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Performance studies of new optics for the time-of-flight detector of the AFP project
No full textWe present the results of performance studies of the upgraded optical part of the time-of-flight subdetector prototype for the AFP (ATLAS Forward Proton) detector obtained during the test campaign in a synchrotron test-beam facility with 5 GeV electrons at the DESY laboratory (Hamburg, Germany) in June 2019. The detection of the particle arrival time is based on generation of Cherenkov light in an L-shaped fused silica bar. In the previous version of the ToF, all bars were made of two pieces (radiator and light guide) glued together with a dedicated glue (Epotek 305). This solution suffers from additional radiation damage of glue. We adopted a new technique of bar production without the need of glue. The new bars have a higher optical throughput by a factor of 1.6, reduced fragility, and better geometrical precision
Testing two-component models on very-high-energy gamma-ray emitting BL Lac objects
No full textContext. It has become evident that one-zone synchrotron self-Compton models are not always adequate for very-high-energy (VHE) gamma-ray emitting blazars. While two-component models are performing better, they are difficult to constrain due to the large number of free parameters. Aims. In this work, we make a first attempt to take into account the observational constraints from Very Long Baseline Interferometry (VLBI) data, long-term light curves (radio, optical, and X-rays) and optical polarisation to limit the parameter space for a two-component model and test if it can still reproduce the observed spectral energy distribution (SED) of the blazars. Methods. We selected five TeV BL Lac objects based on the availability of VHE gamma-ray and optical polarisation data. We collected constraints for the jet parameters from VLBI observations. We evaluated the contributions of the two components to the optical flux by means of decomposition of long-term radio and optical light curves as well as modeling of the optical polarisation variability of the objects. We selected eight epochs for these five objects, based on the variability observed at VHE gamma rays, for which we constructed the SEDs that we then modeled with a two-component model. Results. We found parameter sets which can reproduce the broadband SED of the sources in the framework of two-component models considering all available observational constraints from VLBI observations. Moreover, the constraints obtained from the long-term behavior of the sources in the lower energy bands could be used to determine the region where the emission in each band originates. Finally, we attempted to use optical polarisation data to shed new light on the behavior of the two components in the optical band. Our observationally constrained two zone model allows explanation of the entire SED from radio to VHE with two co-located emission regions
Anomeric Selectivity of Trehalose Transferase with Rare l -Sugars
No full textRetaining LeLoir glycosyltransferases catalyze the formation of glycosidic bonds between nucleotide sugar donors and carbohydrate acceptors. The anomeric selectivity of trehalose transferase from Thermoproteus uzoniensis was investigated for both d- and l-glycopyranose acceptors. The enzyme couples a wide range of carbohydrates, yielding trehalose analogues with conversion and enantioselectivity of >98%. The anomeric selectivity inverts from α,α-(1 → 1)-glycosidic bonds for d-glycopyranose acceptors to α,β-(1 → 1)-glycosidic bonds for l-glycopyranose acceptors, while (S)-selectivity was retained for both types of sugar acceptors. Comparison of protein crystal structures of trehalose transferase in complex with α,α-trehalose and an unnatural α,β-trehalose analogue highlighted the mechanistic rationale for the observed inversion of anomeric selectivity
Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex
No full textHerpesviruses acquire their membrane envelopes in the cytoplasm of infected cells via a molecular mechanism that remains unclear. Herpes simplex virus (HSV)−1 proteins pUL7 and pUL51 form a complex required for efficient virus envelopment. We show that interaction between homologues of pUL7 and pUL51 is conserved across human herpesviruses, as is their association with trans-Golgi membranes. We characterized the HSV-1 pUL7:pUL51 complex by solution scattering and chemical crosslinking, revealing a 1:2 complex that can form higher-order oligomers in solution, and we solved the crystal structure of the core pUL7:pUL51 heterodimer. While pUL7 adopts a previously-unseen compact fold, the helix-turn-helix conformation of pUL51 resembles the cellular endosomal complex required for transport (ESCRT)-III component CHMP4B and pUL51 forms ESCRT-III–like filaments, suggesting a direct role for pUL51 in promoting membrane scission during virus assembly. Our results provide a structural framework for understanding the role of the conserved pUL7:pUL51 complex in herpesvirus assembly
Modelling the spread of Covid19 in Italy using a revised version of the SIR model
No full textIn this paper, we present a model to predict the spread of the Covid-19 epidemic and apply it to the specific case of Italy. We started from a simple Susceptible, Infected, Recovered (SIR) model and we added the condition that, after a certain time, the basic reproduction number exponentially decays in time, as empirically suggested by world data. Using this model, we were able to reproduce the real behavior of the epidemic with an average error of 5\%. Moreover, we illustrate possible future scenarios, associated to different intervals of . This model has been used since the beginning of March 2020, predicting the Italian peak of the epidemic in April 2020 with about 100.000 detected active cases. The real peak of the epidemic happened on the 20th of April 2020, with 108.000 active cases. This result shows that the model had predictive power for the italian case
Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations
No full textNanodiscs are membrane mimetics that consist of a protein belt surrounding a lipid bilayer, and are broadly used for characterization of membrane proteins. Here, we investigate the structure, dynamics and biophysical properties of two small nanodiscs, MSP1D1ΔH5 and ΔH4H5. We combine our SAXS and SANS experiments with molecular dynamics simulations and previously obtained NMR and EPR data to derive and validate a conformational ensemble that represents the structure and dynamics of the nanodisc. We find that it displays conformational heterogeneity with various elliptical shapes, and with substantial differences in lipid ordering in the centre and rim of the discs. Together, our results reconcile previous apparently conflicting observations about the shape of nanodiscs, and pave the way for future integrative studies of larger complex systems such as membrane proteins embedded in nanodiscs
Ultra-high-energy cosmic-ray nuclei and neutrinos in models of gamma-ray bursts and extragalactic propagation
No full textUtrahochenergetische kosmische Strahlung (ultra-high-energy cosmic rays -- UHECR) besteht aus ionisierten Atomkernen mit den höchsten Teilchenergien, die je gemessen wurden. Zwar wurden die Quellen von UHECRs noch nicht eindeutig identifiziert, doch gibt es deutliche Anzeichen, dass sie extragalaktisch sind. Um die Beobachtungen zu interpretieren, wird ein Modell der Wechselwirkungen mit Photofeldern sowohl in der Quelle als auch während der extragalaktischen Propagation benötigt. Bei diesen Wechselwirkungen werden sekundäre Neutrinos erzeugt. Diese Dissertation behandelt Modelle der Quellen von UHECRs und die damit verbundene Produktion von Neutrinos sowohl in den Quellen als auch während der Propagation. Dafür wurde ein neuer Code, PriNCe, für die Propagation von UHECRs entwickelt. Dieser Code wird in einem umfangreichen Parameterscan für ein generisches Quellenmodell angewendet, welches mit dem Spektralindex, der maximalen Rigidität, der kosmologischen Quellenverteilung und der chemischen Komposition als freie Parameter definiert ist. Dabei wird der Einfluss von verschiedenen Photodisintegrations- und Luftschauermodellen auf die erwarteten Eigenschaften der Quellen demonstriert. Der Fluss kosmogenischer Neutrinos, der sich daraus robust vorhersagen lässt, liegt außerhalb der Reichweite aller derzeit geplanten Neutrinodetektoren. GRBs als mögliche Quellen von UHECRs werden im Multi-Collision Internal-Shock Modell simuliert, welches die Abhängigkeit der Strahlungsprozesse von den verschiedenen Dissipationsradien im Plasmajet berücksichtigt. Für dieses Modell wird der Effekt demonstriert, den verschiedene Annahmen über die anfängliche Verteilung des Plasmajets und das hydrodynamische Modell auf die resultierende UHECR- und Neutrinosstrahlung haben. Für den Gammastrahlenblitz GRB170817A, welcher zusammen mit einem Gravitationswellensignal beobachtet wurde, werden Vorhersagen für den Neutrinofluss und ihre Abhängigkeit vom Beobachtungswinkel gemacht.Ultra-high-energy cosmic rays (UHECRs) are the most energetic particles observed in the Universe. While the astrophysical sources of UHECRs have not yet been uniquely identified, there are strong indications for an extragalactic origin. The interpretation of the observations requires both simulations of UHECR acceleration and energy losses inside the source environment as well as interactions during extragalactic propagation. Due to their extreme energies, UHECR will interact with photons in these environments, producing a flux of secondary neutrinos. This dissertation deals with models of UHECR sources and the accompanying neutrino production in the source environment and during extragalactic propagation. We have developed a new, computationally efficient code, PriNCe, for the extragalactic propagation of UHECR nuclei. The PriNCe code is applied for an extensive parameter scan of a generic source model that is described by the spectral index, the maximal rigidity, the cosmological source evolution and the injected mass composition. In this scan, we demonstrate the impact of different disintegration and air-shower models on the inferred source properties. A prediction for the expected flux of cosmogenic neutrinos is also derived. GRBs are discussed as specific UHECR source candidates in the multi-collision internal-shock model. This model takes the radiation from different radii in the GRB outflow into account. We demonstrate how different assumptions about the initial setup of the jet and the hydrodynamic collision model impact the production of UHECRs and neutrinos. Motivated by the multi-messenger observation of GRB170817A, we discuss the expected neutrino production from this GRB and its dependence on the observation angle. We show that the neutrino flux for this event is at least four orders of magnitude below the detection limit for different geometries of the plasma jet
Tetrameric Structures of Inorganic CBS-Pyrophosphatases from Various Bacterial Species Revealed by Small-Angle X-ray Scattering in Solution
No full textQuaternary structure of CBS-pyrophosphatases (CBS-PPases), which belong to the PPases of family II, plays an important role in their function ensuring cooperative behavior of the enzymes. Despite an intensive research, high resolution structures of the full-length CBS-PPases are not yet available making it difficult to determine the signal transmission path from the regulatory to the active center. In the present work, small-angle X-ray scattering (SAXS) combined with size-exclusion chromatography was applied to determine the solution structures of the full-length wild-type CBS-PPases from three different bacterial species. Previously, in the absence of an experimentally determined full-length CBS-PPase structure, a homodimeric model of the enzyme based on known crystal structures of the CBS domain and family II PPase without this domain has been proposed. Our SAXS analyses demonstrate, for the first time, the existence of stable tetramers in solution for all studied CBS-PPases from different sources. Our findings show that further studies are required to establish the functional properties of these enzymes. This is important not only to enhance our understanding of the relation between CBS-PPases structure and function under normal conditions but also because some human pathogens harbor this class of enzymes
BILMIX : a new approach to restore the size polydispersity and electron density profiles of lipid bilayers from liposomes using small-angle X-ray scattering data
No full textSmall-angle X-ray scattering (SAXS) is one of the major tools for the study of model membranes, but interpretation of the scattering data remains non-trivial. Current approaches allow the extraction of some structural parameters and the electron density profile of lipid bilayers. Here it is demonstrated that parametric modelling can be employed to determine the polydispersity of spherical or ellipsoidal vesicles and describe the electron density profile across the lipid bilayer. This approach is implemented in the computer program BILMIX. BILMIX delivers a description of the electron density of a lipid bilayer from SAXS data and simultaneously generates the corresponding size distribution of the unilamellar lipid vesicles
