Opportunities for Structure Determination Using X-ray Free-electron Laser Pulses

One of the exciting prospects enabled by the short, intense pulses of X-ray free-electron lasers (XFELs) is the determination of near-atomic resolution structures of biomolecules and their complexes without the need of crystallisation or cryo-cooling. Using femtosecond pulses that freeze all atomic motion could open up entirely new capabilities and insights into the dynamics, function and interaction of many systems in structural biology. Meeting this goal requires methodological advances beyond those that have already been recently made at XFEL facilities. Here, some of the challenges and opportunities are discussed, starting from considerations of the interactions of X-rays with materials. The destructive nature of XFEL pulses restricts high-resolution imaging experiments to a single shot from a single sample, yet three-dimensional information is needed to properly interpret images from unsectioned samples. This requires the means to obtain multiple-view images of a unique object, such as a cell, in a single pulse or to average data from many reproducible objects as in crystallography or single-particle diffractive imaging. A potential method is presented for the former case and, in addition to the requirement of high peak brightness, the performance in the latter case is dependent on the highest average brightness achievable with future XFEL sources

Chapter 5 - X-Ray Diffraction Structure Measurements

This chapter describes how the structure of molten silicates under high pressures may be measured by synchrotron X-ray diffraction, using either large-volume presses or diamond-anvil cells, the latter combined with resistive-heating or laser-heating techniques. A brief summary of the data obtained so far is given, followed by a description of both energy-dispersive and angle-dispersive techniques, including challenges and how they may be overcome. Three areas of research are then highlighted: (1) structural measurements at extreme pressure conditions up to 100 GPa, (2) tracking the structural environment of minor/trace elements in magmas, and (3) the different ways to obtain the density of melts from X-ray diffraction data. Finally, some future prospects are discussed

A light dimuon resonance in B decays?

The observed deviations from the Standard Model in several $b \to s\mu\mu$ processes can be explained in terms of a new vector boson produced on-shell in B meson decays. A mass of 2.5-3 GeV and a total width of 10-20% allow to hide the associated dimuon bump in the poorly known charmonium region, and the large invisible decay width can be interpreted in terms of Dark Matter. This proposal predicts a contribution to the muon anomalous magnetic moment, that could explain the long-standing tension with the Standard Model. It also predicts sizeable invisible $B$ decays and a peculiar $q^2$-dependence of the lepton flavor universality ratios $R_K$ and $R_{K^{*}}$ , that could be tested at the LHCb and Belle-II. This proceeding is based on arXiv:1704.06188, and slightly extends it with comments about Dark Matter

Development and simulations of Enhanced Lateral Drift Sensors

We present the concept of a new type of silicon tracking sensor called Enhanced Lateral Drift (ELAD) sensor. In ELAD sensors the spatial resolution of the impact position of ionising particles is improved by a dedicated charge sharing mechanism, which is achieved by a non-homogeneous electric field in the lateral direction in the sensor bulk. The non-homogeneous electric field is created by buried doping implants with a higher concentration with respect to the background concentration of the bulk. The resulting position-dependent charge sharing allows for an improved interpolation of the impact position. TCAD-based electric field simulations for 2D and 3D geometries as well as transient simulations with a traversing particle for the 2D geometry have been carried out.The electric field profiles have further been optimised for position resolution.The simulations show a strong dependence of the charge sharing mechanism on the buried implant concentration.Optimal values for the buried implant concentration allow for nearly linear charge sharing between two readout electrodes as a function of the impact position.Additionally, the foreseen production technique combining silicon epitaxy and ion beam implantation is outlined

Climbing the Data Mountain: Processing of SFX Data

Serial femtosecond crystallography experiments produce mountains of data that require FEL facilities to provide many petabytes of storage space and large compute clusters for timely processing of user data. The route to reach the summit of the data mountain requires peak finding, indexing, integration, refinement, and phasing. Those who reach the summit get a crystal clear view of the “radiation damage-free” structure of a protein that is most consistent with the observed measurements. Data processing plays a critical role in the ability to measure accurate structure factor intensities from individual diffraction snapshots and combine them in three-dimensional space. Current developments in SFX aim to take into account the huge complexity of SFX experiments, modeling variations in the beam and crystals, uncertainties in geometry, partiality, mosaicity, and figures of merit that are unique to SFX

Measuring structural inhomogeneity of a helical conjugated polymer at high pressure and temperature

We report on X-ray scattering measurements of heli-cal poly[9,9-bis(2-ethylhexyl)-fluorene-2,7-diyl] by mapping thesample with 10μm spatial resolution from 0.3 GPa to 36 GPa.We follow the strongest 00lreflection, which moves towardhigher scattering angles with pressure indicating planarizationof helical polyfluorene. Lateral inhomogeneity is increased for>10 GPa concomitant with the solidification of the pressure transmitting medium (a 4:1 mixture of methanol and ethanol) We also follow the 00l reflection with increasing temperature atthe constant pressure of 4.3 GPa in neon. We observe a sharpshift toward higher scattering angles indicative of a phase transi-tion at 167–176C

Equations of state of rhodium, iridium and their alloys up to 70 GPa

Knowledge of the compressional and thermal behaviour of metals and alloys is of a high fundamental and applied value. In this work, we studied the behaviour of Ir, Rh, and their fcc-structured alloys, Ir$_{0.42}$Rh$_{0.58}>$ and Ir$_{0.26}$Os$_{0.05}$Pt$_{0.31}$Rh$_{0.23}$Ru$_{0.15}$, up to 70 GPa using the diamond anvil cell technique with synchrotron X-ray diffraction. We found that all these materials are structurally stable upon room-temperature hydrostatic compression in the whole pressure interval, as well as upon heating to 2273 K both at ambient and high pressure. Rh, Ir$_{0.42}$Rh$_{0.58}$ and Ir$_{0.26}$Os$_{0.05}$Pt$_{0.31}$Rh$_{0.23}$Ru$_{0.15}$ were investigated under static compression for the first time. According to our data, the compressibility of Ir, Rh, fcc–Ir$_{0.42}$Rh$_{0.58}$, and fcc–Ir$_{0.26}$Os$_{0.05}$Pt$_{0.31}$Rh$_{0.23}$Ru$_{0.15}$, can be described with the 3rd order Birch-Murnaghan equation of state with the following parameters: V$_0$ = 14.14(6) Å$^3$·atom$^1 {−1}$, B$_0$ = 341(10) GPa, and B0' = 4.7(3); V$_0$ = 13.73(7) Å$^3$·atom$^{−1}$, B$_0$ = 301(9) GPa, and B$_0$' = 3.1(2); V$_0$ = 13.90(8) Å$^3$·atom$^{−1}$, B$_0$ = 317(17) GPa, and B$_0$' = 6.0(5); V$_0$ = 14.16(9) Å$^3$·atom$^{−1}$, B$_0$ = 300(22) GPa, B$_0$' = 6(1), where V$_0$ is the unit cell volume, B$_0$ and B$_0$' – are the bulk modulus and its pressure derivative

Toward Optimization of Centrifugal Barrel Polishing P rocedure for Treatment of Niobium Cavities

Centrifugal barrel polishing (CBP) is a simple and environmentally friendly method that can be applied for mechanical abrasion of the cavity interior in order to remove the mechanically damaged surface after its production. The CBP recipes described in the literature, however, require CBP to be performed in many stages, require long processing times and nevertheless are unable to provide good cavity RF performance without additional chemical processing. Here, we report new results on characterization of cavity surfaces treated with a typical CBP recipe, including the contamination with abrasive particles, plastic deformation and hydrogen contamination, and critically evaluate it. Methods to reduce the depth of significant plastic deformation as well as the modified commercially viable CBP procedure followed by final electropolishing are proposed and tested on samples

A vesicle-to-sponge transition via the proliferation of membrane-linking pores in ω−3ω-3 polyunsaturated fatty acid-containing lipid assemblies

We investigate the nanostructure evolution and the membrane reorganization of diluted lipid dispersions of self-assembled monoolein (MO)/eicosapentaenoic acid (EPA, 20:5) mixtures by synchrotron small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM) microscopy. The nonlamellar lipid phase containing a ω-3 polyunsaturated fatty acid was fragmented into stable nanoscale objects with the help of PEGylated lipids. The Cryo-TEM imaging revealed the transformation pathway of the vesicular bilayer membranes into sponge nanoparticles (spongosomes) in excess aqueous medium. At ambient temperature, the topological transition occurred through the proliferation of membrane-linking pores (MLP) within the individual lipid nanoparticles. The density of the MLP pores varied starting from the nanoparticle center toward the periphery. The generation of MLP is governed by the amphiphilic composition and leads to formation of 3D networks of aqueous channels inside the nanoparticles, i.e. spongosomes. A higher density of MLP pores was established at increasing fraction of EPA in the mixed lipid membranes. This corresponded to sponge particles of less hydrated internal structure, i.e. with smaller-size aqueous compartments. Synchrotron SAXS patterns characterized the overall structural transition from vesicles to sponge membranes in the studied lipid systems. It can be concluded that the incorporation of a ω-3 polyunsaturated fatty acid at increasing concentration causes swelling inhibition (dehydration) of the host liquid crystalline architectures

Probing photodissociation dynamics using ring polymer molecular dynamics

The performance of the ring polymer molecular dynamics (RPMD) approach to simulate typical photodissociation processes is assessed. The correct description of photodissociation requires the calculation of correlation functions or expectation values associated with non-equilibrium initial conditions, which was shown to be possible with RPMD very recently [J. Chem. Phys. 145, 204118 (2016)]. This approach is combined with treatment of the nonadiabatic dynamics employing the ring polymer surface hopping approach (RPSH), which is based on Tully’s fewest switches surface hopping (FSSH) approach. The performance is tested using one-dimensional photodissociation models. It is found that RPSH with non-equilibrium initial conditions can well reproduce the time-dependent dissociation probability, and adiabatic and diabatic populations for cases where the crossing point is below and above the Franck-Condon point, respectively, while standard FSSH fails to reproduce the exact quantum dynamics in the latter case. Thus, it is shown that RPSH is an efficient and accurate alternative to standard FSSH, which is one of the most widely employed approaches to study photochemistry