Effect of Noise on DNA Sequencing via Transverse Electronic Transport

Krems, Matt; Zwolak, Michael; Pershin, Yuriy V.; Di Ventra, Massimiliano

doi:10.1016/j.bpj.2009.06.055

Title: Effect of Noise on DNA Sequencing via Transverse Electronic Transport

Full Record
Other Related Research

Authors:: Krems, Matt; Zwolak, Michael; Pershin, Yuriy V.; Di Ventra, Massimiliano

Publication Date:: Thu Oct 01 00:00:00 EDT 2009

Sponsoring Org.:: USDOE

OSTI Identifier:: 1198025

Resource Type:: Published Article

Journal Name:: Biophysical Journal

Additional Journal Information:: Journal Name: Biophysical Journal Journal Volume: 97 Journal Issue: 7; Journal ID: ISSN 0006-3495

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Citation Formats


                    Krems, Matt, Zwolak, Michael, Pershin, Yuriy V., and Di Ventra, Massimiliano. Effect of Noise on DNA Sequencing via Transverse Electronic Transport.  United States: N. p., 2009. 
Web.  doi:10.1016/j.bpj.2009.06.055.

Copy to clipboard


                    Krems, Matt, Zwolak, Michael, Pershin, Yuriy V., & Di Ventra, Massimiliano. Effect of Noise on DNA Sequencing via Transverse Electronic Transport.  United States.  https://doi.org/10.1016/j.bpj.2009.06.055

Copy to clipboard


                    Krems, Matt, Zwolak, Michael, Pershin, Yuriy V., and Di Ventra, Massimiliano. Thu .  
"Effect of Noise on DNA Sequencing via Transverse Electronic Transport".  United States.  https://doi.org/10.1016/j.bpj.2009.06.055.

Copy to clipboard


                    
@article{osti_1198025,

  title        = {Effect of Noise on DNA Sequencing via Transverse Electronic Transport},

  author       = {Krems, Matt and Zwolak, Michael and Pershin, Yuriy V. and Di Ventra, Massimiliano},

  abstractNote = {},

  doi          = {10.1016/j.bpj.2009.06.055},

  journal      = {Biophysical Journal},

  number       = 7,

  volume       = 97,

  place        = {United States},

  year         = {Thu Oct 01 00:00:00 EDT 2009},

  month        = {Thu Oct 01 00:00:00 EDT 2009}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Publisher's Version of Record
https://doi.org/10.1016/j.bpj.2009.06.055

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 64 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Similar Records in DOE PAGES and OSTI.GOV collections:

Effect of dephasing on DNA sequencing via transverse electronic transport

Journal Article Zwolak, Michael ; Krems, Matt ; Pershin, Yuriy V ; ... - Biophysical Journal

We study theoretically the effects of dephasing on DNA sequencing in a nanopore via transverse electronic transport. To do this, we couple classical molecular dynamics simulations with transport calculations using scattering theory. Previous studies, which did not include dephasing, have shown that by measuring the transverse current of a particular base multiple times, one can get distributions of currents for each base that are distinguishable. We introduce a dephasing parameter into transport calculations to simulate the effects of the ions and other fluctuations. These effects lower the overall magnitude of the current, but have little effect on the current distributionsmore »« less
Full Text Available
Expert system for data acquisition to achieve a constant signal-to-noise ratio: Application to imaging of DNA sequencing gels

Journal Article Koutny, L B ; Yeung, E S - Analytical Chemistry (Washington); (United States)

Normally, data acquisition and processing in chemical measurements are based on equal time (effort) for each data point. This leads to uneven signal-to-noise ratios (S/N) for each point. The authors present an expert system which decides in real time whether adequate S/N has been achieved for each point. If so, that data point will be omitted in all further acquisition or processing operations, greatly increasing the overall efficiency. The special case of analyzing DNA sequencing gels is tested with this scheme. A factor of 7.6 reduction in effort is demonstrated for a data set of 384 [times] 250 pixels, whichmore »« less
https://doi.org/10.1021/ac00050a010
Stochastic realization via invariant system descriptions. [Realization of white noise-driven linear system from autocorrelated measurements of output sequence]

Conference Candy, J V ; Bullock, T E ; Warren, M E

The realization of a linear, constant, multivariable system driven by white noise from the measurement covariance sequence is considered. It is shown that the class of all realizations possessing the same power spectral density can be uniquely characterized by giving an invariant system description. An algorithm to extract this description from the covariance sequence, which does not require solution of a Riccati equation, is presented. The link between the realization from the covariance sequence, white noise model, and the steady-state Kalman filter is also shown.
The effect of electron transport on the characterization of x-ray free-electron laser pulses via ablation

Journal Article Hau-Riege, Stefan P. ; Pardini, Tom - Applied Physics Letters

The spatial intensity distribution of x-ray free-electron laser (XFEL) pulses in-focus is commonly characterized by performing ablative imprints in thin gold films on silica substrates. In many cases, the range of the electrons generated in the gold by x-ray absorption far exceeds the beam size, and so, it is not clear if the results of imprint studies are compromised by electron transport. Thermal conduction could further modify the energy density profile in the material. We used here a combination of Monte-Carlo transport and continuum models to quantify the accuracy of the imprint method for characterizing XFEL beam profiles. We foundmore »« less
Cited by 2
https://doi.org/10.1063/1.4996190

Full Text Available
Whole genome assembly from 454 sequencing output via modified DNA graph concept

Journal Article Jacek, Blazewicz ; Marcin, Bryja ; Marek, Figlerowicz ; ... - Computational Biology and Chemistry
https://doi.org/10.1016/j.compbiolchem.2009.04.005

Similar Records