A simple model for protein thermal denaturation

Whether proteins denature in all-or-none fashion or in a continuous fashion is as yet an unresolved problem. The all-or-none process implies that while the process of denaturation is going on, only two kinds of protein molecules can exist. One is completely unchanged and the other is altered. The altered protein molecules are indistinguishable. Underlying the 'continuum' models is the assumption that all the chains in a protein globule undergo similar changes so that it is enough to consider a single chain.

Spatially dependent zero-frequency response functions and correlation functions in the Kondo model

We present the details of a formalism for calculating spatially varying zero-frequency response functions and equal-time correlation functions in models of magnetic and mixed-valence impurities of metals. The method is based on a combination of perturbative, thermodynamic scaling theory [H. R. Krishna-murthy and C. Jayaprakash, Phys. Rev. B 30, 2806 (1984)] and a nonperturbative technique such as the Wilson renormalization group. We illustrate the formalism for the spin-1/2 Kondo problem and present results for the conduction-spin-density�impurity-spin correlation function and conduction-electron charge density near the impurity. We also discuss qualitative features that emerge from our calculations and discuss how they can be carried over to the case of realistic models for transition-metal impurities.

Constitutive Response of Passivated Copper Films: Experiments and Analyses

The constitutive behavior of passivated copper films is studied. Stresses in copper films of thickness ranging from 1000 nm to 40 nm, passivated with silicon oxide on a quartz or silicon substrate, were measured using the curvature method. The thermal cycling spans a temperature range from - 196 to 600°C. It is seen that the strong relaxation at high temperatures normally found in unpassivated films is nonexistent for passivated films. The copper film did not show any rate-dependent effect over a range of heating/cooling rate from 5 to 25°C/min. Further analyses showed that significant strain hardening exists during the course of thermal loading. In particular, the measured stress- temperature response can only be fitted with a kinematic hardening model, if a simple constitutive law within the continuum plasticity framework is to be used. The analytic procedures for extracting the film properties are presented. Implications to stress modeling of copper interconnects in actual devices are discussed.

Nonlinear cyclic load analysis for lateral response of batter piles in soft clay with a rigorous degradation model

Nonlinear analysis of batter piles in soft clay is performed using the finite element technique. As the batter piles are not only governed by lateral load but also axial load, the effect of P- Delta moment and geometric stiffness matrix is included in the analysis. For implementing the nonlinear soil behavior, reduction in soil strength (degradation), and formation of gap with number of load cycles, a numerical model is developed where a hyperbolic relation is adopted for the soil in static condition and hyperbolic relation considering degradation and gap for cyclic load condition. The numerical model is validated with published experimental results for cyclic lateral loading and the hysteresis loops are developed to predict the load-deflection behavior and soil resistance behavior during consecutive cycles of loading. This paper highlights the importance of a rigorous degradation model for subsequent cycles of loading on the pile-soil system by a hysteretic representation.

A model of coupled thermal, mechanical, and electrostatic field effects in III-N thin film heterostructures

A one-dimensional coupled multi-physics based model has been developed to accurately compute the effects of electrostatic, mechanical, and thermal field interactions on the electronic energy band structure in group III-nitrides thin film heterostructures. Earlier models reported in published literature assumes electro-mechanical field with uniform temperature thus neglecting self-heating. Also, the effects of diffused interface on the energy band structure were not studied. We include these effects in a self-consistent manner wherein the transport equation is introduced along with the electro-mechanical models, and the lattice structural variation as observed in experiments are introduced at the interface. Due to these effects, the electrostatic potential distribution in the heterostructure is altered. The electron and hole ground state energies decrease by 5% and 9%, respectively, at a relative temperature of 700 K, when compared with the results obtained from the previously reported electro-mechanical model assuming constant and uniform temperature distribution. A diffused interface decreases the ground state energy of electrons and holes by about 11% and 9%, respectively, at a relative temperature of 700 K when compared with the predictions based on uniform temperature based electro-mechanical model. (C) 2013 AIP Publishing LLC.

A simple model for spatial disaggregation of evaporative fraction: Comparative study with thermal sharpened land surface temperature data over India

[1] Evaporative fraction (EF) is a measure of the amount of available energy at the earth surface that is partitioned into latent heat flux. The currently operational thermal sensors like the Moderate Resolution Imaging Spectroradiometer (MODIS) on satellite platforms provide data only at 1000 m, which constraints the spatial resolution of EF estimates. A simple model (disaggregation of evaporative fraction (DEFrac)) based on the observed relationship between EF and the normalized difference vegetation index is proposed to spatially disaggregate EF. The DEFrac model was tested with EF estimated from the triangle method using 113 clear sky data sets from the MODIS sensor aboard Terra and Aqua satellites. Validation was done using the data at four micrometeorological tower sites across varied agro-climatic zones possessing different land cover conditions in India using Bowen ratio energy balance method. The root-mean-square error (RMSE) of EF estimated at 1000 m resolution using the triangle method was 0.09 for all the four sites put together. The RMSE of DEFrac disaggregated EF was 0.09 for 250 m resolution. Two models of input disaggregation were also tried with thermal data sharpened using two thermal sharpening models DisTrad and TsHARP. The RMSE of disaggregated EF was 0.14 for both the input disaggregation models for 250 m resolution. Moreover, spatial analysis of disaggregation was performed using Landsat-7 (Enhanced Thematic Mapper) ETM+ data over four grids in India for contrasted seasons. It was observed that the DEFrac model performed better than the input disaggregation models under cropped conditions while they were marginally similar under non-cropped conditions.

Analytical model for stress-strain response of plastic waste mixed soil

Recycling plastic water bottles has become one of the major challenges world wide. The present study provides an approach for the use of plastic waste as reinforcement material in soil, which can be used for ground improvement, subbases, and subgrade preparation in road construction. The experimental results are presented in the form of stress-strain-pore water pressure response and compression paths. On the basis of experimental test results, it is observed that the strength of soil is improved and compressibility reduced significantly with the addition of a small percentage of plastic waste to the soil. In this paper, an analytical model is proposed to evaluate the response of plastic waste mixed soil. It is noted that the model captures the stress-strain and pore water pressure response of all percentages of plastic waste adequately. The paper also provides a comparative study of failure stress obtained from different published models and the proposed model, which are compared with experimental results. The improvement in strength attributable to the inclusion of plastic waste can be advantageously used in ground improvement projects.

Photocatalytic and Thermal Degradation of Poly(methyl methacrylate), Poly(butyl acrylate), and Their Copolymers

The photocatalytic and thermal degradations of poly(methyl methacrylate), poly(butyl acrylate), and their copolymers of different compositions were studied. The photocatalytic degradation was investigated in o-dichlorobenzene in the presence of two different catalysts, namely, Degussa P-25 and combustion synthesized nanotitania (CSN-TiO2). The samples were analyzed by using gel permeation chromatography (GPC) to obtain the molecular weight distributions (MWDs) as a function of reaction time. Experimental data indicated that the photodegradation of these polymers occurs by both random and chain end scission. A continuous distribution kinetic model was used to determine the degradation rate coefficients by fitting the experimental data with the model. Both the random and specific rate coefficients of the copolymers decreased with increasing percentage of butyl acrylate (BA). Thermal degradation of the copolymers was investigated by thermo-gravimetry. The normalized weight loss profiles for the copolymers showed that the thermal stability of the copolymers increased with mole percentage of BA in the copolymer (PMMABA). The Czawa method was used to determine the activation energies at different conversions. At low acrylate content in the copolymer, the activation energy depends on conversion, indicating multiple degradation mechanisms. At high acrylate content in the copolymer, the activation energy is independent of conversion, indicating degradation by a one-step mechanism.

Photoinduced DNA and Protein Cleavage Activity of Ferrocene-Conjugated Ternary Copper(II) Complexes

Ferrocene-conjugated ternary copper(II) complexes [Cu(L)(B)](ClO4)(2), where L is FcCH(2)N(CH2Py)(2) (Fc = (eta(5)-C5H4)Fe-II(eta(5)-C5H5)) and B is a phenanthroline base, viz., 2,2'-bipyridine (bpy, 1), 1, 10-phenanthroline (phen, 2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq, 3), and dipyrido[3,2-a:2',3'-c]phenazine (dppz, 4), have been synthesized and characterized by various spectroscopic and analytical techniques. The bpy complex 1, as its hexafluorophosphate salt, has been structurally characterized by X-ray crystallography. The molecular structure shows the copper(II) center having an essentially square-pyramidal coordination geometry in which L with a pendant ferrocenyl (Fc) moiety and bpy show respective tridentate and bidentate modes of binding to the metal center. The complexes are redox active, showing a reversible cyclic voltammetric response of the Fc(+)-Fc couple near 0.5 V vs SCE and a quasi-reversible Cu(II)-Cu(I) couple near 0.0 V. Complexes 2-4 show binding affinity to calf thymus (CT) DNA, giving binding constant (K-b) values in the range of 4.2 x 10(4) to 2.5 x 10(5) M-1. Thermal denaturation and viscometric titration data suggest groove binding and/or a partial intercalative mode of binding of the complexes to CT DNA. The complexes show good binding propensity to the bovine serum albumin (BSA) protein, giving K-BSA values of similar to 10(4) M-1 for the bpy and phen complexes and similar to 10(5) M-1 for the dpq and dppz complexes. Complexes 2-4 exhibit efficient chemical nuclease activity in the presence of 3-mercapto-propionic acid (MPA) as a reducing agent or hydrogen peroxide (H2O2) as an oxidizing agent. Mechanistic studies reveal formation of hydroxyl radicals as the reactive species. The dpq and dppz complexes are active in cleaving supercoiled (SC) pUC19 DNA on photoexposure to visible light of different wavelengths including red light using an argon-krypton mixed gas ion laser. Mechanistic investigations using various inhibitors reveal the fort-nation of hydroxyl radicals in the DNA photocleavage reactions. The dppz complex 4, which shows efficient photoioduced BSA cleavage activity, is a potent multifunctional model nuclease and protease in the chemistry of photodynamic therapy (PDT) of cancer.

Analysis of a Genomic DNA Expression Library of Mycobacterium tuberculosis Using Tuberculosis Patient Sera: Evidence for Modulation of Host Immune Response

DNA obtained from a human sputum isolate of Mycobacterium tuberculosis, NTI-64719, which showed extensive dissemination in the guinea pig model resulting in a high score for virulence was used to construct an expression library in the lambda ZAP vector. The size of DNA inserts in the library ranged from 1 to 3 kb, and recombinants represented 60% of the total plaques obtained. When probed with pooled serum from chronically infected tuberculosis patients, the library yielded 176 recombinants with a range of signal intensities. Among these, 93 recombinants were classified into 12 groups on the basis of DNA hybridization experiments, The polypeptides synthesized by the recombinants were predominantly LacZ fusion proteins, Serum obtained from patients who were clinically diagnosed to be in the early phase of M. tuberculosis infection was used to probe the 176 recombinants obtained. interestingly, some recombinants that gave very strong signals in the original screen did not react with early-phase serum; conversely, others whose signals were extremely weak in the original screen gave very intense signals with serum from recently infected patients, This indicates the differential nature of either the expression of these antigens or the immune response elicited by them as a function of disease progression.

Response And Stability Of A Stochastic Beam-Column Using Stochastic Fem

A beam-column resting on continuous Winkler foundation and discrete elastic supports is considered. The beam-column is of variable cross-section and the variation of sectional properties along the axis of the beam-column is deterministic. Young's modulus, mass per unit length and distributed axial loadings of the beam-column have a stochastic distribution. The foundation stiffness coefficient of the Winkler model, the stiffnesses of discrete elastic supports, stiffnesses of end springs and the end thrust, are all considered as random parameters. The material property fluctuations and distributed axial loadings are considered to constitute independent, one-dimension uni-variate homogeneous real stochastic fields in space. The foundation stiffness coefficient, stiffnesses of the discrete elastic supports, stiffnesses of end springs and the end thrust are considered to constitute independent random variables. Static response, free vibration and stability behaviour of the beam-column are studied. Hamilton's principle is used to formulate the problem using stochastic FEM. Sensitivity vectors of the response and stability parameters are evaluated. Using these statistics of free vibration frequencies, mode shapes, buckling parameters, etc., are evaluated. A numerical example is given.

Role of Melt Convection on the Thermal Performance of Heat Sinks with Phase Change Material

The role of melt convection oil the performance of beat sinks with Phase Change Material (PCM) is presented in this paper. The beat sink consists of aluminum plate fins embedded in PCM and heat flux is supplied from the bottom. The design of such a heat sink requires optimization with respect to its geometrical parameters. The objective of the optimization is to maximize the heat sink operation time for the prescribed heat flux and the critical chip temperature. The parameters considered for optimization are fin number and fill thickness. The height and base plate thickness of heat sink are kept constant in the present analysis. An enthalpy based CFD model is developed, which is capable Of Simulating phase change and associated melt convection. The CFD model is Coupled with Genetic Algorithm (GA) for carrying out the optimization. Two cases are considered, one without melt convection (conduction regime) and the other with convection. It is found that the geometrical optimizations of heat sinks are different for the two cases, indicating the importance of inch convection in the design of heat sinks with PCMs.