Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme

Experimental studies have observed significant changes in both structure and function of lysozyme (and other proteins) on addition of a small amount of dimethyl sulfoxide (DMSO) in aqueous solution. Our atomistic molecular dynamic simulations of lysozyme in water-DMSO reveal the following sequence of changes on increasing DMSO concentration. (i) At the initial stage (around 5% DMSO concentration) protein's conformational flexibility gets markedly suppressed. From study of radial distribution functions, we attribute this to the preferential solvation of exposed protein hydrophobic residues by the methyl groups of DMSO. (ii) In the next stage (10-15% DMSO concentration range), lysozome partially unfolds accompanied by an increase both in fluctuation and in exposed protein surface area. (iii) Between 15-20% concentration ranges, both conformational fluctuation and solvent accessible protein surface area suddenly decrease again indicating the formation of an intermediate collapse state. These results are in good agreement with near-UV circular dichroism (CD) and fluorescence studies. We explain this apparently surprising behavior in terms of a structural transformation which involves clustering among the methyl groups of DMSO. (iv) Beyond 20% concentration of DMSO, the protein starts its final sojourn towards the unfolding state with further increase in conformational fluctuation and loss in native contacts. Most importantly, analysis of contact map and fluctuation near the active site reveal that both partial unfolding and conformational fluctuations are centered mostly on the hydrophobic core of active site of lysozyme. Our results could offer a general explanation and universal picture of the anomalous behavior of protein structure-function observed in the presence of cosolvents (DMSO, ethanol, tertiary butyl alcohol, dioxane) at their low concentrations. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3694268]

Amplitude death in complex networks induced by environment

We present a mechanism for amplitude death in coupled nonlinear dynamical systems on a complex network having interactions with a common environment like external system. We develop a general stability analysis that is valid for any network topology and obtain the threshold values of coupling constants for the onset of amplitude death. An important outcome of our study is a universal relation between the critical coupling strength and the largest nonzero eigenvalue of the coupling matrix. Our results are fully supported by the detailed numerical analysis for different network topologies.

Temperature gradient induced phase transitions and morphological changes in diamond thin film

The diamond films were deposited onto a wurtzite gallium nitride (GaN) thin film substrate using hot-filament chemical vapor deposition (HFCVD). During the film deposition a lateral temperature gradient was imposed across the substrate by inclining the substrate. As grown films predominantly showed the hexagonal phase, when no inclination was applied to the substrate. Tilting the substrate with respect to the heating filament by 6 degrees imposed a lateral temperature gradient across the substrate, which induced the formation of a cubic diamond phase. Diamond grains were predominantly oriented in the (100) direction. However, a further increase in the substrate tilt angle to 12 degrees, resulted in grains oriented in the (111) direction. The growth rate and hence the morphology of diamond grains varied along the inclined substrate. The present study focuses on the measurements of dominant phase formation and crystal orientation with varying substrate inclination using orientation-imaging microscopy (OIM). This technique enables direct examination of individual diamond grains and their crystallographic orientation. (C) 2012 Elsevier B.V. All rights reserved.

Microbially induced separation of quartz from hematite using yeast cells and metabolites

The utility of yeast, Saccharomyces cerevisiae, in the separation of quartz from hematite is demonstrated. Yeast cells; as well as their metabolites, functioned as flotation collectors, depressants or flocculants and dispersants for hematite and quartz. Interaction between yeast and the above minerals resulted in significant surface chemical changes, rendering quartz surfaces hydrophobic and hematite hydrophilic. Mineral-specific extracellular proteins and exopolysaccharides were secreted by yeast cells when grown in the presence of quartz and hematite, respectively. Quartz could be efficiently separated from hematite through microbially induced flotation and selective flocculation.

Swift heavy ion induced structural, iono and photoluminescence properties of beta-CaSiO3:Dy3+ nanophosphor

CaSiO3:Dy3+ (1-5 mol%) nanophosphors have been prepared by a low temperature solution combustion method. The structural and luminescence (ionoluminescence; IL and photoluminescence; PL) studies have been carried out for pristine and ion irradiated samples. The XRD patterns of pristine sample show a prominent peak at (320) for the monoclinic structure of beta-CaSiO3. Upon ion irradiation, the intensity of the prominent peak is decreased at the fluence of 7.81 x 10(12) ions cm(-2) and at higher fluence of 15.62 x 10(12) ions cm(-2), the prominent peak completely vanishes. The decrease in peak intensity might be due to the stress induced point defects. On-line IL and in situ PL studies have been carried out on pelletized samples bombarded with 100 MeV Si7+ ions with fluences in the range (7.81-15.62) x 10(12) ions cm(-2). The characteristic emission peaks at 481,574, 664 and 754 nm recorded in both IL and PL are attributed to the luminescence centers activated by Dy3+ ions. It is found that IL and PL emissions intensity decreases with increase in Si7+ ion fluence. The decrease in intensity can be due to the destruction of Si-O-Si and O-Si-O type species present on the surface of the sample. FTIR studies also confirm the Si-O-Si and O-Si-O type species observed to be sensitive for swift heavy ion (SHI) irradiated samples. (C) 2012 Elsevier B.V. All rights reserved.

Further evidence for room temperature, indentation-induced nanocrystallization in a bulk metallic glass

Room temperature nanoindentation experiments, employing two different pyramidal (Berkovich and cube-corner) indenters, were performed on a Zr-based bulk metallic glass (BMG) to critically examine the possibility of indentation-induced nanocrystallization in BMGs. Cross-sectional transmission electron microscopy images obtained from high angle annular dark field ( HAADF) and high resolution (HR) modes clearly indicate to the occurrence of nanocrystallization. Pronounced nanocrystallite formation in the case of sharper cube-corner indenter suggests that the structural transformation is favored by the high strains introduced during nanoindentation. (c) 2012 Elsevier B.V. All rights reserved.

Self Repair in Circuits-Automating Open Fault Repair in Integrated Circuits Using Field-Induced Aggregation of Carbon Nanotubes

This paper presents studies on the use of carbon nanotubes dispersed in an insulating fluid to serve as an automaton for healing open-circuit interconnect faults in integrated circuits. The physics behind the repair mechanism is the electric-field-induced diffusion limited aggregation. On the occurrence of an open fault, the repair is automatically triggered due to the presence of an electric field across the gap. We perform studies on the repair time as a function of the electric field and dispersion concentrations with the above application in mind.

Novel Radiation-Induced Properties of Graphene and Related Materials

Interaction of graphene, graphene oxide, and related nanocarbons with radiation gives rise to many novel properties and phenomena. Irradiation of graphene oxide in solid state or in solution by sunlight, UV radiation, or excimer laser radiation reduces it to graphene with negligible oxygen functionalities on the surface. This transformation can be exploited for nanopatterning and for large scale production of reduced graphene oxide (RGO). Laser-induced dehydrogenation of hydrogenated graphene can also be used for this purpose. All such laser-induced transformations are associated with thermal effects. RGO emits blue light on UV excitation, a feature that can be used to generate white light in combination with a yellow emitter. RGO as well as graphene nanoribbons are excellent detectors of infra-red radiation while RGO is a good UV detector.