Analysis of dynamics and mechanism of ligand binding to Artocarpus integrifolia agglutinin. A 13C and 19F NMR study

Binding of 13C-labeled N-acetylgalactosamine (13C-GalNAc) and N-trifluoroacetylgalactosamine (19F-GalNAc) to Artocarpus integrifolia agglutinin has been studied using 13C and 19F nuclear magnetic resonance spectroscopy, respectively. Binding of these saccharides resulted in broadening of the resonances, and no change in chemical shift was observed, suggesting that the alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc experience a magnetically equivalent environment in the lectin combining site. The alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc were found to be in slow exchange between free and protein bound states. Binding of 13C-GalNAc was studied as a function of temperature. From the temperature dependence of the line broadening, the thermodynamic and kinetic parameters were evaluated. The association rate constants obtained for the alpha-anomers of 13C-GalNAc and 19F-GalNAc (k+1 = 1.01 x 10(5) M-1.s-1 and 0.698 x 10(5) M-1.s-1, respectively) are in close agreement with those obtained for the corresponding beta-anomers (k+1 = 0.95 x 10(5) M-1.s-1 and 0.65 x 10(5) M-1.s-1, respectively), suggesting that the two anomers bind to the lectin by a similar mechanism. In addition these values are several orders of magnitude slower than those obtained for diffusion controlled processes. The dissociation rate constants obtained are 49.9, 56.9, 42, and 43 s-1, respectively, for the alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc. A two-step mechanism has been proposed for the interaction of 13C-GalNAc and 19F-GalNAc with A. integrifolia lectin in view of the slow association rates and high activation entropies. The thermodynamic parameters obtained for the association and dissociation reactions suggest that the binding process is entropically favored and that there is a small enthalpic contribution.

Study of thermal fluctuations during thermal denaturation of DNA

In this paper we address the fundamental issue of temperature fluctuation during the thermal denaturation (or the unzipping of the two strands on heating) of double stranded (ds) DNA. From our experiments we observe the presence of extremely high thermal fluctuations during DNA denaturation. This thermal fluctuation is several orders higher than the thermal fluctuation at temperatures away from the denaturation temperature range. This fluctuation is absent in single stranded (ss) DNA. The magnitude of fluctuation is much higher in heteropolymeric DNA and is almost absent in short homopolymeric DNA fragments. The temperature range over which the denaturation occurs (i.e., over which the thermal fluctuation is large) depends on the length of the DNA and is largest for the longest DNA.

Road kills of amphibians in different land use areas from Sharavathi river basin, central Western Ghats, India

A survey of amphibian mortality on roads was carried out in the Sharavathi river basin in the central Western Ghats. Road kills in three different land use areas: agricultural fields, water bodies and forests were recorded for four days along three 100m stretches in each type of area. One-hundred-and-forty-four individuals belonging to two orders, eight families, 11 genera and 13 species were recorded in the survey. Kills/km observed were: in forest 55, agricultural fields 38 and water bodies 27, for an overall average of 40 kills/km. Kill species compositions varied significantly between land use areas, but not overall kill rates.

Kinetics and the mechanism of interaction of the endoplasmic reticulum chaperone, calreticulin, with monoglucosylated (Glc(1)Man(9)GlcNAc(2)) substrate

Calreticulin is a lectin-like molecular chaperone of the endoplasmic reticulum in eukaryotes. Its interaction with N-glycosylated polypeptides is mediated by the glycan, Glc(1)Man(9)GlcNAc(2), present on the target glycoproteins. In this work, binding of monoglucosyl IgG (chicken) substrate to calreticulin has been studied using real time association kinetics of the interaction with the biosensor based on surface plasmon resonance (SPR). By SPR, accurate association and dissociation rate constants were determined, and these yielded a micromolar association constant. The nature of reaction was unaffected by immobilization of either of the reactants. The Scatchard analysis values for K-a agreed web crith the one obtained by the ratio k(1)/k(-1). The interaction was completely inhibited by free oligosaccharide, Glc(1)Man(9)GlcNAc(2), whereas Man(9)GlcNAc(2) did not bind to the calreticulin-substrate complex, attesting to the exquisite specificity of this interaction. The binding of calreticulin to IgG was used for the development of immunoassay and the relative affinity of the lectin-substrate association was indirectly measured. The values are in agreement with those obtained with SPR. Although the reactions are several orders of magnitude slower than the diffusion controlled processes, the data are qualitatively and quantitatively consistent with single-step bimolecular association and dissociation reaction. Analyses of the activation parameters indicate that reaction is enthalpically driven and does not involve a highly ordered transition state. Based on these data, the mechanism of its chaperone activity is briefly discussed.

Temperature and pressure dependence of direct current electrical resistivity in the Na2O-ZnO-B2O3 glass system

Two series of glasses were prepared, xNa2O, yZnO, 100 - x - yB2O3 and 30 - xNa2O, xZnO, 70B2O3 (mol%). The temperature dependence of the direct current resistivity was measured from room temperature to about 700 K and in both series of glasses we observed a simple Arrhenius type of temperature dependence. However, the resistivity of the binary alkali glass increased steeply by as much as two orders of magnitude with the addition of even a small quantity of ZnO and remained virtually unaffected by further addition of ZnO. The resistivity decreases gradually with increasing pressure in Na2O-B2O3 but increases with increasing pressure with the addition of ZnO.

Asynchronous behaviour in some three-atom linear concerted radical-exchange reactions

A few simple three-atom thermoneutral radical exchange reactions (i.e. A + BC --> AB + C) are examined by ab initio SCF methods. Emphasis is laid on the detailed analysis of density matrices rather than on energetics. Results reveal that the sum of the bond orders of the breaking and forming bonds is not conserved to unity, due to development of free valence on the migrating atom 'B' in the transition state. Bond orders, free valence and spin densities on the atoms are calculated. The present analysis shows that the bond-cleavage process is always more advanced than the bond-formation process in the transition state. Further analysis shows a development of the negative spin density on the migrating atom 'B' in the transition state. The depletion of the alpha-spin density on the radical site "A" in the reactant during the reaction lags behind the growth of the alpha-spin density on the terminal atom "C" of the reactant bond, 'B-C' in the transition state. But all these processes are completed simultaneously at the end of the reaction. Hence, the reactions are asynchronous but kinetically concerted in most cases.

Dynamics and local structure of colossal magnetoresistance manganites

We report Extended X-ray Absorption Fine Structure and anelastic spectroscopy measurements on on hole doped manganese oxides La1-xCaxMnO3 which present the colossal magnetoresistance effect. EXAFS measurements were realized both in the absence and presence of an applied magnetic field of 1.1 Tesla, in a wide temperature range (between 330 and 77 K) and at various dopings (x = 0.25 and x = 0.33). The magnetic field orders the magnetic moments so favouring the electron mobility and the reduction of Mn-O octahedra distortions. We observe the presence of four short and two long Mn-O distances (1.93 and 2.05 Angstrom respectively) above and also below the metal-insulator phase transition. The overall distortion decreases but does not completely disappear in the metallic phase suggesting the possible coexistence of metallic and insulating regions at low temperatures. The magnetic field reduces the lattice distortions showing evidence of a microscopic counterpart of the macroscopic colossal magnetoresistance. We also present preliminary anelastic relaxation spectra in a wide temperature range from 900 K to 1 K on a sample with x = 0.40, in order to study the structural phase transitions and the lattice dynamics. A double peak has been observed at the metal-insulator transition in the imaginary part of Young's modulus. This double peak indicates that the metal-insulator transition could be a more complex phenomenon than a simple second order phase transition. In particular the peak at lower temperatures can be connected with the possible presence of inhomogeneous phase structures. Another intense dissipation peak has been observed corresponding to the structural orthorhombic-trigonal transition around 750 K.

Surface Structures of Silicon and Germanium

Si and Ge were cleaved on the (111) plane under ultra high vacuum and exposed to O and subsequent heat treatment. LEED and spot photometric measurements were taken. Cleaved surfaces for both Si and Ge gave the expected (2 x 1) structure. Results for O exposure were qualitatively for Si and Ge. The 1/2 orders disappeared after exposure to approx = 10 exp - exp 7. Integral orders started to weaken at 10 exp -6 to 10 exp - exp 2 torr min., disappearing at 10 exp -1 torr min. Heat treatment of Si at 900 deg C for several seconds restored the integral orders and further heating gave a new pattern with 1/3 orders. Exposure to 2 x 10 exp -6 torr min O without further heating weakened the fractional orders and at 10 exp -5 torr min they disappeared. Integral orders remained after further heating in O. For Ge integral orders were not restored after 0 exposure until heat treatment had continued at 550 deg C for several min. The (1 x 1) structure disappeared after heating at 590 deg C in 7 x 10 exp -1 torr O and further heating at 590 deg C without O restored the integral order Variations of intensity with voltage were measured for the (00) and (20) spots. The results supported a model proposed by Haneman (Phys. Rev., 1968, 170, 705) involving two kinds of atom sites on the cleaved surface. 20 ref.--E.J.S.

Learning dynamic prices in multiseller electronic retail markets with price sensitive customers, stochastic demands, and inventory replenishments

In this paper, we use reinforcement learning (RL) as a tool to study price dynamics in an electronic retail market consisting of two competing sellers, and price sensitive and lead time sensitive customers. Sellers, offering identical products, compete on price to satisfy stochastically arriving demands (customers), and follow standard inventory control and replenishment policies to manage their inventories. In such a generalized setting, RL techniques have not previously been applied. We consider two representative cases: 1) no information case, were none of the sellers has any information about customer queue levels, inventory levels, or prices at the competitors; and 2) partial information case, where every seller has information about the customer queue levels and inventory levels of the competitors. Sellers employ automated pricing agents, or pricebots, which use RL-based pricing algorithms to reset the prices at random intervals based on factors such as number of back orders, inventory levels, and replenishment lead times, with the objective of maximizing discounted cumulative profit. In the no information case, we show that a seller who uses Q-learning outperforms a seller who uses derivative following (DF). In the partial information case, we model the problem as a Markovian game and use actor-critic based RL to learn dynamic prices. We believe our approach to solving these problems is a new and promising way of setting dynamic prices in multiseller environments with stochastic demands, price sensitive customers, and inventory replenishments.

Memory effect in Dy0.5Sr0.5MnO3 single crystals

We have performed a series of magnetic aging experiments on single crystals of Dy0.5Sr0.5MnO3. The results demonstrate striking memory and chaos-like effects in this insulating half-doped perovskite manganite and suggest the existence of strong magnetic relaxation mechanisms of a clustered magnetic state. The spin-glass-like state established below a temperature T-sg approximate to 34 K originates from quenched disorder arising due to the ionic-radii mismatch at the rare earth site. However, deviations from the typical behavior seen in canonical spin glass materials are observed which indicate that the glassy magnetic properties are due to cooperative and frustrated dynamics in a heterogeneous or clustered magnetic state. In particular, the microscopic spin flip time obtained from dynamical scaling near the spin glass freezing temperature is four orders of magnitude larger than microscopic times found in atomic spin glasses. The magnetic viscosity deduced from the time dependence of the zero-field-cooled magnetization exhibits a peak at a temperature T < T-sg and displays a marked dependence on waiting time in zero field.

Interplay between multiple length and time scales in complex chemical systems

Processes in complex chemical systems, such as macromolecules, electrolytes, interfaces, micelles and enzymes, can span several orders of magnitude in length and time scales. The length and time scales of processes occurring over this broad time and space window are frequently coupled to give rise to the control necessary to ensure specificity and the uniqueness of the chemical phenomena. A combination of experimental, theoretical and computational techniques that can address a multiplicity of length and time scales is required in order to understand and predict structure and dynamics in such complex systems. This review highlights recent experimental developments that allow one to probe structure and dynamics at increasingly smaller length and time scales. The key theoretical approaches and computational strategies for integrating information across time-scales are discussed. The application of these ideas to understand phenomena in various areas, ranging from materials science to biology, is illustrated in the context of current developments in the areas of liquids and solvation, protein folding and aggregation and phase transitions, nucleation and self-assembly.

Diagnosis of dominant forcing factors for large-scale vertical velocities during active and break phases of the monsoon

An attempt to diagnose the dominant forcings which drive the large-scale vertical velocities over the monsoon region has been made by computing the forcings like diabatic heating fields,etc. and the large-scale vertical velocities driven by these forcings for the contrasting periods of active and break monsoon situations; in order to understand the rainfall variability associated with them. Computation of diabatic heating fields show us that among different components of diabatic heating it is the convective heating that dominates at mid-tropospheric levels during an active monsoon period; whereas it is the sensible heating at the surface that is important during a break period. From vertical velocity calculations we infer that the prime differences in the large-scale vertical velocities seen throughout the depth of the atmosphere are due to the differences in the orders of convective heating; the maximum rate of latent heating being more than 10 degrees Kelvin per day during an active monsoon period; whereas during a break monsoon period it is of the order of 2 degrees Kelvin per day at mid-tropospheric levels. At low levels of the atmosphere, computations show that there is large-scale ascent occurring over a large spatial region, driven only by the dynamic forcing associated with vorticity and temperature advection during an active monsoon period. However, during a break monsoon period such large-scale spatial organization in rising motion is not seen. It is speculated that these differences in the low-level large-scale ascent might be causing differences in convective heating because the weaker the low level ascent, the lesser the convective instability which produces deep cumulus clouds and hence lesser the associated latent heat release. The forcings due to other components of diabatic heating, namely, the sensible heating and long wave radiative cooling do not influence the large-scale vertical velocities significantly.

Generalized asymptotic expansions for coupled wavenumbers in fluid-filled cylindrical shells

Analytical expressions are found for the coupled wavenumbers in an infinite fluid-filled cylindrical shell using the asymptotic methods. These expressions are valid for any general circumferential order (n).The shallow shell theory (which is more accurate at higher frequencies)is used to model the cylinder. Initially, the in vacua shell is dealt with and asymptotic expressions are derived for the shell wavenumbers in the high-and the low-frequency regimes. Next, the fluid-filled shell is considered. Defining a relevant fluid-loading parameter p, we find solutions for the limiting cases of small and large p. Wherever relevant, a frequency scaling parameter along with some ingenuity is used to arrive at an elegant asymptotic expression. In all cases.Poisson's ratio v is used as an expansion variable. The asymptotic results are compared with numerical solutions of the dispersion equation and the dispersion relation obtained by using the more general Donnell-Mushtari shell theory (in vacuo and fluid-filled). A good match is obtained. Hence, the contribution of this work lies in the extension of the existing literature to include arbitrary circumferential orders(n). (C) 2010 Elsevier Ltd. All rights reserved.

Microstructure related influence on the electrical properties of pulsed laser ablated (Ba, Sr)TiO3 thin films

The microstructural dependence of electrical properties of (Ba, Sr)TiO3(BST) thin films were studied from the viewpoint of dc and ac electrical properties. The films were grown using a pulsed laser deposition technique in a temperature range of 300 to 600 degrees C, inducing changes in grain size, structure, and morphology. Consequently, two different types of films were realized, of which type I, was polycrystalline, multigrained, while type II was [100] oriented possessing a densely packed fibrous microstructure. Leakage current measurements were done at elevated temperatures to provide evidence of the conduction mechanism present in these films. The results revealed a contribution from both electronic and ionic conduction. In the case of type I films, two trapping levels were identified with energies around 0.5 and 2.73 eV, which possibly originate from oxygen vacancies V-O and Ti3+ centers, respectively. These levels act as shallow and deep traps and are reflected in the current-voltage characteristics of the BST thin films. The activation energy associated with oxygen vacancy motion in this case was obtained as 1.28 eV. On the contrary, type II films showed no evidence of deep trap energy levels, while the identified activation energy associated with shallow traps was obtained as 0.38 eV. The activation energy obtained for oxygen vacancy motion in type II films was around 1.02 eV. The dc measurement results were further elucidated through ac impedance analysis, which revealed a grain boundary dominated response in type I in comparison to type II films where grain response is highlighted. A comparison of the mean relaxation time of the two films revealed three orders of magnitude higher relaxation time in the case of type I films. Due to smaller grain size in type I films the grains were considered to be completely depleted giving rise to only grain boundary response for the bulk of the film. The activation energy obtained from conductivity plots agree very well with that of dc measurements giving values 1.3 and 1.07 eV for type I and type II films, respectively. Since oxygen vacancy transport have been identified as the origin of resistance degradation in BST thin films, type I films with their higher value of activation energy for oxygen ion mobility explains the improvement in breakdown characteristics under constant high dc field stress. The role of microstructure in controlling the rate of degradation is found useful in this instance to enhance the film properties under high electric field stresses. (C) 2000 American Institute of Physics. [S0021-8979(00)00418-7].

Saccharide binding to three Gal/GalNAc specific lectins: Fluorescence, spectroscopic and stopped-flow kinetic studies

Fluorescence and stopped-flow spectrophotometric studies on three plant lectins fromPsophocarpus tetragonolobus (winged bean),Glycine max (soybean) andArtocarpus integrifolia (jack fruit) have been studied usingN-dansylgalactosamine as a fluorescent ligand. The best monosaccharide for the winged bean agglutinin I (WBA I) and soybean (SBA) is Me-agrGalNAc and for jack fruit agglutinin (JFA) is Me-agrGal. Examination of the percentage enhancement and association constants (1.51×106, 6.56×106 and 4.17×105 M–1 for SBA, WBA I and JFA, respectively) suggests that the combining regions of the lectins SBA and WBA I are apolar whereas that of JFA is polar. Thermodynamic parameters obtained for the binding of several monosaccharides to these lectins are enthalpically favourable. The binding of monosaccharides to these lectins suggests that the-OH groups at C-1, C-2, C-4 and C-6 in thed-galactose configuration are important loci for interaction with these lectins. An important finding is that the JFA binds specifically to Galß1-3GaINAc with much higher affinity than the other disaccharides which are structurally and topographically similar.The results of stopped-flow spectrometry on the binding ofN-dansylgalactosamine to these lectins are consistent with a bimolecular single step mechanism. The association rate constants (2.4×105, 1.3×104, and 11.7×105 M–1 sec–1 for SBA, WBA I and JFA, respectively) obtained are several orders of magnitude slower than the ones expected for diffusion controlled reactions. The dissociation rate constants (0.2, 3.2×10–2, 83.3 sec–1 for SBA, WBA I and JFA, respectively) obtained for the dissociation ofN-dansylgalactosamine from its lectin complex are slowest for SBA and WBA I when compared with any other lectin-ligand dissociation process.