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.

Vapor pressure and dissociation energy of (In2O)

The vapor pressure of pure liquid indium, and the sum of pressures of (In) and (In2O) species over the condensed phase mixture {In} + , contained in a silica vessel, have been measured by Knudsen effusion and Langmuir free vaporization methods in the temperatue range 600 to 950°C. Mass spectrometric studies reported in the literature show that (In) and (In2O) are the important species in the vapor phase over the {In} + ; mixture. The vapor pressure of (In2O) corresponding to the reaction, deduced from the present measurements is given by the equation, The “apparent evaporation coefficient” for the condensed phase mixture is approximately 0.8. The energy for the dissociation (In2O) molecule into atoms calculated from the above equation is D°0 = 180.0 (± 1.0) kcal mol−1.

Phase equilibria in the system NiO-CaO-SiO2 and Gibbs energy of formation of CaNiSi2O6

Phase relations in the pseudoternary system NiO-CaO-SiO2 at 1373 K are established. The coexisting phases are identified by X-ray diffraction and energy-dispersive X-ray analysis of equilibrated samples. There is only one quaternary oxide CaNiSi2O6 with clinopyroxene structure. The Gibbs energy of formation of CaNiSi2O6 is measured using a solid state galvanic cell incorporating stabilized zirconia as the solid electrolyte in the temperature range of 1000 to 1400 K:Pt, Ni + SiO2 + CaSiO3 + CaNiSi2O6 \ (Y2O3)ZrO2 \ Ni + NiO, Pt From the electromotive force (emf) of the cell, the Gibbs energy of formation of CaNiSi2O6 from NiO, SiO2, and CaSiO3 is obtained. To derive the Gibbs energy of formation of the quaternary oxide from component binary oxides, the free energy of formation of CaSiO, is determined separately using a solid state cell based on single crystal CaF2 as the electrolyte: Pt, O-2, CaO + CaF2 \ CaF2 \ CaSiO3 + SiO2 + CaF2, O-2, Pt The results can be expressed by the following equations: NiO (r.s) + CaO (r.s) + 2SiO(2) (qz) --> CaNiSi2O6 (pyr) Delta G degrees = -115,700 + 10.63T (+/-100) J mol(-1) CaO (r.s) + SiO2 (qz) --> CaSiO3 (wol) Delta G degrees = -90,030 -0.61T (+/-60) J mol(-1).

Microelectromechanical torsional varactors with low parasitic capacitances and high dynamic range

This work focuses on the design of torsional microelectromechanical systems (MEMS) varactors to achieve highdynamic range of capacitances. MEMS varactors fabricated through the polyMUMPS process are characterized at low and high frequencies for their capacitance-voltage characteristics and electrical parasitics. The effect of parasitic capacitances on tuning ratio is studied and an equivalent circuit is developed. Two variants of torsional varactors that help to improve the dynamic range of torsional varactors despite the parasitics are proposed and characterized. A tuning ratio of 1:8, which is the highest reported in literature, has been obtained. We also demonstrate through simulations that much higher tuning ratios can be obtained with the designs proposed. The designs and experimental results presented are relevant to CMOS fabrication processes that use low resistivity substrate. (C) 2012 Society of Photo-Optical Instrumentation Engineers (SPIE). DOI: 10.1117/1.JMM.11.1.013006]

System Ho-Rh-O: Phase Equilibria, Chemical Potentials and Gibbs Energy of Formation of HoRhO3

The thermodynamic properties of the HoRhO3 were determined in the temperature range from 900 to 1300 K by using a solid-state electrochemical cell incorporating calcia-stabilized zirconia as the electrolyte. The standard Gibbs free energy of formation of orthorhombic perovskite HoRhO3, from Ho2O3 with C-rare earth structure and Rh2O3 with orthorhombic structure, can be expressed by the equation; Delta G(f)degrees((ox)) (+/- 78)/(J/mol) = -50535 + 3.85(T/K) Using the thermodynamic data of HoRhO3 and auxiliary data for binary oxides from the literature, the phase relations in the Ho-Rh-O system were computed at 1273 K. Thermodynamic data for intermetallic phases in the binary Ho-Rh were estimated from experimental enthalpy of formation for three compositions from the literature and Miedema's model, consistent with the phase diagram. The oxygen potential-composition diagram and three-dimensional chemical potential diagram at 1273 K, and temperature-composition diagrams at constant oxygen partial pressures were computed for the system Ho-Rh-O. The decomposition temperature of HoRhO3 is 1717(+/- 2) K in pure O-2 and 1610(+/- 2) K in air at a total pressure p(o) = 0.1 MPa.

Catalytic activity of Peptidase N is required for adaptation of Escherichia coli to nutritional downshift and high temperature stress

Peptidase N (PepN), the sole M1 family member in Escherichia coli, displays broad substrate specificity and modulates stress responses: it lowers resistance to sodium salicylate (NaSal)-induced stress but is required during nutritional downshift and high temperature (NDHT) stress. The expression of PepN does not significantly change during different growth phases in LB or NaSal-induced stress; however, PepN amounts are lower during NDHT stress. To gain mechanistic insights on the roles of catalytic activity of PepN in modulating these two stress responses, alanine mutants of PepN replacing E264 (GAMEN motif) and E298 (HEXXH motif) were generated. There are no major structural changes between purified wild type (WT) and mutant proteins, which are catalytically inactive. Importantly, growth profiles of Delta pepN upon expression of WT or mutant proteins demonstrated the importance of catalytic activity during NDHT but not NaSal-induced stress. Further fluorescamine reactivity studies demonstrated that the catalytic activity of PepN is required to generate higher intracellular amounts of free N-terminal amino acids; consequently, the lower growth of Delta pepN during NDHT stress increases with high amounts of casamino acids. Together, this study sheds insights on the expression and functional roles of the catalytic activity of PepN during adaptation to NDHT stress. (C) 2012 Elsevier GmbH. All rights reserved.

Row-buffer reorganization: simultaneously improving performance and reducing energy in DRAMs

In this paper, based on the temporal and spatial locality characteristics of memory accesses in multicores, we propose a re-organization of the existing single large row buffer in a DRAM bank into multiple smaller row-buffers. The proposed configuration helps improve the row hit rates and also brings down the energy required for row-activations. The major contribution of this work is proposing such a reorganization without requiring any significant changes to the existing widely accepted DRAM specifications. Our proposed reorganization improves performance by 35.8%, 14.5% and 21.6% in quad, eight and sixteen core workloads along with a 42%, 28% and 31% reduction in DRAM energy. Additionally, we introduce a Need Based Allocation scheme for buffer management that shows additional performance improvement.

Correlation between enhanced lattice polarizability and high piezoelectric response in BiScO3-PbTiO3

Piezoelectric and ex situ electric-field induced structural studies were carried out on closely spaced compositions in the morphotropic phase boundary region of (1 - x) PbTiO3-(x)BiScO3. While the common approach of zero field structural analysis failed to provide a unique relationship between the anomalous piezoresponse of x = 0.3725 and structural factor(s), ex situ study of electric-field induced structural changes revealed that the composition exhibiting the highest piezoelectric response is the one which also exhibits significantly enhanced polarizability of the lattices of both coexisting (monoclinic and tetragonal) phases. The enhanced lattice polarizability manifests as a significant fraction of the monoclinic phase transforming irreversibly to the tetragonal phase after electric poling. DOI: 10.1103/PhysRevB.87.064106

Polymer Template Assisted Synthesis of Porous Li1.2Mn0.53Ni0.13Co0.13O2 as a High Capacity and High Rate Capability Positive Electrode Material

A porous layered composite of Li2MnO3 and LiMn1/3Co1/3Ni1/3O2 (composition: Li1.2Mn0.53Ni0.13Co0.13O2) is prepared by reverse microemulsion method employing a soft polymer template and studied as a positive electrode material. The precursor is heated at several temperatures between 500 and 900 degrees C. The product samples possess mesoporosity with broadly distributed pores of about 30 nm diameters. There is a decrease in pore volume as well as in surface area by increasing the temperature of preparation. Nevertheless, the electrochemical activity of the composite increases with an increase in temperature. The discharge capacity values of the samples prepared at 800 and 900 degrees C are about 250 mAh g(-1) at a specific current of 40 mA g(-1) with an excellent cycling stability. A value of 225 mAh g(-1) is obtained at the end of 30 charge-discharge cycles. Both these composite samples possess high rate capability, but the 800 degrees C sample is marginally superior to the 900 degrees C sample. A discharge capacity of 100 mAh g(-1) is obtained at a specific current of 1000 mA g(-1). The high rate capability is attributed to porous nature of the composite samples. (C) 2013 The Electrochemical Society. All rights reserved.

In-situ Stabilization of Tin Nanoparticles in Porous Carbon Matrix derived from Metal Organic Framework: High Capacity and High Rate Capability Anodes for Lithium-ion Batteries

It is a formidable challenge to arrange tin nanoparticles in a porous matrix for the achievement of high specific capacity and current rate capability anode for lithium-ion batteries. This article discusses a simple and novel synthesis of arranging tin nanoparticles with carbon in a porous configuration for application as anode in lithium-ion batteries. Direct carbonization of synthesized three-dimensional Sn-based MOF: K2Sn2(1,4-bdc)(3)](H2O) (1) (bdc = benzenedicarboxylate) resulted in stabilization of tin nanoparticles in a porous carbon matrix (abbreviated as Sn@C). Sn@C exhibited remarkably high electrochemical lithium stability (tested over 100 charge and discharge cycles) and high specific capacities over a wide range of operating currents (0.2-5 Ag-1). The novel synthesis strategy to obtain Sn@C from a single precursor as discussed herein provides an optimal combination of particle size and dispersion for buffering severe volume changes due to Li-Sn alloying reaction and provides fast pathways for lithium and electron transport.

Studies on microscopic structure of diesel sprays under atmospheric and high gas pressures

In the present work, the spray structure of diesel from a 200-mu m, single-hole solenoid injector is studied using microscopic imaging at injection pressures of 700, 1000 and 1400 bar for various gas pressures. A long-distance microscope with a high resolution camera is used for spray visualization with a direct imaging technique. This study shows that even at very high injection pressures, the spray structure in an ambient environment of atmospheric pressure reveals presence of entangled ligaments and non-spherical droplets during the injection period. With increase in the injection pressure, the ligaments tend to get smaller and spread radially. The spray structure studies are also conducted at high gas pressures in a specially designed high pressure chamber with optical access. The near nozzle spray structure at the end of the injection shows that the liquid jet breakup is improved with increase in gas density. The droplet size measurement is possible only late in the injection duration when the breakup appears to be complete and mostly spherical droplets are observed. Hence, droplet size measurements are performed after 1.3 ms from start of the injection pulse. Spatial and temporal variation in Sauter Mean `Diameter (SMD) is observed and reported for the case corresponding to an injection pressure of 700 bar. Overall, this study has highlighted the importance of verifying the extentof atomization and droplet shape even in dense sprays before using conventional dropsizing methods such as PDPA.

Polarization switching and high piezoelectric response in Sn-modified BaTiO3

BaTiO3 is shown to exhibit anomalous piezoelectric response, comparable to that of lead-zirconate titanate, by dilute Sn modification (1-4 mol%). Using a newly discovered powder poling technique it is shown that the mechanism associated with this anomalous strain response involves electric-field-induced switching of polarization vector from 001] towards 101] pseudocubic direction. This switchability is significantly enhanced by tuning the tetragonal-orthorhombic first-order criticality near to room temperature.

The contribution of grain boundary sliding in tensile deformation of an ultrafine-grained aluminum alloy having high strength and high ductility

An as-cast Al-7 % Si alloy was processed by high-pressure torsion (HPT) for up to 10 turns at temperatures of 298 or 445 K. The HPT-processed samples had ultrafine-grained structures and they were tested in tension at room temperature at various strain rates in the range from 1.0 x 10(-4) to 1.0 x 10(-2) s(-1). The contributions of grain boundary sliding (GBS) to the total strain were measured directly using atomic force microscopy. Samples simultaneously showing both high strength and high ductility contained the highest fractions of high-angle grain boundaries (HAGB) and exhibited the highest contributions from GBS, whereas samples showing high strength but low ductility gave negligible values for the sliding contributions. It is concluded that high strength and high ductility require both an ultrafine grain size and a high fraction of HAGB.

Estimation of Aboveground Phytomass of Plantations Using Digital Photogrammetry and High Resolution Remote Sensing Data

The study follows an approach to estimate phytomass using recent techniques of remote sensing and digital photogrammetry. It involved tree inventory of forest plantations in Bhakra forest range of Nainital district. Panchromatic stereo dataset of Cartosat-1 was evaluated for mean stand height retrieval. Texture analysis and tree-tops detection analyses were done on Quick-Bird PAN data. The composite texture image of mean, variance and contrast with a 5x5 pixel window was found best to separate tree crowns for assessment of crown areas. Tree tops count obtained by local maxima filtering was found to be 83.4 % efficient with an RMSE+/-13 for 35 sample plots. The predicted phytomass ranged from 27.01 to 35.08 t/ha in the case of Eucalyptus sp. while in the case of Tectona grandis from 26.52 to 156 t/ha. The correlation between observed and predicted phytomass in Eucalyptus sp. was 0.468 with an RMSE of 5.12. However, the phytomass predicted in Tectona grandis was fairly strong with R-2=0.65 and RMSE of 9.89 as there was no undergrowth and the crowns were clearly visible. Results of the study show the potential of Cartosat-1 derived DSM and Quick-Bird texture image for the estimation of stand height, stem diameter, tree count and phytomass of important timber species.