Evolving graphs: dynamical models, inverse problems and propagation

Applications such as neuroscience, telecommunication, online social networking, transport and retail trading give rise to connectivity patterns that change over time. In this work, we address the resulting need for network models and computational algorithms that deal with dynamic links. We introduce a new class of evolving range-dependent random graphs that gives a tractable framework for modelling and simulation. We develop a spectral algorithm for calibrating a set of edge ranges from a sequence of network snapshots and give a proof of principle illustration on some neuroscience data. We also show how the model can be used computationally and analytically to investigate the scenario where an evolutionary process, such as an epidemic, takes place on an evolving network. This allows us to study the cumulative effect of two distinct types of dynamics

Supersymmetric Langevin equation to explore free energy landscapes

The recently discovered supersymmetric generalizations of Langevin dynamics and Kramers equation can be utilized for the exploration of free energy landscapes of systems whose large time-scale separation hampers the usefulness of standard molecular dynamics techniques. The first realistic application is here presented. The system chosen is a minimalist model for a short alanine peptide exhibiting a helix-coil transition.Comment: 9 pages, 9 figures, RevTeX 4 v2: conclusive section enlarged, references adde

Hepatitis C virus (HCV) infection may elicit neutralizing antibodies targeting epitopes conserved in all viral genotypes

Anti-hepatitis C virus (HCV) cross-neutralizing human monoclonal antibodies, directed against conserved epitopes on surface E2 glycoprotein, are central tools for understanding virus-host interplay, and for planning strategies for prevention and treatment of this infection. Recently, we developed a research aimed at identifying these antibody specificities. The characteristics of one of these antibodies (Fab e20) were addressed in this study. Firstly, using immunofluorescence and FACS analysis of cells expressing envelope HCV glycoproteins, Fab e20 was able to recognize all HCV genotypes. Secondly, competition assays with a panel of mouse and rat monoclonals, and alanine scanning mutagenesis analyses located the e20 epitope within the CD81 binding site, documenting that three highly conserved HCV/E2 residues (W529, G530 and D535) are critical for e20 binding. Finally, a strong neutralizing activity against HCV pseudoparticles (HCVpp) incorporating envelope glycoproteins of genotypes 1a, 1b, 2a, 2b and 4, and against the cell culture-grown (HCVcc) JFH1 strain, was observed. The data highlight that neutralizing antibodies against HCV epitopes present in all HCV genotypes are elicited during natural infection. Their availability may open new avenues to the understanding of HCV persistence and to the development of strategies for the immune control of this infection

Adaptive Resolution Simulation of Liquid Water

We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct description of all essential thermodynamic and structural properties of liquid water.Comment: 4 pages, 3 figures; changed figure

Distributed Community Detection in Dynamic Graphs

Inspired by the increasing interest in self-organizing social opportunistic networks, we investigate the problem of distributed detection of unknown communities in dynamic random graphs. As a formal framework, we consider the dynamic version of the well-studied \emph{Planted Bisection Model} \sdG(n,p,q) where the node set $[n]$ of the network is partitioned into two unknown communities and, at every time step, each possible edge $(u,v)$ is active with probability $p$ if both nodes belong to the same community, while it is active with probability $q$ (with $q<<p$) otherwise. We also consider a time-Markovian generalization of this model. We propose a distributed protocol based on the popular \emph{Label Propagation Algorithm} and prove that, when the ratio $p/q$ is larger than $n^{b}$ (for an arbitrarily small constant $b>0$), the protocol finds the right "planted" partition in $O(\log n)$ time even when the snapshots of the dynamic graph are sparse and disconnected (i.e. in the case $p=\Theta(1/n)$).Comment: Version I

The Coulomb Interaction between Pion-Wavepackets: The piplus-piminus Puzzle

The time dependent Schr\"odinger equation for $\pi^+$--$\pi^-$ pairs, which are emitted from the interaction zone in relativistic nuclear collisions, is solved using wavepacket states. It is shown that the Coulomb enhancement in the momentum correlation function of such pairs is smaller than obtained in earlier calculations based on Coulomb distorted plane waves. These results suggest that the experimentally observed positive correlation signal cannot be caused by the Coulomb interaction between pions emitted from the interaction zone. But other processes which involve long-lived resonances and the related extended source dimensions could provide a possible explanation for the observed signal.Comment: 12 pages, LaTeX, 1 figur

Receptor-activated Ca2+ influx. Two independently regulated mechanisms of influx stimulation coexist in neurosecretory PC12 cells.

Receptor-activated Ca2+ influx was investigated in PC12 cells clones loaded with fura-2. Cells were stimulated in a Ca(2+)-free medium and studied after reintroduction of the cation or addition of Mn2+ into the medium. A first influx component, independent of receptor activation and sustained by depletion of the intracellular inositol 1,4,5-trisphosphate sensitive Ca2+ store (store-dependent Ca2+ influx, SDCI), was identified by experiments with carbachol followed by atropine and with agents that induce store discharge without polyphosphoinositide hydrolysis: thapsigargin, an inhibitor of Ca(2+)-ATPase activity; ryanodine and caffeine, activators of the ryanodine receptor. A second component of Ca2+ influx, induced by carbachol and rapidly blocked by atropine, relies on receptor-effector coupling via G protein(s) different from that (those) involved in phospholipase C activation. SDCI and receptor-coupled influx are similar in their voltage dependence and insensitivity to forskolin and phorbol esters but they differ with respect to their Mn2+ permeability and their sensitivity to the SC 38249 imidazole blocker. The two components might play different roles. SDCI might act as a safety device to prevent Ca2+ store depletion whereas receptor-dependent influx might control physiological functions such as secretion and growth

Zero-variance principle for Monte Carlo algorithms

We present a general approach to greatly increase at little cost the efficiency of Monte Carlo algorithms. To each observable to be computed we associate a renormalized observable (improved estimator) having the same average but a different variance. By writing down the zero-variance condition a fundamental equation determining the optimal choice for the renormalized observable is derived (zero-variance principle for each observable separately). We show, with several examples including classical and quantum Monte Carlo calculations, that the method can be very powerful.Comment: 9 pages, Latex, to appear in Phys. Rev. Let

Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_\gamma$ and the catalytic proton moving more than 0.5 \AA. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an \AA in the catalytic site.Comment: revtex4, 7 pages, 4 figures, to be submitted to Scienc

Designing biomimetic-inspired middleware for anticipative sensor-actor networks

© Springer International Publishing Switzerland 2015. Developing software environments for Sensor-Actor Networks (Sanets) is a promising research concern in systems engineering. Current concepts in software would adopt Sanets in a singular communications methodology, but the solution in this work is to take biological inspiration for the systems solution, thus the design of the system achieves a biomimetic construct as a result. Sanets are configurable for a variety of network structures and topologies, with the research aim in designing a network that is interactive and anticipatory to external and internal adaptations. Meanwhile, the event-based changes are composed of scenarios, and the interactivity between external and internal actors. From the requirements of the end-user, the system must be responsive and interactive from the user perspective in real-time, while in addition offering the contextual data to make useful interpretation of systemic conditions from an anticipative view Chiu and Chaczko Design of biomimetic middleware for anticipatory sensor-actor network systems. In: Proceedings of the 2nd Asia-Pacific Conference on Computer-Aided System Engineering, APCASE 2014, pp. 22–23. South Kuta, Indonesia, 10–12 February 2014. ISBN 978-0- 9924518-0-6 [2]