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

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

Infiltration-soil moisture redistribution under natural conditions: experimental evidence as a guideline for realizing simulation models

Abstract. The evolution in time, t, of the experimental soil moisture vertical profile under natural conditions is investigated in order to address the corresponding simulation modelling. The measurements were conducted in a plot with a bare silty loam soil. The soil water content, θ, was continuously monitored at different depths, z, using a Time Domain Reflectometry (TDR) system. Four buriable three-rod waveguides were inserted horizontally at different depths (5, 15, 25 and 35 cm). In addition, we used sensors of air temperature and relative humidity, wind speed, solar radiation, evaporation and rain as supports for the application of selected simulation models, as well as for the detection of elements leading to their improvement. The results indicate that, under natural conditions, very different trends of the θ(z, t) function can be observed in the given fine-textured soil, where the formation of a sealing layer over the parent soil requires an adjustment of the simulation modelling commonly used for hydrological applications. In particular, because of the considerable variations in the shape of the moisture content vertical profile as a function of time, a generalization of the existing models should incorporate a first approximation of the variability in time of the saturated hydraulic conductivity, K1s, of the uppermost soil. This conclusion is supported by the fact that the observed shape of θ(z, t) can be appropriately reproduced by adopting the proposed approach with K1s kept constant during each rainfall event but considered variable from event to event, however the observed rainfall rate and the occurrence of freeze-thaw cycles with high soil moisture contents have to be explicitly incorporated in a functional form for K1s(t)

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

On the production of N-2(+) ions at the N 1s edge of the nitrogen molecule

The N+2 ion yield of the N2 molecule has been measured at the N 1s → Rydberg excitations. It displays Fano-type line shapes due to interference between direct outer-valence photoionization and participator decay of the core-excited Rydberg states. The N+2 ion yield is compared with the total intensity of the outer-valence photoelectron lines obtained recently with electron spectroscopy (Kivimäki et al 2012 Phys. Rev. A 86 012516). The increasing difference between the two curves at the higher core-to-Rydberg excitations is most likely due to soft x-ray emission processes that are followed by autoionization. The results also suggest that resonant Auger decay from the core–valence doubly excited states contributes to the N+2 ion yield at the photon energies that are located on both sides of the N 1s ionization limit

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

Evidence for a diamondlike electronic band structure of Si multilayers on Ag(111)

Silicon multilayers on Ag(111) have been suggested to exhibit the structure of silicene, a material that has been heralded as a novel basis for microelectronic applications. However, our angle-resolved photoemission spectra (ARPES) from silicon multilayers on Ag(111) and of the silver-induced reconstruction of Si(111) demonstrate, from the close match in the valence level band structures, that the films exhibit a sp3 diamondlike structure. This refutes the interpretation o silicon multilayers on Ag(111) as silicene, a conclusion that is strengthened by the observation from core level photoemission that significant silver segregation occurs to the surface of these layers

Valence photoionization of the N2 molecule in the region of the N 1s→Rydberg excitations

The intensities of the X and A valence photoelectron lines of N2 have been found to display Fano line shapes as a function of photon energy around the N 1s→ Rydberg excitations. The vibrational intensity distributions of these photoelectron lines change at the N 1s→3sσ and 3pπ resonances. These effects indicate interference between direct and resonant photoionization channels. Our numerical simulations reproduce quite well the experimental results

Exact Solution of the Munoz-Eaton Model for Protein Folding

A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for a generic protein, for any choice of the energy and entropy parameters, and in principle allows the model to be used as a first tool to characterize the dynamics of a protein of known native state and equilibrium population. Applications to a $\beta$-hairpin and to protein CI-2, with comparisons to previous results, are also shown.Comment: 4 pages, 5 figures, RevTeX 4. To be published in Phys. Rev. Let