Applications of All-Atom Molecular Dynamics to Nanofluidics

Chinappi, Mauro

doi:10.5772/35556

Cited by 2 publications

(3 citation statements)

References 49 publications

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“…Protein sequencing is one of the most transformative potential applications of the nanopore sensing method. 16,17 One of the key challenges is detection of all twenty natural amino acids, which differ from one another just by a handful of atoms. Here we show how SEM can be used to assess distinguishability of the amino acids in biological nanopore MspA.…”

Section: Application Example: Probing Amino Acid Distinguishability Umentioning

confidence: 99%

“…To date, the nanopore sensing principle has been applied to study variety of biomolecular systems, 7,8 from ions 9 to viruses, 10 including determination of the nucleotide sequence of DNA 11 and RNA. 12 Tremendous opportunities lie ahead for nanopore sensing in protein character-ization [13][14][15] and sequencing technologies, 16,17 detection of molecular biomarkers, 18,19 drug design, 20 mass spectrometry 21,22 and general purpose analytics. 23,24 Realizing these goals will require development of custom nanopores that produce well-defined current modulations in the presence of target analytes.…”

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confidence: 99%

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Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model

Wilson

Sarthak

et al. 2019

ACS Sens.

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Nanopore sensing has emerged as a versatile approach to detection and identification of biomolecules. Presently, researchers rely on experience and intuition for choosing or modifying the nanopores to detect a target analyte. The field would greatly bene t from a computational method that could relate the atomic-scale geometry of the nanopores and analytes to the blockade nanopore currents they produce. Existing computational methods are either computationally too expensive to be used routinely in experimental laboratories or not sensitive enough to account for the atomic structure of the pore and the analytes. Here, we demonstrate a robust and inexpensive computational approach-the steric exclusion model (SEM) of nanopore conductance-that is orders of magnitude more efficient than all-atom MD and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. The method combines the computational efficiency of a finite element solver with the atomic precision of a nanopore conductance map to yield unprecedented speed and accuracy of ionic current prediction. We validate our SEM approach through comparison with the current blockades computed using the all-atom molecular dynamics method for a range of proteins confined to a solid-state nanopore, biological channels embedded in a lipid bilayer membranes and blockade currents produced by DNA homopolymers in MspA. We illustrate potential applications of SEM by computing blockade currents produced by nucleosome proteins in a solid-state nanopore, individual amino acids in MspA and by testing the effect of point mutations on amino acid distinguishability. We expect our SEM approach to become an integral part of future development of the nanopore sensing field. * These authors contributed equally to the manuscript Supplementary Information Available The following files are available free of charge: SI Wilson2019.pdf. Simulated dependence of KCl, K + and Cl − conductivity from the center of carbon, hydrogen, nitrogen, oxygen atoms; comparison of the nanopore currents computed using the resistor and SEM models; comparison of SEM and MD blockade currents in MspA done using nominal conductivity of KCl and for 3'-trans systems; supplementary methods detailing MD simulations of biological nanopores; and a table summarizing conditions for the biological nanopores simulations.

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Section: Application Example: Probing Amino Acid Distinguishability Umentioning

confidence: 99%

mentioning

confidence: 99%

Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model

Wilson

Sarthak

et al. 2019

ACS Sens.

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“…The measured slip lengths range from nanometers to tens of nanometers and were shown to almost collapse onto a single curve as a function of the static contact angle θ characterizing the surface wettability [17], thereby suggesting a quasi-universal relationship s ∝ (1 + cos θ) −2 [13], with θ the equilibrium contact angle formed by liquid droplets at the solid surface. Rationalizing this picture in terms of the statistical properties of atomistic motion close to solid boundaries is a challenging task [18,15,19,20,21], especially when different molecular mechanisms of slip may coexist [15,22]: depending on the external driving force (the applied shear), liquid atoms may hop from one equilibrium site to another of the liquid-solid energy landscape, or even display a collective motion of entire layers of atoms slipping together. More recent numerical simulations [14] even suggested that the dichotomy between hydrophobicity and large slip might be purely coincidental and that hydrophilic surfaces can show features typically associated with hydrophobicity.…”

Section: Introductionmentioning

confidence: 99%

The importance of chemical potential in the determination of water slip in nanochannels

et al. 2015

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Abstract. We investigate the slip properties of water confined in graphite-like nano-channels by nonequilibrium molecular dynamics simulations, with the aim of identifying and analyze separately the influence of different physical quantities on the slip length. In a system under confinement but connected to a reservoir of fluid, the chemical potential is the natural control parameter: we show that two nanochannels characterized by the same macroscopic contact angle -but a different microscopic surface potential -do not exhibit the same slip length unless the chemical potential of water in the two channels is matched. Some methodological issues related to the preparation of samples for the comparative analysis in confined geometries are also discussed.

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Applications of All-Atom Molecular Dynamics to Nanofluidics

Cited by 2 publications

References 49 publications

Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model

Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model

The importance of chemical potential in the determination of water slip in nanochannels

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