[Show abstract][Hide abstract] ABSTRACT: We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.
PLoS ONE 07/2015; 10(7):e0131754. DOI:10.1371/journal.pone.0131754 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We present a continuum-based approach to predict the structure and thermodynamic properties of confined fluids at multiple length-scales, ranging from a few angstroms to macro-meters. The continuum approach is based on the empirical potential-based quasi-continuum 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 EQT-cDFT-based grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQT-cDFT approach by simulating Lennard-Jones fluids, namely, methane and argon, confined inside slit-like channels of graphene. We show that the EQT-cDFT 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 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We report on electronic properties of water-filled 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 water-filled 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 water-filled [H
2
O(
n
)@C180 and H
2
O(
n
)@C240] fullerenes. The energy gap decrease of water-filled fullerenes is due to the increased interaction between water and carbon wall under deformation.
[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 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.Keywords: DNA detection; sequencing; mechanosensitive channel of large conductance (MscL); membrane tension; ionic current; MspA
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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 · 2.95 Impact Factor
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[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 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 · 2.95 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 C-C bonds on the C60 surface.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[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.
[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 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.
[Show abstract][Hide abstract] 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 · 2.95 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 out-of-plane mode leads to the absorption of energy from the in-plane motion in graphene. The in-plane vibration modulates the potential energy profile for the out-of-plane modes. For the fundamental out-of-plane mode in the loading direction, the minimum of the potential energy shifts because of in-plane compressive strain. The structure takes a finite amount of time to relax to the new potential energy configuration. A hysteresis in the out-of-plane dynamics is observed when the time period of in-plane excitation becomes comparable to the time required for this relaxation. Increasing the stiffness of the out-of-plane modes by giving an initial tensile strain leads to a considerable decrease in dissipation rate.
[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 ultra-efficient 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.