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Two members of White House virus task force in quarantine




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Rock ‘n’ roll pioneer Little Richard passes away





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Andy Serkis says The Batman will be darker than previous films




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Russo Brothers to recommend and discuss movies as a part of Instagram series




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Chandigarh: Bapu dham resident tests positive after death, UT sees 21 new cases




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Random sampling finds two positive cases in two days in Panchkula




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Punjab: Balbir Singh Senior admitted to a private hospital due to pneumonia




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Punjab and Haryana HC to hold 10 benches for hearing of urgent cases over video conferencing




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Plea in Punjab and Haryana HC seeks directions to health facilities to attend non-Covid cases




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Inside Track: Kishor’s expertise




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The Centre will need to nurse the Constitution and India back to good health




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If the lockdown is not lifted, there may be defiance on a larger scale than at present




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Is your mother getting her essential nutrients? Check here




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On Mother’s Day, relive nostalgia with these 3 recipes for dips




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31 new Covid-19 cases in Punjab, total 1,762




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28 cases take Haryana's corona tally to 675

The Covid-19 count of Haryana on Saturday reached 675 as 28 new cases, which includes 25 from the national capital region (NCR) were reported. A 22-year-old TB patient also succumbed to Covid-19 in Panipat taking death toll to 9 in the state.




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Cops seize Rs 97L, Land Rover, 2 pistols in UT

Five days after nearly 5,500 cases of liquor seized by police went missing in Sonipat, Haryana Police on Saturday raided the Chandigarh hideout of the godown owner's husband and seized Rs 97 lakh, a Range Rover car, two pistols and a three mobile phones.




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Chandigarh extends excise policy till June 30

The UT excise and taxation department has extended the excise policy from May 15 to June 30 due to the Covid-19 pandemic and the ongoing lockdown.




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WhatsApp for Web gets Messenger Rooms support: How it works and other details




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Banned Umar Akmal refuses to divulge details of two meetings with suspected bookies: PCB sources




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Device for source position stabilization and beam parameter monitoring at inverse Compton X-ray sources

Compact X-ray sources based on inverse Compton scattering provide brilliant and partially coherent X-rays in a laboratory environment. The cross section for inverse Compton scattering is very small, requiring high-power laser systems as well as small laser and electron beam sizes at the interaction point to generate sufficient flux. Therefore, these systems are very sensitive to distortions which change the overlap between the two beams. In order to monitor X-ray source position, size and flux in parallel to experiments, the beam-position monitor proposed here comprises a small knife edge whose image is acquired with an X-ray camera specifically designed to intercept only a very small fraction of the X-ray beam. Based on the source position drift recorded with the monitor, a closed-loop feedback stabilizes the X-ray source position by adjusting the laser beam trajectory. A decrease of long-term source position drifts by more than one order of magnitude is demonstrated with this device. Consequently, such a closed-loop feedback system which enables stabilization of source position drifts and flux of inverse Compton sources in parallel to experiments has a significant impact on the performance of these sources.




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Scientific instrument Femtosecond X-ray Experiments (FXE): instrumentation and baseline experimental capabilities

The European X-ray Free-Electron Laser (EuXFEL) delivers extremely intense (>1012 photons pulse−1 and up to 27000 pulses s−1), ultrashort (<100 fs) and transversely coherent X-ray radiation, at a repetition rate of up to 4.5 MHz. Its unique X-ray beam parameters enable novel and groundbreaking experiments in ultrafast photochemistry and material sciences at the Femtosecond X-ray Experiments (FXE) scientific instrument. This paper provides an overview of the currently implemented experimental baseline instrumentation and its performance during the commissioning phase, and a preview of planned improvements. FXE's versatile instrumentation combines the simultaneous application of forward X-ray scattering and X-ray spectroscopy techniques with femtosecond time resolution. These methods will eventually permit exploitation of wide-angle X-ray scattering studies and X-ray emission spectroscopy, along with X-ray absorption spectroscopy, including resonant inelastic X-ray scattering and X-ray Raman scattering. A suite of ultrafast optical lasers throughout the UV–visible and near-IR ranges (extending up to mid-IR in the near future) with pulse length down to 15 fs, synchronized to the X-ray source, serve to initiate dynamic changes in the sample. Time-delayed hard X-ray pulses in the 5–20 keV range are used to probe the ensuing dynamic processes using the suite of X-ray probe tools. FXE is equipped with a primary monochromator, a primary and secondary single-shot spectrometer, and a timing tool to correct the residual timing jitter between laser and X-ray pulses.




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Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays

To investigate the effect of high-energy X-rays on site-specific radiation-damage, low-dose diffraction data were collected from radiation-sensitive crystals of the metal enzyme cytochrome c oxidase. Data were collected at the Structural Biology I beamline (BL41XU) at SPring-8, using 30 keV X-rays and a highly sensitive pixel array detector equipped with a cadmium telluride sensor. The experimental setup of continuous sample translation using multiple crystals allowed the average diffraction weighted dose per data set to be reduced to 58 kGy, and the resulting data revealed a ligand structure featuring an identical bond length to that in the damage-free structure determined using an X-ray free-electron laser. However, precise analysis of the residual density around the ligand structure refined with the synchrotron data showed the possibility of a small level of specific damage, which might have resulted from the accumulated dose of 58 kGy per data set. Further investigation of the photon-energy dependence of specific damage, as assessed by variations in UV-vis absorption spectra, was conducted using an on-line spectrometer at various energies ranging from 10 to 30 keV. No evidence was found for specific radiation damage being energy dependent.




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Fast identification of mineral inclusions in diamond at GSECARS using synchrotron X-ray microtomography, radiography and diffraction

Mineral inclusions in natural diamond are widely studied for the insight that they provide into the geochemistry and dynamics of the Earth's interior. A major challenge in achieving thorough yet high rates of analysis of mineral inclusions in diamond derives from the micrometre-scale of most inclusions, often requiring synchrotron radiation sources for diffraction. Centering microinclusions for diffraction with a highly focused synchrotron beam cannot be achieved optically because of the very high index of refraction of diamond. A fast, high-throughput method for identification of micromineral inclusions in diamond has been developed at the GeoSoilEnviro Center for Advanced Radiation Sources (GSECARS), Advanced Photon Source, Argonne National Laboratory, USA. Diamonds and their inclusions are imaged using synchrotron 3D computed X-ray microtomography on beamline 13-BM-D of GSECARS. The location of every inclusion is then pinpointed onto the coordinate system of the six-circle goniometer of the single-crystal diffractometer on beamline 13-BM-C. Because the bending magnet branch 13-BM is divided and delivered into 13-BM-C and 13-BM-D stations simultaneously, numerous diamonds can be examined during coordinated runs. The fast, high-throughput capability of the methodology is demonstrated by collecting 3D diffraction data on 53 diamond inclusions from Juína, Brazil, within a total of about 72 h of beam time.




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X-ray reflecto-interferometer based on compound refractive lenses

An X-ray amplitude-splitting interferometer based on compound refractive lenses, which operates in the reflection mode, is proposed and realized. The idea of a reflecto-interferometer is to use a very simplified experimental setup where a focused X-ray beam reflected from parallel flat surfaces creates an interference pattern in a wide angular range. The functional capabilities of the interferometer were experimentally tested at the European Synchrotron Radiation Facility (ESRF) ID06 beamline in the X-ray energy range from 10 keV to 15 keV. The main features of the proposed approach, high spatial and temporal resolution, were demonstrated experimentally. The reflections from free-standing Si3N4 membranes, gold and resist layers were studied. Experimentally recorded interferograms are in good agreement with our simulations. The main advantages and future possible applications of the reflecto-interferometer are discussed.




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Soft X-ray varied-line-spacing gratings fabricated by near-field holography using an electron beam lithography-written phase mask

A fabrication method comprising near-field holography (NFH) with an electron beam lithography (EBL)-written phase mask was developed to fabricate soft X-ray varied-line-spacing gratings (VLSGs). An EBL-written phase mask with an area of 52 mm × 30 mm and a central line density greater than 3000 lines mm−1 was used. The introduction of the EBL-written phase mask substantially simplified the NFH optics for pattern transfer. The characterization of the groove density distribution and diffraction efficiency of the fabricated VLSGs indicates that the EBL–NFH method is feasible and promising for achieving high-accuracy groove density distributions with corresponding image properties. Vertical stray light is suppressed in the soft X-ray spectral range.




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Microsecond time-resolved X-ray diffraction for the investigation of fatigue behavior during ultrasonic fatigue loading

A new method based on time-resolved X-ray diffraction is proposed in order to measure the elastic strain and stress during ultrasonic fatigue loading experiments. Pure Cu was chosen as an example material for the experiments using a 20 kHz ultrasonic fatigue machine mounted on the six-circle diffractometer available at the DiffAbs beamline on the SOLEIL synchrotron facility in France. A two-dimensional hybrid pixel X-ray detector (XPAD3.2) was triggered by the strain gage signal in a synchronous data acquisition scheme (pump–probe-like). The method enables studying loading cycles with a period of 50 µs, achieving a temporal resolution of 1 µs. This allows a precise reconstruction of the diffraction patterns during the loading cycles. From the diffraction patterns, the position of the peaks, their shifts and their respective broadening can be deduced. The diffraction peak shift allows the elastic lattice strain to be estimated with a resolution of ∼10−5. Stress is calculated by the self-consistent scale-transition model through which the elastic response of the material is estimated. The amplitudes of the cyclic stresses range from 40 to 120 MPa and vary linearly with respect to the displacement applied by the ultrasonic machine. Moreover, the experimental results highlight an increase of the diffraction peak broadening with the number of applied cycles.




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BioStruct-Africa: empowering Africa-based scientists through structural biology knowledge transfer and mentoring – recent advances and future perspectives

Being able to visualize biology at the molecular level is essential for our understanding of the world. A structural biology approach reveals the molecular basis of disease processes and can guide the design of new drugs as well as aid in the optimization of existing medicines. However, due to the lack of a synchrotron light source, adequate infrastructure, skilled persons and incentives for scientists in addition to limited financial support, the majority of countries across the African continent do not conduct structural biology research. Nevertheless, with technological advances such as robotic protein crystallization and remote data collection capabilities offered by many synchrotron light sources, X-ray crystallography is now potentially accessible to Africa-based scientists. This leap in technology led to the establishment in 2017 of BioStruct-Africa, a non-profit organization (Swedish corporate ID: 802509-6689) whose core aim is capacity building for African students and researchers in the field of structural biology with a focus on prevalent diseases in the African continent. The team is mainly composed of, but not limited to, a group of structural biologists from the African diaspora. The members of BioStruct-Africa have taken up the mantle to serve as a catalyst in order to facilitate the information and technology transfer to those with the greatest desire and need within Africa. BioStruct-Africa achieves this by organizing workshops onsite at our partner universities and institutions based in Africa, followed by post-hoc online mentoring of participants to ensure sustainable capacity building. The workshops provide a theoretical background on protein crystallography, hands-on practical experience in protein crystallization, crystal harvesting and cryo-cooling, live remote data collection on a synchrotron beamline, but most importantly the links to drive further collaboration through research. Capacity building for Africa-based researchers in structural biology is crucial to win the fight against the neglected tropical diseases, e.g. ascariasis, hookworm, trichuriasis, lymphatic filariasis, active trachoma, loiasis, yellow fever, leprosy, rabies, sleeping sickness, onchocerciasis, schistosomiasis, etc., that constitute significant health, social and economic burdens to the continent. BioStruct-Africa aims to build local and national expertise that will have direct benefits for healthcare within the continent.




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Generating three-color pulses in high-gain harmonic-generation free-electron lasers with a tilted electron bunch

A multi-color light source is a significant tool for nonlinear optics experiments, pump–dump/repump–probe experiments and in other fields. Here, a novel method is proposed to create three-color pulses based on a high-gain harmonic-generation (HGHG) free-electron laser with a tilted electron bunch. In this method, the initial bunch tilt is created by transverse wakefields after the bunch passes through a corrugated structure with an off-axis orbit, and is further enlarged in a following drift section. Then the tilted bunch experiences the off-axis field of a quadrupole magnet to cool down the large transverse velocity induced before. After that, it enters an HGHG configuration adopting a transverse gradient undulator (TGU) as the radiator, where only three separated fractions of the tilted bunch will resonate at three adjacent harmonics of the seed wavelength and are enabled to emit three-color pulses simultaneously. In addition, the use of the natural transverse gradient of a normal planar undulator instead of the TGU radiator to emit three-color pulses is also studied in detail. Numerical simulations including the generation of the tilted bunch and the free-electron laser radiation confirm the validity and feasibility of this scheme both for the TGU radiator and the natural gradient in the extreme-ultraviolet waveband.




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Reducing sample consumption for serial crystallography using acoustic drop ejection

Efficient sample delivery is an essential aspect of serial crystallography at both synchrotrons and X-ray free-electron lasers. Rastering fixed target chips through the X-ray beam is an efficient method for serial delivery from the perspectives of both sample consumption and beam time usage. Here, an approach for loading fixed targets using acoustic drop ejection is presented that does not compromise crystal quality, can reduce sample consumption by more than an order of magnitude and allows serial diffraction to be collected from a larger proportion of the crystals in the slurry.




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Performance of nearly fixed offset asymmetric channel-cut crystals for X-ray monochromators

X-ray double-crystal monochromators face a shift of the exit beam when the Bragg angle and thus the transmitted photon energy changes. This can be compensated for by moving one or both crystals accordingly. In the case of monolithic channel-cut crystals, which exhibit utmost stability, the shift of the monochromated beam is inevitable. Here we report performance tests of novel, asymmetrically cut, channel-cut crystals which reduce the beam movements by more than a factor of 20 relative to the symmetric case over the typical energy range of an EXAFS spectrum at the Cu K-edge. In addition, the presented formulas for the beam offset including the asymmetry angle directly indicate the importance of this value, which has been commonly neglected so far in the operation of double-crystal monochromators.




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Picosecond pump–probe X-ray scattering at the Elettra SAXS beamline

A new setup for picosecond pump–probe X-ray scattering at the Austrian SAXS beamline at Elettra-Sincrotrone Trieste is presented. A high-power/high-repetion-rate laser has been installed on-site, delivering UV/VIS/IR femto­second-pulses in-sync with the storage ring. Data acquisition is achieved by gating a multi-panel detector, capable of discriminating the single X-ray pulse in the dark-gap of the Elettra hybrid filling mode. Specific aspects of laser- and detection-synchronization, on-line beam steering as well protocols for spatial and temporal overlap of laser and X-ray beam are also described. The capabilities of the setup are demonstrated by studying transient heat-transfer in an In/Al/GaAs superlattice structure and results are confirmed by theoretical calculations.




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A semi-analytical approach for the characterization of ordered 3D nanostructures using grazing-incidence X-ray fluorescence

Following the recent demonstration of grazing-incidence X-ray fluorescence (GIXRF)-based characterization of the 3D atomic distribution of different elements and dimensional parameters of periodic nanoscale structures, this work presents a new computational scheme for the simulation of the angular-dependent fluorescence intensities from such periodic 2D and 3D nanoscale structures. The computational scheme is based on the dynamical diffraction theory in many-beam approximation, which allows a semi-analytical solution to the Sherman equation to be derived in a linear-algebraic form. The computational scheme has been used to analyze recently published GIXRF data measured on 2D Si3N4 lamellar gratings, as well as on periodically structured 3D Cr nanopillars. Both the dimensional and structural parameters of these nanostructures have been reconstructed by fitting numerical simulations to the experimental GIXRF data. Obtained results show good agreement with nominal parameters used in the manufacturing of the structures, as well as with reconstructed parameters based on the previously published finite-element-method simulations, in the case of the Si3N4 grating.




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X-ray fluorescence detection for serial macromolecular crystallography using a JUNGFRAU pixel detector

Detection of heavy elements, such as metals, in macromolecular crystallography (MX) samples by X-ray fluorescence is a function traditionally covered at synchrotron MX beamlines by silicon drift detectors, which cannot be used at X-ray free-electron lasers because of the very short duration of the X-ray pulses. Here it is shown that the hybrid pixel charge-integrating detector JUNGFRAU can fulfill this function when operating in a low-flux regime. The feasibility of precise position determination of micrometre-sized metal marks is also demonstrated, to be used as fiducials for offline prelocation in serial crystallography experiments, based on the specific fluorescence signal measured with JUNGFRAU, both at the synchrotron and at SwissFEL. Finally, the measurement of elemental absorption edges at a synchrotron beamline using JUNGFRAU is also demonstrated.




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The HXD95: a modified Bassett-type hydrothermal diamond-anvil cell for in situ XRD experiments up to 5 GPa and 1300 K

A new diamond-anvil cell apparatus for in situ synchrotron X-ray diffraction measurements of liquids and glasses, at pressures from ambient to 5 GPa and temperatures from ambient to 1300 K, is reported. This portable setup enables in situ monitoring of the melting of complex compounds and the determination of the structure and properties of melts under moderately high pressure and high temperature conditions relevant to industrial processes and magmatic processes in the Earth's crust and shallow mantle. The device was constructed according to a modified Bassett-type hydro­thermal diamond-anvil cell design with a large angular opening (θ = 95°). This paper reports the successful application of this device to record in situ synchrotron X-ray diffraction of liquid Ga and synthetic PbSiO3 glass to 1100 K and 3 GPa.




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A portable on-axis laser-heating system for near-90° X-ray spectroscopy: application to ferropericlase and iron silicide

A portable IR fiber laser-heating system, optimized for X-ray emission spectroscopy (XES) and nuclear inelastic scattering (NIS) spectroscopy with signal collection through the radial opening of diamond anvil cells near 90°with respect to the incident X-ray beam, is presented. The system offers double-sided on-axis heating by a single laser source and zero attenuation of incoming X-rays other than by the high-pressure environment. A description of the system, which has been tested for pressures above 100 GPa and temperatures up to 3000 K, is given. The XES spectra of laser-heated Mg0.67Fe0.33O demonstrate the potential to map the iron spin state in the pressure–temperature range of the Earth's lower mantle, and the NIS spectra of laser-heated FeSi give access to the sound velocity of this candidate of a phase inside the Earth's core. This portable system represents one of the few bridges across the gap between laser heating and high-resolution X-ray spectroscopies with signal collection near 90°.




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X-ray free-electron laser wavefront sensing using the fractional Talbot effect

Wavefront sensing at X-ray free-electron lasers is important for quantitatively understanding the fundamental properties of the laser, for aligning X-ray instruments and for conducting scientific experimental analysis. A fractional Talbot wavefront sensor has been developed. This wavefront sensor enables measurements over a wide range of energies, as is common on X-ray instruments, with simplified mechanical requirements and is compatible with the high average power pulses expected in upcoming X-ray free-electron laser upgrades. Single-shot measurements were performed at 500 eV, 1000 eV and 1500 eV at the Linac Coherent Light Source. These measurements were applied to study both mirror alignment and the effects of undulator tapering schemes on source properties. The beamline focal plane position was tracked to an uncertainty of 0.12 mm, and the source location for various undulator tapering schemes to an uncertainty of 1 m, demonstrating excellent sensitivity. These findings pave the way to use the fractional Talbot wavefront sensor as a routine, robust and sensitive tool at X-ray free-electron lasers as well as other high-brightness X-ray sources.




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The HARE chip for efficient time-resolved serial synchrotron crystallography

Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided.




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Time dependence of X-ray polarizability of a crystal induced by an intense femtosecond X-ray pulse

The time evolution of the electron density and the resulting time dependence of the X-ray polarizability of a crystal irradiated by highly intense XFEL femtosecond pulses is investigated theoretically. Rate equations for bound electrons and the Boltzmann equation for the unbound electron gas are used in calculations.




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Contributions of charge-density research to medicinal chemistry

Contributions of experimental and selected theoretical charge-density research to medicinal chemistry are reviewed; combining experimental methods from high-resolution small-molecule and macromolecular crystallography with theory proves to be fruitful.




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Pressure effects on lipids and bio-membrane assemblies

Pressure can play a key role in probing the structure and dynamics of membrane assemblies, and is also critical to the biology and adaptation of deep-sea organisms. This article presents an overview of the effect of pressure on the structure of membranes and recent developments in high-pressure instrumentation.




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Viruses and viral proteins

The X-ray structures of viruses and viral proteins currently available are providing high-resolution snapshots of viral molecular machineries, expanding our vision of the virus world and giving crucial information on potential targets for future antiviral therapies.




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Molecular self-assembly of nylon-12 nanorods cylindrically confined to nanoporous alumina

It has been revealed that in cylindrical nano-confinement, the hydrogen-bonding direction of nylon-12 crystals in the rod could self-assemble to be parallel to the long axis of the rod. The dominant growth direction and hydrogen-bonding direction of the γ-form crystal in the long axis of the rod has been revealed by TEM–SAED and WAXD.




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The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm

An expectation maximization algorithm is implemented to resolve the indexing ambiguity which arises when merging data from many crystals in protein crystallography, especially in cases where partial reflections are recorded in serial femtosecond crystallography (SFX) at XFELs.




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Reconciling the regulatory role of Munc18 proteins in SNARE-complex assembly

Mammalian Munc18 proteins are essential for membrane fusion and human health. Here, we review the literature describing structural and in vitro data, and identify a possible explanation for the conflicting functional roles that have been reported.




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Diffuse scattering and partial disorder in complex structures

This review discusses the state of the field of single-crystal diffuse scattering (SCDS), including detectors, data collection and the modelling techniques. High quality, three-dimensional volumes of SCDS data can now be collected at synchrotron light sources, allowing increasingly detailed and quantitative analyses to be undertaken.




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Structure and function of dioxygenases in histone demethylation and DNA/RNA demethylation

The structure and function of dioxygenases in histone demethylation and DNA/RNA dimethylation are discussed.




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Rochelle salt – a structural reinvestigation with improved tools. I. The high-T paraelectric phase at 308 K

A novel sample cell with control of temperature and relative humidity permitted collection of data of excellent quality, enabling unrestrained refinement of all atomic parameters. One of the K atoms in the structure is disordered; very strong anisotropy in three of the four water O atoms indicates partial static disorder, which does not involve the bonded H atoms.