Molecule transport in nanopores with applications to water purification, power generation and disease diagnosis

Heiranian, Mohammad

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https://hdl.handle.net/2142/108510 Copy

Description

Title

Molecule transport in nanopores with applications to water purification, power generation and disease diagnosis

Author(s)

Heiranian, Mohammad

Issue Date

2020-07-17

Director of Research (if dissertation) or Advisor (if thesis)

Aluru, Narayana

Doctoral Committee Chair(s)

Aluru, Narayana

Committee Member(s)

• Bashir, Rashid
• Nam, SungWoo
• Shukla, Diwakar

Department of Study

Mechanical Sci & Engineering

Discipline

Theoretical & Applied Mechans

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

Nanopores, Nanofluidics, biophysics, DNA sequencing, Desalination, Graphene, Carbon Nanotubes, Molybdenum disulfide, Electric double layers, Hydrodynamics

Abstract

High performance water transport in nanopores has drawn a great deal of attention in a variety of applications, such as water desalination, power generation and biosensing. A single-layer MoS2 nanopore is shown, here, to possess high water transport rate and strong salt rejection rate making it ideal for water desilation. High water transport enhancement factors in carbon-based nanopores have been reported over the classical Hagen-Poiseuille (HP) equation which does not account for the physics of transport at molecular scale. Instead, comparing the experimentally measured transport rates to that of a theory, that accounts for the microscopic physics of transport, would result in enhancement factors approaching unity. Here, molecular corrections are introduced into HP equation by considering the variation of key hydrodynamical properties (viscosity and friction) with thickness and diameter of pores in ultrathin graphene and finite-length carbon nanotubes (CNTs) using Green-Kubo relations and molecular dynamics (MD) simulations. The corrected HP (CHP) theory, successfully predicts the permeation rates from non-equilibrium MD pressure driven flows. The previously reported enhancement factors over no-slip HP (of the order of 1000) approach unity when the permeations are normalized by the CHP flow rates. In a follow-up study, we revisit Sampson’s theory after more than a century to account for the surface chemistry of nanopores by incorporating slippage and interfacial viscosity variation into the original Sampson’s theory. The HP theory works for flow in infinitely long tubes where end effects are neglected. In 1891, Ralph Allen Sampson came up with a formula, known as Sampson formula, within the fluid mechanics framework to describe flow in an infinitesimally thin orifice. Zeev Dagan, Sheldon Weinbaum and Robert Pfeffer published an article in the Journal of Fluid Mechanics in 1982, where the HP and Sampson formulas were combined to successfully describe flow in circular tubes of finite length. Although the Sampson formula is a powerful theory for end effects, it has been shown to lack accuracy for relatively small-radius pores (e.g., nanopores in single-layer graphene membranes) since it does not account for the molecular interface chemistry. We show that the corrected Sampson’s theory is able to accurately describe flow in ultrathin nanopores when compared to the data from molecular dynamics simulations. Combining our corrected Sampson formula with the HP equation, we can remarkably predict flow in not only ultrathin pores but also finite-length pores such as carbon nanotubes. We also explored the structure and dynamics of aqueous ions in nanopores. At the nanopore interfaces, properties of ions are shown to differ largely from those of predicted by the classical ionic layering models (e.g., Gouy-Chapman electric double layer (EDL)) when the thickness of the nanopore is scaled down to the limit of ultrathin membranes (e.g, single-layer graphene). Here, using extensive molecular dynamics, the structure and dynamics of aqueous ions inside nanopores are studied for different thicknesses, diameters and surface charge densities of carbon-based nanopores (ultrathin graphene and finite-length carbon nanotubes (CNTs)). The ion concentration and diffusion coefficient in ultrathin nanopores show no indication of Stern layer formation (an immobile counter-ionic layer) as the counter-ions and nanopore atoms are weakly correlation with time compared to the strong correlation in thick nanopores. Adsorption constants of counter-ions onto the nanopore surface are shown to be many orders of magnitudes smaller than that of thick nanopores. The vanishing counter-ion adsorption in ultrathin nanopores explains the lack of Stern layer formation leading to fast dynamics of ions with picosecond scale residence times. Finally, we investigated DNA transport through biological nanopores. Distinguishing bases of nucleic acids by passing them through nanopores has so far primarily relied on electrical signals – specifically, ionic currents through the nanopores. However, the low signal-to-noise ratio makes detection of ionic currents difficult. We show that the initially closed Mechano-Sensitive Channel of Large Conductance (MscL) protein pore opens for single stranded DNA (ssDNA) translocation under an applied electric field. As each nucleotide translocates through the pore, a unique mechanical signal is observed – specifically, the tension in the membrane containing the MscL pore is different for each nucleotide. In addition to the membrane tension, we found that the ionic current is also different for the 4 nucleotide types. The initially closed MscL adapts its opening for nucleotide translocation due to the flexibility of the pore. This unique operation of MscL provides single nucleotide resolution in both electrical and mechanical signals.

Graduation Semester

2020-08

Type of Resource

Thesis

Permalink

http://hdl.handle.net/2142/108510

Copyright and License Information

Copyright 2020 Mohammad Heiranian

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