Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism

Pyrrolysyl-tRNA synthetase (PyIRS) is an atypical enzyme responsible for charging tRNA(Pyl) with pyrrolysine, despite lacking precise tRNA anticodon recognition. This dimeric protein exhibits allosteric regulation of function, like any other tRNA synthetases. In this study we examine the paths of allosteric communication at the atomic level, through energy-weighted networks of Desulfitobacterium hafniense PyIRS (DhPyIRS) and its complexes with tRNA(Pyl) and activated pyrrolysine. We performed molecular dynamics simulations of the structures of these complexes to obtain an ensemble conformation-population perspective. Weighted graph parameters relevant to identifying key players and ties in the context of social networks such as edge/node betweenness, closeness index, and the concept of funneling are explored in identifying key residues and interactions leading to shortest paths of communication in the structure networks of DhPylRS. Further, the changes in the status of important residues and connections and the costs of communication due to ligand induced perturbations are evaluated. The optimal, suboptimal, and preexisting paths are also investigated. Many of these parameters have exhibited an enhanced asymmetry between the two subunits of the dimeric protein, especially in the pretransfer complex, leading us to conclude that encoding of function goes beyond the sequence/structure of proteins. The local and global perturbations mediated by appropriate ligands and their influence on the equilibrium ensemble of conformations also have a significant role to play in the functioning of proteins. Taking a comprehensive view of these observations, we propose that the origin of many functional aspects (allostery rand half-sites reactivity in the case of DhPyIRS) lies in subtle rearrangements of interactions and dynamics at a global level.

Influence of the highest occupied molecular orbital energy level of the donor material on the effectiveness of the anode buffer layer in organic solar cells

Efficiency of organic photovoltaic cells based on organic electron donor/organic electron acceptor junctions can be strongly improved when the transparent conductive Anode is coated with a Buffer Layer (ABL). Here, the effects of a metal (gold) or oxide (molybdenum oxide) ABL are reported, as a function of the Highest Occupied Molecular Orbital (HOMO) of different electron donors. The results indicate that a good matching between the work function of the anode and the highest occupied molecular orbital of the donor material is the major factor limiting the hole transfer efficiency. Indeed, gold is efficient as ABL only when the HOMO of the organic donor is close to its work function Phi(Au). Therefore we show that the MoO(3) oxide has a wider field of application as ABL than gold. (C) 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Compiler Assisted Leakage Energy Optimization for Clustered VLIW Architectures

Miniaturization of devices and the ensuing decrease in the threshold voltage has led to a substantial increase in the leakage component of the total processor energy consumption. Relatively simpler issue logic and the presence of a large number of function units in the VLIW and the clustered VLIW architectures attribute a large fraction of this leakage energy consumption in the functional units. However, functional units are not fully utilized in the VLIW architectures because of the inherent variations in the ILP of the programs. This underutilization is even more pronounced in the context of clustered VLIW architectures because of the contentions for the limited number of slow intercluster communication channels which lead to many short idle cycles.In the past, some architectural schemes have been proposed to obtain leakage energy bene .ts by aggressively exploiting the idleness of functional units. However, presence of many short idle cycles cause frequent transitions from the active mode to the sleep mode and vice-versa and adversely a ffects the energy benefits of a purely hardware based scheme. In this paper, we propose and evaluate a compiler instruction scheduling algorithm that assist such a hardware based scheme in the context of VLIW and clustered VLIW architectures. The proposed scheme exploits the scheduling slacks of instructions to orchestrate the functional unit mapping with the objective of reducing the number of transitions in functional units thereby keeping them off for a longer duration. The proposed compiler-assisted scheme obtains a further 12% reduction of energy consumption of functional units with negligible performance degradation over a hardware-only scheme for a VLIW architecture. The benefits are 15% and 17% in the context of a 2-clustered and a 4-clustered VLIW architecture respectively. Our test bed uses the Trimaran compiler infrastructure.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.

Effect of pairing fluctuations on low-energy electronic spectra in cuprate superconductors

We describe here a minimal theory of tight-binding electrons moving on the square planar Cu lattice of the hole-doped cuprates and mixed quantum mechanically with their own Cooper pairs. The superconductivity occurring at the transition temperature T(c) is the long-range, d-wave symmetry phase coherence of these Cooper pairs. Fluctuations, necessarily associated with incipient long-range superconducting order, have a generic large-distance behavior near T(c). We calculate the spectral density of electrons coupled to such Cooper-pair fluctuations and show that features observed in angle resolved photoemission spectroscopy (ARPES) experiments on different cuprates above T(c) as a function of doping and temperature emerge naturally in this description. These include ``Fermi arcs'' with temperature-dependent length and an antinodal pseudogap, which fills up linearly as the temperature increases toward the pseudogap temperature. Our results agree quantitatively with experiment. Below T(c), the effects of nonzero superfluid density and thermal fluctuations are calculated and compared successfully with some recent ARPES experiments, especially the observed bending or deviation of the superconducting gap from the canonical d-wave form.

Gibbs energy of formation of nickel orthosilicate (Ni2SiO4)

Two solid state galvanic cells:Pt, Ni + Ni2Si04 + Si02/(Y203)Zr02/Ni + + NiO, Pt (1) and Pt, Ni + NizSiOj + Si02/CaF2/Ni + + NiO, Pt (11) have been employed for the determination of the Gibbs' energy of formation of nickel orthosilicate(Ni2Si04) from nickel oxide and quartz. The emf of cell (I) was reversible and reproducible in the temperature range 925 to 1375K whereas emf of cell (11) drifted with time and changed polarity. From the results of cell (I), the Gibbs' energy of formation of nickel silicate is obtained as,2Ni0 (r.s.) + Si02 (quartz) + Ni2Si04 (olivine)Gibbs' energy of formation of the spinel form of Ni2Si04 is obtained by combining the data for olivine obtained in this study with high pressure data on olivine to spinel transition reported in the literature. The complex time dependence of the emf of cell (11) can be rationalised on the basis of formation of calcium silicates from calcium oxide, generally present as an impurity in the calcium fluoride electrolyte, and silica. The emf of cell (11) is shown to be the function of the activity of calcium oxide at the electrolyte/ electrode interface. The results provide strong evidence against the recent suggestion of mixed anionic conduction in calcium fluoride.

Measurement of the Gibbs energy of formation of URh3 using an oxide solid electrolyte

The Gibbs' energy offormation of the intermetallic compound URh3has been measured in the temperature range 980 to 1320 K using an oxide solid state cell incorporating yttria-doped thoria as the solid electrolyte and a mixture of manganese and manganese oxide as the reference electrode. The cell can be represented as Pt, Mn + MnO I (Y203)Th02 I Rh + URh3 + U02 + x' Rh, Pt The reversible emf of the cell was a linear function of temperature E = 15.60 +0.0237 T (±0.8) mY. Using auxiliary thermodynamic data for MnO and U02+ x the Gibbs' energy of formation of URh3 from component metals has been computed. The results can be expressed by the equation L'.G?< URh3 > = -316240 + 13.22 T (± 3000) J mol-1. The "third-law" enthalpy of formation of URh3at 298 K is -293.2 (± 4) kJ mol-1, significantly more negative than the value of -181.5 kJ mol-1 calculated using Miedema's model.

Gibbs energy of formation of CaCu3Ti4O12 and phase relations in the system CaO-CUO/CU2O-TiO2

he standard Gibbs energy of formation of CaCu3Ti4O12 (CCTO) from CaTiO3, CuO and TiO2 has been determined as a function of temperature from 925 to 1350 K using a solid-state electrochemical cell with yttria-stabilized zirconia as the solid electrolyte. Combining this result with information in the literature on CaTiO3, the standard Gibbs energy of formation of CCTO from its component binary oxides, CaO, CuO and TiO2, has been obtained: View the MathML source (CaCu3Ti4O12)/J mol−1 (±600) = −125231 + 6.57 (T/K). The oxygen chemical potential corresponding to the reduction of CCTO to CaTiO3, TiO2 and Cu2O has been calculated from the electrochemical measurements as a function of temperature and compared on an Ellingham diagram with those for the reduction of CuO to Cu2O and Cu2O to Cu. The oxygen partial pressures corresponding to the reduction reactions at any chosen temperature can be read using the nomograms provided on either side of the diagram. The effect of the oxygen partial pressure on phase relations in the pseudo-ternary system CaO–CuO/Cu2O–TiO2 at 1273 K has been evaluated. The phase diagrams allow identification of secondary phases that may form during the synthesis of the CCTO under equilibrium conditions. The secondary phases may have a significant effect on the extrinsic component of the colossal dielectric response of CCTO.

Phase Equilibria in the System Al2O3-CaO-CoO and Gibbs Energy of Formation of Ca3CoAl4O10

An isothermal section of the system Al2O3-CaO-CoO at 1500 K has been established by equilibrating 22 samples of different compositions at high temperature and phase identification by optical and scanning electron microscopy, X-ray diffraction, and energy dispersive spectroscopy after quenching to room temperature. Only one quaternary oxide, Ca3CoAl4O10, was identified inside the ternary triangle. Based on the phase relations, a solid-state electrochemical cell was designed to measure the Gibbs energy of formation of Ca3CoAl4O10 in the temperature range from 1150 to 1500 K. Calcia-stabilized zirconia was used as the solid electrolyte and a mixture of Co + CoO as the reference electrode. The cell can be represented as: ( - )\textPt,\textCaAl 2 \textO 4 + \textCa 1 2 \textAl 1 4 \textO 3 3 + \textCa 3 \textCoAl 4 \textO 10 + \textCo//(CaO)ZrO 2 \text// \textCoO + \textCo,\text Pt ( + ). (−)PtCaAl2O4+Ca12Al14O33+Ca3CoAl4O10+Co//(CaO)ZrO2//CoO+Co Pt (+) From the emf of the cell, the standard Gibbs energy change for the Ca3CoAl4O10 formation reaction, CoO + 3/5CaAl2O4 + 1/5Ca12Al14O33 → Ca3CoAl4O10, is obtained as a function of temperature: \Updelta Gr\texto Unknown control sequence '\Updelta'/J mol−1 (±50) = −2673 + 0.289 (T/K). The standard Gibbs energy of formation of Ca3CoAl4O10 from its component binary oxides, Al2O3, CaO, and CoO is derived as a function of temperature. The standard entropy and enthalpy of formation of Ca3CoAl4O10 at 298.15 K are evaluated. Chemical potential diagrams for the system Al2O3-CaO-CoO at 1500 K are presented based on the results of this study and auxiliary information from the literature.

Modern energy access to all in rural India: An integrated implementation strategy

Expanding energy access to the rural population of India presents a critical challenge for its government. The presence of 364 million people without access to electricity and 726 million who rely on biomass for cooking indicate both the failure of past policies and programs, and the need for a radical redesign of the current system. We propose an integrated implementation framework with recommendations for adopting business principles with innovative institutional, regulatory, financing and delivery mechanisms. The framework entails establishment of rural energy access authorities and energy access funds, both at the national and regional levels, to be empowered with enabling regulatory policies, capital resources and the support of multi-stakeholder partnership. These institutions are expected to design, lead, manage and monitor the rural energy interventions. At the other end, trained entrepreneurs would be expected to establish bioenergy-based micro-enterprises that will produce and distribute energy carriers to rural households at an affordable cost. The ESCOs will function as intermediaries between these enterprises and the international carbon market both in aggregating carbon credits and in trading them under CDM. If implemented, such a program could address the challenges of rural energy empowerment by creating access to modern energy carriers and climate change mitigation. (C) 2011 Elsevier Ltd. All rights reserved.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

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.

Perturbative expansion of the QCD Adler function improved by renormalization-group summation and analytic continuation in the Borel plane

We examine the large-order behavior of a recently proposed renormalization-group-improved expansion of the Adler function in perturbative QCD, which sums in an analytically closed form the leading logarithms accessible from renormalization-group invariance. The expansion is first written as an effective series in powers of the one-loop coupling, and its leading singularities in the Borel plane are shown to be identical to those of the standard ``contour-improved'' expansion. Applying the technique of conformal mappings for the analytic continuation in the Borel plane, we define a class of improved expansions, which implement both the renormalization-group invariance and the knowledge about the large-order behavior of the series. Detailed numerical studies of specific models for the Adler function indicate that the new expansions have remarkable convergence properties up to high orders. Using these expansions for the determination of the strong coupling from the hadronic width of the tau lepton we obtain, with a conservative estimate of the uncertainty due to the nonperturbative corrections, alpha(s)(M-tau(2)) = 0.3189(-0.0151)(+0.0173), which translates to alpha(s)(M-Z(2)) = 0.1184(-0.0018)(+0.0021). DOI: 10.1103/PhysRevD.87.014008

k.p based closed form energy band gap and transport electron effective mass model for 100] and 110] relaxed and strained Silicon nanowire

In this paper, we address a physics based closed form model for the energy band gap (E-g) and the transport electron effective mass in relaxed and strained 100] and 110] oriented rectangular Silicon Nanowire (SiNW). Our proposed analytical model along 100] and 110] directions are based on the k.p formalism of the conduction band energy dispersion relation through an appropriate rotation of the Hamiltonian of the electrons in the bulk crystal along 001] direction followed by the inclusion of a 4 x 4 Luttinger Hamiltonian for the description of the valance band structure. Using this, we demonstrate the variation in Eg and the transport electron effective mass as function of the cross-sectional dimensions in a relaxed 100] and 110] oriented SiNW. The behaviour of these two parameters in 100] oriented SiNW has further been studied with the inclusion of a uniaxial strain along the transport direction and a biaxial strain, which is assumed to be decomposed from a hydrostatic deformation along 001] with the former one. In addition, the energy band gap and the effective mass of a strained 110] oriented SiNW has also been formulated. Using this, we compare our analytical model with that of the extracted data using the nearest neighbour empirical tight binding sp(3)d(5)s* method based simulations and has been found to agree well over a wide range of device dimensions and applied strain. (C) 2012 Elsevier Ltd. All rights reserved.

Clusters of bound particles in the derivative delta-function Bose gas

In this paper we discuss a novel procedure for constructing clusters of bound particles in the case of a quantum integrable derivative delta-function Bose gas in one dimension. It is shown that clusters of bound particles can be constructed for this Bose gas for some special values of the coupling constant, by taking the quasi-momenta associated with the corresponding Bethe state to be equidistant points on a single circle in the complex momentum plane. We also establish a connection between these special values of the coupling constant and some fractions belonging to the Farey sequences in number theory. This connection leads to a classification of the clusters of bound particles associated with the derivative delta-function Bose gas and allows us to study various properties of these clusters like their size and their stability under the variation of the coupling constant. (C) 2013 Elsevier B.V. All rights reserved.