Direct detection of molecular intermediates from first-passage times

Thorneywork, Alice L.; Gladrow, Jannes; Qing, Yujia; Rico-Pasto, Marc; Ritort, Fèlix; Bayley, Hagan; Kolomeisky, Anatoly B.; Keyser, Ulrich F.

doi:10.1126/sciadv.aaz4642

Cited by 36 publications

(21 citation statements)

References 40 publications

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“…Our results can readily be tested by existing experiments probing colloidal particle systems (see e.g. [85][86][87] ), and may furthermore be relevant for a theoretical description of transport in ion-channels [88][89][90][91] . Our results can be extended in diverse ways, most immediately by including other types of interparticle interactions 92 and time-depended energy barriers 93 .…”

Section: Discussionmentioning

confidence: 73%

Single-file diffusion in a bi-stable potential: signatures of memory in the barrier-crossing of a tagged-particle

Lapolla,

Godec

2020

Preprint

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We investigate memory effects in barrier-crossing in the overdamped setting. We focus on the scenario where the hidden degrees of freedom relax on exactly the same time scale as the observable. As a prototypical model we analyze taggedparticle diffusion in a single-file confined to a bi-stable potential. We identify the signatures of memory and explain their origin. The emerging memory is a result of the projection of collective many-body eigenmodes onto the motion of a tagged-particle. We are interested in the 'confining' (all background particles in front of the tagged-particle) and 'pushing' (all background particles behind the tagged-particle) scenarios for which we find non-trivial and qualitatively different relaxation behavior. Notably and somewhat unexpectedly, at fixed particle number we find that the higher the barrier the more prominent are the signatures of memory. Our results can readily be tested experimentally and may be relevant for understanding transport in biological ion-channels.

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Section: Discussionmentioning

confidence: 73%

Single-file diffusion in a bi-stable potential: signatures of memory in the barrier-crossing of a tagged-particle

Lapolla,

Godec

2020

Preprint

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“…Thermal vibrations of the pore's structure affect the motion of analytes [61,62]. The number of analytes within the pore is also strongly fluctuating, as there are only a few particles within at a time [63][64][65]. Moreover, the analyte undergoes Brownian motion, so the interest in not on the analysis of a single capture event, but on a statistical description of the capture [10,66,67].…”

Section: Modeling and Computational Challengesmentioning

confidence: 99%

Electroosmosis in nanopores: Computational methods and technological applications

Gubbiotti¹,

Baldelli²,

Muccio³

et al. 2021

Preprint

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Electroosmosis is a fascinating effect where liquid motion is induced by an applied electric field. Counter ions accumulate in the vicinity of charged surfaces, triggering a coupling between liquid mass transport and external electric field. In nanofluidic technologies, where surfaces play an exacerbated role, electroosmosis is thus of primary importance. Its consequences on the transport properties in biological and synthetic nanopores are subtle and intricate. Thorough understanding is therefore challenging yet crucial to fully assess the mechanisms at play. Here, we review recent progress on computational techniques for the analysis of electroosmosis and discuss technological applications, in particular for sensing devices.

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“…In particular, they have been shown to successfully discriminate diffusion on fractal objects from other types of dynamics ( 37 ). Nevertheless, first-passage time distributions are rarely measured in experiments and are only slowly emerging as powerful experimental observables ( 38 , 39 ), which have not yet been applied to fractals.…”

Section: Introductionmentioning

confidence: 99%

First-passage statistics of colloids on fractals: Theory and experimental realization

et al. 2022

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In nature and technology, particle dynamics frequently occur in complex environments, for example in restricted geometries or crowded media. These dynamics have often been modeled invoking a fractal structure of the medium although the fractal structure was only indirectly inferred through the dynamics. Moreover, systematic studies have not yet been performed. Here, colloidal particles moving in a laser speckle pattern are used as a model system. In this case, the experimental observations can be reliably traced to the fractal structure of the underlying medium with an adjustable fractal dimension. First-passage time statistics reveal that the particles explore the speckle in a self-similar, fractal manner at least over four decades in time and on length scales up to 20 times the particle radius. The requirements for fractal diffusion to be applicable are laid out, and methods to extract the fractal dimension are established.

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Direct detection of molecular intermediates from first-passage times

Cited by 36 publications

References 40 publications

Single-file diffusion in a bi-stable potential: signatures of memory in the barrier-crossing of a tagged-particle

Single-file diffusion in a bi-stable potential: signatures of memory in the barrier-crossing of a tagged-particle

Electroosmosis in nanopores: Computational methods and technological applications

First-passage statistics of colloids on fractals: Theory and experimental realization

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