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DY: Fachverband Dynamik und Statistische Physik

DY 38: Focus Session: Innovations in Research Software Engineering (joint session BP/DY)

DY 38.6: Vortrag

Donnerstag, 20. März 2025, 16:30–16:45, H44

Estimation of kinetic rates by constrained optimization — •Federico Marotta¹, Maria Zimmermann-Kogadeeva¹, Peer Bork¹, Julia Mahamid¹, and Sophia Rudorf² — ¹European Molecular Biology Laboratory — ²Leibniz Universität Hannover

Biological systems often rely on molecular motors to perform useful work. The kinetics of the reactions in a motor’s cycle can be easily investigated in vitro or in model organisms, but it is difficult to generalize them to a different system. We present a method to estimate the transition kinetics in an uncharacterized system, where minimal data are available, by leveraging a reference system where the kinetics have been elucidated. The motor’s activity is represented as a continuous-time Markov chain, characterized by an infinitesimal generator matrix Q whose entries are functions of the transition rates of the cycle (the vector ω) and possibly of the concentrations of external molecules. In the uncharacterized system, the available data induce a constraint on the admissible rates. By employing an extremum principle, we estimate the rates ω_unc that minimize the kinetic distance with respect to the reference rates ω_ref while respecting such constraint. As an application of this strategy, we describe a model of the translation elongation cycle, where reference data are available for E. coli in vitro, and estimate the rates either in vivo or in a different organism, under constraints on the total elongation time or the steady-state occupancies, respectively.

Keywords: ribosome; optimization; markov chain