The structure and dynamics of multilayer networks

In the past years, network theory has successfully characterized the interaction among the constituents of a variety of complex systems, ranging from biological to technological, and social systems. However, up until recently, attention was almost exclusively given to networks in which all components were treated on equivalent footing, while neglecting all the extra information about the temporal- or context-related properties of the interactions under study. Only in the last years, taking advantage of the enhanced resolution in real data sets, network scientists have directed their interest to the multiplex character of real-world systems, and explicitly considered the time-varying and multilayer nature of networks. We offer here a comprehensive review on both structural and dynamical organization of graphs made of diverse relationships (layers) between its constituents, and cover several relevant issues, from a full redefinition of the basic structural measures, to understanding how the multilayer nature of the network affects processes and dynamics.     

Laser irradiation of atomic chains: A study based on the Density Functional Theory

This study is motivated by recent applications of short laser pulses to the manipulation of structures at the atomic scale and is based on the Density Functional Theory. The structures considered are linear monatomic chains formed by covalent and metallic atoms (i.e. Si, As and Al, Ag). The study is divided into two parts. The first part analyzes the structural and electronic properties of the chain ground states and the second part illustrates their evolution under laser irradiation. These calculations show the modification of the chain structure and illustrate the relationship between those changes, on one side, and the chain length and composition and the parameters of the laser light, on the other side.     

Continuous thermal collapse of the intrinsically disordered protein tau is driven by its entropic flexible domain

The tau protein belongs to the category of Intrinsically Disordered Proteins (IDP), which in their native state lack a folded structure and fluctuate between many conformations. In its physiological state, tau helps nucleating and stabilizing the microtubules' (MTs) surfaces in the axons of the neurons. Tau is mainly composed by two domains: (i) the binding domain that tightly bounds the MT surfaces and (ii) the projection domain that exerts a long-range entropic repulsive force and thus provides the proper spacing between adjacent MTs. Tau is also involved in the genesis and in the development of the Alzheimer disease when it detaches from MT surfaces and aggregates in paired helical filaments. Unfortunately, the molecular mechanisms behind these phenomena are still unclear. Temperature variation, rarely considered in biological studies, is here used to provide structural information on tau correlated to its role as an entropic spacer between adjacent MTs surfaces. In this paper, by means of small-angle X-ray scattering and molecular dynamics simulation, we demonstrate that tau undergoes a counterintuitive collapse phenomenon with increasing temperature. A detailed analysis of our results, performed by the Ensemble Optimization Method, shows that the thermal collapse is coupled to the occurrence of a transient long-range contact between a region encompassing the end of the proline-rich domain P2 and the first part of the repeats domain, and the region of the N-terminal domain entailing residues 80-150. Interestingly these two regions involved in the tau temperature collapse belong to the flexible projection domain that acts as an entropic bristle and regulates the MTs' architecture. Our results show that temperature is an important parameter that influences the dynamics of the tau projection domain, and hence its entropic behavior.     

Azimuthal asymmetries in exclusive four-particle “Drell-Yan” events

I study hard collisions between unpolarized protons and antiprotons where a lepton-antilepton pair is detected in coincidence with a final proton-antiproton pair, and no more particles are produced, in the regime 10 GeV2 ≪ s ≪ 1000 GeV2 , M > 4 GeV, q _T < 3 GeV/c. The present work is centered on azimuthal asymmetries. Because of momentum conservation, a Boer-Mulders term in the momentum distribution of a quark implies a balancing effect in the momentum distribution of some spectators. This produces azimuthal asymmetries of the final hadrons. To analyze this, I have organized a parton-level Monte Carlo generator where a standard cos(2f \phi) -asymmetry of the dilepton distribution is produced, thanks to a soft rescattering process between an active quark coming from a hadron and a spectator antidiquark coming from the other hadron. This produces cos(2f \phi) -asymmetries of the final hadron pair. Hadron and lepton asymmetries have the same size.     

Thermodynamic and structural characterization of zwitterionic micelles of the membrane protein solubilizing amidosulfobetaine surfactants ASB-14 and ASB-16

Surface tension and isothermal titration calorimetry (ITC) were used to determine the critical micelle concentration (cmc) of the zwitterionic amidosulfobetaine surfactants ASB-14 and ASB-16 (linear-alkylamidopropyldimethylammoniopropanosulfonates) at 25 °C. The cmc and the heat of micellization were determined from 15 to 75 °C by ITC for both surfactants. The increase in temperature caused significant changes in the enthalpy and in the entropy of micellization, with small changes in the standard Gibbs energy (ΔG(mic)), which is consistent to an enthalpy?entropy compensation with a compensatory temperature of 311 K (ASB-14) and 314 K (ASB-16). In the studied temperature range, the heat capacity of micellization (ΔC(p)(mic)) was essentially constant. The experimental ΔC(p)(mic) was lower than that expected if only hydrophobic interactions were considered, suggesting that polar interactions at the head groups are of significant importance in the thermodynamics of micelle formation by these surfactants. Indeed, a NMR NOESY spectrum showed NOEs that are improbable to occur within the same monomer, resulting from interactions at the polar head groups involving more than one monomer. The ITC and NMR results indicate a tilt in the polar headgroup favoring the polar interactions. We have also observed COSY correlations typical of dipolar interactions that could be recovered with the partial alignment of the molecule in solution, which results in an anisotropic tumbling. The anisotropy suggested an ellipsoidal shape of the micelles, which results in a positive magnetic susceptibility, and ultimately in orientation induced by the magnetic field. Such an ellipsoidal shape was confirmed from results obtained by SAXS experiments that revealed aggregation numbers of 108 and 168 for ASB-14 and ASB-16 micelles, respectively. This study characterizes an interesting micelle system that can be used in the study of membrane proteins by solution NMR spectroscopy.     

Photo-Induced Phase Transition to a Striped Polaron Crystal in Cuprates

Here we report the evidence of a disorder-to-order photo-induced phase transition (PIPT) under X-ray (h x = 12.4 keV) illumination in oxygen doped La 2 CuO 4 + i . The commensurate striped polaron crystalline phase is induced by the irradiation of X-rays in a cuprate perovskite at hole doping i ¨ 1/8 and high Cu-O micro-strain, k >7%. The nucleation of long range crystalline phases of holes on the oxygen 2 p x,y orbitals in the CuO 2 plane associated with pseudo Jahn Teller local lattice distortions (LLD) is favored by mobile counter-ions (interstitial oxygen ions in the La 2 O 2 layer) in the temperature range 200-350 K. The PIPT appears beyond a threshold dose of 10 17 photons/cm 2 at 220 K and a power law of the polaron crystal growth is observed as a function of the X-ray illumination dose.     

Design-Oriented Modelling of Different Quenching Solutions in Induction Plasma Synthesis of Copper Nanoparticles

The aim of this paper is to compare the effects of different mechanisms underlying the synthesis of copper nanoparticles using an atmospheric pressure radio-frequency induction thermal plasma. A design oriented modelling approach was used to parametrically investigate trends and impact of different parameters on the synthesis process through a thermo-fluid dynamic model coupled with electromagnetic field equations for describing the plasma behaviour and a moment method for describing nanoparticles nucleation, growth and transport. The effect of radiative losses from Cu vapour on the precursor evaporation efficiency is highlighted, with occurrence of loading effect even with low precursor feed rate due to the decrease in plasma temperature. A method to model nanoparticle deposition on a porous wall is proposed, in which a sticking coefficient is employed to model particle sticking on the porous wall used to carry a quench gas flow into the chamber. Two different reaction chamber designs combined with different quench gas injection strategies (injection through a porous wall for “active” quenching; injection of a shroud gas for “passive” quenching) are analysed in terms of process yield and size distribution of the synthetized nanoparticles. Conclusion can be drawn on the characteristics of each quenching strategy in terms of throughput and mean diameter of the synthesized nanoparticles.     

Accuracy of the multipole expansion applied to a sphere in a creeping flow parallel to a wall

An example system is studied to discuss precision of the multipoleexpansion, applied to determine forces exerted on particlesby a viscous low-Reynolds-number fluid flow. A single spherein an ambient flow (pure shear, quadratic, and modulated shear)parallel to a close plane wall is considered. Forces and torquesexerted by the ambient flow on a motionless sphere are evaluated.Their precision is determined and related to a multipole orderof the truncation. Similar analysis is performed for a movingsphere with no ambient flow and for a freely moving sphere.Relative motion of the sphere with respect to the wall givesrise to strong lubrication interactions. It is analysed howthese interactions affect accuracy of the pure multipole expansion,and what are the smallest distances where it becomes insufficient.An alternative precise method is applied, in which lubricationexpressions are subtracted from the hydrodynamic forces andtorques, and the residue is evaluated as a fast-convergent seriesof inverse powers of the distance between the sphere centreand the wall. The accuracy of this procedure is carefully analysed.