Geometry of compact tubes and protein structures

Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures the well-known characteristics of polymers and their phases but also provides a natural explanation for many of the key features of protein behavior. There are two natural length scales associated with a tube subject to compaction -- the thickness of the tube and the range of the attractive interactions. For short tubes, when these length scales become comparable, one obtains marginally compact structures, which are relatively few in number compared to those in the generic compact phase of polymers. The motifs associated with the structures in this new phase include helices, hairpins and sheets. We suggest that Nature has selected this phase for the structures of proteins because of its many advantages including the few candidate strucures, the ability to squeeze the water out from the hydrophobic core and the flexibility and versatility associated with being marginally compact. Our results provide a framework for understanding the common features of all proteins.Comment: 15 pages, 3 eps figure

Nuclear loads and nuclear shielding performance of EU DEMO divertor: A comparative neutronics evaluation of two interim design options

In a demonstrational fusion power plant (DEMO), divertor is supposed to protect vacuum vessel and superconducting magnets against neutron flux in the bottom region of the vessel. The vessel is subject to a strict design limit in irradiation damage dose and the magnets in nuclear heating power, respectively. Thus, the DEMO divertor must have the capability to protect sufficiently the vessel and the magnets against neutron flux being substantially stronger than in ITER.In this paper, a first systematic neutronics study for the European DEMO divertor is reported. Results of the extensive assessment of key nuclear loading features (nuclear heating, irradiation damage & helium production) are presented for two optional concepts, namely, dome and shielding liner including minor geometrical variants. The shielding performance of the two competing design options is discussed together with the case of a bare cassette (no shielding), particularly in terms of damage dose compared with the design limits specified for the European DEMO.It was found that both the dome and shielding liner were able to significantly reduce the nuclear loads in the cassette body and the vessel. The maximum damage dose at the end of the lifetime remained subcritical for the cassette body for both cases whereas it exceeded the limit for the vessel under the dome, but only locally on the surface underneath the pumping duct. But, the damage could be reduced below the limit for the vessel by increasing the size of the dome or by deploying the shielding liner. The most critical feature was the excessive damage occurring in the own body of the shielding components where the maximum damage dose in the steel heat sink of the dome and the shielding liner far exceeded the design limit at the end of the lifetime

The Digital Evolution of Occupy Wall Street

We examine the temporal evolution of digital communication activity relating to the American anti-capitalist movement Occupy Wall Street. Using a high-volume sample from the microblogging site Twitter, we investigate changes in Occupy participant engagement, interests, and social connectivity over a fifteen month period starting three months prior to the movement's first protest action. The results of this analysis indicate that, on Twitter, the Occupy movement tended to elicit participation from a set of highly interconnected users with pre-existing interests in domestic politics and foreign social movements. These users, while highly vocal in the months immediately following the birth of the movement, appear to have lost interest in Occupy related communication over the remainder of the study period.Comment: Open access available at: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.006467

Observation of Fermi-Pasta-Ulam-Tsingou Recurrence and Its Exact Dynamics

One of the most controversial phenomena in nonlinear dynamics is the reappearance of initial conditions. Celebrated as the Fermi-Pasta-Ulam-Tsingou problem, the attempt to understand how these recurrences form during the complex evolution that leads to equilibrium has deeply influenced the entire development of nonlinear science. The enigma is rendered even more intriguing by the fact that integrable models predict recurrence as exact solutions, but the difficulties involved in upholding integrability for a sufficiently long dynamic has not allowed a quantitative experimental validation. In natural processes, coupling with the environment rapidly leads to thermalization, and finding nonlinear multimodal systems presenting multiple returns is a long-standing open challenge. Here, we report the observation of more than three Fermi-Pasta-Ulam-Tsingou recurrences for nonlinear optical spatial waves and demonstrate the control of the recurrent behavior through the phase and amplitude of the initial field. The recurrence period and phase shift are found to be in remarkable agreement with the exact recurrent solution of the nonlinear Schrödinger equation, while the recurrent behavior disappears as integrability is lost. These results identify the origin of the recurrence in the integrability of the underlying dynamics and allow us to achieve one of the basic aspirations of nonlinear dynamics: the reconstruction, after several return cycles, of the exact initial condition of the system, ultimately proving that the complex evolution can be accurately predicted in experimental conditions

Guest editorial special section on sensor applications

[No abstract available

The quantum nature of the OH stretching mode in ice and water probed by neutron scattering experiments

The OH stretching vibrational spectrum of water was measured in a wide range of temperatures across the triple point, 269 K <T < 296 K, using Inelastic Neutron Scattering (INS). The hydrogen projected density of states and the proton mean kinetic energy, ⟨E K ⟩ OH , were determined for the first time within the framework of a harmonic description of the proton dynamics. We found that in the liquid the value of ⟨E K ⟩ OH is nearly constant as a function of T, indicating that quantum effects on the OH stretching frequency are weakly dependent on temperature. In the case of ice, ab initio electronic structure calculations, using non-local van der Waals functionals, provided ⟨E K ⟩ OH values in agreement with INS experiments. We also found that the ratio of the stretching (⟨E K ⟩ OH ) to the total (⟨E K ⟩ exp ) kinetic energy, obtained from the present measurements, increases in going from ice, where hydrogen bonding is the strongest, to the liquid at ambient conditions and then to the vapour phase, where hydrogen bonding is the weakest. The same ratio was also derived from the combination of previous deep inelastic neutron scattering data, which does not rely upon the harmonic approximation, and the present measurements. We found that the ratio of stretching to the total kinetic energy shows a minimum in the metastable liquid phase. This finding suggests that the strength of intermolecular interactions increases in the supercooled phase, with respect to that in ice, contrary to the accepted view that supercooled water exhibits weaker hydrogen bonding than ice

The Chemical Origin of SEY at Technical Surfaces

The secondary emission yield (SEY) properties of colaminated Cu samples for LHC beam screens are correlated to the surface chemical composition determined by X-ray photoelectron spectroscopy. The surface of the "as received" samples is characterized by the presence of significant quantities of contaminating adsorbates and by the maximum of the SEY curve (dmax) being as high as 2.2. After extended electron scrubbing at kinetic energy of 10 and 500 eV, the dmax value drops to the ultimate values of 1.35 and 1.1, respectively. In both cases the surface oxidized phases are significantly reduced, whereas only in the sample scrubbed at 500 eV the formation of a graphitic-like C layer is observed. We find that the electron scrubbing of technical Cu surfaces can be described as occurring in two steps, where the first step consists in the electron induced desorption of weakly bound contaminants that occurs indifferently at 10 and at 500 eV and corresponds to a partial decrease of dmax, and the second step, activated by more energetic electrons and becoming evident at high doses, which increases the number of graphitic-like C-C bonds via the dissociation of adsorbates already contaminating the "as received" surface or accumulating on this surface during irradiation. Our results demonstrate how the kinetic energy of impinging electrons is a crucial parameter when conditioning technical surfaces of Cu and other metals by means of electron induced chemical processing.Comment: 6 pages, contribution to the Joint INFN-CERN-EuCARD-AccNet Workshop on Electron-Cloud Effects: ECLOUD'12; 5-9 Jun 2012, La Biodola, Isola d'Elba, Italy; CERN Yellow Report CERN-2013-002, pp.99-10

Short period attractors and non-ergodic behavior in the deterministic fixed energy sandpile model

We study the asymptotic behaviour of the Bak, Tang, Wiesenfeld sandpile automata as a closed system with fixed energy. We explore the full range of energies characterizing the active phase. The model exhibits strong non-ergodic features by settling into limit-cycles whose period depends on the energy and initial conditions. The asymptotic activity $\rho_a$ (topplings density) shows, as a function of energy density $\zeta$, a devil's staircase behaviour defining a symmetric energy interval-set over which also the period lengths remain constant. The properties of $\zeta$-$\rho_a$ phase diagram can be traced back to the basic symmetries underlying the model's dynamics.Comment: EPL-style, 7 pages, 3 eps figures, revised versio

Characterizing and modeling the dynamics of online popularity

Online popularity has enormous impact on opinions, culture, policy, and profits. We provide a quantitative, large scale, temporal analysis of the dynamics of online content popularity in two massive model systems, the Wikipedia and an entire country's Web space. We find that the dynamics of popularity are characterized by bursts, displaying characteristic features of critical systems such as fat-tailed distributions of magnitude and inter-event time. We propose a minimal model combining the classic preferential popularity increase mechanism with the occurrence of random popularity shifts due to exogenous factors. The model recovers the critical features observed in the empirical analysis of the systems analyzed here, highlighting the key factors needed in the description of popularity dynamics.Comment: 5 pages, 4 figures. Modeling part detailed. Final version published in Physical Review Letter