Modularity revisited: A novel dynamics-based concept for decomposing complex networks

Finding modules (or clusters) in large, complex networks is a challenging task, in particular if one is not interested in a full decomposition of the whole network into modules. We consider modular networks that also contain nodes that do not belong to one of modules but to several or to none at all. A new method for analyzing such networks is presented. It is based on spectral analysis of random walks on modular networks. In contrast to other spectral clustering approaches, we use different transition rules of the random walk. This leads to much more prominent gaps in the spectrum of the adapted random walk and allows for easy identification of the network's modular structure, and also identifying the nodes belonging to these modules. We also give a characterization of that set of nodes that do not belong to any module, which we call transition region. Finally, by analyzing the transition region, we describe an algorithm that identifies so called hub-nodes inside the transition region that are important connections between modules or between a module and the rest of the network. The resulting algorithms scale linearly with network size (if the network connectivity is sparse) and thus can also be applied to very large networks

Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs

Background: Proteases play an essential part in a variety of biological processes. Besides their importance under healthy conditions they are also known to have a crucial role in complex diseases like cancer. In recent years, it has been shown that not only the fragments produced by proteases but also their dynamics, especially ex vivo, can serve as biomarkers. But so far, only a few approaches were taken to explicitly model the dynamics of proteolysis in the context of mass spectrometry. Results: We introduce a new concept to model proteolytic processes, the degradation graph. The degradation graph is an extension of the cleavage graph, a data structure to reconstruct and visualize the proteolytic process. In contrast to previous approaches we extended the model to incorporate endoproteolytic processes and present a method to construct a degradation graph from mass spectrometry time series data. Based on a degradation graph and the intensities extracted from the mass spectra it is possible to estimate reaction rates of the underlying processes. We further suggest a score to rate different degradation graphs in their ability to explain the observed data. This score is used in an iterative heuristic to improve the structure of the initially constructed degradation graph. Conclusion: We show that the proposed method is able to recover all degraded and generated peptides, the underlying reactions, and the reaction rates of proteolytic processes based on mass spectrometry time series data. We use simulated and real data to demonstrate that a given process can be reconstructed even in the presence of extensive noise, isobaric signals and false identifications. While the model is currently only validated on peptide data it is also applicable to proteins, as long as the necessary time series data can be produced

Covalency effects on the magnetism of EuRh2P2

In experiments, the ternary Eu pnictide EuRh2P2 shows an unusual coexistence of a non-integral Eu valence of about 2.2 and a rather high Neel temperature of 50 K. In this paper, we present a model which explains the non-integral Eu valence via covalent bonding of the Eu 4f-orbitals to P2 molecular orbitals. In contrast to intermediate valence models where the hybridization with delocalized conduction band electrons is known to suppress magnetic ordering temperatures to at most a few Kelvin, covalent hybridization to the localized P2 orbitals avoids this suppression. Using perturbation theory we calculate the valence, the high temperature susceptibility, the Eu single-ion anisotropy and the superexchange couplings of nearest and next-nearest neighbouring Eu ions. The model predicts a tetragonal anisotropy of the Curie constants. We suggest an experimental investigation of this anisotropy using single crystals. From experimental values of the valence and the two Curie constants, the three free parameters of our model can be determined.Comment: 9 pages, 5 figures, submitted to J. Phys.: Condens. Matte

Compact intense extreme-ultraviolet source

High-intensity laser pulses covering the ultraviolet to terahertz spectral regions are nowadays routinely generated in a large number of laboratories. In contrast, intense extreme-ultraviolet (XUV) pulses have only been demonstrated using a small number of sources including free-electron laser facilities and long high-harmonic generation (HHG) beamlines. Here, we demonstrate a concept for a compact intense XUV source based on HHG that is focused to an intensity of 2×1014W/cm2, with a potential increase up to 1017W/cm2 in the future. Our approach uses tight focusing of the near-infrared (NIR) driving laser and minimizes the XUV virtual source size by generating harmonics several Rayleigh lengths away from the NIR focus. Accordingly, the XUV pulses can be refocused to a small beam waist radius of 600 nm, enabling the absorption of up to four XUV photons by a single Ar atom in a setup that fits on a modest (2 m) laser table. Our concept represents a straightforward approach for the generation of intense XUV pulses in many laboratories, providing exciting opportunities for XUV strong-field and nonlinear optics experiments, for XUV-pump XUV-probe spectroscopy and for the coherent diffractive imaging of nanoscale structures

Regelung eines elastischen Fahrwegs unter Verwendung eines variablen Beobachters

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Low cost microfluidic device for partial cell separation: micromilling approach

Several studies have already demonstrated that it is possible to perform blood flow studies in microfluidic systems fabricated by using low-cost techniques. However, most of these techniques do not produce microchannels smaller than 100 microns and as a result they have several limitations related to blood cell separation. Recently, manufacturers have been able to produce milling tools smaller than 100 microns, which consequently have promoted the ability of micromilling machines to fabricate microfluidic devices able to perform separation of red blood cells (RBCs) from plasma. In this work, we show the ability of a micromilling machine to manufacture microchannels with dimensions down to 30 microns. Additionally, we show for the first time the ability of the proposed microfluidic device to enhance the cell-free layer close to the walls, leading to perform partial separation of RBCs from plasma.The authors acknowledge the financial support provided by PTDC/SAU-ENB/116929/2010 and EXPL/EMSSIS/2215/2013 from FCT (Science and Technology Foundation), COMPETE, QREN and European Union (FEDER). RR and DP acknowledge, respectively, the PhD scholarships SFRH/BD/97658/2013 and SFRH/BD/89077/2012 attributed by FCT.info:eu-repo/semantics/publishedVersio

A schematic model for QCD at finite temperature

The simplest version of a class of toy models for QCD is presented. It is a Lipkin-type model, for the quark-antiquark sector, and, for the gluon sector, gluon pairs with spin zero are treated as elementary bosons. The model restricts to mesons with spin zero and to few baryonic states. The corresponding energy spectrum is discussed. We show that ground state correlations are essential to describe physical properties of the spectrum at low energies. Phase transitions are described in an effective manner, by using coherent states. The appearance of a Goldstone boson for large values of the interaction strength is discussed, as related to a collective state. The formalism is extended to consider finite temperatures. The partition function is calculated, in an approximate way, showing the convenience of the use of coherent states. The energy density, heat capacity and transitions from the hadronic phase to the quark-gluon plasma are calculated.Comment: 33 pages, 11 figure

Single- and double-beta decay Fermi-transitions in an exactly solvable model

An exactly solvable model suitable for the description of single and double-beta decay processes of the Fermi-type is introduced. The model is equivalent to the exact shell-model treatment of protons and neutrons in a single j-shell. Exact eigenvalues and eigenvectors are compared to those corresponding to the hamiltonian in the quasiparticle basis (qp) and with the results of both the standard quasiparticle random phase approximation (QRPA) and the renormalized one (RQRPA). The role of the scattering term of the quasiparticle hamiltonian is analyzed. The presence of an exact eigenstate with zero energy is shown to be related to the collapse of the QRPA. The RQRPA and the qp solutions do not include this zero-energy eigenvalue in their spectra, probably due to spurious correlations. The meaning of this result in terms of symmetries is presented.Comment: 29 pages, 9 figures included in a Postsript file. Submitted to Physcal Review

Fermion-Boson Interactions and Quantum Algebras

Quantum Algebras (q-algebras) are used to describe interactions between fermions and bosons. Particularly, the concept of a su_q(2) dynamical symmetry is invoked in order to reproduce the ground state properties of systems of fermions and bosons interacting via schematic forces. The structure of the proposed su_q(2) Hamiltonians, and the meaning of the corresponding deformation parameters, are discussed.Comment: 20 pages, 10 figures. Physical Review C (in press