Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

Our ability to infer the protein quaternary structure automatically from atom and lattice information is inadequate, especially for weak complexes, and heteromeric quaternary structures. Several approaches exist, but they have limited performance. Here, we present a new scheme to infer protein quaternary structure from lattice and protein information, with all-around coverage for strong, weak and very weak affinity homomeric and heteromeric complexes. The scheme combines naive Bayes classifier and point group symmetry under Boolean framework to detect quaternary structures in crystal lattice. It consistently produces >= 90% coverage across diverse benchmarking data sets, including a notably superior 95% coverage for recognition heteromeric complexes, compared with 53% on the same data set by current state-of-the-art method. The detailed study of a limited number of prediction-failed cases offers interesting insights into the intriguing nature of protein contacts in lattice. The findings have implications for accurate inference of quaternary states of proteins, especially weak affinity complexes.

Symmetry-breaking transition in a two-level system coupled to an Ohmic bath: A squeezed-state approach

Displaced squeezed states are proposed as variational ground states for phonons (Bose fields) coupled to two-level systems (spin systems). We have investigated the zero-temperature phase diagram for the localization-delocalization transition of a tunneling particle interacting with an Ohmic heat bath. Our results are compared with known existing approximate treatments. A modified phase diagram using the displaced squeezed state is presented.

Levitation Effect: Role of Symmetry and Dependence of Diffusivity on the Bond Length of Homonuclear and Heteronuclear Diatomic Species

Molecular dynamics investigation of model diatomic species confined to the alpha-cages of zeolite NaY is reported. The dependence of self-diffusivity on the bond length of the diatomic species has been investigated. Three different sets of runs have been carried out. In the first set, the two atoms of the diatomic molecule interact with the zeolite atoms with equal strength (example, O-2, the symmetric case). In the second and third sets which correspond to asymmetric cases, the two atoms of the diatomic molecule interact with unequal strengths (example, CO). The result for the symmetric case exhibits a well-defined maximum in self-diffusivity for an intermediate bond length. In contrast to this, the intermediate asymmetry leads to a less pronounced maximum. For the large asymmetric case, the maximum is completely absent. These findings are analyzed by computing a number of related properties. These results provide a direct confirmation at the microscopic level of the suggestion by Derouane that the supermobility observed experimentally by Kemball has its origin in the mutual cancellation of forces. The maximum in diffusivity from molecular dynamics is seen at the value predicted by the levitation effect. Further, these findings suggest a role for symmetry in the existence of a diffusivity maximum as a function of diameter of the diffusant often referred to as the levitation effect. The nature of the required symmetry for the existence of anomalous diffusivity is interaction symmetry which is different from that normally encountered in crystallography.

Cyclization of enediyne radical cations through chemical, photochemical, and electrochemical oxidation: The role of state symmetry

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Strength Symmetry Index: A measure of seizure adequacy in ECT

Seizure electroencephalography (EEG) was recorded from two channels-right (Rt) and left (Lt)-during bilateral electroconvulsive therapy (ECT) (n = 12) and unilateral ECT (n = 12). The EEG was also acquired into a microcomputer and was analyzed without knowledge of the clinical details. EEG recordings of both ECT procedures yielded seizures of comparable duration. The Strength Symmetry Index (SSI) was computed from the early- and midseizure phases using the fractal dimension of the EEG. The seizures of unilateral ECT were characterized by significantly smaller SSI in both phases. More unilateral than bilateral ECT seizures had a smaller than median SSI in both phases. The seizures also differed on other measures as reported in the literature. The findings indicate that SSI may be a potential measure of seizure adequacy that remains to be validated in future research.

AC breakdown characteristics of epoxy alumina nanocomposites

Experiments were conducted to measure the ac breakdown strength of 0.5 mm, thick epoxy alumina nanocomposites with different filler concentrations of 0.1, 1 and 5wt%. The experiments were performed as per the ASTM D 149 standard. It was observed that the ac breakdown strength was marginally lower up to 1wt% filler concentration and then increased at 5wt% filler concentration as compared to the unfilled epoxy. The Weibull shape parameter (β) increased with the addition of nanoparticles to epoxy. The dependence of thickness on the ac breakdown strength was also analyzed by conducting experiments on 1mm and 3mm thick unfilled epoxy and epoxy alumina nanocomposites of 1wt% and 5wt% filler concentrations. The DSC analysis was done to understand the material properties at the filler resin interface in order to study the effect of the filler concentration and thereby the influence of the interface on the ac breakdown strength of epoxy nanocomposites.

Symmetry-breaking transitions in equilibrium shapes of coherent precipitates: Effect of elastic anisotropy and inhomogeneity

We examine the symmetry-breaking transitions in equilibrium shapes of coherent precipitates in two-dimensional (2-D) systems under a plane-strain condition with the principal misfit strain components epsilon(xx)*. and epsilon(yy)*. For systems with cubic elastic moduli, we first show all the shape transitions associated with different values of t = epsilon(yy)*/epsilon(xx)*. We also characterize each of these transitions, by studying its dependence on elastic anisotropy and inhomogeneity. For systems with dilatational misfit (t = 1) and those with pure shear misfit (t = -1), the transition is from an equiaxed shape to an elongated shape, resulting in a break in rotational symmetry. For systems with nondilatational misfit (-1 < t < 1; t not equal 0), the transition involves a break in mirror symmetries normal to the x- and y-axes. The transition is continuous in all cases, except when 0 < t < 1. For systems which allow an invariant line (-1 less than or equal to t < 0), the critical size increases with an increase in the particle stiffness. However, for systems which do not allow an invariant line (0 < t less than or equal to 1), the critical size first decreases, reaches a minimum, and then starts increasing with increasing particle stiffness; moreover, the transition is also forbidden when the particle stiffness is greater than a critical value.

AC Breakdown Characteristics of Epoxy Nanocomposites

Experiments were conducted to measure the ac breakdown strength of epoxy alumina nanocomposites with different filler loadings of 0.1, 1 and 5 wt%. The experiments were performed as per the ASTM D 149 standard on samples of thickness 0.5 mm, 1 mm and 3 mm in order to study the effect of thickness on the ac breakdown strength of epoxy nanocomposites. In the case of epoxy alumina nanocomposites it was observed that the ac breakdown strength was marginally lower for 0.1 wt% and 1 wt% filler loadings and then increased at 5 wt% filler loading as compared to the unfilled epoxy. The Weibull shape parameter (beta) increased with the addition of nanoparticles to epoxy as well as with the increasing sample thickness for all the filler loadings considered. DSC analysis was done to study the material properties at the filler resin interface in order to understand the effect of the filler loading and thereby the influence of the interface on the ac breakdown strength of epoxy nanocomposites. It was also observed that the decrease in ac electric breakdown strength with an increase in sample thickness follows an inverse power-law dependence. In addition, the ac breakdown strength of epoxy silica nanocomposites have also been studied in order to understand the influence of the filler type on the breakdown strength.

Symmetry in Scalar Field Topology

Study of symmetric or repeating patterns in scalar fields is important in scientific data analysis because it gives deep insights into the properties of the underlying phenomenon. Though geometric symmetry has been well studied within areas like shape processing, identifying symmetry in scalar fields has remained largely unexplored due to the high computational cost of the associated algorithms. We propose a computationally efficient algorithm for detecting symmetric patterns in a scalar field distribution by analysing the topology of level sets of the scalar field. Our algorithm computes the contour tree of a given scalar field and identifies subtrees that are similar. We define a robust similarity measure for comparing subtrees of the contour tree and use it to group similar subtrees together. Regions of the domain corresponding to subtrees that belong to a common group are extracted and reported to be symmetric. Identifying symmetry in scalar fields finds applications in visualization, data exploration, and feature detection. We describe two applications in detail: symmetry-aware transfer function design and symmetry-aware isosurface extraction.

Insulating State and Breakdown of Fermi Liquid Description in Molecular-Scale Single-Crystalline Wires of Gold

Electrical transport measurements on ultrathin single-crystalline Au nanowires, synthesized via a wet chemical route, show an unexpected insulating behavior. The linear response electrical resistance exhibits a power-law dependence on temperature. In addition, the variation of current over a wide range of temperature and voltage obeys a universal scaling relation that provides compelling evidence for a non-Fermi liquid behavior. Our results demonstrate that the quantum ground state In ultrathin nanowires of simple metallic systems can be radically different from their bulk counterparts and can be described In terms of a Tomonaga-Luttinger liquid (TLL), in the presence of remarkably strong electron-electron interactions.

Symmetry of one-dimensional dynamical systems in terms of transfer matrix parameters

The concept of symmetry for passive, one-dimensional dynamical systems is well understood in terms of the impedance matrix, or alternatively, the mobility matrix. In the past two decades, however, it has been established that the transfer matrix method is ideally suited for the analysis and synthesis of such systems. In this paper an investigatiob is described of what symmetry means in terms of the transfer matrix parameters of an passive element or a set of elements. One-dimensional flexural systems with 4 × 4 transfer matrices as well as acoustical and mechanical systems characterized by 2 × 2 transfer matrices are considered. It is shown that the transfer matrix of a symmetrical system, defined with respect to symmetrically oriented state variables, is involutory, and that a physically symmetrical system may not necessarily be functionally or dynamically symmetrical.

Electrical Breakdown of Gases Between Coaxial Cylindrical Electrodes in Crossed Electric and Magnetic Fields

Sparking potentials have been measured in nitrogen and dry air between coaxial cylindrical electrodes for values of n = R2/R1 = approximately 1 to 30 (R1 = inner electrode radius, R2 = outer electrode radius) in the presence of crossed uniform magnetic fields. The magnetic flux density was varied from 0 to 3000 Gauss. It has been shown that the minimum sparking potentials in the presence of the crossed magnetic field can be evaluated on the basis of the equivalent pressure concept when the secondary ionization coefficient does not vary appreciably with B/p (B = magnetic flux density, p = gas pressure). The values of secondary ionization coefficients �¿B in nitrogen in crossed fields calculated from measured values of sparking potentials and Townsend ionization coefficients taken from the literature, have been reported. The calculated values of collision frequencies in nitrogen from minimum sparking potentials in crossed fields are found to increase with increasing B/p at constant E/pe (pe = equivalent pressure). Studies on the similarity relationship in crossed fields has shown that the similarity theorem is obeyed in dry air for both polarities of the central electrode in crossed fields.

Full spin and spatial symmetry adapted technique for correlated electronic hamiltonians: Application to an icosahedral cluster

One of the long standing problems in quantum chemistry had been the inability to exploit full spatial and spin symmetry of an electronic Hamiltonian belonging to a non-Abelian point group. Here, we present a general technique which can utilize all the symmetries of an electronic (magnetic) Hamiltonian to obtain its full eigenvalue spectrum. This is a hybrid method based on Valence Bond basis and the basis of constant z-component of the total spin. This technique is applicable to systems with any point group symmetry and is easy to implement on a computer. We illustrate the power of the method by applying it to a model icosahedral half-filled electronic system. This model spans a huge Hilbert space (dimension 1,778,966) and in the largest non-Abelian point group. The C60 molecule has this symmetry and hence our calculation throw light on the higher energy excited states of the bucky ball. This method can also be utilized to study finite temperature properties of strongly correlated systems within an exact diagonalization approach. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012