Anomalous dynamics of translocation

Chuang, Jeffrey H.; Kantor, Yacov; Kardar, Mehran

doi:10.1103/physreve.65.011802

Cited by 292 publications

(458 citation statements)

References 31 publications

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“…In order for this approximation to be valid, the polymer on each side of the membrane is implicitly assumed to relax on a time scale much smaller than the one on which the translocation process is taking place. Even if experimental results do support some of the conclusions arising from current models, the separation of time scales assumption is probably not valid in the general case [28]. To our knowledge, [19] is the only theoretical paper to forgo this assumption.…”

Section: Nanopore Technologiesmentioning

confidence: 64%

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

et al. 2002

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Over the last two decades, the introduction of new methods such as pulsed-field gel electrophoresis and capillary array electrophoresis has made it possible to map and sequence entire genomes, including our own. The development of these experimental methods has been helped by the progress of theoretical and computational sciences, and the interactions between these three modi operandi of modern science are still pushing the limits of our technologies. We now see a clear trend towards proteomics and microfluidic (even nanofluidic!) devices. In this review, we take a look at the progress of the field over the last 3 years using the glasses of the theoretical scientist and focusing mostly on new ideas and concepts. About a dozen different subfields are discussed and reviewed. We conclude by giving a commented list of some of the best review articles published over the last 2-3 years.

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Section: Nanopore Technologiesmentioning

confidence: 64%

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

et al. 2002

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“…This corresponds to the simple scaling consideration [30], which claims that the variance of the translocation coordinate (t) ≡ s 2 − s 2 in the long-time limit should go as (t) ∝ t α , where α = 2/(2ν + 1) ≈ 0.92 for the three-dimensional case. This power is obtained by the requirement that the translocation time τ tr should scale like the maximal relaxation time of the polymer chain, i.e., τ tr ∝ N 2ν+1 .…”

Section: Simulation Resultsmentioning

confidence: 99%

Fractional Brownian motion approach to polymer translocation: The governing equation of motion

et al. 2011

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We suggest a governing equation that describes the process of polymer-chain translocation through a narrow pore and reconciles the seemingly contradictory features of such dynamics: (i) a Gaussian probability distribution of the translocated number of polymer segments at time t after the process has begun, and (ii) a subdiffusive increase of the distribution variance (t) with elapsed time (t) ∝ t α . The latter quantity measures the meansquared number s of polymer segments that have passed through the pore (t) = [s(t) − s(t = 0)] 2 , and is known to grow with an anomalous diffusion exponent α < 1. Our main assumption [i.e., a Gaussian distribution of the translocation velocity v(t)] and some important theoretical results, derived recently, are shown to be supported by extensive Brownian dynamics simulation, which we performed in 3D. We also numerically confirm the predictions made recently that the exponent α changes from 0.91 to 0.55 to 0.91 for short-, intermediate-, and long-time regimes, respectively.

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“…There are two fruitful approaches to this complex issue: phenomenological models and molecular dynamics. The phenomenological models provide a highly reduced description of the polymer dynamics, but they are able to elucidate the dependence of the dynamics on parameters such as the polymer length, pore dimensions, and applied field ͑Sung and Park, 1996; Lubensky and Nelson, 1999;Muthukumar, 1999Muthukumar, , 2001Chern et al, 2001;Chuang et al, 2001;Ambjörnsson et al, 2002;Kong and Muthukumar, 2002;Loebl et al, 2003;Meller, 2003;Slonkina and Kolomeisky, 2003;Luo et al, 2006;Matysiak et al, 2006;Tsai and Chen, 2007͒. On the other hand, if one wants to understand how to probe physical differences between the bases, an atomistic description of the polynucleotide dynamics is necessary.…”

Section: Nanopores and Polynucleotidesmentioning

confidence: 99%

Colloquium: Physical approaches to DNA sequencing and detection

2008

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With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, a revolutionary sequencing method is needed for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single-nucleotide level. This is in sharp contrast to current techniques and instruments that probe ͑through chemical elongation, electrophoresis, and optical detection͒ length differences and terminating bases of strands of DNA. Several physical approaches to DNA detection have the potential to deliver fast and low-cost sequencing. Central to these approaches is the concept of nanochannels or nanopores, which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. This Colloquium emphasizes the physics behind these methods and ideas, critically describes their advantages and drawbacks, and discusses future research opportunities in the field.

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Anomalous dynamics of translocation

Cited by 292 publications

References 31 publications

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

Fractional Brownian motion approach to polymer translocation: The governing equation of motion

Colloquium: Physical approaches to DNA sequencing and detection

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