N. R. Aluru

University of Illinois, Urbana-Champaign, Urbana, Illinois, United States

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Publications (204)650.5 Total impact

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    ABSTRACT: The current rectification factor can be tailored by changing the degree of asymmetry between the fluid baths on opposite sides of a nanocapillary membrane (NCM). A symmetric device with symmetric fluid baths connected to opposite sides of the NCM did not rectify ionic current; while a NCM connected between fluid baths with a 32-fold difference in cross-sectional area produced a rectification factor of 75. The data suggests that the primary mechanism for the current rectification is the change in cross-sectional area of the fluid baths and the polarity dependent propagation of the enriched and depleted concentration polarization (CP) zones into these regions. An additional contribution to the increasing rectification factor with increasing bath asymmetry appears to be a result of electroconvection in the macropore, with inside diameters (IDs) of 625 and 850-μm. Power spectral density (PSD) analysis reveals chaotic oscillations that are consistent with electroconvection in the I-t data of the 625 and 850-μm ID macropore devices. In the ON state, current rectification keeps ionic transport toward the NCM high, increasing the speed of processes like sample enrichment. A simple means is provided to fabricate fluidic diodes with tailored current rectification factors.
    Analytical Chemistry 03/2015; DOI:10.1021/ac5019638 · 5.83 Impact Factor
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    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 signals−specifically, ionic currents through the nanopores. However, the low signal-to-noise 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 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 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. N anopore-based DNA sequencing is attractive as it is a label-free, single-molecule approach that can be utilized for high-precision DNA analysis. 1−3 Biological nanopores have been investigated for DNA base detection since they offer several advantages for single-molecule DNA analysis. 2−8 First, mutagenesis can be used to tailor the physical and chemical properties of biological nanopores; 1,8 Second, biological nanopores are synthesized by cells with an atomic level precision that may not be possible with solid-state fabrication approaches; 9 Third, crystallography data of protein channels is available at angstrom length scales. 1,2,4,9 The first biological nanopore investigated for sequencing DNA was staphylococcal α-hemolysin (αHL) protein pore; 10 an applied potential translocated a single-stranded DNA (ssDNA) molecule through the pore giving rise to modulation of the ionic current. 5
    Journal of Physical Chemistry Letters 01/2015; 6. DOI:10.1021/jz5025417 · 6.69 Impact Factor
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    ABSTRACT: The ability of silicon to dissolve in physiological environments allows its use as the basis of a high-performance inorganic integrated circuit technology for active, bioresorbable implant devices. N. R. Aluru, J. A. Rogers, and co-workers perform systematic experimental and theoretical studies of hydrolysis of silicon nanomembranes at near neutral pH, as described on page 1857. This image shows a molecular-dynamics rendering of nucleophilic attack of a silicon surface immersed in water and the resulting formation of molecules of silicic acid. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Advanced Materials 01/2015; 27(11). DOI:10.1002/adma.201404579 · 15.41 Impact Factor
  • Namjung Kim, N R Aluru
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    ABSTRACT: Advances made in the fabrication of micro/nano-electromechanical (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 Kramer-Kronig 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 pull-in voltage, pull-in gap, detachment length, etc, are calculated for devices operating in the transition region. Our results show that accurate predictions for the pull-in 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:10.1088/0957-4484/25/48/485204 · 3.67 Impact Factor
  • T Sanghi, N R Aluru
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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 cross-correlation of the mean force with the molecular velocity that gives rise to the spatial anisotropy in the velocity-autocorrelation 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 non-Gaussian. 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) carbon-nanotube (CNT). It is observed that inside the (6,6) CNT, in which water arranges itself in a highly concerted single-file 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
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    ABSTRACT: We report the intrinsic water contact angle (WCA) of multilayer graphene, explore different methods of cleaning multilayer graphene, and evaluate the efficiency of those methods based on spectroscopic analysis. Highly oriented pyrolytic graphite (HOPG) was used as a model material system to study the wettability of the multilayer graphene surface by WCA measurements. A WCA value of 45 ± 3° was measured for a clean HOPG surface, which can serve as the intrinsic WCA for multilayer graphene. A 1-min plasma treatment (100 W) decreased the WCA to 6° owing to the creation of surface defects and functionalization by oxygen-containing groups. Molecular dynamics simulations of water droplets on the HOPG surface with or without the oxygen-containing defect sites confirmed the experimental results. Heat treatment at near atmospheric pressure and wet chemical cleaning methods using hydrofluoric acid and chloroform did not change the WCA significantly. Low-pressure, high-temperature annealing under argon and hydrogen reduced the WCA to 54°, close to the intrinsic WCA of HOPG. Raman spectroscopy and atomic force microscopy did not show any significant change for the HOPG surface after this treatment, confirming low-pressure, high-temperature annealing as an effective technique to clean multilayer graphene without damaging the surface. Time-of-flight secondary ion mass spectroscopy indicated the existence of hydrocarbon species on the surface of the HOPG sample that was exposed to air for <5 min and the absence of these impurities in the bulk. X-ray photoelectron spectroscopy analyses of the sample surfaces after the different cleaning techniques were performed to correlate the WCA to the surface chemistry. X-ray photoelectron spectroscopy results revealed that the WCA value changed drastically, depending on the amounts of oxygen-containing and hydrocarbon-containing groups on the surface.
    Langmuir 10/2014; 30(43). DOI:10.1021/la503089k · 4.38 Impact Factor
  • K. Kunal, N.R. Aluru
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    ABSTRACT: We investigate the effect of size on intrinsic dissipation in nano-structures. 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):094304-094304-11. DOI:10.1063/1.4894282 · 2.19 Impact Factor
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    ABSTRACT: We report here a detailed thermodynamic description of water molecules inside a biological water channel. Taking advantage of high-resolution 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 Asn-Pro-Ala 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):083702-083702-5. DOI:10.1063/1.4893782 · 3.52 Impact Factor
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    Amir Barati Farimani, Kyoungmin Min, Narayana R Aluru
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    Amir Barati Farimani, Kyoungmin Min, Narayana R Aluru
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    ABSTRACT: Nanopore-based DNA sequencing has led to fast and high resolution recognition and detection of DNA bases. Solid-state and biological nanopores have low signal to noise ratio (SNR) (<10) and are generally too thick (>5 nm) to be able to read at single base resolution. A nanopore in graphene, a 2-D material with sub-nanometer thickness, has a SNR of ~ 3 under DNA ionic current. In this report, using atomistic and quantum simulations, we find that a single-layer MoS2 is an extraordinary material (with a SNR > 15) for DNA sequencing by two competing technologies, i.e., nanopore and nano-channel. A MoS2 nanopore shows 4 distinct ionic current signals for single nucleobase detection with low noise. In addition, a single layer MoS2 shows a characteristic change/response in the total Density of States (DOS) for each base. The band gap of MoS2 is significantly changed compared to other nano-materials (e.g. graphene, h-BN, and silicon nanowire) when bases are placed on top of the pristine MoS2 and armchair MoS2 nanoribbon, thus making MoS2 a promising material for base detection via transverse current tunneling measurement. MoS2 nanopore benefits from a craftable pore architecture (combination of Mo, and S atoms at the edge) which can be engineered to obtain the optimum sequencing signals.
    ACS Nano 07/2014; 8(8). DOI:10.1021/nn5029295 · 12.03 Impact Factor
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    ABSTRACT: Crosslinking can fundamentally change the mechanical properties of a linear glassy polymer. It has been experimentally observed that when lightly crosslinked, poly(methyl-methacrylate) (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. 2014
    Journal of Polymer Science Part B Polymer Physics 03/2014; 52(6). DOI:10.1002/polb.23437 · 2.55 Impact Factor
  • Myung E Suk, N R Aluru
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    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 sub-5-nm 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 pore-axial 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 bio-molecular sensors.
    The Journal of Chemical Physics 02/2014; 140(8):084707. DOI:10.1063/1.4866643 · 3.12 Impact Factor
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    K. Min, A. Barati Farimani, N.R. Aluru
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    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 C-C bonds on the C60 surface.
    Applied Physics Letters 12/2013; 103(26):263112-263112-4. DOI:10.1063/1.4858486 · 3.52 Impact Factor
  • Aravind Alwan, N. R. Aluru
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    ABSTRACT: This paper presents a data-driven 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; DOI:10.1016/j.jcp.2013.08.024 · 2.49 Impact Factor
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    ABSTRACT: The integration of a microchannel with an ion-selective nanochannel exhibits nonlinear current-voltage characteristics owing to the concentration polarization effects. In this paper, an efficient computational impedance spectroscopic technique (CIS) is developed using an area averaged multi-ion transport model (MM). Using this technique, we investigate the ion transport dynamics in the Ohmic and non-Ohmic regions. Under no external DC bias and in the Ohmic regime, we observe two distinct arcs. The low frequency diffusional arc characterizes the diffusion-transport 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.
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    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
  • K. Kunal, N. R. Aluru
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    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 nano-string. We utilize classical molecular dynamics and study the scaling of dissipation rate (Q factor) with frequency. The dissipation is shown to result from strong non-linear coupling between the stretching vibration and the out-of-plane thermal phonons. A Langevin dynamics framework is developed to describe the out-of-plane phonon dynamics under in-plane stretching. The dissipation mechanism is analyzed using this framework. From the analysis, a bi-relaxation 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
  • Ravi Bhadauria, N R Aluru
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    ABSTRACT: We propose a quasi-continuum hydrodynamic model for isothermal transport of Lennard-Jones 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 empirical-potential based quasi-continuum 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 center-of-mass motion of fluid particles is used, the parameters of which are dependent on the fluctuations of total wall-fluid force from an equilibrium molecular dynamics simulation. Different types of corrugated surfaces are considered to study wall-fluid friction effects on boundary conditions. Proposed hydrodynamic model yields good agreement of velocity profiles obtained from non-equilibrium 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
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    ABSTRACT: Mechanically induced reactivity is a promising means for designing self-reporting materials. Mechanically sensitive chemical groups called mechanophores are covalently linked into polymers in order to trigger specific chemical reactions upon mechanical loading. These mechanophores can be linked either within the backbone or as crosslinks between backbone segments. Mechanophore response is sensitive to both the matrix properties and placement within the matrix, providing two avenues for material design. A model framework is developed to describe reactivity of mechanophores located as crosslinks in a glassy polymer matrix. Simulations are conducted at the molecular and macromolecular scales in order to develop macroscale constitutive relations. The model is developed specifically for the case of spiropyran (SP) in lightly crosslinked polymethylmethacrylate (PMMA). This optically trackable mechanophore (fluorescent when activated) allows the model to be assessed in terms of observed experimental behavior. The force modified potential energy surface (FMPES) framework is used in conjunction with ab initio steered molecular dynamics (MD) simulations of SP to determine the mechanophore kinetics. MD simulations of the crosslinked PMMA structure under shear deformation are used to determine the relationship between macroscale stress and local force on the crosslinks. A continuum model implemented in a finite element framework synthesizes these mechanochemical relations with the mechanical behavior. The continuum model with parameters taken directly from the FMPES and MD analyses under predicts stress-driven activation relative to experimental data. The continuum model, with the physically motivated modification of force fluctuations, provides an accurate prediction for monotonic loading across three decades of strain rate and creep loading, suggesting that the fundamental physics are captured.
    Journal of Applied Physics 07/2013; 114(2). DOI:10.1063/1.4812581 · 2.19 Impact Factor
  • Yanbin Wu, Narayana R Aluru
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    ABSTRACT: In this study, we develop graphitic carbon-water non-bonded interaction parameters entirely from ab initio calculation data. First, we employ the MØller-Plesset perturbation theory of the 2nd order (MP2) method to compute the polycyclic aromatic hydrocarbon(PAH)-water interaction energies, with proper size of basis sets and energy component analysis to extrapolate to infinite-sized graphene limit. Then, we develop graphitic carbon-water interaction parameters based on the MP2 data from this work and the ab initio data available in the literature from other methods such as random-phase approximation (RPA), density functional theory-symmetry-adapted perturbation theory (DFT-SAPT) and couple cluster treatment with single and double excitations and perturbative triples (CCSD(T)). The accuracy of the interaction parameters is evaluated by predicting water contact angle on graphite and carbon nanotube (CNT) radial breathing mode (RBM) frequency shift and comparing them with experimental data. The interaction parameters obtained from MP2 data predict the CNT RBM frequency shift that is in good agreement with experiments. The interaction parameters obtained from RPA and DFT-SAPT data predict the contact angles and the CNT RBM frequency shift that agree well with experiments. The interaction parameters obtained from CCSD(T) data underestimate the contact angles and overestimate the CNT RBM frequency shift probably due to the use of small basis sets in CCSD(T) calculations.
    The Journal of Physical Chemistry B 06/2013; 117(29). DOI:10.1021/jp402051t · 3.38 Impact Factor

Publication Stats

5k Citations
650.50 Total Impact Points

Institutions

  • 1999–2015
    • University of Illinois, Urbana-Champaign
      • • Department of Materials Science and Engineering
      • • Department of Mechanical Science and Engineering
      • • Beckman Institute for Advanced Science and Technology
      • • Department of Electrical and Computer Engineering
      Urbana, Illinois, United States
  • 2006
    • Clemson University
      • Department of Mechanical Engineering
      CEU, South Carolina, United States
  • 1996–1997
    • Massachusetts Institute of Technology
      • • Research Laboratory of Electronics
      • • Department of Electrical Engineering and Computer Science
      Cambridge, MA, United States