scholarly journals P13, the EMBL macromolecular crystallography beamline at the low-emittance PETRA III ring for high- and low-energy phasing with variable beam focusing

2017 ◽  
Vol 24 (1) ◽  
pp. 323-332 ◽  
Author(s):  
Michele Cianci ◽  
Gleb Bourenkov ◽  
Guillaume Pompidor ◽  
Ivars Karpics ◽  
Johanna Kallio ◽  
...  
Keyword(s):  
Heavy Atom ◽  
Low Energy ◽  
Photon Flux ◽  
Macromolecular Crystallography ◽  
Large Area ◽  
Area Detector ◽  
Beam Focusing ◽  
High Photon Flux ◽  
Wide Range ◽  
Integrated Facility

The macromolecular crystallography P13 beamline is part of the European Molecular Biology Laboratory Integrated Facility for Structural Biology at PETRA III (DESY, Hamburg, Germany) and has been in user operation since mid-2013. P13 is tunable across the energy range from 4 to 17.5 keV to support crystallographic data acquisition exploiting a wide range of elemental absorption edges for experimental phase determination. An adaptive Kirkpatrick–Baez focusing system provides an X-ray beam with a high photon flux and tunable focus size to adapt to diverse experimental situations. Data collections at energies as low as 4 keV (λ = 3.1 Å) are possible due to a beamline design minimizing background and maximizing photon flux particularly at low energy (up to 1011 photons s−1 at 4 keV), a custom calibration of the PILATUS 6M-F detector for use at low energies, and the availability of a helium path. At high energies, the high photon flux (5.4 × 1011 photons s−1 at 17.5 keV) combined with a large area detector mounted on a 2θ arm allows data collection to sub-atomic resolution (0.55 Å). A peak flux of about 8.0 × 1012 photons s−1 is reached at 11 keV. Automated sample mounting is available by means of the robotic sample changer `MARVIN' with a dewar capacity of 160 samples. In close proximity to the beamline, laboratories have been set up for sample preparation and characterization; a laboratory specifically equipped for on-site heavy atom derivatization with a library of more than 150 compounds is available to beamline users.

scholarly journals EMBL beamlines for macromolecular crystallography at PETRA III

2014 ◽  
Vol 70 (a1) ◽  
pp. C345-C345 ◽  
Author(s):  
Thomas Schneider ◽  
Gleb Bourenkov ◽  
Michele Cianci ◽  
Johanna Kallio ◽  
Guillaume Pompidor ◽  
...  
Keyword(s):  
Data Collection ◽  
Heavy Atom ◽  
Photon Flux ◽  
Wide Energy Range ◽  
Macromolecular Crystallography ◽  
Experimental Conditions ◽  
High Photon Flux ◽  
Small Crystals ◽  
Wide Range ◽  
Integrated Facility

Since 2012, EMBL Hamburg operates two new beamlines for macromolecular crystallography - P13 and P14 - at PETRA III at DESY (Hamburg, Germany). We exploit the high brilliance and the wide energy range offered by PETRA III to offer a wide range of conditions to fit the experimental conditions to the challenges posed by the samples. P13 provides high photon flux down to 4 keV. With a helium cone and a kappa goniostat, this allows optimized data collection for SAD phasing. Using adaptive mirrors, the focus size (H x V) can be adjusted between 30 x 20 μm^2 and 150 x 100 μm^2 to match the size of the sample. A MARVIN sample changer is in operation for rapid loading and unloading of samples. P14 offers a high photon flux (>10^12 ph/sec at 12 keV into 5 x 5 µm^2). The beamsize can be varied between 1 x 1.5 mm^2 (unfocused) and 5 x 5 µm^2 (fully focused) in less than a minute by moving the KB mirrors in and out of the beam. For small crystals, an MD3 vertical diffractometer with a sphere of confusion smaller than 100 nm offers excellent conditions. Both beamlines are equipped with PILATUS 6M-F detectors for shutter-less data collection and dedicated data processing computers. The beamlines are embedded into the 'Integrated Facility for Structural Biology' offering facilities for sample preparation and characterization, a laboratory specifically equipped for the preparation of heavy atom derivatives, and downstream facilities for data evaluation We will report about the status of the beamlines and describe typical experimental situations (small crystals, large unit cells, serial crystallography, low-energy phasing, small molecules and others).

A unique high-performance wide-range (10–1500 eV) spherical grating monochromator beamline

1998 ◽  
Vol 5 (3) ◽  
pp. 723-725 ◽  
Author(s):  
P.-C. Tseng ◽  
C.-C. Chen ◽  
T.-E. Dann ◽  
S.-C. Chung ◽  
C. T. Chen ◽  
...  
Keyword(s):  
High Performance ◽  
Low Energy ◽  
Resolving Power ◽  
Photon Flux ◽  
Wide Spectral Range ◽  
Experimental Station ◽  
Wide Range ◽  
Grating Monochromator ◽  
Overall Performance ◽  
Under Construction

A wide-spectral-range high-performance 6 m-spherical grating monochromator (6 m-SGM) beamline has been designed and is under construction at SRRC. Two different entrance slits, instead of additional mirrors, are used to optimize the overall performance. Six gratings are used to cover photon energies from 10 to 1500 eV. Movable entrance slits and bendable vertical focusing mirrors are used to enhance further the beamline performance. A bendable horizontal focusing mirror is used to improve the resolution and to focus the photon beam at the experimental station immediately after the exit slit. Several end-stations can be installed at the same time to utilize the beam time fully. The expected energy-resolving power, with both slit openings set at 10 µm, is up to 15 000 and 40 000 for the high- and low-energy branches, respectively. A photon flux of 1 × 1011 photons s−1 can be obtained with an energy-resolving power of 20 000.

PROXIMA 2A: A New Micro-focus Beamline for Macromolecular Crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1672-C1672
Author(s):  
Denis Duran ◽  
Sebastien Le Couster ◽  
Gavin Fox ◽  
Roger Fourme ◽  
Rob Meijers ◽  
...  
Keyword(s):  
High Performance ◽  
Protein Structures ◽  
Photon Flux ◽  
First Year ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
Fluorescence Detector ◽  
Beam Position ◽  
X Ray ◽  
Area Detector

PROXIMA 2A is a new micro-focus and energy tunable beamline dedicated to biological macromolecular crystallography at Synchrotron SOLEIL. The beamline officially opened in March 2013, and its first year of user operation has yielded excellent results. The X-ray source is a powerful in-vacuum U24 undulator coupled to a cryo-cooled Si[111] channel-cut monochromator and a pair of focussing bimorph mirrors in Kirpatrick-Baez configuration. This combination delivers a photon flux of over 10**12 ph/s into a focal spot of 10 μm × 5 μm (H×V FWHM), which is tunable over 6 – 15 keV. The supports of the optical elements have been designed to minimise the effects of vibrations and thermal dilations on the X-ray beam position, which is stable to within 5 microns over a day. The experimental station consists of a high performance micro-diffractometer, a cryostream, an area detector (ADSC Q315r), and an X-ray fluorescence detector. The X-ray energies for MAD experiments are directly calibrated on the sample. A robot equipped with a large 9 uni-puck dewar (CATS Irelec) is available to users for the automated transfer and screening of cryo-cooled samples. The users launch their experiments via an MXCuBE interface [1], which permits the centering of the sample, collecting of diffraction images, recording of X-ray spectra and the transfer of samples. The X-ray diffraction data are of an excellent quality, and the users readily exploit the micro-focused X-rays to select the best zones of their crystals. The first year of results from users has yielded a variety of success stories including novel protein structures resolved from crystals as small as 5 microns, as well as those solved by SAD & MAD methods. The future perspectives include automated helical and grid scans, in situ plate screening and multi-crystal merging techniques.

KLEIN–NISHINA EFFECTS IN THE PROMPT AND EXTENDED HIGH-ENERGY GAMMA-RAY EMISSION OF GAMMA-RAY BURSTS

2011 ◽  
Vol 20 (10) ◽  
pp. 2023-2027 ◽  
Author(s):  
XIANG-YU WANG ◽  
HAO-NING HE ◽  
ZHUO LI
Keyword(s):  
Gamma Ray ◽  
Early Time ◽  
High Energy ◽  
Gamma Ray Bursts ◽  
Low Energy ◽  
Large Area ◽  
Wide Range ◽  
Inverse Compton ◽  
Energy Gamma ◽  
Gamma Ray Emission

Prompt and extended high-energy (> 100 MeV) gamma-ray emission has been observed from more than ten gamma-ray bursts by Fermi Large Area Telescope (LAT). Such emission is likely to be produced by synchrotron radiation of electrons accelerated in internal or external shocks. We show that IC scattering of these electrons with synchrotron photons are typically in the Klein–Nishina (KN) regime. For the prompt emission, the KN effect can suppress the IC component and as a result, one single component is seen in some strong bursts. The KN inverse-Compton cooling may also affect the low-energy electron number distribution and hence result in a hard low-energy synchrotron photon spectrum. During the afterglow, KN effect makes the Compton-Y parameter generally less than 1 in the first seconds for a wide range of parameter space. Furthermore, we suggest that the KN effect can explain the somewhat faster-than-expected decay of the early-time high-energy emission observed in GRB090510 and GRB090902B.

scholarly journals Large area detector of low-energy gamma radiation

2017 ◽  
Vol 24 (4) ◽  
pp. 678-681
Author(s):  
T.A. Nepokupnaya ◽  
Keyword(s):  
Gamma Radiation ◽  
Low Energy ◽  
Large Area ◽  
Area Detector ◽  
Energy Gamma ◽  
Large Area Detector

scholarly journals BL-11C Micro-MX: a high-flux microfocus macromolecular-crystallography beamline for micrometre-sized protein crystals at Pohang Light Source II

2021 ◽  
Vol 28 (4) ◽  
Author(s):  
Do-Heon Gu ◽  
Cheolsoo Eo ◽  
Seung-A Hwangbo ◽  
Sung-Chul Ha ◽  
Jin Hong Kim ◽  
...  
Keyword(s):  
Technical Information ◽  
Photon Flux ◽  
Macromolecular Crystallography ◽  
Wide Range ◽  
Multi Wavelength ◽  
Pohang Light Source ◽  
Sample Position ◽  
Sample Exchanger ◽  
New Protein

BL-11C, a new protein crystallography beamline, is an in-vacuum undulator-based microfocus beamline used for macromolecular crystallography at the Pohang Accelerator Laboratory and it was made available to users in June 2017. The beamline is energy tunable in the range 5.0–20 keV to support conventional single- and multi-wavelength anomalous-dispersion experiments against a wide range of heavy metals. At the standard working energy of 12.659 keV, the monochromated beam is focused to 4.1 µm (V) × 8.5 µm (H) full width at half-maximum at the sample position and the measured photon flux is 1.3 × 1012 photons s−1. The experimental station is equipped with a Pilatus3 6M detector, a micro-diffractometer (MD2S) incorporating a multi-axis goniometer, and a robotic sample exchanger (CATS) with a dewar capacity of 90 samples. This beamline is suitable for structural determination of weakly diffracting crystalline substances, such as biomaterials, including protein, nucleic acids and their complexes. In addition, serial crystallography experiments for determining crystal structures at room temperature are possible. Herein, the current beamline characteristics, technical information for users and some recent scientific highlights are described.

Direct STEM ADF imaging of gold on silicon (111)

1989 ◽  
Vol 47 ◽  
pp. 472-473
Author(s):  
P. Xu ◽  
E. J. Kirkland ◽  
J. Silcox
Keyword(s):  
Film Growth ◽  
Heavy Atom ◽  
High Vacuum ◽  
Dark Field ◽  
Thin Metal Film ◽  
Base Pressure ◽  
Ultra High Vacuum ◽  
Specimen Preparation ◽  
Dark Field Imaging ◽  
Wide Range

Many studies of thin metal film growth and the formation of metal-semiconductor contacts have been performed using a wide range of experimental methods. STEM annular dark field imaging could be an important complement since it may allow direct imaging of a single heavy atom on a thin silicon substrate. This would enable studies of the local atomic arrangements and defects in the initial stage of metal silicide formation.Preliminary experiments were performed in an ultra-high vacuum VG HB501A STEM with a base pressure of 1 × 10-10 mbar. An antechamber directly attached to the microscope for specimen preparation has a base pressure of 2×l0-10 mbar. A thin single crystal membrane was fabricated by anodic etching and subsequent reactive etching. The specimen was cleaned by the Shiraki method and had a very thin oxide layer left on the surface. 5 Å of gold was deposited on the specimen at room temperature from a tungsten filament coil monitored by a quartz crystal monitor.

Understanding Conformational Entropy in Small Molecules

2020 ◽  
Author(s):  
Lucian Chan ◽  
Garrett Morris ◽  
Geoffrey Hutchison
Keyword(s):  
Small Molecules ◽  
Degrees Of Freedom ◽  
Absolute Error ◽  
Low Energy ◽  
Standard Entropy ◽  
Free Energies ◽  
Conformational Entropy ◽  
Wide Range ◽  
High Degree ◽  
Empirical Corrections

The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers grows exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, including performing thermochemistry calculations with all possible stable conformations, and developing empirical corrections from experimental data. We have performed conformer sampling on over 120,000 small molecules generating some 12 million conformers, to develop models to predict conformational entropy across a wide range of molecules. Using insight into the nature of conformational disorder, our cross-validated physically-motivated statistical model can outperform common machine learning and deep learning methods, with a mean absolute error ≈4.8 J/mol•K, or under 0.4 kcal/mol at 300 K. Beyond predicting molecular entropies and free energies, the model implies a high degree of correlation between torsions in most molecules, often as- sumed to be independent. While individual dihedral rotations may have low energetic barriers, the shape and chemical functionality of most molecules necessarily correlate their torsional degrees of freedom, and hence restrict the number of low-energy conformations immensely. Our simple models capture these correlations, and advance our understanding of small molecule conformational entropy.

scholarly journals Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

2021 ◽  
Vol 22 (15) ◽  
pp. 7879
Author(s):  
Yingxia Gao ◽  
Yi Zheng ◽  
Léon Sanche
Keyword(s):  
Condensed Phase ◽  
Genetic Material ◽  
High Energy ◽  
Dna Lesions ◽  
Low Energy ◽  
Experimental Investigations ◽  
Experimental Conditions ◽  
Strand Breaks ◽  
Sequence Of Events ◽  
Wide Range

The complex physical and chemical reactions between the large number of low-energy (0–30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.

scholarly journals The Growth of Semiconductor Thin Films Studied by RHEED

1990 ◽  
Vol 43 (5) ◽  
pp. 583
Author(s):  
GL Price
Keyword(s):  
Thin Films ◽  
Surface Science ◽  
High Vacuum ◽  
High Energy ◽  
Ultra High Vacuum ◽  
Large Area ◽  
Growth Modes ◽  
Semiconductor Thin Films ◽  
Wide Range ◽  
Recent Developments

Recent developments in the growth of semiconductor thin films are reviewed. The emphasis is on growth by molecular beam epitaxy (MBE). Results obtained by reflection high energy electron diffraction (RHEED) are employed to describe the different kinds of growth processes and the types of materials which can be constructed. MBE is routinely capable of heterostructure growth to atomic precision with a wide range of materials including III-V, IV, II-VI semiconductors, metals, ceramics such as high Tc materials and organics. As the growth proceeds in ultra high vacuum, MBE can take advantage of surface science techniques such as Auger, RHEED and SIMS. RHEED is the essential in-situ probe since the final crystal quality is strongly dependent on the surface reconstruction during growth. RHEED can also be used to calibrate the growth rate, monitor growth kinetics, and distinguish between various growth modes. A major new area is lattice mismatched growth where attempts are being made to construct heterostructures between materials of different lattice constants such as GaAs on Si. Also described are the new techniques of migration enhanced epitaxy and tilted superlattice growth. Finally some comments are given On the means of preparing large area, thin samples for analysis by other techniques from MBE grown films using capping, etching and liftoff.

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