Stochastic (thermo)dynamics of molecular coupled processes
by Michalis Chatzittofi
Date of Examination:2024-10-23
Date of issue:2024-12-18
Advisor:Prof. Dr. Ramin Golestanian
Referee:Prof. Dr. Ramin Golestanian
Referee:Prof. Dr. Marcus Mueller
Referee:Prof. Dr. Helmut Grubmüller
Referee:Prof. Dr. Stefan Klumpp
Referee:Dr. Aljaz Godec
Persistent Address:
http://dx.doi.org/10.53846/goediss-10903
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Abstract
English
Out of equilibrium biological processes are the key for life. From large animals to the smallest proteins, life is sustained by a continuous throughput of free energy. This happens through the exchange of some form of energy to another. Interestingly, the properties of a broad class of these different systems can be described by simple models in the language of non-equilibrium statistical physics. In this thesis, we focus on the smallest existing machines; these are enzymes, molecular motors and microswimmers, which can either be biological or synthetic. At the simplest level these machines convert chemical energy into mechanical work. Our goal is to provide a minimal description of molecular processes and to study the impact of the mechanical degrees of freedom on the chemical dynamics. We consider both single particle as well as multiple interacting processes. Our study leads to some new results including mechanisms for the coordination of stochastic dynamics, simple models for designing bio-inspired systems, inference protocols of non-equilibrium driving forces and the importance of external forces in the internal dynamics of nano-machines. We begin with a short introduction to provide some background information from statistical and biological physics including some examples and models from the literature. We then set out on our journey and first examine the collective dynamics described by thermally activated identical coupled phase oscillators and establish a new model of synchronization. This becomes possible via a mobility matrix that couples the chemical forces of the different processes, referred as the dissipative coupling. Following this, we study the effect of the dissipative coupling in the case of non-identical processes. Strikingly, this leads to topological phase locking and boosted stochastic dynamics. Using the same principles, we consider an out-of-equilibrium process of an enzyme mechanically coupled to a passive molecule, and study the steady-state dynamics of the whole system and how the non-equilibrium conformational changes affect the molecule state. We demonstrate that the coupling in this case is controlled by the geometry of the enzyme which promotes the thermodynamically unfavorable state of the passive molecule to become favorable. These lead to three golden rules for designing an enzyme. To model relevant biological processes we need to respect thermodynamics. To this end, we utilize tools from the literature of stochastic thermodynamics and suggest a simple way of inferring correlations in non-equilibrium coupled systems. This is achieved by applying thermodynamic uncertainty relations to problems of many coupled processes. We then provide a framework to describe the total entropy production rate of stochastic microswimmers and we propose an experimental protocol which allows for the exact inference of the chemical driving force that generates the active-swimming of the swimmer. Finally, focusing on the individual processes, we construct a nonlinear response theory for molecular machines. We find that their activity changes in a non-monotonic way when subjected to external forces. We conclude with a summary, discussion and future perspectives.
Keywords: non-equilibrium statistical physics; active matter; stochastic thermodynamics; molecular oscillators; coupled processes; microswimmers
