Hu Qiu

Exceptionally fast water desalination at complete salt rejection by pristine graphyne monolayers

Desalination that produces clean freshwater from seawater holds the promise of solving the global water shortage for drinking, agriculture and industry. However, conventional desalination technologies such as reverse osmosis and thermal distillation involve large amounts of energy consumption, and the semipermeable membranes widely used in reverse osmosis face the challenge to provide a high throughput at high salt rejection. Here we find by comprehensive molecular dynamics simulations and first principles modeling that pristine graphyne, one of the graphene-like one-atom-thick carbon allotropes, can achieve 100% rejection of nearly all ions in seawater including Na(+), Cl(-), Mg(2+), K(+) and Ca(2+), at an exceptionally high water permeability about two orders of magnitude higher than those for commercial state-of-the-art reverse osmosis membranes at a salt rejection of ~98.5%. This complete ion rejection by graphyne, independent of the salt concentration and the operating pressure, is revealed to be originated from the significantly higher energy barriers for ions than for water. This intrinsic specialty of graphyne should provide a new possibility for the efforts to alleviate the global shortage of freshwater and other environmental problems.

Electromelting of confined monolayer ice.

In sharp contrast to the prevailing view that electric fields promote water freezing, here we show by molecular dynamics simulations that monolayer ice confined between two parallel plates can melt into liquid water under a perpendicularly applied electric field. The melting temperature of the monolayer ice decreases with the increasing strength of the external field due to the field-induced disruption of the water-wall interaction induced well-ordered network of the hydrogen bond. This electromelting process should add an important new ingredient to the physics of water.

Ion solvation and structural stability in a sodium channel investigated by molecular dynamics calculations

The stability and ion binding properties of the homo-tetrameric pore domain of a prokaryotic, voltage-gated sodium channel are studied by extensive all-atom molecular dynamics simulations, with the channel protein being embedded in a fully hydrated lipid bilayer. It is found that Na(+) ion presents in a mostly hydrated state inside the wide pore of the selectivity filter of the sodium channel, in sharp contrast to the nearly fully dehydrated state for K(+) ions in potassium channels. Our results also indicate that Na(+) ions make contact with only one or two out of the four polypeptide chains forming the selectivity filter, and surprisingly, the selectivity filter exhibits robust stability for various initial ion configurations even in the absence of ions. These findings are quite different from those in potassium channels. Furthermore, an electric field above 0.5V/nm is suggested to be able to induce Na(+) permeation through the selectivity filter.

Detecting ssDNA at single-nucleotide resolution by sub-2-nanometer pore in monoatomic graphene: A molecular dynamics study

Obtaining a sequence-based signal at a resolution of single nucleotide during the passage of a DNA strand through nanopores remains a challenging problem. Here, we demonstrate by molecular dynamics simulations that the single-base resolution detection can be realized by pulling a single-stranded DNA through graphene nanopores with diameters down to ∼1 nm. By simply monitoring and analyzing the peak values of the pulling force profile, each nucleotide in the DNA strand can be identified and characterized, except for cytosine and thymine which remain indistinguishable. This intriguing character through narrow nanopores should help realize the low-cost and time-efficient DNA sequencing.

Dynamic and energetic mechanisms for the distinct permeation rate in AQP1 and AQP0

Despite sharing overall sequence and structural similarities, water channel aquaporin 0 (AQP0) transports water more slowly than other aquaporins. Using molecular dynamics simulations of AQP0 and AQP1, we find that there is a sudden decrease in the distribution profile of water density along the pore of AQP0 in the region of residue Tyr23, which significantly disrupts the single file water chain by forming hydrogen bond with permeating water molecules. Comparisons of free-energy and interaction-energy profiles for water conduction between AQP0 and AQP1 indicate that this interruption of the water chain causes a huge energy barrier opposing water translocation through AQP0. We further show that a mutation of Tyr23 to phenylalanine leads to a 2- to 4-fold enhancement in water permeability of AQP0, from (0.5+/-0.2) x 10(-14) cm(3)s(-1) to (1.9+/-0.6) x 10(-14) cm(3)s(-1). Therefore, Tyr23 is a dominate factor leading to the low water permeability in AQP0.

Water in Inhomogeneous Nanoconfinement: Coexistence of Multilayered Liquid and Transition to Ice Nanoribbons

Phase behavior and the associated phase transition of water within inhomogeneous nanoconfinement are investigated using molecular dynamics simulations. The nanoconfinement is constructed by a flat bottom plate and a convex top plate. At 300 K, the confined water can be viewed as a coexistence of monolayer, bilayer, and trilayer liquid domains to accommodate the inhomogeneous confinement. With increasing liquid density, the confined water with uneven layers transforms separately into two-dimensional ice crystals with unchanged layer number and rhombic in-plane symmetry for oxygen atoms. The monolayer water undergoes the transition first into a puckered ice nanoribbon, and the bilayer water transforms into a rhombic ice nanoribbon next, followed by the transition of trilayer water into a trilayer ice nanoribbon. The sequential localized liquid-to-solid transition within the inhomogeneous confinement can also be achieved by gradually decreasing the temperature at low liquid densities. These findings of phase behaviors of water under the inhomogeneous nanoconfinement not only extend the phase diagram of confined water but also have implications for realistic nanofluidic systems and microporous materials.

Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores

We investigate by means of molecular dynamics simulations stretch-induced stepwise translocation of single-stranded DNA (ssDNA) through graphene nanopores. The intrinsic stepwise DNA motion, found to be largely independent of size and shape of the graphene nanopore, is brought about through alternating conformational changes between spontaneous adhesion of DNA bases to the rim of the graphene nanopore and unbinding due to mechanical force or electric field. The adhesion reduces the DNA bases’ vertical conformational fluctuations, facilitating base detection and recognition. A graphene membrane shaped as a quantum point contact permits, by means of transverse electronic conductance measurement, detection of the stepwise translocation of the DNA as predicted through quantum mechanical Green’s function-based transport calculations. The measurement scheme described opens a route to enhance the signal-to-noise ratio not only by slowing down DNA translocation to provide sufficient time for base recognition but also by stabilizing single DNA bases and, thereby, reducing thermal noise.

Electrically Tunable Quenching of DNA Fluctuations in Biased Solid-State Nanopores

Nanopores offer sensors for a broad range of nanoscale materials, in particular ones of biological origin such as single- and double-stranded DNA or DNA-protein complexes. In order to increase single-molecule sensitivity, it is desirable to control biomolecule motion inside nanopores. In the present study, we investigate how in the case of a double-stranded DNA the single-molecule sensitivity can be improved through bias voltages. For this purpose we carry out molecular dynamics simulations of the DNA inside nanopores in an electrically biased metallic membrane. Stabilization of DNA, namely, a reduction in thermal fluctuations, is observed under positive bias voltages, while negative voltages bring about only negligible stabilization. For positive biases the stabilization arises from electrostatic attraction between the negatively charged DNA backbone and the positively charged pore surface. Simulations on a teardrop-shaped pore show a transverse shift of DNA position toward the sharp end of the pore under positive bias voltages, suggesting the possibility to control DNA alignment inside nanopores through geometry shaping. The present findings open a feasible and efficient route to reduce thermal noise and, in turn, enhance the signal-to-noise ratio in single-molecule nanopore sensing.

Detection and mapping of DNA methylation with 2D material nanopores

DNA methylation is an epigenetic modification involving the addition of a methyl group to DNA, which is heavily involved in gene expression and regulation, thereby critical to the progression of diseases such as cancer. In this work we show that detection and localization of DNA methylation can be achieved with nanopore sensors made of two-dimensional materials such as graphene and molybdenum di-sulfide. We label each DNA methylation site with a methyl-CpG binding domain protein (MBD1), and combine molecular dynamics simulations with electronic transport calculations to investigate the translocation of the methylated DNA–MBD1 complex through two-dimensional material nanopores under external voltage biases. The passage of the MBD1-labeled methylation site through the pore is identified by dips in the current blockade induced by the DNA strand, as well as by peaks in the transverse electronic sheet current across the two-dimensional layer. The position of the methylation sites can be clearly recognized by the relative positions of the dips in the recorded ionic current blockade with an estimated error ranging from 0 to 16%. Finally, we define the spatial resolution of the two-dimensional material nanopore device as the minimal distance between two methylation sites identified within a single measurement, which is 15 base pairs by ionic current recognition, but as low as 10 base pairs by transverse electronic conductance detection, indicating better resolution with this latter technique. The present approach opens a new route for precise and efficient profiling of DNA methylation.Epigenetics: DNA methylation electronically detected by 2D nanoporesAs one the most common epigenetic modifications in eukaryotic genomes, DNA methylation plays a crucial role in the expression of genes in mammalian cells. It holds great promise as a biomarker to investigate cell development and aging, and to be used in risk assessment and early diagnosis of diseases such as cancer. A team lead by Jean–Pierre Leburton at the University of Illinois in the USA shows by numerical simulation that the use of a few angstrom wide nanopores in a tri-atomic membrane of semiconducting molybdenum di-sulfide (MoS2) offers a powerful way to detect and map electronically and with high resolution the presence of individual methyl groups on a DNA molecule, thereby paving the way towards fast and low-cost DNA sequencing techniques for personal medicine.

Graphene Nanopores for Electronic Recognition of DNA Methylation

We investigate theoretically the ability of graphene nanopore membranes to detect methylated sites along a DNA molecule by electronic sheet current along the two-dimensional (2D) materials. Special emphasis is placed on the detection sensitivity changes due to pore size, shape, position, and the presence of defects around the nanopore in a membrane with constricted geometry. Enhanced sensitivity for detecting methylated CpG sites, labeled by methyl-CpG binding domain (MBD) proteins along a DNA molecule, is obtained for electronic transport through graphene midgap states caused by the constriction. A large square deviation from the graphene conductance with respect to the open nanopore is observed during the translocation of MBD proteins. This approach exhibits superior resolution in the detection of multiple methylated sites along the DNA compared to conventional ionic current blockade techniques.