Publications (201)577.37 Total impact
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ABSTRACT: We present a continuumbased approach to predict the structure and thermodynamic properties of confined fluids at multiple lengthscales, ranging from a few angstroms to macrometers. The continuum approach is based on the empirical potentialbased quasicontinuum theory (EQT) and classical density functional theory (cDFT). EQT is a simple and fast approach to predict inhomogeneous density and potential profiles of confined fluids. We use EQT potentials to construct a grand potential functional for cDFT. The EQTcDFTbased grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQTcDFT approach by simulating LennardJones fluids, namely, methane and argon, confined inside slitlike channels of graphene. We show that the EQTcDFT can accurately predict the structure and thermodynamic properties, such as density profiles, adsorption, local pressure tensor, surface tension, and solvation force, of confined fluids as compared to the molecular dynamics simulation results.The Journal of Chemical Physics 06/2015; 142(24):244116. DOI:10.1063/1.4922956 · 3.12 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We report on electronic properties of waterfilled fullerenes [H 2 O( n )@C60, H 2 O( n )@C180, and H 2 O( n )@C240] under mechanical deformation using density functional theory. Under a point load, energy gap change of empty and waterfilled fullerenes is investigated. For C60 and H 2 O( n )@C60, the energy gap decreases as the tensile strain increases. For H 2 O( n )@C60, under compression, the energy gap decreases monotonously while for C60, it first decreases and then increases. Similar behavior is observed for other empty (C180 and C240) and waterfilled [H 2 O( n )@C180 and H 2 O( n )@C240] fullerenes. The energy gap decrease of waterfilled fullerenes is due to the increased interaction between water and carbon wall under deformation.MRS Communications 05/2015; DOI:10.1557/mrc.2015.22 · 1.55 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: Biological nanopores have been extensively used for DNA base detection since these pores are widely available and tunable through mutations. Distinguishing bases of nucleic acids by passing them through nanopores has so far primarily relied on electrical signalsspecifically, ionic currents through the nanopores. However, the low signaltonoise ratio makes detection of ionic currents difficult. In this study, we show that the initially closed mechanosensitive channel of large conductance (MscL) protein pore opens for singlestranded 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 four 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. Finally, we also show that the speed of DNA translocation is roughly 1 order of magnitude slower in MscL compared to Mycobacterium smegmatis porin A (MspA), suggesting MscL to be an attractive protein pore for DNA sequencing.Keywords: DNA detection; sequencing; mechanosensitive channel of large conductance (MscL); membrane tension; ionic current; MspAJournal of Physical Chemistry Letters 01/2015; 6(4). DOI:10.1021/jz5025417 · 7.46 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: Advances made in the fabrication of micro/nanoelectromechanical (M/NEM) devices over the last ten years necessitate the understanding of the attractive force that arises from quantum fluctuations (generally referred to as Casimir effects) [Casimir H B G 1948 Proc. K. Ned. Akad. Wet. 51 793]. The fundamental mechanisms underlying quantum fluctuations have been actively investigated through various theoretical and experimental approaches. However, the effect of the force on M/NEM devices has not been fully understood yet, especially in the transition region involving gaps ranging from 10 nm to 1 μm, due to the complexity of the force. Here, we numerically calculate the Casimir effects in M/NEM devices by using the Lifshitz formula, the general expression for the Casimir effects [Lifshitz E 1956 Sov. Phys. JETP 2 73]. Since the Casimir effects are highly dependent on the permittivity of the materials, the KramerKronig relation [Landau L D, Lifshitz E M and Pitaevskii L P 1984 Electrodynamics of Continuous Media (New York: Pergamon Press)] and the optical data for metals and dielectrics are used in order to obtain the permittivity. Several simplified models for the permittivity of the materials, such as the Drude and Lorentz models [Jackson J D 1975 Classical Electrodynamics (New York: Wiley)], are also used to extrapolate the optical data. Important characteristic values of M/NEM devices, such as the pullin voltage, pullin gap, detachment length, etc, are calculated for devices operating in the transition region. Our results show that accurate predictions for the pullin behaviour are possible when the Lifshitz formula is used instead of the idealized expressions for Casimir effects. We expand this study into the dynamics of M/NEM devices, so that the time and frequency response of M/NEM devices with Casimir effects can be explored.Nanotechnology 11/2014; 25(48):485204. DOI:10.1088/09574484/25/48/485204 · 3.67 Impact Factor 
Article: Thermal noise in confined fluids
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ABSTRACT: In this work, we discuss a combined memory function equation (MFE) and generalized Langevin equation (GLE) approach (referred to as MFE/GLE formulation) to characterize thermal noise in confined fluids. Our study reveals that for fluids confined inside nanoscale geometries, the correlation time and the time decay of the autocorrelation function of the thermal noise are not significantly different across the confinement. We show that it is the strong crosscorrelation of the mean force with the molecular velocity that gives rise to the spatial anisotropy in the velocityautocorrelation function of the confined fluids. Further, we use the MFE/GLE formulation to extract the thermal force a fluid molecule experiences in a MD simulation. Noise extraction from MD simulation suggests that the frequency distribution of the thermal force is nonGaussian. Also, the frequency distribution of the thermal force near the confining surface is found to be different in the direction parallel and perpendicular to the confinement. We also use the formulation to compute the noise correlation time of water confined inside a (6,6) carbonnanotube (CNT). It is observed that inside the (6,6) CNT, in which water arranges itself in a highly concerted singlefile arrangement, the correlation time of thermal noise is about an order of magnitude higher than that of bulk water.The Journal of Chemical Physics 11/2014; 141(17):174707. DOI:10.1063/1.4900501 · 3.12 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We investigate the effect of size on intrinsic dissipation in nanostructures. We use molecular dynamics simulation and study dissipation under two different modes of deformation: stretching and bending mode. In the case of stretching deformation (with uniform strain field), dissipation takes place due to Akhiezer mechanism. For bending deformation, in addition to the Akhiezer mechanism, the spatial temperature gradient also plays a role in the process of entropy generation. Interestingly, we find that the bending modes have a higher Q factor in comparison with the stretching deformation (under the same frequency of operation). Furthermore, with the decrease in size, the difference in Q factor between the bending and stretching deformation becomes more pronounced. The lower dissipation for the case of bending deformation is explained to be due to the surface scattering of phonons. A simple model, for phonon dynamics under an oscillating strain field, is considered to explain the observed variation in dissipation rate. We also studied the scaling of Q factor with initial tension, in a beam under flexure. We develop a continuum theory to explain the observed results.Journal of Applied Physics 09/2014; 116(9):09430409430411. DOI:10.1063/1.4894282 · 2.19 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We report here a detailed thermodynamic description of water molecules inside a biological water channel. Taking advantage of highresolution molecular dynamics trajectories calculated for an aquaporin (AQP) channel, we compute the spatial translational and rotational components of water diffusion and entropy in AQP. Our results reveal that the spontaneous filling and entry of water into the pore in AQPs are driven by an entropic gain. Specifically, water molecules exhibit an elevated degree of rotational motion inside the pore, while their translational motion is slow compared with bulk. The partial charges of the lining asparagine residues at the conserved signature AsnProAla motifs play a key role in enhancing rotational diffusion and facilitating dipole flipping of water inside the pore. The frequencies of the translational and rotational motions in the power spectra overlap indicating a strong coupling of these motions in AQPs. A shooting mechanism with diffusive behavior is observed in the extracellular region which might be a key factor in the fast conduction of water in AQPs.Applied Physics Letters 08/2014; 105(8):0837020837025. DOI:10.1063/1.4893782 · 3.52 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: Crosslinking can fundamentally change the mechanical properties of a linear glassy polymer. It has been experimentally observed that when lightly crosslinked, poly(methylmethacrylate) (PMMA) has a characteristically more ductile response to mechanical loading than does linear PMMA despite having a higher glass transition temperature. Here, molecular dynamics (MD) simulations are used to investigate conformational and energetic differences between linear PMMA and lightly crosslinked PMMA under shear deformation. As consistent with experiments, crosslinked PMMA is found to have a reduced yield stress relative to linear PMMA. Using the probing capabilities of our explicit atom MD approach, it is observed that while the crosslinks have a minimal direct energy contribution to the total system, they can alter how the main chains conform to macroscopic loading. In crosslinked PMMA, the backbone aligns more with the direction of external loading, thereby reducing the force applied to (and associated deformation of) the polymer bonds. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014Journal of Polymer Science Part B Polymer Physics 03/2014; 52(6). DOI:10.1002/polb.23437 · 2.55 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: Graphene nanopore is a promising device for single molecule sensing, including DNA bases, as its single atom thickness provides high spatial resolution. To attain high sensitivity, the size of the molecule should be comparable to the pore diameter. However, when the pore diameter approaches the size of the molecule, ion properties and dynamics may deviate from the bulk values and continuum analysis may not be accurate. In this paper, we investigate the static and dynamic properties of ions with and without an external voltage drop in sub5nm graphene nanopores using molecular dynamics simulations. Ion concentration in graphene nanopores sharply drops from the bulk concentration when the pore radius is smaller than 0.9 nm. Ion mobility in the pore is also smaller than bulk ion mobility due to the layered liquid structure in the poreaxial direction. Our results show that a continuum analysis can be appropriate when the pore radius is larger than 0.9 nm if pore conductivity is properly defined. Since many applications of graphene nanopores, such as DNA and protein sensing, involve ion transport, the results presented here will be useful not only in understanding the behavior of ion transport but also in designing biomolecular sensors.The Journal of Chemical Physics 02/2014; 140(8):084707. DOI:10.1063/1.4866643 · 3.12 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We present the mechanical properties of H2O(n)@C60 under hydrostatic strain and a point load using Density Functional Theory. In each case, we performed mechanical tests under both tension and compression. The bulk modulus and elastic modulus increase as the number of water molecules increases. For fracture behavior, two mechanisms are observed: First, under compression, due to the interaction and bond formation between water and C60, structures with more water molecules begin to exhibit fracture at a lower strain. Second, under tension, fracture is initiated from the bond dissociation of CC bonds on the C60 surface.Applied Physics Letters 12/2013; 103(26):2631122631124. DOI:10.1063/1.4858486 · 3.52 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: This paper presents a datadriven framework for performing uncertainty quantification (UQ) by choosing a stochastic model that accurately describes the sources of uncertainty in a system. This model is propagated through an appropriate response surface function that approximates the behavior of this system using stochastic collocation. Given a sample of data describing the uncertainty in the inputs, our goal is to estimate a probability density function (PDF) using the kernel moment matching (KMM) method so that this PDF can be used to accurately reproduce statistics like mean and variance of the response surface function. Instead of constraining the PDF to be optimal for a particular response function, we show that we can use the properties of stochastic collocation to make the estimated PDF optimal for a wide variety of response functions. We contrast this method with other traditional procedures that rely on the Maximum Likelihood approach, like kernel density estimation (KDE) and its adaptive modification (AKDE). We argue that this modified KMM method tries to preserve what is known from the given data and is the better approach when the available data is limited in quantity. We test the performance of these methods for both univariate and multivariate density estimation by sampling random datasets from known PDFs and then measuring the accuracy of the estimated PDFs, using the known PDF as a reference. Comparing the output mean and variance estimated with the empirical moments using the raw data sample as well as the actual moments using the known PDF, we show that the KMM method performs better than KDE and AKDE in predicting these moments with greater accuracy. This improvement in accuracy is also demonstrated for the case of UQ in electrostatic and electrothermomechanical microactuators. We show how our framework results in the accurate computation of statistics in micromechanical systems.Journal of Computational Physics 12/2013; 255:521539. DOI:10.1016/j.jcp.2013.08.024 · 2.49 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: The integration of a microchannel with an ionselective nanochannel exhibits nonlinear currentvoltage characteristics owing to the concentration polarization effects. In this paper, an efficient computational impedance spectroscopic technique (CIS) is developed using an area averaged multiion transport model (MM). Using this technique, we investigate the ion transport dynamics in the Ohmic and nonOhmic regions. Under no external DC bias and in the Ohmic regime, we observe two distinct arcs. The low frequency diffusional arc characterizes the diffusiontransport and the electrical double layer (EDL) charging effects at the interface of the micro nanochannel, while the high frequency geometric arc characterizes the electric migration and displacement current effects inside the nanochannel and in the microchannel. Further, we observe an anomalous inductive arc at low frequencies (fL(m)(2)/D <= 1), in the overlimiting regime. This arc is primarily attributed to the phase effects between the first harmonic contribution of the total ionic concentration and the electric field in the induced space charge region. The microscopic diffusion boundary layer (DBL) lengths observed in the microchannel are also efficiently characterized from the impedance spectrum. Equivalent circuit models are designed to interpret the impedance response.  [Show abstract] [Hide abstract]
ABSTRACT: Encapsulation of a single water molecule in a buckyball (C60) can provide fundamental insights into the properties of water. Investigation of a single water molecule is feasible through its solitary confinement in C60. In this paper, we performed a detailed study of the properties and dynamics of a single water molecule in a buckyball using DFT and MD simulations. We report on the enhancement of rotational diffusion and entropy of a water molecule in C60, compared to a bulk water molecule. H2O@C60 has zero translational diffusion and terahertz revolution frequency. The harmonic, high amplitude rotation of a single water molecule in C60 is compared to stochastic behavior of bulk water molecules. The combination of large rotational and negligible translational motion of water in C60 creates new opportunities in nanotechnology applications.Physical Chemistry Chemical Physics 09/2013; 15(41). DOI:10.1039/c3cp53277a · 4.20 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: Periodic stretching of a string, under adiabatic condition (no thermal coupling with the environment), will increase its temperature. This represents the case of intrinsic damping where the energy associated with stretching motion is converted into thermal energy. We study this phenomenon in a graphene nanoribbon (GNR), a nanostring. We utilize classical molecular dynamics and study the scaling of dissipation rate (Q factor) with frequency. The dissipation is shown to result from strong nonlinear coupling between the stretching vibration and the outofplane thermal phonons. A Langevin dynamics framework is developed to describe the outofplane phonon dynamics under inplane stretching. The dissipation mechanism is analyzed using this framework. From the analysis, a birelaxation time model is obtained to explain the observed scaling of Q factor with frequency. We also compute the size and temperature dependence of Q factor. The decrease in Q factor with decrease in size (width) is shown to result from the elastic softening of GNR.Journal of Applied Physics 08/2013; 114(8). DOI:10.1063/1.4818612 · 2.19 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We propose a quasicontinuum hydrodynamic model for isothermal transport of LennardJones fluid confined in slit shaped nanochannels. In this work, we compute slip and viscous contributions independently and superimpose them to obtain the total velocity profile. Layering of fluid near the interface plays an important role in viscous contribution to the flow, by apparent viscosity change along the confining dimension. This relationship necessitates computing density profiles, which is done using the recently proposed empiricalpotential based quasicontinuum theory [A. V. Raghunathan, J. H. Park, and N. R. Aluru, J. Chem. Phys. 127, 174701 (2007)]. Existing correlations for density dependent viscosity provided by Woodcock [AIChE J. 52, 438 (2006)] are used to compute viscosity profile in the nanopores. A Dirichlet type slip boundary condition based on a static Langevin friction model describing centerofmass motion of fluid particles is used, the parameters of which are dependent on the fluctuations of total wallfluid force from an equilibrium molecular dynamics simulation. Different types of corrugated surfaces are considered to study wallfluid friction effects on boundary conditions. Proposed hydrodynamic model yields good agreement of velocity profiles obtained from nonequilibrium molecular dynamics simulations for gravity driven flow.The Journal of Chemical Physics 08/2013; 139(7):074109. DOI:10.1063/1.4818165 · 3.12 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: The mechanism of dissipation operative at the nanoscale remains poorly understood for most cases. In this work, using molecular dynamics simulations, we show that the unstable outofplane mode leads to the absorption of energy from the inplane motion in graphene. The inplane vibration modulates the potential energy profile for the outofplane modes. For the fundamental outofplane mode in the loading direction, the minimum of the potential energy shifts because of inplane compressive strain. The structure takes a finite amount of time to relax to the new potential energy configuration. A hysteresis in the outofplane dynamics is observed when the time period of inplane excitation becomes comparable to the time required for this relaxation. Increasing the stiffness of the outofplane modes by giving an initial tensile strain leads to a considerable decrease in dissipation rate.Nanotechnology 06/2013; 24(27):275701. DOI:10.1088/09574484/24/27/275701 · 3.67 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: An ultrathin graphene membrane is a promising candidate for various applications such as gas separation, water purification, biosensors, etc. In this study, we investigate water transport mechanisms and hydrodynamic properties such as water flux, pressure variation, velocity, viscosity, slip length, etc. Due to the unique water structure, confined in the radial direction and layered in the axial direction of the pore, water viscosity and slip length increase with a decrease in the pore radius, in contrast to water confined in a carbon nanotube. As the diameter of the pore increases, the water transport mechanism transitions from collective diffusion to frictional flow described by the modified Hagen–Poiseuille equation. Graphene membrane is shown to be ultraefficient by comparing the permeation coefficient of graphene membrane to that of a carbon nanotube and an ultrathin silicon membrane. We envision that the study presented here will help to understand and design various membrane separation processes using graphene membrane.RSC Advances 05/2013; 3(24):93659372. DOI:10.1039/C3RA40661J · 3.84 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: Recent experiments have indicated a strong influence of the substrate grain orientation on the selfordering in anodic porous alumina. Anodic porous alumina with straight pore channels grown in a stable, selfordered manner is formed on (001) oriented Al grain, while disordered porous pattern is formed on (101) oriented Al grain with tilted pore channels growing in an unstable manner. In this work, numerical simulation of the pore growth process is carried out to understand this phenomenon. The ratedetermining step of the oxide growth is assumed to be the CabreraMott barrier at the oxide/electrolyte (o/e) interface, while the substrate is assumed to determine the ratio β between the ionization and oxidation reactions at the metal/oxide (m/o) interface. By numerically solving the electric field inside a growing porous alumina during anodization, the migration rates of the ions and hence the evolution of the o/e and m/o interfaces are computed. The simulated results show that pore growth is more stable when β is higher. A higher β corresponds to more Al ionized and migrating away from the m/o interface rather than being oxidized, and hence a higher retained O:Al ratio in the oxide. Experimentally measured oxygen content in the selfordered porous alumina on (001) Al is indeed found to be about 3% higher than that in the disordered alumina on (101) Al, in agreement with the theoretical prediction. The results, therefore, suggest that ionization on (001) Al substrate is relatively easier than on (101) Al, and this leads to the more stable growth of the pore channels on (001) Al.Journal of Applied Physics 05/2013; 113(20). DOI:10.1063/1.4807295 · 2.19 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: Molecular dynamics simulations are used to investigate the mechanical properties of a silicon nanofilm covered with a defective graphene. Our results show that graphene not only enhances the mechanical properties of a silicon nanofilm but also unifies the mechanical properties of the ultrathin silicon nanofilms among different crystal orientations. The Young's modulus and critical stress of the silicon nanofilm along four crystal orientations covered with graphene decrease as the thickness of the silicon nanofilm increases. In addition, we study the effects of monoatomic vacancies and Stone–Wales (SW) defects with various concentrations on the mechanical properties of a silicon nanofilm covered with defective graphene. The results show that Young's modulus reduces linearly for monoatomic vacancies and a relatively smaller dependence is observed on SW defects, while the critical stress is more sensitive to the presence of both types of defects. The results in this paper demonstrate the significance of graphene in enhancing the mechanical properties of the silicon nanofilm.Surface Science 05/2013; 611:80–85. DOI:10.1016/j.susc.2013.01.019 · 1.87 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: In this work, we combine our earlier proposed empirical potential based quasicontinuum theory, (EQT) [A. V. Raghunathan, J. H. Park, and N. R. Aluru, J. Chem. Phys. 127, 174701 (2007)], which is a coarsegrained 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 selfdiffusivity 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 selfdiffusivity 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 carbondioxide, water, and LennardJones 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 selfdiffusion dynamics of confined fluids.The Journal of Chemical Physics 03/2013; 138(12):124109. DOI:10.1063/1.4796387 · 3.12 Impact Factor
Publication Stats
5k  Citations  
577.37  Total Impact Points  
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Institutions

1999–2015

University of Illinois, UrbanaChampaign
 • Department of Mechanical Science and Engineering
 • Beckman Institute for Advanced Science and Technology
 • Department of Electrical and Computer Engineering
Urbana, Illinois, United States


1996–1997

Massachusetts Institute of Technology
 • Research Laboratory of Electronics
 • Department of Electrical Engineering and Computer Science
Cambridge, MA, United States


1993–1996

Stanford University
 Center for Integrated Systems
Palo Alto, California, United States
