Sterically driven current reversal in a molecular motor model

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(33)

Опубликована: Авг. 7, 2023

Simulations can help unravel the complicated ways in which molecular structure determines function. Here, we use simulations to show how slight alterations of a motor's cause typical dynamical behavior reverse directions. Inspired by autonomous synthetic catenane motors, study dynamics minimal motor model, consisting shuttling ring that moves along track containing interspersed binding sites and catalytic sites. The attract while speed up reaction between species, be thought as fuel waste. When waste are held nonequilibrium steady-state concentrations, free energy from drives directed motion track. Using this model dynamics, ring's direction reversed simply adjusting spacing on We present steric mechanism behind current reversal, supported kinetic measurements simulations. These results demonstrate simulation guide future development artificial motors.

Язык: Английский

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A [3]-catenane non-autonomous molecular motor model: Geometric phase, no-pumping theorem, and energy transduction

The Journal of Chemical Physics, Год журнала: 2023, Номер 158(22)

Опубликована: Июнь 13, 2023

We study a model of synthetic molecular motor-a [3]-catenane consisting two small macrocycles mechanically interlocked with bigger one-subjected to time-dependent driving using stochastic thermodynamics. The presents nontrivial features due the interacting but is simple enough be treated analytically in limiting regimes. Among results obtained, we find mapping into an equivalent [2]-catenane that reveals implications no-pumping theorem stating generate net motion macrocycles, both energies and barriers need change. In adiabatic limit (slow driving), fully characterize motor's dynamics show expressed as surface integral parameter space, which corrects previous erroneous results. also analyze performance motor subjected step-wise protocols absence presence applied load. Optimization strategies for generating large currents maximizing free energy transduction are proposed. This provides interesting clues working principles non-autonomous motors their optimization.

Язык: Английский

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On the Emergence of Autonomous Chemical Systems through Dissipation Kinetics

Life, Год журнала: 2023, Номер 13(11), С. 2171 - 2171

Опубликована: Ноя. 6, 2023

This work addresses the kinetic requirements for compensating entropic cost of self-organization and natural selection, thereby revealing a fundamental principle in biology. Metabolic evolutionary features life cannot therefore be separated from an origin perspective. Growth, self-organization, evolution dissipation processes need to metabolically coupled fueled by low-entropy energy harvested environment. The process requires reproduction cycle involving out-of-equilibrium intermediates barriers that prevent reproductive proceeding reverse. Model analysis leads unexpectedly simple relationship system should fed with potential exceeding value related ratio generation time transition state lifetime, enabling mimicking selection take place. Reproducing life’s main features, particular its Darwinian behavior, satisfying constraints relate energy. Irreversible reaction cycles made only unstable entities reproduce some these essential offering physical/chemical basis possible emergence autonomy. Such Emerging Autonomous Systems (EASs) are found capable maintaining reproducing their kind through transmission stable state, what could deemed epigenetic process.

Язык: Английский

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A Minimalistic Covalent Bond‐Forming Chemical Reaction Cycle that Consumes Adenosine Diphosphate

Angewandte Chemie, Год журнала: 2024, Номер 136(22)

Опубликована: Март 27, 2024

Abstract The development of synthetic active matter requires the ability to design materials capable harnessing energy from a source carry out work. Nature achieves this using chemical reaction cycles in which released an exergonic is used drive biochemical processes. Although many chemically fuelled that control transient responses, such as self‐assembly, have been reported, generally high complexity reported systems hampers full understanding how available actually exploited by these systems. This lack limiting factor matter. Here, we report minimalistic responsive cycle adenosine diphosphate (ADP) triggers formation catalyst for its own hydrolysis. establishes interdependence between concentrations network components resulting catalyst. sufficiently simple all kinetic and thermodynamic parameters governing behaviour can be characterised, allowing models built simulate progress reactions within network. While current does not enable ADP‐hydrolysis populate non‐equilibrium composition, provide insight into way dissipates energy. Furthermore, essential principles are revealed constructing driven systems, composition away equilibrium through consumption

Язык: Английский

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Power Strokes in Molecular Motors: Predictive, Irrelevant, or Somewhere in Between?

Journal of the American Chemical Society, Год журнала: 2024, Номер unknown

Опубликована: Дек. 20, 2024

For several decades, molecular motor directionality has been rationalized in terms of the free energy conformations visited before and after takes a step, so-called power stroke mechanism with analogues macroscopic engines. Despite theoretical experimental demonstrations its flaws, language is quite ingrained, some communities still value intuition. By building catalysis-driven into simulated numerical experiments, we here systematically report on how responds when modified accordingly to We confirm that generally does not predict directionality. Nevertheless, simulations illustrate relative stability should be included as potential design element adjust directional bias. Though strokes are formally unimportant for determining directionality, show practical attempts alter have side effects can fact The change bias align what intuition would suggested, offering explanation why flawed retain apparent utility engineering specific systems.

Язык: Английский

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