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Monitoring Protein Adsorption with Solid-state Nanopores
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Modeling thermophoretic effects in solid-state nanopores.

Maxim Belkin1, Shu-Han Chao2, Gino Giannetti2

  • 1Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801.

Journal of Computational Electronics
|November 15, 2014
PubMed
Summary
This summary is machine-generated.

New simulation protocols enable modeling of local temperature variations in nanopore systems. These methods predict how temperature gradients affect molecular transport, aiding the design of temperature-responsive nanopore devices.

Keywords:
Molecular dynamicsSoret coefficientboundary-driven MDnanofluidicsnon-equilibrium MDplasmonic heatingthermodiffusionthermophoresis

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Area of Science:

  • Computational physics and biophysics
  • Nanotechnology and materials science
  • Molecular dynamics simulations

Background:

  • Local temperature modulation is a novel mechanism for controlling molecular transport through nanopores.
  • Existing molecular dynamics (MD) methods with single thermostats cannot simulate non-uniform temperature gradients.
  • Accurate simulation protocols are needed to predict the effects of temperature gradients on nanopore transport.

Purpose of the Study:

  • To develop and present simulation protocols for modeling nanopore systems with non-uniform temperature distributions.
  • To investigate the thermophoretic effect of temperature gradients on ion and DNA nucleotide distribution.
  • To demonstrate the application of these protocols in solid-state nanopores and for DNA motion analysis.

Main Methods:

  • Boundary-driven non-equilibrium MD protocol for imposing temperature gradients in all-atom simulations.
  • Direct computation of effective forces from thermal gradients on biomolecules.
  • Coupling continuum calculations with coarse-grained DNA models for plasmonic nanopore simulations.

Main Results:

  • Demonstrated differential response of DNA nucleotides to temperature gradients.
  • Showcased regulation of ionic current in solid-state nanopores via local heating.
  • Validated methods for studying local temperature effects on DNA electrophoretic motion.

Conclusions:

  • Developed versatile simulation protocols for analyzing temperature-gradient effects in nanopore systems.
  • These methods facilitate the rational design of novel temperature-responsive nanopore technologies.
  • The study provides a computational framework for understanding thermophoresis in complex nanoscale systems.