S. Gowtham

Physisorption of nucleobases on graphene: Density-functional calculations

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 with ...

First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes

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.

Theoretical study of physisorption of nucleobases on boron nitride nanotubes : a new class of hybrid nano-biomaterials

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 approximately C approximately T approximately 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.

First-principles computation of structural, elastic and magnetic properties of Ni2FeGa across the martensitic transformation

The structural stabilities, elastic, electronic and magnetic properties of the Heusler-type shape memory alloy Ni(2)FeGa are calculated using density functional theory. The volume conserving tetragonal distortion of the austenite Ni(2)FeGa find an energy minimum at c/a = 1.33. Metastable behaviour 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 shows a depression in the minority spin channel of the cubic Ni(2)FeGa just above the Fermi level which gets partially filled up in the tetragonal phase. In contrast to Ni(2)MnGa, the transition metal spin-down states show partial hybridization in Ni(2)FeGa and there is a relatively high electron density of states near the Fermi level in both phases.

Diffusion of Water Molecules in Amorphous Silica

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-m 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.

Applicability of carbon and boron nitride nanotubes as biosensors: Effect of biomolecular adsorption on the transport properties of carbon and boron nitride nanotubes

The effect of molecular adsorption on the transport properties of single walled carbon and boron nitride nanotubes (CNTs and BNNTs) is investigated using density functional theory and non-equilibrium Greens function methods. The calculated I-V characteristics predict noticeable changes in the conductivity of semiconducting BNNTs due to physisorption of nucleic acid base molecules. Specifically, guanine which binds to the side wall 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 relatively small changes in current due to the biomolecular adsorption. The results therefore suggest the suitability of BNNTs for biosensing applications.

A numerical investigation into possible mechanisms by that the A629P mutant of ATP7A causes Menkes Disease

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.

Revision Control System (RCS) in computational sciences and engineering curriculum

The Revision Control System (RCS) is an essential aspect of software development process and software configuration management. While continuing to be an integral component of the real world, it is often left out of the main stream curriculum in most academic institutions. Instead, students are expected to learn it on their own, as a hobby or as an independent study, out of personal interest. The author describes the experiences gained from attempting to implement a distributed Revision Control System, Git, as part of the computational sciences and engineering curriculum at the undergraduate and graduate levels. The author also describes the advantages for both parties involved: improving the competency of students and preparing them for the real world expectations while providing the teacher an opportunity to provide timely feedback to the students and monitor their progress. The availability of free and open source tools used to analyze and visualize the commit history to the repository helps teachers and students observe submission and feedback patterns respectively.