Thermal Fluctuation Spectroscopy of DNA Thermal Denaturation

We have developed the technique of thermal fluctuation spectroscopy to measure the thermal fluctuations in a system. This technique is particularly useful to study the denaturation dynamics of biomolecules like DNA. Here we present a study of the thermal fluctuations during the thermal denaturation (or melting) of double-stranded DNA. We find that the thermal denaturation of heteropolymeric DNA is accompanied by large, non-Gaussian thermal fluctuations. The thermal fluctuations show a two-peak structure as a function of temperature. Calculations of enthalpy exchanged show that the first peak comes from the denaturation of AT rich regions and the second peak from denaturation of GC rich regions. The large fluctuations are almost absent in homopolymeric DNA. We suggest that bubble formation and cooperative opening and closing dynamics of basepairs causes the additional fluctuation at the first peak and a large cooperative transition from a partially molten DNA to a completely denatured state causes the additional fluctuation at the second peak.

Design and fabrication of an automated thermal desorption gas-solid reaction system: Oxidation of ammonia and methanol over YBa2Cu3O7−δ(123) oxide systems

A fully automated, versatile Temperature Programmed Desorption (TDP), Temperature Programmed Reaction (TPR) and Evolved Gas Analysis (EGA) system has been designed and fabricated. The system consists of a micro-reactor which can be evacuated to 10−6 torr and can be heated from 30 to 750°C at a rate of 5 to 30°C per minute. The gas evolved from the reactor is analysed by a quadrupole mass spectrometer (1–300 amu). Data on each of the mass scans and the temperature at a given time are acquired by a PC/AT system to generate thermograms. The functioning of the system is exemplified by the temperature programmed desorption (TPD) of oxygen from YBa2Cu3−xCoxO7 ± δ, catalytic ammonia oxidation to NO over YBa2Cu3O7−δ and anaerobic oxidation of methanol to CO2, CO and H2O over YBa2Cu3O7−δ (Y123) and PrBa2Cu3O7−δ (Pr123) systems.

The role of hydrogen in hardening/softening steel: Influence of the charging process

Thermal desorption spectroscopy and nanoindentation techniques were employed to elucidate the key differences in the hydrogen (H) charging methods (electrochemical versus gaseous) and their consequences on the mechanical response of a low carbon steel. While electrochemical charging enhances the hardness, gaseous charging reduces it. This contrasting behavior is rationalized in terms of the dependency of the strength on the absorbed amount of H during charging and the H concentration gradient in the specimen. (C) 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Nature of nitrogen adsorbed on transition metal surfaces as revealed by electron spectroscopy and cognate techniques

The nature of the chemisorbed states of nitrogen on various transition metal surfaces is discussed comprehensively on the basis of the results of electron spectroscopic investigations augmented by those from other techniques such as LEED and thermal desorption. A brief discussion of the photoemission spectra of free N2, a comparison of adsorbed N2 and CO as well as of physisorption of N2 on metal surfaces is also presented. We discuss the chemisorption of N2 on the surfaces of certain metals (e.g. Ni, Fe, Ru and W) in some detail, paying considerable attention to the effect of electropositive and electronegative surface modifiers. Features of the various chemisorbed states (one or more weakly chemisorbed gamma-states, strongly chemisorbed alpha-states with bond orders between 1 and 2. and dissociative chemisorbed beta-states) on different surfaces are described and relations between them indicated. While the gamma-state could be a precursor of the alpha-state, the alpha-state could be the precursor of the beta-state and this kind of information is of direct relevance to ammonia synthesis. The nature of adsorption of N2 on the surfaces of some metals (e.g. Cr, Co) deserves further study and such investigations might as well suggest alternative catalysts for ammonia synthesis.

Reduction of oxygen impurity at GaN/beta-Si(3)N(4)/Si interface via SiO(2) to Ga(2)O conversion by exposing of Si surface under Ga flux

The removal of native oxide from Si (1 1 1) surfaces was investigated by X-ray photoelectron spectroscopy (XPS) and secondary ion mass spectra (SIMS) depth profiles. Two different oxide removal methods, performed under ultrahigh-vacuum (UHV) conditions, were carried out and compared. The first cleaning method is thermal desorption of oxide at 900 degrees C. The second method is the deposition of metallic gallium followed by redesorption. A significant decrease in oxygen was achieved by thermal desorption at 900 degrees C under UHV conditions. By applying a subsequent Ga deposition/redesorption, a further reduction in oxygen could be achieved. We examine the merits of an alternative oxide desorption method via conversion of the stable SiO(2) surface oxide into a volatile Ca(2)O oxide by a supply of Ga metals. Furthermore, ultra thin films of pure silicon nitride buffer layer were grown on a Si (1 1 1) surface by exposing the surface to radio-frequency (RF) nitrogen plasma followed by GaN growth. The SIMS depth profile shows that the oxygen impurity can be reduced at GaN/beta-Si(3)N(4)/Si interfaces by applying a subsequent Ga deposition/redesorption. (C) 2011 Elsevier B.V. All rights reserved.

Palladium(II) and platinum(II) complexes of beta-functionalized ethyl selenolates: Effect of substitution on synthesis, reactivity, spectroscopy, structures and thermal behavior

Sodium ethylselenolates with functional groups X (where X = -OH, -COOH, -COOMe and -COOEt) at beta-carbon were prepared in situ by reductive cleavage of corresponding diselenide with NaBH4 either in methanol or aqueous ammonia. Treatment of these selenolates with [M2Cl2(mu-Cl)(2)(PR'(3))(2)] (M = Pd or Pt; PR'(3) = PMePh2, PnPr(3)) in different stoichiometry yielded various bi- and tri-nuclear complexes. The homoleptic hexanuclear complexes [Pd(mu-SeCH2CH2X)(2)](6) (X = OH, COOH, COOEt), were obtained by reacting Na2PdCl4 with NaSeCH2CH2X. All these complexes have been fully characterized. Molecular structures of ethylselenolates containing hydroxyl and carboxylic acid groups revealed solid state associated structures through inter-molecular hydrogen bond interactions. Trinuclear complex, [Pd3Cl2(mu-SeCH2CH2COOH)(4)(PnPr(3))(2)] (3a), was disposed in a boat form unlike chair conformation observed for the corresponding methylester complex. The effect of beta-functionality in ethylselenolate ligands towards reactivity, structures and thermal properties of palladium and platinum complexes has been extensively Studied.

Synthesis, structural characterization, thermal studies and chain dynamics of poly(methacrylonitrile peroxide) by NMR spectroscopy

Poly(methacrylonitrile peroxide) (PMNP) has been synthesized from methacrylonitrile by free radical initiated oxidative polymerization and characterized by different spectroscopic methods. NMR spectroscopy confirmed the alternating copolymer structure with labile peroxy bonds in the main chain. The extreme instability of PMNP was noted from FTIR spectroscopy. Thermal degradation studies by using differential scanning calorimetry and thermogravimetry have revealed that PMNP degrades highly exothermically and the heat of degradation, 42.5 kcal mol−1, is of the same order as that reported for other vinyl polyperoxides. Mass spectral fragmentation pattern under electron impact (EI) condition has also been investigated. The mechanism of the primary exothermic degradation has been substantiated by thermochemical calculations. The chain dynamics of the polyperoxide chain has been studied by means of 13C spin–lattice relaxation times (T1) of the main chain as well as the side chain carbons. The temperature dependence of the spin–lattice relaxation times shows that the PMNP is more flexible compared to the analogous poly(styrene peroxide).

Structural, thermal and electrical characterization of NdLiMo2O8 electroceramics, using impedance spectroscopy

We report electrical property of a polycrystalline NdLiMo2O8 ceramics using complex impedance analysis. The material shows temperature dependent electrical relaxation phenomena. The d.c. conductivity shows typical Arrhenius behavior, when observed as a function of temperature. The a.c. conductivity is found to obey Jonscher's universal power law. The material was prepared in powder form by a standard solid-state reaction technique. Material formation and crystallinity have been confirmed by X-ray diffraction studies. Impedance measurements have been performed over a range of temperatures and frequencies. The results have been analyzed in the complex plane formalism and suitable equivalent circuits have been proposed in different regions. The role of bulk and grain boundary effect in the overall electrical conduction process is discussed with proper justification. (C) 2011 Elsevier Ltd. All rights reserved.

Study of thermal relaxation of Poly (HDDA-co-MMA) by temperature modulated DSC and dielectric spectroscopy

The thermal transitions in the copolymer of 1,6-hexanediol diacrylate (HDDA) and methyl methacrylate (MMA) was investigated to understand its use in microstereolithography. The glass transition temperature and the effect of interaction on this transition process was investigated by means of temperature modulated differential scanning calorimetry (TMDSC). The heat capacities were determined and PHDDA rich phases showed lower heat capacity than PMMA rich phases. The frequency dependence of glass transitions were studied by varying the modulation period of TMDSC and confirmed by dielectric relaxation spectroscopy. Vogel Fulcher Tammann Hesse (VFTH) parameters of homo and copolymers have also been reported.

Identification of the nature of platinum related midgap state in silicon by deep level transient spectroscopy

In this article, we present the detailed investigations on platinum related midgap state corresponding to E-c -0.52 eV probed by deep level transient spectroscopy. By irradiating the platinum doped samples with high-energy (1.1 MeV) gamma rays, we observed that the concentration of the midgap state increases and follows a square dependence with irradiation dose. However, the concentration of the acceptor corresponding to E-c -20.28 eV remained constant. Furthermore, from the studies on passivation by atomic hydrogen and thermal reactivation, we noticed that the E-c -0.52 eV level reappears in the samples annealed at high temperatures after hydrogenation. The interaction of platinum with various defects and the qualitative arguments based on the law of mass action suggest that the platinum related midgap defect might possibly correspond to the interstitial platinum-divacancy complex (V-Pt-V).

Studies of Phosphazenes. Part 13.' Thermal Rearrangement Reactions of Some Met hoxycyclo phosp hazenes

The methoxycyclophosphazenes [NP(OMe),], (n = 3-6) rearrange on heating to give oxocyclophosphazanes, [N(Me)PO(OMe)],. Isomeric products are formed when n = 4-6. The lH, ,lP, and 13C n.m.r. data for the starting materials and the products are presented. The ethoxy- and n-propoxy-derivatives N,P,( OR)* do not undergo the above rearrangement. The geminal derivatives N,P,R,(OMe), (R = Ph or NHBut) on heating yield both fully and partially rearranged products, namely dioxophosphaz-1 -enes and oxophosphazadienes, as shown by 270- MHz lH n.m.r. spectroscopy. The non-geminal derivative N,P,( NMe,),(OMe), gives only the fully rearranged product N,Me,P,(NMe,),O,(OMe), whose structure has been established from its lH and 31P n.m.r. spectra.

Internal nitride formation during gas-phase thermal nitridation of titanium

Titanium nitride surface layers were prepared by gas-phase thermal nitridation of pure titanium in an ammonia atmosphere at 1373 K for different times. In addition to the surface nitride layer, nitride/hydride formation was observed in the bulk of the specimen. The cross-section of the specimen was characterized by various techniques such as optical microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, secondary ion mass spectrometry and nanomechanical testing, and the mechanism of formation of these phases is discussed.

Interaction of rat testis protein, TP, with nucleic acids in vitro. Fluorescence quenching, UV absorption, and thermal denaturation studies

The nucleic acid binding properties of the testis protein, TP, were studied with the help of physical techniques, namely, fluorescence quenching, UV difference absorption spectroscopy, and thermal melting. Results of quenching of tyrosine fluorescence of TP upon its binding to double-stranded and denatured rat liver nucleosome core DNA and poly(rA) suggest that the tyrosine residues of TP interact/intercalate with the bases of these nucleic acids. From the fluorescence quenching data, obtained at 50 mM NaCl concentration, the apparent association constants for binding of TP to native and denatured DNA and poly(rA) were calculated to be 4.4 X 10(3) M-1, 2.86 X 10(4) M-1, and 8.5 X 10(4) M-1, respectively. UV difference absorption spectra upon TP binding to poly(rA) and rat liver core DNA showed a TP-induced hyperchromicity at 260 nm which is suggestive of local melting of poly(rA) and DNA. The results from thermal melting studies of binding of TP to calf thymus DNA at 1 mM NaCl as well as 50 mM NaCl showed that although at 1 mM NaCl TP brings about a slight stabilization of the DNA against thermal melting, a destabilization of the DNA was observed at 50 mM NaCl. From these results it is concluded that TP, having a higher affinity for single-stranded nucleic acids, destabilizes double- stranded DNA, thus behaving like a DNA-melting protein.

Surface segregation and oxidation studies of Cu-Sn and Cu-Pd alloys by x-ray photoelectron and auger spectroscopy

X-ray photoelectron and Auger spectroscopic techniques have been employed to study surface segregation and oxidation of Cu-1 at%Sn, Cu-9at%Pd and Cu-25at%Pd alloys. Both Cu-Pd(9%) and Cu-Pd(25%) alloys show segregation of Cu when heated above 500 K. The Pd concentration was reduced by 50% at 750 K compared to the bulk composition; the enthalpy of segregation of Cu is around - 6kJ/mol. Sn segregation is seen from 470 to 650 K in the Cu-Sn(1%) alloy, and a saturation plateau of Sn concentration above 650 K is observed. Surface oxidation of Cu-Sn(1%) and Cu-Pd(9%) alloys at 500 K showed the formation of Cu2O on the surface with total suppression of Sn or Pd on the respective alloy surfaces. On vacuum annealing the oxidised Cu-Sn alloy surface at 550 K, a displacement reaction 2Cu2O+Sn→4Cu+SnO2 was observed. However, under similar annealing of the oxidised Cu-Pd(9%) alloy surface at 500 K, oxide oxygen was totally desorbed leaving the Cu-Pd alloy surface clean. In the case of the Cu-Pd(25%) alloy, only dissociatively chemisorbed oxygen was seen at 500 K which desorbed at the same temperature. Oxygen spill-over from copper to palladium is suggested as the mechanism of oxygen desorption from the oxidised Cu-Pd alloy surfaces.

Structure-thermal behaviour studies on the salicylato complex of cobalt

The salicylato complex of cobalt was synthesized and its structure established to be [Co(sal)2] · 4 H2O, where, sal =, from elemental analysis, IR spectroscopy, magnetic susceptibility, cryoscopy and conductivity. The X-ray diffractogram of the complex has been given. Thermal decomposition has been studied in air by thermogravimetry (TG), differential thermal analysis and differential scanning calorimetry. TG shows three main steps of decomposition. The intermediates formed at various stages were collected and analysed. From the TG results and chemical analysis of the intermediates, a mechanism has been proposed for the thermal decomposition of the complex, leading to the oxide formation in the final stage.