Open Conference Systems, StatPhys 27 Main Conference

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Stochastic Thermodynamics of Ribosome: A network theoretic perspective
Annwesha Dutta, Gunter M. Schütz, Debashish Chowdhury

##manager.scheduler.building##: Edificio Santa Maria
##manager.scheduler.room##: Auditorio San Agustin
Date: 2019-07-08 11:45 AM – 03:30 PM
Last modified: 2019-06-15

Abstract


The ribosome is a complex molecular machine that synthesizes protein by decoding the genetic information present in the messenger RNA. Due to its complexity, the chemical processes and mechanochemical couplings that are involved in the translations are not well understood. To address this problem, we develop a stochastic thermodynamic description by constructing a continuous time Markov network of the different conformational states of the ribosome at every codon step, based on single-molecule experimental observations. We describe the ribosomal system as coupled to a heat reservoir, a work reservoir, and particle reservoirs of the different chemical species involved in the process. We then obtain the exact steady-state probabilities from graph-theoretical considerations. The heat dissipated by the ribosome while converting chemical energy into mechanical energy is computed in terms of its experimentally observed transition rates. Further, we obtain the trajectory of the ribosome on the mRNA track by performing Monte Carlo (MC) simulations of the network. We then applied the steady state fluctuation theorem to estimate the effective force acting on the ribosome by investigating the fluctuations in the trajectory. These results gives us a quantitative picture of the interesting thermodynamic quantities for translation by ribosome.