Length-independent transport rates in biomolecules by quantum mechanical unfurling

Levine, Ariel D.; Michael, Cassia; Peskin, Uri

doi:10.1039/c5sc03495g

Cited by 17 publications

(41 citation statements)

References 69 publications

(80 reference statements)

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“…One may also examine the unfurling, length independent transport behavior, theoretically suggested in Ref. 56 for related DNA junctions. Finally, DNA nanojunctions show promise for a broad range of applications, including nonlinear charge and energy transport, signaling, and sensing [59][60][61] .…”

Section: Discussionmentioning

confidence: 99%

Controlling charge transport mechanisms in molecular junctions: Distilling thermally induced hopping from coherent-resonant conduction

Kim

Segal

2017

The Journal of Chemical Physics

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The electrical conductance of molecular junctions may strongly depend on the temperature, and weakly on molecular length, under two distinct mechanisms: phase-coherent resonant conduction, with charges proceeding via delocalized molecular orbitals, and incoherent thermally-assisted multi-step hopping. While in the case of coherent conduction the temperature dependence arises from the broadening of the Fermi distribution in the metal electrodes, in the latter case it corresponds to electron-vibration interaction effects on the junction. With the objective to distill the thermally-activated hopping component, thus expose intrinsic electron-vibration interaction phenomena on the junction, we suggest the design of molecular junctions with "spacers", extended anchoring groups that act to filter out phase-coherent resonant electrons. Specifically, we study the electrical conductance of fixed-gap and variable-gap junctions that include a tunneling block, with spacers at the boundaries. Using numerical simulations and analytical considerations, we demonstrate that in our design, resonant conduction is suppressed. As a result, the electrical conductance is dominated by two (rather than three) mechanisms: superexchange (deep tunneling), and multi-step thermally-induced hopping. We further exemplify our analysis on DNA junctions with an A:T block serving as a tunneling barrier. Here, we show that the electrical conductance is insensitive to the number of G:C base-pairs at the boundaries. This indicates that the tunneling-to-hopping crossover revealed in such sequences truly corresponds to the properties of the A:T barrier.

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Section: Discussionmentioning

confidence: 99%

Controlling charge transport mechanisms in molecular junctions: Distilling thermally induced hopping from coherent-resonant conduction

Kim

Segal

2017

The Journal of Chemical Physics

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“…ET mechanisms, aside from nearest-neighbor hopping, variable-range hopping, coherent bandlike transport, and polaron transport, can produce weakly distance-dependent rates. For example, a photoexcited state with substantial D-to-B charge transfer character may produce soft distance dependences, as the initial state may be delocalized onto the B by the photoexcitation (73,74).…”

Section: Donor-acceptor Chemistry With Dna Basesmentioning

confidence: 99%

Why Are DNA and Protein Electron Transfer So Different?

Beratan

2019

Annu. Rev. Phys. Chem.

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The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.

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“…It would be interesting to generate datasets using other (relatively cheap) methods that perturbatively include electron-vibration interaction effects, see e.g. [72][73][74] and explore the ability of the ML technique to reproduce other transport mechanisms.…”

Section: Discussionmentioning

confidence: 99%

Machine Learning Prediction of DNA Charge Transport

Korol¹,

Segal²

2019

J. Phys. Chem. C

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First principle calculations of charge transfer in DNA molecules are computationally expensive given that charge carriers migrate in interaction with intra-and inter-molecular atomic motion. Screening sequences, e.g. to identify excellent electrical conductors is challenging even when adopting coarse-grained models and effective computational schemes that do not explicitly describe atomic dynamics. In this work, we present a machine learning (ML) model that allows the inexpensive prediction of the electrical conductance of millions of long double-stranded DNA (dsDNA) sequences, reducing computational costs by orders of magnitude. The algorithm is trained on short DNA nanojunctions with n = 3 − 7 base pairs. The electrical conductance of the training set is computed with a quantum scattering method, which captures charge-nuclei scattering processes. We demonstrate that the ML method accurately predicts the electrical conductance of varied dsDNA junctions tracing different transport mechanisms: coherent (short-range) quantum tunneling, onresonance (ballistic) transport, and incoherent site-to-site hopping. Furthermore, the ML approach supports physical observations that clusters of nucleotides regulate DNA transport behavior. The input features tested in this work could be used in other ML studies of charge transport in complex polymers, in the search for promising electronic and thermoelectric materials.

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Length-independent transport rates in biomolecules by quantum mechanical unfurling

Abstract: A new mechanism termed quantum unfurling is consistent with length independent charge transport rates as observed in biomolecules.

Cited by 17 publications

References 69 publications

Controlling charge transport mechanisms in molecular junctions: Distilling thermally induced hopping from coherent-resonant conduction

Controlling charge transport mechanisms in molecular junctions: Distilling thermally induced hopping from coherent-resonant conduction

Why Are DNA and Protein Electron Transfer So Different?

Machine Learning Prediction of DNA Charge Transport

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