Conformational Choices for the Stereochemically Constrained gamma-Amino Acid Residue Gabapentin: Theoretical Studies and Correlation With Experimental Results

Gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn) is an achiral, conformationally constrained gamma amino acid residue. A survey of available crystal structures of Gpn peptides reveals that the torsion angles about the C-gamma-C-beta (theta(1)) and C-beta-C-alpha(theta(2)) bonds are overwhelmingly limited to gauche, gauche (g(+)g(+)/g(-)g(-)) conformations. The Gpn residue forms C-7 and C-9 hydrogen bonds in which the donor and acceptor atoms come from the flanking peptide units. In combination with alpha amino acid residues alpha gamma and gamma alpha segments can adopt C-12 hydrogen bonded structures. The conformational choices available to the Gpn residue have been probed using energy calculations, adopting a grid search strategy. Ramachandran phi-psi maps have been constructed for fixed values of theta(1) and theta(2), corresponding to the gauche and trans conformations. The sterically allowed and energetically favorable regions of conformational space have been defined and experimental observations compared. C-7 and C-9 hydrogen bonded conformational families have been identified using a grid search approach in which theta(1) and theta(2) values are varied over a range of +/- 10 degrees about ideal values at 1 degrees intervals. The theoretical analysis together with experimental observations for 59 Gpn residues from 35 crystal structures permits definition of the limited range of conformational possibilities at this gamma amino acid residue. .

Urban Growth Analysis Using Spatial and Temporal Data

Urban growth identification, quantification, knowledge of rate and the trends of growth would help in regional planning for better infrastructure provision in environmentally sound way. This requires analysis of spatial and temporal data, which help in quantifying the trends of growth on spatial scale. Emerging technologies such as Remote Sensing, Geographic Information System (GIS) along with Global Positioning System (GPS) help in this regard. Remote sensing aids in the collection of temporal data and GIS helps in spatial analysis. This paper focuses on the analysis of urban growth pattern in the form of either radial or linear sprawl along the Bangalore - Mysore highway. Various GIS base layers such as builtup areas along the highway, road network, village boundary etc. were generated using collateral data such as the Survey of India toposheet, etc. Further, this analysis was complemented with the computation of Shannon's entropy, which helped in identifying prevalent sprawl zone, rate of growth and in delineating potential sprawl locations. The computation Shannon's entropy helped in delineating regions with dispersed and compact growth. This study reveals that the Bangalore North and South taluks contributed mainly to the sprawl with 559% increase in built-up area over a period of 28 years and high degree of dispersion. The Mysore and Srirangapatna region showed 128% change in built-up area and a high potential for sprawl with slightly high dispersion. The degree of sprawl was found to be directly proportional to the distances from the cities.

Spatial correlation in grain misorientation distribution

Grain misorientation was studied in relation to the nearest neighbor's mutual distance using electron back-scattered diffraction measurements. The misorientation correlation function was defined as the probability density for the occurrence of a certain misorientation between pairs of grains separated by a certain distance. Scale-invariant spatial correlation between neighbor grains was manifested by a power law dependence of the preferred misorientation vs. inter-granular distance in various materials after diverse strain paths. The obtained negative scaling exponents were in the range of -2 +/- 0.3 for high-angle grain boundaries. The exponent decreased in the presence of low-angle grain boundaries or dynamic recrystallization, indicating faster decay of correlations. The correlations vanished in annealed materials. The results were interpreted in terms of lattice incompatibility and continuity conditions at the interface between neighboring grains. Grain-size effects on texture development, as well as the implications of such spatial correlations on texture modeling, were discussed.

Inferring neuronal network connectivity from spike data: A temporal data mining approach

Understanding the functioning of a neural system in terms of its underlying circuitry is an important problem in neuroscience. Recent d evelopments in electrophysiology and imaging allow one to simultaneously record activities of hundreds of neurons. Inferring the underlying neuronal connectivity patterns from such multi-neuronal spike train data streams is a challenging statistical and computational problem. This task involves finding significant temporal patterns from vast amounts of symbolic time series data. In this paper we show that the frequent episode mining methods from the field of temporal data mining can be very useful in this context. In the frequent episode discovery framework, the data is viewed as a sequence of events, each of which is characterized by an event type and its time of occurrence and episodes are certain types of temporal patterns in such data. Here we show that, using the set of discovered frequent episodes from multi-neuronal data, one can infer different types of connectivity patterns in the neural system that generated it. For this purpose, we introduce the notion of mining for frequent episodes under certain temporal constraints; the structure of these temporal constraints is motivated by the application. We present algorithms for discovering serial and parallel episodes under these temporal constraints. Through extensive simulation studies we demonstrate that these methods are useful for unearthing patterns of neuronal network connectivity.

Search for chaos in neutron star systems: Is Cyg X-3 a black hole?

The accretion disk around a compact object is a nonlinear general relativistic system involving magnetohydrodynamics. Naturally, the question arises whether such a system is chaotic (deterministic) or stochastic (random) which might be related to the associated transport properties whose origin is still not confirmed. Earlier, the black hole system GRS 1915+105 was shown to be low-dimensional chaos in certain temporal classes. However, so far such nonlinear phenomena have not been studied fairly well for neutron stars which are unique for their magnetosphere and kHz quasi-periodic oscillation (QPO). On the other hand, it was argued that the QPO is a result of nonlinear magnetohydrodynamic effects in accretion disks. If a neutron star exhibits chaotic signature, then what is the chaotic/correlation dimension? We analyze RXTE/PCA data of neutron stars Sco X-1 and Cyg X-2, along with the black hole Cyg X-1 and the unknown source Cyg X-3, and show that while Sco X-1 and Cyg X-2 are low dimensional chaotic systems, Cyg X-1 and Cyg X-3 are stochastic sources. Based on our analysis, we argue that Cyg X-3 may be a black hole.

Extending temporal simulations

Direct numerical simulations (DNS) of spatially growing turbulent shear layers may be performed as temporal simulations by solving the governing equations with some additional terms while imposing streamwise periodicity. These terms are functions of the means whose spatial growth is calculated easily and accurately from statistics of the temporal DNS. Equations for such simulations are derived.

Convergence analysis of the Newton algorithm and a pseudo-time marching scheme for diffuse correlation tomography

We propose a self-regularized pseudo-time marching scheme to solve the ill-posed, nonlinear inverse problem associated with diffuse propagation of coherent light in a tissuelike object. In particular, in the context of diffuse correlation tomography (DCT), we consider the recovery of mechanical property distributions from partial and noisy boundary measurements of light intensity autocorrelation. We prove the existence of a minimizer for the Newton algorithm after establishing the existence of weak solutions for the forward equation of light amplitude autocorrelation and its Frechet derivative and adjoint. The asymptotic stability of the solution of the ordinary differential equation obtained through the introduction of the pseudo-time is also analyzed. We show that the asymptotic solution obtained through the pseudo-time marching converges to that optimal solution provided the Hessian of the forward equation is positive definite in the neighborhood of optimal solution. The superior noise tolerance and regularization-insensitive nature of pseudo-dynamic strategy are proved through numerical simulations in the context of both DCT and diffuse optical tomography. (C) 2010 Optical Society of America.

Deuterium-carbon correlation in static oriented systems using DAPT - A windowless multiple pulse sequence

We present a new method for establishing correlation between deuterium and its attached carbon in a deuterated liquid crystal. The method is based on transfer of polarization using the DAPT pulse sequence proposed originally for two spin half nuclei, now extended to a spin-1 and a spin-1/2 nuclei. DAPT utilizes the evolution of magnetization of the spin pair under two blocks of phase shifted BLEW-12 pulses on one of the spins separated by a 90 degree pulse on the other spin. The method is easy to implement and does not need to satisfy matching conditions unlike the Hartmann-Hahn cross-polarization. Experimental results presented demonstrate the efficacy of the method.

Correlation between conductivity or diffusivity and activation energy in amorphous solids

There exist many investigations of ionic transport in a variety of glasses. These studies exhibit strong correlation between ionic conductivity and activation energy: Typically, it is found that higher conductivity is associated with lower activation energies and vice versa. Although there are explanations for this at a phenomenological level, there is no consistent physical picture to explain the correlation between conductivity and activation energy. We have carried out molecular dynamics simulation as a function of the size of the impurity atom or diffusant (both neutral and charged) in a host amorphous matrix. We find that there is a maximum in self-diffusivity as a function of the size of the impurity atom suggesting that there is an appropriate size for which the diffusivity is maximum. The activation energy is found to be the lowest for this size of the impurity. A similar maximum has been previously found in other condensed phases, such as confined fluids and dense liquids, and has its origin in the levitation effect. The implications of this result for understanding ionic conductivity in glasses are discussed. Our results suggest that there is a relation between microscopic structure of the amorphous solid, diffusivity or conductivity, and activation energy. The nature of this relationship is discussed in terms of the levitation parameter showing that diffusivity is maximum when the size of the neck or doorway radius is comparable with the size of the diffusant. Our computational results here are in excellent agreement with independent experimental results of Nascimento et al. [Braz. J. Phys. 35, 626 (2005)] that structural features of the glass are important in determining the ionic conductivity.

Correlation, Coding, and Cooperation in Wireless Sensor Networks

We consider a single-hop data-gathering sensor network, consisting of a set of sensor nodes that transmit data periodically to a base-station. We are interested in maximizing the lifetime of this network. With our definition of network lifetime and the assumption that the radio transmission energy consumption forms the most significant portion of the total energy consumption at a sensor node, we attempt to enhance the network lifetime by reducing the transmission energy budget of sensor nodes by exploiting three system-level opportunities. We pose the problem of maximizing lifetime as a max-min optimization problem subject to the constraint of successful data collection and limited energy supply at each node. This turns out to be an extremely difficult optimization to solve. To reduce the complexity of this problem, we allow the sensor nodes and the base-station to interactively communicate with each other and employ instantaneous decoding at the base-station. The chief contribution of the paper is to show that the computational complexity of our problem is determined by the complex interplay of various system-level opportunities and challenges.

Low correlation sequences over AM-PSK and QAM alphabets

A construction for a family of sequences over the 8-ary AM-PSK constellation that has maximum nontrivial correlation magnitude bounded as theta(max) less than or similar to root N is presented here. The famfly is asymptotically optimal with respect to the Welch bound on maximum magnitude of correlation. The 8-ary AM-PSK constellation is a subset of the 16-QAM constellation. We also construct two families of sequences over 16-QAM with theta(max) less than or similar to root 2 root N. These families are constructed by interleaving sets of sequences. A construction for a famBy of low-correlation sequences over QAM alphabet of size 2(2m) is presented with maximum nontrivial normalized correlation parameter bounded above by less than or similar to a root N, where N is the period of the sequences in the family and where a ranges from 1.61 in the case of 16-QAM modulation to 2.76 for large m. When used in a CDMA setting, the family will permit each user to modulate the code sequence with 2m bits of data. Interestingly, the construction permits users on the reverse link of the CDMA channel to communicate using varying data rates by switching between sequence famflies; associated to different values of the parameter m. Other features of the sequence families are improved Euclidean distance between different data symbols in comparison with PSK signaling and compatibility of the QAM sequence families with sequences belonging to the large quaternary sequence families {S(p)}.

ZnO nanocrystalline thin films: a correlation of microstructural, optoelectronic properties

The compositional, structural, microstructural, dc electrical conductivity and optical properties of undoped zinc oxide films prepared by the sol-gel process using a spin-coating technique were investigated. The ZnO films were obtained by 5 cycle spin-coated and dried zinc oxide films followed by annealing in air at 600 A degrees C. The films deposited on the platinum coated silicon substrate were crystallized in a hexagonal wurtzite form. The energy-dispersive X-ray (EDX) spectrometry shows Zn and O elements in the products with an approximate molar ratio. TEM image of ZnO thin film shows that a grain of about 60-80 nm in size is really an aggregate of many small crystallites of around 10-20 nm. Electron diffraction pattern shows that the ZnO films exhibited hexagonal structure. The SEM micrograph showed that the films consist in nanocrystalline grains randomly distributed with voids in different regions. The dc conductivity found in the range of 10(-5)-10(-6) (Omega cm)(-1). The optical study showed that the spectra for all samples give the transparency in the visible range.

Context-dependency of a complex fruit-frugivore mutualism: temporal variation in crop size and neighborhood effects

The quantity of fruit consumed by dispersers is highly variable among individuals within plant populations. The outcome Of Such selection operated by firugivores has been examined mostly with respect to changing spatial contexts. The influence of varying temporal contexts on frugivore choice, and their possible demographic and evolutionary consequences is poorly understood. We examined if temporal variation in fruit availability across a hierarchy of nested temporal levels (interannual, intraseasonal, 120 h, 24 h) altered frugivore choice for a complex seed dispersal system in dry tropical forests of southern India. The interactions between Phyllanthus emblica and its primary disperser (ruminants) was mediated by another frugivore (a primate),which made large quantities of fruit available on the ground to ruminants. The direction and strength of crop size and neighborhood effects on this interaction varied with changing temporal contexts.Fruit availability was higher in the first of the two study years, and at the start of the season in both years. Fruit persistence on trees,determined by primate foraging, was influenced by crop size andconspecific neighborhood densities only in the high fruit availability year. Fruit removal by ruminants was influenced by crop size in both years and neighborhood densities only in the high availability year. In both years, these effects were stronger at the start of the season.Intraseasonal reduction in fruit availability diminished inequalities in fruit removal by ruminants and the influence of crop size and fruiting neighborhoods. All trees were not equally attractive to frugivores in a P. emblica population at all points of time. Temporal asymmetry in frugivore-mediated selection could reduce potential for co-evolution between firugivores and plants by diluting selective pressures. Inter-dependencies; formed between disparate animal consumers can add additional levels of complexity to plant-frugivore mutualistic networks and have potential reproductive consequences for specific individuals within populations.

A dynamical approach to the spatio-temporal features of the Portevin-Le Chatelier effect

We show that the extended Ananthakrishna's model exhibits all the features of the Portevin - Le Chatelier effect including the three types of bands. The model reproduces the recently observed crossover from a low dimensional chaotic state at low and medium strain rates to a high dimensional power law state of stress drops at high strain rates. The dynamics of crossover is elucidated through a study of the Lyapunov spectrum.

Large latitudinal gradients and temporal heterogeneity in aerosol black carbon and its mass mixing ratio over southern and northern oceans observed during a trans-continental cruise experiment

Extensive, and collocated measurements of the mass concentrations (M-B) of aerosol black carbon (BC) and (M-T) of composite aerosols were made over the Arabian Sea, tropical Indian Ocean and the Southern Ocean during a trans-continental cruise experiment. Our investigations show that MB remains extremely low(<50 ng m(-3)) and remarkably steady (in space and time) in the Southern Ocean (20 degrees S to 56 degrees S). In contrast, large latitudinal gradients exist north of similar to 20 degrees S; M-B increasing exponentially to reach as high as 2000 ng m(-3) in the Arabian Sea (similar to 8 degrees N). Interestingly, the share of BC showed a distinctly different latitudinal variation, with a peak close to the equator and decreasing on either side. Large fluctuations were seen in M-T over Southern Ocean associated with enhanced production of sea-salt aerosols in response to sea-surface wind speed. These spatio-temporal changes in M-B and its mixing ratio have important implications to regional and global climate.