Energy flows in biomolecular and synthetic machines

• Applicant: Dr. Deepak Gupta, Ph.D.
• Subject Area: Statistical Physics, Nonlinear Dynamics, Complex Systems, Soft and Fluid Matter, Biological Physics
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 522145273

This project explores the design and operational principles of biomolecular and synthetic machines. We aim to develop both analytical and numerical computational schemes to estimate different energy fluxes responsible for these machines’ steady-state operations and relaxation mechanisms. The overall objective of this project is divided into two tasks. Task 1: Computation of thermodynamic observables, such as heat, work, efficiency, and entropy production of biomolecular and synthetic machines. Task 2: Relaxation of a system under restart protocol in Brownian particle systems in one and two dimensions. Task 1 consists of two work packages A and B, and task 2 has one work package C. Work package A focuses on designing a model for a biomolecular machine—the FoF1-ATP synthase. Herein, we aim to investigate the role of different chemical drives on its steady-state, input and output powers, information exchanges between its subunits, and performance. This project goes beyond previous research in two aspects: 1) We model FoF1 with its accurate potential energy profiles. 2) This machine will be investigated in a far from equilibrium state (in stark contrast to earlier work of the applicant). The project will uncover how intricate connections between subunits and their underlying landscapes affect the energy conversion mechanism of this machine and will hint at the possible driving control protocol for the F1 crankshaft to synthesize ATP in vivo. Further, researchers are interested in understanding the nonequilibrium thermodynamic properties of synthetic machines. Therefore, in work package B, we investigate a synthetic machine—the Brownian gyrator of one and two particles, in the presence of colored noise. We aim to compute the exact finite-time fluctuations of its thermodynamic observables (heat, work, efficiency, stochastic area, …) by extending the Green’s function method to a finite-time regime. We emphasize that such an extension has never been explored. Another open problem that we aim to solve is to develop a connection between the path-integral and the Green’s function methods. Finally, work package C discusses the relaxation of the Brownian particle systems (motivated from above machines) to their stationary state. Here, we aim to devise a technique by which a machine can relax faster to its stationary state with a low dissipation cost using the restart protocol.

• DFG Programme: WBP Position