Biomedical subjects

Nisanth N Nair

Publications and source records attributed to Nisanth N Nair.

5 recordsLinked to original sources

PubMed2006

Glycine at the pyrite-water interface: the role of surface defects.

Ab initio molecular dynamics simulations were performed in order to study chemisorption, electronic properties, and desorption of glycine at wet pyrite surfaces focusing on the role of surface point defects. The change in the electronic structure and its influence on the chemical reactivity of the free FeS(2)(100) surface due to sulfur vacancies was studied in detail yielding several adsorption modes of glycine and water molecules. Energetically preferred adsorption modes were furthermore investigated in the presence of hot pressurized water mimicking "Iron Sulfur World" prebiotic conditions. The metadynamics Car-Parrinello technique was employed to map the free energy landscape including paths and barriers for desorption of glycine from such wet defective surfaces. The ubiquitous sulfur vacancies are found to increase the retention time of the adsorbed amino acid by many orders of magnitudes in comparison to the ideal pyrite-water interface. The importance of these findings in terms of a possible two-dimensional primordial chemistry on mineral surfaces is discussed.

Journal Article↗

PubMed2006

Molecular dynamics study of the thermal entropy in mixed zinc chalcogenides.

Molecular dynamics (MD) calculations were performed to determine the vibrational contribution to the entropy of mixing and its importance for the mixing of ZnO/ZnS and ZnS/Zn3P2. These systems were modeled by cyclic clusters Zn48O48, Zn32S32, and Zn48P32. The mixed cyclic clusters considered were Zn48O47S, Zn32S31O, Zn33S30P2, and Zn47S2P30. For each of the clusters, the entropy was calculated in the range of the experimental temperature of the mixing process. The convergence of the entropy with respect to the number of MD steps was studied. Finally, the thermal part of the entropy of mixing was determined, and its dependence on the number of MD steps was investigated. It was found that the thermal entropy is important for the Gibbs free energy of mixing near the miscibility gaps.

Journal Article↗

PubMed2005

Toward an understanding of the formation of vanadia-titania catalysts.

Structures of hydrated vanadia species on the TiO2-anatase surfaces were investigated using the semiempirical molecular orbital method MSINDO. The (101), (001), and (100) surfaces of anatase were considered. They were modeled by appropriate two-dimensional cyclic clusters of TiO2. Monomeric and dimeric hydrated vanadia species on the anatase surfaces were simulated by adsorbing VO4H3 and V2O7H4 molecules, respectively. Different adsorption structures were considered, and their stabilities at 300 and 600 K were tested by constant-temperature Born-Oppenheimer molecular dynamics simulations in the framework of MSINDO. Structural features of the vanadia-titania catalysts found in extended X-ray absorption fine structure, secondary ion mass spectrometry, IR, Raman, and NMR spectroscopy and conductivity experiments can be explained by the present calculations.

Journal Article↗

PubMed2005

Molecular dynamics investigation of oxygen vacancy diffusion in rutile.

Oxygen vacancy diffusion in rutile was studied by Born-Oppenheimer molecular dynamics techniques in the framework of the semiempirical molecular orbital method MSINDO. Migration of an oxygen vacancy from the rutile (110) surface towards the bulk was simulated. The metadynamics technique was employed to accelerate the diffusion processes. In this way, transition state structures and activation energies for the diffusion processes were obtained. Rate constants and the time scale of diffusion processes were estimated for different temperatures using the calculated activation energy. It was found that the vacancies in the bulk are less stable than on the surface. The feasibility of oxygen vacancy diffusion under experimental conditions is discussed.

Computer Simulation↗

PubMed2004

Molecular dynamics implementation in MSINDO: study of silicon clusters.

Born-Oppenheimer molecular dynamics is implemented in the semiempirical self-consistent field molecular orbital method MSINDO. The method is employed for the investigation of the structure and dynamics of silicon clusters of various sizes. The reliability of the present parameterization for silicon compounds is demonstrated by a comparison of the results of simulated annealing and of density functional calculations of Si(n) clusters (n = 5-7). The melting behavior of the Si(7) cluster is investigated and the MSINDO results are compared to previous high-level calculations. The efficiency of the present approach for the treatment of large systems is demonstrated by an extensive simulated annealing study of the Si(45) and Si(60) clusters. New Si(45) and Si(60) structures are found and evaluated. The relative stability of various energy minimum structures is compared with density functional calculations and available literature data.

Journal Article↗