Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Adaptive selection of search space in look ahead orthogonal matching pursuit

Compressive Sensing theory combines the signal sampling and compression for sparse signals resulting in reduction in sampling rate and computational complexity of the measurement system. In recent years, many recovery algorithms were proposed to reconstruct the signal efficiently. Look Ahead OMP (LAOMP) is a recently proposed method which uses a look ahead strategy and performs significantly better than other greedy methods. In this paper, we propose a modification to the LAOMP algorithm to choose the look ahead parameter L adaptively, thus reducing the complexity of the algorithm, without compromising on the performance. The performance of the algorithm is evaluated through Monte Carlo simulations.

A novel MCMC algorithm for near-optimal detection in large-scale uplink mulituser MIMO systems

In this paper, we propose a low-complexity algorithm based on Markov chain Monte Carlo (MCMC) technique for signal detection on the uplink in large scale multiuser multiple input multiple output (MIMO) systems with tens to hundreds of antennas at the base station (BS) and similar number of uplink users. The algorithm employs a randomized sampling method (which makes a probabilistic choice between Gibbs sampling and random sampling in each iteration) for detection. The proposed algorithm alleviates the stalling problem encountered at high SNRs in conventional MCMC algorithm and achieves near-optimal performance in large systems with M-QAM. A novel ingredient in the algorithm that is responsible for achieving near-optimal performance at low complexities is the joint use of a randomized MCMC (R-MCMC) strategy coupled with a multiple restart strategy with an efficient restart criterion. Near-optimal detection performance is demonstrated for large number of BS antennas and users (e.g., 64, 128, 256 BS antennas/users).

MRT Letter: Experimental Verification of Vectorial Theory to Determine Field at the Geometrical Focus of a Cylindrical Lens

We provide experimental evidence supporting the vectorial theory for determining electric field at and near the geometrical focus of a cylindrical lens. This theory provides precise distribution of field and its polarization effects. Experimental results show a close match (approximate to 95% using (2)-test) with the simulation results (obtained using vectorial theory). Light-sheet generated both at low and high NA cylindrical lens shows the importance of vectorial theory for further development of light-sheet techniques. Potential applications are in planar imaging systems (such as, SPIM, IML-SPIM, imaging cytometry) and spectroscopy. Microsc. Res. Tech. 77:105-109, 2014. (c) 2014 Wiley Periodicals, Inc.

Simulation of inhomogeneous distributions of ultracold atoms in an optical lattice via a massively parallel implementation of nonequilibrium strong-coupling perturbation theory

We present a nonequilibrium strong-coupling approach to inhomogeneous systems of ultracold atoms in optical lattices. We demonstrate its application to the Mott-insulating phase of a two-dimensional Fermi-Hubbard model in the presence of a trap potential. Since the theory is formulated self-consistently, the numerical implementation relies on a massively parallel evaluation of the self-energy and the Green's function at each lattice site, employing thousands of CPUs. While the computation of the self-energy is straightforward to parallelize, the evaluation of the Green's function requires the inversion of a large sparse 10(d) x 10(d) matrix, with d > 6. As a crucial ingredient, our solution heavily relies on the smallness of the hopping as compared to the interaction strength and yields a widely scalable realization of a rapidly converging iterative algorithm which evaluates all elements of the Green's function. Results are validated by comparing with the homogeneous case via the local-density approximation. These calculations also show that the local-density approximation is valid in nonequilibrium setups without mass transport.

Enhanced Gas Adsorption on Graphitic Substrates via Defects and Local Curvature: A Density Functional Theory Study

Using van-der-Waals-corrected density functional theory calculations, we explore the possibility of engineering the local structure and morphology of high-surface-area graphene-derived materials to improve the uptake of methane and carbon dioxide for gas storage and sensing. We test the sensitivity of the gas adsorption energy to the introduction of native point defects, curvature, and the application of strain. The binding energy at topological point defect sites is inversely correlated with the number of missing carbon atoms, causing Stone-Wales defects to show the largest enhancement with respect to pristine graphene (similar to 20%). Improvements of similar magnitude are observed at concavely curved surfaces in buckled graphene sheets under compressive strain, whereas tensile strain tends to weaken gas binding. Trends for CO2 and CH4 are, similar, although CO2 binding is generally stronger by similar to 4 to 5 kJ mol(-1). However, the differential between the adsorption of CO2 and CH4 is much higher on folded graphene sheets and at concave curvatures; this could possibly be leveraged for CH4/CO2 flow separation and gasselective sensors.

Anomalous power law decay in solvation dynamics of DNA: a mode coupling theory analysis of ion contribution

Several time dependent fluorescence Stokes shift (TDFSS) experiments have reported a slow power law decay in the hydration dynamics of a DNA molecule. Such a power law has neither been observed in computer simulations nor in some other TDFSS experiments. Here we observe that a slow decay may originate from collective ion contribution because in experiments DNA is immersed in a buffer solution, and also from groove bound water and lastly from DNA dynamics itself. In this work we first express the solvation time correlation function in terms of dynamic structure factors of the solution. We use mode coupling theory to calculate analytically the time dependence of collective ionic contribution. A power law decay in seen to originate from an interplay between long-range probe-ion direct correlation function and ion-ion dynamic structure factor. Although the power law decay is reminiscent of Debye-Falkenhagen effect, yet solvation dynamics is dominated by ion atmosphere relaxation times at longer length scales (small wave number) than in electrolyte friction. We further discuss why this power law may not originate from water motions which have been computed by molecular dynamics simulations. Finally, we propose several experiments to check the prediction of the present theoretical work.

Bayesian Accelerated Life Testing under Competing Weibull Causes of Failure

Consider a J-component series system which is put on Accelerated Life Test (ALT) involving K stress variables. First, a general formulation of ALT is provided for log-location-scale family of distributions. A general stress translation function of location parameter of the component log-lifetime distribution is proposed which can accommodate standard ones like Arrhenius, power-rule, log-linear model, etc., as special cases. Later, the component lives are assumed to be independent Weibull random variables with a common shape parameter. A full Bayesian methodology is then developed by letting only the scale parameters of the Weibull component lives depend on the stress variables through the general stress translation function. Priors on all the parameters, namely the stress coefficients and the Weibull shape parameter, are assumed to be log-concave and independent of each other. This assumption is to facilitate Gibbs sampling from the joint posterior. The samples thus generated from the joint posterior is then used to obtain the Bayesian point and interval estimates of the system reliability at usage condition.

Spectral finite element based on an efficient layerwise theory for wave propagation analysis of composite and sandwich beams

In this paper, we present a spectral finite element model (SFEM) using an efficient and accurate layerwise (zigzag) theory, which is applicable for wave propagation analysis of highly inhomogeneous laminated composite and sandwich beams. The theory assumes a layerwise linear variation superimposed with a global third-order variation across the thickness for the axial displacement. The conditions of zero transverse shear stress at the top and bottom and its continuity at the layer interfaces are subsequently enforced to make the number of primary unknowns independent of the number of layers, thereby making the theory as efficient as the first-order shear deformation theory (FSDT). The spectral element developed is validated by comparing the present results with those available in the literature. A comparison of the natural frequencies of simply supported composite and sandwich beams obtained by the present spectral element with the exact two-dimensional elasticity and FSDT solutions reveals that the FSDT yields highly inaccurate results for the inhomogeneous sandwich beams and thick composite beams, whereas the present element based on the zigzag theory agrees very well with the exact elasticity solution for both thick and thin, composite and sandwich beams. A significant deviation in the dispersion relations obtained using the accurate zigzag theory and the FSDT is also observed for composite beams at high frequencies. It is shown that the pure shear rotation mode remains always evanescent, contrary to what has been reported earlier. The SFEM is subsequently used to study wavenumber dispersion, free vibration and wave propagation time history in soft-core sandwich beams with composite faces for the first time in the literature. (C) 2014 Elsevier Ltd. All rights reserved.

Bayesian Accelerated Life Testing under Competing Weibull Causes of Failure

Consider a J-component series system which is put on Accelerated Life Test (ALT) involving K stress variables. First, a general formulation of ALT is provided for log-location-scale family of distributions. A general stress translation function of location parameter of the component log-lifetime distribution is proposed which can accommodate standard ones like Arrhenius, power-rule, log-linear model, etc., as special cases. Later, the component lives are assumed to be independent Weibull random variables with a common shape parameter. A full Bayesian methodology is then developed by letting only the scale parameters of the Weibull component lives depend on the stress variables through the general stress translation function. Priors on all the parameters, namely the stress coefficients and the Weibull shape parameter, are assumed to be log-concave and independent of each other. This assumption is to facilitate Gibbs sampling from the joint posterior. The samples thus generated from the joint posterior is then used to obtain the Bayesian point and interval estimates of the system reliability at usage condition.

Cu-II-Azide Polynuclear Complexes of Three Different Building Clusters with the Same Schiff-Base Ligand: Synthesis, Structures, Magnetic Behavior, and Density Functional Theory Studies

Three copper-azido complexes Cu-4(N-3)(8)(L-1)(2)(MeOH)(2)](n) (1), Cu-4(N-3)(8)(L-1)(2)] (2), and Cu-5(N-3)(10)(L-1)(2)](n) (3) L-1 is the imine resulting from the condensation of pyridine-2-carboxaldehyde with 2-(2-pyridyl)ethylamine] have been synthesized using lower molar equivalents of the Schiff base ligand with Cu(NO3)(2)center dot 3H(2)O and an excess of NaN3. Single crystal X-ray structures show that the basic unit of the complexes 1 and 2 contains Cu-4(II) building blocks; however, they have distinct basic and overall structures due to a small change in the bridging mode of the peripheral pair of copper atoms in the linear tetranudear structures. Interestingly, these changes are the result of changing the solvent system (MeOH/H2O to EtOH/H2O) used for the synthesis, without changing the proportions of the components (metal to ligand ratio 2:1). Using even lower proportions of the ligand, another unique complex was isolated with Cu-5(II) building units, forming a two-dimensional complex (3). Magnetic susceptibility measurements over a wide range of temperature exhibit the presence of both antiferromagnetic (very weak) and ferromagnetic exchanges within the tetranuclear unit structures. Density functional theory calculations (using B3LYP functional, and two different basis sets) have been performed on the complexes 1 and 2 to provide a qualitative theoretical interpretation of their overall magnetic behavior.

Evaluation of TRMM PR Sampling Error Over a Subtropical Basin Using Bootstrap Technique

Quantitative use of satellite-derived rainfall products for various scientific applications often requires them to be accompanied with an error estimate. Rainfall estimates inferred from low earth orbiting satellites like the Tropical Rainfall Measuring Mission (TRMM) will be subjected to sampling errors of nonnegligible proportions owing to the narrow swath of satellite sensors coupled with a lack of continuous coverage due to infrequent satellite visits. The authors investigate sampling uncertainty of seasonal rainfall estimates from the active sensor of TRMM, namely, Precipitation Radar (PR), based on 11 years of PR 2A25 data product over the Indian subcontinent. In this paper, a statistical bootstrap technique is investigated to estimate the relative sampling errors using the PR data themselves. Results verify power law scaling characteristics of relative sampling errors with respect to space-time scale of measurement. Sampling uncertainty estimates for mean seasonal rainfall were found to exhibit seasonal variations. To give a practical example of the implications of the bootstrap technique, PR relative sampling errors over a subtropical river basin of Mahanadi, India, are examined. Results reveal that the bootstrap technique incurs relative sampling errors < 33% (for the 2 degrees grid), < 36% (for the 1 degrees grid), < 45% (for the 0.5 degrees grid), and < 57% (for the 0.25 degrees grid). With respect to rainfall type, overall sampling uncertainty was found to be dominated by sampling uncertainty due to stratiform rainfall over the basin. The study compares resulting error estimates to those obtained from latin hypercube sampling. Based on this study, the authors conclude that the bootstrap approach can be successfully used for ascertaining relative sampling errors offered by TRMM-like satellites over gauged or ungauged basins lacking in situ validation data. This technique has wider implications for decision making before incorporating microwave orbital data products in basin-scale hydrologic modeling.

The opportunity for sampling: the ecological context of female mate choice

Female mate choice decisions, which influence sexual selection, involve complex interactions between the 2 sexes and the environment. Theoretical models predict that male movement and spacing in the field should influence female sampling tactics, and in turn, females should drive the evolution of male movement and spacing to sample them optimally. Theoretically, simultaneous sampling of males using the best-of-n or comparative Bayes strategy should yield maximum mating benefits to females. We examined the ecological context of female mate sampling based on acoustic signals in the tree cricket Oecanthus henryi to determine whether the conditions for such optimal strategies were met in the field. These strategies involve recall of the quality and location of individual males, which in turn requires male positions to be stable within a night. Calling males rarely moved within a night, potentially enabling female sampling strategies that require recall. To examine the possibility of simultaneous acoustic sampling of males, we estimated male acoustic active spaces using information on male spacing, call transmission, and female hearing threshold. Males were found to be spaced far apart, and active space overlap was rare. We then examined female sampling scenarios by studying female spacing relative to male acoustic active spaces. Only 15% of sampled females could hear multiple males, suggesting that simultaneous mate sampling is rare in the field. Moreover, the relatively large distances between calling males suggest high search costs, which may favor threshold strategies that do not require memory.

Influence of Spatial Variability on Pavement Responses Using Latin Hypercube Sampling on Two-Dimensional Random Fields

Although uncertainties in material properties have been addressed in the design of flexible pavements, most current modeling techniques assume that pavement layers are homogeneous. The paper addresses the influence of the spatial variability of the resilient moduli of pavement layers by evaluating the effect of the variance and correlation length on the pavement responses to loading. The integration of the spatially varying log-normal random field with the finite-difference method has been achieved through an exponential autocorrelation function. The variation in the correlation length was found to have a marginal effect on the mean values of the critical strains and a noticeable effect on the standard deviation which decreases with decreases in correlation length. This reduction in the variance arises because of the spatial averaging phenomenon over the softer and stiffer zones generated because of spatial variability. The increase in the mean value of critical strains with decreasing correlation length, although minor, illustrates that pavement performance is adversely affected by the presence of spatially varying layers. The study also confirmed that the higher the variability in the pavement layer moduli, introduced through a higher value of coefficient of variation (COV), the higher the variability in the pavement response. The study concludes that ignoring spatial variability by modeling the pavement layers as homogeneous that have very short correlation lengths can result in the underestimation of the critical strains and thus an inaccurate assessment of the pavement performance. (C) 2014 American Society of Civil Engineers.