Bio-inspired novel design principles for artificial molecular motors

Hugel, Thorsten; Lumme, Christina

doi:10.1016/j.copbio.2010.06.003

Cited by 13 publications

(5 citation statements)

References 50 publications

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“…Breaking detailed balance due to the presence of unbalanced forces acting on a system causes rectification of thermal fluctuations and leads to new dynamical behaviors, very different from those observed in equilibrium situations [1,2]. Typical realizations of rectified motion include the transport of particles under the action of unbiased forces of optical [3,4], mechanical [5,6], or chemical [7,8] origin. Hence, the implications of rectification has attracted the interest of researchers in a variety of fields, ranging from biology to nanoscience, due to its relevance in the transport and motion at small scales [2,9].…”

Section: Introductionmentioning

confidence: 99%

“…1,2 Typical realizations of rectified motion include the transport of particles under the action of unbiased forces of optical, 3,4 mechanical, 5,6 or chemical 7,8 origin. Hence, the implications of rectification has attracted the interest of researchers in a variety of fields, ranging from biology to nanoscience, due to its relevance in the transport and motion at small scales.…”

Section: Introductionmentioning

confidence: 99%

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Confined Brownian ratchets

Malgaretti

Pagonabarraga

Rubı́

2013

The Journal of Chemical Physics

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We analyze the dynamics of Brownian ratchets in a confined environment. The motion of the particles is described by a Fick-Jakobs kinetic equation in which the presence of boundaries is modeled by means of an entropic potential. The cases of a flashing ratchet, a two-state model, and a ratchet under the influence of a temperature gradient are analyzed in detail. We show the emergence of a strong cooperativity between the inherent rectification of the ratchet mechanism and the entropic bias of the fluctuations caused by spatial confinement. Net particle transport may take place in situations where none of those mechanisms leads to rectification when acting individually. The combined rectification mechanisms may lead to bidirectional transport and to new routes to segregation phenomena. Confined Brownian ratchets could be used to control transport in mesostructures and to engineer new and more efficient devices for transport at the nanoscale. © 2013 AIP Publishing LLC.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Confined Brownian ratchets

Malgaretti

Pagonabarraga

Rubı́

2013

The Journal of Chemical Physics

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“…As shown below, enabled by the large extensional changes achievable in DNA, the power-strokedriven steps of IW could be as large as a micrometer, much larger than the typical nanometer-scale step size of natural and synthetic molecular motors. Furthermore, we predict a stall force of the order of 0.1 pN, implying the ability to do work of the order of 100 pN nm or tens of k B T per step, a very large number compared to what can be expected for existing diffusively driven artificial molecular motors, [27][28][29] and at least comparable to biological motors with a typical work output of 10k B T per step. 2 In the following, we introduce the IW concept in more detail.…”

Section: Introductionmentioning

confidence: 76%

“…Inchworm (IW) is based on a several-kbp-long, double-stranded DNA molecule confined in a nanochannel (NC) in an extended, quasi-linear conformation (Fig. Furthermore, we predict a stall force of the order of 0.1 pN, implying the ability to do work of the order of 100 pN nm or tens of k B T per step, a very large number compared to what can be expected for existing diffusively driven artificial molecular motors, [27][28][29] and at least comparable to biological motors with a typical work output of 10k B T per step. [20][21][22][23] A power stroke can be realized by changing the salt concentration in the NC, controlling the DNA's persistence length by altering the electrostatic repulsion along its backbone, and effectively changing the length of the DNA molecule's configuration.…”

Section: Introductionmentioning

confidence: 83%

Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke

et al. 2014

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Synthetic molecular motors typically take nanometer-scale steps through rectification of thermal motion. Here we propose Inchworm, a DNA-based motor that employs a pronounced power stroke to take micrometer-scale steps on a time scale of seconds, and we design, fabricate, and analyze the nanofluidic device needed to operate the motor. Inchworm is a kbp-long, double-stranded DNA confined inside a nanochannel in a stretched configuration. Motor stepping is achieved through externally controlled changes in salt concentration (changing the DNA's extension), coordinated with ligand-gated binding of the DNA's ends to the functionalized nanochannel surface. Brownian dynamics simulations predict that Inchworm's stall force is determined by its entropic spring constant and is ∼ 0.1 pN. Operation of the motor requires periodic cycling of four different buffers surrounding the DNA inside a nanochannel, while keeping constant the hydrodynamic load force on the DNA. We present a two-layer fluidic device incorporating 100 nm-radius nanochannels that are connected through a few-nm-wide slit to a microfluidic system used for in situ buffer exchanges, either diffusionally (zero flow) or with controlled hydrodynamic flow. Combining experiment with finite-element modeling, we demonstrate the device's key performance features and experimentally establish achievable Inchworm stepping times of the order of seconds or faster.

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“…Several variants 5 of Brownian ratchet have been proposed to explain this transport mechanism under different nonequilibrium situations. Typical examples of Brownian ratchet include the transport of particles under the action of unbiased forces of chemical, 7,8 optical, 9,10 or mechanical 11 origin. In general, Brownian ratchets have been studied with an ad hoc physical periodic barrier imposed externally.…”

Section: Introductionmentioning

confidence: 99%

Ratchet rectification effect on the translocation of a flexible polyelectrolyte chain

Mondal

Muthukumar

2016

The Journal of Chemical Physics

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We report a three dimensional Langevin dynamics simulation of a uniformly charged flexible polyelectrolyte chain, translocating through an asymmetric narrow channel with periodically varying cross sections under the influence of a periodic external electric field. When reflection symmetry of the channel is broken, a rectification effect is observed with a favored direction for the chain translocation. For a given volume of the channel unit and polymer length, the rectification occurs below a threshold frequency of the external periodic driving force. We have also observed that the extent of the rectification varies non-monotonically with increasing molecular weight and the strength of geometric asymmetry of the channel. Observed non-monotonicity of the rectification performance has been interpreted in terms of a competition between two effects arising from the channel asymmetry and change in conformational entropy. An analytical model is presented with predictions consistent with the simulation results.

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Bio-inspired novel design principles for artificial molecular motors

Cited by 13 publications

References 50 publications

Confined Brownian ratchets

Confined Brownian ratchets

Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke

Ratchet rectification effect on the translocation of a flexible polyelectrolyte chain

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