Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws

In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated to nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation $a + b = s^Y$ between the number of fundamental affinities $a$, that of broken conservation laws $b$ and the number of chemostats $s^Y$. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction and of thermodynamic constraints for network reconstruction.Comment: 18 page

Modeling the interactions of biomatter and biofluid

The internal motions of biomatter immersed in biofluid are investigated. The interactions between the fragments of biomatter and its surrounding biofluid are modeled using field theory. In the model, the biomatter is coupled to the gauge field representing the biofluid. It is shown that at non-relativistic limit various equation of motions, from the well-known Sine-Gordon equation to the simultaneous nonlinear equations, can be reproduced within a single framework.Comment: 10 pages, 3 figure

Ab initio study of alanine polypeptide chains twisting

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles Phi and Psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.Comment: 24 pages, 10 figure

Scenarios for zinc and copper: a strong sustainability and weak sustainability approach

VakpublicatieInstitute of Environmental Science

Haalbaarheidsstudie naar indicatoren voor ketenbeheer in de Milieubalans : voorbeeldstudie voor cadmium in Nederland 1985-1990

VakpublicatieInstitute of Environmental Science

Integraal ketenbeheer in de provincie Limburg: bouwmaterialen, automobiliteit, champignons en PVC

VakpublicatieInstitute of Environmental Science