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]

Dependence of climate forcing and response on the altitude of black carbon aerosols

Black carbon aerosols absorb solar radiation and decrease planetary albedo, and thus can contribute to climate warming. In this paper, the dependence of equilibrium climate response on the altitude of black carbon is explored using an atmospheric general circulation model coupled to a mixed layer ocean model. The simulations model aerosol direct and semi-direct effects, but not indirect effects. Aerosol concentrations are prescribed and not interactive. It is shown that climate response of black carbon is highly dependent on the altitude of the aerosol. As the altitude of black carbon increases, surface temperatures decrease; black carbon near the surface causes surface warming, whereas black carbon near the tropopause and in the stratosphere causes surface cooling. This cooling occurs despite increasing planetary absorption of sunlight (i.e. decreasing planetary albedo). We find that the trend in surface air temperature response versus the altitude of black carbon is consistent with our calculations of radiative forcing after the troposphere, stratosphere, and land surface have undergone rapid adjustment, calculated as ``regressed'' radiative forcing. The variation in climate response from black carbon at different altitudes occurs largely from different fast climate responses; temperature dependent feedbacks are not statistically distinguishable. Impacts of black carbon at various altitudes on the hydrological cycle are also discussed; black carbon in the lowest atmospheric layer increases precipitation despite reductions in solar radiation reaching the surface, whereas black carbon at higher altitudes decreases precipitation.

Quenching across quantum critical points in periodic systems: Dependence of scaling laws on periodicity

We study the quenching dynamics of a many-body system in one dimension described by a Hamiltonian that has spatial periodicity. Specifically, we consider a spin-1/2 chain with equal xx and yy couplings and subject to a periodically varying magnetic field in the (z) over cap direction or, equivalently, a tight-binding model of spinless fermions with a periodic local chemical potential, having period 2q, where q is a positive integer. For a linear quench of the strength of the magnetic field (or chemical potential) at a rate 1/tau across a quantum critical point, we find that the density of defects thereby produced scales as 1/tau(q/(q+1)), deviating from the 1/root tau scaling that is ubiquitous in a range of systems. We analyze this behavior by mapping the low-energy physics of the system to a set of fermionic two-level systems labeled by the lattice momentum k undergoing a nonlinear quench as well as by performing numerical simulations. We also show that if the magnetic field is a superposition of different periods, the power law depends only on the smallest period for very large values of tau, although it may exhibit a crossover at intermediate values of tau. Finally, for the case where a zz coupling is also present in the spin chain, or equivalently, where interactions are present in the fermionic system, we argue that the power associated with the scaling law depends on a combination of q and the interaction strength.

Compositional dependence optical properties study of As40Se60-xSbx thin films

Thin films were thermally evaporated from the bulk glasses of As40Se60-xSbx (with x = 0, 5, 10, 15 at.%) under high vacuum. We have characterized the deposited films by Fourier Transform Infrared spectroscopy. The relationship between the structural and optical properties and the compositional variation has been investigated. Increasing Sb content was found to affect the thermal and optical properties of these films. Non-direct electronic transition was found to be responsible for the photon absorption inside the investigated films. It was found that, the optical band gap E-o decreases while the width of localized states (Urbach energy) E-e increases. (C) 2011 Elsevier B.V. All rights reserved.

Dependence of Protein Adsorption on Wetting Behavior of UHMWPE-HA-Al2O3-CNT Hybrid Biocomposites

Ultrahigh-molecular-weight polyethylene (UHMWPE) is used as an articulating surface in total hip and knee joint replacement. In order to enhance long-term durability/wear resistance properties, UHMWPE-based polymer-ceramic hybrid composites are being developed. Surface properties such as wettability and protein adsorption alter with reinforcement or with change in surface chemistry. From this perspective, the wettability and protein adsorption behavior of compression-molded UHMWPE-hydroxyapatite (HA)-aluminum oxide (Al2O3)-carbon nanotube (CNT) composites were analyzed in conjunction with surface roughness. The combined effect of Al2O3 and CNT shows enhancement of the contact angle by similar to 37A degrees compared with the surface of the UHMWPE matrix reinforced with HA. In reference to unreinforced UHMWPE, protein adsorption density also increased by similar to 230% for 2 wt.%HA-5 wt.%Al2O3-2 wt.%CNT addition to UHMWPE. An important conclusion is that the polar and dispersion components of the surface free energy play a significant role in wetting and protein adsorption than do the total free energy or chemistry of the surface. The results of this study have major implications for the biocompatibility of these newly developed biocomposites.

Transport in nanoporous zeolites: Relationships between sorbate size, entropy, and diffusivity

Molecular dynamics simulations have been performed on monatomic sorbates confined within zeolite NaY to obtain the dependence of entropy and self-diffusivity on the sorbate diameter. Previously, molecular dynamics simulations by Santikary and Yashonath J. Phys. Chem. 98, 6368 (1994)], theoretical analysis by Derouane J. Catal. 110, 58 (1988)] as well as experiments by Kemball Adv. Catal. 2, 233 (1950)] found that certain sorbates in certain adsorbents exhibit unusually high self-diffusivity. Experiments showed that the loss of entropy for certain sorbates in specific adsorbents was minimum. Kemball suggested that such sorbates will have high self-diffusivity in these adsorbents. Entropy of the adsorbed phase has been evaluated from the trajectory information by two alternative methods: two-phase and multiparticle expansion. The results show that anomalous maximum in entropy is also seen as a function of the sorbate diameter. Further, the experimental observation of Kemball that minimum loss of entropy is associated with maximum in self-diffusivity is found to be true for the system studied here. A suitably scaled dimensionless self-diffusivity shows an exponential dependence on the excess entropy of the adsorbed phase, analogous to excess entropy scaling rules seen in many bulk and confined fluids. The two trajectory-based estimators for the entropy show good semiquantitative agreement and provide some interesting microscopic insights into entropy changes associated with confinement.

Carrier concentration dependence of donor activation energy in n-type GaN epilayers grown on Si (111) by plasma-assisted MBE

The n-type GaN layers were grown by plasma-assisted MBE and either intentionally doped with Si or unintentionally doped. The optical characteristics of a donor level in Si-doped, GaN were studied in terms of photoluminescence (PL) spectroscopy as a function of electron concentration. Temperature dependent PL measurements allowed us to estimate the activation energy of a Si-related donor from temperature-induced decay of PL intensity. PL peak positions, full width at half maximum of PL and activation energies are found to be proportional to the cube root of carrier density. The involvement of donor levels is supported by the temperature-dependent electron concentration measurements. (C) 2012 Elsevier Ltd. All rights reserved.

Mechanical properties of ZnS nanowires and thin films: Microscopic origin of the dependence on size and growth direction

Mechanical properties of ZnS nanowires and thin films are studied as a function of size and growth direction using all-atom molecular dynamics simulations. Using the stress-strain relationship we extract Young's moduli of nanowires and thin films at room temperature. Our results show that Young's modulus of 0001] nanowires has strong size dependence. On the other hand, 01 (1) over bar0] nanowires do not exhibit a strong size dependence of Young's modulus in the size range we have investigated. We provide a microscopic understanding of this behavior on the basis of bond stretching and contraction due to the rearrangement of atoms in the surface layers. The ultimate tensile strengths of the nanowires do not show much size dependence. To investigate the mechanical behavior of ZnS in two dimensions, we calculate Young's modulus of thin films under tensile strain along the 0001] direction. Young's modulus of thin films converges to the bulk value more rapidly than that of the 0001] nanowire.

Temperature dependence of spin lifetime of conduction electrons in bulk germanium

Optically generated spin polarized electrons in bulk n-type Ge samples have been detected by using a radio-frequency modulation technique. Using the Hanle effect in an external magnetic field, the spin lifetime was measured as a function of temperature in the range 90 K to 180 K. The lifetime decreases with increasing temperature from similar to 5 ns at 100 K to similar to 2 ns at 180 K. We show that the temperature dependence is consistent with the Elliott-Yafet spin relaxation mechanism R. J. Elliot, Phys. Rev. 96, 266 (1954)]. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4772500]

Study of Submerged Jet for Suction of Fluid

This paper deals with the study of a submerged jet for the suction of unwanted fluid. This submerged jet is caused by the fluid coming out from a source. The presence of a sink in front of this source facilitates the suction of the fluid depending upon the source and sink flow rates, the axial and lateral separations of the source and sink, and the angle between the axes of the source and sink. The main purpose is the determination of the sink flow rate for 100% removal of the source fluid as a function of these parameters. The experiments have been carried using a source nozzle 6 mm in diameter and two sizes for the sink pipe diameter: 10 mm and 20 mm. The main diagnostics used are flow visualization using dye and particle image velocimetry (PIV). The dependence of the required suction flow rate to obtain 100% effectiveness on the suction tube diameter and angle is relatively weak compared to the lateral separation. DOI: 10.1115/1.4007266]

Quantitative interactions between the A-type K+ current and inositol trisphosphate receptors regulate intraneuronal Ca2+ waves and synaptic plasticity

Key points center dot Active calcium signal propagation occurs when an initial calcium trigger elicits calcium release through endoplasmic reticulum (ER) receptors. A high concentration of the calcium trigger in thin-calibre dendrites would suppress release of calcium through hippocampal inositol trisphosphate receptors (InsP3Rs). center dot Could the high-density expression of A-type K+ channels in thin-calibre dendrites be a mechanism for inhibiting this suppression, thereby restoring the utility of the ER as a substrate for active calcium propagation? center dot Quantitative analyses involving experimentally constrained models reveal a bell-shaped dependence of calcium released through InsP3Rs on the A-type K+ channel density, during the propagation of a calcium wave. center dot A-type K+ channels regulated the relative contribution of ER calcium to the induction of synaptic plasticity in the presence of model metabotropic glutamate receptors. center dot These results identify a novel form of interaction between active dendrites and the ER membrane and suggest that A-type K+ channels are ideally placed for inhibiting the suppression of InsP3Rs in thin-calibre dendrites. Abstract The A-type potassium current has been implicated in the regulation of several physiological processes. Here, we explore a role for the A-type potassium current in regulating the release of calcium through inositol trisphosphate receptors (InsP3R) that reside on the endoplasmic reticulum (ER) of hippocampal pyramidal neurons. To do this, we constructed morphologically realistic, conductance-based models equipped with kinetic schemes that govern several calcium signalling modules and pathways, and constrained the distributions and properties of constitutive components by experimental measurements from these neurons. Employing these models, we establish a bell-shaped dependence of calcium release through InsP3Rs on the density ofA-type potassium channels, during the propagation of an intraneuronal calcium wave initiated through established protocols. Exploring the sensitivities of calcium wave initiation and propagation to several underlying parameters, we found that ER calcium release critically depends on dendritic diameter and that wave initiation occurred at branch points as a consequence of a high surface area to volume ratio of oblique dendrites. Furthermore, analogous to the role ofA-type potassium channels in regulating spike latency, we found that an increase in the density ofA-type potassium channels led to increases in the latency and the temporal spread of a propagating calcium wave. Next, we incorporated kinetic models for the metabotropic glutamate receptor (mGluR) signalling components and a calcium-controlled plasticity rule into our model and demonstrate thatthe presence of mGluRs induced a leftward shift in a BienenstockCooperMunro-like synaptic plasticity profile. Finally, we show that the A-type potassium current could regulate the relative contribution of ER calcium to synaptic plasticity induced either through 900 pulses of various stimulus frequencies or through theta burst stimulation. Our results establish a novel form of interaction between active dendrites and the ER membrane, uncovering a powerful mechanism that could regulate biophysical/biochemical signal integration and steer the spatiotemporal spread of signalling microdomains through changes in dendritic excitability.

Dependence of electron recombination time and light to electricity conversion efficiency on shape of the nanocrystal light sensitizer

Tunability of electron recombination time and light to electricity conversion efficiency to superior values in semiconductor sensitized solar cells via optimized design of nanocrystal light sensitizer shape is discussed here.

Chemical unfolding of chicken villin headpiece in aqueous dimethyl sulfoxide solution: cosolvent concentration dependence, pathway, and microscopic mechanism

Unfolding of a protein often proceeds through partial unfolded intermediate states (PUIS). PUIS have been detected in several experimental and simulation studies. However, complete analyses of transitions between different PUIS and the unfolding trajectory are sparse. To understand such dynamical processes, we study chemical unfolding of a small protein, chicken villin head piece (HP-36), in aqueous dimethyl sulfoxide (DMSO) solution. We carry out molecular dynamics simulations at various solution compositions under ambient conditions. In each concentration, the initial step of unfolding involves separation of two adjacent native contacts, between phenyl alanine residues (11-18 and 7-18). This first step induces, under appropriate conditions, subsequent separation among other hydrophobic contacts, signifying a high degree of cooperativity in the unfolding process. The observed sequence of structural changes in HP-36 on increasing DMSO concentration and the observed sequence of PUIS, are in approximate agreement with earlier simulation results (in pure water) and experimental observations on unfolding of HP-36. Peculiar to water-DMSO mixture, an intervening structural transformation (around 15% of DMSO) in the binary mixture solvent retards the progression of unfolding as composition is increased. This is reflected in a remarkable nonmonotonic composition dependence of RMSD, radius of gyration and the fraction of native contacts. At 30% mole fraction of DMSO, we find the extended randomly coiled structure of the unfolded protein. The molecular mechanism of DMSO induced unfolding process is attributed to the initial preferential solvation of the hydrophobic side chain atoms through the methyl groups of DMSO, followed by the hydrogen bonding of the oxygen atom of DMSO to the exposed backbone NH groups of HP-36.

Runtime dependence computation and execution of loops on heterogeneous systems

GPUs have been used for parallel execution of DOALL loops. However, loops with indirect array references can potentially cause cross iteration dependences which are hard to detect using existing compilation techniques. Applications with such loops cannot easily use the GPU and hence do not benefit from the tremendous compute capabilities of GPUs. In this paper, we present an algorithm to compute at runtime the cross iteration dependences in such loops. The algorithm uses both the CPU and the GPU to compute the dependences. Specifically, it effectively uses the compute capabilities of the GPU to quickly collect the memory accesses performed by the iterations by executing the slice functions generated for the indirect array accesses. Using the dependence information, the loop iterations are levelized such that each level contains independent iterations which can be executed in parallel. Another interesting aspect of the proposed solution is that it pipelines the dependence computation of the future level with the actual computation of the current level to effectively utilize the resources available in the GPU. We use NVIDIA Tesla C2070 to evaluate our implementation using benchmarks from Polybench suite and some synthetic benchmarks. Our experiments show that the proposed technique can achieve an average speedup of 6.4x on loops with a reasonable number of cross iteration dependences.