scholarly journals Recent Advances in X-Ray Hydroxyl Radical Footprinting at the Advanced Light Source Synchrotron

2019 ◽  
Vol 26 (1) ◽  
pp. 70-75 ◽  
Author(s):  
Simon A. Morton ◽  
Sayan Gupta ◽  
Christopher J. Petzold ◽  
Corie Y. Ralston
Keyword(s):  
Hydroxyl Radical ◽  
Light Source ◽  
Conformational Changes ◽  
National Laboratory ◽  
Structural Features ◽  
Brookhaven National Laboratory ◽  
Structural Method ◽  
Response Curves ◽  
Advanced Light Source ◽  
Hydroxyl Radical Footprinting

Background: Synchrotron hydroxyl radical footprinting is a relatively new structural method used to investigate structural features and conformational changes of nucleic acids and proteins in the solution state. It was originally developed at the National Synchrotron Light Source at Brookhaven National Laboratory in the late nineties, and more recently, has been established at the Advanced Light Source at Lawrence Berkeley National Laboratory. The instrumentation for this method is an active area of development, and includes methods to increase dose to the samples while implementing high-throughput sample delivery methods. Conclusion: Improving instrumentation to irradiate biological samples in real time using a sample droplet generator and inline fluorescence monitoring to rapidly determine dose response curves for samples will significantly increase the range of biological problems that can be investigated using synchrotron hydroxyl radical footprinting.

scholarly journals Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

2013 ◽  
Vol 46 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Scott Classen ◽  
Greg L. Hura ◽  
James M. Holton ◽  
Robert P. Rambo ◽  
Ivan Rodic ◽  
...  
Keyword(s):  
Data Collection ◽  
Light Source ◽  
Small Angle ◽  
National Laboratory ◽  
Department Of Energy ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
X Ray Scattering ◽  
Advanced Light Source ◽  
Ray Scattering

The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B4C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.

Development and testing of stable supports for the National Synchrotron Light Source II RF beam position monitors

2010 ◽  
Vol 1 (MEDSI-6) ◽  
Author(s):  
B. Kosciuk ◽  
V. Ravindranath ◽  
O. Singh ◽  
S. Sharma
Keyword(s):  
Light Source ◽  
Coefficient Of Thermal Expansion ◽  
National Laboratory ◽  
Brookhaven National Laboratory ◽  
National Synchrotron Light Source ◽  
Beam Position ◽  
Vacuum Chambers ◽  
Synchrotron Light ◽  
Under Construction ◽  
Beam Position Monitors

The National Synchrotron Light Source II currently under construction at the Brookhaven National Laboratory is expected to provide unprecedented orbit stability in the storage ring in order to fully utilize the very small emittance of the electron beam. The desire to measure the position of such small beams to high resolution imposes stringent requirements on the thermal and structural stability of the supports for the beam postion monitor (BPM) pick-up electrodes located on multi-pole vacuum chambers and more so on those located upstream and downstream of insertion device sources where the beam size is the smallest. Even with tunnel air temperature expected to be controlled to ±0.1°C, low coefficient of thermal expansion materials is required to meet this level of thermal stability. Here, we present the application of these materials to the design of stable supports for radio frequency (RF)-BPMs as well as the methods of testing their performance.

A SOFT X-RAY UNDULATOR BEAMLINE AT THE ADVANCED LIGHT SOURCE WITH CIRCULAR AND VARIABLE LINEAR POLARIZATION FOR THE SPECTROSCOPY AND MICROSCOPY OF MAGNETIC MATERIALS

2002 ◽  
Vol 09 (01) ◽  
pp. 549-554 ◽  
Author(s):  
ANTHONY T. YOUNG ◽  
ELKE ARENHOLZ ◽  
JUN FENG ◽  
HOWARD PADMORE ◽  
STEVE MARKS ◽  
...  
Keyword(s):  
Light Source ◽  
National Laboratory ◽  
X Rays ◽  
X Ray ◽  
Advanced Light Source ◽  
Linearly Polarized ◽  
Linearly Polarized Radiation ◽  
Elliptically Polarized ◽  
Photoemission Electron ◽  
Polarized Radiation

A new undulator beamline at the Advanced Light Source, Lawrence Berkeley National Laboratory is described. This new beamline has an Apple II type undulator which produces linearly and elliptically polarized X-rays. A high resolution monochromator directs the radiation to two branchlines. The first branchline is optimized for spectroscopy and accommodates multiple endstations simultaneously. The second branchline features a photoemission electron microscope. A novel feature of the beamline is the ability to produce linearly polarized radiation at arbitrary, user-selectable angles. Applications of the new beamline are also described.

Overview of diagnostics and instrumentation for National Synchrotron Light Source II

2010 ◽  
Vol 1 (MEDSI-6) ◽  
Author(s):  
B. Kosciuk ◽  
A. Blednykh ◽  
D. Padrazo ◽  
O. Singh
Keyword(s):  
Light Source ◽  
State Of The Art ◽  
National Laboratory ◽  
Brookhaven National Laboratory ◽  
Beam Diagnostics ◽  
Third Generation ◽  
National Synchrotron Light Source ◽  
Beam Stability ◽  
Synchrotron Light ◽  
Under Construction

National Synchrotron Light Source II (NSLS-II), a new state-of-the-art third-generation light source under construction at Brookhaven National Laboratory is expected to have extremely small emittance and extraordinary beam stability. The mechanical requirements for beam diagnostics and instrumentation are exceptionally challenging. Here we present an overview of the mechanical aspects of some NSLS-II diagnostics as well as the performance levels of some systems currently under development.

scholarly journals Biological soft X-ray tomography on beamline 2.1 at the Advanced Light Source

2014 ◽  
Vol 21 (6) ◽  
pp. 1370-1377 ◽  
Author(s):  
Mark A. Le Gros ◽  
Gerry McDermott ◽  
Bertrand P. Cinquin ◽  
Elizabeth A. Smith ◽  
Myan Do ◽  
...  
Keyword(s):  
Data Collection ◽  
Light Source ◽  
Mammalian Cells ◽  
National Laboratory ◽  
Three Dimensional ◽  
Imaging Method ◽  
X Rays ◽  
X Ray ◽  
Correlative Imaging ◽  
Advanced Light Source

Beamline 2.1 (XM-2) is a transmission soft X-ray microscope in sector 2 of the Advanced Light Source at Lawrence Berkeley National Laboratory. XM-2 was designed, built and is now operated by the National Center for X-ray Tomography as a National Institutes of Health Biomedical Technology Research Resource. XM-2 is equipped with a cryogenic rotation stage to enable tomographic data collection from cryo-preserved cells, including large mammalian cells. During data collection the specimen is illuminated with `water window' X-rays (284–543 eV). Illuminating photons are attenuated an order of magnitude more strongly by biomolecules than by water. Consequently, differences in molecular composition generate quantitative contrast in images of the specimen. Soft X-ray tomography is an information-rich three-dimensional imaging method that can be applied either as a standalone technique or as a component modality in correlative imaging studies.

scholarly journals A cantilevered liquid-nitrogen-cooled silicon mirror for the Advanced Light Source Upgrade

2020 ◽  
Vol 27 (5) ◽  
pp. 1131-1140 ◽  
Author(s):  
Grant Cutler ◽  
Daniele Cocco ◽  
Elaine DiMasi ◽  
Simon Morton ◽  
Manuel Sanchez del Rio ◽  
...  
Keyword(s):  
Liquid Nitrogen ◽  
Light Source ◽  
National Laboratory ◽  
Lawrence Berkeley National Laboratory ◽  
Strehl Ratio ◽  
X Ray ◽  
Polarization Control ◽  
Insertion Device ◽  
Entire Energy ◽  
Advanced Light Source

This paper presents a novel cantilevered liquid-nitrogen-cooled silicon mirror design for the first optic in a new soft X-ray beamline that is being developed as part of the Advanced Light Source Upgrade (ALS-U) (Lawrence Berkeley National Laboratory, USA). The beamline is optimized for photon energies between 400 and 1400 eV with full polarization control. Calculations indicate that, without correction, this design will achieve a Strehl ratio greater than 0.85 for the entire energy and polarization ranges of the beamline. With a correction achieved by moving the focus 7.5 mm upstream, the minimum Strehl ratio is 0.99. This design is currently the baseline plan for all new ALS-U insertion device beamlines.

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