The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism...

1. Integrating Epistemology of Thermodynamics and of Biological Evolutionary Systems 1.1 Entropy and Biological Evolution 1.2 Biosphere, Entropy, and Dissipative Structures 2. Thermodynamics of Ecosystems and of Biological Evolution 2.1 The Time Paradox: Towards an Evolutionary Thermodynamics 2.2 Non-equilibrium Thermodynamics 3. Towards an Evolutionary Physics 3.1 A New Concept: Ecodynamics 4....

Fundamental relationships between the thermodynamics and kinetics of protein folding were investigated using chain models of natural proteins with diverse folding rates by extensive comparisons between the distribution of conformations in thermodynamic equilibrium and the distribution of conformations sampled along folding trajectories. Consistent with theory and single-molecule experiment, dur...

The protein folding problem can be viewed as three different problems: defining the thermodynamic folding code; devising a good computational structure prediction algorithm; and answering Levinthal's question regarding the kinetic mechanism of how proteins can fold so quickly. Once regarded as a grand challenge, protein folding has seen much progress in recent years. Folding codes are now being...

In the present study we characterize the thermodynamics of binding of histamine to recombinant histamine-binding protein (rRaHBP2), a member of the lipocalin family isolated from the brown-ear tick Rhipicephalus appendiculatus. The binding pocket of this protein contains a number of charged residues, consistent with histamine binding, and is thus a typical example of a "hydrophilic" binder. In ...

We discuss a phenomenon regarding water that was until recently subject of scientific interest: i.e., the dynamical crossover, from fragile to strong glass forming material, for both bulk and protein hydration water. Such crossover is characterized by temperature TL in which significant changes like decoupling (or violation Stokes-Einstein relation) homologous transport parameters, e.g., densit...

Finite-time thermodynamics is the extension of traditional reversible thermodynamics to include the extra requirement that the process in question goes to completion in a specified finite length of time. As such it is by definition a branch of irreversible thermodynamics, but unlike most other versions of irreversible thermodynamics, finite-time thermodynamics does not require or assume any kno...

Over the past two decades there has been an increase in appreciation for the role of surface charge-charge interactions in protein folding and stability. The perception shifted from the belief that charge-charge interactions are not important for protein folding and stability to the near quantitative understanding of how these interactions shape the folding energy landscape. This led to the abi...