate the law of individual growth and development (ontogenesis) of the living…
We develop a framework describing the dynamics and thermodynamics of open non-ideal reaction-diffusion systems, which embodies Flory-Huggins theories of mixtures and chemical reaction network theories. Our theory elucidates the mechanisms…
Small thermodynamic systems exhibit peculiar behavior different from that observed in long-scale systems. Non-equilibrium processes taking place in those systems are strongly influenced by the presence of fluctuations which can be large.…