Thermodynamics and kinetics for Biology

Transcription bursting and stochastics

From thermodynamics through kinetics and non equilibrium thermodynamics to control analysis

Chapter on non equilibrium thermodynamics. The chapter discusses both phenomenological and mechanistic non equilibrium thermodynamics. The phenomenological part has as asset compared to earlier treatments that it also considers the phenomenological stoichiometry as a parameter that may be adjusted by systems to attain optimal performance. In the mechanistic part, this feature of variable stoichiometry and 'slips' as well as redistribution of fluxes over parallel branches of metabolism is discussed. ...

A chapter on generalized thermodynamics. The chapter is not specifically about biology although it uses many examples in biology due to the richness of the topic. It deals with the first and second law of thermodynamics, catalysts, and engines. This includes heat engines, heat pumps, and protonmotive ATP synthase.

The first sheet in this excel file is a Table that collects the standard Gibbs energies of formation (from the elements) of a large number of chemical species that are relevant for metabolism. It obtained these from a substantial number of sources, including Thauer et al and Alberty, as indicated at the bottom of the first sheet of the Table. Following Alberty, (2006) the Table also computes the further transformed Gibbs energies of formation, under the standard conditions also used by Alberty, ...

Westerhoff H.V. and Van Dam K. (1987) Thermodynamics and control of biological free-energy transduction, Elsevier, Amsterdam ISBN: 0-444-80783-7 (U.S.)

This monograph gives the basis of both non equilibrium thermodynamics and metabolic control analysis in biology. It is rife with examples from bioenergetics.

It is also a compilation of mathematical equations and text and hence serves as a data file for mathematical biology and biological modelling

working document 31 January 2022 Context is the equilibrium constants measurement standardization

In this short book written by Hans V. Westerhoff, it is argued that scientific rationality as further developed in systems biology should be used to tackle the complex problems of society. This is promoted as one way to battle the disinformation strategies followed by a great many political leaders with the aim of staying in power through populism.

To be cited as: Westerhoff, H.V., (2020) Trumping the Trumps: Addressing complexities through biological rationality, SysBA press, Amsterdam.

Work document version 31 January 2020