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ABSTRACT: In this work, we combine our earlier proposed empirical potential based quasi-continuum theory, (EQT) [A. V. Raghunathan, J. H. Park, and N. R. Aluru, J. Chem. Phys. 127, 174701 (2007)], which is a coarse-grained multiscale framework to predict the static structure of confined fluids, with a phenomenological Langevin equation to simulate the dynamics of confined fluids in thermal equilibrium. An attractive feature of this approach is that all the input parameters to the Langevin equation (mean force profile of the confined fluid and the static friction coefficient) can be determined using the outputs of the EQT and the self-diffusivity data of the corresponding bulk fluid. The potential of mean force profile, which is a direct output from EQT is used to compute the mean force profile of the confined fluid. The density profile, which is also a direct output from EQT, along with the self-diffusivity data of the bulk fluid is used to determine the static friction coefficient of the confined fluid. We use this approach to compute the mean square displacement and survival probabilities of some important fluids such as carbon-dioxide, water, and Lennard-Jones argon confined inside slit pores. The predictions from the model are compared with those obtained using molecular dynamics simulations. This approach of combining EQT with a phenomenological Langevin equation provides a mathematically simple and computationally efficient means to study the impact of structural inhomogeneity on the self-diffusion dynamics of confined fluids.
The Journal of chemical physics 03/2013; 138(12):124109. · 3.09 Impact Factor
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ABSTRACT: The surface property of the nanochannel plays an important role in controlling the ion transport through the nanochannel.
Embedding electrodes outside the nanochannel (referred to as gated nanochannels) is a simple way to control the surface charge
density of the nanochannel. Based on the numerical simulations using coupled Poisson–Nernst–Planck and Stokes equations, we
show that a relative difference between the applied voltage and the gate voltage would alter the space charge density along
the nanochannel. Thus, the gate voltage can tune the nanochannel into a p- or n-type field effect transistor, enabling the control of fluid flow in the nanochannel. The ionic currents reveal that the ionic
flux can be controlled by the gate voltage. Analytical expressions are derived to estimate the effective space charge density
and the fluid flow in the nanochannels for a fixed gate voltage. We also suggest potential applications of the gated nanochannels.
KeywordsNanofluidic–Gate–Space charge–Diodes–Preconcentration
Microfluidics and Nanofluidics 04/2012; 11(3):297-306. · 3.37 Impact Factor
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ABSTRACT: In this paper, we propose coarse-grained single-site (CGSS), wall-CO(2), and CO(2)-CO(2) interaction potential models to study the structure of carbon dioxide under confinement. The CGSS potentials are used in an empirical potential based quasi-continuum theory, EQT, to compute the center-of-mass density and potential profiles of CO(2) confined inside different size graphite slit pores. Results obtained from EQT are compared with those obtained from all-atom molecular dynamics (AA-MD) simulations, and are found to be in good agreement with each other. Though these CGSS interaction potentials are primarily developed and parameterized for EQT, they are also used to perform coarse-grained molecular dynamics (CG-MD) simulations. The results obtained from CG-MD simulations are also found to be in reasonable agreement with AA-MD simulation results.
The Journal of chemical physics 01/2012; 136(2):024102. · 3.09 Impact Factor
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ABSTRACT: In this letter, we investigate the mechanical properties of graphene under shear deformation. Specifically, using molecular dynamics simulations, we compute the shear modulus, shear fracture strength, and shear fracture strain of zigzag and armchair graphene structures at various temperatures. To predict shear strength and fracture shear strain, we also present an analytical theory based on the kinetic analysis. We show that wrinkling behavior of graphene under shear deformation can be significant. We compute the amplitude to wavelength ratio of wrinkles using molecular dynamics and compare it with existing theory. Our results indicate that graphene can be a promising mechanical material under shear deformation.
Applied Physics Letters 02/2011; · 3.84 Impact Factor
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ABSTRACT: The characterization of physical properties of cells such as their mass and stiffness has been of great interest and can have profound implications in cell biology, tissue engineering, cancer, and disease research. For example, the direct dependence of cell growth rate on cell mass for individual adherent human cells can elucidate the mechanisms underlying cell cycle progression. Here we develop an array of micro-electro-mechanical systems (MEMS) resonant mass sensors that can be used to directly measure the biophysical properties, mass, and growth rate of single adherent cells. Unlike conventional cantilever mass sensors, our sensors retain a uniform mass sensitivity over the cell attachment surface. By measuring the frequency shift of the mass sensors with growing (soft) cells and fixed (stiff) cells, and through analytical modeling, we derive the Young's modulus of the unfixed cell and unravel the dependence of the cell mass measurement on cell stiffness. Finally, we grew individual cells on the mass sensors and measured their mass for 50+ hours. Our results demonstrate that adherent human colon epithelial cells have increased growth rates with a larger cell mass, and the average growth rate increases linearly with the cell mass, at 3.25%/hr. Our sensitive mass sensors with a position-independent mass sensitivity can be coupled with microscopy for simultaneous monitoring of cell growth and status, and provide an ideal method to study cell growth, cell cycle progression, differentiation, and apoptosis.
Proceedings of the National Academy of Sciences 11/2010; 107(48):20691-6. · 9.68 Impact Factor
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ABSTRACT: We investigate the variation in fracture strength of graphene with temperature, strain rate, and crack length using molecular dynamics (MD) simulations, kinetic analysis of fracture with a nonlinear elastic relation, and the quantized fracture mechanics theory. Young’s modulus does not vary significantly with temperature until about 1200 K, beyond which the material becomes softer. Temperature plays a more important role in determining the fracture strength of graphene. Our studies suggest that graphene can be a strong material even, when subjected to variations in temperature, strain rate, and cracks.
Journal of Applied Physics 10/2010; · 2.17 Impact Factor
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Zhu Chen,
Yingbing Jiang,
Darren R Dunphy,
David P Adams,
Carter Hodges,
Nanguo Liu,
Nan Zhang,
George Xomeritakis,
Xiaozhong Jin, N R Aluru,
Steven J Gaik,
Hugh W Hillhouse,
C Jeffrey Brinker
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ABSTRACT: Synthetic solid-state nanopores are being intensively investigated as single-molecule sensors for detection and characterization of DNA, RNA and proteins. This field has been inspired by the exquisite selectivity and flux demonstrated by natural biological channels and the dream of emulating these behaviours in more robust synthetic materials that are more readily integrated into practical devices. So far, the guided etching of polymer films, focused ion-beam sculpting, and electron-beam lithography and tuning of silicon nitride membranes have emerged as three promising approaches to define synthetic solid-state pores with sub-nanometre resolution. These procedures have in common the formation of nominally cylindrical or conical pores aligned normal to the membrane surface. Here we report the formation of 'kinked' silica nanopores, using evaporation-induced self-assembly, and their further tuning and chemical derivatization using atomic-layer deposition. Compared with 'straight through' proteinaceous nanopores of comparable dimensions, kinked nanopores exhibit up to fivefold reduction in translocation velocity, which has been identified as one of the critical issues in DNA sequencing. Additionally, we demonstrate an efficient two-step approach to create a nanopore array exhibiting nearly perfect selectivity for ssDNA over dsDNA. We show that a coarse-grained drift-diffusion theory with a sawtooth-like potential can reasonably describe the velocity and translocation time of DNA through the pore. By control of pore size, length and shape, we capture the main functional behaviours of protein pores in our solid-state nanopore system.
Nature Material 08/2010; 9(8):667-75. · 32.84 Impact Factor
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ABSTRACT: In this paper, we investigate, using molecular dynamics simulations, the conformation and diffusion of longer and shorter single-strand DNA (ssDNA) as a function of water film thickness. While the conformation of the shorter ssDNA is significantly affected and the diffusion is suppressed with reduction in water film thickness, the conformation and diffusion of the longer DNA is not influenced. We explain our observations by considering the competition between stacking interaction of bases and solvation tendency of ssDNA. This paper suggests an approach to control the surface motion of ssDNA in nanoscale water films using film thickness.
Applied Physics Letters 03/2010; 96(12):123703. · 3.84 Impact Factor
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ABSTRACT: In this paper, we develop a transferable coarse-grained interatomic potential to study the structure of simple (spherical and nonpolar) Lennard-Jones (LJ) fluids confined at supercritical temperatures. The potential is used in empirical potential based quasicontinuum theory, [A. V. Raghunathan et al., J. Chem. Phys. 127, 174701 (2007)] to study the structure of three simple LJ fluids (oxygen, methane, and argon) confined in slitlike geometries. The results obtained using the coarse-grained interatomic potential are found to be in good agreement with those predicted by equilibrium molecular dynamics simulations.
The Journal of chemical physics 01/2010; 132(4):044703. · 3.09 Impact Factor
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ABSTRACT: We show that ordering in nanoscale water film on a hydrophobic surface gives rise to fast diffusion of water. Specifically, as the surface coverage of water increases, the diffusion coefficient of water increases until a critical surface coverage and a further increase in surface coverage results in a decrease of water diffusion coefficient. For thin nanoscale films that form two layers of waters on a hydrophobic surface, the first layer of water forms a hexagonal structure, very similar to the ice Ih structure, that is independent of the surface coverage. As the surface coverage increases, the ordering of water molecules in the second layer increases and for a critical surface coverage the ordering in the second layer is maximized and the hydrogen bonding between first and second layers is minimal giving rise to fast diffusion. As the surface coverage further increases, the hydrogen bonding between the first and second layers increases and the diffusion coefficient of water is reduced. This “ordering-induced diffusion enhancement” on hydrophobic surfaces is contrary to the ordering-induced slow mobility in hydrophobic nanotubes (e.g., in a carbon nanotube).
01/2010;
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ABSTRACT: An empirical potential based quasicontinuum theory (EQT) is proposed to predict the structure, concentration, and various potential profiles of water in confined environments. EQT seamlessly unifies the continuum theory given by the Nernst-Planck equation and the atomistic theory governed by interatomic potentials. In particular, the interatomic potentials describing various interactions in water are directly incorporated into the Nernst-Planck theory. We introduce a new empirical potential to compute electrostatic interactions in water. The results from the EQT formalism are compared with molecular dynamics simulations and a good match is observed for channels with widths ranging from 2sigma(ow) to 20sigma(ow), where sigma(ow) is the water-oxygen Lennard-Jones distance parameter. While molecular dynamics can be limited to small length scales, EQT can be used at various length scales to effectively and accurately capture both the interfacial structure and bulk properties of water making it a robust and fast method that can predict properties in widths ranging from the macroscale down to the nanoscale.
The Journal of chemical physics 11/2009; 131(18):184703. · 3.09 Impact Factor
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ABSTRACT: We investigated the effect of the electric field on single-file reverse osmosis (RO) water flux using molecular dynamics simulations. The electric field is generated by introducing oppositely charged biomolecules to the salt solution and pure water chambers attached to the nanopore. Simulation results indicate that an electric field in the direction of RO enhances the water flux while in the direction opposite to RO it suppresses the water flux. When the RO water flux is enhanced, the single-file water dipoles are aligned in the direction of the electric field. The addition of an electric field in the direction of RO led to a flux of 3 water molecules ns(-1) by constantly maintaining water dipole vectors in the direction of the electric field, and this water flux is superimposed on the pressure driven water flux.
Physical Chemistry Chemical Physics 10/2009; 11(38):8614-9. · 3.57 Impact Factor
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ABSTRACT: A tight-binding method combined with molecular dynamics (MD) is used to investigate the electrostatic signals generated by DNA segments inside short semiconducting single-wall carbon nanotubes (CNTs). The trajectories of DNA, ions, and waters, obtained from MD, are used in the tight-binding method to compute the electrostatic potential. The electrostatic signals indicate that when the DNA translocates through the CNT, it is possible to identify the total number of base pairs and the relative positions of the defective base pairs in DNA chains. Our calculations suggest that it is possible to differentiate Dickerson and hairpin DNA structures by comparing the signals.
Applied Physics Letters 09/2009; 95(11):113116-113116-3. · 3.84 Impact Factor
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ABSTRACT: We investigate the mechanical strength and properties of graphene under uniaxial tensile test as a function of size and chirality using the orthogonal tight-binding method and molecular dynamics simulations with the AIREBO potential. Our results on Young's modulus, fracture strain, and fracture strength of bulk graphene are in reasonable agreement with the recently published experimental data. Our results indicate that fracture strain and fracture strength of bulk graphene under uniaxial tension can have a significant dependence on the chirality. Mechanical properties such as Young's modulus and Poisson's ratio can depend strongly on the size and chirality of the graphene nanoribbon.
Nano Letters 09/2009; 9(8):3012-5. · 13.20 Impact Factor
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ABSTRACT: a b s t r a c t Combined density functional theory and molecular dynamics simulations were performed to investigate ionic selectivity of boron nitride nanotubes (BNNTs). A finite-length (10, 10) BNNT with a diameter of 1.356 nm immersed in a reservoir of 1 M KCl solution can selectively conduct Cl À ions, while K + ions barely reach the center of the nanotube and do not conduct. In contrast, a (10, 10) single-walled carbon nanotube of approximately the same diameter immersed in a 1 M KCl solution can selectively conduct K + ions through the nanotube. We investigate the potential of mean force analysis, binding energy calcula-tions, the water structure, and its orientation, to explain the selectivity of BNNT.
08/2009;
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ABSTRACT: We perform classical molecular dynamics simulations based on the Tersoff interatomic potential to investigate the size and surface orientation dependence of lattice constant and thermal expansion coefficient of one-dimensional silicon nanostructures. Three different surface orientations of silicon are considered, i.e., Si(110), Si(111), and Si(100) with 2×1 reconstruction. For each surface orientation, we investigate nanostructures with thicknesses ranging from 0.3 to 5.0 nm. We compute the vibrational amplitude of surface atoms, lattice constant, and thermal expansion coefficient as a function of size and temperature, and compare them for different surface orientations. An analytical expression is developed to compute the variation of the thermal expansion coefficient with size of the nanostructure.
Journal of Applied Physics 06/2009; · 2.17 Impact Factor
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ABSTRACT: The present study reports on molecular dynamics investigations of chemically cross-linked poly(ethylene glycol) hydrogels with the aim of exploring the diffusion properties of water, ions, and rhodamine within the polymer at the molecular level. The water structure and diffusion properties were studied at various cross-linking densities with molecular weights of the chains ranging from 572 to 3400. As the cross-linking density is increased, the water diffusion decreases and the slowdown in diffusion is more severe at the polymer-water interface. The water diffusion at various cross-linking densities is correlated with the water hydrogen bonding dynamics. The diffusion of ions and rhodamine also decreased as the cross-linking density is increased. The variation of diffusion coefficient with cross-linking density is related to the variation of water content at different cross-linking densities. Comparison of simulation results and obstruction scaling theory for hydrogels showed similar trends.
The Journal of Physical Chemistry B 03/2009; 113(11):3512-20. · 3.70 Impact Factor
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ABSTRACT: In this letter, we investigate using molecular dynamics simulations the diffusion of water submonolayers on hydrophilic surfaces. In contrast to a strong hydrophilic Ag surface, on a weak hydrophilic Pb surface, the diffusion coefficient is remarkably enhanced at a critical surface coverage and a Lambda-shape anomaly with surface coverage is observed, i.e., the diffusion coefficient increases with the increase in surface coverage until a critical surface coverage, beyond which the diffusion coefficient decreases. We explain the anomalous diffusion of water on hydrophilic surfaces by a detailed understanding of molecular cavities and monolayer tail contributing to three-dimensional hydrogen bonding.
Applied Physics Letters 01/2009; 93(25):253104. · 3.84 Impact Factor
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ABSTRACT: Bidirectional single file water transport in a carbon nanotube is known to occur in "bursts" in short nanotubes. Here we show that in long carbon nanotubes, when the orientation of the water molecules is maintained along one direction, a net water transport along that direction can be attained due to coupling between rotational and translational motions. The rotations of the water molecules are correlated more with the translation of the neighboring water molecule with the acceptor oxygen than the neighbor with the donor hydrogen. This mechanism can be used to pump water through nanotubes.
Physical Review Letters 09/2008; 101(6):064502. · 7.37 Impact Factor
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ABSTRACT: A self-consistent tight-binding method is used to investigate the screening effects of semiconducting and metallic single-wall carbon nanotubes (SWCNTs) when the water molecules and various charged ions pass through the nanotubes. The trajectories of ions and water molecules are obtained from molecular dynamics simulations. It is shown that metallic SWCNTs have much stronger screening abilities than semiconducting SWCNTs. Our results indicate that it is possible to distinctly identify different ions and also to differentiate between armchair and zig-zag nanotubes.
Applied Physics Letters 08/2008; · 3.84 Impact Factor
