Since 2011, I have been a part of Michigan Tech's Information Technology Services while continuing to pursue research in inter-disciplinary fields and teach [under]graduate courses in Physics & Mathematical Sciences.
Collecting & reading books, sports, photography, exploring Upper Michigan's wilderness and toying around with computers -- designing & writing software/code to meet various personal needs, designing websites for good friends, etc. -- keep me busy during free-er times. Pretending to make the internet a better place, I ramble [not so] frequently about these & other topics - sometimes I tweet and facebook too. And for the record, I adore & idolize Vishweshwaraiah, Vince Lombardi and few scientists.
As much of what I do [or don't do] appears to make little or no sense, it is quite possible that I might be perceived as a very boring, obsessive & socially unacceptable entity, at times arrogant & insensitive as well. But, if you still decide to hang out, shoot me a message or stalk one or more of my alternate identities -- LinkedIn, twitter, facebook -- and I will make it worth your time.
Work
In my current role as the HPC Research Scientist at Michigan Tech, I support just about every aspect of research computing -- from desktop to high performance computing (HPC) and high performance visualization (HPV) clusters -- finding additional computing resources, when necessary, through the National Science Foundation's XSEDE Campus Champion program.
Teaching
- PH4390: Computational Methods in Physics
- PH4395: Computer Simulations in Physics
- PH4999: MATLAB & LaTeX in Physics
- MA5903: Introduction to Scientific Programming
Research
Current research interests include
- Design, development, customization, maintenance and optimization of parallel computing platform.
- Development of technological tools that assist research and classroom teaching.
- Development of computational sciences & engineering curriculum with an emphasis on high performance computing.
- Interaction of biological matter with nanomaterials.
- Electronic structure calculations of nanoclusters.
Publications
With a spread of citations on a Google map
Journal Article
Book Chapter
Conference Proceeding
MS Thesis
PhD Dissertation
# 01
Applicability of CNTs and BNNTs as Biosensors: Effect of Biomolecular Adsorption on the Transport Properties of Carbon and Boron Nitride Nanotubes
Applied Physics Letters, vol. 102, pp. 13370, 2013
DOI: 10.1063/1.4801442
Density functional theory coupled with non-equilibrium Green’s function is employed to investigate the effect of molecular adsorption on the transport properties of single walled- carbon (CNT) and boron nitride nanotubes (BNNT). The calculated I-V characteristics predict noticeable changes in the conductivity of BNNTs due to physisorption of nucleic acid base molecules, though electronic conductivity of CNTs remained unaltered upon biomolecular physisorption. Specifically, guanine which binds to the sidewall of BNNT significantly enhances its conductivity by introducing conduction channels near the Fermi energy of the bioconjugated system. For metallic CNTs, a large background current masks relative small changes in current due to the biomolecular adsorption. The results therefore suggest the suitability of BNNTs for biosensing applications.
# 02
First-Principles Computation of Structural, Elastic and Magnetic Properties of Ni2FeGa Across the Martensitic Transformation
Journal of Physics: Condensed Matter, vol. 25, pp. 02550, 2013
The structural stabilities, elastic, electronic and magnetic properties of the Heusler-type shape memory alloy Ni2FeGa are calculated using density functional theory. The volume conserving tetragonal distortion of the austenite Ni2FeGa find an energy minimum at
c/a = 1.33. A metastable behavior of the high temperature cubic austenite phase is predicted due to elastic softening in the [110] direction. Calculations of the total and partial magnetic moments show a dominant contribution from Fe atoms of the alloy. The calculated density of states show a finite gap in the minority spin channel of the cubic Ni2FeGa just below the Fermi level which gets partially filled up for the tetragonal phase. The relatively high electron density of states near the Fermi level in both the phases indicate that the Fermi surface effects may be pronounced in Ni2FeGa.
# 03
Diffusion of Water Molecules in Amorphous Silica
IEEE Electron Device Letters, vol. 33, pp. 864, 2012
The diffusive penetration of atmospheric water vapor into amorphous silica (
a-SiO2) degrades the performance of electronic devices. In this letter, we calculate the range of activation energies for water diffusion in a-SiO2 such that the diffusion time through, for example, a 0.5-µm protective layer is on the order of the decadal time scale, as required in typical applications. We find that for all practical purposes, silica composed of n-member rings is impenetrable to water vapor for n <= 5. Thus, we conclude that the distribution of n-member rings in a-SiO2 and, specifically, the n > 5 fraction is the critical parameter for predicting device performance.
# 04
Electronic Structure Calculations of Substitutional and Interstitial Hydrogen in Nb
Solid State Communications, vol. 152, pp. 788, 2012
We report the results of a theoretical study on the effects of substitutional and interstitial hydrogen atoms in niobium. We confirm that any contaminated hydrogen will occupy the interstitial site over the substitutional site in niobium. For interstitial hydrogens, the lattice deformation increases with the percentage content of hydrogen, though it is negligible at low concentrations. Substitutional hydrogens are found to prefer off-center sites in the host lattice.
# 05
10 Citations for 2010_MGSPK
Theoretical Study of Physisorption of Nucleobases on Boron Nitride Nanotubes: A New Class of Hybrid Nano-Bio Materials
Nanotechnology, vol. 21, pp. 16570, 2010
10 Citations for 2010_MGSPK
We investigate the adsorption of the nucleic acid bases -- adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) -- on the outer wall of a high curvature semiconducting single-walled boron nitride nanotube (BNNT) by first-principles density functional theory calculations. The calculated binding energy shows the order: G
> A ~ C ~ T ~ U, implying that the interaction strength of the high curvature BNNT with the nucleobases, G being an exception, is nearly the same. A higher binding energy for the G-BNNT conjugate appears to result from hybridization of the molecular orbitals of G and the BNNT. A smaller energy gap predicted for the G-BNNT conjugate relative to that of the pristine BNNT may be useful in the application of this class of biofunctional materials to the design of next-generation sensing devices.
# 06
3 Citations for 2010_MGPC
Theoretical Study of Small Clusters of Indium Oxide: InO, In2O, InO2, In2O2
Journal of Molecular Structure: THEOCHEM, vol. 948, pp. 31, 2010
3 Citations for 2010_MGPC
The structural, vibrational and electronic properties of small clusters of indium oxide (InmOn;
m,n = 1,2) in the neutral and the ionic state are studied using first-principles method based on density functional theory. The linear structures are preferred over all the other possible structures for the neutral InO clusters. The structural deformations and the instability in InO, In2O, InO2 and In2O2 are relatively higher when an electron is removed than the case when an electron is added to it. InO2, with negative electron affinity, is predicted to be highly unstable. The calculated results suggest that the neutral InO clusters are likely to become unstable when the metal to oxygen ratio is larger than unity.
# 07
2 Citations for 2010_KGSH
A Numerical Investigation Into Possible Mechanisms By That The A629P Mutant of ATP7A Causes Menkes Disease
Physical Chemistry Chemical Physics, vol. 12, pp. 11390, 2010
DOI: 10.1039/C003568H
2 Citations for 2010_KGSH
We study in silico possible mechanisms by that the A629P mutant of ATP7A causes Menkes Disease. Our results indicate that the mutation does not have appreciable affects on the stability of copper-bound states but rather destabilizes the characteristic end-to-end
β-sheet. In this way, the mutation presumably increases the probability for aggregation and/or degradation leading to decreased concentration of the monomer.
# 08
62 Citations for 2008_GSPKA
First-Principles Study of Physisorption of Nucleic Acid Bases on Small-Diameter Carbon Nanotubes
Nanotechnology, vol. 19, pp. 12570, 2008
62 Citations for 2008_GSPKA
We report the results of our first-principles study based on density functional theory on the interaction of the nucleic acid base molecules adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U), with a single-walled carbon nanotube (CNT). Specifically, the focus is on the physisorption of base molecules on the outer wall of a (5, 0) metallic CNT possessing one of the smallest diameters possible. Compared to the case for CNTs with large diameters, the physisorption energy is found to be reduced in the high-curvature case. The base molecules exhibit significantly different interaction strengths and the calculated binding energies follow the hierarchy G
> A > T > C > U, which appears to be independent of the tube curvature. The stabilizing factor in the interaction between the base molecule and CNT is dominated by the molecular polarizability that allows a weakly attractive dispersion force to be induced between them. The present study provides an improved understanding of the role of the base sequence in deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) in their interactions with carbon nanotubes of varying diameters.
# 09
79 Citations for 2007_GSAPK
Physisorption of Nucleobases on Graphene: Density Functional Calculations
Physical Review B, vol. 76, pp. 33401, 2007
79 Citations for 2007_GSAPK
We report the results of our first-principles investigation on the interaction of the nucleobases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) with graphene, carried out within the density-functional theory framework, with additional calculations utilizing Hartree-Fock plus second-order Møller-Plesset perturbation theory. The calculated binding energy of the nucleobases shows the following hierarchy: G
> A ~ T ~ C > U, with the equilibrium configuration being rather similar for all five of them. Our results clearly demonstrate that the nucleobases exhibit significantly different interaction strengths when physisorbed on graphene. The stabilizing factor in the interaction between the base molecule and graphene sheet is dominated by the molecular polarizability that allows a weakly attractive dispersion force to be induced between them. The present study represents a significant step toward a first-principles understanding of how the base sequence of DNA can affect its interaction with carbon nanotubes, as observed experimentally.
# 10
13 Citations for 2006_LGHLPK
Geometry, Electronic Properties, and Thermodynamics of Pure and Al-Doped Li Clusters
Physical Review B, vol. 74, pp. 24541, 2006
13 Citations for 2006_LGHLPK
The first-principles density functional molecular dynamics simulations have been carried out to investigate the geometric, the electronic, and the finite temperature properties of pure Li clusters (Li10, Li12) and Al-doped Li clusters (Li10Al, Li10Al2). We find that the addition of two Al impurities in Li10 results in a substantial structural change, while the addition of one Al impurity causes a rearrangement of atoms. Introduction of Al impurities in Li10 establishes a polar bond between Li and nearby Al atom(s), leading to a multicentered bonding, which weakens the Li-Li metallic bonds in the system. These weakened Li-Li bonds lead to a premelting feature to occur at lower temperatures in Al-doped clusters. In Li10Al2, Al atoms also form a weak covalent bond, resulting in their dimerlike behavior. This causes Al atoms not to "melt" until 800 K, in contrast to the Li atoms which show a complete diffusive behavior above 400 K. Thus, although one Al impurity in Li10 cluster does not change its melting characteristics significantly, two impurities results in "surface melting" of Li atoms whose motions are confined around an Al dimer.
# 11
5 Citations for 2006_GCP
Theoretical Study of Sequential Oxidation of Clusters of Gallium Oxide: Ga3On (
n: 4-8)
Chemical Physics Letters, vol. 431, pp. 358, 2006
5 Citations for 2006_GCP
We report the results of a theoretical study of sequential oxidation of gallium oxide clusters from Ga3O4 to Ga3O8. These results, based on density functional theory calculations, find the ground state of the neutral clusters to be in the lowest spin state with nearly the same binding energy of 3.5 eV per atom. Electron affinity, ionization potential and HOMO-LUMO gap values of these oxygen-rich clusters show an oscillatory trend which may be due to the fact that sequential oxidation as well as addition (and removal) of an electron leads to significant changes in the geometry of the respective neutral clusters.
# 12
15 Citations for 2005_GDCP
Structural, Energetic, Electronic, Bonding, and Vibrational Properties of Ga3O, Ga3O2, Ga3O3, Ga2O3, and GaO3 Clusters
Journal of Physical Chemistry B, vol. 109, pp. 14836, 2005
DOI: 10.1021/jp050801u
15 Citations for 2005_GDCP
The results of density functional theory based calculations on Ga3O, Ga3O2, Ga3O3, Ga2O3, and GaO3 clusters are reported here. A preference for planar arrangement of the constituent atoms maximizing the ionic interactions is found in the ground state of the clusters considered. The sequential oxidation of the metal-excess clusters increases the binding energy, but the sequential removal of a metal atom from the oxygen-excess clusters decreases the binding energy. The increase in the oxygen to metal ratio in these clusters is accompanied by increase in both electron affinity and ionization potential. The ionization induced structural distortions in the neutral clusters are relatively small, except those for Ga3O2. In anionic (cationic) clusters, the added (ionized) electron is shared by the Ga atoms, except in the case of GaO3. The vibrational frequencies and charge density analysis reveal the importance of the ionic Ga-O bond in stabilizing the gallium oxide clusters considered in this study.
# 13
21 Citations for 2004_GLDPGG
Structure, Energetics, Electronic, and Hydration Properties of Neutral and Anionic Al3O6, Al3O7 and Al3O8 Clusters
Journal of Physical Chemistry A, vol. 108, pp. 5081, 2004
DOI: 10.1021/jp038040n
21 Citations for 2004_GLDPGG
We report the results of a theoretical study of neutral and anionic Al3On (
n = 6-8) and an experimental investigation of Al3O6H2- clusters, focusing on their structural and electronic properties. Our results, based on density functional calculations, reveal that sequential oxidation of Al3O5 induces significant structural changes in the cluster configurations in which an O2 molecule tends to replace an O atom. The neutral Al3On (n = 6-8) clusters are found to be in doublet electronic states, with a planar to three-dimensional close-packed structure being most stable. The triplet state is found to be the optimum electronic state for the ground state of anionic Al3On (n = 6-8). The clusters showed an energetic preference for a twisted-pair rhombic structure, although for n = 6 and 8, a planar hexagonal structure was only 0.16 eV higher in energy. It is also shown that the strength of the oxygen-oxygen bond dominates the preferred fragmentation path for both neutral and anionic clusters. The hydration behavior of an n = 6 cluster Al3O6H2- was examined experimentally using an ion trap-secondary ion mass spectrometer under vacuum conditions, and the gas-phase clusters were shown to add three H2O molecules. Since H2O addition is consistent with the presence of under-coordinated metals in oxide clusters, the experimental result for n = 6 was consistent with the planar hexagonal structure, which contained three under-coordinated Al sites.
# 14
13 Citations for 2004_GCP
Theoretical Study of Neutral & Ionic States of Small Clusters of GamOn (
m, n = 1, 2)
Journal of Physical Chemistry B, vol. 108, pp. 17295, 2004
DOI: 10.1021/jp049305g
13 Citations for 2004_GCP
The structure, bonding, vibrational, and electronic properties of small clusters of gallium oxide, GamOn (
m, n = 1, 2) are studied here with a focus on the changes induced by the addition or removal of an electron from the neutral species. It is found that the addition of an electron introduces relatively larger structural changes than the removal of an electron from the neutral cluster. The values of ionization potential and electron affinity of these clusters are calculated, for the first time, in this study. Analysis of the atomic charges and electronic properties predicts a kind of instability in Ga2O-. In Ga2O2, the linear Ga-O-Ga-O isomer forms the ground state of the neutral cluster. The cationic structure also prefers the linear configuration, since the ionized electron comes out of an antibonding molecular orbitals of the neutral Ga2O2. The anionic Ga2O2, on the other hand, prefers the rhombus structure as a ground state since LUMO of the neutral Ga2O2 consists of a Ga-O bonding orbital.