Design of logical topologies for wavelength-routed optical networks

his paper studies the problem of designing a logical topology over a wavelength-routed all-optical network (AON) physical topology, The physical topology consists of the nodes and fiber links in the network, On an AON physical topology, we can set up lightpaths between pairs of nodes, where a lightpath represents a direct optical connection without any intermediate electronics, The set of lightpaths along with the nodes constitutes the logical topology, For a given network physical topology and traffic pattern (relative traffic distribution among the source-destination pairs), our objective is to design the logical topology and the routing algorithm on that topology so as to minimize the network congestion while constraining the average delay seen by a source-destination pair and the amount of processing required at the nodes (degree of the logical topology), We will see that ignoring the delay constraints can result in fairly convoluted logical topologies with very long delays, On the other hand, in all our examples, imposing it results in a minimal increase in congestion, While the number of wavelengths required to imbed the resulting logical topology on the physical all optical topology is also a constraint in general, we find that in many cases of interest this number can be quite small, We formulate the combined logical topology design and routing problem described above (ignoring the constraint on the number of available wavelengths) as a mixed integer linear programming problem which we then solve for a number of cases of a six-node network, Since this programming problem is computationally intractable for larger networks, we split it into two subproblems: logical topology design, which is computationally hard and will probably require heuristic algorithms, and routing, which can be solved by a linear program, We then compare the performance of several heuristic topology design algorithms (that do take wavelength assignment constraints into account) against that of randomly generated topologies, as well as lower bounds derived in the paper.

Basis set dependence of the molecular electrostatic potential topography. A case study of substituted benzenes

The basis set dependence of the topographical structure of the molecular electrostatic potential (MESP), as well as the effect of substituents on the MESP distribution, has been investigated with substituted benzenes as test cases. The molecules are studied at HF-SCF 3�21G and 6�31G** levels, with a further MESP topographical investigation at the 3�21G, double-zeta, 6�31G*, 6�31G**, double-zeta polarized and triple-zeta polarized levels. The MESP critical points for a 3�21G optimized/6�31G** basis are similar to the corresponding 6�31G** optimized/6�31G** ones. More generally, the qualitative features of the MESP topography computed at the polarized level are independent of the level at which optimization is carried out. For a proper representation of oxygen lone pairs, however, optimization using a polarized basis set is required. The nature of the substituent drastically changes the MESP distribution over the phenyl ring. The values and positions of MESP minima indicate the most active site for electrophilic attack. This point is strengthened by a study of disubstituted benzenes.

Important role of the amino acid attached to tRNA in formylation and in initiation of protein synthesis in Escherichia coli

In attempts to convert an elongator tRNA to an initiator tRNA, we previously generated a mutant elongator methionine tRNA carrying an anticodon sequence change from CAU to CUA along with the two features important for activity of Escherichia coli initiator tRNA in initiation. This mutant tRNA (Mi:2 tRNA) was active in initiation in vivo but only when aminoacylated with methionine by overproduction of methionyl-tRNA synthetase. Here we show that the Mi:2 tRNA is normally aminoacylated in vivo with lysine and that the tRNA aminoacylated with lysine is a very poor substrate for formylation compared with the same tRNA aminoacylated with methionine. By introducing further changes at base pairs 4:69 and 5:68 in the acceptor stem of the Mi:2 tRNA to those found in the E. coli initiator tRNA, we show that change of the U4:A69 base pair to G4:C69 and overproduction of lysyl-tRNA synthetase and methionyl-tRNA transformylase results in partial formylation of the mutant tRNA and activity of the formyllysyl-tRNAs in initiation of protein synthesis. Thus, the G4:C69 base pair contributes toward formylation of the tRNA and protein synthesis in E. coli can be initiated with formyllysine. We also discuss the implications of these and other results on recognition of tRNAs by E. coli lysyl-tRNA synthetase and on competition in cells among aminoacyl-tRNA synthetases.

Microstructure of copolyperoxides of alpha-methylstyrene with styrene and methyl methacrylate

This paper reports a study on the microstructure of two series of copolyperoxides of alpha-methylstyrene, with styrene and with methylmethacrylate. The copolyperoxides were synthesized by the free radical-initiated oxidative copolymerization of the vinyl monomer pairs. The copolyperoxide compositions obtained from the H-1 and C-13 NMR spectra led to the determination of the reactivity ratios. The product of the reactivity ratios indicates that alpha-methylstyrene forms a block copolyperoxide with styrene and a random copolyperoxide with methylmethacrylate. Microstructural parameters like average sequence length, run number, etc. have been determined for the latter copolyperoxide from analysis of its C-13 NMR spectrum. The aromatic quaternary and carbonyl carbons were found to be sensitive to triad sequences. The end groups of the copolyperoxides have been identified by H-1 NMR as well as FTIR spectroscopic techniques. The thermal degradation of the copolyperoxides has been studied by differential scanning calorimetry, which confirms the alternating peroxide units in the copolyperoxide chain.

Modulation of vesicular properties by variation of shapes of bolaform counter ions in hybrid-ion paired surfactants

Four new vesicle-forming bolaphile/amphiphile ion pairs are synthesized; the bolaphile shapes in such hybrid systems strongly control their vesicular properties.

Production of Dirac particles due to riccion coupling

It has been noted that at high energy the Ricci scalar is manifested in two different ways, as a matter field as well as a geometrical field (which is its usual nature even at low energy). Here, using the material aspect of the Ricci scalar, its interaction with Dirac spinors is considered in four-dimensional curved spacetime. We find that a large number of fermion-antifermion pairs can be produced by the exponential expansion of the early universe.

Engineered dimer interface mutants of triosephosphate isomerase: the role of inter-subunit interactions in enzyme function and stability

The role of inter-subunit interactions in maintaining optimal catalytic activity in triosephosphate isomerase (TIM) has been probed, using the Plasmodium falciparum enzyme as a model. Examination of subunit interface contacts in the crystal structures suggests that residue 75 (Thr, conserved) and residue 13 (Cys, variable) make the largest number of inter-subunit contacts. The mutants Cys13Asp (C13D) and Cys13Glu (C13E) have been constructed and display significant reduction in catalytic activity when compared with wild-type (WT) enzyme (similar to 7.4-fold decrease in k(cat) for the C13D and similar to 3.3-fold for the C13E mutants). Analytical gel filtration demonstrates that the C13D mutant dissociates at concentrations < 1.25 mu M, whereas the WT and the C13E enzymes retain the dimeric structure. The order of stability of the mutants in the presence of chemical denaturants, like urea and guanidium chloride, is WT > Cys13Glu > Cys13Asp. Irreversible thermal precipitation temperatures follow the same order as well. Modeling studies establish that the Cys13Asp mutation is likely to cause a significantly greater structural perturbation than Cys13Glu. Analysis of sequence and structural data for TIMs from diverse sources suggests that residues 13 and 82 form a pair of proximal sites, in which a limited number of residue pairs may be accommodated.

Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria

Molecular understanding of disease processes can be accelerated if all interactions between the host and pathogen are known. The unavailability of experimental methods for large-scale detection of interactions across host and pathogen organisms hinders this process. Here we apply a simple method to predict protein-protein interactions across a host and pathogen organisms. We use homology detection approaches against the protein-protein interaction databases. DIP and iPfam in order to predict interacting proteins in a host-pathogen pair. In the present work, we first applied this approach to the test cases involving the pairs phage T4 - Escherichia coli and phage lambda - E. coli and show that previously known interactions could be recognized using our approach. We further apply this approach to predict interactions between human and three pathogens E. coli, Salmonella enterica typhimurium and Yersinia pestis. We identified several novel interactions involving proteins of host or pathogen that could be thought of as highly relevant to the disease process. Serendipitously, many interactions involve hypothetical proteins of yet unknown function. Hypothetical proteins are predicted from computational analysis of genome sequences with no laboratory analysis on their functions yet available. The predicted interactions involving such proteins could provide hints to their functions. (C) 2011 Elsevier B.V. All rights reserved.

Structure of Ethyl 5-Methoxy-3-phenyl-2-indolecarboxylate

C18H17NO3, M r = 295"34, monoclinic, C2/c, a = 11.689 (2), b = 22.934 (4), c = 11.592 (2) A, fl=100.16(3) ° , V =3058.8(8) A 3, Z=8, D,n= 1.30 (5), Dx = 1.28 Mg m -3, A(Mo Ka) = 0.7107 A, tz(Mo Ka) = 0.094 mm- 1, F(000) = 1248, T = 300 K, final R = 0.046 for 1849 observed reflections [I > 30"(/)]. The indole nucleus is slightly bent along the C(8)---C(9) bond. The phenyl ring connected to the indole moiety is rotated about the C(3)---C(10) bond by 45.8 (3) °. The carboxyl group makes a dihedral angle of 8.1 (4) ° with the mean plane of the indole moiety. Centrosymmetrically related pairs of molecules are linked through hydrogen bonds across the centre of symmetry and form dimers.

Interfacial Regions Governing Internal Cavities of Dendrimers. Studies of Poly(alkyl aryl ether) Dendrimers Constituted with Linkers of Varying Alkyl Chain Length

This report deals with a study of the properties of internal cavities of dendritic macromolecules that are capable Of encapsulating and mediating photoreactions of guest molecules. The internal cavity structures of dendrimers are determined by the interfacial regions between the aqueous exterior and hydrocarbon like interior constituted by the linkers that connect symmetrically sited branch points constituting the dendrimer and head groups that cap the dendrimers. Phloroglucinol-based poly(alkyl aryl ether) dendrimers constituted with a homologous series of alkyl linkers were undertaken for the current study. Twelve dendrimers within first, second, and third generations, having ethyl, n-propyl, n-butyl, and n-pentyl groups as the linkers and hydroxyl groups at peripheries in each generation, were synthesized. Encapsulation of pyrene and coumarins by aqueous basic solutions of dendrimers were monitored-by UV-vis and fluorescence spectroscopies, which showed that a lower generation dendrimer with an optimal alkyl linker presented better encapsulation abilities than a higher generation dendrimer. Norrish type I photoreaction of dibenzyl ketone was carried out within the above: series of dendrimers to probe their abilities to hold guests and reactive inthermediate radical pairs within themselves. The extent of cage effect from the series of third generation dendrimers was observed to be higher with dendrimers having an n-pentyl group as the linker.

Block coherence: a method for measuring the interdependence between two blocks of neurobiological time series

Multisensor recordings are becoming commonplace. When studying functional connectivity between different brain areas using such recordings, one defines regions of interest, and each region of interest is often characterized by a set (block) of time series. Presently, for two such regions, the interdependence is typically computed by estimating the ordinary coherence for each pair of individual time series and then summing or averaging the results over all such pairs of channels (one from block 1 and other from block 2). The aim of this paper is to generalize the concept of coherence so that it can be computed for two blocks of non-overlapping time series. This quantity, called block coherence, is first shown mathematically to have properties similar to that of ordinary coherence, and then applied to analyze local field potential recordings from a monkey performing a visuomotor task. It is found that an increase in block coherence between the channels from V4 region and the channels from prefrontal region in beta band leads to a decrease in response time.

Mechanism of seizure of aluminium-silicon alloys dry sliding against steel

A steel ball was slid on aluminium-silicon alloys at different temperatures. After the coefficient of friction had been measured, the surface shear stress was deconvoluted using a two-term model of friction. The ratio of surface shear stress to bulk hardness was calculated as a function of temperature, silicon content and alloying additions. These results are qualitatively similar to those recorded for pre-seizure specimens slid against an En24 disc in a pin-on-disc machine. This similarity, when viewed in the context of the phenomenon of bulk shear, provides a model for seizure of these alloys.

1H and 13C NMR spectral studies of conformation of some N-(2-pyridinyl)-3-pyridinecarboxamides

The 1H and 13C NMR spectra of N-(2-pyridinyl)-, N-(4-methyl2-pyridinyl)-, and N-(6-methyl-2-pyridinyl)-3-pyridine-carboxamides (1�3, respectively) and 3-pyridinecarboxamide (4) in different solvents have been analysed using COSY, HETCOR, chemical shift and coupling constant correlations. The conformations of 1�4 have been obtained by utilizing the NMR spectra, NOE experiments and MINDO/3 calculations. In dilute solutions, the 2-pyridyl ring is coplanar with the amide group while the 3-pyridyl ring is apparently not. Compounds 1�3 dimerize through cooperative hydrogen bonding in concentrated CDCl3 solution (approximately 0.1 M) and the structure of the dimer resembles some of the DNA base-pairs. Hydrogen bonding between N---H and the solvent molecules hinders dimerization in (CD3)2CO and CD3CN.

Maintaining dynamic sequences under equality tests in polylogarithmic time

We present a randomized and a deterministic data structure for maintaining a dynamic family of sequences under equality tests of pairs of sequences and creations of new sequences by joining or splitting existing sequences. Both data structures support equality tests in O(1) time. The randomized version supports new sequence creations in O(log(2) n) expected time where n is the length of the sequence created. The deterministic solution supports sequence creations in O(log n (log m log* m + log n)) time for the mth operation.

Phenomenological aspects of phase fluctuation in high Tc superconductors: Cooper pair droplets

We point out how fluctuation of the phase of the superconducting order parameter can play a key role in our understanding of high Te superconductors. A simple universal criterion is given which illustrates why all oxide superconductors in contrast to classical superconductors ought to behave as a lattice of cooper pairs. T-c is to be thought of as the temperature of phase coherence or the temperature above which the lattice of Cooperpair 'melts' into a phase of Cooper-pair droplets that starts forming at T approximate to T-* . This is the pseudo-gap region. Quantum fluctuation of the phase predicts a superconductor to insulator phase transition for all underdoped materials.