Optimal Control of the F₁-ATPase Molecular Motor

Abstract

F1-ATPase is a rotary molecular motor that in vivo is subject to strong nonequilibrium driving forces. There is great interest in understanding the operational principles governing its high efficiency of free-energy transduction. Here we use a near-equilibrium framework to design a nontrivial control protocol to minimize dissipation in rotating F1 to synthesize adenosine triphosphate. We find that the designed protocol requires much less work than a naive (constant-velocity) protocol across a wide range of protocol durations. Our analysis points to a possible mechanism for energetically efficient driving of F1 in vivo and provides insight into free-energy transduction for a broader class of biomolecular and synthetic machines.

Limits on the Precision of Catenane Molecular Motors: Insights from Thermodynamics and Molecular Dynamics Simulations

“…Here, we demonstrate how a high-dimensional particle-based model of an artificial molecular motor can be used in conjunction with molecular dynamics simulations to generate a direct comparison against the TUR and explain how it can be employed in studying molecular motors. This effort complements current research on the optimal control of and performance trade-offs for molecular motors. − …”

Optimal control in stochastic thermodynamics

“…This system represents a simplified model of hairpin pulling experiments and Landauer erasure [50,51,77]. The two-state nature of the system is also representative of activated processes such as chemical reactions, and the barrier crossing mimics the main features of experiments performed on ATP synthase, whose dynamics can be approximated as a series of barrier crossings [22,69,109]. This model is also typical of steered molecular-dynamics simulations, which use a time-dependent quadratic potential to drive reactions [110][111][112].…”

Waiting Time Distributions in Hybrid Models of Motor–Bead Assays: A Concept and Tool for Inference

“…Discrete Markov network models emphasize the changes in the biochemical configuration of the motor protein [11][12][13][14][15], whereas continuous models based on an overdamped Langevin equation focus on the observable diffusive dynamics of the bead [16][17][18][19]. Hybrid models include the dynamics of both assay constituents by coupling the discrete dynamics of the motor with the continuous dynamics of the bead via an effective potential [20][21][22][23][24][25][26][27].…”