The Thermodynamic Machinery of LifeSpringer Science & Business Media, 9 lip 2006 - 431 Thermodynamics was created in the ?rst half of the 19th century as a theory designed to explain the functioning of heat engines converting heat into mechanical work. In the course of time, while the scope of research in this ?eld was being extended to a wider and wider class of energy transformations, thermodynamics came to be considered as a general theory of machines identi?ed with energy transducers. Imp- tant progress in biochemistry in the ?rst half of the 20th century, and in molecular biology in the second half, made it possible to think of treating even living organisms as machines, at least on the subcellular level. However, success in applying thermodynamics to elucidate the phenomenon of life has been rather mitigated. Two reasons seem to be responsible for this unsatisfactory s- uation. Nineteenth century thermodynamics dealt only with simple (homogeneous) systems in complete equilibrium. Although during the 20th century a nonequilibrium thermodynamics was developed, sta- ing with the Onsager theory of linear response and ending with the Prigogine nonlinear theory of dissipative structures, these theories still concern the originally homogeneous systems. Because living organisms are complex systems with a historically frozen spatial and functional structure, a thermodynamics of both nonequilibrium and complex s- tems is needed for their description. The ?rst goal of the present book is to formulate the foundations of such a thermodynamics. |
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actin actin filament active amino acids Appendix assumed atoms bacteria basis of pdb binding Biol biological Biophys carbon catalytic cell channels Chap chemical reactions complex component concentration conformational substates conformational transitions considered const corresponding covalent bonds cycle cytochrome degrees of freedom denotes density determined diffusion dissipation domain dynamical variables electron ensemble entropy enzyme equation flux free energy function H H H hydrogen bonds hydrolysis initial ions kinase kinetic Kurzyński macroscopic mean first-passage mechanism membrane microtubules molecular molecules monosaccharides motion motor myosin myosin head organisms oxygen pdb entry phase phosphorylation physical potential Prigogine program Rasmol protein proton pumps purple bacteria Rasmol rate constants reaction rate reaction rate constants receptors relaxation rotation Sect spatial statistical statistical ensemble stochastic subsystems subunit temperature theory thermodynamic equilibrium thermodynamic forces thermodynamic variables tion trajectories transduction transfer vibrational