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

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

Molybdenum disulfide nanoporous membranes for water desalination

We demonstrate molybdenum disulfide (MoS2) as a nano porous membrane for water desalination. By performing extensive molecular dynamics simulations, we find that a nanopore in a single-layer MoS2 can effectively reject salt ions and allow transport of water at a high rate. More than 88% of ions are rejected by membranes having pore areas ranging from 20 to 60 A^2. Water flux through the nanoporous MoS2 membrane is found to be 2 to 5 orders of magnitude greater than that of other known nanoporous membranes (MFI-type zeolite, commercial polymeric seawater Reverse Osmosis (RO), brackish RO, Nanofiltration and High-flux RO). Pore chemistry and architecture are shown to play a significant role in modulating the water flux. MoS2 pores with only molybdenum atoms on their edges give rise to higher fluxes which are about 70% greater than that of graphene nanopores. These observations are explained by the permeation coefficients, energy barriers, water density and velocity distributions in the pores. Our findings pave way towards identifying efficient membranes for water desalination

Strain Modulation of Graphene by Nanoscale Substrate Curvatures: A Molecular View

Spatially nonuniform strain is important for engineering the pseudomagnetic field and band structure of graphene. Despite the wide interest in strain engineering, there is still a lack of control on device-compatible strain patterns due to the limited understanding of the structure-strain relationship. Here, we study the effect of substrate corrugation and curvature on the strain profiles of graphene via combined experimental and theoretical studies of a model system: graphene on closely packed SiO2 nanospheres with different diameters (20-200 nm). Experimentally, via quantitative Raman analysis, we observe partial adhesion and wrinkle features and find that smaller nanospheres induce larger tensile strain in graphene, theoretically, molecular dynamics simulations confirm the same microscopic structure and size dependence of strain and reveal that a larger strain is caused by a stronger, inhomogeneous interaction force between smaller nanospheres and graphene. This molecular-level understanding of the strain mechanism is important for strain engineering of graphene and other two-dimensional materials.Comment: Nano Letters (2018

Revisiting Sampson's theory for hydrodynamic transport in ultrathin nanopores

Sampson's theory for hydrodynamic resistance across a zero-length orifice was developed over a century ago. Although a powerful theory for entrance/exit resistance in nanopores, it lacks accuracy for relatively small-radius pores since it does not account for the molecular interface chemistry. Here, Sampson's theory is revisited for the finite slippage and interfacial viscosity variation near the pore wall. The corrected Sampson's theory can accurately predict the hydrodynamic resistance from molecular dynamics simulations of ultrathin nanopores

Antibody Subclass Detection Using Graphene Nanopores

Solid-state nanopores are promising for label-free protein detection. The large thickness, ranging from several tens of nanometers to micrometers and larger, of solid-state nanopores prohibits atomic-scale scanning or interrogation of proteins. Here, a single-atom thick graphene nanopore is shown to be highly capable of sensing and discriminating between different subclasses of IgG antibodies despite their minor and subtle variation in atomic structure. Extensive molecular dynamics (MD) simulations, rigorous statistical analysis with a total aggregate simulation time of 2.7 μs, supervised machine learning (ML), and classification techniques are employed to distinguish IgG2 from IgG3. The water flux and ionic current during IgG translocation reveal distinct clusters for IgG subclasses facilitating an additional recognition mechanism. In addition, the histogram of ionic current for each segment of IgG can provide high-resolution spatial detection. Our results show that nanoporous graphene can be used to detect and distinguish antibody subclasses with good accuracy