An introduction to ratchets in chemistry and biology

Lau, Bryan; Kedem, O.; Schwabacher, James C.; Kwasnieski, Daniel; Weiss, Emily A.

doi:10.1039/c7mh00062f

Cited by 73 publications

(47 citation statements)

References 87 publications

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“…In the simplest incarnation of Feynman's ratchet, the height of a saw-tooth barrier fluctuates (34,35), giving rise to directed motion if the saw-tooth potential is asymmetric. This simple model had captured the imagination of scientists working in a very wide range of disciplines from quantum dots (36) to the ribosome (37) and synthetic molecular machines (38,39) and has led to many experimental tests in numerous different contexts (40)(41)(42). A key idea in these systems with significant thermal noise is that input energy can be used to prevent backward (undesired) motion, leaving behind the desired forward motion.…”

Section: Tomar Portugal 2004mentioning

confidence: 99%

Stochastically pumped adaptation and directional motion of molecular machines

Astumian

2018

Proc. Natl. Acad. Sci. U.S.A.

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Recent developments in synthetic molecular motors and pumps have sprung from a remarkable confluence of experiment and theory. Synthetic accomplishments have facilitated the ability to design and create molecules, many of them featuring mechanically bonded components, to carry out specific functions in their environment-walking along a polymeric track, unidirectional circling of one ring about another, synthesizing stereoisomers according to an external protocol, or pumping rings onto a long rod-like molecule to form and maintain high-energy, complex, nonequilibrium structures from simpler antecedents. Progress in the theory of nanoscale stochastic thermodynamics, specifically the generalization and extension of the principle of microscopic reversibility to the single-molecule regime, has enhanced the understanding of the design requirements for achieving strong unidirectional motion and high efficiency of these synthetic molecular machines for harnessing energy from external fluctuations to carry out mechanical and/or chemical functions in their environment. A key insight is that the interaction between the fluctuations and the transition state energies plays a central role in determining the steady-state concentrations. Kinetic asymmetry, a requirement for stochastic adaptation, occurs when there is an imbalance in the effect of the fluctuations on the forward and reverse rate constants. Because of strong viscosity, the motions of the machine can be viewed as mechanical equilibrium processes where mechanical resonances are simply impossible but where the probability distributions for the state occupancies and trajectories are very different from those that would be expected at thermodynamic equilibrium. molecular machine | stochastic pumping | kinetic asymmetry The molecular machines necessary for life must carry out their function in the fluctuating environment of a biological cell. Nowhere is the dynamic aspect of biology at the molecular level more evident than in the bilayer membrane surrounding most cells and organelles, a small portion of which is shown schematically in Fig. 1. Three transmembrane proteins are included in the depiction: (i) an ion channel that provides a conduit for conduction of ions across the membrane; (ii) a molecule that facilitates the transport of some substance, S, across the membrane; and (iii), an NaATPase that uses energy from ATP hydrolysis to maintain ion gradients across the membrane. The transporter acts as a catalyst to reduce the barrier for transport of S. In and of itself, the transporter cannot drive the substance S from low to high chemical potential. The transporter, however, is near a possible source of energy, the ion channel. The ion channel provides a path for conduction of ions from high to low electrochemical potential, thus dissipating energy. Every time the ion channel opens or closes, the local electric field across the membrane changes, and because the flow of ions down the electrochemical gradient when the channel is open dissipates energy, the resulting ...

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Section: Tomar Portugal 2004mentioning

confidence: 99%

Stochastically pumped adaptation and directional motion of molecular machines

Astumian

2018

Proc. Natl. Acad. Sci. U.S.A.

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“…At the micrometric scale, it describes the mechanism of protrusion elongation (Fig 5b) (45), and at the mesoscopic scale (the aim of this paper), it is used to describe the directional motion of cells by using a ratchetlike microarray (Fig 5c) (29)(30)(31). Interestingly, this framework has also been applied in more complex in vivo systems to describe the mechanism of embryonic development in Drosophila (46,47), among other applications in biology (29,48,49).…”

Section: A Implications Of the Feynman Ratchet In Biophysicsmentioning

confidence: 99%

The Biophysics of Cell Migration: Biasing Cell Motion with Feynman Ratchets

2020

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ABSTRACT The concepts and frameworks of soft matter physics and the laws of thermodynamics can be used to describe relevant developmental, physiologic, and pathologic events in which directed cell migration is involved, such as in cancer. Typically, this directionality has been associated with the presence of soluble long-range gradients of a chemoattractant, synergizing with many other guidance cues to direct the motion of cells. In particular, physical inputs have been shown to strongly influence cell locomotion. However, this type of cue has been less explored despite the importance in biology. In this paper, we describe recent in vitro works at the interface between physics and biology, showing how the motion of cells can be directed by using gradient-free environments with repeated local asymmetries. This rectification of cell migration, from random to directed, is a process reminiscent of the Feynman ratchet; therefore, this framework can be used to explain the mechanism behind directed cell motion.

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“…Increasing attention has been focused on techniques for transporting micrometer-sized particles using asymmetric periodic potential [1,2,3,4,5]. Generally, such transport is called ratchet transport, where an asymmetric ratchet-shaped potential rectifies particle motion, resulting in unidirectional particle motion, even if the particles intrinsically exhibit nondirectional motion.…”

Section: Introductionmentioning

confidence: 99%

“…migrating cells) and passive (nonself-propelled) particles (ex. molecules) [1,2,3,4,5]. Of late, techniques to rectify the motion of self-propelled particles are being developed using static asymmetric potential.…”

Section: Introductionmentioning

confidence: 99%

“…Although the particles themselves do not exhibit ballistic motion, unidirectional motion is extracted through the time-dependency and asymmetricity of the potential. Typical examples for varying the potential have been proposed [1,2,3]; in a flashing ratchet, the asymmetric potential switches between the on/off states, whereas in a rocking ratchet, the asymmetric potential is tilted by an oscillating force. Based on these principals, it has been experimentally demonstrated that passive small particles can be transported.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Collective Ratchet Transport Generated by Particle Crowding under Asymmetric Sawtooth‐Shaped Static Potential

Hayakawa

Kishino

Takinoue

2020

Advanced Intelligent Systems

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AbstructIn this study, we describe the ratchet transport of particles under static asymmetric potential with periodicity. Ratchet transport has garnered considerable attention due to its potential for developing smart transport techniques on a micrometer scale. In previous studies, either particle self-propulsion or time varying potential was introduced to realize unidirectional transport.Without utilizing these two factors, we experimentally demonstrate ratchet transport through particle interactions during crowding. Such ratchet transport induced by particle interaction has not been experimentally demonstrated thus far, although some theoretical studies had suggested that particle crowding enhances ratchet transport. In addition, we constructed a model for such transport in which the potential varies depending on the particle density, which agrees well with our experimental results. This study can accelerate the development of transport techniques on a micrometer scale. arXiv:1912.04659v1 [cond-mat.soft]

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An introduction to ratchets in chemistry and biology

Abstract: This article describes the functions and mechanisms of particle and electron ratchets, and the interplay between theory and experiment in this field of non-equilibrium transport.

Cited by 73 publications

References 87 publications

Stochastically pumped adaptation and directional motion of molecular machines

Stochastically pumped adaptation and directional motion of molecular machines

The Biophysics of Cell Migration: Biasing Cell Motion with Feynman Ratchets

Collective Ratchet Transport Generated by Particle Crowding under Asymmetric Sawtooth‐Shaped Static Potential

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