Free Energy and Entropy Changes: From Molecular Dynamics Simulations to the Developing Theories of Small Systems

Dear Colleagues

Non-equilibrium systems, natural, biological or man-made, pose new challenges to the development of a general theory, capable of predicting the main macroscopic behaviors from the microscopic dynamics. Nevertheless, recently, important general results have been obtained, pushing the range of applicability of concepts of standard thermodynamics into the realm of out-of-equilibrium phenomena.

For instance, one of the central problems in molecular biology is the estimation of the affinity of macromolecules forming macromolecular complexes as well as affinities of small molecules (possible inhibitors) towards macromolecules (proteins or nucleic acids). The latter process is especially important because of its possible practical applications in the drug design process. These mechanisms depend on a delicate balance between enthalpy change, which usually favors the association process, and entropy change, which usually opposes the complexation. Estimation of configurational entropy change of solute and solvent is therefore a particularly challenging and important task.

On the theoretical side, one of the most relevant results in the theory of non-equilibrium systems is the Jarzynski equality, relating the statistics of the exponential of the mechanical work done by external agents and the free energy difference between initial and final equilibrium states. Although the derivations of the Jarzynski equality seem to be quite general, the definitions of the quantities appearing in it, the work in particular, and the interpretation of certain experiments are still at the core of an intense debate.  As a matter of fact, the Jarzynski equality falls within the set of theories meant to describe small, strongly coupled, and long ranged interacting systems. This is a wide open although long-established field, of particular interest in nanotechnology, and well beyond.

This Special Issue serves as a platform for presentation of results in the wide context of non-equilibrium systems, with specific focus on new and improved techniques developed for estimation of free energy changes in macromolecular systems, or more in general on the study of the fluctuations of thermodynamics quantities such as heat, work or entropy production in different systems.  Original research papers, reviews/perspectives and short communications covering theory and applications are welcome.

Dr. Alessandro Sarracino
Prof. Dr. Owen Jepps
Dr. Maciej Maciejczyk
Guest Editors

 

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