Chain motifs: The tails and handles of complex networks

A great part of the interest in complex networks has been motivated by the presence of structured, frequently nonuniform, connectivity. Because diverse connectivity patterns tend to result in distinct network dynamics, and also because they provide the means to identify and classify several types of complex network, it becomes important to obtain meaningful measurements of the local network topology. In addition to traditional features such as the node degree, clustering coefficient, and shortest path, motifs have been introduced in the literature in order to provide complementary descriptions of the network connectivity. The current work proposes a different type of motif, namely, chains of nodes, that is, sequences of connected nodes with degree 2. These chains have been subdivided into cords, tails, rings, and handles, depending on the type of their extremities (e.g., open or connected). A theoretical analysis of the density of such motifs in random and scale-free networks is described, and an algorithm for identifying these motifs in general networks is presented. The potential of considering chains for network characterization has been illustrated with respect to five categories of real-world networks including 16 cases. Several interesting findings were obtained, including the fact that several chains were observed in real-world networks, especially the world wide web, books, and the power grid. The possibility of chains resulting from incompletely sampled networks is also investigated.

Charm and longitudinal structure functions within the Kharzeev-Levin-Nardi model

We use the Kharzeev-Levin-Nardi (KLN) model of the low x gluon distributions to fit recent HERA data on F(L) and F(2)(c)(F(2)(b)). Having checked that this model gives a good description of the data, we use it to predict F(L) and F(2)(c) to be measured in a future electron-ion collider. The results are similar to those obtained with the de Florian-Sassot and Eskola-Paukkunen-Salgado nuclear gluon distributions. The conclusion of this exercise is that the KLN model, simple as it is, may still be used as an auxiliary tool to make estimates for both heavy-ion and electron-ion collisions.

Electron collisions with the CH(2)O-H(2)O complex

We report cross sections for elastic collisions of low-energy electrons with the CH(2)O-H(2)O complex. We employed the Schwinger multichannel method with pseudopotentials in the static-exchange and in the static-exchange-polarization approximations for energies from 0.1 to 20 eV. We considered four different hydrogen-bonded structures for the complex that were generated by classical Monte Carlo simulations. Our aim is to investigate the effect of the water molecule on the pi* shape resonance of formaldehyde. Previous studies reported a pi* shape resonance for CH(2)O at around 1 eV. The resonance positions of the complexes appear at lower energies in all cases due to the mutual polarization between the two molecules. This indicates that the presence of water may favor dissociation by electron impact and may lead to an important effect on strand breaking in wet DNA by electron impact.

Experimental observation of a complex periodic window

The existence of a special periodic window in the two-dimensional parameter space of an experimental Chua's circuit is reported. One of the main reasons that makes such a window special is that the observation of one implies that other similar periodic windows must exist for other parameter values. However, such a window has never been experimentally observed, since its size in parameter space decreases exponentially with the period of the periodic attractor. This property imposes clear limitations for its experimental detection.

Use of correlated potential harmonic basis functions for the description of the (4)He trimer and small clusters

A correlated many-body basis function is used to describe the (4)He trimer and small helium clusters ((4)HeN) with N = 4-9. A realistic helium dimer potential is adopted. The ground state results of the (4)He dimer and trimer are in close agreement with earlier findings. But no evidence is found for the existence of Efimov state in the trimer for the actual (4)He-(4)He interaction. However, decreasing the potential strength we calculate several excited states of the trimer which exhibit Efimov character. We also solve for excited state energies of these clusters which are in good agreement with Monte Carlo hyperspherical description. (C) 2011 American Institute of Physics. [doi:10.1063/1.3583365]

Jensen inequalities for tunneling probabilities in complex systems

The Jensen theorem is used to derive inequalities for semiclassical tunneling probabilities for systems involving several degrees of freedom. These Jensen inequalities are used to discuss several aspects of sub-barrier heavy-ion fusion reactions. The inequality hinges on general convexity properties of the tunneling coefficient calculated with the classical action in the classically forbidden region.

Balance functions from Au+Au, d+Au, and p+p collisions at root s(NN)=200 GeV

Balance functions have been measured for charged-particle pairs, identified charged-pion pairs, and identified charged-kaon pairs in Au + Au, d + Au, and p + p collisions at root s(NN) = 200 GeV at the Relativistic Heavy Ion Collider using the STAR detector. These balance functions are presented in terms of relative pseudorapidity, Delta eta, relative rapidity, Delta y, relative azimuthal angle, Delta phi, and invariant relative momentum, q(inv). For charged-particle pairs, the width of the balance function in terms of Delta eta scales smoothly with the number of participating nucleons, while HIJING and UrQMD model calculations show no dependence on centrality or system size. For charged-particle and charged-pion pairs, the balance functions widths in terms of Delta eta and Delta y are narrower in central Au + Au collisions than in peripheral collisions. The width for central collisions is consistent with thermal blast-wave models where the balancing charges are highly correlated in coordinate space at breakup. This strong correlation might be explained by either delayed hadronization or limited diffusion during the reaction. Furthermore, the narrowing trend is consistent with the lower kinetic temperatures inherent to more central collisions. In contrast, the width of the balance function for charged-kaon pairs in terms of Delta y shows little centrality dependence, which may signal a different production mechanism for kaons. The widths of the balance functions for charged pions and kaons in terms of q(inv) narrow in central collisions compared to peripheral collisions, which may be driven by the change in the kinetic temperature.

The clusters Abell 222 and Abell 223: a multi-wavelength view

Context. The Abell 222 and 223 clusters are located at an average redshift z similar to 0.21 and are separated by 0.26 deg. Signatures of mergers have been previously found in these clusters, both in X-rays and at optical wavelengths, thus motivating our study. In X-rays, they are relatively bright, and Abell 223 shows a double structure. A filament has also been detected between the clusters both at optical and X-ray wavelengths. Aims. We analyse the optical properties of these two clusters based on deep imaging in two bands, derive their galaxy luminosity functions (GLFs) and correlate these properties with X-ray characteristics derived from XMM-Newton data. Methods. The optical part of our study is based on archive images obtained with the CFHT Megaprime/Megacam camera, covering a total region of about 1 deg(2), or 12.3 x 12.3 Mpc(2) at a redshift of 0.21. The X-ray analysis is based on archive XMM-Newton images. Results. The GLFs of Abell 222 in the g' and r' bands are well fit by a Schechter function; the GLF is steeper in r' than in g'. For Abell 223, the GLFs in both bands require a second component at bright magnitudes, added to a Schechter function; they are similar in both bands. The Serna & Gerbal method allows to separate well the two clusters. No obvious filamentary structures are detected at very large scales around the clusters, but a third cluster at the same redshift, Abell 209, is located at a projected distance of 19.2 Mpc. X-ray temperature and metallicity maps reveal that the temperature and metallicity of the X-ray gas are quite homogeneous in Abell 222, while they are very perturbed in Abell 223. Conclusions. The Abell 222/Abell 223 system is complex. The two clusters that form this structure present very different dynamical states. Abell 222 is a smaller, less massive and almost isothermal cluster. On the other hand, Abell 223 is more massive and has most probably been crossed by a subcluster on its way to the northeast. As a consequence, the temperature distribution is very inhomogeneous. Signs of recent interactions are also detected in the optical data where this cluster shows a ""perturbed"" GLF. In summary, the multiwavelength analyses of Abell 222 and Abell 223 are used to investigate the connection between the ICM and the cluster galaxy properties in an interacting system.

Border detection in complex networks

One important issue implied by the finite nature of real-world networks regards the identification of their more external (border) and internal nodes. The present work proposes a formal and objective definition of these properties, founded on the recently introduced concept of node diversity. It is shown that this feature does not exhibit any relevant correlation with several well-established complex networks measurements. A methodology for the identification of the borders of complex networks is described and illustrated with respect to theoretical (geographical and knitted networks) as well as real-world networks (urban and word association networks), yielding interesting results and insights in both cases.

Iridium(III)-surfactant complex immobilized in mesoporous silica via templated synthesis: a new route to optical materials

In this work we report the preparation of a new blue-emitting material based on the templated synthesis of mesoporous silica (MCM-41) using micellar solutions of the newly synthesized monocationic metallosurfactant complex bis[1-benzyl-4-(2,4-difluorophenyl)-1H-1,2,3-triazole](4,4'-diheptadecyl-2,2'- bipyridine)-iridium(III) chloride in hexadecyl-trimethyl-ammonium bromide (CTAB). Under ambient conditions, significant increases in excited state lifetime and quantum yield values (up to 45%), were obtained for the solid materials in comparison to the corresponding micellar solutions. Solid state (1)H and (19)F NMR spectroscopies were successfully employed for quantifying the luminophore content in terms of Ir-surfactant to CTAB and Ir-surfactant to silica ratios.

Purine nucleoside phosphorylase from Schistosoma mansoni in complex with ribose-1-phosphate

Schistosomes are blood flukes which cause schistosomiasis, a disease affecting approximately 200 million people worldwide. Along with several other important human parasites including trypanosomes and Plasmodium, schistosomes lack the de novo pathway for purine synthesis and depend exclusively on the salvage pathway for their purine requirements, making the latter an attractive target for drug development. Part of the pathway involves the conversion of inosine (or guanosine) into hypoxanthine (or guanine) together with ribose-1-phosphate (R1P) or vice versa. This inter-conversion is undertaken by the enzyme purine nucleoside phosphorylase (PNP) which has been used as the basis for the development of novel anti-malarials, conceptually validating this approach. It has been suggested that, during the reverse reaction, R1P binding to the enzyme would occur only as a consequence of conformational changes induced by hypoxanthine, thus making a binary PNP-R1P complex unlikely. Contradictory to this statement, a crystal structure of just such a binary complex involving the Schistosoma mansoni enzyme has been successfully obtained. The ligand shows an intricate hydrogen-bonding network in the phosphate and ribose binding sites and adds a further chapter to our knowledge which could be of value in the future development of selective inhibitors.

Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni

Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.

Spin-polarized current and shot noise in the presence of spin flip in a quantum dot via nonequilibrium Green's functions

Using nonequilibrium Green's functions we calculate the spin-polarized current and shot noise in a ferromagnet-quantum-dot-ferromagnet system. Both parallel (P) and antiparallel (AP) magnetic configurations are considered. Coulomb interaction and coherent spin flip (similar to a transverse magnetic field) are taken into account within the dot. We find that the interplay between Coulomb interaction and spin accumulation in the dot can result in a bias-dependent current polarization p. In particular, p can be suppressed in the P alignment and enhanced in the AP case depending on the bias voltage. The coherent spin flip can also result in a switch of the current polarization from the emitter to the collector lead. Interestingly, for a particular set of parameters it is possible to have a polarized current in the collector and an unpolarized current in the emitter lead. We also found a suppression of the Fano factor to values well below 0.5.

Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.