Aalto University, P.O. Box 11000, FI-00076 Aalto www.aalto.fi Author Aki Kutvonen Name of the doctoral dissertation Non-Markovian environments and information exchange in stochastic thermodynamics Publisher School of Science Unit Department of Applied Physics Series Aalto University publication series DOCTORAL DISSERTATIONS 15/2016 Field of research Theoretical and Computational Physics Manuscr...

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All proteins are capable of recognizing and binding specific molecules such as other proteins, cofactors, prosthetic groups or drugs. Efforts to understand the mechanisms controlling selective binding were initially prompted by the realization that recognition and binding are universal features of all biochemical processes. These efforts have intensified with the awareness that knowledge-based ...

Thermodynamics is a physical branch of science that governs the thermal behavior of dynamical systems from those as simple as refrigerators to those as complex as our expanding universe. The laws of thermodynamics involving conservation of energy and nonconservation of entropy are, without a doubt, two of the most useful and general laws in all sciences. The first law of thermodynamics, accordi...

The structure of a protein-protein interaction, its affinity and thermodynamic characteristics depict a 'frozen' state of a complex. This picture ignores the kinetic nature of complex formation and dissociation, which are of major biological and biophysical interest. This review highlights recent advances in deciphering the kinetic pathway of protein-protein complexation, the nature of the enco...

Cooperative interactions mediate information transfer between structural domains of a protein molecule and are major determinants of protein function and modulation. The prevalent theories to understand the thermodynamic origins of cooperativity have been developed to reproduce the complex behavior of a global thermodynamic observable such as ligand binding or enzyme activity. However, in most ...

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters, e.g. the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows, however, that the evolution of the statistical measures, e.g. Gibbs free energy, h...

Life on Earth is capable of growing from temperatures well below freezing to above the boiling point of water, with some organisms preferring cooler and others hotter conditions. The growth rate of each organism ultimately depends on its intracellular chemical reactions. Here we show that a thermodynamic model based on a single, rate-limiting, enzyme-catalysed reaction accurately describes popu...