In-vacuum long-wavelength macromolecular crystallography.

Science.gov (United States)

Wagner, Armin; Duman, Ramona; Henderson, Keith; Mykhaylyk, Vitaliy

2016-03-01

Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline.

AR-NE3A, a New Macromolecular Crystallography Beamline for Pharmaceutical Applications at the Photon Factory

International Nuclear Information System (INIS)

Yamada, Yusuke; Hiraki, Masahiko; Sasajima, Kumiko; Matsugaki, Naohiro; Igarashi, Noriyuki; Kikuchi, Takashi; Mori, Takeharu; Toyoshima, Akio; Kishimoto, Shunji; Wakatsuki, Soichi; Amano, Yasushi; Warizaya, Masaichi; Sakashita, Hitoshi

2010-01-01

Recent advances in high-throughput techniques for macromolecular crystallography have highlighted the importance of structure-based drug design (SBDD), and the demand for synchrotron use by pharmaceutical researchers has increased. Thus, in collaboration with Astellas Pharma Inc., we have constructed a new high-throughput macromolecular crystallography beamline, AR-NE3A, which is dedicated to SBDD. At AR-NE3A, a photon flux up to three times higher than those at existing high-throughput beams at the Photon Factory, AR-NW12A and BL-5A, can be realized at the same sample positions. Installed in the experimental hutch are a high-precision diffractometer, fast-readout, high-gain CCD detector, and sample exchange robot capable of handling more than two hundred cryo-cooled samples stored in a Dewar. To facilitate high-throughput data collection required for pharmaceutical research, fully automated data collection and processing systems have been developed. Thus, sample exchange, centering, data collection, and data processing are automatically carried out based on the user's pre-defined schedule. Although Astellas Pharma Inc. has a priority access to AR-NE3A, the remaining beam time is allocated to general academic and other industrial users.

The bio-crystallography beamline (BL41XU) at SPring-8

CERN Document Server

Kawamoto, M; Kamiya, N

2001-01-01

The bio-crystallography beamline (BL41XU), one of two pilot beamlines at SPring-8, was constructed using a standard in-vacuum-type undulator and opened for general users from domestic and overseas countries. Many tests and improvements were carried out on beamline elements and equipment for macromolecular crystallography, especially on the so-called 'pin-post' water cooling crystal of rotated-inclined double crystal monochromator. The maximum brilliance at sample position reached to 4x10 sup 1 sup 5 photons/s/mm sup 2 /mrad sup 2 at an X-ray energy of 11 keV. Commercially available X-ray detectors of CCD and imaging plate were installed in the experimental station. A beamline control software system for beam tracking and an on-line reader for large-format imaging plate were newly developed.

New Paradigm for Macromolecular Crystallography Experiments at SSRL: Automated Crystal Screening And Remote Data Collection

International Nuclear Information System (INIS)

Soltis, S.M.; Cohen, A.E.; Deacon, A.; Eriksson, T.; Gonzalez, A.; McPhillips, S.; Chui, H.; Dunten, P.; Hollenbeck, M.; Mathews, I.; Miller, M.; Moorhead, P.; Phizackerley, R.P.; Smith, C.; Song, J.; Bedem, H. van dem; Ellis, P.; Kuhn, P.; McPhillips, T.; Sauter, N.; Sharp, K.

2009-01-01

Complete automation of the macromolecular crystallography experiment has been achieved at Stanford Synchrotron Radiation Lightsource (SSRL) through the combination of robust mechanized experimental hardware and a flexible control system with an intuitive user interface. These highly reliable systems have enabled crystallography experiments to be carried out from the researchers' home institutions and other remote locations while retaining complete control over even the most challenging systems. A breakthrough component of the system, the Stanford Auto-Mounter (SAM), has enabled the efficient mounting of cryocooled samples without human intervention. Taking advantage of this automation, researchers have successfully screened more than 200 000 samples to select the crystals with the best diffraction quality for data collection as well as to determine optimal crystallization and cryocooling conditions. These systems, which have been deployed on all SSRL macromolecular crystallography beamlines and several beamlines worldwide, are used by more than 80 research groups in remote locations, establishing a new paradigm for macromolecular crystallography experimentation.

Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline.

Science.gov (United States)

Shimizu, Nobutaka; Shimizu, Tetsuya; Baba, Seiki; Hasegawa, Kazuya; Yamamoto, Masaki; Kumasaka, Takashi

2013-11-01

Measurement of the UV-visible absorption spectrum is a convenient technique for detecting chemical changes of proteins, and it is therefore useful to combine spectroscopy and diffraction studies. An online microspectrophotometer for the UV-visible region was developed and installed on the macromolecular crystallography beamline, BL38B1, at SPring-8. This spectrophotometer is equipped with a difference dispersive double monochromator, a mercury-xenon lamp as the light source, and a photomultiplier as the detector. The optical path is mostly constructed using mirrors, in order to obtain high brightness in the UV region, and the confocal optics are assembled using a cross-slit diaphragm like an iris to eliminate stray light. This system can measure optical densities up to a maximum of 4.0. To study the effect of radiation damage, preliminary measurements of glucose isomerase and thaumatin crystals were conducted in the UV region. Spectral changes dependent on X-ray dose were observed at around 280 nm, suggesting that structural changes involving Trp or Tyr residues occurred in the protein crystal. In the case of the thaumatin crystal, a broad peak around 400 nm was also generated after X-ray irradiation, suggesting the cleavage of a disulfide bond. Dose-dependent spectral changes were also observed in cryo-solutions alone, and these changes differed with the composition of the cryo-solution. These responses in the UV region are informative regarding the state of the sample; consequently, this device might be useful for X-ray crystallography.

10 years of protein crystallography at AR-NW12A beamline

Science.gov (United States)

Chavas, L. M. G.; Yamada, Y.; Hiraki, M.; Igarashi, N.; Matsugaki, N.; Wakatsuki, S.

2013-03-01

The exponential growth of protein crystallography can be observed in the continuously increasing demand for synchrotron beam time, both from academic and industrial users. Nowadays, the screening of a profusion of sample crystals for more and more projects is being implemented by taking advantage of fully automated procedures at every level of the experiments. The insertion device AR-NW12A beamline is one of the five macromolecular crystallography (MX) beamlines at the Photon Factory (PF). Currently the oldest MX beamline operational at the High Energy Accelerator Research Organization (KEK), the end-station was launched in 2001 as part of an upgrade of the PF Advanced Ring. Since its commissioning, AR-NW12A has been operating as a high-throughput beamline, slowly evolving to a multipurpose end-station for MX experiments. The development of the beamline took place about a decade ago, in parallel with a drastic development of protein crystallography and more general synchrotron technology. To keep the beamline up-to-date and competitive with other MX stations in Japan and worldwide, new features have been constantly added, with the goal of user friendliness of the various beamline optics and other instruments. Here we describe the evolution of AR-NW12A for its tenth anniversary. We also discuss the plans for upgrades for AR-NW12A, the future objectives in terms of the beamline developments, and especially the strong desire to open the beamline to a larger user community.

JBluIce-EPICS control system for macromolecular crystallography

International Nuclear Information System (INIS)

Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J.L.; Fischetti, R.F.

2011-01-01

The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline component. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallographic experiments, especially in the field of microcrystallography.

An acoustic on-chip goniometer for room temperature macromolecular crystallography.

Science.gov (United States)

Burton, C G; Axford, D; Edwards, A M J; Gildea, R J; Morris, R H; Newton, M I; Orville, A M; Prince, M; Topham, P D; Docker, P T

2017-12-05

This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

International Nuclear Information System (INIS)

Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

2013-01-01

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully

Macromolecular crystallography using synchrotron radiation

International Nuclear Information System (INIS)

Bartunik, H.D.; Phillips, J.C.; Fourme, R.

1982-01-01

The use of synchrotron X-ray sources in macromolecular crystallography is described. The properties of synchrotron radiation relevant to macromolecular crystallography are examined. The applications discussed include anomalous dispersion techniques, the acquisition of normal and high resolution data, and kinetic studies of structural changes in macromolecules; protein data are presented illustrating these applications. The apparatus used is described including information on the electronic detectors, the monitoring of the incident beam and crystal cooling. (U.K.)

Outrunning free radicals in room-temperature macromolecular crystallography

International Nuclear Information System (INIS)

Owen, Robin L.; Axford, Danny; Nettleship, Joanne E.; Owens, Raymond J.; Robinson, James I.; Morgan, Ann W.; Doré, Andrew S.; Lebon, Guillaume; Tate, Christopher G.; Fry, Elizabeth E.; Ren, Jingshan; Stuart, David I.; Evans, Gwyndaf

2012-01-01

A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector. A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A 2A adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macromolecular crystallography

Outrunning free radicals in room-temperature macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Owen, Robin L., E-mail: robin.owen@diamond.ac.uk; Axford, Danny [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Nettleship, Joanne E.; Owens, Raymond J. [Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Robinson, James I.; Morgan, Ann W. [University of Leeds, Leeds LS9 7FT (United Kingdom); Doré, Andrew S. [Heptares Therapeutics Ltd, BioPark, Welwyn Garden City AL7 3AX (United Kingdom); Lebon, Guillaume; Tate, Christopher G. [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom); Fry, Elizabeth E.; Ren, Jingshan [The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Evans, Gwyndaf [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

2012-06-15

A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector. A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A{sub 2A} adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macromolecular crystallography.

ISPyB: an information management system for synchrotron macromolecular crystallography.

Science.gov (United States)

Delagenière, Solange; Brenchereau, Patrice; Launer, Ludovic; Ashton, Alun W; Leal, Ricardo; Veyrier, Stéphanie; Gabadinho, José; Gordon, Elspeth J; Jones, Samuel D; Levik, Karl Erik; McSweeney, Seán M; Monaco, Stéphanie; Nanao, Max; Spruce, Darren; Svensson, Olof; Walsh, Martin A; Leonard, Gordon A

2011-11-15

Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

International Nuclear Information System (INIS)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L.; Armour, Wes; Waterman, David G.; Iwata, So; Evans, Gwyndaf

2013-01-01

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Aller, Pierre [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz; Cameron, Alex [Imperial College, London SW7 2AZ (United Kingdom); Axford, Danny; Owen, Robin L. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Armour, Wes [Oxford e-Research Centre (OeRC), Keble Road, Oxford OX1 3QG (United Kingdom); Waterman, David G. [Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

2013-08-01

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

NSLS-II biomedical beamlines for micro-crystallography, FMX, and for highly automated crystallography, AMX: New opportunities for advanced data collection

Energy Technology Data Exchange (ETDEWEB)

Fuchs, Martin R., E-mail: mfuchs@bnl.gov; Bhogadi, Dileep K.; Jakoncic, Jean; Myers, Stuart; Sweet, Robert M.; Berman, Lonny E.; Skinner, John; Idir, Mourad; Chubar, Oleg; McSweeney, Sean; Schneider, Dieter K. [National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973 (United States)

2016-07-27

We present the final design of the x-ray optics and experimental stations of two macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source-II. The microfocusing FMX beamline will deliver a flux of ∼5×10{sup 12} ph/s at 1 Å into a 1 – 20 µm spot, its flux density surpassing current MX beamlines by up to two orders of magnitude. It covers an energy range from 5 – 30 keV. The highly automated AMX beamline is optimized for high throughput, with beam sizes from 4 – 100 µm, an energy range of 5 – 18 keV and a flux at 1 Å of ∼10{sup 13} ph/s. A focus in designing the beamlines lay on achieving high beam stability, for example by implementing a horizontal bounce double crystal monochromator at FMX. A combination of compound refractive lenses and bimorph mirror optics at FMX supports rapid beam size changes. Central components of the in-house developed experimental stations are horizontal axis goniometers with a target sphere of confusion of 100 nm, piezo-slits for dynamic beam size changes during diffraction experiments, dedicated secondary goniometers for data collection from specimen in crystallization plates, and next generation pixel array detectors. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and room temperature data collection of crystals in trays.

Facilities for small-molecule crystallography at synchrotron sources.

Science.gov (United States)

Barnett, Sarah A; Nowell, Harriott; Warren, Mark R; Wilcox, Andrian; Allan, David R

2016-01-01

Although macromolecular crystallography is a widely supported technique at synchrotron radiation facilities throughout the world, there are, in comparison, only very few beamlines dedicated to small-molecule crystallography. This limited provision is despite the increasing demand for beamtime from the chemical crystallography community and the ever greater overlap between systems that can be classed as either small macromolecules or large small molecules. In this article, a very brief overview of beamlines that support small-molecule single-crystal diffraction techniques will be given along with a more detailed description of beamline I19, a dedicated facility for small-molecule crystallography at Diamond Light Source.

The protein micro-crystallography beamlines for targeted protein research program

International Nuclear Information System (INIS)

Hirata, Kunio; Yamamoto, Masaki; Matsugaki, Naohiro; Wakatsuki, Soichi

2010-01-01

In order to collect proper diffraction data from outstanding micro-crystals, a brand-new data collection system should be designed to provide high signal-to noise ratio in diffraction images. SPring-8 and KEK-PF are currently developing two micro-beam beamlines for Targeted Proteins Research Program by MEXT of Japan. The program aims to reveal the structure and function of proteins that are difficult to solve but have great importance in both academic research and industrial application. At SPring-8, a new 1-micron beam beamline for protein micro-crystallography, RIKEN Targeted Proteins Beamline (BL32XU), is developed. At KEK-PF a new low energy micro-beam beamline, BL-1A, is dedicated for SAD micro-crystallography. The two beamlines will start operation in the end of 2010. The present status of the research and development for protein micro-crystallography will be presented. (author)

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography.

Science.gov (United States)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L; Armour, Wes; Waterman, David G; Iwata, So; Evans, Gwyndaf

2013-08-01

The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

Conceptual design report for the high-throughput macromolecular crystallography beamline at the Indus-2

International Nuclear Information System (INIS)

Kumar, Ashwani; Jagannath

2007-07-01

Studies aimed at understanding the functionality of several bio-molecules as well as related efficacy of drugs necessitate determination of the structure of relevant molecules. Based on the presumption that the structure of these molecules does not undergo any dramatic change on crystallization, these structures are being reliably determined with the help of x-ray diffraction technique. With the availability of intense x-ray beams from the synchrotrons, along with the tunability of the x-ray energies, the progress in this field has been phenomenal. Presently, all over the world, most of the high quality investigations in this field are being carried out at the synchrotron sources. So as to facilitate the scientists working in this field in India, we at BARC have undertaken to build a protein crystallography beamline for Indus-2 synchrotron. In this report we present the design features of this beamline as determined through our extensive calculations. (author)

Quickly Getting the Best Data from Your Macromolecular Crystals with a New Generation of Beamline Instruments

International Nuclear Information System (INIS)

Cipriani, Florent; Felisaz, Franck; Lavault, Bernard; Brockhauser, Sandor; Ravelli, Raimond; Launer, Ludovic; Leonard, Gordon; Renier, Michel

2007-01-01

While routine Macromolecular x-ray (MX) crystallography has relied on well established techniques for some years all the synchrotrons around the world are improving the throughput of their MX beamlines. Third generation synchrotrons provide small intense beams that make data collection of 5-10 microns sized crystals possible. The EMBL/ESRF MX Group in Grenoble has developed a new generation of instruments to easily collect data on 10 μm size crystals in an automated environment. This work is part of the Grenoble automation program that enables FedEx like crystallography using fully automated data collection and web monitored experiments. Seven ESRF beamlines and the MRC BM14 ESRF/CRG beamline are currently equipped with these latest instruments. We describe here the main features of the MD2x diffractometer family and the SC3 sample changer robot. Although the SC3 was primarily designed to increase the throughput of MX beamlines, it has also been shown to be efficient in improving the quality of the data collected. Strategies in screening a large number of crystals, selecting the best, and collecting a full data set from several re-oriented micro-crystals can now be run with minimum time and effort. The MD2x and SC3 instruments are now commercialised by the company ACCEL GmbH

Status and prospects of macromolecular crystallography

Indian Academy of Sciences (India)

technique that could be completely automated in most cases. ... major challenge in macromolecular crystallography today is ... tial characterization of crystals in the home source and make a ... opportunities for a generation of structural biolo-.

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

Science.gov (United States)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L.; Armour, Wes; Waterman, David G.; Iwata, So; Evans, Gwyndaf

2013-01-01

The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein. PMID:23897484

Macromolecular crystallography with a large format CMOS detector

Energy Technology Data Exchange (ETDEWEB)

Nix, Jay C., E-mail: jcnix@lbl.gov [Molecular Biology Consortium 12003 S. Pulaski Rd. #166 Alsip, IL 60803 U.S.A (United States)

2016-07-27

Recent advances in CMOS technology have allowed the production of large surface area detectors suitable for macromolecular crystallography experiments [1]. The Molecular Biology Consortium (MBC) Beamline 4.2.2 at the Advanced Light Source in Berkeley, CA, has installed a 2952 x 2820 mm RDI CMOS-8M detector with funds from NIH grant S10OD012073. The detector has a 20nsec dead pixel time and performs well with shutterless data collection strategies. The sensor obtains sharp point response and minimal optical distortion by use of a thin fiber-optic plate between the phosphor and sensor module. Shutterless data collections produce high-quality redundant datasets that can be obtained in minutes. The fine-sliced data are suitable for processing in standard crystallographic software packages (XDS, HKL2000, D*TREK, MOSFLM). Faster collection times relative to the previous CCD detector have resulted in a record number of datasets collected in a calendar year and de novo phasing experiments have resulted in publications in both Science and Nature [2,3]. The faster collections are due to a combination of the decreased overhead requirements of shutterless collections combined with exposure times that have decreased by over a factor of 2 for images with comparable signal to noise of the NOIR-1 detector. The overall increased productivity has allowed the development of new beamline capabilities and data collection strategies.

SPring-8 Structural Biology Beamlines / Current Status of Public Beamlines for Protein Crystallography at SPring-8

International Nuclear Information System (INIS)

Kawamoto, Masahide; Hasegawa, Kazuya; Shimizu, Nobutaka; Sakai, Hisanobu; Shimizu, Tetsuya; Nisawa, Atsushi; Yamamoto, Masaki

2007-01-01

SPring-8 has 2 protein crystallography beamlines for public use, BL38B1 (Structural Biology III) and BL41XU (Structural Biology I). The BL38B1 is a bending magnet beamline for routine data collection, and the BL41XU is an undulator beamline specially customized for micro beam and ultra-high resolutional experiment. The designs and the performances of each beamline are presented

Distributed control of protein crystallography beamline 5.0 using CORBA

International Nuclear Information System (INIS)

Timossi, Chris

1999-01-01

The Protein Crystallography Beamline at Berkeley Lab's Advanced Light Source is a facility that is being used to solve the structure of proteins. The software that is being used to control this beamline uses Java for user interface applications which communicate via CORBA with workstations that control the beamline hardware. We describe the software architecture for the beamline and our experiences after two years of operation

Macromolecular neutron crystallography at the Protein Crystallography Station (PCS)

OpenAIRE

Kovalevsky, Andrey; Fisher, Zoe; Johnson, Hannah; Mustyakimov, Marat; Waltman, Mary Jo; Langan, Paul

2010-01-01

The Protein Crystallography Station user facility at Los Alamos National Laboratory not only offers open access to a high-performance neutron beamline, but also actively supports and develops new methods in protein expression, deuteration, purification, robotic crystallization and the synthesis of substrates with stable isotopes and provides assistance with data-reduction and structure-refinement software and comprehensive neutron structure analysis.

A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source

International Nuclear Information System (INIS)

Pompidor, Guillaume; Dworkowski, Florian S. N.; Thominet, Vincent; Schulze-Briese, Clemens; Fuchs, Martin R.

2013-01-01

The new version MS2 of the in situ on-axis micro-spectrophotometer at the macromolecular crystallography beamline X10SA of the Swiss Light Source supports the concurrent acquisition of Raman, resonance Raman, fluorescence and UV/Vis absorption spectra along with diffraction data. The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years

Design of a High-Throughput Biological Crystallography Beamline for Superconducting Wiggler

International Nuclear Information System (INIS)

Tseng, P.C.; Chang, C.H.; Fung, H.S.; Ma, C.I.; Huang, L.J.; Jean, Y.C.; Song, Y.F.; Huang, Y.S.; Tsang, K.L.; Chen, C.T.

2004-01-01

We are constructing a high-throughput biological crystallography beamline BL13B, which utilizes the radiation generated from a 3.2 Tesla, 32-pole superconducting multipole wiggler, for multi-wavelength anomalous diffraction (MAD), single-wavelength anomalous diffraction (SAD), and other related experiments. This beamline is a standard double crystal monochromator (DCM) x-ray beamline equipped with a collimating mirror (CM) and a focusing mirror (FM). Both the CM and FM are one meter long and made of Si substrate, and the CM is side-cooled by water. Based on detailed thermal analysis, liquid nitrogen (LN2) cooling for both crystals of the DCM has been adopted to optimize the energy resolution and photon beam throughput. This beamline will deliver, through a 100 μm diameter pinhole, photon flux of greater than 1011 photons/sec in the energy range from 6.5 keV to 19 keV, which is comparable to existing protein crystallography beamlines from bending magnet source at high energy storage rings

Protein crystallography beamline (PX-BL21); its utilization and research highlights

International Nuclear Information System (INIS)

Kumar, Ashwani; Ghosh, Biplab; Singh, Rahul; Makde, Ravindra; Sharma, Surinder M.

2016-01-01

The protein crystallography beamline (PX-BL21) is sourced on 1.5 T bending magnet of 2.5 GeV Indus-2 synchrotron. This beamline has been designed to perform monochromatic and anomalous diffraction experiments on single crystals of biological macromolecules such as protein, DNA and their complexes. PX beamline also has a state-of-art ancillary biochemical laboratory to prepare single crystals of biological macromolecules. Since the commissioning of the beamline, it has been utilized by more than 70% of research groups working in the area of protein crystallography in India. About 30 crystal structures of proteins, determined using this beamline, have been deposited in Protein Data Bank (PDB). Some of these structures have been determined using experimental phasing, such as the single wavelength anomalous diffraction (SAD) experiments. The energy tunability of the synchrotron have been exploited to carry our various SAD experiments: Selenium-SAD, Zinc-SAD and Manganese-SAD and Sulphar-SAD. In the present talk, the key results from the PX-BL21 beamline will be discussed. (author)

Acoustic methods for high-throughput protein crystal mounting at next-generation macromolecular crystallographic beamlines.

Science.gov (United States)

Roessler, Christian G; Kuczewski, Anthony; Stearns, Richard; Ellson, Richard; Olechno, Joseph; Orville, Allen M; Allaire, Marc; Soares, Alexei S; Héroux, Annie

2013-09-01

To take full advantage of advanced data collection techniques and high beam flux at next-generation macromolecular crystallography beamlines, rapid and reliable methods will be needed to mount and align many samples per second. One approach is to use an acoustic ejector to eject crystal-containing droplets onto a solid X-ray transparent surface, which can then be positioned and rotated for data collection. Proof-of-concept experiments were conducted at the National Synchrotron Light Source on thermolysin crystals acoustically ejected onto a polyimide `conveyor belt'. Small wedges of data were collected on each crystal, and a complete dataset was assembled from a well diffracting subset of these crystals. Future developments and implementation will focus on achieving ejection and translation of single droplets at a rate of over one hundred per second.

A pixel detector for the protein crystallography beamline at the SLS

CERN Document Server

Brönnimann, C; Eikenberry, E F; Fischer, P; Florin, S; Horisberger, R P; Lindner, Manfred; Schmitt, B; Schulze, C

2002-01-01

At the Paul Scherrer Institute a new synchrotron light source is currently under construction, the Swiss Light Source (SLS), which will be operational in summer 2001. Among the first beamlines is a high brightness, micro-focusing protein crystallography beamline. It will be equipped with a pixel detector, which has several features of interest for the next generation of protein crystallography detectors. The point spread function and the effect of charge sharing was measured with a prototype detector in a test experiment at the European Synchrotron Radiation Facility in Grenoble. The concepts of the SLS pixel detector is presented as well as test results from radiation hard prototype chips.

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

International Nuclear Information System (INIS)

Brockhauser, Sandor; Svensson, Olof; Bowler, Matthew W.; Nanao, Max; Gordon, Elspeth; Leal, Ricardo M. F.; Popov, Alexander; Gerring, Matthew; McCarthy, Andrew A.; Gotz, Andy

2012-01-01

A powerful and easy-to-use workflow environment has been developed at the ESRF for combining experiment control with online data analysis on synchrotron beamlines. This tool provides the possibility of automating complex experiments without the need for expertise in instrumentation control and programming, but rather by accessing defined beamline services. The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE

Towards a compact and precise sample holder for macromolecular crystallography.

Science.gov (United States)

Papp, Gergely; Rossi, Christopher; Janocha, Robert; Sorez, Clement; Lopez-Marrero, Marcos; Astruc, Anthony; McCarthy, Andrew; Belrhali, Hassan; Bowler, Matthew W; Cipriani, Florent

2017-10-01

Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines. This situation provided the motivation for the development of a compact and precise sample holder with corresponding pucks, handling tools and robotic transfer protocols. The development process included four main phases: design, prototype manufacture, testing with a robotic sample changer and validation under real conditions on a beamline. Two sample-holder designs are proposed: NewPin and miniSPINE. They share the same robot gripper and allow the storage of 36 sample holders in uni-puck footprint-style pucks, which represents 252 samples in a dry-shipping dewar commonly used in the field. The pucks are identified with human- and machine-readable codes, as well as with radio-frequency identification (RFID) tags. NewPin offers a crystal-repositioning precision of up to 10 µm but requires a specific goniometer socket. The storage density could reach 64 samples using a special puck designed for fully robotic handling. miniSPINE is less precise but uses a goniometer mount compatible with the current SPINE standard. miniSPINE is proposed for the first implementation of the new standard, since it is easier to integrate at beamlines. An upgraded version of the SPINE sample holder with a corresponding puck named SPINEplus is also proposed in order to offer a homogenous and interoperable system. The project involved several European synchrotrons and industrial companies in the fields of consumables and sample-changer robotics. Manual handling of mini

Development of sample exchange robot PAM-HC for beamline BL-1A at the photon factory

Energy Technology Data Exchange (ETDEWEB)

Hiraki, Masahiko, E-mail: masahiko.hiraki@kek.jp [Mechanical Engineering Center, Applied Research Laboratory, KEK (High Energy Accelerator Research Organization), 1-1 Oho, Tsukuba, Ibaraki 305-0801 Japan (Japan); Department of Accelerator Science, SOKENDAI (the Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801 Japan (Japan); Matsugaki, Naohiro; Yamada, Yusuke; Senda, Toshiya [Structural Biology research Center, Institute of Materials Structure Science, KEK (Japan); Department of Materials Structure Science, SOKENDAI (Japan)

2016-07-27

A macromolecular crystallography beamline, BL-1A, has been built at the Photon Factory (PF) for low energy experiments and has been operational since 2010. We have installed a sample exchange robot, PAM (PF Automated Mounting system), similar to other macromolecular crystallography beamlines. However, following the installation of a helium chamber to reduce the absorption of the diffraction signal by air, we developed a new sample exchange robot to replace PAM. The new robot, named PAM-HC (Helium Chamber), is designed with the goal of minimizing leakage of helium gas from the chamber. Here, the PAM-HC hardware and the flow of its movement are described. Furthermore, measurements of temperature changes during sample exchange are presented in this paper.

Development of sample exchange robot PAM-HC for beamline BL-1A at the photon factory

International Nuclear Information System (INIS)

Hiraki, Masahiko; Matsugaki, Naohiro; Yamada, Yusuke; Senda, Toshiya

2016-01-01

A macromolecular crystallography beamline, BL-1A, has been built at the Photon Factory (PF) for low energy experiments and has been operational since 2010. We have installed a sample exchange robot, PAM (PF Automated Mounting system), similar to other macromolecular crystallography beamlines. However, following the installation of a helium chamber to reduce the absorption of the diffraction signal by air, we developed a new sample exchange robot to replace PAM. The new robot, named PAM-HC (Helium Chamber), is designed with the goal of minimizing leakage of helium gas from the chamber. Here, the PAM-HC hardware and the flow of its movement are described. Furthermore, measurements of temperature changes during sample exchange are presented in this paper.

PRIGo: a new multi-axis goniometer for macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Waltersperger, Sandro; Olieric, Vincent, E-mail: vincent.olieric@psi.ch; Pradervand, Claude [Paul Scherrer Institute, Villigen PSI (Switzerland); Glettig, Wayne [Centre Suisse d’Electronique et Microtechnique SA, Neuchâtel 2002 (Switzerland); Salathe, Marco; Fuchs, Martin R.; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias [Paul Scherrer Institute, Villigen PSI (Switzerland); Schulze-Briese, Clemens [Dectris Ltd, Baden 5400 (Switzerland); Wang, Meitian, E-mail: vincent.olieric@psi.ch [Paul Scherrer Institute, Villigen PSI (Switzerland)

2015-05-09

The design and performance of the new multi-axis goniometer PRIGo developed at the Swiss Light Source at Paul Scherrer Institute is described. The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0–90°), followed by a ϕ stage (0–360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

Celebrating macromolecular crystallography: A personal perspective

Directory of Open Access Journals (Sweden)

Abad-Zapatero, Celerino

2015-04-01

Full Text Available The twentieth century has seen an enormous advance in the knowledge of the atomic structures that surround us. The discovery of the first crystal structures of simple inorganic salts by the Braggs in 1914, using the diffraction of X-rays by crystals, provided the critical elements to unveil the atomic structure of matter. Subsequent developments in the field leading to macromolecular crystallography are presented with a personal perspective, related to the cultural milieu of Spain in the late 1950’s. The journey of discovery of the author, as he developed professionally, is interwoven with the expansion of macromolecular crystallography from the first proteins (myoglobin, hemoglobin to the ‘coming of age’ of the field in 1971 and the discoveries that followed, culminating in the determination of the structure of the ribosomes at the turn of the century. A perspective is presented exploring the future of the field and also a reflection about the future generations of Spanish scientists.El siglo XX ha sido testigo del increíble avance que ha experimentado el conocimiento de la estructura atómica de la materia que nos rodea. El descubrimiento de las primeras estructuras atómicas de sales inorgánicas por los Bragg en 1914, empleando difracción de rayos X con cristales, proporcionó los elementos clave para alcanzar tal conocimiento. Posteriores desarrollos en este campo, que condujeron a la cristalografía macromolecular, se presentan aquí desde una perspectiva personal, relacionada con el contexto cultural de la España de la década de los 50. La experiencia del descubrimiento científico, durante mi desarrollo profesional, se integra en el desarrollo de la cristalografía macromolecular, desde las primeras proteínas (míoglobina y hemoglobina, hasta su madurez en 1971 que, con los posteriores descubrimientos, culmina con la determinación del la estructura del ribosoma. Asimismo, se explora el futuro de esta disciplina y se

The Joint Structural Biology Group beam lines at the ESRF: Modern macromolecular crystallography

CERN Document Server

Mitchell, E P

2001-01-01

Macromolecular crystallography has evolved considerably over the last decade. Data sets in under an hour are now possible on high throughput beam lines leading to electron density and, possibly, initial models calculated on-site. There are five beam lines currently dedicated to macromolecular crystallography: the ID14 complex and BM-14 (soon to be superseded by ID-29). These lines handle over five hundred projects every six months and demand is increasing. Automated sample handling, alignment and data management protocols will be required to work efficiently with this demanding load. Projects developing these themes are underway within the JSBG.

Macromolecular crystallography research at Trombay

International Nuclear Information System (INIS)

Kannan, K.K.; Chidamrabam, R.

1983-01-01

Neutron diffraction studies of hydrogen positions in small molecules of biological interest at Trombay have provided valuable information that has been used in protein and enzyme structure model-building and in developing hydrogen bond potential functions. The new R-5 reactor is expected to provide higher neutron fluxes and also make possible small-angle neutron scattering studies of large biomolecules and bio-aggregates. In the last few years infrastructure facilities have also been established for macromolecular x-ray crystallography research. Meanwhile, the refinement of carbonic hydrases and lyysozyme structures have been carried out and interesting results obtained on protein dynamics and structure-function relationships. Some interesting presynaptic toxin phospholipases have also taken up for study. (author)

Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

Energy Technology Data Exchange (ETDEWEB)

A Soares; D Schneider; J Skinner; M Cowan; R Buono; H Robinson; A Heroux; M Carlucci-Dayton; A Saxena; R Sweet

2011-12-31

The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

International Nuclear Information System (INIS)

Soares, A.; Schneider, D.; Skinner, J.; Cowan, M.; Buono, R.; Robinson, H.; Heroux, A.; Carlucci-Dayton, M.; Saxena, A.; Sweet, R.

2008-01-01

The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

Conceptual design of novel IP-conveyor-belt Weissenberg-mode data-collection system with multi-readers for macromolecular crystallography. A comparison between Galaxy and Super Galaxy.

Science.gov (United States)

Sakabe, N; Sakabe, K; Sasaki, K

2004-01-01

Galaxy is a Weissenberg-type high-speed high-resolution and highly accurate fully automatic data-collection system using two cylindrical IP-cassettes each with a radius of 400 mm and a width of 450 mm. It was originally developed for static three-dimensional analysis using X-ray diffraction and was installed on bending-magnet beamline BL6C at the Photon Factory. It was found, however, that Galaxy was also very useful for time-resolved protein crystallography on a time scale of minutes. This has prompted us to design a new IP-conveyor-belt Weissenberg-mode data-collection system called Super Galaxy for time-resolved crystallography with improved time and crystallographic resolution over that achievable with Galaxy. Super Galaxy was designed with a half-cylinder-shaped cassette with a radius of 420 mm and a width of 690 mm. Using 1.0 A incident X-rays, these dimensions correspond to a maximum resolutions of 0.71 A in the vertical direction and 1.58 A in the horizontal. Upper and lower screens can be used to set the frame size of the recorded image. This function is useful not only to reduce the frame exchange time but also to save disk space on the data server. The use of an IP-conveyor-belt and many IP-readers make Super Galaxy well suited for time-resolved, monochromatic X-ray crystallography at a very intense third-generation SR beamline. Here, Galaxy and a conceptual design for Super Galaxy are described, and their suitability for use as data-collection systems for macromolecular time-resolved monochromatic X-ray crystallography are compared.

Design and Construction of a High-speed Network Connecting All the Protein Crystallography Beamlines at the Photon Factory

International Nuclear Information System (INIS)

Matsugaki, Naohiro; Yamada, Yusuke; Igarashi, Noriyuki; Wakatsuki, Soichi

2007-01-01

A private network, physically separated from the facility network, was designed and constructed which covered all the four protein crystallography beamlines at the Photon Factory (PF) and Structural Biology Research Center (SBRC). Connecting all the beamlines in the same network allows for simple authentication and a common working environment for a user who uses multiple beamlines. Giga-bit Ethernet wire-speed was achieved for the communication among the beamlines and SBRC buildings

FlexED8: the first member of a fast and flexible sample-changer family for macromolecular crystallography.

Science.gov (United States)

Papp, Gergely; Felisaz, Franck; Sorez, Clement; Lopez-Marrero, Marcos; Janocha, Robert; Manjasetty, Babu; Gobbo, Alexandre; Belrhali, Hassan; Bowler, Matthew W; Cipriani, Florent

2017-10-01

Automated sample changers are now standard equipment for modern macromolecular crystallography synchrotron beamlines. Nevertheless, most are only compatible with a single type of sample holder and puck. Recent work aimed at reducing sample-handling efforts and crystal-alignment times at beamlines has resulted in a new generation of compact and precise sample holders for cryocrystallography: miniSPINE and NewPin [see the companion paper by Papp et al. (2017, Acta Cryst., D73, 829-840)]. With full data collection now possible within seconds at most advanced beamlines, and future fourth-generation synchrotron sources promising to extract data in a few tens of milliseconds, the time taken to mount and centre a sample is rate-limiting. In this context, a versatile and fast sample changer, FlexED8, has been developed that is compatible with the highly successful SPINE sample holder and with the miniSPINE and NewPin sample holders. Based on a six-axis industrial robot, FlexED8 is equipped with a tool changer and includes a novel open sample-storage dewar with a built-in ice-filtering system. With seven versatile puck slots, it can hold up to 112 SPINE sample holders in uni-pucks, or 252 miniSPINE or NewPin sample holders, with 36 samples per puck. Additionally, a double gripper, compatible with the SPINE sample holders and uni-pucks, allows a reduction in the sample-exchange time from 40 s, the typical time with a standard single gripper, to less than 5 s. Computer vision-based sample-transfer monitoring, sophisticated error handling and automatic error-recovery procedures ensure high reliability. The FlexED8 sample changer has been successfully tested under real conditions on a beamline.

A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits.

Science.gov (United States)

Jaskolski, Mariusz; Dauter, Zbigniew; Wlodawer, Alexander

2014-09-01

As a contribution to the celebration of the year 2014, declared by the United Nations to be 'The International Year of Crystallography', the FEBS Journal is dedicating this issue to papers showcasing the intimate union between macromolecular crystallography and structural biology, both in historical perspective and in current research. Instead of a formal editorial piece, by way of introduction, this review discusses the most important, often iconic, achievements of crystallographers that led to major advances in our understanding of the structure and function of biological macromolecules. We identified at least 42 scientists who received Nobel Prizes in Physics, Chemistry or Medicine for their contributions that included the use of X-rays or neutrons and crystallography, including 24 who made seminal discoveries in macromolecular sciences. Our spotlight is mostly, but not only, on the recipients of this most prestigious scientific honor, presented in approximately chronological order. As a summary of the review, we attempt to construct a genealogy tree of the principal lineages of protein crystallography, leading from the founding members to the present generation. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

WIFIP: a web-based user interface for automated synchrotron beamlines.

Science.gov (United States)

Sallaz-Damaz, Yoann; Ferrer, Jean Luc

2017-09-01

The beamline control software, through the associated graphical user interface (GUI), is the user access point to the experiment, interacting with synchrotron beamline components and providing automated routines. FIP, the French beamline for the Investigation of Proteins, is a highly automatized macromolecular crystallography (MX) beamline at the European Synchrotron Radiation Facility. On such a beamline, a significant number of users choose to control their experiment remotely. This is often performed with a limited bandwidth and from a large choice of computers and operating systems. Furthermore, this has to be possible in a rapidly evolving experimental environment, where new developments have to be easily integrated. To face these challenges, a light, platform-independent, control software and associated GUI are required. Here, WIFIP, a web-based user interface developed at FIP, is described. Further than being the present FIP control interface, WIFIP is also a proof of concept for future MX control software.

Suite of three protein crystallography beamlines with single superconducting bend magnet as the source

International Nuclear Information System (INIS)

MacDowell, Alastair A.; Celestre, Richard S.; Howells, Malcolm; McKinney, Wayne; Krupnick, James; Cambie, Daniella; Domning, Edward E; Duarte, Robert M.; Kelez, Nicholas; Plate, David W.; Cork, Carl W.; Earnest, Thomas N.; Dickert, Jeffery; Meigs, George; Ralston, Corie; Holton, James M.; Alber, Thomas; Berger, James M.; Agard, David A.; Padmore, Howard A.

2004-01-01

At the Advanced Light Source (ALS), three protein crystallography (PX) beamlines have been built that use as a source one of the three 6 Tesla single pole superconducting bending magnets (superbends) that were recently installed in the ring. The use of such single pole superconducting bend magnets enables the development of a hard x-ray program on a relatively low energy 1.9 GeV ring without taking up insertion device straight sections. The source is of relatively low power, but due to the small electron beam emittance, it has high brightness. X-ray optics are required to preserve the brightness and to match the illumination requirements for protein crystallography. This was achieved by means of a collimating premirror bent to a plane parabola, a double crystal monochromator followed by a toroidal mirror that focuses in the horizontal direction with a 2:1 demagnification. This optical arrangement partially balances aberrations from the collimating and toroidal mirrors such that a tight focused spot size is achieved. The optical properties of the beamline are an excellent match to those required by the small protein crystals that are typically measured. The design and performance of these new beamlines are described

Suite of three protein crystallography beamlines with single superconducting bend magnet as the source.

Science.gov (United States)

MacDowell, Alastair A; Celestre, Rich S; Howells, Malcolm; McKinney, Wayne; Krupnick, James; Cambie, Daniella; Domning, Edward E; Duarte, Robert M; Kelez, Nicholas; Plate, David W; Cork, Carl W; Earnest, Thomas N; Dickert, Jeffery; Meigs, George; Ralston, Corie; Holton, James M; Alber, Tom; Berger, James M; Agard, David A; Padmore, Howard A

2004-11-01

At the Advanced Light Source, three protein crystallography beamlines have been built that use as a source one of the three 6 T single-pole superconducting bending magnets (superbends) that were recently installed in the ring. The use of such single-pole superconducting bend magnets enables the development of a hard X-ray program on a relatively low-energy 1.9 GeV ring without taking up insertion-device straight sections. The source is of relatively low power but, owing to the small electron beam emittance, it has high brightness. X-ray optics are required to preserve the brightness and to match the illumination requirements for protein crystallography. This was achieved by means of a collimating premirror bent to a plane parabola, a double-crystal monochromator followed by a toroidal mirror that focuses in the horizontal direction with a 2:1 demagnification. This optical arrangement partially balances aberrations from the collimating and toroidal mirrors such that a tight focused spot size is achieved. The optical properties of the beamline are an excellent match to those required by the small protein crystals that are typically measured. The design and performance of these new beamlines are described.

Suite of three protein crystallography beamlines with single superconducting bend magnet as the source

Energy Technology Data Exchange (ETDEWEB)

MacDowell, Alastair A.; Celestre, Richard S.; Howells, Malcolm; McKinney, Wayne; Krupnick, James; Cambie, Daniella; Domning, Edward E; Duarte, Robert M.; Kelez, Nicholas; Plate, David W.; Cork, Carl W.; Earnest, Thomas N.; Dickert, Jeffery; Meigs, George; Ralston, Corie; Holton, James M.; Alber, Thomas; Berger, James M.; Agard, David A.; Padmore, Howard A.

2004-08-01

At the Advanced Light Source (ALS), three protein crystallography (PX) beamlines have been built that use as a source one of the three 6 Tesla single pole superconducting bending magnets (superbends) that were recently installed in the ring. The use of such single pole superconducting bend magnets enables the development of a hard x-ray program on a relatively low energy 1.9 GeV ring without taking up insertion device straight sections. The source is of relatively low power, but due to the small electron beam emittance, it has high brightness. X-ray optics are required to preserve the brightness and to match the illumination requirements for protein crystallography. This was achieved by means of a collimating premirror bent to a plane parabola, a double crystal monochromator followed by a toroidal mirror that focuses in the horizontal direction with a 2:1 demagnification. This optical arrangement partially balances aberrations from the collimating and toroidal mirrors such that a tight focused spot size is achieved. The optical properties of the beamline are an excellent match to those required by the small protein crystals that are typically measured. The design and performance of these new beamlines are described.

Automated data collection based on RoboDiff at the ESRF beamline MASSIF-1

Energy Technology Data Exchange (ETDEWEB)

Nurizzo, Didier, E-mail: Didier.nurizzo@esrf.fr; Guichard, Nicolas; McSweeney, Sean; Theveneau, Pascal; Guijarro, Matias; Svensson, Olof; Mueller-Dieckmann, Christoph; Leonard, Gordon [ESRF, The European Synchrotron, 71, Avenue des Martyrs,CS 40220, 38043 Grenoble (France); Bowler, Matthew W. [EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS90181, 38042 Grenoble Cedex 9 (France)

2016-07-27

The European Synchrotron Radiation Facility has a long standing history in the automation of experiments in Macromolecular Crystallography. MASSIF-1 (Massively Automated Sample Screening and evaluation Integrated Facility), a beamline constructed as part of the ESRF Upgrade Phase I program, has been open to the external user community since July 2014 and offers a unique completely automated data collection service to both academic and industrial structural biologists.

Protein crystal growth studies at the Center for Macromolecular Crystallography

International Nuclear Information System (INIS)

DeLucas, Lawrence J.; Long, Marianna M.; Moore, Karen M.; Harrington, Michael; McDonald, William T.; Smith, Craig D.; Bray, Terry; Lewis, Johanna; Crysel, William B.; Weise, Lance D.

2000-01-01

The Center for Macromolecular Crystallography (CMC) has been involved in fundamental studies of protein crystal growth (PCG) in microgravity and in our earth-based laboratories. A large group of co-investigators from academia and industry participated in these experiments by providing protein samples and by performing the x-ray crystallographic analysis. These studies have clearly demonstrated the usefulness of a microgravity environment for enhancing the quality and size of protein crystals. Review of the vapor diffusion (VDA) PCG results from nineteen space shuttle missions is given in this paper

Progress in rational methods of cryoprotection in macromolecular crystallography

International Nuclear Information System (INIS)

Alcorn, Thomas; Juers, Douglas H.

2010-01-01

Measurements of the average thermal contractions (294→72 K) of 26 different cryosolutions are presented and discussed in conjunction with other recent advances in the rational design of protocols for cryogenic cooling in macromolecular crystallography. Cryogenic cooling of macromolecular crystals is commonly used for X-ray data collection both to reduce crystal damage from radiation and to gather functional information by cryogenically trapping intermediates. However, the cooling process can damage the crystals. Limiting cooling-induced crystal damage often requires cryoprotection strategies, which can involve substantial screening of solution conditions and cooling protocols. Here, recent developments directed towards rational methods for cryoprotection are described. Crystal damage is described in the context of the temperature response of the crystal as a thermodynamic system. As such, the internal and external parts of the crystal typically have different cryoprotection requirements. A key physical parameter, the thermal contraction, of 26 different cryoprotective solutions was measured between 294 and 72 K. The range of contractions was 2–13%, with the more polar cryosolutions contracting less. The potential uses of these results in the development of cryocooling conditions, as well as recent developments in determining minimum cryosolution soaking times, are discussed

Polycapillary x-ray optics for macromolecular crystallography

International Nuclear Information System (INIS)

Owens, S.M.; Gibson, W.M.; Carter, D.C.; Sisk, R.C.; Ho, J.X.

1996-01-01

Polycapillary x-ray optics have found potential application in many different fields, including antiscatter and magnification in mammography, radiography, x-ray fluorescence, x-ray lithography, and x-ray diffraction techniques. In x-ray diffraction, an optic is used to collect divergent x-rays from a point source and redirect them into a quasi-parallel, or slightly focused beam. Monolithic polycapillary optics have been developed recently for macromolecular crystallography and have already shown considerable gains in diffracted beam intensity over pinhole collimation. Development is being pursued through a series of simulations and prototype optics. Many improvements have been made over the stage 1 prototype reported previously, which include better control over the manufacturing process, reducing the diameter of the output beam, and addition of a slight focusing at the output of the optic to further increase x-ray flux at the sample. The authors report the characteristics and performance of the stage 1 and stage 2 optics

A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source

Science.gov (United States)

Pompidor, Guillaume; Dworkowski, Florian S. N.; Thominet, Vincent; Schulze-Briese, Clemens; Fuchs, Martin R.

2013-01-01

The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years. PMID:23955041

A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source.

Science.gov (United States)

Pompidor, Guillaume; Dworkowski, Florian S N; Thominet, Vincent; Schulze-Briese, Clemens; Fuchs, Martin R

2013-09-01

The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years.

The structural biology center at the APS: an integrated user facility for macromolecular crystallography

International Nuclear Information System (INIS)

Rosenbaum, G.; Westbrook, E.M.

1997-01-01

The Structural Biology Center (SBC) has developed and operates a sector (undulator and bending magnet) of the APS as a user facility for macromolecular crystallography. Crystallographically determined structures of proteins, nucleic acids and their complexes with proteins, viruses, and complexes between macromolecules and small ligands have become of central importance in molecular and cellular biology. Major design goals were to make the extremely high brilliance of the APS available for brilliance limited studies, and to achieve a high throughput of less demanding studies, as well as optimization for MAS-phasing. Crystal samples will include extremely small crystals, crystals with large unit cells (viruses, ribosomes, etc.) and ensembles of closely similar crystal structures for drug design, protein engineering, etc. Data are recorded on a 3000x3000 pixel CCD-area detector (optionally on image plates). The x-ray optics of both beamlines has been designed to produce a highly demagnified image of the source in order to match the focal size with the sizes of the sample and the resolution element of the detector. Vertical focusing is achieved by a flat, cylindrically bent mirror. Horizontal focusing is achieved by sagitally bending the second crystal of the double crystal monochromator. Monochromatic fluxes of 1.3 * 10 13 ph/s into focal sizes of 0.08 mm (horizontal)x0.04 mm (vertical) FWHM (flux density 3.5 * 10 15 ph/s/mm 2 ) have been recorded.copyright 1997 American Institute of Physics

Current status and future prospects of an automated sample exchange system PAM for protein crystallography

Science.gov (United States)

Hiraki, M.; Yamada, Y.; Chavas, L. M. G.; Matsugaki, N.; Igarashi, N.; Wakatsuki, S.

2013-03-01

To achieve fully-automated and/or remote data collection in high-throughput X-ray experiments, the Structural Biology Research Centre at the Photon Factory (PF) has installed PF automated mounting system (PAM) for sample exchange robots at PF macromolecular crystallography beamlines BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. We are upgrading the experimental systems, including the PAM for stable and efficient operation. To prevent human error in automated data collection, we installed a two-dimensional barcode reader for identification of the cassettes and sample pins. Because no liquid nitrogen pipeline in the PF experimental hutch is installed, the users commonly add liquid nitrogen using a small Dewar. To address this issue, an automated liquid nitrogen filling system that links a 100-liter tank to the robot Dewar has been installed on the PF macromolecular beamline. Here we describe this new implementation, as well as future prospects.

Web-Ice: Integrated Data Collection and Analysis for Macromolecular Crystallography

International Nuclear Information System (INIS)

Gonzalez, Ana; Gonzalez, Ana; Moorhead, Penjit; McPhillips, Scott E.; Song, Jinhu; Sharp, Ken; Taylor, John R.; Adams, Paul D.; Sauter, Nicholas K.; Soltis, S. Michael

2007-01-01

New software tools are introduced to facilitate diffraction experiments involving large numbers of crystals. While existing programs have long provided a framework for lattice indexing, Bragg spot integration, and symmetry determination, these initial data processing steps often require significant manual effort. This limits the timely availability of data analysis needed for high-throughput procedures, including the selection of the best crystals from a large sample pool, and the calculation of optimal data collection parameters to assure complete spot coverage with minimal radiation damage. To make these protocols more efficient, we developed a network of software applications and application servers, collectively known as Web-Ice. When the package is installed at a crystallography beamline, a programming interface allows the beamline control software (e.g., Blu-Ice/DCSS) to trigger data analysis automatically. Results are organized based on a list of samples that the user provides, and are examined within a Web page, accessible both locally at the beamline or remotely. Optional programming interfaces permit the user to control data acquisition through the Web browser. The system as a whole is implemented to support multiple users and multiple processors, and can be expanded to provide additional scientific functionality. Web-Ice has a distributed architecture consisting of several stand-alone software components working together via a well defined interface. Other synchrotrons or institutions may integrate selected components or the whole of Web-Ice with their own data acquisition software. Updated information about current developments may be obtained at http://smb.slac.stanford.edu/research/developments/webice

PILATUS: a two-dimensional X-ray detector for macromolecular crystallography

CERN Document Server

Eikenberry, E F; Huelsen, G; Toyokawa, H; Horisberger, R P; Schmitt, B; Schulze-Briese, C; Tomizaki, T

2003-01-01

A large quantum-limited area X-ray detector for protein crystallography is under development at the Swiss Light Source. The final detector will be 2kx2k pixels covering 40x40 cm sup 2. A three-module prototype with 1120x157 pixels covering an active area of 24.3x3.4 cm sup 2 has been tested. X-rays above 6 keV with peak count rates exceeding 5x10 sup 5 X-ray/pixel/s could be detected in single photon counting mode. Statistics of module production and results of threshold trimming are presented. To demonstrate the potential of this new detector, protein crystal data were collected at beamline 6S of the SLS.

A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

Science.gov (United States)

Chatake, Toshiyuki; Fujiwara, Satoru

2016-01-01

A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

Radiation damage to nucleoprotein complexes in macromolecular crystallography

International Nuclear Information System (INIS)

Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary; Ravelli, Raimond B. G.; Carmichael, Ian; Kneale, Geoff; McGeehan, John E.

2015-01-01

Quantitative X-ray induced radiation damage studies employing a model protein–DNA complex revealed a striking partition of damage sites. The DNA component was observed to be far more resistant to specific damage compared with the protein. Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein–DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07–44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N 1 —C and sugar-phosphate C—O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses

Long-wavelength macromolecular crystallography - First successful native SAD experiment close to the sulfur edge

Science.gov (United States)

Aurelius, O.; Duman, R.; El Omari, K.; Mykhaylyk, V.; Wagner, A.

2017-11-01

Phasing of novel macromolecular crystal structures has been challenging since the start of structural biology. Making use of anomalous diffraction of natively present elements, such as sulfur and phosphorus, for phasing has been possible for some systems, but hindered by the necessity to access longer X-ray wavelengths in order to make most use of the anomalous scattering contributions of these elements. Presented here are the results from a first successful experimental phasing study of a macromolecular crystal structure at a wavelength close to the sulfur K edge. This has been made possible by the in-vacuum setup and the long-wavelength optimised experimental setup at the I23 beamline at Diamond Light Source. In these early commissioning experiments only standard data collection and processing procedures have been applied, in particular no dedicated absorption correction has been used. Nevertheless the success of the experiment demonstrates that the capability to extract phase information can be even further improved once data collection protocols and data processing have been optimised.

MolProbity: all-atom structure validation for macromolecular crystallography

International Nuclear Information System (INIS)

Chen, Vincent B.; Arendall, W. Bryan III; Headd, Jeffrey J.; Keedy, Daniel A.; Immormino, Robert M.; Kapral, Gary J.; Murray, Laura W.; Richardson, Jane S.; Richardson, David C.

2010-01-01

MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction. MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database

Direct methods in protein crystallography.

Science.gov (United States)

Karle, J

1989-11-01

It is pointed out that the 'direct methods' of phase determination for small-structure crystallography do not have immediate applicability to macromolecular structures. The term 'direct methods in macromolecular crystallography' is suggested to categorize a spectrum of approaches to macromolecular structure determination in which the analyses are characterized by the use of two-phase and higher-order-phase invariants. The evaluation of the invariants is generally obtained by the use of heavy-atom techniques. The results of a number of the more recent algebraic and probabilistic studies involving isomorphous replacement and anomalous dispersion thus become valid subjects for discussion here. These studies are described and suggestions are also presented concerning future applicability. Additional discussion concerns the special techniques of filtering, the use of non-crystallographic symmetry, some features of maximum entropy and attempts to apply phase-determining formulas to the refinement of macromolecular structure. It is noted that, in addition to the continuing remarkable progress in macromolecular crystallography based on the traditional applications of isomorphous replacement and anomalous dispersion, recent valuable advances have been made in the application of non-crystallographic symmetry, in particular, to virus structures and in applications of filtering. Good progress has also been reported in the application of exact linear algebra to multiple-wavelength anomalous-dispersion investigations of structures containing anomalous scatterers of only moderate scattering power.

Mix and Inject: Reaction Initiation by Diffusion for Time-Resolved Macromolecular Crystallography

Directory of Open Access Journals (Sweden)

Marius Schmidt

2013-01-01

Full Text Available Time-resolved macromolecular crystallography unifies structure determination with chemical kinetics, since the structures of transient states and chemical and kinetic mechanisms can be determined simultaneously from the same data. To start a reaction in an enzyme, typically, an initially inactive substrate present in the crystal is activated. This has particular disadvantages that are circumvented when active substrate is directly provided by diffusion. However, then it is prohibitive to use macroscopic crystals because diffusion times become too long. With small micro- and nanocrystals diffusion times are adequately short for most enzymes and the reaction can be swiftly initiated. We demonstrate here that a time-resolved crystallographic experiment becomes feasible by mixing substrate with enzyme nanocrystals which are subsequently injected into the X-ray beam of a pulsed X-ray source.

Automated sample mounting and technical advance alignment system for biological crystallography at a synchrotron source

International Nuclear Information System (INIS)

Snell, Gyorgy; Cork, Carl; Nordmeyer, Robert; Cornell, Earl; Meigs, George; Yegian, Derek; Jaklevic, Joseph; Jin, Jian; Stevens, Raymond C.; Earnest, Thomas

2004-01-01

High-throughput data collection for macromolecular crystallography requires an automated sample mounting system for cryo-protected crystals that functions reliably when integrated into protein-crystallography beamlines at synchrotrons. Rapid mounting and dismounting of the samples increases the efficiency of the crystal screening and data collection processes, where many crystals can be tested for the quality of diffraction. The sample-mounting subsystem has random access to 112 samples, stored under liquid nitrogen. Results of extensive tests regarding the performance and reliability of the system are presented. To further increase throughput, we have also developed a sample transport/storage system based on 'puck-shaped' cassettes, which can hold sixteen samples each. Seven cassettes fit into a standard dry shipping Dewar. The capabilities of a robotic crystal mounting and alignment system with instrumentation control software and a relational database allows for automated screening and data collection to be developed

OCTOPUS: an innovative multimodal diffractometer for neutron macromolecular crystallography across the length scales

International Nuclear Information System (INIS)

Blakeley, M.P.; Andersen, K.; Kreuz, M.; Giroud, B.; McSweeney, S.; Mitchell, E.; Teixeira, S.C.M.; Forsyth, V.T.

2011-01-01

We propose to construct a novel protein diffractometer at position H112B. The new instrument will deliver major efficiency gains, as well as offering greatly extended flexibility through the option of several easily interchangeable modes of operation. This proposal builds on the demonstrable need to extend ILL's capacity for high resolution structural studies of protein systems, as well as a need to widen the scope of biological crystallography - in particular for monochromatic studies at both high and low resolution. The development will be carried out in close collaboration with structural biologists at the ESRF, and engineered in such a way that the user interface of the instrument (from sample to software) will be transparently identifiable to a large, dynamic, and driven community of European synchrotron X-ray macromolecular crystallographers. (authors)

Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.

Science.gov (United States)

Blakeley, Matthew P; Hasnain, Samar S; Antonyuk, Svetlana V

2015-07-01

The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron

Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential

Directory of Open Access Journals (Sweden)

Matthew P. Blakeley

2015-07-01

Full Text Available The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden and Sirius (Brazil under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å, for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59% were released since 2010. Sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+ remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place

Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves.

Science.gov (United States)

Guo, Feng; Zhou, Weijie; Li, Peng; Mao, Zhangming; Yennawar, Neela H; French, Jarrod B; Huang, Tony Jun

2015-06-01

Advances in modern X-ray sources and detector technology have made it possible for crystallographers to collect usable data on crystals of only a few micrometers or less in size. Despite these developments, sample handling techniques have significantly lagged behind and often prevent the full realization of current beamline capabilities. In order to address this shortcoming, a surface acoustic wave-based method for manipulating and patterning crystals is developed. This method, which does not damage the fragile protein crystals, can precisely manipulate and pattern micrometer and submicrometer-sized crystals for data collection and screening. The technique is robust, inexpensive, and easy to implement. This method not only promises to significantly increase efficiency and throughput of both conventional and serial crystallography experiments, but will also make it possible to collect data on samples that were previously intractable. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Remote Access Revolution: Chemical Crystallographers Enter a New Era at Diamond Light Source Beamline I19

Directory of Open Access Journals (Sweden)

Natalie T. Johnson

2017-12-01

Full Text Available Since the inception of the use of synchrotron radiation in the structural characterisation of crystalline materials by single-crystal diffraction in the late 20th century, the field has undergone an explosion of technological developments. These cover all aspects of the experiments performed, from the construction of the storage rings and insertion devices, to the end user functionalities in the experimental hutches. Developments in automation have most frequently been driven by the macromolecular crystallography community. The drive towards greater access to ever-brighter X-ray sources has benefited the entire field. Herein, we detail the revolution that is now occurring within the chemical crystallography community, utilising many of the tools developed by their more biologically oriented colleagues, along with specialised functionalities that are tailored to the small-molecule world. We discuss the benefits of utilising the advanced features of Diamond Light Source beamline I19 in the newly developed remote access mode and the step-change in productivity that can be established as a result.

Control system for the 2nd generation Berkeley automounters (BAM2) at GM/CA-CAT macromolecular crystallography beamlines

Energy Technology Data Exchange (ETDEWEB)

Makarov, O., E-mail: makarov@anl.gov [GM/CA-CAT, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Hilgart, M.; Ogata, C.; Pothineni, S. [GM/CA-CAT, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Cork, C. [Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)

2011-09-01

GM/CA-CAT at Sector 23 of the Advanced Photon Source (APS) is an NIH funded facility for crystallographic structure determination of biological macromolecules by X-ray diffraction. A second-generation Berkeley automounter is being integrated into the beamline control system at the 23BM experimental station. This new device replaces the previous all-pneumatic gripper motions with a combination of pneumatics and XYZ motorized linear stages. The latter adds a higher degree of flexibility to the robot including auto-alignment capability, accommodation of a larger capacity sample Dewar of arbitrary shape, and support for advanced operations such as crystal washing, while preserving the overall simplicity and efficiency of the Berkeley automounter design.

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging.

Science.gov (United States)

Warren, Anna J; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R; Horrell, Sam; McAuley, Katherine E; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-07-01

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

History of protein crystallography in China

OpenAIRE

Rao, Zihe

2007-01-01

China has a strong background in X-ray crystallography dating back to the 1920s. Protein crystallography research in China was first developed following the successful synthesis of insulin in China in 1966. The subsequent determination of the three-dimensional structure of porcine insulin made China one of the few countries which could determine macromolecular structures by X-ray diffraction methods in the late 1960s and early 1970s. After a slow period during the 1970s and 1980s, protein cry...

History of protein crystallography in China.

Science.gov (United States)

Rao, Zihe

2007-06-29

China has a strong background in X-ray crystallography dating back to the 1920s. Protein crystallography research in China was first developed following the successful synthesis of insulin in China in 1966. The subsequent determination of the three-dimensional structure of porcine insulin made China one of the few countries which could determine macromolecular structures by X-ray diffraction methods in the late 1960s and early 1970s. After a slow period during the 1970s and 1980s, protein crystallography in China has reached a new climax with a number of outstanding accomplishments. Here, I review the history and progress of protein crystallography in China and detail some of the recent research highlights, including the crystal structures of two membrane proteins as well as the structural genomics initiative in China.

Automation in structural biology beamlines of the Photon Factory

International Nuclear Information System (INIS)

Igarashi, Noriyuki; Hiraki, Masahiko; Matsugaki, Naohiro; Yamada, Yusuke; Wakatsuki, Soichi

2007-01-01

The Photon Factory currently operates four synchrotron beamlines for protein crystallography and two more beamlines are scheduled to be constructed in the next years. Over the last years these beamlines have been upgraded and equipped with a fully automated beamline control system based on a robotic sample changer. The current system allows for remote operation, controlled from the user's area, of sample mounting, centering and data collection of pre-frozen crystals mounted in Hampton-type cryo-loops on goniometer head. New intuitive graphical user interfaces have been developed so as to control the complete beamline operation. Furthermore, algorithms for automatic sample centering based on pattern matching and X-ray beam scanning are being developed and combined with newly developed diffraction evaluation programs in order to complete entire automation of the data collection. (author)

Macromolecular crystallization in microgravity

International Nuclear Information System (INIS)

Snell, Edward H; Helliwell, John R

2005-01-01

Density difference fluid flows and sedimentation of growing crystals are greatly reduced when crystallization takes place in a reduced gravity environment. In the case of macromolecular crystallography a crystal of a biological macromolecule is used for diffraction experiments (x-ray or neutron) so as to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal then the greater the molecular structure detail that can be extracted. It is this structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences, with major potential in understanding disease pathologies. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyse the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural advances. Finally, limitations and alternatives to microgravity and future directions for this research are covered. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry and mathematics meet to enable insight to the fundamentals of life. As the reader will see, there is a great deal of physics involved when the microgravity environment is applied to crystallization, some of it known, and undoubtedly much yet to

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

Directory of Open Access Journals (Sweden)

C. Mueller

2015-09-01

Full Text Available We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA. The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.

Serial Femtosecond Crystallography

OpenAIRE

Chapman, Henry N.

2015-01-01

X-ray free-electron lasers produce brief flashes of X-rays that are of about a billion times higher peak brightness than achievable from storage ring sources. Such a tremendous jump in X-ray source capabilities, which came in 2009 when the Linac Coherent Light Source began operations, was unprecedented in the history of X-ray science. Protein structure determination through the method of macromolecular crystallography has consistently benefited from the many increases in source performance fr...

Performance of PILATUS detector technology for long-wavelength macromolecular crystallography

International Nuclear Information System (INIS)

Marchal, J.; Wagner, A.

2011-01-01

The long-wavelength MX beamline I23 currently under design at Diamond Light Source will be optimized in the X-ray energy range between 3 and 5 keV. At the moment no commercial off-the-shelf detector with high quantum efficiency and dynamic range is available to cover the large area required for diffraction experiments in this energy range. The hybrid pixel detector technology used in PILATUS detectors could overcome these limitations as the modular design could allow a large coverage in reciprocal space and high detection efficiency. Experiments were carried out on the Microfocus Spectroscopy beamline I18 at Diamond Light Source to test the performance of a 100K PILATUS module in the low-energy range from 2.3 to 3.7 keV.

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

International Nuclear Information System (INIS)

Warren, Anna J.; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R.; Horrell, Sam; McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-01-01

A comparison of X-ray diffraction and radiographic techniques for the location and characterization of protein crystals is demonstrated on membrane protein crystals mounted within lipid cubic phase material. The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

Energy Technology Data Exchange (ETDEWEB)

Warren, Anna J. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Armour, Wes [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Oxford e-Research Centre, 7 Keble Road, Oxford OX1 3QG (United Kingdom); Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Horrell, Sam [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); University of Liverpool, Liverpool L69 3BX (United Kingdom); McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

2013-07-01

A comparison of X-ray diffraction and radiographic techniques for the location and characterization of protein crystals is demonstrated on membrane protein crystals mounted within lipid cubic phase material. The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

Fragment-based screening by protein crystallography: successes and pitfalls.

Science.gov (United States)

Chilingaryan, Zorik; Yin, Zhou; Oakley, Aaron J

2012-10-08

Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality.

Fragment-Based Screening by Protein Crystallography: Successes and Pitfalls

Directory of Open Access Journals (Sweden)

Aaron J. Oakley

2012-10-01

Full Text Available Fragment-based drug discovery (FBDD concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality.

A history of experimental phasing in macromolecular crystallography

OpenAIRE

Isaacs, Neil

2016-01-01

It was just over a century ago that W. L. Bragg published a paper describing the first crystal structures to be determined using X-ray diffraction data. These structures were obtained from considerations of X-ray diffraction (Bragg equation), crystallography (crystal lattices and symmetry) and the scattering power of different atoms. Although W. H. Bragg proposed soon afterwards, in 1915, that the periodic electron density in crystals could be analysed using Fourier transforms, it took some d...

A smooth and differentiable bulk-solvent model for macromolecular diffraction

Energy Technology Data Exchange (ETDEWEB)

Fenn, T. D. [Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, California (United States); Schnieders, M. J. [Department of Chemistry, Stanford, California (United States); Brunger, A. T., E-mail: brunger@stanford.edu [Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, California (United States); Departments of Neurology and Neurological Sciences, Structural Biology and Photon Science, Stanford, California (United States)

2010-09-01

A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates. Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R{sub free} and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography.

A smooth and differentiable bulk-solvent model for macromolecular diffraction

International Nuclear Information System (INIS)

Fenn, T. D.; Schnieders, M. J.; Brunger, A. T.

2010-01-01

A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates. Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R free and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography

Development of the XFP beamline for x-ray footprinting at NSLS-II

Energy Technology Data Exchange (ETDEWEB)

Bohon, Jen, E-mail: jbohon@bnl.gov; Sullivan, Michael; Abel, Don; Toomey, John; Chance, Mark R., E-mail: mark.chance@case.edu [Case Center for Synchrotron Biosciences, Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH (United States); Dvorak, Joseph [Brookhaven National Laboratory, Upton, NY (United States)

2016-07-27

For over a decade, synchrotron-based footprinting studies at the NSLS X28C beamline have provided unique insights and approaches for examining the solution-state structures of large macromolecular assemblies, membrane proteins, and soluble proteins, for time-resolved studies of macromolecular dynamics, and most recently for in vivo studies of RNA-protein complexes. The transition from NSLS to NSLS-II has provided the opportunity to create an upgraded facility for the study of increasingly complex systems; progress on the development of the XFP (X-ray Footprinting for In Vitro and In Vivo Structural Studies of Biological Macromolecules) beamline at NSLS-II is presented here. The XFP beamline will utilize a focused 3-pole wiggler source to deliver a high flux density x-ray beam, where dynamics can be studied on the microsecond to millisecond timescales appropriate for probing biological macromolecules while minimizing sample perturbation. The beamline optics and diagnostics enable adaptation of the beam size and shape to accommodate a variety of sample morphologies with accurate measurement of the incident beam, and the upgrades in sample handling and environment control will allow study of highly sensitive or unstable samples. The XFP beamline is expected to enhance relevant flux densities more than an order of magnitude from that previously available at X28C, allowing static and time-resolved structural analysis of highly complex samples that have previously pushed the boundaries of x-ray footprinting technology. XFP, located at NSLS-II 17-BM, is anticipated to become available for users in 2016.

EPICS controlled sample mounting robots at the GM/CA CAT

Energy Technology Data Exchange (ETDEWEB)

Makarov, O.A. [GM/CA-CAT, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439-4861 (United States)], E-mail: makarov@anl.gov; Benn, R.; Corcoran, S.; Devarapalli, S.; Fischetti, R.; Hilgart, M.; Smith, W.W.; Stepanov, S.; Xu, S. [GM/CA-CAT, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 436D, Argonne, IL 60439-4861 (United States)

2007-11-11

GM/CA CAT at Sector 23 of the advanced photon source (APS) is an NIH funded facility for crystallographic structure determination of biological macromolecules by X-ray diffraction [R.F. Fischetti, et al., GM/CA canted undulator beamlines for protein crystallography, Acta Crystallogr. A 61 (2005) C139]. The facility consists of three beamlines; two based on canted undulators and one on a bending magnet. The scientific and technical goals of the CAT emphasize streamlined, efficient throughput for a variety of sample types, sizes and qualities, representing the cutting edge of structural biology research. For this purpose all three beamlines are equipped with the ALS-style robots [C.W.Cork, et al. Status of the BCSB automated sample mounting and alignment system for macromolecular crystallography at the Advanced Light Source, SRI-2003, San-Francisco, CA, USA, August 25-29, 2003] for an automated mounting of cryo-protected macromolecular crystals. This report summarizes software and technical solutions implemented with the first of the three operational robots at beamline 23-ID-B. The automounter's Dewar can hold up to 72 or 96 samples residing in six Rigaku ACTOR magazines or ALS-style pucks, respectively. Mounting of a crystal takes approximately 2 s, during which time the temperature of the crystal is maintained near that of liquid nitrogen.

Correlated single-crystal electronic absorption spectroscopy and X-ray crystallography at NSLS beamline X26-C

International Nuclear Information System (INIS)

Orville, A.M.; Buono, R.; Cowan, M.; Heroux, A.; Shea-McCarthy, G.; Schneider, D.K.; Skinner, J.M.; Skinner, M.J.; Stoner-Ma, D.; Sweet, R.M.

2011-01-01

The research philosophy and new capabilities installed at NSLS beamline X26-C to support electronic absorption and Raman spectroscopies coupled with X-ray diffraction are reviewed. This beamline is dedicated full time to multidisciplinary studies with goals that include revealing the relationship between the electronic and atomic structures in macromolecules. The beamline instrumentation has been fully integrated such that optical absorption spectra and X-ray diffraction images are interlaced. Therefore, optical changes induced by X-ray exposure can be correlated with X-ray diffraction data collection. The installation of Raman spectroscopy into the beamline is also briefly reviewed. Data are now routinely generated almost simultaneously from three complementary types of experiments from the same sample. The beamline is available now to the NSLS general user population.

Application of in situ diffraction in high-throughput structure determination platforms.

Science.gov (United States)

Aller, Pierre; Sanchez-Weatherby, Juan; Foadi, James; Winter, Graeme; Lobley, Carina M C; Axford, Danny; Ashton, Alun W; Bellini, Domenico; Brandao-Neto, Jose; Culurgioni, Simone; Douangamath, Alice; Duman, Ramona; Evans, Gwyndaf; Fisher, Stuart; Flaig, Ralf; Hall, David R; Lukacik, Petra; Mazzorana, Marco; McAuley, Katherine E; Mykhaylyk, Vitaliy; Owen, Robin L; Paterson, Neil G; Romano, Pierpaolo; Sandy, James; Sorensen, Thomas; von Delft, Frank; Wagner, Armin; Warren, Anna; Williams, Mark; Stuart, David I; Walsh, Martin A

2015-01-01

Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.

A public database of macromolecular diffraction experiments.

Science.gov (United States)

Grabowski, Marek; Langner, Karol M; Cymborowski, Marcin; Porebski, Przemyslaw J; Sroka, Piotr; Zheng, Heping; Cooper, David R; Zimmerman, Matthew D; Elsliger, Marc André; Burley, Stephen K; Minor, Wladek

2016-11-01

The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics

A history of experimental phasing in macromolecular crystallography.

Science.gov (United States)

Isaacs, Neil

2016-03-01

It was just over a century ago that W. L. Bragg published a paper describing the first crystal structures to be determined using X-ray diffraction data. These structures were obtained from considerations of X-ray diffraction (Bragg equation), crystallography (crystal lattices and symmetry) and the scattering power of different atoms. Although W. H. Bragg proposed soon afterwards, in 1915, that the periodic electron density in crystals could be analysed using Fourier transforms, it took some decades before experimental phasing methods were developed. Many scientists contributed to this development and this paper presents the author's own perspective on this history. There will be other perspectives, so what follows is a history, rather than the history, of experimental phasing.

Metalloprotein Crystallography: More than a Structure.

Science.gov (United States)

Bowman, Sarah E J; Bridwell-Rabb, Jennifer; Drennan, Catherine L

2016-04-19

Metal ions and metallocofactors play important roles in a broad range of biochemical reactions. Accordingly, it has been estimated that as much as 25-50% of the proteome uses transition metal ions to carry out a variety of essential functions. The metal ions incorporated within metalloproteins fulfill functional roles based on chemical properties, the diversity of which arises as transition metals can adopt different redox states and geometries, dictated by the identity of the metal and the protein environment. The coupling of a metal ion with an organic framework in metallocofactors, such as heme and cobalamin, further expands the chemical functionality of metals in biology. The three-dimensional visualization of metal ions and complex metallocofactors within a protein scaffold is often a starting point for enzymology, highlighting the importance of structural characterization of metalloproteins. Metalloprotein crystallography, however, presents a number of implicit challenges including correctly incorporating the relevant metal or metallocofactor, maintaining the proper environment for the protein to be purified and crystallized (including providing anaerobic, cold, or aphotic environments), and being mindful of the possibility of X-ray induced damage to the proteins or incorporated metal ions. Nevertheless, the incorporated metals or metallocofactors also present unique advantages in metalloprotein crystallography. The significant resonance that metals undergo with X-ray photons at wavelengths used for protein crystallography and the rich electronic properties of metals, which provide intense and spectroscopically unique signatures, allow a metalloprotein crystallographer to use anomalous dispersion to determine phases for structure solution and to use simultaneous or parallel spectroscopic techniques on single crystals. These properties, coupled with the improved brightness of beamlines, the ability to tune the wavelength of the X-ray beam, the availability of

I19, the small-molecule single-crystal diffraction beamline at Diamond Light Source.

Science.gov (United States)

Nowell, Harriott; Barnett, Sarah A; Christensen, Kirsten E; Teat, Simon J; Allan, David R

2012-05-01

The dedicated small-molecule single-crystal X-ray diffraction beamline (I19) at Diamond Light Source has been operational and supporting users for over three years. I19 is a high-flux tunable-wavelength beamline and its key details are described in this article. Much of the work performed on the beamline involves structure determination from small and weakly diffracting crystals. Other experiments that have been supported to date include structural studies at high pressure, studies of metastable species, variable-temperature crystallography, studies involving gas exchange in porous materials and structural characterizations that require analysis of the diffuse scattering between Bragg reflections. A range of sample environments to facilitate crystallographic studies under non-ambient conditions are available as well as a number of options for automation. An indication of the scope of the science carried out on the beamline is provided by the range of highlights selected for this paper.

Serial Millisecond Crystallography of Membrane Proteins.

Science.gov (United States)

Jaeger, Kathrin; Dworkowski, Florian; Nogly, Przemyslaw; Milne, Christopher; Wang, Meitian; Standfuss, Joerg

2016-01-01

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) is a powerful method to determine high-resolution structures of pharmaceutically relevant membrane proteins. Recently, the technology has been adapted to carry out serial millisecond crystallography (SMX) at synchrotron sources, where beamtime is more abundant. In an injector-based approach, crystals grown in lipidic cubic phase (LCP) or embedded in viscous medium are delivered directly into the unattenuated beam of a microfocus beamline. Pilot experiments show the application of microjet-based SMX for solving the structure of a membrane protein and compatibility of the method with de novo phasing. Planned synchrotron upgrades, faster detectors and software developments will go hand-in-hand with developments at free-electron lasers to provide a powerful methodology for solving structures from microcrystals at room temperature, ligand screening or crystal optimization for time-resolved studies with minimal or no radiation damage.

Development of Control Applications for High-Throughput Protein Crystallography Experiments

International Nuclear Information System (INIS)

Gaponov, Yurii A.; Matsugaki, Naohiro; Honda, Nobuo; Sasajima, Kumiko; Igarashi, Noriyuki; Hiraki, Masahiko; Yamada, Yusuke; Wakatsuki, Soichi

2007-01-01

An integrated client-server control system (PCCS) with a unified relational database (PCDB) has been developed for high-throughput protein crystallography experiments on synchrotron beamlines. The major steps in protein crystallographic experiments (purification, crystallization, crystal harvesting, data collection, and data processing) are integrated into the software. All information necessary for performing protein crystallography experiments is stored in the PCDB database (except raw X-ray diffraction data, which is stored in the Network File Server). To allow all members of a protein crystallography group to participate in experiments, the system was developed as a multi-user system with secure network access based on TCP/IP secure UNIX sockets. Secure remote access to the system is possible from any operating system with X-terminal and SSH/X11 (Secure Shell with graphical user interface) support. Currently, the system covers the high-throughput X-ray data collection stages and is being commissioned at BL5A and NW12A (PF, PF-AR, KEK, Tsukuba, Japan)

X-ray crystallography facility for the international space station

International Nuclear Information System (INIS)

McdDonald, William T.; Lewis, Johanna L.; Smith, Craig D.; DeLucas, Lawrence J.

1997-01-01

Directed by NASA's Office of Space Access and Technology (OSAT), the University of Alabama at Birmingham (UAB) Center for Macromolecular Crystallography (CMC) recently completed a Design Feasibility Study for the X-ray Crystallography Facility (XCF) for the International Space Station (ISS). The XCF is a facility for growing macromolecular protein crystals; harvesting, selecting, and mounting sample crystals, and snap-freezing the samples, if necessary; performing x-ray diffraction; and downlinking the diffraction data to the ground. Knowledge of the structure of protein molecules is essential for the development of pharmaceuticals by structure-based drug design techniques. Currently, x-ray diffraction of high quality protein crystals is the only method of determining the structure of these macromolecules. High quality protein crystals have been grown in microgravity onboard the Space Shuttle Orbiter for more than 10 years, but these crystals always have been returned to Earth for x-ray diffraction. The XCF will allow crystal growth, harvesting, mounting, and x-ray diffraction onboard the ISS, maximizing diffraction data quality and timeliness. This paper presents the XCF design concept, describing key feasibility issues for the ISS application and advanced technologies and operational features which resolve those issues. The conclusion is that the XCF design is feasible and can be operational onboard the ISS by early in 2002

Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal

Directory of Open Access Journals (Sweden)

Sam Horrell

2016-07-01

Full Text Available Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07–1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a `catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.

Watching proteins function with time-resolved x-ray crystallography

Science.gov (United States)

Šrajer, Vukica; Schmidt, Marius

2017-09-01

Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron x-ray sources. An expansive database of more than 100 000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al 2005a Methods Mol. Biol. 305 115-54, Schmidt 2008 Ultrashort Laser Pulses in Biology and Medicine (Berlin: Springer) pp 201-41, Neutze and Moffat 2012 Curr. Opin. Struct. Biol. 22 651-9, Šrajer 2014 The Future of Dynamic Structural Science (Berlin: Springer) pp 237-51). In this approach, short and intense x-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron x-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard x-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond x-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al 2014 Science 346 1242-6, Barends et al 2015 Science 350 445-50, Pande et al 2016 Science 352 725-9). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline

Automation and Remote Synchrotron Data Collection

International Nuclear Information System (INIS)

Gilski, M.

2008-01-01

X-ray crystallography is the natural choice for macromolecular structure determination by virtue of its accuracy, speed, and potential for further speed gains, while synchrotron radiation is indispensable because of its intensity and tuneability. Good X-ray crystallographic diffraction patterns are essential and frequently this is achievable through using the few large synchrotrons located worldwide. Beamline time on these facilities have long queues, and increasing the efficiency of utilization of these facilities will help in expediting the structure determination process. Automation and remote data collection are therefore essential steps in ensuring that macromolecular structure determination becomes a very high throughput process. (author)

New beamline dedicated to solution scattering from biological macromolecules at the ESRF

International Nuclear Information System (INIS)

Pernot, P; Theveneau, P; Giraud, T; Fernandes, R Nogueira; Nurizzo, D; Spruce, D; Surr, J; McSweeney, S; Round, A; Felisaz, F; Foedinger, L; Gobbo, A; Huet, J; Villard, C; Cipriani, F

2010-01-01

The new bio-SAXS beamline (ID14-3 at the ESRF, Grenoble, France) is dedicated exclusively to small-angle scattering experiments of biological macromolecules in solution and has been in user operation since November 2008. Originally a protein crystallography beamline, ID14-3 was refurbished, still as a part of the ESRF Structural Biology group, with the main aim to provide a facility with 'quick and easy' access to satisfy rapidly growing demands from crystallographers, biochemists and structural biologists. The beamline allows manual and automatic sample loading/unloading, data collection, processing (conversion of a 2D image to a normalized 1D X-ray scattering profile) and analysis. The users obtain on-line standard data concerning the size (radius of gyration, maximum dimension and volume) and molecular weight of samples which allow on-the fly ab-inito shape reconstruction in order to provide feedback enabling the data collection strategies to be optimized. Automation of sample loading is incorporated on the beamline using a device constructed in collaboration between the EMBL (Grenoble and Hamburg outstations) and the ESRF. Semi/automated data analysis is implemented following the model of the SAXS facility at X33, EMBL Hamburg. This paper describes the bio-SAXS beamline and set-up characteristics together with the examples of user data obtained.

Trichromatic concept at the SPring-8 RIKEN beamline I

International Nuclear Information System (INIS)

Yamamoto, Masaki; Kumasaka, Takashi; Ueki, Tatzuo

1998-01-01

At the SPring-8, RIKEN beamline I has been designed and developed for structural biology research by the Institute of Physical and Chemical Research (RIKEN). RIKEN beamline I consists of two experimental stations, protein crystallography (PX) and small-angle X-ray scattering (SAXS). Both experiments can be carried out simultaneously, with dichromatic synchrotron radiation emitted from two coaxial undulators with vertical polarization. The branched beams are generated by a transparent diamond crystal. With synchrotron radiation, the multi-wavelength anomalous diffraction (MAD) method, which gives phases from a single anomalous scatterer, has been developed. Anomalous scattering contributes a small portion of diffraction intensity so that the accuracy of intensity data is definitely important. The PX branch of RIKEN beamline I has been designed based on a 'trichromatic concept' to optimize for the MAD data collection. This concept is that three kinds of intensity data sets with three different wavelengths are taken quasi-simultaneously for the single protein crystal without changing any setting by 'trichromator'. The main feature of this concept is to minimize systematic errors in the measurements of anomalous diffraction for the MAD method. The construction of RIKEN beamline I had been progressed satisfactorily until June 1997. The initial commissioning successfully provided the three different monochromatized undulator beams were successfully observed on the phosphor screen, which located at the near end of the trichromator. (author)

Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

Directory of Open Access Journals (Sweden)

Przemyslaw Nogly

2015-03-01

Full Text Available Lipidic cubic phases (LCPs have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX at X-ray free-electron lasers (XFELs. Here, the adaptation of this technology to perform serial millisecond crystallography (SMX at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.

In meso in situ serial X-ray crystallography of soluble and membrane proteins

International Nuclear Information System (INIS)

Huang, Chia-Ying; Olieric, Vincent; Ma, Pikyee; Panepucci, Ezequiel; Diederichs, Kay; Wang, Meitian; Caffrey, Martin

2015-01-01

A method for performing high-throughput in situ serial X-ray crystallography with soluble and membrane proteins in the lipid cubic phase is described. It works with microgram quantities of protein and lipid (and ligand when present) and is compatible with the most demanding sulfur SAD phasing. The lipid cubic phase (LCP) continues to grow in popularity as a medium in which to generate crystals of membrane (and soluble) proteins for high-resolution X-ray crystallographic structure determination. To date, the PDB includes 227 records attributed to the LCP or in meso method. Among the listings are some of the highest profile membrane proteins, including the β 2 -adrenoreceptor–G s protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at macromolecular

Missed opportunities in crystallography.

Science.gov (United States)

Dauter, Zbigniew; Jaskolski, Mariusz

2014-09-01

Scrutinized from the perspective of time, the giants in the history of crystallography more than once missed a nearly obvious chance to make another great discovery, or went in the wrong direction. This review analyzes such missed opportunities focusing on macromolecular crystallographers (using Perutz, Pauling, Franklin as examples), although cases of particular historical (Kepler), methodological (Laue, Patterson) or structural (Pauling, Ramachandran) relevance are also described. Linus Pauling, in particular, is presented several times in different circumstances, as a man of vision, oversight, or even blindness. His example underscores the simple truth that also in science incessant creativity is inevitably connected with some probability of fault. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

OpenAIRE

Warren, Anna J.; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R.; Horrell, Sam; McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-01-01

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolec...

Watching proteins function with time-resolved x-ray crystallography

Energy Technology Data Exchange (ETDEWEB)

Šrajer, Vukica; Schmidt, Marius

2017-08-22

Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron x-ray sources. An expansive database of more than 100 000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al 2005a Methods Mol. Biol. 305 115–54, Schmidt 2008 Ultrashort Laser Pulses in Biology and Medicine (Berlin: Springer) pp 201–41, Neutze and Moffat 2012 Curr. Opin. Struct. Biol. 22 651–9, Šrajer 2014 The Future of Dynamic Structural Science (Berlin: Springer) pp 237–51). In this approach, short and intense x-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron x-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard x-rays (XFELs; 5–20 keV), which provide exceptionally intense, femtosecond x-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al 2014 Science 346 1242–6, Barends et al 2015 Science 350 445–50, Pande et al 2016 Science 352 725–9). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We

Watching proteins function with time-resolved x-ray crystallography

International Nuclear Information System (INIS)

Šrajer, Vukica; Schmidt, Marius

2017-01-01

Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron x-ray sources. An expansive database of more than 100 000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al 2005a Methods Mol. Biol . 305 115–54, Schmidt 2008 Ultrashort Laser Pulses in Biology and Medicine (Berlin: Springer) pp 201–41, Neutze and Moffat 2012 Curr. Opin. Struct. Biol . 22 651–9, Šrajer 2014 The Future of Dynamic Structural Science (Berlin: Springer) pp 237–51). In this approach, short and intense x-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron x-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard x-rays (XFELs; 5–20 keV), which provide exceptionally intense, femtosecond x-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al 2014 Science 346 1242–6, Barends et al 2015 Science 350 445–50, Pande et al 2016 Science 352 725–9). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs

Operational experience of a large area x-ray camera for protein crystallography

International Nuclear Information System (INIS)

Joachimiak, A.; Jorden, A. R.; Loeffen, P. W.; Naday, I.; Sanishvili, R.; Westbrook, E. M.

1999-01-01

After 3 years experience of operating very large area (210mm x 210mm) CCD-based detectors at the Advanced Photon Source, operational experience is reported. Four such detectors have been built, two for Structural Biology Center (APS-1 and SBC-2), one for Basic Energy Sciences Synchrotrons Radiation Center (Gold-2) at Argonne National Laboratory's Advanced Photon Source and one for Osaka University by Oxford Instruments, for use at Spring 8 (PX-21O). The detector is specifically designed as a high resolution and fast readout camera for macromolecular crystallography. Design trade-offs for speed and size are reviewed in light of operational experience and future requirements are considered. Operational data and examples of crystallography data are presented, together with plans for more development

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation.

Science.gov (United States)

Martin-Garcia, Jose M; Conrad, Chelsie E; Nelson, Garrett; Stander, Natasha; Zatsepin, Nadia A; Zook, James; Zhu, Lan; Geiger, James; Chun, Eugene; Kissick, David; Hilgart, Mark C; Ogata, Craig; Ishchenko, Andrii; Nagaratnam, Nirupa; Roy-Chowdhury, Shatabdi; Coe, Jesse; Subramanian, Ganesh; Schaffer, Alexander; James, Daniel; Ketwala, Gihan; Venugopalan, Nagarajan; Xu, Shenglan; Corcoran, Stephen; Ferguson, Dale; Weierstall, Uwe; Spence, John C H; Cherezov, Vadim; Fromme, Petra; Fischetti, Robert F; Liu, Wei

2017-07-01

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5-20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A 2A adenosine receptor (A 2A AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A 2A AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A 2A AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5-20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

Directory of Open Access Journals (Sweden)

Jose M. Martin-Garcia

2017-07-01

Full Text Available Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX is severely limited by the scarcity of X-ray free-electron laser (XFEL sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX. As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS, are reported. Microcrystals (5–20 µm of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2A adenosine receptor (A2AAR, the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP or a high-molecular-weight poly(ethylene oxide (PEO; molecular weight 8 000 000 were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the

Electron crystallography with the EIGER detector

Directory of Open Access Journals (Sweden)

Gemma Tinti

2018-03-01

Full Text Available Electron crystallography is a discipline that currently attracts much attention as method for inorganic, organic and macromolecular structure solution. EIGER, a direct-detection hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland, has been tested for electron diffraction in a transmission electron microscope. EIGER features a pixel pitch of 75 × 75 µm2, frame rates up to 23 kHz and a dead time between frames as low as 3 µs. Cluster size and modulation transfer functions of the detector at 100, 200 and 300 keV electron energies are reported and the data quality is demonstrated by structure determination of a SAPO-34 zeotype from electron diffraction data.

NATO Advanced Study Institute on Evolving Methods for Macromolecular Gystallography

CERN Document Server

Read, Randy J

2007-01-01

X-ray crystallography is the pre-eminent technique for visualizing the structures of macromolecules at atomic resolution. These structures are central to understanding the detailed mechanisms of biological processes, and to discovering novel therapeutics using a structure-based approach. As yet, structures are known for only a small fraction of the proteins encoded by human and pathogenic genomes. To counter the myriad modern threats of disease, there is an urgent need to determine the structures of the thousands of proteins whose structure and function remain unknown. This volume draws on the expertise of leaders in the field of macromolecular crystallography to illuminate the dramatic developments that are accelerating progress in structural biology. Their contributions span the range of techniques from crystallization through data collection, structure solution and analysis, and show how modern high-throughput methods are contributing to a deeper understanding of medical problems.

Structural analysis of nanoparticulate carriers for encapsulation of macromolecular drugs

Czech Academy of Sciences Publication Activity Database

Angelov, Borislav; Garamus, V.M.; Drechsler, M.; Angelova, A.

2017-01-01

Roč. 235, Jun (2017), s. 83-89 ISSN 0167-7322 R&D Projects: GA MŠk EF15_003/0000447; GA MŠk EF15_008/0000162 Grant - others:OP VVV - ELIBIO(XE) CZ.02.1.01/0.0/0.0/15_003/0000447; ELI Beamlines(XE) CZ.02.1.01/0.0/0.0/15_008/0000162 Institutional support: RVO:68378271 Keywords : self-assembled nanocarriers * liquid crystalline phase transitions * cationic lipids * macromolecular drugs Subject RIV: BO - Biophysics OBOR OECD: Biophysics Impact factor: 3.648, year: 2016

The success story of crystallography.

Science.gov (United States)

Schwarzenbach, Dieter

2012-01-01

Diffractionists usually place the birth of crystallography in 1912 with the first X-ray diffraction experiment of Friedrich, Knipping and Laue. This discovery propelled the mathematical branch of mineralogy to global importance and enabled crystal structure determination. Knowledge of the geometrical structure of matter at atomic resolution had revolutionary consequences for all branches of the natural sciences: physics, chemistry, biology, earth sciences and material science. It is scarcely possible for a single person in a single article to trace and appropriately value all of these developments. This article presents the limited, subjective view of its author and a limited selection of references. The bulk of the article covers the history of X-ray structure determination from the NaCl structure to aperiodic structures and macromolecular structures. The theoretical foundations were available by 1920. The subsequent success of crystallography was then due to the development of diffraction equipment, the theory of the solution of the phase problem, symmetry theory and computers. The many structures becoming known called for the development of crystal chemistry and of data banks. Diffuse scattering from disordered structures without and with partial long-range order allows determination of short-range order. Neutron and electron scattering and diffraction are also mentioned.

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy.

Science.gov (United States)

Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit

2017-09-17

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

Structure of the cyanobactin oxidase ThcOx from Cyanothece sp. PCC 7425, the first structure to be solved at Diamond Light Source beamline I23 by means of S-SAD.

Science.gov (United States)

Bent, Andrew F; Mann, Greg; Houssen, Wael E; Mykhaylyk, Vitaliy; Duman, Ramona; Thomas, Louise; Jaspars, Marcel; Wagner, Armin; Naismith, James H

2016-11-01

diffraction data for native sulfur phasing on a standard macromolecular crystallography beamline using a wavelength of 1.77 Å did not yield a structure. The new beamline thus has the potential to facilitate structure determination by native S-SAD phasing for what would previously have been regarded as very challenging cases with modestly diffracting crystals and low sulfur content.

Data acquisition and analysis at the Structural Biology Center

International Nuclear Information System (INIS)

Westbrook, M.L.; Coleman, T.A.; Daly, R.T.; Pflugrath, J.W.

1996-01-01

The Structural Biology Center (SBC), a national user facility for macromolecular crystallography located at Argonne National Laboratory's Advanced Photon Source, is currently being built and commissioned. SBC facilities include a bending-magnet beamline, an insertion-device beamline, laboratory and office space adjacent to the beamlines, and associated instrumentation, experimental apparatus, and facilities. SBC technical facilities will support anomalous dispersion phasing experiments, data collection from microcrystals, data collection from crystals with large molecular structures and rapid data collection from multiple related crystal structures for protein engineering and drug design. The SBC Computing Systems and Software Engineering Group is tasked with developing the SBC Control System, which includes computing systems, network, and software. The emphasis of SBC Control System development has been to provide efficient and convenient beamline control, data acquisition, and data analysis for maximal facility and experimenter productivity. This paper describes the SBC Control System development, specifically data acquisition and analysis at the SBC, and the development methods used to meet this goal

Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography

Energy Technology Data Exchange (ETDEWEB)

Wall, Michael E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-10-16

X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins.

The protein crystallography beamline BW6 at DORIS - automatic operation and high-throughput data collection

CERN Document Server

Blume, H; Bourenkov, G P; Kosciesza, D; Bartunik, H D

2001-01-01

The wiggler beamline BW6 at DORIS has been optimized for de-novo solution of protein structures on the basis of MAD phasing. Facilities for automatic data collection, rapid data transfer and storage, and online processing have been developed which provide adequate conditions for high-throughput applications, e.g., in structural genomics.

A convolutional neural network-based screening tool for X-ray serial crystallography.

Science.gov (United States)

Ke, Tsung Wei; Brewster, Aaron S; Yu, Stella X; Ushizima, Daniela; Yang, Chao; Sauter, Nicholas K

2018-05-01

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization. open access.

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

Energy Technology Data Exchange (ETDEWEB)

Coquelle, Nicolas [Université Grenoble Alpes, IBS, 38044 Grenoble (France); CNRS, IBS, 38044 Grenoble (France); CEA, IBS, 38044 Grenoble (France); Brewster, Aaron S. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta [European Synchrotron Radiation Facility, BP 220, 38043 Grenoble (France); Burghammer, Manfred, E-mail: burgham@esrf.fr [European Synchrotron Radiation Facility, BP 220, 38043 Grenoble (France); Ghent University, Ghent B-9000 (Belgium); Colletier, Jacques-Philippe, E-mail: burgham@esrf.fr [Université Grenoble Alpes, IBS, 38044 Grenoble (France); CNRS, IBS, 38044 Grenoble (France); CEA, IBS, 38044 Grenoble (France)

2015-05-01

A raster scanning serial protein crystallography approach is presented, that consumes as low ∼200–700 nl of sedimented crystals. New serial data pre-analysis software, NanoPeakCell, is introduced. High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

Room-temperature macromolecular serial crystallography using synchrotron radiation

Directory of Open Access Journals (Sweden)

Francesco Stellato

2014-07-01

Full Text Available A new approach for collecting data from many hundreds of thousands of microcrystals using X-ray pulses from a free-electron laser has recently been developed. Referred to as serial crystallography, diffraction patterns are recorded at a constant rate as a suspension of protein crystals flows across the path of an X-ray beam. Events that by chance contain single-crystal diffraction patterns are retained, then indexed and merged to form a three-dimensional set of reflection intensities for structure determination. This approach relies upon several innovations: an intense X-ray beam; a fast detector system; a means to rapidly flow a suspension of crystals across the X-ray beam; and the computational infrastructure to process the large volume of data. Originally conceived for radiation-damage-free measurements with ultrafast X-ray pulses, the same methods can be employed with synchrotron radiation. As in powder diffraction, the averaging of thousands of observations per Bragg peak may improve the ratio of signal to noise of low-dose exposures. Here, it is shown that this paradigm can be implemented for room-temperature data collection using synchrotron radiation and exposure times of less than 3 ms. Using lysozyme microcrystals as a model system, over 40 000 single-crystal diffraction patterns were obtained and merged to produce a structural model that could be refined to 2.1 Å resolution. The resulting electron density is in excellent agreement with that obtained using standard X-ray data collection techniques. With further improvements the method is well suited for even shorter exposures at future and upgraded synchrotron radiation facilities that may deliver beams with 1000 times higher brightness than they currently produce.

Structure analysis of molecular systems in the Institute of Macromolecular Chemistry of the Czech Academy of Sciences

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich

2010-01-01

Roč. 17, 2a (2010), k32-k34 ISSN 1211-5894. [Struktura 2010. Soláň, 14.06.2010-17.06.2010] R&D Projects: GA AV ČR IAA500500701; GA ČR GA305/07/1073 Institutional research plan: CEZ:AV0Z40500505 Keywords : Academy of Sciences of the Czech Republic * X-ray structure analysis * crystallography Subject RIV: CD - Macromolecular Chemistry http:// xray .cz/ms/bul2010-2a/hasek.pdf

The development of structural x-ray crystallography

Science.gov (United States)

Woolfson, M. M.

2018-03-01

From its birth in 1912, when only the simplest structures could be solved, x-ray structural crystallography is now able to solve macromolecular structures containing many thousands of independent non-hydrogen atoms. This progress has depended on, and been driven by, great technical advances in the development of powerful synchrotron x-ray sources, advanced automated equipment for the collection and storage of large data sets and powerful computers to deal with everything from data processing to running programmes employing complex algorithms for the automatic solution of structures. The sheer number of developments in the subject over the past century makes it impossible for this review to be exhaustive, but it will describe some major developments that will enable the reader to understand how the subject has grown from its humble beginnings to what it is today.

Neutron beam-line shield design for the protein crystallography instrument at the Lujan Center

International Nuclear Information System (INIS)

Russell, G.J.; Pitcher, E.J.; Muhrer, G.; Ferguson, P.D.

2001-01-01

We have developed a very useful methodology for calculating absolute total (neutron plus gamma-ray) dose equivalent rates for use in the design of neutron beam line shields at a spallation neutron source. We have applied this technique to the design of beam line shields for several new materials science instruments being built at the Manuel Lujan Jr. Neutron Scattering Center. These instruments have a variety of collimation systems and different beam line shielding issues. We show here some specific beam line shield designs for the Protein Crystallography Instrument. (author)

Collecting data in the home laboratory: evolution of X-ray sources, detectors and working practices

Energy Technology Data Exchange (ETDEWEB)

Skarzynski, Tadeusz, E-mail: tadeusz.skarzynski@agilent.com [Agilent Technologies, 10 Mead Road, Yarnton, Oxfordshire (United Kingdom)

2013-07-01

Recent developments in X-ray crystallographic hardware related to structural biology research are presented and discussed. While the majority of macromolecular X-ray data are currently collected using highly efficient beamlines at an ever-increasing number of synchrotrons, there is still a need for high-performance reliable systems for in-house experiments. In addition to crystal screening and optimization of data-collection parameters before a synchrotron trip, the home system allows the collection of data as soon as the crystals are produced to obtain the solution of novel structures, especially by the molecular-replacement method, and is invaluable in achieving the quick turnover that is often required for ligand-binding studies in the pharmaceutical industry. There has been a continuous evolution of X-ray sources, detectors and software developed for in-house use in recent years and a diverse range of tools for structural biology laboratories are available. An overview of the main directions of these developments and examples of specific solutions available to the macromolecular crystallography community are presented in this paper, showing that data collection ‘at home’ is still an attractive proposition complementing the use of synchrotron beamlines.

Secure network for beamline control

International Nuclear Information System (INIS)

Ohata, T.; Fukui, T.; Ishii, M.; Furukawa, Y.; Nakatani, T.; Matsushita, T.; Takeuchi, M.; Tanaka, R.; Ishikawa, T.

2001-01-01

In SPring-8, beamline control system is constructed with a highly available distributed network system. The socket based communication protocol is used for the beamline control mainly. Beamline users can control the equipment by sending simple control commands to a server process, which is running on a beamline-managing computer (Ohata et al., SPring-8 beamline control system, ICALEPCS'99, Trieste, Italy, 1999). At the beginning the network was based on the shared topology at all beamlines. Consequently, it has a risk for misapplication of the user's program to access different machines on the network system cross over beamlines. It is serious problem for the SPring-8 beamline control system, because all beamlines controlled with unified software interfaces. We introduced the switching technology and the firewalls to support network access control. Also the virtual networking (VLAN: IEEE 802.1Q) and the gigabit Ethernet technology (IEEE 802.3ab) are introduced. Thus the network security and the reliability are guaranteed at the higher level in SPring-8 beamline

Protein energy landscapes determined by five-dimensional crystallography

International Nuclear Information System (INIS)

Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

2013-01-01

Barriers of activation within the photocycle of a photoactive protein were extracted from comprehensive time courses of time resolved crystallographic data collected at multiple temperature settings. Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012 ▶), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001 ▶), Chem. Rev.101, 1569–1581; Schmidt et al. (2005 ▶), Methods Mol. Biol.305, 115–154; Schmidt (2008 ▶), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallography, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010 ▶), Acta Cryst. A66, 198–206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallographic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes

Beamline 9.0.1 - a high-resolution undulator beamline for gas-phase spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Bozek, J.D.; Heimann, P.A.; Mossessian, D. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)

1997-04-01

Beamline 9.0.1 at the Advanced Light Source is an undulator beamline with a Spherical Grating Monochromator (SGM) which provides very high resolution and flux over the photon energy range 20-320eV. The beamline has been used primarily by the atomic and molecular science community to conduct spectroscopy experiments using electron, ion and fluorescence photon detection. A description of the beamline and its performance will be provided in this abstract.

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

Science.gov (United States)

Keedy, Daniel A; Hill, Zachary B; Biel, Justin T; Kang, Emily; Rettenmaier, T Justin; Brandao-Neto, Jose; Pearce, Nicholas M; von Delft, Frank; Wells, James A; Fraser, James S

2018-06-07

Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. © 2018, Keedy et al.

APS beamline standard components handbook

International Nuclear Information System (INIS)

Kuzay, T.M.

1992-01-01

It is clear that most Advanced Photon Source (APS) Collaborative Access Team (CAT) members would like to concentrate on designing specialized equipment related to their scientific programs rather than on routine or standard beamline components. Thus, an effort is in progress at the APS to identify standard and modular components of APS beamlines. Identifying standard components is a nontrivial task because these components should support diverse beamline objectives. To assist with this effort, the APS has obtained advice and help from a Beamline Standardization and Modularization Committee consisting of experts in beamline design, construction, and operation. The staff of the Experimental Facilities Division identified various components thought to be standard items for beamlines, regardless of the specific scientific objective of a particular beamline. A generic beamline layout formed the basis for this identification. This layout is based on a double-crystal monochromator as the first optical element, with the possibility of other elements to follow. Pre-engineering designs were then made of the identified standard components. The Beamline Standardization and Modularization Committee has reviewed these designs and provided very useful input regarding the specifications of these components. We realize that there will be other configurations that may require special or modified components. This Handbook in its current version (1.1) contains descriptions, specifications, and pre-engineering design drawings of these standard components. In the future, the APS plans to add engineering drawings of identified standard beamline components. Use of standard components should result in major cost reductions for CATs in the areas of beamline design and construction

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

Science.gov (United States)

Tsujino, Soichiro; Tomizaki, Takashi

2016-05-01

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

A new small-angle X-ray scattering set-up on the crystallography beamline I711 at MAX-lab

DEFF Research Database (Denmark)

Knaapila, M.; Svensson, C.; Barauskas, J.

2009-01-01

A small-angle X-ray scattering (SAXS) set-up has recently been developed at beamline I711 at the MAX II storage ring in Lund (Sweden). An overview of the required modifications is presented here together with a number of application examples. The accessible q range in a SAXS experiment is 0.009-0...

Some Aspects of Crystal Centering During X-ray High-throughput Protein Crystallography Experiment

Science.gov (United States)

Gaponov, Yu. A.; Matsugaki, N.; Sasajima, K.; Igarashi, N.; Wakatsuki, S.

A set of algorithms and procedures of a crystal loop centering during X-ray high-throughput protein crystallography experiment has been designed and developed. A simple algorithm of the crystal loop detection and preliminary recognition has been designed and developed. The crystal loop detection algorithm is based on finding out the crystal loop ending point (opposite to the crystal loop pin) using image cross section (digital image column) profile analysis. The crystal loop preliminary recognition procedure is based on finding out the crystal loop sizes and position using image cross section profile analysis. The crystal loop fine recognition procedure based on Hooke-Jeeves pattern search method with an ellipse as a fitting pattern has been designed and developed. The procedure of restoring missing coordinate of the crystal loop is described. Based on developed algorithms and procedures the optimal auto-centering procedure has been designed and developed. A procedure of optimal manual crystal centering (Two Clicks Procedure) has been designed and developed. Developed procedures have been integrated into control software system PCCS installed at crystallography beamlines Photon Factory BL5A and PF-AR NW12, KEK.

Status of the ELIMED multidisciplinary and medical beam-line at ELI-Beamlines

International Nuclear Information System (INIS)

Romano, F; Cirrone, G A P; Cuttone, G; Schillaci, F; Scuderi, V; Amico, A; Candiano, G; Larosa, G; Leanza, R; Manna, R; Marchese, V; Milluzzo, G; Petringa, G; Pipek, J; Giordanengo, S; Guarachi, L F; Marchetto, F; Sacchi, R; Korn, G; Margarone, D

2017-01-01

Nowadays, one of the biggest challenges consists in using high intensity laser-target interaction to generate high-energy ions for medical purposes, eventually replacing the old paradigm of acceleration characterized by huge and complex machines. In order to investigate the feasibility of using laser-driven ion beams for multidisciplinary application, a dedicated beam transport line will be installed at the ELI-Beamlines facility in Prague (CZ), as a part of the User-oriented ELIMAIA beam-line dedicated to ion acceleration and their potential applications. The beam-line section dedicated to transport and dosimetric endpoints is called ELIMED (ELI-Beamlines MEDical and multidisciplinary applications) and will be developed by the INFN-LNS. (paper)

Racemic DNA Crystallography

OpenAIRE

Mandal , Pradeep K.; Collie , Gavin W.; Kauffmann , Brice; Huc , Ivan

2014-01-01

International audience; Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of Land D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propens...

Racemic DNA crystallography.

Science.gov (United States)

Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

2014-12-22

Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An object model for beamline descriptions

International Nuclear Information System (INIS)

Hill, B.W.; Martono, H.; Gillespie, J.S.

1997-01-01

Translation of beamline model descriptions between different accelerator codes presents a unique challenge due to the different representations used for various elements and subsystems. These differences range from simple units conversions to more complex translations involving multiple beamline components. A representation of basic accelerator components is being developed in order to define a meta-structure from which beamline models, in different codes, can be described and to facilitate the translation of models between these codes. Sublines of basic components will be used to represent more complex beamline descriptions and bridge the gap between codes which may represent a beamline element as a single entity, and those which use multiple elements to describe the same physical device. A C++ object model for supporting this beamline description and a grammar for describing beamlines in terms of these components is being developed. The object model will support a common graphic user interface and translation filters for representing native beamline descriptions for a variety of accelerator codes. An overview of our work on the object model for beamline descriptions is presented here. copyright 1997 American Institute of Physics

Performance characteristics needed for protein crystal diffraction x-ray detectors

International Nuclear Information System (INIS)

Westbrook, E. M.

1999-01-01

During the 1990's, macromolecular crystallography became progressively more dependent on synchrotrons X-ray sources for diffraction data collection. Detectors of this diffraction data at synchrotrons beamlines have evolved over the decade, from film to image phosphor plates, and then to CCD systems. These changes have been driven by the data quality and quantity improvements each newer detector technology provided. The improvements have been significant. It is likely that newer detector technologies will be adopted at synchrotron beamlines for crystallographic diffraction data collection in the future, but these technologies will have to compete with existing CCD detector systems which are already excellent and are getting incrementally better in terms of size, speed, efficiency, and resolving power. Detector development for this application at synchrotrons must concentrate on making systems which are bigger and faster than CCDs and which can capture weak data more efficiently. And there is a need for excellent detectors which are less expensive than CCD systems

Multigrain crystallography

DEFF Research Database (Denmark)

Sørensen, Henning Osholm; Schmidt, Søren; Wright, Jonathan P.

2012-01-01

We summarize exploratory work on multigrain crystallography. The experimental arrangement comprises a monochromatic beam, a fully illuminated sample with up to several hundred grains in transmission geometry on a rotary table and a 2D detector. Novel algorithms are presented for indexing, integra......We summarize exploratory work on multigrain crystallography. The experimental arrangement comprises a monochromatic beam, a fully illuminated sample with up to several hundred grains in transmission geometry on a rotary table and a 2D detector. Novel algorithms are presented for indexing...... of the methodology in terms of number of grains, size of unit cell and direct space resolution. First experimental results in the fields of chemistry, structural biology and time-resolved studies in photochemistry are presented. As an outlook, the concept of TotalCrystallography is introduced, defined...

Modeling of X-ray beamlines and devices

International Nuclear Information System (INIS)

Ice, G.E.

1996-01-01

X-ray beamlines on synchrotron sources are similar in size and complexity to beamlines at state-of-the-art neutron sources. The design principles, tools, and optimization strategies for synchrotron beamlines are also similar to those of neutron beamlines. The authors describe existing design tools for modeling synchrotron radiation beamlines and describe how these tools have evolved over the last two decades. The development of increasingly powerful modeling tools has been driven by the escalating cost and sophistication of state-of-the-art beamlines and by a world-wide race to exploit advanced synchrotron radiation sources

Design and performance of U7B beamline and X-ray diffraction and scattering station at NSRL and its preliminary experiments in protein crystallography

International Nuclear Information System (INIS)

Pan Guoqiang; Xu, Chaoyin; Fan Rong; Gao Chen; Lou Xiaohua; Teng Maikun; Huang Qingqiu; Niu Liwen

2005-01-01

This publication describes the design and performance of the U7B beamline and X-ray diffraction and diffuse scattering station at National Synchrotron Radiation Laboratory (NSRL). The beamline optics comprise a Pt-coated toroidal focusing mirror and a double-crystal Si(1 1 1) monochromator. A preliminary experiment of diffraction data collection and processing was carried out using a commercial imaging plate detector system (Mar345). The data collected from one single crystal of acutohaemolysin, a Lys49-type PLA2 from Agkistrodon acutus venom, are of high quality

Timely deposition of macromolecular structures is necessary for peer review

International Nuclear Information System (INIS)

Joosten, Robbie P.; Soueidan, Hayssam; Wessels, Lodewyk F. A.; Perrakis, Anastassis

2013-01-01

Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature

Timely deposition of macromolecular structures is necessary for peer review

Energy Technology Data Exchange (ETDEWEB)

Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Soueidan, Hayssam; Wessels, Lodewyk F. A. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam (Netherlands); Perrakis, Anastassis, E-mail: a.perrakis@nki.nl [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)

2013-12-01

Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature.

Improvement of an automated protein crystal exchange system PAM for high-throughput data collection

International Nuclear Information System (INIS)

Hiraki, Masahiko; Yamada, Yusuke; Chavas, Leonard M. G.; Wakatsuki, Soichi; Matsugaki, Naohiro

2013-01-01

A special liquid-nitrogen Dewar with double capacity for the sample-exchange robot has been created at AR-NE3A at the Photon Factory, allowing continuous fully automated data collection. In this work, this new system is described and the stability of its calibration is discussed. Photon Factory Automated Mounting system (PAM) protein crystal exchange systems are available at the following Photon Factory macromolecular beamlines: BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. The beamline AR-NE3A has been constructed for high-throughput macromolecular crystallography and is dedicated to structure-based drug design. The PAM liquid-nitrogen Dewar can store a maximum of three SSRL cassettes. Therefore, users have to interrupt their experiments and replace the cassettes when using four or more of them during their beam time. As a result of investigation, four or more cassettes were used in AR-NE3A alone. For continuous automated data collection, the size of the liquid-nitrogen Dewar for the AR-NE3A PAM was increased, doubling the capacity. In order to check the calibration with the new Dewar and the cassette stand, calibration experiments were repeatedly performed. Compared with the current system, the parameters of the novel system are shown to be stable

Improvement of an automated protein crystal exchange system PAM for high-throughput data collection

Energy Technology Data Exchange (ETDEWEB)

Hiraki, Masahiko, E-mail: masahiko.hiraki@kek.jp; Yamada, Yusuke; Chavas, Leonard M. G. [High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Wakatsuki, Soichi [High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025-7015 (United States); Stanford University, Beckman Center B105, Stanford, CA 94305-5126 (United States); Matsugaki, Naohiro [High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan)

2013-11-01

A special liquid-nitrogen Dewar with double capacity for the sample-exchange robot has been created at AR-NE3A at the Photon Factory, allowing continuous fully automated data collection. In this work, this new system is described and the stability of its calibration is discussed. Photon Factory Automated Mounting system (PAM) protein crystal exchange systems are available at the following Photon Factory macromolecular beamlines: BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. The beamline AR-NE3A has been constructed for high-throughput macromolecular crystallography and is dedicated to structure-based drug design. The PAM liquid-nitrogen Dewar can store a maximum of three SSRL cassettes. Therefore, users have to interrupt their experiments and replace the cassettes when using four or more of them during their beam time. As a result of investigation, four or more cassettes were used in AR-NE3A alone. For continuous automated data collection, the size of the liquid-nitrogen Dewar for the AR-NE3A PAM was increased, doubling the capacity. In order to check the calibration with the new Dewar and the cassette stand, calibration experiments were repeatedly performed. Compared with the current system, the parameters of the novel system are shown to be stable.

Beamline Design and Instrumentation for the Imaging and Coherence Beamline I13L at the Diamond Light Source

Science.gov (United States)

Wagner, U. H.; Pešić, Z. D.; De Fanis, A.; Rau, C.

2013-03-01

I13L is a 250 m long hard x-ray beamline (6 keV to 35 keV) at the Diamond Light Source. The beamline comprises of two independent experimental endstations: one for imaging in direct space using x-ray microscopy and one for imaging in reciprocal space using coherent diffraction based imaging techniques. In this paper we will discuss the fundamental design concepts of the beamline and explain their implications for the civil engineering of the endstation building and the beamline instrumentation. For the latter this paper will focus on the beamline mirror systems and monochromators.

Beamline Design and Instrumentation for the Imaging and Coherence Beamline I13L at the Diamond Light Source

International Nuclear Information System (INIS)

Wagner, U H; Pešić, Z D; Fanis, A De; Rau, C

2013-01-01

I13L is a 250 m long hard x-ray beamline (6 keV to 35 keV) at the Diamond Light Source. The beamline comprises of two independent experimental endstations: one for imaging in direct space using x-ray microscopy and one for imaging in reciprocal space using coherent diffraction based imaging techniques. In this paper we will discuss the fundamental design concepts of the beamline and explain their implications for the civil engineering of the endstation building and the beamline instrumentation. For the latter this paper will focus on the beamline mirror systems and monochromators.

Fluid Physics and Macromolecular Crystal Growth in Microgravity

Science.gov (United States)

Helliwell, John R.; Snell, Edward H.; Chayen, Naomi E.; Judge, Russell A.; Boggon, Titus J.; Pusey, M. L.; Rose, M. Franklin (Technical Monitor)

2000-01-01

The first protein crystallization experiment in microgravity was launched in April, 1981 and used Germany's Technologische Experimente unter Schwerelosigkeit (TEXUS 3) sounding rocket. The protein P-galactosidase (molecular weight 465Kda) was chosen as the sample with a liquid-liquid diffusion growth method. A sliding device brought the protein, buffer and salt solution into contact when microgravity was reached. The sounding rocket gave six minutes of microgravity time with a cine camera and schlieren optics used to monitor the experiment, a single growth cell. In microgravity a strictly laminar diffusion process was observed in contrast to the turbulent convection seen on the ground. Several single crystals, approx 100micron in length, were formed in the flight which were of inferior but of comparable visual quality to those grown on the ground over several days. A second experiment using the same protocol but with solutions cooled to -8C (kept liquid with glycerol antifreeze) again showed laminar diffusion. The science of macromolecular structural crystallography involves crystallization of the macromolecule followed by use of the crystal for X-ray diffraction experiments to determine the three dimensional structure of the macromolecule. Neutron protein crystallography is employed for elucidation of H/D exchange and for improved definition of the bound solvent (D20). The structural information enables an understanding of how the molecule functions with important potential for rational drug design, improved efficiency of industrial enzymes and agricultural chemical development. The removal of turbulent convection and sedimentation in microgravity, and the assumption that higher quality crystals will be produced, has given rise to the growing number of crystallization experiments now flown. Many experiments can be flown in a small volume with simple, largely automated, equipment - an ideal combination for a microgravity experiment. The term "protein crystal growth

Limiting effects in double EEX beamline

Science.gov (United States)

Ha, G.; Power, J. G.; Conde, M.; Doran, D. S.; Gai, W.

2017-07-01

The double emittance exchange (EEX) beamline is suggested to overcome the large horizontal emittance and transverse jitter issues associated with the single EEX beamline while preserving its powerful phase-space manipulation capability. However, the double EEX beamline also has potential limitations due to coherent synchrotron radiation (CSR) and transverse jitter. The former limitation arises because double EEX uses twice as many bending magnets as single EEX which means stronger CSR effects degrading the beam quality. The latter limitation arises because a longitudinal jitter in front of the first EEX beamline is converted into a transverse jitter in the middle section (between the EEX beamlines) which can cause beam loss or beam degradation. In this paper, we numerically explore the effects of these two limitations on the emittance and beam transport.

Limiting effects in double EEX beamline

International Nuclear Information System (INIS)

Ha, G; Power, J G; Conde, M; Doran, D S; Gai, W

2017-01-01

The double emittance exchange (EEX) beamline is suggested to overcome the large horizontal emittance and transverse jitter issues associated with the single EEX beamline while preserving its powerful phase-space manipulation capability. However, the double EEX beamline also has potential limitations due to coherent synchrotron radiation (CSR) and transverse jitter. The former limitation arises because double EEX uses twice as many bending magnets as single EEX which means stronger CSR effects degrading the beam quality. The latter limitation arises because a longitudinal jitter in front of the first EEX beamline is converted into a transverse jitter in the middle section (between the EEX beamlines) which can cause beam loss or beam degradation. In this paper, we numerically explore the effects of these two limitations on the emittance and beam transport. (paper)

On macromolecular refinement at subatomic resolution with interatomic scatterers

Energy Technology Data Exchange (ETDEWEB)

Afonine, Pavel V., E-mail: pafonine@lbl.gov; Grosse-Kunstleve, Ralf W.; Adams, Paul D. [Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720 (United States); Lunin, Vladimir Y. [Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290 (Russian Federation); Urzhumtsev, Alexandre [IGMBC, 1 Rue L. Fries, 67404 Illkirch and IBMC, 15 Rue R. Descartes, 67084 Strasbourg (France); Faculty of Sciences, Nancy University, 54506 Vandoeuvre-lès-Nancy (France); Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720 (United States)

2007-11-01

Modelling deformation electron density using interatomic scatters is simpler than multipolar methods, produces comparable results at subatomic resolution and can easily be applied to macromolecules. A study of the accurate electron-density distribution in molecular crystals at subatomic resolution (better than ∼1.0 Å) requires more detailed models than those based on independent spherical atoms. A tool that is conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8–1.0 Å, the number of experimental data is insufficient for full multipolar model refinement. As an alternative, a simpler model composed of conventional independent spherical atoms augmented by additional scatterers to model bonding effects has been proposed. Refinement of these mixed models for several benchmark data sets gave results that were comparable in quality with the results of multipolar refinement and superior to those for conventional models. Applications to several data sets of both small molecules and macromolecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package.

Macromolecular therapeutics.

Science.gov (United States)

Yang, Jiyuan; Kopeček, Jindřich

2014-09-28

This review covers water-soluble polymer-drug conjugates and macromolecules that possess biological activity without attached low molecular weight drugs. The main design principles of traditional and backbone degradable polymer-drug conjugates as well as the development of a new paradigm in nanomedicines - (low molecular weight) drug-free macromolecular therapeutics are discussed. To address the biological features of cancer, macromolecular therapeutics directed to stem/progenitor cells and the tumor microenvironment are deliberated. Finally, the future perspectives of the field are briefly debated. Copyright © 2014 Elsevier B.V. All rights reserved.

Doublet III beamline: as-built

International Nuclear Information System (INIS)

Harder, C.R.; Holland, M.M.; Parker, J.W.; Gunn, J.; Resnick, L.

1980-03-01

In order to fully exploit Doublet III capabilities and to study new plasma physics regimes, a Neutral Beam Injector System has been constructed. Initially, a two beamline system will supply 7 MW of heat to the plasma. The system is currently being expanded to inject approx. 20 MW of power (6 beamlines). Each beamline is equipped with two Lawrence Berkeley Laboratory type rectangular ion sources with 10 cm x 40 cm extraction grids. These sources will accelerate hydrogen ions to 80 keV, with extracted beam currents in excess of 80 A per source expected. The first completed source is currently being tested and conditioned on the High Voltage Test Stand at Lawrence Livermore Laboratory. This paper pictorially reviews the as-built Doublet III neutral beamline with emphasis on component relation and configuration relative to spatial and source imposed design constraints

Human factors design for the BMIT biomedical beamlines

International Nuclear Information System (INIS)

Miller, C Denise; Wysokinski, Tomasz W; Belev, George; Chapman, L Dean

2013-01-01

Operation of a biomedical beamline poses a unique set of operational and instrumentation challenges for a synchrotron facility. From proper handling and care of live animals and animal tissues, to a user community drawn primarily from the medical and veterinary realms, the work of a biomedical beamline is unique when compared to other beamlines. At the Biomedical Imaging and Therapy (BMIT) beamlines at Canadian Light Source (CLS), operation of the beamlines is geared towards our user community of medical personnel, in addition to basic science researchers. Human factors considerations have been incorporated wherever possible on BMIT, including in the design of software and hardware, as well as ease-of-use features of beamline control stations and experiment hutches. Feedback from users continues to drive usability improvements to beamline operations.

Structure determination by X-ray crystallography

CERN Document Server

Ladd, M F C

1977-01-01

Crystallography may be described as the science of the structure of materi­ als, using this word in its widest sense, and its ramifications are apparent over a broad front of current scientific endeavor. It is not surprising, therefore, to find that most universities offer some aspects of crystallography in their undergraduate courses in the physical sciences. It is the principal aim of this book to present an introduction to structure determination by X-ray crystal­ lography that is appropriate mainly to both final-year undergraduate studies in crystallography, chemistry, and chemical physics, and introductory post­ graduate work in this area of crystallography. We believe that the book will be of interest in other disciplines, such as physics, metallurgy, biochemistry, and geology, where crystallography has an important part to play. In the space of one book, it is not possible either to cover all aspects of crystallography or to treat all the subject matter completely rigorously. In particular, certain ...

Beamlines on the SPring-8 project

Energy Technology Data Exchange (ETDEWEB)

Ohno, Hideo [Japan Atomic Energy Research Inst., Kamigori, Hyogo (Japan). Kansai Research Establishment

1997-03-01

SPring-8 project is going to construct a ultrahigh-brilliance X-ray synchrotron radiation facility and commissioning of the storage ring is expected in Spring 1977. The facility will be available to scientists and engineers of universities, national laboratories and industries not only from Japan but also from abroad. 20 proposals for public beamlines are submitted to the Beamline Committee and the ten public beamlines are scheduled for completion by the end of 1997. (author)

Status of Indus-1 and Indus-2 beamlines

CERN Document Server

Nandedkar, R V

2003-01-01

Indus-1 and Indus-2 are two synchrotron radiation sources that are planned in India. Indus-1 is a 450 MeV electron storage ring for vacuum ultra-violet soft X-ray radiation. This source is operational. Two beamlines, viz. a soft X-ray/vacuum ultra-violet reflectometry beamline and an angle integrated photoelectron spectroscopy beamline are already operational. Angle resolved photoelectron spectroscopy and photophysics beamlines are going to be operational soon. The second Indian synchrotron source is the 2.5 GeV Indus-2 electron storage ring that is under construction and is expected to be ready for commissioning in the year 2003. Of the total 27 beamlines possible on this ring, about 10 beamlines are already planned and are in the design stage.

Status of Indus-1 and Indus-2 beamlines

International Nuclear Information System (INIS)

Nandedkar, R.V.; Sawhney, K.J.S.

2003-01-01

Indus-1 and Indus-2 are two synchrotron radiation sources that are planned in India. Indus-1 is a 450 MeV electron storage ring for vacuum ultra-violet soft X-ray radiation. This source is operational. Two beamlines, viz. a soft X-ray/vacuum ultra-violet reflectometry beamline and an angle integrated photoelectron spectroscopy beamline are already operational. Angle resolved photoelectron spectroscopy and photophysics beamlines are going to be operational soon. The second Indian synchrotron source is the 2.5 GeV Indus-2 electron storage ring that is under construction and is expected to be ready for commissioning in the year 2003. Of the total 27 beamlines possible on this ring, about 10 beamlines are already planned and are in the design stage

Rotary Valve & Beamline Highlights for Fiscal Year 2017

Energy Technology Data Exchange (ETDEWEB)

Fitsos, P [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2017-09-21

This Fiscal Year (FY) work was divided between continued testing and characterization work of the Rotary Valve (RV) and mechanical engineering support for the beamline hardware stands. This configuration is more like the final setup with the accelerator firing deuterons down the evacuated beamline toward the RV for interaction with the deuterium and neutron production. The beamline cells were part of an experiment to reduce the impact that RV gas would have on the beamline vacuum. This work will be reported separately from this report. Previous testing had been with the beamline at atmospheric pressure and now the goal was to get test results of the RV with it connected to a beamline that’s running at some level of vacuum.

Beamline instrumentation and experiment automation for the Rossendorf Beamline at ESRF/Grenoble (F)

International Nuclear Information System (INIS)

Oehme, W.; Dienel, S.; Proehl, D.

2000-03-01

The Rossendorf research center finished the work (from 1996 - 1998) for building its own beamline for experiments with synchrotron radiation at the ESRF (European Synchrotron Radiation Facility) at Grenoble/France. The beamline has two measuring systems for alternative use for experiments investigating radioactive samples by means of X-ray absorption spectrometry, and materials structures by means of X-ray diffraction analyses. The report in hand focuses on work performed required for the control equipment for optical systems and performance of the measuring systems with respect to electronics, calculation methods, and software. Hardware components of importance to system instrumentation are explained, as well as the basic computing tasks and general software principles, and are illustrated with some examples. The general setting of the beamline is represented in a tabulated overview. The literature list serves as a guideline for detailed documentation. (orig./CB) [de

Recent advances in racemic protein crystallography.

Science.gov (United States)

Yan, Bingjia; Ye, Linzhi; Xu, Weiliang; Liu, Lei

2017-09-15

Solution of the three-dimensional structures of proteins is a critical step in deciphering the molecular mechanisms of their bioactivities. Among the many approaches for obtaining protein crystals, racemic protein crystallography has been developed as a unique method to solve the structures of an increasing number of proteins. Exploiting unnatural protein enantiomers in crystallization and resolution, racemic protein crystallography manifests two major advantages that are 1) to increase the success rate of protein crystallization, and 2) to obviate the phase problem in X-ray diffraction. The requirement of unnatural protein enantiomers in racemic protein crystallography necessitates chemical protein synthesis, which is hitherto accomplished through solid phase peptide synthesis and chemical ligation reactions. This review highlights the fundamental ideas of racemic protein crystallography and surveys the harvests in the field of racemic protein crystallography over the last five years from early 2012 to late 2016. Copyright © 2017. Published by Elsevier Ltd.

Beamline 9.3.2 - a high-resolution, bend-magnet beamline with circular polarization capability

Energy Technology Data Exchange (ETDEWEB)

Moler, E.J.; Hussain, Z.; Howells, M.R. [Lawrence Berkeley National Lab., CA (United States)] [and others

1997-04-01

Beamline 9.3.2 is a high resolution, SGM beamline on an ALS bending magnet with access to photon energies from 30-1500 eV. Features include circular polarization capability, a rotating chamber platform that allows switching between experiments without breaking vacuum, an active feedback system that keeps the beam centered on the entrance slit of the monochromator, and a bendable refocusing mirror. The beamline optics consist of horizontally and vertically focussing mirrors, a Spherical Grating Monochromator (SGM) with movable entrance and exit slits, and a bendable refocussing mirror. In addition, a movable aperature has been installed just upstream of the vertically focussing mirror which can select the x-rays above or below the plane of the synchrotron storage ring, allowing the user to select circularly or linearly polarized light. Circularly polarized x-rays are used to study the magnetic properties of materials. Beamline 9.3.2 can supply left and right circularly polarized x-rays by a computer controlled aperture which may be placed above or below the plane of the synchrotron storage ring. The degree of linear and circular polarization has been measured and calibrated.

Macromolecular refinement by model morphing using non-atomic parameterizations.

Science.gov (United States)

Cowtan, Kevin; Agirre, Jon

2018-02-01

Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.

SUNY beamline facilities at the National Synchrotron Light Source

International Nuclear Information System (INIS)

Coppens, P.

1993-01-01

This document presents information concerning: crystallography (single crystal studies); crystallography (powder diffraction); crystallography (surface structure); exafs and interface studies; and small angle scattering

A Test Beamline on Diamond Light Source

International Nuclear Information System (INIS)

Sawhney, K. J. S.; Dolbnya, I. P.; Tiwari, M. K.; Alianelli, L.; Scott, S. M.; Preece, G. M.; Pedersen, U. K.; Walton, R. D.

2010-01-01

A Test beamline B16 has been built on the 3 GeV Diamond synchrotron radiation source. The beamline covers a wide photon energy range from 2 to 25 keV. The beamline is highly flexible and versatile in terms of the available beam size (a micron to 100 mm) and the range of energy resolution and photon flux; by virtue of its several operational modes, and the different inter-changeable instruments available in the experiments hutch. Diverse experimental configurations can be flexibly configured using a five-circle diffractometer, a versatile optics test bench, and a suite of detectors. Several experimental techniques including reflectivity, diffraction and imaging are routinely available. Details of the beamline and its measured performance are presented.

The INE-Beamline for Actinide Research at ANKA

Science.gov (United States)

Brendebach, Boris; Denecke, Melissa A.; Rothe, Jörg; Dardenne, Kathy; Römer, Jürgen

2007-02-01

The INE-Beamline for actinide research at the synchrotron source ANKA is now fully operational. This beamline was designed, built, and commissioned by the Institut für Nukleare Entsorgung (INE) at the Forschungszentrum Karlsruhe (FZK), Germany. It is dedicated to actinide speciation investigations related to nuclear waste disposal as well as applied and basic actinide research. Experiments on radioactive samples with activities up to 106 times the limit of exemption inside a safe and flexible double containment concept are possible. The close proximity of the beamline to INE's active laboratories is unique in Europe. Currently, experiments can be performed in an X-ray energy range from around 2.15 keV (P K edge) to 24.35 keV (Pd K edge). The INE-Beamline design is optimized for spectroscopy with emphasis on surface sensitive techniques. A microfocus option is presently being installed at the INE-Beamline. Access to the INE-Beamline is possible through cooperation with INE, through the ANKA proposal system and via the European Network of Excellence for Actinide Sciences (ACTINET).

Radiation-resistant beamline components at LAMPF

International Nuclear Information System (INIS)

Macek, R.J.; Grisham, D.L.; Lambert, J.e.; Werbeck, R.

1983-01-01

A variety of highly radiation-resistant beamline components have been successfully developed at LAMPF primarily for use in the target cells and beam stop area of the intense proton beamline. Design features and operating experience are reviewed for magnets, instrumentation, targets, vacuum seals, vacuum windows, collimators, and beam stops

UV-Visible Absorption Spectroscopy Enhanced X-ray Crystallography at Synchrotron and X-ray Free Electron Laser Sources.

Science.gov (United States)

Cohen, Aina E; Doukov, Tzanko; Soltis, Michael S

2016-01-01

This review describes the use of single crystal UV-Visible Absorption micro-Spectrophotometry (UV-Vis AS) to enhance the design and execution of X-ray crystallography experiments for structural investigations of reaction intermediates of redox active and photosensitive proteins. Considerations for UV-Vis AS measurements at the synchrotron and associated instrumentation are described. UV-Vis AS is useful to verify the intermediate state of an enzyme and to monitor the progression of reactions within crystals. Radiation induced redox changes within protein crystals may be monitored to devise effective diffraction data collection strategies. An overview of the specific effects of radiation damage on macromolecular crystals is presented along with data collection strategies that minimize these effects by combining data from multiple crystals used at the synchrotron and with the X-ray free electron laser.

National synchrotron light source. Activity report, October 1, 1994--September 30, 1995

Energy Technology Data Exchange (ETDEWEB)

Rothman, E.Z.; Hastings, J. [eds.

1996-05-01

This report discusses research conducted at the National Synchrotron Light Source in the following areas: atomic and molecular science; energy dispersive diffraction; lithography, microscopy, and tomography; nuclear physics; scattering and crystallography studies of biological materials; time resolved spectroscopy; UV photoemission and surface science; x-ray absorption spectroscopy; x-ray scattering and crystallography; x-ray topography; the 1995 NSLS annual users` meeting; 17th international free electron laser conference; micro bunches workshop; VUV machine; VUV storage ring parameters; beamline technical improvements; x-ray beamlines; x-ray storage ring parameters; the NSLS source development laboratory; the accelerator test facility (ATF); NSLS facility improvements; NSLS advisory committees; NSLS staff; VUV beamline guide; and x-ray beamline guide.

National synchrotron light source. Activity report, October 1, 1994--September 30, 1995

International Nuclear Information System (INIS)

Rothman, E.Z.; Hastings, J.

1996-05-01

This report discusses research conducted at the National Synchrotron Light Source in the following areas: atomic and molecular science; energy dispersive diffraction; lithography, microscopy, and tomography; nuclear physics; scattering and crystallography studies of biological materials; time resolved spectroscopy; UV photoemission and surface science; x-ray absorption spectroscopy; x-ray scattering and crystallography; x-ray topography; the 1995 NSLS annual users' meeting; 17th international free electron laser conference; micro bunches workshop; VUV machine; VUV storage ring parameters; beamline technical improvements; x-ray beamlines; x-ray storage ring parameters; the NSLS source development laboratory; the accelerator test facility (ATF); NSLS facility improvements; NSLS advisory committees; NSLS staff; VUV beamline guide; and x-ray beamline guide

Beamline for Schools Safety Awareness Day

CERN Multimedia

Photo Service, CERN

2014-01-01

The first two teams to participate in CERN's Beamline for Schools project spent their first day at CERN at the Safety Training Center in Prévessin. They covered amongst others radiation protection, cryogenics and fire-fighting. The teams will spend the rest of the week at the T9 beamline.

The BEAR Beamline at Elettra

International Nuclear Information System (INIS)

Nannarone, S.; Pasquali, L.; Selvaggi, G.; Borgatti, F.; DeLuisa, A.; Doyle, B.P.; Gazzadi, G.C.; Giglia, A.; Finetti, P.; Pedio, M.; Mahne, N.; Naletto, G.; Pelizzo, M.G.; Tondello, G.

2004-01-01

The BEAR (Bending Magnet for Emission Absorption and Reflectivity) beamline is installed at the right exit of the 8.1 bending magnet at ELETTRA. The beamline - in operation since January 2003 - delivers linear and circularly polarized radiation in the 5 - 1600 eV energy range. The experimental station is composed of a UHV chamber for reflectivity, absorption, fluorescence and angle resolved photoemission measurements and a UHV chamber for in-situ sample preparation

EPICS and its role in data acquisition and beamline control

International Nuclear Information System (INIS)

Mooney, T. M.; Arnold, N. D.; Boucher, E.; Cha, B. K.; Goetze, K. A.; Kraimer, M. R.; Rivers, M. L.; Sluiter, R. L.; Sullivan, J. P.; Wallis, D. B.

1999-01-01

Beamline-control and data-acquisition software based on EPICS (a tool kit for building distributed control systems) has been running on many Advanced Photon Source beamlines for several years. EPICS itself, the collaborative software-development effort surrounding it, and EPICS-based beamline software have been described previously in general terms. This talk will review and update that material, focusing on the role EPICS core software plays in beamline applications and on the effects of a few defining characteristics of EPICS on the beamline software we have developed with it

The Stanford Automated Mounter: Enabling High-Throughput Protein Crystal Screening at SSRL

International Nuclear Information System (INIS)

Smith, C.A.; Cohen, A.E.

2009-01-01

The macromolecular crystallography experiment lends itself perfectly to high-throughput technologies. The initial steps including the expression, purification, and crystallization of protein crystals, along with some of the later steps involving data processing and structure determination have all been automated to the point where some of the last remaining bottlenecks in the process have been crystal mounting, crystal screening, and data collection. At the Stanford Synchrotron Radiation Laboratory, a National User Facility that provides extremely brilliant X-ray photon beams for use in materials science, environmental science, and structural biology research, the incorporation of advanced robotics has enabled crystals to be screened in a true high-throughput fashion, thus dramatically accelerating the final steps. Up to 288 frozen crystals can be mounted by the beamline robot (the Stanford Auto-Mounting System) and screened for diffraction quality in a matter of hours without intervention. The best quality crystals can then be remounted for the collection of complete X-ray diffraction data sets. Furthermore, the entire screening and data collection experiment can be controlled from the experimenter's home laboratory by means of advanced software tools that enable network-based control of the highly automated beamlines.

Fully Automated Data Collection Using PAM and the Development of PAM/SPACE Reversible Cassettes

Science.gov (United States)

Hiraki, Masahiko; Watanabe, Shokei; Chavas, Leonard M. G.; Yamada, Yusuke; Matsugaki, Naohiro; Igarashi, Noriyuki; Wakatsuki, Soichi; Fujihashi, Masahiro; Miki, Kunio; Baba, Seiki; Ueno, Go; Yamamoto, Masaki; Suzuki, Mamoru; Nakagawa, Atsushi; Watanabe, Nobuhisa; Tanaka, Isao

2010-06-01

To remotely control and automatically collect data in high-throughput X-ray data collection experiments, the Structural Biology Research Center at the Photon Factory (PF) developed and installed sample exchange robots PAM (PF Automated Mounting system) at PF macromolecular crystallography beamlines; BL-5A, BL-17A, AR-NW12A and AR-NE3A. We developed and installed software that manages the flow of the automated X-ray experiments; sample exchanges, loop-centering and X-ray diffraction data collection. The fully automated data collection function has been available since February 2009. To identify sample cassettes, PAM employs a two-dimensional bar code reader. New beamlines, BL-1A at the Photon Factory and BL32XU at SPring-8, are currently under construction as part of Targeted Proteins Research Program (TPRP) by the Ministry of Education, Culture, Sports, Science and Technology of Japan. However, different robots, PAM and SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), will be installed at BL-1A and BL32XU, respectively. For the convenience of the users of both facilities, pins and cassettes for PAM and SPACE are developed as part of the TPRP.

The BESSY X-ray microfocus beamline project

International Nuclear Information System (INIS)

Erko, A.; Schaefers, F.; Firsov, A.; Peatman, W.B.; Eberhardt, W.; Signorato, R.

2004-01-01

The design and construction of a beamline dedicated to X-ray absorption spectroscopy, X-ray fluorescence analysis, X-ray diffraction and X-ray small-angle scattering measurements with micron and submicron spatial resolution in the photon energy range of 1.9-30 keV are reported here. The main feature of the beamline is a combination of all these methods in one experimental station. The source will be a BESSY 7-T wavelength shifter, which is already in operation. Such a wavelength shifter with its continuous spectrum is an optimum source for these experiments. Glass capillaries and the combination of a linear Bragg-Fresnel lens and bimorph mirror were chosen as the special optical components in the beamline. This beamline will open for BESSY users the possibility to perform experiments on the same sample applying a microfocused X-ray beam in combination with advanced experimental methods

Practical macromolecular cryocrystallography

Energy Technology Data Exchange (ETDEWEB)

Pflugrath, J. W., E-mail: jim.pflugrath@gmail.com [Rigaku Americas Corp., 9009 New Trails Drive, The Woodlands, TX 77381 (United States)

2015-05-27

Current methods, reagents and experimental hardware for successfully and reproducibly flash-cooling macromolecular crystals to cryogenic temperatures for X-ray diffraction data collection are reviewed. Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100 K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented.

The Upgrade Programme for the Structural Biology beamlines at the European Synchrotron Radiation Facility - High throughput sample evaluation and automation

Science.gov (United States)

Theveneau, P.; Baker, R.; Barrett, R.; Beteva, A.; Bowler, M. W.; Carpentier, P.; Caserotto, H.; de Sanctis, D.; Dobias, F.; Flot, D.; Guijarro, M.; Giraud, T.; Lentini, M.; Leonard, G. A.; Mattenet, M.; McCarthy, A. A.; McSweeney, S. M.; Morawe, C.; Nanao, M.; Nurizzo, D.; Ohlsson, S.; Pernot, P.; Popov, A. N.; Round, A.; Royant, A.; Schmid, W.; Snigirev, A.; Surr, J.; Mueller-Dieckmann, C.

2013-03-01

Automation and advances in technology are the key elements in addressing the steadily increasing complexity of Macromolecular Crystallography (MX) experiments. Much of this complexity is due to the inter-and intra-crystal heterogeneity in diffraction quality often observed for crystals of multi-component macromolecular assemblies or membrane proteins. Such heterogeneity makes high-throughput sample evaluation an important and necessary tool for increasing the chances of a successful structure determination. The introduction at the ESRF of automatic sample changers in 2005 dramatically increased the number of samples that were tested for diffraction quality. This "first generation" of automation, coupled with advances in software aimed at optimising data collection strategies in MX, resulted in a three-fold increase in the number of crystal structures elucidated per year using data collected at the ESRF. In addition, sample evaluation can be further complemented using small angle scattering experiments on the newly constructed bioSAXS facility on BM29 and the micro-spectroscopy facility (ID29S). The construction of a second generation of automated facilities on the MASSIF (Massively Automated Sample Screening Integrated Facility) beam lines will build on these advances and should provide a paradigm shift in how MX experiments are carried out which will benefit the entire Structural Biology community.

Generic radiation safety design for SSRL synchrotron radiation beamlines

Energy Technology Data Exchange (ETDEWEB)

Liu, James C. [Radiation Protection Department, Stanford Linear Accelerator Center (SLAC), MS 48, P.O. Box 20450, Stanford, CA 94309 (United States)]. E-mail: james@slac.stanford.edu; Fasso, Alberto [Radiation Protection Department, Stanford Linear Accelerator Center (SLAC), MS 48, P.O. Box 20450, Stanford, CA 94309 (United States); Khater, Hesham [Radiation Protection Department, Stanford Linear Accelerator Center (SLAC), MS 48, P.O. Box 20450, Stanford, CA 94309 (United States); Prinz, Alyssa [Radiation Protection Department, Stanford Linear Accelerator Center (SLAC), MS 48, P.O. Box 20450, Stanford, CA 94309 (United States); Rokni, Sayed [Radiation Protection Department, Stanford Linear Accelerator Center (SLAC), MS 48, P.O. Box 20450, Stanford, CA 94309 (United States)

2006-12-15

To allow for a conservative, simple, uniform, consistent, efficient radiation safety design for all SSRL beamlines, a generic approach has been developed, considering both synchrotron radiation (SR) and gas bremsstrahlung (GB) hazards. To develop the methodology and rules needed for generic beamline design, analytic models, the STAC8 code, and the FLUKA Monte Carlo code were used to pre-calculate sets of curves and tables that can be looked up for each beamline safety design. Conservative beam parameters and standard targets and geometries were used in the calculations. This paper presents the SPEAR3 beamline parameters that were considered in the design, the safety design considerations, and the main pre-calculated results that are needed for generic shielding design. In the end, the rules and practices for generic SSRL beamline design are summarized.

Racemic protein crystallography.

Science.gov (United States)

Yeates, Todd O; Kent, Stephen B H

2012-01-01

Although natural proteins are chiral and are all of one "handedness," their mirror image forms can be prepared by chemical synthesis. This opens up new opportunities for protein crystallography. A racemic mixture of the enantiomeric forms of a protein molecule can crystallize in ways that natural proteins cannot. Recent experimental data support a theoretical prediction that this should make racemic protein mixtures highly amenable to crystallization. Crystals obtained from racemic mixtures also offer advantages in structure determination strategies. The relevance of these potential advantages is heightened by advances in synthetic methods, which are extending the size limit for proteins that can be prepared by chemical synthesis. Recent ideas and results in the area of racemic protein crystallography are reviewed.

Insertion Device Upgrade Plans at the NSLS

CERN Document Server

Tanabe, Toshiya; Harder, David; Lehecka, Michael; Rakowsky, George; Skaritka, John

2005-01-01

This paper describes plans to upgrade insertion devices at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, U.S.A. The aging wiggler (W80) at X25 is being replaced by a 1 m long in-vacuum mini-gap undulator (MGU-18) optimized for a dedicated macromolecular crystallography program. A new, 1/3 m long, in-vacuum undulator (MGU-13.5), will be installed between a pair of RF cavities at X9, and will serve a new beamline dedicated for small angle x-ray scattering (SAXS). Both MGU’s will have provision for cryocooling the NdFeB hybrid arrays to 150K to raise the field and K-value and to obtain better spectral coverage. Design issues of the devices and other considerations, especially magnetic measurement methods in low temperature will be discussed.

Distributed computing for macromolecular crystallography.

Science.gov (United States)

Krissinel, Evgeny; Uski, Ville; Lebedev, Andrey; Winn, Martyn; Ballard, Charles

2018-02-01

Modern crystallographic computing is characterized by the growing role of automated structure-solution pipelines, which represent complex expert systems utilizing a number of program components, decision makers and databases. They also require considerable computational resources and regular database maintenance, which is increasingly more difficult to provide at the level of individual desktop-based CCP4 setups. On the other hand, there is a significant growth in data processed in the field, which brings up the issue of centralized facilities for keeping both the data collected and structure-solution projects. The paradigm of distributed computing and data management offers a convenient approach to tackling these problems, which has become more attractive in recent years owing to the popularity of mobile devices such as tablets and ultra-portable laptops. In this article, an overview is given of developments by CCP4 aimed at bringing distributed crystallographic computations to a wide crystallographic community.

Muon Beamline Commissioning and Feasibility Study for μSR at a New DC Muon Beamline, MuSIC-RCNP, Osaka University

Science.gov (United States)

Tomono, Dai; Fukuda, Mitsuhiro; Hatanaka, Kichiji; Higemoto, Wataru; Kawashima, Yoshitaka; Kojima, Kenji M.; Kuno, Yoshitaka; Matsuda, Yugo; Matsuzaki, Teiichiro; Miyake, Yasuhiro; Miyamoto, Koichiro; Morita, Yasuyuki; Motoishi, Takahiro; Nakazawa, Yu; Ninomiya, Kazuhiko; Nishikawa, Ryo; Ohta, Saki; Sato, Akira; Shimomura, Koichiro; Takahisa, Keiji; Weichao, Yao; Wong, Ming L.

At the new DC muon beamline MuSIC at Research Center for Nuclear Physics (RCNP), Osaka University, the beamline construction from the solenoid system of the muon production to the experimental port was completed. A beamline commissioning and a feasibility study for μSR are now in progress. With newly refurbished spectrometer installed at the experimental port, we succeeded in observing μSR spectra and μ-e decay asymmetry in a simple setup down to 4 K. We are still under development of other μSR appratuses.

Upgrade of Spring-8 Beamline Network with Vlan Technology Over Gigabit Ethernet

OpenAIRE

Ishii, M.; Fukui, T.; Furukawa, Y.; Nakatani, T.; Ohata, T.; Tanaka, R.

2001-01-01

The beamline network system at SPring-8 consists of three LANs; a BL-LAN for beamline component control, a BL-USER-LAN for beamline experimental users and an OA-LAN for the information services. These LANs are interconnected by a firewall system. Since the network traffic and the number of beamlines have increased, we upgraded the backbone of BL-USER-LAN from Fast Ethernet to Gigabit Ethernet. And then, to establish the independency of a beamline and to raise flexibility of every beamline, we...

The Upgrade Programme for the Structural Biology beamlines at the European Synchrotron Radiation Facility – High throughput sample evaluation and automation

International Nuclear Information System (INIS)

Theveneau, P; Baker, R; Barrett, R; Beteva, A; Bowler, M W; Carpentier, P; Caserotto, H; Sanctis, D de; Dobias, F; Flot, D; Guijarro, M; Giraud, T; Lentini, M; Leonard, G A; Mattenet, M; McSweeney, S M; Morawe, C; Nurizzo, D; McCarthy, A A; Nanao, M

2013-01-01

Automation and advances in technology are the key elements in addressing the steadily increasing complexity of Macromolecular Crystallography (MX) experiments. Much of this complexity is due to the inter-and intra-crystal heterogeneity in diffraction quality often observed for crystals of multi-component macromolecular assemblies or membrane proteins. Such heterogeneity makes high-throughput sample evaluation an important and necessary tool for increasing the chances of a successful structure determination. The introduction at the ESRF of automatic sample changers in 2005 dramatically increased the number of samples that were tested for diffraction quality. This 'first generation' of automation, coupled with advances in software aimed at optimising data collection strategies in MX, resulted in a three-fold increase in the number of crystal structures elucidated per year using data collected at the ESRF. In addition, sample evaluation can be further complemented using small angle scattering experiments on the newly constructed bioSAXS facility on BM29 and the micro-spectroscopy facility (ID29S). The construction of a second generation of automated facilities on the MASSIF (Massively Automated Sample Screening Integrated Facility) beam lines will build on these advances and should provide a paradigm shift in how MX experiments are carried out which will benefit the entire Structural Biology community.

Baking controller for synchrotron beamline vacuum systems

International Nuclear Information System (INIS)

Garg, C.K.; Kane, S.R.; Dhamgaye, V.P.

2003-01-01

The 2.5 GeV electron storage ring Indus-2 is a hard X-ray Synchrotron Radiation (SR) Source. Nearly 27 beamlines will be installed on Indus-2 and they will cater to different experiments and applications. Most of the beamlines will be in Ultra High Vacuum (UHV) the only exception being hard X-rays beamlines. However the front ends of all the beamlines will be in UHV. Practicing UHV requires efforts and patience. Evacuating any chamber, volume gases can be removed easily. However, outgassing phenomena like desorption, diffusion and permeation restricts the system to attain UHV. All processes except the volume gas removal are temperature dependent. At ambient temperature, gas pressure decreases so slowly that outgassing limit (i.e. 10 -10 1/s/cm 2 ) can hardly be achieved on a practical time scale. Also there are three orders of magnitude difference in outgassing between baked and unbaked systems. Depending on the vacuum chamber and the components inside it, the thermal outgassing (baking) of system is required and can be done at various temperatures between 150 degC to 450 deg C. For whole baking cycle, constant monitoring and controlling of the systems is required which takes tens of hours. This paper describes the automation for such baking system, which will be used for SR beamlines

Diamond Beamline I16 (Materials and Magnetism)

International Nuclear Information System (INIS)

Collins, S. P.; Bombardi, A.; Marshall, A. R.; Williams, J. H.; Barlow, G.; Day, A. G.; Pearson, M. R.; Woolliscroft, R. J.; Walton, R. D.; Beutier, G.; Nisbet, G.

2010-01-01

We describe the key features and performance specifications of a facility for high-resolution single-crystal x-ray diffraction at Diamond Light Source. The scientific emphasis of the beamline is materials- and x-ray-physics, including resonant and magnetic scattering. We highlight some of the more novel aspects of the beamline design.

Beamline for Schools 2016: How to be a CERN scientist

CERN Document Server

2016-01-01

Two teams of high-school students from the UK and Poland had the opportunity to conduct their own experiments at a fully equipped CERN beamline.   Students from the 2016 Beamline for Schools competition working on their experiment. (Image: Noemí Carabán Gonzalez/CERN) Two teams of high-school students from the UK and Poland had the opportunity to conduct their own experiments at a fully equipped CERN beamline, after winning the Beamline for Schools competition. The teams, ”Pyramid Hunters” from Poland and “Relatively Special” from the United Kingdom, spent 10 days at CERN conducting the experiments they had dreamt up in their winning proposals. The Beamline for Schools competition gives high-school students the chance to run an experiment on a fully equipped CERN beamline, in the same way researchers do at the Large Hadron Collider and other CERN facilities every day. To know more about their stay at CERN and the experiments they&r...

NATO Advanced Study Institute on Electron Crystallography

CERN Document Server

Weirich, Thomas E; Zou, Xiaodong

2006-01-01

During the last decade we have been witness to several exciting achievements in electron crystallography. This includes structural and charge density studies on organic molecules complicated inorganic and metallic materials in the amorphous, nano-, meso- and quasi-crystalline state and also development of new software, tailor-made for the special needs of electron crystallography. Moreover, these developments have been accompanied by a now available new generation of computer controlled electron microscopes equipped with high-coherent field-emission sources, cryo-specimen holders, ultra-fast CCD cameras, imaging plates, energy filters and even correctors for electron optical distortions. Thus, a fast and semi-automatic data acquisition from small sample areas, similar to what we today know from imaging plates diffraction systems in X-ray crystallography, can be envisioned for the very near future. This progress clearly shows that the contribution of electron crystallography is quite unique, as it enables to r...

Computer control of the ISX-B neutral injection beamlines

International Nuclear Information System (INIS)

Hanna, P.C.

1982-09-01

A system of controls for the Impurity Study Experiment (ISX-B) neutral injection beamlines at the Oak Ridge National Laboratory is presented. The system uses standard CAMAC equipment interfaced to the actual beamline controls and driven by a PDP-11/34 mini-computer. It is designed to relieve the operator of most of the mundane tasks of beam injection and also to reduce the number of operators needed to monitor multiple beamlines

The ELIMED transport and dosimetry beamline for laser-driven ion beams

Energy Technology Data Exchange (ETDEWEB)

Romano, F., E-mail: francesco.romano@lns.infn.it [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Schillaci, F.; Cirrone, G.A.P.; Cuttone, G. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Scuderi, V. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); ELI-Beamlines Project, Institute of Physics ASCR, v.v.i. (FZU), 182 21 Prague (Czech Republic); Allegra, L.; Amato, A.; Amico, A.; Candiano, G.; De Luca, G.; Gallo, G. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Giordanengo, S.; Guarachi, L. Fanola [Istituto Nazionale di Fisica Nucleare, Sezione di Torino, Via P. Giuria 1, Torino (Italy); Universita' di Torino, Dipartimento di Fisica, Via P. Giuria 1, Torino (Italy); Korn, G. [ELI-Beamlines Project, Institute of Physics ASCR, v.v.i. (FZU), 182 21 Prague (Czech Republic); Larosa, G. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Leanza, R. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Universita' di Catania, Dipartimento di Fisica e Astronomia, Via S. Sofia 64, Catania (Italy); Manna, R.; Marchese, V. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Marchetto, F. [Istituto Nazionale di Fisica Nucleare, Sezione di Torino, Via P. Giuria 1, Torino (Italy); Margarone, D. [ELI-Beamlines Project, Institute of Physics ASCR, v.v.i. (FZU), 182 21 Prague (Czech Republic); and others

2016-09-01

A growing interest of the scientific community towards multidisciplinary applications of laser-driven beams has led to the development of several projects aiming to demonstrate the possible use of these beams for therapeutic purposes. Nevertheless, laser-accelerated particles differ from the conventional beams typically used for multiscipilinary and medical applications, due to the wide energy spread, the angular divergence and the extremely intense pulses. The peculiarities of optically accelerated beams led to develop new strategies and advanced techniques for transport, diagnostics and dosimetry of the accelerated particles. In this framework, the realization of the ELIMED (ELI-Beamlines MEDical and multidisciplinary applications) beamline, developed by INFN-LNS (Catania, Italy) and that will be installed in 2017 as a part of the ELIMAIA beamline at the ELI-Beamlines (Extreme Light Infrastructure Beamlines) facility in Prague, has the aim to investigate the feasibility of using laser-driven ion beams for multidisciplinary applications. In this contribution, an overview of the beamline along with a detailed description of the main transport elements as well as the detectors composing the final section of the beamline will be presented.

Pharmaceutical crystallography: is there a devil in the details?

DEFF Research Database (Denmark)

Bond, A. D.

2012-01-01

Modern instruments for small-molecule crystallography continue to become more sophisticated and more automated. This technical progress provides a basis for frontier research in chemical and pharmaceutical crystallography, but it also encourages analytical crystallographers to become more...... are presented for pharmaceutical compounds, and the potential importance of the "details" in pharmaceutical crystallography is discussed....

The Pharmaceutical Industry Beamline of Pharmaceutical Consortium for Protein Structure Analysis

International Nuclear Information System (INIS)

Nishijima, Kazumi; Katsuya, Yoshio

2002-01-01

The Pharmaceutical Industry Beamline was constructed by the Pharmaceutical Consortium for Protein Structure Analysis which was established in April 2001. The consortium is composed of 22 pharmaceutical companies affiliating with the Japan Pharmaceutical Manufacturers Association. The beamline is the first exclusive on that is owned by pharmaceutical enterprises at SPring-8. The specification and equipments of the Pharmaceutical Industry Beamline is almost same as that of RIKEN Structural Genomics Beamline I and II. (author)

Crystallography taken to the extreme

Science.gov (United States)

Dubrovinskaia, Natalia; Dubrovinsky, Leonid

2018-06-01

This article is a brief autobiographical account of our life in science and the path that we took in performing the research for which we were awarded the Gregori Aminoff Prize in Crystallography 2017 by the Royal Swedish Academy of Sciences. We were invited to write it by the editor-in-chief of Physica Scripta, Suzy Lidström, who charged us with the task of contributing to a series of autobiographical articles published since 2014, the International Year of Crystallography, on the lives of the Aminoff Prize winners. As this series is intended to be of particular interest to young scientists, teachers and lecturers and those researching the history of science, we tried to adhere to this purpose while writing our story. It does not pretend to be a comprehensive review either of our own scientific results or, especially, of covering the complete history of the research field of high-pressure crystallography in which we are active.

Crystallography: past and present

Science.gov (United States)

Hodeau, J.-L.; Guinebretiere, R.

2007-12-01

In the 19th century, crystallography referred to the study of crystal shapes. Such studies by Haüy and Bravais allowed the establishment of important hypotheses such as (i) “les molécules intégrantes qui sont censées être les plus petits solides que l’on puisse extraire d’un minéral” [1], (ii) the definition of the crystal lattice and (iii) “le cristal est clivable parallèlement à deux ou trois formes cristallines” [2]. This morphological crystallography defined a crystal like “a chemically homogeneous solid, wholly or partly bounded by natural planes that intersect at predetermined angles” [3]. It described the main symmetry elements and operations, nomenclatures of different crystal forms and also the theory of twinning. A breakthrough appeared in 1912 with the use of X-rays by M. von Laue and W.H. and W.L. Bragg. This experimental development allowed the determination of the atomic content of each unit cell constituting the crystal and defined a crystal as “any solid in which an atomic pattern is repeated periodically in three dimensions, that is, any solid that “diffracts” an incident X-ray beam” [3]. Mathematical tools like the Patterson methods, the direct methods, were developed. The way for solving crystalline structure was opened first for simple compounds and at that time crystallography was associated mainly with perfect crystals. In the fifties, crystallographers already had most apparatus and fundamental methods at their disposal; however, we had to wait for the development of computers to see the full use of these tools. Furthermore the development of new sources of neutrons, electrons and synchrotron X-rays allowed the studies of complex compounds like large macromolecules in biology. Nowadays, one of the new frontiers for crystallographers is to relate the crystal structure to its physical-chemical-biological properties, this means that an accurate structural determination is needed to focus on a selective part of the

A hard X-ray nanoprobe beamline for nanoscale microscopy

Energy Technology Data Exchange (ETDEWEB)

Winarski, Robert P., E-mail: winarski@anl.gov; Holt, Martin V. [Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60441 (United States); Rose, Volker [Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60441 (United States); Fuesz, Peter; Carbaugh, Dean; Benson, Christa; Shu, Deming; Kline, David; Stephenson, G. Brian; McNulty, Ian [Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60441 (United States); Maser, Jörg [Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60441 (United States)

2012-11-01

The Hard X-ray Nanoprobe Beamline is a precision platform for scanning probe and full-field microscopy with 3–30 keV X-rays. A combination of high-stability X-ray optics and precision motion sensing and control enables detailed studies of the internal features of samples with resolutions approaching 30 nm. The Hard X-ray Nanoprobe Beamline (or Nanoprobe Beamline) is an X-ray microscopy facility incorporating diffraction, fluorescence and full-field imaging capabilities designed and operated by the Center for Nanoscale Materials and the Advanced Photon Source at Sector 26 of the Advanced Photon Source at Argonne National Laboratory. This facility was constructed to probe the nanoscale structure of biological, environmental and material sciences samples. The beamline provides intense focused X-rays to the Hard X-ray Nanoprobe (or Nanoprobe) which incorporates Fresnel zone plate optics and a precision laser sensing and control system. The beamline operates over X-ray energies from 3 to 30 keV, enabling studies of most elements in the periodic table, with a particular emphasis on imaging transition metals.

The Project for the High Energy Materials Science Beamline at Petra III

International Nuclear Information System (INIS)

Martins, R. V.; Lippmann, T.; Beckmann, F.; Schreyer, A.

2007-01-01

The high energy materials science beamline will be among the first fourteen beamlines planned to be operational in 2009 at the new third generation synchrotron light source Petra III at DESY, Germany. The operation and funding of this beamline is assured by GKSS. 70% of the beamline will be dedicated to materials science. The remaining 30% are reserved for physics and are covered by DESY. The materials science activities will be concentrating on three intersecting topics which are industrial, applied, and fundamental research. The beamline will combine three main features: Firstly, the high flux, fast data acquisition systems, and the beamline infrastructure will allow carrying out complex and highly dynamic in-situ experiments. Secondly, a high flexibility in beam shaping will be available, fully exploiting the high brilliance of the source. Thirdly, the beamline will provide the possibility to merge in one experiment different analytical techniques such as diffraction and tomography

Langmuir-Blodgett nanotemplates for protein crystallography.

Science.gov (United States)

Pechkova, Eugenia; Nicolini, Claudio

2017-12-01

The new generation of synchrotrons and microfocused beamlines has enabled great progress in X-ray protein crystallography, resulting in new 3D atomic structures for proteins of high interest to the pharmaceutical industry and life sciences. It is, however, often still challenging to produce protein crystals of sufficient size and quality (order, intensity of diffraction, radiation stability). In this protocol, we provide instructions for performing the Langmuir-Blodgett (LB) nanotemplate method, a crystallization approach that can be used for any protein (including membrane proteins). We describe how to produce highly ordered 2D LB protein monolayers at the air-water interface and deposit them on glass slides. LB-film formation can be observed by surface-pressure measurements and Brewster angle microscopy (BAM), although its quality can be characterized by atomic force microscopy (AFM) and nanogravimetry. Such films are then used as a 2D template for triggering 3D protein crystal formation by hanging-drop vapor diffusion. The procedure for forming the 2D template takes a few minutes. Structural information about the protein reorganization in the LB film during the crystallization process on the nano level can be obtained using an in situ submicron GISAXS (grazing-incidence small-angle X-ray scattering) method. MicroGISAXS spectra, measured directly at the interface of the LB films and protein solution in real time, as described in this protocol, can be interpreted in terms of the buildup of layers, islands, or holes. In our experience, the obtained LB crystals take 1-10 d to prepare and they are more ordered and radiation stable as compared with those produced using other crystallization methods.

Sequential recovery of macromolecular components of the nucleolus.

Science.gov (United States)

Bai, Baoyan; Laiho, Marikki

2015-01-01

The nucleolus is involved in a number of cellular processes of importance to cell physiology and pathology, including cell stress responses and malignancies. Studies of macromolecular composition of the nucleolus depend critically on the efficient extraction and accurate quantification of all macromolecular components (e.g., DNA, RNA, and protein). We have developed a TRIzol-based method that efficiently and simultaneously isolates these three macromolecular constituents from the same sample of purified nucleoli. The recovered and solubilized protein can be accurately quantified by the bicinchoninic acid assay and assessed by polyacrylamide gel electrophoresis or by mass spectrometry. We have successfully applied this approach to extract and quantify the responses of all three macromolecular components in nucleoli after drug treatments of HeLa cells, and conducted RNA-Seq analysis of the nucleolar RNA.

National synchrotron light source user's manual: Guide to the VUV and x-ray beamlines: Third edition

International Nuclear Information System (INIS)

Gmuer, N.F.; Thomlinson, W.; White-DePace, S.

1989-01-01

This report contains information on the following topics: A Word on the Writing of Beamline Descriptions; Beamline Equipment Utilization for General Users; the Vacuum Ultraviolet (VUV) Storage Ring and Beamlines; VUV Beamline Descriptions--An Explanation; VUV Beamline Descriptions; X-Ray Storage Ring and Beamlines; X-Ray Beamline Descriptions--An Explanation; and X-Ray Beamline Descriptions

Radiation protection of a proton beamline at ELI-Beamlines

Czech Academy of Sciences Publication Activity Database

Bechet, Sabrina; Versaci, Roberto; Rollet, S.; Olšovcová, Veronika; Fajstavr, Antonín; Žáková, Martina; Margarone, Daniele

2016-01-01

Roč. 11, č. 12 (2016), 1-5, č. článku C12019. ISSN 1748-0221 R&D Projects: GA MŠk EF15_008/0000162 Grant - others:ELI Beamlines(XE) CZ.02.1.01/0.0/0.0/15_008/0000162 Institutional support: RVO:68378271 Keywords : models * simulations * wake-field acceleration Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 1.220, year: 2016

The Scanning Nanoprobe Beamline Nanoscopium at Synchrotron Soleil

Science.gov (United States)

Somogyi, A.; Kewish, C. M.; Polack, F.; Moreno, T.

2011-09-01

The Nanoscopium beamline at Synchrotron Soleil will offer advanced scanning-based hard x-ray imaging techniques in the 5- to 20-keV energy range, for user communities working in the earth, environmental, and life sciences. Two dedicated end stations will exploit x-ray coherence to produce images in which contrast is based on a range of physical processes. In the first experiment hutch, coherent scatter imaging techniques will produce images in which contrast arises from spatial variations in the complex refractive index, and orientation in the nanostructure of samples. In the second experiment hutch, elemental mapping will be carried out at the trace (ppm) level by scanning x-ray fluorescence, speciation mapping by XANES, and phase gradient mapping by scanning differential phase contrast imaging. The beamline aims to reach sub-micrometric, down to 30 nm, spatial resolution. This ˜155-meter-long beamline will share the straight section with a future tomography beamline by using canted undulators having 6.5-mrad separation angle. The optical design of Nanoscopium aims to reduce the effect of instabilities on the probing nanobeam by utilizing an all-horizontal geometry for the reflections of the primary beamline mirrors, which focus onto a slit, creating an over-filled secondary source. Kirkpatrick-Baez mirrors and Fresnel zone plates will be used as focusing devices in the experiment hutches. Nanoscopium is expected to commence user operation in 2013.

Development of the protein crystallography by synchrotron radiation

International Nuclear Information System (INIS)

Yamamoto, Masaki

2014-01-01

Since crystal structure determination of the first protein by Kendrew in 1959, protein crystallography developed into the leading role of the protein structure study by various technology developments. Especially the utilization of synchrotron radiation from the 1990s brought innovative progress of protein crystallography on the data quality and the phasing method and had expanded the samples targets including membrane proteins and suprarmolecular complexes. Here I give the outline of the history and the future prospects of the protein crystallography from the role of synchrotron radiation. (author)

A second beam-diagnostic beamline for the advanced light source

International Nuclear Information System (INIS)

Sannibale, Fernando; Baum, Dennis; Kelez, Nicholas; Scarvie, Tom; Holldack, Karsten

2003-01-01

A second beamline, BL 7.2, completely dedicated to beam diagnostics is being installed at the Advanced Light Source (ALS). The design has been optimized for the measurement of the momentum spread and emittance of the stored beam in combination with the existing diagnostic beamline, BL 3.1. A detailed analysis of the experimental error has allowed the definition of the system parameters. The obtained requirements found a good matching with a simple and reliable system based on the detection of X-ray synchrotron radiation (SR) through a pinhole system. The actual beamline, which also includes a port for visible and infrared SR as well as an X-ray beam position monitor (BPM), is mainly based on the design of two similar diagnostic beamlines at BESSY II. This approach allowed a significant saving in time, cost and engineering effort. The design criteria, including a summary of the experimental error analysis, as well as a brief description of the beamline are presented

Kannan, Dr Kazhiur Kothandapani

Indian Academy of Sciences (India)

Date of birth: 30 September 1939. Specialization: X-ray & Macromolecular Crystallography and Macromolecular Computer Graphics Address: F-206, Redwood, Reheja Residency, III Block, Koramangala, Bengaluru 560 034, Karnataka Contact: Residence: (080) 2550 5829. Mobile: 87627 80061

Inelastic X-ray Scattering Beamline Collaborative Development Team Final Report

International Nuclear Information System (INIS)

Burns, Clement

2008-01-01

This is the final report for the project to create a beam line for inelastic x-ray scattering at the Advanced Photon Source. The facility is complete and operating well, with spectrometers for both high resolution and medium resolution measurements. With the advent of third generation synchrotron sources, inelastic x-ray scattering (IXS) has become a valuable technique to probe the electronic and vibrational states of a wide variety of systems of interest in physics, chemistry, and biology. IXS is a weak probe, and experimental setups are complex and require well-optimized spectrometers which need a dedicated beamline to function efficiently. This project was the result of a proposal to provide a world-class, user friendly beamline for IXS at the Advanced Photon Source. The IXS Collaborative Development Team (IXS-CDT) was formed from groups at the national laboratories and a number of different universities. The beamline was designed from the front end to the experimental stations. Two different experimental stations were provided, one for medium resolution inelastic x-ray scattering (MERIX) and a spectrometer for high resolution inelastic x-ray scattering (HERIX). Funding for this project came from several sources as well as the DOE. The beamline is complete with both spectrometers operating well. The facility is now open to the general user community and there has been a tremendous demand to take advantage of the beamline's capabilities. A large number of different experiments have already been carried out on the beamline. A detailed description of the beamline has been given in the final design report (FDR) for the beamline from which much of the material in this report came. The first part of this report contains a general overview of the project with more technical details given later.

LNLS soft x-ray spectroscopy (SXS) beamline

International Nuclear Information System (INIS)

Tolentino, Helio; Rocha, Milton C.; Tamura, Edilson; Cezar, Julio C.; Vicentin, Flavio C.; Giles, Carlos; Compagnon-Cailhol, Valerie; Abbate, Miguel; Cruz, Daniela Z.N.; Mocellin, Alexandra

1996-01-01

The Soft X-ray Spectroscopy beamline will be dedicated to the study of structural, electronic and magnetic properties of materials by using photoabsorption and photoemission techniques, X-ray dischroism will be used to study magnetism of transition metals and rare earths compounds. This beamline is one of the first seven beamlines which were decided to start operation along with the storage ring. Part of the beamline - mostly importations - has been granted by fundings from the state of Sao Paulo (Fapesp). The electron energy analyser came through EEC from a cooperation with a French group at LURE. All components of the beamline are either constructed or bougth and being mounted at the storage ring. The monochromator has already been commissioned under UHV, attaining the specification of 5x10 -9 Torr. To cover the whole energy range, from 800 eV up to 4000 eV, many crystals have been bought, cut and tested. The mirror has been specified in order to focus the source in both directions. Simulations using the Shadow code (source simulation and ray tracing technique) were performed in order to optimize the performance of the optics. We expert to focus 10 mrad down to a spot of 3.0x1.5 mm 2 . The mirror chamber has already been constructed and commissioned under UHV conditions (pressure -9 Torr). The mechanics (mechanical feedthroughs, stability, etc..) has been tested using an X-ray source and has been approved. The experimental chamber has already been used for photoemission experiments using a conventional AL/Mg X-ray source. Many results have been obtained and two master thesis have been performed using this set-up. (author)

VUV-soft x-ray beamline for spectroscopy and calibration

International Nuclear Information System (INIS)

Bartlett, R.J.; Trela, W.J.; Michaud, F.D.; Southworth, S.H.; Rothe, R.; Alkire, R.W.

1986-01-01

The authors describe the design and performance of the Los Alamos VUV synchrotron radiation beamline, U3C, on the VUV ring of the National Synchrotron Light Source at Brookhaven National Laboratory. The beamline uses separate function optics to collect and focus the horizontally and vertically diverging beam. The monochromator is a grazing incidence Roland circle instrument of the extended grasshopper design (ERG). A post monochromator refocusing mirror is used to focus or collimate the diverging beam from the monochromator. The beamline control and diagnostics systems are also discussed

Beamline for X-ray Free Electron Laser of SACLA

International Nuclear Information System (INIS)

Tono, K; Togashi, T; Ohashi, H; Kimura, H; Takahashi, S; Takeshita, K; Tomizawa, H; Goto, S; Inubushi, Y; Sato, T; Yabashi, M

2013-01-01

A beamline for X-ray free electron laser (XFEL) has been developed at SACLA, SPring-8 Angstrom Compact free electron LAser. The beamline delivers and diagnoses an XFEL beam without degrading the beam quality. The transport optics are applicable in the range of 4–30 keV with a double-crystal monochromator or 4–15 keV with either of two double-mirror systems. A photon diagnostic system of the beamline monitors intensity, photon energy, center-of-mass position, and spatial profile in shot-by-shot and non-destructive manners.

Low cost ESR based X-ray beamline for lithography experimentation

Energy Technology Data Exchange (ETDEWEB)

Kovacs, S.; Doumas, A.; Truncale, M. (Grumman Corp., Bethpage, NY (United States). Space and Electronics Div.)

1992-08-01

Any application of the electron storage ring (ESR) based X-ray lithography technology requires an X-ray radiation transport system to transfer the synchrotron radiation into a spectrum defined by the lithography process requirements. Structure of this transport system (i.e. the beamline) depends on the nature of the application. In this paper a beamline conceptual design will be discussed. The beamline is intended for the developmment of X-ray lithography technology. (orig.).

Advanced light source vacuum policy and vacuum guidelines for beamlines and experiment endstations

International Nuclear Information System (INIS)

Hussain, Z.

1995-08-01

The purpose of this document is to: (1) Explain the ALS vacuum policy and specifications for beamlines and experiment endstations. (2) Provide guidelines related to ALS vacuum policy to assist in designing beamlines which are in accordance with ALS vacuum policy. This document supersedes LSBL-116. The Advanced Light Source is a third generation synchrotron radiation source whose beam lifetime depends on the quality of the vacuum in the storage ring and the connecting beamlines. The storage ring and most of the beamlines share a common vacuum and are operated under ultra-high-vacuum (UHV) conditions. All endstations and beamline equipment must be operated so as to avoid contamination of beamline components, and must include proper safeguards to protect the storage ring vacuum from an accidental break in the beamline or endstation vacuum systems. The primary gas load during operation is due to thermal desorption and electron/photon induced desorption of contaminants from the interior of the vacuum vessel and its components. The desorption rates are considerably higher for hydrocarbon contamination, thus considerable emphasis is placed on eliminating these sources of contaminants. All vacuum components in a beamline and endstation must meet the ALS vacuum specifications. The vacuum design of both beamlines and endstations must be approved by the ALS Beamline Review Committee (BRC) before vacuum connections to the storage ring are made. The vacuum design is first checked during the Beamline Design Review (BDR) held before construction of the beamline equipment begins. Any deviation from the ALS vacuum specifications must be approved by the BRC prior to installation of the equipment on the ALS floor. Any modification that is incorporated into a vacuum assembly without the written approval of the BRC is done at the user's risk and may lead to rejection of the whole assembly

The role of macromolecular stability in desiccation tolerance

NARCIS (Netherlands)

Wolkers, W.F.

1998-01-01

The work presented in this thesis concerns a study on the molecular interactions that play a role in the macromolecular stability of desiccation-tolerant higher plant organs. Fourier transform infrared microspectroscopy was used as the main experimental technique to assess macromolecular

Construction of Bending Magnet Beamline at the APS for Environmental Studies

International Nuclear Information System (INIS)

Stern, E.A.

1999-01-01

The objective of this research was to design and construct a bending magnet beamline at the Advanced Photon Source. The beamline is to be optimized for x-ray absorption spectroscopy (XAS) studies with a major focus on environmental issues. The beamline will share the experimental facilities under development at the neighboring undulator-based insertion device beamline. It will utilize these facilities for XAS of both bulk and surface samples, with spatial and elemental imaging, on toxic and radioactive samples. It will help meet the rapidly growing need for the application of these techniques to environmental problems

Wavefront propagation simulations for a UV/soft x-ray beamline: Electron Spectro-Microscopy beamline at NSLS-II

Science.gov (United States)

Canestrari, N.; Bisogni, V.; Walter, A.; Zhu, Y.; Dvorak, J.; Vescovo, E.; Chubar, O.

2014-09-01

A "source-to-sample" wavefront propagation analysis of the Electron Spectro-Microscopy (ESM) UV / soft X-ray beamline, which is under construction at the National Synchrotron Light Source II (NSLS-II) in the Brookhaven National Laboratory, has been conducted. All elements of the beamline - insertion device, mirrors, variable-line-spacing gratings and slits - are included in the simulations. Radiation intensity distributions at the sample position are displayed for representative photon energies in the UV range (20 - 100 eV) where diffraction effects are strong. The finite acceptance of the refocusing mirrors is the dominating factor limiting the spatial resolution at the sample (by ~3 μm at 20 eV). Absolute estimates of the radiation flux and energy resolution at the sample are also obtained from the electromagnetic calculations. The analysis of the propagated UV range undulator radiation at different deflection parameter values demonstrates that within the beamline angular acceptance a slightly "red-shifted" radiation provides higher flux at the sample and better energy resolution compared to the on-axis resonant radiation of the fundamental harmonic.

Emittance Measurement for Beamline Extension at the PET Cyclotron

Directory of Open Access Journals (Sweden)

Sae-Hoon Park

2016-01-01

Full Text Available Particle-induced X-ray emission is used for determining the elemental composition of materials. This method uses low-energy protons (of several MeV, which can be obtained from high-energy (of tens MeV accelerators. Instead of manufacturing an accelerator for generating the MeV protons, the use of a PET cyclotron has been suggested for designing the beamline for multipurpose applications, especially for the PIXE experiment, which has a dedicated high-energy (of tens MeV accelerator. The beam properties of the cyclotron were determined at this experimental facility by using an external beamline before transferring the ion beam to the experimental chamber. We measured the beam profile and calculated the emittance using the pepper-pot method. The beam profile was measured as the beam current using a wire scanner, and the emittance was measured as the beam distribution at the beam dump using a radiochromic film. We analyzed the measurement results and are planning to use the results obtained in the simulations of external beamline and aligned beamline components. We will consider energy degradation after computing the beamline simulation. The experimental study focused on measuring the emittance from the cyclotron, and the results of this study are presented in this paper.

Discussions for the shielding materials of synchrotron radiation beamline hutches

International Nuclear Information System (INIS)

Asano, Y.

2006-01-01

Many synchrotron radiation facilities are now under operation such as E.S.R.F., APS, and S.P.ring-8. New facilities with intermediated stored electron energy are also under construction and designing such as D.I.A.M.O.N.D., S.O.L.E.I.L., and S.S.R.F.. At these third generation synchrotron radiation facilities, the beamline shielding as well as the bulk shield is very important for designing radiation safety because of intense and high energy synchrotron radiation beam. Some reasons employ lead shield wall for the synchrotron radiation beamlines. One is narrow space for the construction of many beamlines at the experimental hall, and the other is the necessary of many movable mechanisms at the beamlines, for examples. Some cases are required to shield high energy neutrons due to stored electron beam loss and photoneutrons due to gas Bremsstrahlung. Ordinary concrete and heavy concrete are coming up to shield material of synchrotron radiation beamline hutches. However, few discussions have been performed so far for the shielding materials of the hutches. In this presentation, therefore, we will discuss the characteristics of the shielding conditions including build up effect for the beamline hutches by using the ordinary concrete, heavy concrete, and lead for shielding materials with 3 GeV and 8 GeV class synchrotron radiation source. (author)

The Nanoscience Beamline (I06) at Diamond Light Source

International Nuclear Information System (INIS)

Dhesi, S. S.; Cavill, S. A.; Potenza, A.; Marchetto, H.; Mott, R. A.; Steadman, P.; Peach, A.; Shepherd, E. L.; Ren, X.; Wagner, U. H.; Reininger, R.

2010-01-01

The Nanoscience beamline (I06) is one of seven Diamond Phase-I beamlines which has been operational since January 2007 delivering polarised soft x-rays, for a PhotoEmission Electron Microscope (PEEM) and branchline, in the energy range 80-2100 eV. The beamline is based on a collimated plane grating monochromator with sagittal focusing elements, utilising two APPLE II helical undulator sources, and has been designed for high flux density at the PEEM sample position. A ∼5 μm (σ) diameter beam is focussed onto the sample in the PEEM allowing a range of experiments using x-ray absorption spectroscopy (XAS), x-ray magnetic circular dichroism (XMCD) and x-ray magnetic linear dichroism (XMLD) as contrast mechanisms. The beamline is also equipped with a branchline housing a 6T superconducting magnet for XMCD and XMLD experiments. The magnet is designed to move on and off the branchline which allows a diverse range of experiments.

Insertion devices and beamlines for the proposed Australian synchrotron light source

International Nuclear Information System (INIS)

Garrett, R.F.; Boldeman, J.W.

1999-01-01

Full text: The proposed Australian synchrotron light source, Boomerang, is a third generation 3 GeV storage ring which is designed to provide for the great majority of Australian requirements for synchrotron radiation well into the next century. The storage ring could accommodate up to 60 experimental stations, including beamlines from 9 insertion devices, which far exceeds the projected Australian requirements over the life of the facility. Undulator radiation will be available up to 20 keV. The first phase construction of Boomerang includes funding for 9 beamlines, comprising 5 bending magnet and 4 insertion device beamlines. The beamline complement has been chosen to cater for approximately 95% of the current and projected Australian demand for synchrotron radiation over the first 5 years operation of the facility. Details will be shown of the performance of the proposed insertion devices, and the initial beamline complement will be presented

SPring-8 beamline control system.

Science.gov (United States)

Ohata, T; Konishi, H; Kimura, H; Furukawa, Y; Tamasaku, K; Nakatani, T; Tanabe, T; Matsumoto, N; Ishii, M; Ishikawa, T

1998-05-01

The SPring-8 beamline control system is now taking part in the control of the insertion device (ID), front end, beam transportation channel and all interlock systems of the beamline: it will supply a highly standardized environment of apparatus control for collaborative researchers. In particular, ID operation is very important in a third-generation synchrotron light source facility. It is also very important to consider the security system because the ID is part of the storage ring and is therefore governed by the synchrotron ring control system. The progress of computer networking systems and the technology of security control require the development of a highly flexible control system. An interlock system that is independent of the control system has increased the reliability. For the beamline control system the so-called standard model concept has been adopted. VME-bus (VME) is used as the front-end control system and a UNIX workstation as the operator console. CPU boards of the VME-bus are RISC processor-based board computers operated by a LynxOS-based HP-RT real-time operating system. The workstation and the VME are linked to each other by a network, and form the distributed system. The HP 9000/700 series with HP-UX and the HP 9000/743rt series with HP-RT are used. All the controllable apparatus may be operated from any workstation.

ALS beamline design requirements: A guide for beamline designers

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-06-01

This manual is written as a guide for researchers in designing beamlines and endstations acceptable for use at the ALS. It contains guidelines and policies related to personnel safety and equipment and vacuum protection. All equipment and procedures must ultimately satisfy the safety requirements set aside in the Lawrence Berkeley National Laboratory (LBNL) Health and Safety Manual (PUB-3000) which is available from the ALS User Office or on the World WideWeb from the LBNL Homepage (http:// www.lbl.gov).

G4Beamline Program for Radiation Simulations

International Nuclear Information System (INIS)

Beard, Kevin; Roberts, Thomas J.; Degtiarenko, Pavel

2008-01-01

G4beamline, a program that is an interface to the Geant4 toolkit that we have developed to simulate accelerator beamlines, is being extended with a graphical user interface to quickly and efficiently model experimental equipment and its shielding in experimental halls. The program is flexible, user friendly, and requires no programming by users, so that even complex systems can be simulated quickly. This improved user interface is of much wider application than just the shielding simulations that are the focus of this project. As an initial application, G4beamline is being extended to provide the simulations that are needed to determine the radiation sources for the proposed experiments at Jefferson Laboratory so that shielding issues can be evaluated. Since the program already has the capabilities needed to simulate the transport of all known particles, including scattering, attenuation, interactions, and decays, the extension involves implementing a user-friendly graphical user inter

How good can our beamlines be?

Energy Technology Data Exchange (ETDEWEB)

Liebschner, Dorothee; Dauter, Miroslawa; Rosenbaum, Gerold, E-mail: rosenbaum@anl.gov; Dauter, Zbigniew, E-mail: rosenbaum@anl.gov [Argonne National Laboratory, Argonne, IL 60439 (United States)

2012-10-01

A repetitive measurement of the same diffraction image allows to judge the performance of a data collection facility. The accuracy of X-ray diffraction data depends on the properties of the crystalline sample and on the performance of the data-collection facility (synchrotron beamline elements, goniostat, detector etc.). However, it is difficult to evaluate the level of performance of the experimental setup from the quality of data sets collected in rotation mode, as various crystal properties such as mosaicity, non-uniformity and radiation damage affect the measured intensities. A multiple-image experiment, in which several analogous diffraction frames are recorded consecutively at the same crystal orientation, allows minimization of the influence of the sample properties. A series of 100 diffraction images of a thaumatin crystal were measured on the SBC beamline 19BM at the APS (Argonne National Laboratory). The obtained data were analyzed in the context of the performance of the data-collection facility. An objective way to estimate the uncertainties of individual reflections was achieved by analyzing the behavior of reflection intensities in the series of analogous diffraction images. The multiple-image experiment is found to be a simple and adequate method to decompose the random errors from the systematic errors in the data, which helps in judging the performance of a data-collection facility. In particular, displaying the intensity as a function of the frame number allows evaluation of the stability of the beam, the beamline elements and the detector with minimal influence of the crystal properties. Such an experiment permits evaluation of the highest possible data quality potentially achievable at the particular beamline.

Simulating the Beam-line at CERN's ISOLDE Experiment

CERN Document Server

McGrath, Casey

2013-01-01

Maximizing the optical matching along portions of the ISOLDE beam-line and automating this procedure will make it easier for scientists to determine what the strengths of the electrical elds of each beam-line element should be in order to reduce particle loss. Simulations are run using a program called MAD-X, however, certain issues were discovered that hindered an immediate success of the simulations. Specifically, the transfer matrices for electrostatic components like the switchyards, kickers, and electric quadrupoles were missing from the original coding. The primary aim of this project was to design these components using AutoCAD and then extract the transfer matrices using SIMION. Future work will then implement these transfer matrices into the MAD-X code to make the simulations of the beam-line more accurate.

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

Energy Technology Data Exchange (ETDEWEB)

Borbulevych, Oleg Y.; Plumley, Joshua A.; Martin, Roger I. [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States); Merz, Kenneth M. Jr [University of Florida, Gainesville, Florida (United States); Westerhoff, Lance M., E-mail: lance@quantumbioinc.com [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States)

2014-05-01

Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX is described. Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

Construction and maintenance of SUNY facilities at the National Synchrotron Light Source. Progress report, 1 July 1983-1 July 1984. Final report

International Nuclear Information System (INIS)

Bigeleisen, J.

1984-01-01

Research reported includes beamline facilities, X-21 beamline update, SUNY-PRT participation in the design and commissioning of the CHESS crystallography facility, surface physics, material and structure studies using EXAFS, x-ray standing wave studies of surfaces and interfaces, and surface diffraction of adsorbed polyatomic molecules

I20; the Versatile X-ray Absorption spectroscopy beamline at Diamond Light Source

International Nuclear Information System (INIS)

Diaz-Moreno, S; Hayama, S; Amboage, M; Freeman, A; Sutter, J; Duller, G

2009-01-01

The Versatile Spectroscopy beamline at Diamond Light Source, I20, is currently under construction and aims to begin operation in late 2009 and early 2010. The beamline aims to cover applications from physics, chemistry and biology through materials, environmental and geological science. Three very distinctive modes of operation will be offered at the beamline: scanning X-ray Absorption spectroscopy (XAS), XAS in dispersive mode, and X-ray emission spectroscopy (XES). To achieve this, the beamline has been designed around two independent experimental end-stations operating from a pair of canted wigglers located in a 5m diamond straight section. One branch of the beamline will deliver monochromatic x-ray radiation of high spectral purity to one of the experimental hutches, whilst the other branch will constitute an energy dispersive spectrometer. The novel design of the beamline allows both branches to operate simultaneously.

Safety upgrades for NSRRC beamlines in the upcoming top-up operation

International Nuclear Information System (INIS)

Liu, Joseph C.; Sheu, R.-J.; Wang, J.-P.; Chen, C.-R.; Chang, F.-D.; Kao, S.-P.

2006-01-01

The original beamline shielding of NSRRC was designed for the decay mode operation that safety shutter was closed during injection. The proposed top-up operation that opens safety shutter during top-up injection will introduce additional beam loss scenarios and radiation sources, especially when the injection efficiency needs to be improved. Careful comparison was made to differentiate the radiation doses into beamlines for both operation modes. Detailed evaluation was made to identify the possible inadequacies of the old beamline shielding and safety control procedures. Remedy actions and safety upgrades for each individual beamline were issued to ensure that dose limit of 2 mSv/yr for users can be fulfilled when running top-up operation

X-Ray Crystallography: One Century of Nobel Prizes

Science.gov (United States)

Galli, Simona

2014-01-01

In 2012, the United Nations General Assembly declared 2014 the International Year of Crystallography. Throughout the year 2014 and beyond, all the crystallographic associations and societies active all over the world are organizing events to attract the wider public toward crystallography and the numerous topics to which it is deeply interlinked.…

A national facility for biological cryo-electron microscopy.

Science.gov (United States)

Saibil, Helen R; Grünewald, Kay; Stuart, David I

2015-01-01

Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback.

SynchLink: an iOS app for ISPyB.

Science.gov (United States)

Ginn, Helen Mary; Mostefaoui, Ghita Kouadri; Levik, Karl Erik; Grimes, Jonathan Mark; Walsh, Martin Austin; Ashton, Alun William; Stuart, David Ian

2014-10-01

The macromolecular crystallography (MX) user experience at synchrotron radiation facilities continues to evolve, with the impact of developments in X-ray detectors, computer hardware and automation methods making it possible for complete data sets to be collected on timescales of tens of seconds. Data can be reduced in a couple of minutes and in favourable cases structures solved and refined shortly after. The information-rich database ISPyB, automatically populated by data acquisition software, data processing and structure solution pipelines at the Diamond Light Source beamlines, allows users to automatically track MX experiments in real time. In order to improve the synchrotron users' experience, efficient access to the data contained in ISPyB is now provided via an iOS 6.0+ app for iPhones and iPads. This provides users, both local and remote, with a succinct summary of data collection, visualization of diffraction images and crystals, and key metrics for data quality in real time.

High-pressure crystallography

Science.gov (United States)

Katrusiak, A.

2008-01-01

The history and development of high-pressure crystallography are briefly described and examples of structural transformations in compressed compounds are given. The review is focused on the diamond-anvil cell, celebrating its 50th anniversary this year, the principles of its operation and the impact it has had on high-pressure X-ray diffraction.

Fab Chaperone-Assisted RNA Crystallography (Fab CARC).

Science.gov (United States)

Sherman, Eileen; Archer, Jennifer; Ye, Jing-Dong

2016-01-01

Recent discovery of structured RNAs such as ribozymes and riboswitches shows that there is still much to learn about the structure and function of RNAs. Knowledge learned can be employed in both biochemical research and clinical applications. X-ray crystallography gives unparalleled atomic-level structural detail from which functional inferences can be deduced. However, the difficulty in obtaining high-quality crystals and their phasing information make it a very challenging task. RNA crystallography is particularly arduous due to several factors such as RNA's paucity of surface chemical diversity, lability, repetitive anionic backbone, and flexibility, all of which are counterproductive to crystal packing. Here we describe Fab chaperone assisted RNA crystallography (CARC), a systematic technique to increase RNA crystallography success by facilitating crystal packing as well as expediting phase determination through molecular replacement of conserved Fab domains. Major steps described in this chapter include selection of a synthetic Fab library displayed on M13 phage against a structured RNA crystallization target, ELISA for initial choice of binding Fabs, Fab expression followed by protein A affinity then cation exchange chromatography purification, final choice of Fab by binding specificity and affinity as determined by a dot blot assay, and lastly gel filtration purification of a large quantity of chosen Fabs for crystallization.

The INE-Beamline for actinide science at ANKA

Science.gov (United States)

Rothe, J.; Butorin, S.; Dardenne, K.; Denecke, M. A.; Kienzler, B.; Löble, M.; Metz, V.; Seibert, A.; Steppert, M.; Vitova, T.; Walther, C.; Geckeis, H.

2012-04-01

Since its inauguration in 2005, the INE-Beamline for actinide research at the synchrotron source ANKA (KIT North Campus) provides dedicated instrumentation for x-ray spectroscopic characterization of actinide samples and other radioactive materials. R&D work at the beamline focuses on various aspects of nuclear waste disposal within INE's mission to provide the scientific basis for assessing long-term safety of a final nuclear waste repository. The INE-Beamline is accessible for the actinide and radiochemistry community through the ANKA proposal system and the European Union Integrated Infrastructure Initiative ACTINET-I3. Experiments with activities up to 1 × 10+6 times the European exemption limit are feasible within a safe but flexible containment concept. Measurements with monochromatic radiation are performed at photon energies varying between ˜2.1 keV (P K-edge) and ˜25 keV (Pd K-edge), including the lanthanide L-edges and the actinide M- and L3-edges up to Cf. The close proximity of the INE-Beamline to INE controlled area labs offers infrastructure unique in Europe for the spectroscopic and microscopic characterization of actinide samples. The modular beamline design enables sufficient flexibility to adapt sample environments and detection systems to many scientific questions. The well-established bulk techniques x-ray absorption fine structure (XAFS) spectroscopy in transmission and fluorescence mode have been augmented by advanced methods using a microfocused beam, including (confocal) XAFS/x-ray fluorescence detection and a combination of (micro-)XAFS and (micro-)x-ray diffraction. Additional instrumentation for high energy-resolution x-ray emission spectroscopy has been successfully developed and tested.

The INE-Beamline for actinide science at ANKA

International Nuclear Information System (INIS)

Rothe, J.; Dardenne, K.; Denecke, M. A.; Kienzler, B.; Loeble, M.; Metz, V.; Steppert, M.; Vitova, T.; Geckeis, H.; Butorin, S.; Seibert, A.; Walther, C.

2012-01-01

Since its inauguration in 2005, the INE-Beamline for actinide research at the synchrotron source ANKA (KIT North Campus) provides dedicated instrumentation for x-ray spectroscopic characterization of actinide samples and other radioactive materials. R and D work at the beamline focuses on various aspects of nuclear waste disposal within INE's mission to provide the scientific basis for assessing long-term safety of a final nuclear waste repository. The INE-Beamline is accessible for the actinide and radiochemistry community through the ANKA proposal system and the European Union Integrated Infrastructure Initiative ACTINET-I3. Experiments with activities up to 1 x 10 +6 times the European exemption limit are feasible within a safe but flexible containment concept. Measurements with monochromatic radiation are performed at photon energies varying between ∼2.1 keV (P K-edge) and ∼25 keV (Pd K-edge), including the lanthanide L-edges and the actinide M- and L3-edges up to Cf. The close proximity of the INE-Beamline to INE controlled area labs offers infrastructure unique in Europe for the spectroscopic and microscopic characterization of actinide samples. The modular beamline design enables sufficient flexibility to adapt sample environments and detection systems to many scientific questions. The well-established bulk techniques x-ray absorption fine structure (XAFS) spectroscopy in transmission and fluorescence mode have been augmented by advanced methods using a microfocused beam, including (confocal) XAFS/x-ray fluorescence detection and a combination of (micro-)XAFS and (micro-)x-ray diffraction. Additional instrumentation for high energy-resolution x-ray emission spectroscopy has been successfully developed and tested.

Wavefront propagation through the beamline designed for seeding the DESY XUV FEL

CERN Document Server

Reininger, R; Gürtler, P; Bahrdt, J

2001-01-01

A beamline designed to reduce the spectral bandwidth of the DESY XUV FEL is described. The beamline is intended to cover the wavelength range from 6.4 to 50 nm with three variable line spacing gratings. A plane mirror in front of the grating is used to maintain constant magnification in the dispersion direction. The electric field generated by the first undulator at three wavelengths, 6.4, 13, and 25 nm, is propagated through the beamline. The results show that the beamline has the resolution and imaging properties required for seeding the second undulator at these wavelengths.

An overview of what is required and when for developing a beamline at the ALS

International Nuclear Information System (INIS)

Hussain, Z.

1995-08-01

This report discusses these topics: reviews required for developing a beamline at the ALS; work items and documentation required for the beamline design review; information to be communicated to the ALS staff before the beamline readiness review; work items and documentation required for the beamline readiness review; contacts for information, technical questions, and sources of additional information; and checklist of what is required and when for developing a beamline

The microspectroscopy beamline for the Australian synchrotron project

International Nuclear Information System (INIS)

Boldeman, J.W.; Ryan, C.; Cohen, D.D.

2005-01-01

A new multi-million dollar synchrotron facility is currently being built in Clayton, Victoria. This is a 3GeV electron machine, it will be a world class machine and contain state of the art beamline facilities for both Australian and overseas scientists. It is due for completion in mid-2007. This specialised beamline will provide sub-micron spatial resolution with the highest flux possible. It will combine 2D mapping with micro X-ray fluorescence (μ-XRF), micro X-ray absorption near edge spectroscopy (μ-XANES) and micro X-ray absorption fine structure spectroscopy (μ-XAFS) for elemental and chemical analysis to solve scientific problems that can only be understood using X-ray beams with sub-micron resolutions. In this paper we describe some key beamline components and give details about their performance specifications. 7 refs., 4 figs.; 1 tab

High-brightness beamline for x-ray spectroscopy at the ALS

Energy Technology Data Exchange (ETDEWEB)

Perera, R.C.C.; Jones, G. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States); Lindle, D.W. [Univ. of Nevada, Las Vegas, NV (United States)

1997-04-01

Beamline 9.3.1 at the Advanced Light Source (ALS) is a windowless beamline, covering the 1-6 keV photon-energy range, designed to achieve the goals of high energy resolution, high flux, and high brightness at the sample. When completed later this year, it will be the first ALS monochromatic hard x-ray beamline, and its brightness will be an order of magnitude higher than presently available in this energy range. In addition, it will provide flux and resolution comparable to any other beamline now in operation. To achieve these goals, two technical improvements, relative to existing x-ray beamlines, were incorporated. First, a somewhat novel optical design for x-rays, in which matched toroidal mirrors are positioned before and after the double-crystal monochromator, was adopted. This configuration allows for high resolution by passing a collimated beam through the monochromator, and for high brightness by focusing the ALS source on the sample with unit magnification. Second, a new {open_quotes}Cowan type{close_quotes} double-crystal monochromator based on the design used at NSLS beamline X-24A was developed. The measured mechanical precision of this new monochromator shows significant improvement over existing designs, without using positional feedback available with piezoelectric devices. Such precision is essential because of the high brightness of the radiation and the long distance (12 m) from the source (sample) to the collimating (focusing) mirror. This combination of features will provide a bright, high resolution, and stable x-ray beam for use in the x-ray spectroscopy program at the ALS.

Performance of beamline 9.3.1 at the ALS: Flux and resolution measurements

Energy Technology Data Exchange (ETDEWEB)

Uehara, Y. [Univ. of Nevada, Las Vegas, NV (United States); Fischer, G.; Kring, J.; Perera, R.C.C. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)

1997-04-01

Beamline 9.3.1 at the ALS is a windowless beamline, covering the 1-6 keV photon-energy range. This beamline is the first monochromatic hard x-ray beamline in the ALS, and designed to achieve the goals of high energy resolution, and preservation of the high brightness from the ALS. It consists of a new {open_quotes}Cowan type{close_quotes} double-crystal monochromator and two toroidal mirrors which are positioned before and after the monochromator. The construction of the beamline was completed in December of 1995, with imperfect mirrors. In this report, the authors describe the experimental results of absolute flux measurements and x-ray absorption measurements of gases and solid samples using the present set of mirrors.

Energy-dispersive X-ray diffraction beamline at Indus-2 synchrotron ...

Indian Academy of Sciences (India)

An energy-dispersive X-ray diffraction beamline has been designed, developed and commissioned at BL-11 bending magnet port of the Indian synchrotron source, Indus-2. The performance of this beamline has been benchmarked by measuring diffraction patterns from various elemental metals and standard inorganic ...

Moly99 Production Facility: Report on Beamline Components, Requirements, Costs

Energy Technology Data Exchange (ETDEWEB)

Bishofberger, Kip A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-12-23

In FY14 we completed the design of the beam line for the linear accelerator production design concept. This design included a set of three bending magnets, quadrupole focusing magnets, and octopoles to flatten the beam on target. This design was generic and applicable to multiple different accelerators if necessary. In FY15 we built on that work to create specifications for the individual beam optic elements, including power supply requirements. This report captures the specification of beam line components with initial cost estimates for the NorthStar production facility.This report is organized as follows: The motivation of the beamline design is introduced briefly, along with renderings of the design. After that, a specific list is provided, which accounts for each beamline component, including part numbers and costs, to construct the beamline. After that, this report details the important sections of the beamline and individual components. A final summary and list of follow-on activities completes this report.

The ELSA laser beamline for electron polarization measurements via Compton backscattering

Energy Technology Data Exchange (ETDEWEB)

Switka, Michael; Hinterkeuser, Florian; Koop, Rebecca; Hillert, Wolfgang [Electron Stretcher Facility ELSA, Physics Institute of Bonn University (Germany)

2016-07-01

The Electron Stretcher Facility ELSA provides a spin polarized electron beam with energies of 0.5 - 3.2 GeV for double polarization hadron physics experiments. As of 2015, the laser beamline of the polarimeter based on Compton backscattering restarted operation. It consists of a cw disk laser with design total beam power of 40 W and features two polarized 515 nm photon beams colliding head-on with the stored electron beam in ELSA. The polarization measurement is based on the vertical profile asymmetry of the back-scattered photons, which is dependent on the polarization degree of the stored electron beam. After recent laser repairs, beamline and detector modifications, the properties of the beamline have been determined and first measurements of the electron polarization degree were conducted. The beamline performance and first measurements are presented.

I18--the microfocus spectroscopy beamline at the Diamond Light Source.

Science.gov (United States)

Mosselmans, J Frederick W; Quinn, Paul D; Dent, Andrew J; Cavill, Stuart A; Moreno, Sofia Diaz; Peach, Andrew; Leicester, Peter J; Keylock, Stephen J; Gregory, Simon R; Atkinson, Kirk D; Rosell, Josep Roque

2009-11-01

The design and performance of the microfocus spectroscopy beamline at the Diamond Light Source are described. The beamline is based on a 27 mm-period undulator to give an operable energy range between 2 and 20.7 keV, enabling it to cover the K-edges of the elements from P to Mo and the L(3)-edges from Sr to Pu. Micro-X-ray fluorescence, micro-EXAFS and micro-X-ray diffraction have all been achieved on the beamline with a spot size of approximately 3 microm. The principal optical elements of the beamline consist of a toroid mirror, a liquid-nitrogen-cooled double-crystal monochromator and a pair of bimorph Kirkpatrick-Baez mirrors. The performance of the optics is compared with theoretical values and a few of the early experimental results are summarized.

Nanoflow electrospinning serial femtosecond crystallography

International Nuclear Information System (INIS)

Sierra, Raymond G.; Laksmono, Hartawan; Kern, Jan; Tran, Rosalie; Hattne, Johan; Alonso-Mori, Roberto; Lassalle-Kaiser, Benedikt; Glöckner, Carina; Hellmich, Julia; Schafer, Donald W.; Echols, Nathaniel; Gildea, Richard J.; Grosse-Kunstleve, Ralf W.; Sellberg, Jonas; McQueen, Trevor A.; Fry, Alan R.; Messerschmidt, Marc M.; Miahnahri, Alan; Seibert, M. Marvin; Hampton, Christina Y.; Starodub, Dmitri; Loh, N. Duane; Sokaras, Dimosthenis; Weng, Tsu-Chien; Zwart, Petrus H.; Glatzel, Pieter; Milathianaki, Despina; White, William E.; Adams, Paul D.; Williams, Garth J.; Boutet, Sébastien; Zouni, Athina; Messinger, Johannes; Sauter, Nicholas K.; Bergmann, Uwe; Yano, Junko; Yachandra, Vittal K.; Bogan, Michael J.

2012-01-01

A low flow rate liquid microjet method for delivery of hydrated protein crystals to X-ray lasers is presented. Linac Coherent Light Source data demonstrates serial femtosecond protein crystallography with micrograms, a reduction of sample consumption by orders of magnitude. An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14–3.1 µl min −1 to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min −1 and diffracted to beyond 4 Å resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption

Nanoflow electrospinning serial femtosecond crystallography

Energy Technology Data Exchange (ETDEWEB)

Sierra, Raymond G.; Laksmono, Hartawan [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Kern, Jan [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Tran, Rosalie; Hattne, Johan [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Alonso-Mori, Roberto [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Lassalle-Kaiser, Benedikt [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Glöckner, Carina; Hellmich, Julia [Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin (Germany); Schafer, Donald W. [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Echols, Nathaniel; Gildea, Richard J.; Grosse-Kunstleve, Ralf W. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Sellberg, Jonas [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Stockholm University, S-106 91 Stockholm (Sweden); McQueen, Trevor A. [Stanford University, Stanford, CA 94025 (United States); Fry, Alan R.; Messerschmidt, Marc M.; Miahnahri, Alan; Seibert, M. Marvin; Hampton, Christina Y.; Starodub, Dmitri; Loh, N. Duane; Sokaras, Dimosthenis; Weng, Tsu-Chien [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Zwart, Petrus H. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Glatzel, Pieter [European Synchrotron Radiation Facility, Grenoble (France); Milathianaki, Despina; White, William E. [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Williams, Garth J.; Boutet, Sébastien [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Zouni, Athina [Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin (Germany); Messinger, Johannes [Umeå Universitet, Umeå (Sweden); Sauter, Nicholas K. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bergmann, Uwe [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Yano, Junko; Yachandra, Vittal K. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bogan, Michael J., E-mail: mbogan@slac.stanford.edu [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States)

2012-11-01

A low flow rate liquid microjet method for delivery of hydrated protein crystals to X-ray lasers is presented. Linac Coherent Light Source data demonstrates serial femtosecond protein crystallography with micrograms, a reduction of sample consumption by orders of magnitude. An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14–3.1 µl min{sup −1} to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min{sup −1} and diffracted to beyond 4 Å resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.

TARA beamline and injection system

International Nuclear Information System (INIS)

Post, R.S.; Brindza, P.; Coleman, J.W.; Torti, R.P.; Blackfield, D.T.; Goodrich, P.

1983-01-01

The TARA beamline for neutral beam injection will permit one to three sources to fire into each plug (60 degree or optional 90 degree injection with respect to the TARA axis) or into each anchor (90 degree injection only). The sources, pre-aimed on their mounting plate at the NB test stand, may be fired into neutralizer ducts or optionally through a magnesium curtain, and the unneutralized fraction is dumped by the TARA fringing field onto a receiver plate. The beamline is housed in a cylindrical tank with the beam axis along the tank diameter at the midplane. The tank will be sorption pumped using LN + T/sub I/ or N/sub B/ and/or e-beam gettering. The beam burial tank contains sed arrays and a thin foil dump which reaches sufficiently high temperatures during the shot to boil out gas between shots

Soft x-ray beamline BL7A at the UVSOR

International Nuclear Information System (INIS)

Murata, T.; Matsukawa, T.; Naoe, S.; Horigome, T.; Matsudo, O.; Watanabe, M.

1992-01-01

A vacuum-compatible double-crystal monochromator with constant exit-beam height has been installed and operated for several years at beamline BL7A at the UVSOR facility at the Institute for Molecular Science, Okazaki, Japan, The beamline is used both for the photons from a normal bending-magnet section and those from a 4 T superconducting three-pole horizontal wiggler. Various pairs of monochromator crystals are being used with sufficient intensity and signal to noise ratio of the output signal. Basic structure of the beamline, the mechanism of the monochromator, and some typical spectra of materials with absorption edges between 850 eV and 4 keV are reported

EMA beamline at SIRIUS: extreme condition X-ray methods of analysis

International Nuclear Information System (INIS)

Souza Neto, Narcizo

2016-01-01

Full text: The EMA beamline (Extreme condition X-ray Methods of Analysis) is one of the hard x-ray undulator beamlines within the first phase of the new synchrotron source in Brazil (Sirius project). This beamline is thought to make a difference where a high brilliance (high flux of up to 2 x 10 14 photons/sec with beam size down to 0.5 x 0.5 μm 2 ) is essential, which is the case for extreme pressures that require small focus and time-resolved that require high photon flux. With that in mind we propose the beamline to have two experimental hutches to cover most of the extreme condition techniques today employed at synchrotron laboratories worldwide. These two stations are thought to provide the general infrastructure for magnets and lasers experiments, which may evolve as new scientific problems appear. In addition to the hutches, support laboratories will be strongly linked and supportive to the experiments at the beamline, covering high pressure instrumentations using diamond anvil cells and pump-and-probe requirements for ultrafast and high power lasers. Along these lines, we will describe the following techniques covered at this beamline: magnetic spectroscopy (XMCD) and scattering (XRMS) under high pressure and very low temperature in order to fully probe both ferromagnetic and antiferromagnetic materials and the dependence with pressure; extreme pressure and temperature XRD and XAS experiments using very small diamond culet anvils and high power lasers. (author)

EMA beamline at SIRIUS: extreme condition X-ray methods of analysis

Energy Technology Data Exchange (ETDEWEB)

Souza Neto, Narcizo, E-mail: narcizo.souza@lnls.br [Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP (Brazil)

2016-07-01

Full text: The EMA beamline (Extreme condition X-ray Methods of Analysis) is one of the hard x-ray undulator beamlines within the first phase of the new synchrotron source in Brazil (Sirius project). This beamline is thought to make a difference where a high brilliance (high flux of up to 2 x 10{sup 14} photons/sec with beam size down to 0.5 x 0.5 μm{sup 2}) is essential, which is the case for extreme pressures that require small focus and time-resolved that require high photon flux. With that in mind we propose the beamline to have two experimental hutches to cover most of the extreme condition techniques today employed at synchrotron laboratories worldwide. These two stations are thought to provide the general infrastructure for magnets and lasers experiments, which may evolve as new scientific problems appear. In addition to the hutches, support laboratories will be strongly linked and supportive to the experiments at the beamline, covering high pressure instrumentations using diamond anvil cells and pump-and-probe requirements for ultrafast and high power lasers. Along these lines, we will describe the following techniques covered at this beamline: magnetic spectroscopy (XMCD) and scattering (XRMS) under high pressure and very low temperature in order to fully probe both ferromagnetic and antiferromagnetic materials and the dependence with pressure; extreme pressure and temperature XRD and XAS experiments using very small diamond culet anvils and high power lasers. (author)

Quantum crystallography: A perspective.

Science.gov (United States)

Massa, Lou; Matta, Chérif F

2018-06-30

Extraction of the complete quantum mechanics from X-ray scattering data is the ultimate goal of quantum crystallography. This article delivers a perspective for that possibility. It is desirable to have a method for the conversion of X-ray diffraction data into an electron density that reflects the antisymmetry of an N-electron wave function. A formalism for this was developed early on for the determination of a constrained idempotent one-body density matrix. The formalism ensures pure-state N-representability in the single determinant sense. Applications to crystals show that quantum mechanical density matrices of large molecules can be extracted from X-ray scattering data by implementing a fragmentation method termed the kernel energy method (KEM). It is shown how KEM can be used within the context of quantum crystallography to derive quantum mechanical properties of biological molecules (with low data-to-parameters ratio). © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Crystallography and environment development

International Nuclear Information System (INIS)

Radwan, M.M.

1992-01-01

Crystallography, the study of atomic and molecular structure, has given detailed information about the fine-structure of the inorganic and living world-i.e. about the environment (in the widest sense of the world)-. It has contributed to geology (at the atomic level), crystal chemistry, the structure of minerals, soils and clays. In the case of the living world it has contributed to structural studies of biological molecules; proteins, nucleic acids (DNA and RNA), and polysaccharides. knowing how the atoms in a material are arranged allows to understand the relationship between atomic structure and properties of these materials. Today we are entering a new age in crystallography-the age of genetic engineering in the living world, and inorganic crystallographic engineering, where we use crystallographic information from the structures nature has given us, to begin to design and build structure of our own, of specified properties, aiming at the welfare of man and the development of his environment

The Beamline X28C of the Center for Synchrotron Biosciences: a National Resource for Biomolecular Structure and Dynamics Experiments Using Synchrotron Footprinting

International Nuclear Information System (INIS)

Gupta, S.; Sullivan, M.; Toomey, J.; Kiselar, J.; Chance, M.

2007-01-01

Structural mapping of proteins and nucleic acids with high resolution in solution is of critical importance for understanding their biological function. A wide range of footprinting technologies have been developed over the last ten years to address this need. Beamline X28C, a white-beam X-ray source at the National Synchrotron Light Source of Brookhaven National Laboratory, functions as a platform for synchrotron footprinting research and further technology development in this growing field. An expanding set of user groups utilize this national resource funded by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health. The facility is operated by the Center for Synchrotron Biosciences and the Center for Proteomics of Case Western Reserve University. The facility includes instrumentation suitable for conducting both steady-state and millisecond time-resolved footprinting experiments based on the production of hydroxyl radicals by X-rays. Footprinting studies of nucleic acids are routinely conducted with X-ray exposures of tens of milliseconds, which include studies of nucleic acid folding and their interactions with proteins. This technology can also be used to study protein structure and dynamics in solution as well as protein-protein interactions in large macromolecular complexes. This article provides an overview of the X28C beamline technology and defines protocols for its adoption at other synchrotron facilities. Lastly, several examples of published results provide illustrations of the kinds of experiments likely to be successful using these approaches

Long-pulse beamlines for the mirror fusion test facility

International Nuclear Information System (INIS)

Stone, R.R.; Goldner, A.I.; Poulsen, P.

1984-01-01

We have recently obtained test results indicating that a beam of pure full-energy deuterium particles can be delivered to the plasma targets in MFTF-B. We used a close-coupled separator magnet with the ion source to separate the impurities from the full-energy deuterium particles. Our completed studies show that the usual iron-core sweep magnet and shielding used in neutral beamlines can be eliminated and the gas flow out of the beamline decreased. This design also reduces beam losses. We will use smooth-bore OFHC tube arrays brazed to manifolds for the active heat transfer surfaces. Tests indicate that both burnout and life requirements are met by this design. In this paper, we present test results and discuss the MFTF-B long-pulse beamline configuration

Macromolecular crowding directs extracellular matrix organization and mesenchymal stem cell behavior.

Directory of Open Access Journals (Sweden)

Adam S Zeiger

Full Text Available Microenvironments of biological cells are dominated in vivo by macromolecular crowding and resultant excluded volume effects. This feature is absent in dilute in vitro cell culture. Here, we induced macromolecular crowding in vitro by using synthetic macromolecular globules of nm-scale radius at physiological levels of fractional volume occupancy. We quantified the impact of induced crowding on the extracellular and intracellular protein organization of human mesenchymal stem cells (MSCs via immunocytochemistry, atomic force microscopy (AFM, and AFM-enabled nanoindentation. Macromolecular crowding in extracellular culture media directly induced supramolecular assembly and alignment of extracellular matrix proteins deposited by cells, which in turn increased alignment of the intracellular actin cytoskeleton. The resulting cell-matrix reciprocity further affected adhesion, proliferation, and migration behavior of MSCs. Macromolecular crowding can thus aid the design of more physiologically relevant in vitro studies and devices for MSCs and other cells, by increasing the fidelity between materials synthesized by cells in vivo and in vitro.

Macromolecular crowding directs extracellular matrix organization and mesenchymal stem cell behavior.

Science.gov (United States)

Zeiger, Adam S; Loe, Felicia C; Li, Ran; Raghunath, Michael; Van Vliet, Krystyn J

2012-01-01

Microenvironments of biological cells are dominated in vivo by macromolecular crowding and resultant excluded volume effects. This feature is absent in dilute in vitro cell culture. Here, we induced macromolecular crowding in vitro by using synthetic macromolecular globules of nm-scale radius at physiological levels of fractional volume occupancy. We quantified the impact of induced crowding on the extracellular and intracellular protein organization of human mesenchymal stem cells (MSCs) via immunocytochemistry, atomic force microscopy (AFM), and AFM-enabled nanoindentation. Macromolecular crowding in extracellular culture media directly induced supramolecular assembly and alignment of extracellular matrix proteins deposited by cells, which in turn increased alignment of the intracellular actin cytoskeleton. The resulting cell-matrix reciprocity further affected adhesion, proliferation, and migration behavior of MSCs. Macromolecular crowding can thus aid the design of more physiologically relevant in vitro studies and devices for MSCs and other cells, by increasing the fidelity between materials synthesized by cells in vivo and in vitro.

CHARACTERIZATION OF THE NEW NSLS INFARED MICROSPECTROSCOPY BEAMLINE U10B.

Energy Technology Data Exchange (ETDEWEB)

CARR,G.L.

1999-07-19

The first of several new infrared beamlines, built on a modified bending magnet port of the NSLS VUV ring, is now operational for mid-infrared microspectroscopy. The port simultaneously delivers 40 mrad by 40 mrad to two separate beamlines and spectrometer endstations designated U10A and U10B. The latter is equipped with a scanning infrared microspectrometer. The combination of this instrument and high brightness synchrotron radiation makes diffraction-limited microspectroscopy practical. This paper describes the beamline's performance and presents quantitative information on the diffraction-limited resolution.

Characterization of the new NSLS infrared microspectroscopy beamline U10B

Energy Technology Data Exchange (ETDEWEB)

Carr, G.L.

1999-07-19

The first of several new infrared beamlines, built on a modified bending magnet port of the NSLS VUV ring, is now operational for mid-infrared microspectroscopy. The port simultaneously delivers 40 mrad by 40 mrad to two separate beamlines and spectrometer endstations designated U10A and U10B. The latter is equipped with a scanning infrared microspectrometer. The combination of this instrument and high brightness synchrotron radiation makes diffraction-limited microspectroscopy practical. This paper describes the beamline's performance and presents quantitative information on the diffraction-limited resolution.

Status of the Nanoscopium Scanning Hard X-ray Nanoprobe Beamline of Synchrotron Soleil

Science.gov (United States)

Somogyi, A.; Kewish, C. M.; Ribbens, M.; Moreno, T.; Polack, F.; Baranton, G.; Desjardins, K.; Samama, J. P.

2013-10-01

The Nanoscopium 155 m-long scanning hard X-ray nanoprobe beamline of Synchrotron Soleil (St Aubin, France) is dedicated to quantitative multi-modal 2D/3D imaging. The beamline aims to reach down to 30 nm spatial resolution in the 5-20 keV energy range. Two experimental stations working in consecutive operation mode will be dedicated to coherent diffractive imaging and scanning X-ray nanoprobe techniques. The beamline is in the construction phase, the first user experiments are expected in 2014. The main characteristics of the beamline and an overview of its status are given in this paper.

Status of the Nanoscopium Scanning Hard X-ray Nanoprobe Beamline of Synchrotron Soleil

International Nuclear Information System (INIS)

Somogyi, A; Kewish, C M; Ribbens, M; Moreno, T; Polack, F; Baranton, G; Desjardins, K; Samama, J P

2013-01-01

The Nanoscopium 155 m-long scanning hard X-ray nanoprobe beamline of Synchrotron Soleil (St Aubin, France) is dedicated to quantitative multi-modal 2D/3D imaging. The beamline aims to reach down to 30 nm spatial resolution in the 5–20 keV energy range. Two experimental stations working in consecutive operation mode will be dedicated to coherent diffractive imaging and scanning X-ray nanoprobe techniques. The beamline is in the construction phase, the first user experiments are expected in 2014. The main characteristics of the beamline and an overview of its status are given in this paper

PF-AR NW14, a new time-resolved diffraction/scattering beamline

Science.gov (United States)

Nozawa, Shunsuke; Adachi, Shin-ichi; Tazaki, Ryoko; Takahashi, Jun-ichi; Itatani, Jiro; Daimon, Masahiro; Mori, Takeharu; Sawa, Hiroshi; Kawata, Hiroshi; Koshihara, Shin-ya

2005-01-01

NW14 is a new insertion device beamline at the Photon Factory Advanced Ring (PF-AR), which is a unique ring with full-time single-bunched operation, aiming for timeresolved x-ray diffraction/scattering and XAFS experiments. The primary scientific goal of this beamline is to observe the ultrafast dynamics of condensed matter systems such as organic and inorganic crystals, biological systems and liquids triggered by optical pulses. With the large photon fluxes derived from the undulator, it should become possible to take a snapshoot an atomic-scale image of the electron density distribution. By combining a series of images it is possible to produce a movie of the photo-induced dynamics with 50-ps resolution. The construction of the beamline is being funded by the ERATO Koshihara Non-equilibrium Dynamics Project of the Japan Science and Technology Agency (JST), and the beamline will be operational from autumn 2005.

PF-AR NW14, a new time-resolved diffraction/scattering beamline

International Nuclear Information System (INIS)

Nozawa, Shunsuke; Adachi, Shin-ichi; Tazaki, Ryoko; Takahashi, Jun-ichi; Itatani, Jiro; Daimon, Masahiro; Mori, Takeharu; Sawa, Hiroshi; Kawata, Hiroshi; Koshihara, Shin-ya

2005-01-01

NW14 is a new insertion device beamline at the Photon Factory Advanced Ring (PF-AR), which is a unique ring with full-time single-bunched operation, aiming for timeresolved x-ray diffraction/scattering and XAFS experiments. The primary scientific goal of this beamline is to observe the ultrafast dynamics of condensed matter systems such as organic and inorganic crystals, biological systems and liquids triggered by optical pulses. With the large photon fluxes derived from the undulator, it should become possible to take a snapshoot an atomic-scale image of the electron density distribution. By combining a series of images it is possible to produce a movie of the photo-induced dynamics with 50-ps resolution. The construction of the beamline is being funded by the ERATO Koshihara Non-equilibrium Dynamics Project of the Japan Science and Technology Agency (JST), and the beamline will be operational from autumn 2005

Crystallography of quasicrystals concepts, methods and structures

CERN Document Server

Walter, Steurer

2009-01-01

From tilings to quasicrystal structures and from surfaces to the n-dimensional approach, this book gives a full, self-contained in-depth description of the crystallography of quasicrystals. It aims not only at conveying the concepts and a precise picture of the structures of quasicrystals, butit also enables the interested reader to enter the field of quasicrystal structure analysis. Going beyond metallic quasicrystals, it also describes the new, dynamically growing field of photonic quasicrystals. The readership will be graduate students and researchers in crystallography, solid-state physics, materials science, solid- state chemistry and applied mathematics.

Crystallography and Drug Design

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 12. Crystallography and Drug Design. K Suguna. General Article Volume 19 Issue 12 December 2014 pp 1093-1103. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/019/12/1093-1103. Keywords.

APS beamline standard components handbook, Version 1.3

International Nuclear Information System (INIS)

Hahn, U.; Shu, D.; Kuzay, T.M.

1993-02-01

This Handbook in its current version (1.3) contains descriptions, specifications, and preliminary engineering design drawings for many of the standard components. The design status and schedules have been provided wherever possible. In the near future, the APS plans to update engineering drawings of identified standard beamline components and complete the Handbook. The completed version of this Handbook will become available to both the CATs and potential vendors. Use of standard components should result in major cost reductions for CATs in the areas of beamline design and construction

The materials science synchrotron beamline EDDI for energy-dispersive diffraction analysis

International Nuclear Information System (INIS)

Genzel, Ch.; Denks, I.A.; Gibmeier, J.; Klaus, M.; Wagener, G.

2007-01-01

In April 2005 the materials science beamline EDDI (Energy Dispersive DIffraction) at the Berlin synchrotron storage ring BESSY started operation. The beamline is operated in the energy-dispersive mode of diffraction using the high energy white photon beam provided by a superconducting 7 T multipole wiggler. Starting from basic information on the beamline set-up, its measuring facilities and data processing concept, the wide range of applications for energy-dispersive diffraction is demonstrated by a series of examples coming from different fields in materials sciences. It will be shown, that the EDDI beamline is especially suitable for the investigation of structural properties and gradients in the near surface region of polycrystalline materials. In particular, this concerns the analysis of multiaxial residual stress fields in the highly stressed surface zone of technical parts. The high photon flux further facilitates fast in situ experiments at room as well as high temperature to monitor for example the growth kinetics and reaction in thin film growth

ADLIB: A simple database framework for beamline codes

International Nuclear Information System (INIS)

Mottershead, C.T.

1993-01-01

There are many well developed codes available for beamline design and analysis. A significant fraction of each of these codes is devoted to processing its own unique input language for describing the problem. None of these large, complex, and powerful codes does everything. Adding a new bit of specialized physics can be a difficult task whose successful completion makes the code even larger and more complex. This paper describes an attempt to move in the opposite direction, toward a family of small, simple, single purpose physics and utility modules, linked by an open, portable, public domain database framework. These small specialized physics codes begin with the beamline parameters already loaded in the database, and accessible via the handful of subroutines that constitute ADLIB. Such codes are easier to write, and inherently organized in a manner suitable for incorporation in model based control system algorithms. Examples include programs for analyzing beamline misalignment sensitivities, for simulating and fitting beam steering data, and for translating among MARYLIE, TRANSPORT, and TRACE3D formats

Nitrogen isotopic composition of macromolecular organic matter in interplanetary dust particles

Science.gov (United States)

Aléon, Jérôme; Robert, François; Chaussidon, Marc; Marty, Bernard

2003-10-01

Nitrogen concentrations and isotopic compositions were measured by ion microprobe scanning imaging in two interplanetary dust particles L2021 K1 and L2036 E22, in which imaging of D/H and C/H ratios has previously evidenced the presence of D-rich macromolecular organic components. High nitrogen concentrations of 10-20 wt% and δ 15N values up to +400‰ are observed in these D-rich macromolecular components. The previous study of D/H and C/H ratios has revealed three different D-rich macromolecular phases. The one previously ascribed to macromolecular organic matter akin the insoluble organic matter (IOM) from carbonaceous chondrites is enriched in nitrogen by one order of magnitude compared to the carbonaceous chondrite IOM, although its isotopic composition is still similar to what is known from Renazzo (δ 15N = +208‰). The correlation observed in macromolecular organic material between the D- and 15N-excesses suggests that the latter originate probably from chemical reactions typical of the cold interstellar medium. These interstellar materials preserved to some extent in IDPs are therefore macromolecular organic components with various aliphaticity and aromaticity. They are heavily N-heterosubstituted as shown by their high nitrogen concentrations >10 wt%. They have high D/H ratios >10 -3 and δ 15N values ≥ +400‰. In L2021 K1 a mixture is observed at the micron scale between interstellar and chondritic-like organic phases. This indicates that some IDPs contain organic materials processed at various heliocentric distances in a turbulent nebula. Comparison with observation in comets suggests that these molecules may be cometary macromolecules. A correlation is observed between the D/H ratios and δ 15N values of macromolecular organic matter from IDPs, meteorites, the Earth and of major nebular reservoirs. This suggests that most macromolecular organic matter in the inner solar system was probably issued from interstellar precursors and further processed

Indus-I beamlines for condensed matter physics

International Nuclear Information System (INIS)

Nandedkar, R.V.

2001-01-01

Full text: A 450 MeV electron storage ring Indus-I is now operational. This storage ring gives synchrotron radiation in soft x-ray vacuum ultra violet (VUV) and to visible region. On this storage ring six beamlines are now being set up for atomic and molecular spectroscopy experiments, solid state spectroscopy experiments and soft and VUV reflectivity experiments. In this talk, present status of beamlines which condense matter physicists will be interested in will be given along with some commissioning experiments. These beam lines are based on a toroidal grating monochromators in the range 40 - 1000 A with moderate energy resolution. Some experiments which can be conducted using these beam lines will be discussed

Imaging in real and reciprocal space at the Diamond beamline I13

International Nuclear Information System (INIS)

Rau, C.; Wagner, U. H.; Vila-Comamala, J.; Bodey, A.; Parson, A.; García-Fernández, M.; Pešić, Z.; De Fanis, A.

2016-01-01

The Diamond Imaging and Coherence beamline I13 consists of two independent branchlines for imaging in real and reciprocal space. Different microscopies are available providing a range of spatial resolution from 5µm to potentially 5nm. The beamline operates in the energy range of 6-35keV covering different scientific areas such as biomedicine, materials science and geophysics. Several original devices have been developed at the beamline, such as the EXCALIBUR photon counting detector and the combined robot arms for coherent X-ray diffraction

Imaging in real and reciprocal space at the Diamond beamline I13

Energy Technology Data Exchange (ETDEWEB)

Rau, C., E-mail: Christoph.rau@diamond.ac.uk [Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX 11 0DE (United Kingdom); University of Manchester, School of Materials Grosvenor St., Manchester, M1 7HS (United Kingdom); Northwestern University School of Medicine, 303 E. Chicago Avenue, Chicago, IL 60611-3008 (United States); Wagner, U. H.; Vila-Comamala, J.; Bodey, A.; Parson, A.; García-Fernández, M.; Pešić, Z. [Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX 11 0DE (United Kingdom); De Fanis, A. [Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX 11 0DE (United Kingdom); European XFEL GmbH, Notkestraße 85, 22607 Hamburg (Germany)

2016-01-28

The Diamond Imaging and Coherence beamline I13 consists of two independent branchlines for imaging in real and reciprocal space. Different microscopies are available providing a range of spatial resolution from 5µm to potentially 5nm. The beamline operates in the energy range of 6-35keV covering different scientific areas such as biomedicine, materials science and geophysics. Several original devices have been developed at the beamline, such as the EXCALIBUR photon counting detector and the combined robot arms for coherent X-ray diffraction.

A short history of structure based research on the photocycle of photoactive yellow protein.

Science.gov (United States)

Schmidt, Marius

2017-05-01

The goals of time-resolved macromolecular crystallography are to extract the molecular structures of the reaction intermediates and the reaction dynamics from time-resolved X-ray data alone. To develop the techniques of time-resolved crystallography, biomolecules with special properties are required. The Photoactive Yellow Protein is the most sparkling of these.

Microspectroscopy At Beamline 73 MAX-lab

International Nuclear Information System (INIS)

Engdahl, Anders

2010-01-01

Presentation of some projects at the infrared microspectroscopy experimental station at beamline 73 MAX-lab. Among the subjects are found identification of organic residues in fossil material and examination of the chemistry in an old oak wood wreck.

Upgrade of the Proton West secondary beamline

International Nuclear Information System (INIS)

Spiegel, L.

1989-01-01

As originally designed and operated, protons entering PW6 were steered by a series of EPB dipoles into a single interaction length beryllium target, some 43 feet from the enclosure wall. Ensuing secondary beams, either p + /π + or p - /π - , were collected by a string of quadrupoles following the target, steered westward, away from the Proton Center line, through PW6 and PW7, and ultimately focussed on experiment production targets located within the large PW8 hall. Around the Spring of 1988 it was decided to upgrade the existing Proton West secondary beamline to allow for transport of a primary proton beam, anticipated to be either 800 or 900 GeV/c, through PW8. This upgrade project, which is now nearing completion, was largely motivated by the then recent approval of E-771, a hadronic beauty production experiment located in PW8. E-771 represents the third in a series of experiments for the large-acceptance dimuon spectrometer presently located at the end of the Proton West beamline. This Technical Memo is a summary of the upgrade --- an explanation of the underlying strategy and a documentation of the final locations of the secondary beamline elements. 6 refs., 2 figs., 2 tabs

Nuclear resonant scattering beamline at SPring-8

Energy Technology Data Exchange (ETDEWEB)

Harami, Taikan [Japan Atomic Energy Research Inst., Kamigori, Hyogo (Japan). Kansai Research Establishment

1996-04-01

Mainly by Japan Atomic Energy Research Institute, the Institute of Physical and Chemical Research and Japan Synchrotron Radiation Research Institute, the construction of the Super Photon ring-8 GeV (SPring-8) which is the large scale synchrotron radiation facility for a high luminance light source placing emphasis on short wavelength region (shorter than about 1 nm) is in progress at the Harima Science Park City, Hyogo Prefecture. The features of the SPring-8 are the high luminance of light, the good parallelism and directionality of light, the quasi-monochromatic light with variable wavelength, and the possibility of design from straight polarization to circular polarization. The injection system that accelerates electrons up to 8 GeV and the storage ring storing the 8 GeV electrons for long hours, and 61 beamlines are explained. The manufacture of the nuclear resonant scattering beamline as the beamline for joint utilization was begun. Its transport channel and the experiment hutch are shown. By the features of undulator synchrotron radiation, the research on the matters with small recoilless fraction such as biological substances, liquid, gas and others and the research on time-dependent phenomena become feasible anew. The research on the dynamic structural analysis of heme protein is planned. (K.I.)

Soft x-ray spectroscopy undulator beamline at the Advanced Photon Source

Energy Technology Data Exchange (ETDEWEB)

Randall, K.J.; Xu, Z.; Moore, J.F.; Gluskin, E.

1997-09-01

Construction of the high-resolution soft x ray spectroscopy undulator beamline, 2ID-C, at the Advanced Photon Source (APS) has been completed. The beamline, one of two soft x ray beamlines at the APS, will cover the photon energy range from 500 to 3,000 eV, with a maximum resolving power between 7,000 and 14,000. The optical design is based on a spherical grating monochromator (SGM) giving both high resolution and high flux throughput. Photon flux is calculated to be approximately 10{sup 12}--10{sup 13} photons per second with a beam size of approximately 1 x 1 mm{sup 2} at the sample.

eBooking of beam-time over internet for beamlines of Indus synchrotron radiation sources

International Nuclear Information System (INIS)

Jain, Alok; Verma, Rajesh; Rajan, Alpana; Modi, M.H.; Rawat, Anil

2015-01-01

Users from various research labs and academic institutes carry out experiments on beamlines of two Synchrotron Radiation Sources Indus-1 and Indus-2 available at RRCAT, Indore. To carry out experimental work on beamlines of both synchrotron radiation sources, beam-time is booked over Internet by the users of beamlines using user portal designed, developed and deployed over Internet. This portal has made the process of beamtime booking fast, hassle free and paperless as manual booking of beam-time for carrying out experiment on a particular beamline is cumbersome. The portal facilitates in-charge of Indus-1 and Indus-2 beamlines to keep track of users' records, work progress and other activities linked to experiments carried on beamlines. It is important to keep record and provide statistics about the usage of the beam lines from time-to-time. The user portal for e-booking of beam-time has been developed in-house using open source software development tools. Multi-step activities of users and beamline administrators are workflow based with seamless flow of information across various modules and fully authenticated using role based mechanism for different roles of software usage. The software is in regular use since November 2013 and has helped beamline in- charges in efficiently managing various activities related to user registration, booking of beam-time, booking of Guest House, Generation of Security permits, User feedback etc. Design concept, role based authentication mechanism and features provided by the web portal are discussed in detail in this paper. (author)

Construction Status of the Beamline for Radio-Isotope Production in the Korea Multi-purpose Accelerator Complex

Energy Technology Data Exchange (ETDEWEB)

Chung, B. H.; Yoon, S. P.; Seol, K. T.; Kim, H. S.; Kwon, H. J.; Cho, Y. S. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2015-10-15

The 100-MeV beamline consist of 5 target room, a TR 103 as one of these is operating beamline, and a TR 101 as the other beamline is under construction as shown in Fig. 1. The TR 101 as beamline target room will be used for the high value-added medical isotope production and increased utilization of the proton accelerator. The optical system of the beamline consisted of dipole and quadrupole, and it included beam position monitor (BPM) and current transformer (CT) for beam diagnostics. The beamline was inserted into the carbon block and the aluminum collimator, the end of pipe as beam window was used for the aluminum to reduce the radioactive of materials. The target transfer equipment is being installed for RI production. The RI Beamline was aligned using the laser tracker, and vacuum leak was not detected by the helium leak detector. This facility is expected to the high value-added medical isotope production and increased utilization of the proton accelerator.

Analytical model for macromolecular partitioning during yeast cell division

International Nuclear Information System (INIS)

Kinkhabwala, Ali; Khmelinskii, Anton; Knop, Michael

2014-01-01

Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell — which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles — can be achieved by both passive (e.g. diffusion, localized retention sites) and active (e.g. motor-driven transport) processes operating in the presence of external polarity cues, internal asymmetries, spontaneous symmetry breaking, or stochastic effects. However, the quantitative contribution of different processes to the partitioning of macromolecular content is difficult to evaluate. Here we developed an analytical model that allows rapid quantitative assessment of partitioning as a function of various parameters in the budding yeast Saccharomyces cerevisiae. This model exposes quantitative degeneracies among the physical parameters that govern macromolecular partitioning, and reveals regions of the solution space where diffusion is sufficient to drive asymmetric partitioning and regions where asymmetric partitioning can only be achieved through additional processes such as motor-driven transport. Application of the model to different macromolecular assemblies suggests that partitioning of protein aggregates and episomes, but not prions, is diffusion-limited in yeast, consistent with previous reports. In contrast to computationally intensive stochastic simulations of particular scenarios, our analytical model provides an efficient and comprehensive overview of partitioning as a function of global and macromolecule-specific parameters. Identification of quantitative degeneracies among these parameters highlights the importance of their careful measurement for a given macromolecular species in order to understand the dominant processes responsible for its observed partitioning

High Power Primary Slits For The ESRF Beamlines

International Nuclear Information System (INIS)

Marion, Philippe; Zhang Lin

2004-01-01

At the ESRF, in order to face the increased heatload on the beamlines, new Primary slits have been developed. The main features of the new slits are: beam size = 0 to 4mm; accuracy = 10μm; acceptable power density: 600 W/mm2; acceptable total power: 7kW; total length: 740mm. The adopted design offers a wide water cooled area; the shapes of the heated parts have been optimized to reduce the local thermal stresses. The maximum calculated temperature and stress are 353C and 606MPa. Six of these new slits are now in operation on ESRF Beamlines

Kinematic mounting systems for NSLS beamlines and experiments

International Nuclear Information System (INIS)

Oversluizen, T.; Stoeber, W.; Johnson, E.D.

1991-01-01

Methods for kinematically mounting equipment are well established, but applications at synchrotron radiation facilities are subject to constraints not always encountered in more traditional laboratory settings. Independent position adjustment of beamline components can have significant benefits in terms of minimizing time spent aligning, and maximizing time spent acquiring data. In this paper, we use examples taken from beamlines at the NSLS to demonstrate approaches for optimization of the reproducibility, stability, excursion, and set-up time for various situations. From our experience, we extract general principles which we hope will be useful for workers at other synchrotron radiation facilities. 7 refs., 4 figs

Ronchi test for characterization of X-ray nanofocusing optics and beamlines.

Science.gov (United States)

Uhlén, Fredrik; Rahomäki, Jussi; Nilsson, Daniel; Seiboth, Frank; Sanz, Claude; Wagner, Ulrich; Rau, Christoph; Schroer, Christian G; Vogt, Ulrich

2014-09-01

A Ronchi interferometer for hard X-rays is reported in order to characterize the performance of the nanofocusing optics as well as the beamline stability. Characteristic interference fringes yield qualitative data on present aberrations in the optics. Moreover, the visibility of the fringes on the detector gives information on the degree of spatial coherence in the beamline. This enables the possibility to detect sources of instabilities in the beamline like vibrations of components or temperature drift. Examples are shown for two different nanofocusing hard X-ray optics: a compound refractive lens and a zone plate.

Current schemes for National Synchrotron Light Source UV beamlines

International Nuclear Information System (INIS)

Williams, G.P.; Howells, M.R.; McKinney, W.R.

1979-01-01

We describe in some detail four beamlines proposed for the National Synchrotron Light Source uv ring at Brookhaven National Laboratory. Three grazing-incidence instruments, one of the plane grating Mijake type and two with toroidal gratings at grazing angles of 2-1/2 0 and 15 0 are described. Two normal incidence instruments, one using the source as entrance slit and accepting 75 milliradians horizontally are also discussed. In each case we have estimated the output fluxes expected from such beamlines

What Macromolecular Crowding Can Do to a Protein

Science.gov (United States)

Kuznetsova, Irina M.; Turoverov, Konstantin K.; Uversky, Vladimir N.

2014-01-01

The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area. PMID:25514413

NSLS [National Synchrotron Light Source] X-19A beamline performance for x-ray absorption measurements

International Nuclear Information System (INIS)

Yang, C.Y.; Penner-Hahn, J.E.; Stefan, P.M.

1989-01-01

Characterization of the X-19A beamline at the National Synchrotron Light Source (NSLS) is described. The beamline is designed for high resolution x-ray absorption spectroscopy over a wide energy range. All of the beamline optical components are compatible with ultrahigh vacuum (UHV) operation. This permits measurements to be made in a window-less mode, thereby facilitating lower energy (<4 KeV) studies. To upgrade the beamline performance, several possible improvements in instrumentation and practice are discussed to increase photon statistics with an optimum energy resolution, while decreasing the harmonic contamination and noise level. A special effort has been made to improve the stability and UHV compatibility of the monochromator system. Initial x-ray absorption results demonstrate the capabilities of this beamline for x-ray absorption studies of low Z elements (e.g. S) in highly dilute systems. The future use of this beamline for carrying out various x-ray absorption experiments is presented. 10 refs., 4 figs

BNL ATF II beamlines design

Energy Technology Data Exchange (ETDEWEB)

Fedurin, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Jing, Y. [Brookhaven National Lab. (BNL), Upton, NY (United States); Stratakis, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Swinson, C. [Brookhaven National Lab. (BNL), Upton, NY (United States)

2015-05-03

The Brookhaven National Laboratory. Accelerator Test Facility (BNL ATF) is currently undergoing a major upgrade (ATF-II). Together with a new location and much improved facilities, the ATF will see an upgrade in its major capabilities: electron beam energy and quality and CO₂ laser power. The electron beam energy will be increased in stages, first to 100-150 MeV followed by a further increase to 500 MeV. Combined with the planned increase in CO₂ laser power (from 1-100 TW), the ATF-II will be a powerful tool for Advanced Accelerator research. A high-brightness electron beam, produced by a photocathode gun, will be accelerated and optionally delivered to multiple beamlines. Besides the energy range (up to a possible 500 MeV in the final stage) the electron beam can be tailored to each experiment with options such as: small transverse beam size (<10 um), short bunch length (<100 fsec) and, combined short and small bunch options. This report gives a detailed overview of the ATFII capabilities and beamlines configuration.

A short history of structure based research on the photocycle of photoactive yellow protein

Directory of Open Access Journals (Sweden)

Marius Schmidt

2017-05-01

Full Text Available The goals of time-resolved macromolecular crystallography are to extract the molecular structures of the reaction intermediates and the reaction dynamics from time-resolved X-ray data alone. To develop the techniques of time-resolved crystallography, biomolecules with special properties are required. The Photoactive Yellow Protein is the most sparkling of these.

The founding and development of X-ray crystallography

International Nuclear Information System (INIS)

Mai Zhenhong

2014-01-01

2014 is the centennial of X-ray crystallography. Crystals have played an important role in our lives and in the development of society throughout these 100 years. In July 2012 the 66th General Assembly of the United Nations declared 2014 to be the official International Year of Crystallography (IYCr2014). The discovery of X-ray diffraction by crystals has had a profound impact on science and technology worldwide. It provides for us a distinct image of the arrangement of atoms or/and molecules in crystals. The development of X-ray spectroscopy has made it possible for us to understand the laws of atomic structure, and thus to identify the elements in all kinds of matter. In this article the greatest events in the history of X-ray crystallography, including the development of X-ray sources, detectors, experimental data analysis, and experimental methods are reviewed to commemorate the pioneers who made such important contributions to science and technology. (author)

Physical optics simulations with PHASE for SwissFEL beamlines

Energy Technology Data Exchange (ETDEWEB)

Flechsig, U.; Follath, R.; Reiche, S. [Paul Scherrer Institut, Swiss Light Source, 5232 Villigen PSI (Switzerland); Bahrdt, J. [Helmholtz Zentrum Berlin (Germany)

2016-07-27

PHASE is a software tool for physical optics simulation based on the stationary phase approximation method. The code is under continuous development since about 20 years and has been used for instance for fundamental studies and ray tracing of various beamlines at the Swiss Light Source. Along with the planning for SwissFEL a new hard X-ray free electron laser under construction, new features have been added to permit practical performance predictions including diffraction effects which emerge with the fully coherent source. We present the application of the package on the example of the ARAMIS 1 beamline at SwissFEL. The X-ray pulse calculated with GENESIS and given as an electrical field distribution has been propagated through the beamline to the sample position. We demonstrate the new features of PHASE like the treatment of measured figure errors, apertures and coatings of the mirrors and the application of Fourier optics propagators for free space propagation.

Macromolecular nanotheranostics for multimodal anticancer therapy

Science.gov (United States)

Huis in't Veld, Ruben; Storm, Gert; Hennink, Wim E.; Kiessling, Fabian; Lammers, Twan

2011-10-01

Macromolecular carrier materials based on N-(2-hydroxypropyl)methacrylamide (HPMA) are prototypic and well-characterized drug delivery systems that have been extensively evaluated in the past two decades, both at the preclinical and at the clinical level. Using several different imaging agents and techniques, HPMA copolymers have been shown to circulate for prolonged periods of time, and to accumulate in tumors both effectively and selectively by means of the Enhanced Permeability and Retention (EPR) effect. Because of this, HPMA-based macromolecular nanotheranostics, i.e. formulations containing both drug and imaging agents within a single formulation, have been shown to be highly effective in inducing tumor growth inhibition in animal models. In patients, however, as essentially all other tumor-targeted nanomedicines, they are generally only able to improve the therapeutic index of the attached active agent by lowering its toxicity, and they fail to improve the efficacy of the intervention. Bearing this in mind, we have recently reasoned that because of their biocompatibility and their beneficial biodistribution, nanomedicine formulations might be highly suitable systems for combination therapies. In the present manuscript, we briefly summarize several exemplary efforts undertaken in this regard in our labs in the past couple of years, and we show that long-circulating and passively tumor-targeted macromolecular nanotheranostics can be used to improve the efficacy of radiochemotherapy and of chemotherapy combinations.

Phase II and III the next generation of CLS beamline control and data acquisition systems

International Nuclear Information System (INIS)

Matias, E.; Beauregard, D.; Berg, R.; Black, G.; Boots, M.J.; Dolton, W.; Hunter, D.; Igarashi, R.; Liu, D.; Maxwell, D.; Miller, C.D.; Wilson, T.; Wright, G.

2012-01-01

The Canadian Light Source (CLS) is nearing the completion of its suite of Phase II Beamlines and in detailed design of its Phase III Beamlines. The paper presents an overview of the overall approach adopted by CLS in the development of beamline control and data acquisition systems. Building on the experience of our first phase of beamlines the CLS has continued to make extensive use of EPICS with EDM and QT based user interfaces. Increasing interpretive languages such as Python are finding a place in the beamline control systems. Web based environment such as ScienceStudio have also found a prominent place in the control system architecture as we move to tighter integration between data acquisition, visualization and data analysis. (authors)

SUNY beam line X3, National Synchrotron Light Source

International Nuclear Information System (INIS)

1991-01-01

This report discusses: beamline change and upgrades at NSLS; crystallography; surface structure; small angle scattering; EXAFS, glazing angle and fluorescence studies; and high temperature superconductors. (LSP)

SUNY beam line X3, National Synchrotron Light Source

Energy Technology Data Exchange (ETDEWEB)

1991-01-01

This report discusses: beamline change and upgrades at NSLS; crystallography; surface structure; small angle scattering; EXAFS, glazing angle and fluorescence studies; and high temperature superconductors. (LSP).

Crystallography across the Sciences 2

NARCIS (Netherlands)

Schenk, H.

2008-01-01

This second commemorative compilation from the IUCr contains 24 invited articles, all refereed, from some of today's most eminent crystallographers. The articles describe state-of-the-art research in which crystallography has played a major role, and are intended to be attractive for a broad

Diamond beamline I07: a beamline for surface and interface diffraction.

Science.gov (United States)

Nicklin, Chris; Arnold, Tom; Rawle, Jonathan; Warne, Adam

2016-09-01

Beamline I07 at Diamond Light Source is dedicated to the study of the structure of surfaces and interfaces for a wide range of sample types, from soft matter to ultrahigh vacuum. The beamline operates in the energy range 8-30 keV and has two endstations. The first houses a 2+3 diffractometer, which acts as a versatile platform for grazing-incidence techniques including surface X-ray diffraction, grazing-incidence small- (and wide-) angle X-ray scattering, X-ray reflectivity and grazing-incidence X-ray diffraction. A method for deflecting the X-rays (a double-crystal deflector) has been designed and incorporated into this endstation, extending the surfaces that can be studied to include structures formed on liquid surfaces or at liquid-liquid interfaces. The second experimental hutch contains a similar diffractometer with a large environmental chamber mounted on it, dedicated to in situ ultrahigh-vacuum studies. It houses a range of complementary surface science equipment including a scanning tunnelling microscope, low-energy electron diffraction and X-ray photoelectron spectroscopy ensuring that correlations between the different techniques can be performed on the same sample, in the same chamber. This endstation allows accurate determination of well ordered structures, measurement of growth behaviour during molecular beam epitaxy and has also been used to measure coherent X-ray diffraction from nanoparticles during alloying.

CERN’s 2016 Beamline for Schools competition starts on 17 November

CERN Document Server

2015-01-01

Spread the word: CERN is offering high-school students from around the world the chance to create and perform a scientific experiment on a CERN accelerator beamline. What better way to learn about physics?    (Video: Noemi Caraban​/CERN ) Now in its third year, the Beamline for Schools competition is open to teams of at least five students aged 16 and with at least one adult supervisor or “coach”. Students can find out about the beamline and facilities via http://cern.ch/bl4s, then think of a simple, creative experiment. They can register their team from 17 November to start receiving e-mail updates. They then submit a written proposal and a short video by 31 March 2016. The winners will be announced in June and will come to CERN, preferably in September 2016. Previous winners have tested webcams and classroom-grown crystals at the beamline, others have studied how particles decay and investigated high-energy gamma rays. All participants will receive...

Experimental stations at I13 beamline at Diamond Light Source

Science.gov (United States)

Pešić, Z. D.; De Fanis, A.; Wagner, U.; Rau, C.

2013-03-01

The I13 beamline of Diamond Light Source has been operational since December 2011. The beamline encompass two fully independent branches devoted to coherent imaging experiments (coherent x-ray diffraction, coherent diffraction imaging and ptychography) and x-ray imaging (in-line phase contrast imaging, tomography and full-field microscopy). This paper gives an overview of the current status of experimental stations on both branches and outlines planned developments.

Experimental stations at I13 beamline at Diamond Light Source

International Nuclear Information System (INIS)

Pešić, Z D; Fanis, A De; Wagner, U; Rau, C

2013-01-01

The I13 beamline of Diamond Light Source has been operational since December 2011. The beamline encompass two fully independent branches devoted to coherent imaging experiments (coherent x-ray diffraction, coherent diffraction imaging and ptychography) and x-ray imaging (in-line phase contrast imaging, tomography and full-field microscopy). This paper gives an overview of the current status of experimental stations on both branches and outlines planned developments.

Recent advances in macromolecular prodrugs

DEFF Research Database (Denmark)

Riber, Camilla Frich; Zelikin, Alexander N.

2017-01-01

Macromolecular prodrugs (MP) are high molar mass conjugates, typically carrying several copies of a drug or a drug combination, designed to optimize delivery of the drug, that is — its pharmacokinetics. From its advent several decades ago, design of MP has undergone significant development and es...

Neutron imaging options at the BOA beamline at Paul Scherrer Institut

International Nuclear Information System (INIS)

Morgano, M.; Peetermans, S.; Lehmann, E.H.; Panzner, T.; Filges, U.

2014-01-01

The BOA beamline at the Swiss spallation neutron source SINQ at Paul Scherrer Institut is a flexible instrument used mainly for testing novel techniques and devices for neutron scattering and optics, but, due to the large and relatively homogeneous field of view, it can be successfully used for experiments in the field of neutron imaging. The beamline allows also for the exploitation of advanced imaging concepts such as polarized neutron imaging and diffractive neutron imaging. In this paper we present the characterization of the BOA beamline in the light of its neutron imaging capabilities. We show also the different techniques that can be employed there as user-friendly plugins for non-standard neutron imaging experiments

First results from the high-brightness x-ray spectroscopy beamline at ALS

Energy Technology Data Exchange (ETDEWEB)

Perera, R.C.C.; Ng, W.; Jones, G. [Lawrence Berkeley National Lab., CA (United States)] [and others

1997-04-01

Beamline 9.3.1 at the Advanced Light Source (ALS) is a windowless beamline, covering the 1-6 keV photon-energy range, designed to achieve the goal of high brightness at the sample for use in the X-ray Atomic and Molecular Spectroscopy (XAMS) science, surface and interface science, biology and x-ray optical development programs at ALS. X-ray absorption and time of flight photo emission measurements in 2 - 5 keV photon energy in argon along with the flux, resolution, spot size and stability of the beamline will be discussed. Prospects for future XAMS measurements will also be presented.

Performance of a novel VUV bending magnet beamline

CERN Document Server

Song, Y F; Hsieh, T F; Huang, L R; Chung, S C; Cheng, N F; Hsiung, G Y; Wang, D J; Chen, C T; Tsang, K L

2001-01-01

A novel high resolution, high flux bending magnet beamline with an energy range from 5 to 40 eV has been constructed at SRRC. This Dragon-like beamline, which horizontally collects 50 mrad of synchrotron radiation from a bending magnet source, uses four cylindrical gratings with an included angle of 140 deg. and a movable curved exit slit. The average photon flux with an energy resolving power of 1000 is about 2x10 sup 1 sup 2 photons/s, which is among the highest of all existing VUV bending magnet beamlines. An energy resolving power of 24,000 at 6.8 eV has been obtained from the Schumann-Runge bands (B sup 3 limit construction operator in a limit construction/sum L: summation operator operator End lower limit of a limit construction u lower limit End limit End sup - /leftarrow/gets A: =leftward arrow X sup 3 limit construction operator in a limit construction/sum L: summation operator operator End lower limit of a limit construction g lower limit End limit End sup -) absorption spectra of O sub 2 gas. A pho...

Pulsed beam tests at the SANAEM RFQ beamline

Science.gov (United States)

Turemen, G.; Akgun, Y.; Alacakir, A.; Kilic, I.; Yasatekin, B.; Ergenlik, E.; Ogur, S.; Sunar, E.; Yildiz, V.; Ahiska, F.; Cicek, E.; Unel, G.

2017-07-01

A proton beamline consisting of an inductively coupled plasma (ICP) source, two solenoid magnets, two steerer magnets and a radio frequency quadrupole (RFQ) is developed at the Turkish Atomic Energy Authority’s (TAEA) Saraykoy Nuclear Research and Training Center (SNRTC-SANAEM) in Ankara. In Q4 of 2016, the RFQ was installed in the beamline. The high power tests of the RF power supply and the RF transmission line were done successfully. The high power RF conditioning of the RFQ was performed recently. The 13.56 MHz ICP source was tested in two different conditions, CW and pulsed. The characterization of the proton beam was done with ACCTs, Faraday cups and a pepper-pot emittance meter. Beam transverse emittance was measured in between the two solenoids of the LEBT. The measured beam is then reconstructed at the entrance of the RFQ by using computer simulations to determine the optimum solenoid currents for acceptance matching of the beam. This paper will introduce the pulsed beam test results at the SANAEM RFQ beamline. In addition, the high power RF conditioning of the RFQ will be discussed.

CAT Guide and Beamline Directory. A key to APS Collaborative Access Teams

International Nuclear Information System (INIS)

1999-01-01

The Advanced Photon Source (APS), a national user facility for synchrotrons radiation research, is located at Argonne National Laboratory, approximately 25 miles southwest of Chicago, Illinois. The APS is considered a third-generation synchrotrons radiation facility (specifically designed to accommodate insertion devices to serve as radiation sources) and is one of three such facilities in the world. Currently, it is the most brilliant source in the United States for research in such diverse fields as biology, medicine, materials science, chemistry, geology, agriculture and soil science, physics, and manufacturing technology. Researchers use the APS either as members of Collaborative Access Teams (CATS) or as Independent Investigators (IIs). CATS are responsible for designing, building, and operating beamlines in one or more sectors, each sector consisting of an insertion-device (ID) beamline and a bending-magnet (BM) beamline. Each beamline is designed to accommodate a specific type of research program(s) and is optimized accordingly. CAT members are entitled to use 75% of the available beam time to pursue CAT research goals. The remaining 25% of the available beam time must be made available to IIs. This document was written to help prospective IIs determine which beamlines are suitable for their specific experiments

The High Energy Materials Science Beamline (HEMS) at PETRA III

International Nuclear Information System (INIS)

Schell, Norbert; King, Andrew; Beckmann, Felix; Ruhnau, Hans-Ulrich; Kirchhof, Rene; Kiehn, Ruediger; Mueller, Martin; Schreyer, Andreas

2010-01-01

The HEMS Beamline at the German high-brilliance synchrotron radiation storage ring PETRA III is fully tunable between 30 and 250 keV and optimized for sub-micrometer focusing. Approximately 70 % of the beamtime will be dedicated to Materials Research. Fundamental research will encompass metallurgy, physics and chemistry with first experiments planned for the investigation of the relationship between macroscopic and micro-structural properties of polycrystalline materials, grain-grain-interactions, and the development of smart materials or processes. For this purpose a 3D-microsctructure-mapper has been designed. Applied research for manufacturing process optimization will benefit from high flux in combination with ultra-fast detector systems allowing complex and highly dynamic in-situ studies of micro-structural transformations, e.g. during welding processes. The beamline infrastructure allows accommodation of large and heavy user provided equipment. Experiments targeting the industrial user community will be based on well established techniques with standardized evaluation, allowing full service measurements, e.g. for tomography and texture determination. The beamline consists of a five meter in-vacuum undulator, a general optics hutch, an in-house test facility and three independent experimental hutches working alternately, plus additional set-up and storage space for long-term experiments. HEMS is under commissioning as one of the first beamlines running at PETRA III.

Markus Alahuhta | NREL

Science.gov (United States)

Macromolecular X-ray crystallography Biochemical characterization of enzymes Education Ph.D., Biochemistry thermophilic Caldicellulosiruptor species to cellulose," J. Biol. Chem. (2015) "The Unique Binding

Nanoscopium: a Scanning Hard X-ray Nanoprobe Beamline at Synchrotron Soleil

Science.gov (United States)

Somogyi, A.; Polack, F.; Moreno, T.

2010-06-01

Nanoscopium is the single scanning hard X-ray nano-probe beamline planned at SOLEIL. This ˜155 m long beamline will fully exploit the high brilliance and coherence characteristics of the X-ray beam both for diffraction limited focusing and for contrast formation. It will offer the most advanced imaging techniques in multimodal mode and will be a research tool for a wide user community working in the fields of earth-, environmental-, and life-sciences. The different μ-μnano-probe techniques offered by the beamline will permit elemental mapping at trace (ppm) levels (scanning XRF), speciation mapping (XANES), phase gradient mapping (scanning differential phase contrast), and density-contrast based imaging of internal structures (coherent diffraction imaging) in the 30 nm to 1 μm spatial resolution range, also in "in situ conditions". Nanoscopium will cover the 5-20 keV energy range. The stability of the nanobeam will be ensured by horizontally reflecting beamline optics (a sagitally and a tangentially pre-focusing mirror, horizontally reflecting monochromators) in front of the overfilled secondary source. Trade-off between high energy resolution (ΔE/E˜10-4) and high flux (1011 ph/s with ΔE/E˜10-2) will be achieved by two interchangeable monochromators (a double crystal and a double multilayer one). KB mirror and FZP lenses will be used as focusing devices. The beamline is in the design and construction phase. It is foreseen to be open for users at the beginning of 2013.

Affinity maturation of a portable Fab–RNA module for chaperone-assisted RNA crystallography

Science.gov (United States)

Koirala, Deepak; Shelke, Sandip A; Dupont, Marcel; Ruiz, Stormy; DasGupta, Saurja; Bailey, Lucas J; Benner, Steven A; Piccirilli, Joseph A

2018-01-01

Abstract Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3–6 binds to an AAACA RNA pentaloop closed by a GC pair with ∼100 nM affinity. The Fab and hairpin have served as a portable module for RNA crystallization. The potential for general application make it desirable to adjust the properties of this crystallization module in a manner that facilitates its use for RNA structure determination, such as ease of purification, surface entropy or binding affinity. In this work, we used both in vitro RNA selection and phage display selection to alter the epitope and paratope sides of the binding interface, respectively, for improved binding affinity. We identified a 5′-GNGACCC-3′ consensus motif in the RNA and S97N mutation in complimentarity determining region L3 of the Fab that independently impart about an order of magnitude improvement in affinity, resulting from new hydrogen bonding interactions. Using a model RNA, these modifications facilitated crystallization under a wider range of conditions and improved diffraction. The improved features of the Fab–RNA module may facilitate its use as an affinity tag for RNA purification and imaging and as a chaperone for RNA crystallography. PMID:29309709

Ultra-high resolution protein crystallography

International Nuclear Information System (INIS)

Takeda, Kazuki; Hirano, Yu; Miki, Kunio

2010-01-01

Many protein structures have been determined by X-ray crystallography and deposited with the Protein Data Bank. However, these structures at usual resolution (1.5< d<3.0 A) are insufficient in their precision and quantity for elucidating the molecular mechanism of protein functions directly from structural information. Several studies at ultra-high resolution (d<0.8 A) have been performed with synchrotron radiation in the last decade. The highest resolution of the protein crystals was achieved at 0.54 A resolution for a small protein, crambin. In such high resolution crystals, almost all of hydrogen atoms of proteins and some hydrogen atoms of bound water molecules are experimentally observed. In addition, outer-shell electrons of proteins can be analyzed by the multipole refinement procedure. However, the influence of X-rays should be precisely estimated in order to derive meaningful information from the crystallographic results. In this review, we summarize refinement procedures, current status and perspectives for ultra high resolution protein crystallography. (author)

Circular dichroism beamline B23 at the Diamond Light Source.

Science.gov (United States)

Hussain, Rohanah; Jávorfi, Tamás; Siligardi, Giuliano

2012-01-01

Synchrotron radiation circular dichroism (SRCD) is a well established technique in structural biology. The first UV-VIS beamline, dedicated to circular dichroism, at Diamond Light Source Ltd, a third-generation synchrotron facility in south Oxfordshire, UK, has recently become operational and it is now available for the user community. Herein the main characteristics of the B23 SRCD beamline, the ancillary facilities available for users, and some of the recent advances achieved are summarized.

Infrared Spectroscopy Beamline Based on a Tabletop Storage Ring

OpenAIRE

Haque, Md. Monirul; Moon, Ahsa; Yamada, Hironari

2012-01-01

An optical beamline dedicated to the infrared (IR) spectroscopy has been constructed at MIRRORCLE, a tabletop storage ring. The beamline has been designed for the use of infrared synchrotron radiation (IRSR) emitted from a bending magnet of 156 mm bending radius with the acceptance angle of 355(H) × 138(V) mrad to obtain high flux. The IR emission is forced by an exactly circular optics, named photon storage ring (PhSR), placed around the electron orbit and is collected by a “magic mirror” as...

A compact cost-effective beamline for a PET Cyclotron

International Nuclear Information System (INIS)

Dehnel, M.P.; Jackle, P.; Roeder, M.; Stewart, T.; Theroux, J.; Brasile, J.P.; Sirot, P.; Buckley, K.R.; Bedue, M.

2007-01-01

Most commercial PET Cyclotrons have targets mounted on or near the main cyclotron vacuum chamber. There is often little or no system capability for centering or focusing the extracted beam on target to achieve maximum production. This paper describes the ion-optics, design and development of a compact cost-effective beamline comprised of low activation and radiation resistant materials. The beamline, complete with suitable diagnostic devices, permits the extracted proton beam to be centered (X-Y steering magnet), and focused (quadrupole doublet) on target eliminating unnecessary beamspill and ensuring high production

Beamline for low-energy transport of highly charged ions at HITRAP

International Nuclear Information System (INIS)

Andelkovic, Z.; Herfurth, F.; Kotovskiy, N.; König, K.; Maaß, B.; Murböck, T.; Neidherr, D.; Schmidt, S.; Steinmann, J.; Vogel, M.; Vorobjev, G.

2015-01-01

A beamline for transport of highly charged ions with energies as low as a few keV/charge has been constructed and commissioned at GSI. Complementary to the existing infrastructure of the HITRAP facility for deceleration of highly charged ions from the GSI accelerator, the new beamline connects the HITRAP ion decelerator and an EBIT with the associated experimental setups. Therefore, the facility can now transport the decelerated heavy highly charged ions to the experiments or supply them offline with medium-heavy highly charged ions from the EBIT, both at energies as low as a few keV/charge. Here we present the design of the 20 m long beamline with the corresponding beam instrumentation, as well as its performance in terms of energy and transport efficiency

A comparison of three different ray trace programs for x-ray and infrared synchrotron beamline designs

International Nuclear Information System (INIS)

Irick, S.C.; Jung, C.R.

1997-07-01

There are a number of ray trace programs currently used for the design of synchrotron beamlines. While several of these programs have been written and used mostly within the programmer''s institution, many have also been available to the general public. This paper discusses three such programs. One is a commercial product oriented for the general optical designer (not specifically for synchrotron beamlines). One is designed for synchrotron beamlines and is free with restricted availability. Finally, one is designed for synchrotron beamlines and is used primarily in one institution. The wealth of information from general optical materials and components catalogs is readily available in the commercial program for general optical designs. This makes the design of an infrared beamline easier from the standpoint of component selection. However, this program is not easily configured for synchrotron beamline designs, particularly for a bending magnet source. The synchrotron ray trace programs offer a variety of sources, but generally are not as easy to use from the standpoint of the user interface. This paper shows ray traces of the same beamline Optikwerks, SHADOW, and RAY, and compares the results

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.; Adams, Paul D.; Moriarty, Nigel W.; Zwart, Peter; Read, Randy J.; Turk, Dusan; Hung, Li-Wei

2007-01-01

Heterogeneity in ensembles generated by independent model rebuilding principally reflects the limitations of the data and of the model-building process rather than the diversity of structures in the crystal. Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ‘perfect’ structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models

The Materials Science beamline upgrade at the Swiss Light Source

Energy Technology Data Exchange (ETDEWEB)

Willmott, P. R., E-mail: philip.willmott@psi.ch; Meister, D.; Leake, S. J.; Lange, M.; Bergamaschi, A. [Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen (Switzerland); and others

2013-07-16

The wiggler X-ray source of the Materials Science beamline at the Swiss Light Source has been replaced with a 14 mm-period cryogenically cooled in-vacuum undulator. In order to best exploit the increased brilliance of this new source, the entire front-end and optics have been redesigned. The Materials Science beamline at the Swiss Light Source has been operational since 2001. In late 2010, the original wiggler source was replaced with a novel insertion device, which allows unprecedented access to high photon energies from an undulator installed in a medium-energy storage ring. In order to best exploit the increased brilliance of this new source, the entire front-end and optics had to be redesigned. In this work, the upgrade of the beamline is described in detail. The tone is didactic, from which it is hoped the reader can adapt the concepts and ideas to his or her needs.

The actinide beamline - A new AMS facility at ANTARES

International Nuclear Information System (INIS)

Hotchkis, M.A.C.; Lee, P.J.; Mino, N.

1998-01-01

At the ANTARES accelerator a new beamline has been commissioned, incorporating new magnetic and electrostatic analysers, to optimise the efficiency for Actinides detection by Accelerator Mass Spectrometry. The detection of Actinides, particularly the isotopic ratios of uranium and plutonium, provide unique signatures for nuclear safeguards purposes. We are currently engaged in a project to evaluate the application of AMS to the measurement of Actinides in environmental samples for nuclear safeguards. Measurement of 236 U is of particular interest as a means of tracing the anthropogenic component of uranium. 236 U is expected to be present in natural samples at an extremely low level ( 236 U: 238 U ratio ∼10 -10 ). It has recently been demonstrated that AMS has sufficient sensitivity to detect 236 U at this level. The principal components of the new beamline include: an electrostatic quadrupole, a 12 deg electrostatic deflector, a 90 deg electrostatic analyser, a multi-isotope detection system including ion counters and Faraday cups. The beamline was completed in September 1998 and initial tests have been performed with iodine samples

Beamlines on Indus-1 and Indus-2: present status

International Nuclear Information System (INIS)

Lodha, G.S.; Deb, S.K.

2010-01-01

Indus-1 (450 MeV) is an efficient synchrotron radiation (SR) source in the soft X-ray/vacuum ultra violet region of the electromagnetic spectrum. For Indus-1 the higher order energy contamination in soft X-ray region, heat load and radiation safety problems are also significantly low. At present five beamlines are operational. This SR source is a national science facility being used by various research group across the country. Strong efforts are underway to increase the user base of Indus-1. The talk presents some of the recent studies carried out using Indus-1. Indus-2 (2.5 GeV) synchrotron source is one of the most important accelerator based science facilities being setup in India. A few beamlines have been commissioned and are being used by researchers from different institutes. This talk gives present status of the various beamlines and experimental stations on Indus-2. It is envisaged that the atomic and molecular science community can actively participate in planning experiments on Indus-1 and Indus-2 and setup experimental stations on Indus-2. (author)

Design and simulation of the nuSTORM pion beamline

Energy Technology Data Exchange (ETDEWEB)

Liu, A., E-mail: aoliu@fnal.gov; Neuffer, D.; Bross, A.

2015-11-21

The nuSTORM (neutrinos from STORed Muons) proposal presents a detailed design for a neutrino facility based on a muon storage ring, with muon decay in the production straight section of the ring providing well defined neutrino beams. The facility includes a primary high-energy proton beam line, a target station with pion production and collection, and a pion beamline for pion transportation and injection into a muon decay ring. The nuSTORM design uses “stochastic injection”, in which pions are directed by a chicane, referred to as the Orbit Combination Section (OCS), into the production straight section of the storage ring. Pions that decay within that straight section provide muons within the circulating acceptance of the ring. The design enables injection without kickers or a separate pion decay transport line. The beam line that the pions traverse before being extracted from the decay ring is referred to as the pion beamline. This paper describes the design and simulation of the pion beamline, and includes full beam dynamics simulations of the system.

Characterization of γ-ray background at IMAT beamline of ISIS Spallation Neutron Source

Science.gov (United States)

Festa, G.; Andreani, C.; Arcidiacono, L.; Burca, G.; Kockelmann, W.; Minniti, T.; Senesi, R.

2017-08-01

The environmental γ -ray background on the IMAT beamline at ISIS Spallation Neutron Source, Target Station 2, is characterized via γ spectroscopy. The measurements include gamma exposure at the imaging detector position, along with the gamma background inside the beamline. Present results are discussed and compared with previous measurements recorded at INES and VESUVIO beamlines operating at Target Station 1. They provide new outcome for expanding and optimizing the PGAA experimental capability at the ISIS neutron source for the investigation of materials, engineering components and cultural heritage objects at the ISIS neutron source.

Characterization of γ-ray background at IMAT beamline of ISIS Spallation Neutron Source

International Nuclear Information System (INIS)

Festa, G.; Andreani, C.; Arcidiacono, L.; Senesi, R.; Burca, G.; Kockelmann, W.; Minniti, T.

2017-01-01

The environmental γ -ray background on the IMAT beamline at ISIS Spallation Neutron Source, Target Station 2, is characterized via γ  spectroscopy. The measurements include gamma exposure at the imaging detector position, along with the gamma background inside the beamline. Present results are discussed and compared with previous measurements recorded at INES and VESUVIO beamlines operating at Target Station 1. They provide new outcome for expanding and optimizing the PGAA experimental capability at the ISIS neutron source for the investigation of materials, engineering components and cultural heritage objects at the ISIS neutron source.

Workshop on cooling of x-ray monochromators on high power beamlines

International Nuclear Information System (INIS)

Matsushita, T.; Ishikawa, T.

1989-03-01

This report is a Workshop on Cooling of X-ray Monochromators on High Power Beamlines held on August 31, 1988 at the Photon Factory during the Third International Conference on Synchrotron Radiation Instrumentation (SRI88). On high power beamlines, especially on insertion device beamlines, heating of crystal monochromators is becoming a serious problem: Researchers observe that the intensity of the X-ray beam on the sample is not proportional to the source intensity because of thermal distortion of the monochromator crystal. This problem will be even more serious on beamlines for the next generation X-ray rings. In the very tight program of the SRI88 conference, only 2 speakers were able to give invited talks closely related to this problem in the session of OPTICAL COMPONENTS FOR HIGH POWER BEAMLINES on Wednesday morning of August 31, 1988. We held this workshop in the afternoon of the same day with the intention of offering further opportunities to exchange information on efforts underway at various laboratories and to discuss ideas how to solve this problem. We also intended that the workshop would be a 'follow-up' to the X-ray optics workshop held at ESRF, Grenoble in September 1987, where the importance of crystal cooling was strongly pointed out. There were 32 participants from 7 countries. 12 people represented their experiences and ideas for reducing thermal distortion of crystal monochromators. Following those presentations, there were discussions on collaborations for solving this important problem. The attendees agreed that exchange of information should be continued by holding such meetings at reasonable intervals. (J.P.N.)

Commissioning and first results of scanning type EXAFS beamline (BL-09) at INDUS-2 synchrotron source

Energy Technology Data Exchange (ETDEWEB)

Poswal, A. K., E-mail: poswalashwini@gmail.com; Agrawal, A., E-mail: poswalashwini@gmail.com; Yadav, A. K., E-mail: poswalashwini@gmail.com; Nayak, C., E-mail: poswalashwini@gmail.com; Basu, S., E-mail: poswalashwini@gmail.com; Bhattachryya, D.; Jha, S. N.; Sahoo, N. K. [Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai -400085 (India); Kane, S. R.; Garg, C. K. [Indus Synchrotrons Utilization Division, Raja Ramanna Centre for Advanced Technology, Indore- 452013 (India)

2014-04-24

An Energy Scanning X-ray Absorption Fine Structure spectroscopy beamline has recently been installed and commissioned at BL-09 bending magnet port of INDUS-2 synchrotron source, Indore. The beamline uses an UHV compatible fixed exit double crystal monochromator (DCM) with two Si (111) crystals. Two grazing incidence cylindrical mirrors are also used in this beamline; the pre-mirror is used as a collimating mirror while the post mirror is used for vertical focusing and higher harmonic rejection. In this beamline it is possible to carry out EXAFS measurements both in transmission and fluorescence mode on various types of samples, using Ionization chamber detectors and solid state drift detector respectively. In this paper, results from first experiments of the Energy Scanning EXAFS beamline are presented.

Design and development of PEEM/ARPES beamline for Indus-2 synchrotron radiation source

International Nuclear Information System (INIS)

Goutam, U.K.; Sharma, R.K.; Jagannath; Gadkari, S.C.; Yakhmi, J.V.; Sahni, V.C.

2008-06-01

A high resolution beamline having two branches dedicated to Photo Emission Electron Microscopy (PEEM) and Angle Resolved Photo Electron Spectroscopy (ARPES) is planned for Indus-2 synchrotron radiation source. These two techniques open a wide field of new applications in materials research and have proven to be powerful tools to investigate topological, elemental, chemical state, electronic and magnetic properties of surfaces, thin films, and multilayers at high resolutions.The beamline will cover a large energy range from 10 to 4000 eV and is expected to deliver a flux of the order of ∼10 13 ph/s/0.1%B.W. with an energy resolution of ∼10 -4 . This report describes the optical design, beamline layout, effects of heat load on various components and the expected performance of the beamline. This beamline would have a collimating mirror for vertical collimation of the beam, plane grating/double crystal monochromator to make the white synchrotron beam monochromatic in entire energy range, toroidal mirror for splitting the beam as well as for intermediate focusing and a Kirkpatrick-Baez (K-B) mirror system for focusing the beam both in vertical and horizontal directions at the final sample location. Total beamline will be 36m long. Optical design has been carried out involving various computer codes such as XOP2.1, SHADOWVUI, SPECTRA 8.0 etc. Head load calculations have been performed using ANSYS, a finite element analysis code. Using this code, temperature distribution, thermal deformation and slope error values for collimating mirror, grating monochromator and double crystal monochromator using several possible cooling arrangements have been calculated and depending on these parameters, best options for different components have been selected for the beamline. Experimental stations of this beamline consist of ultra-high vacuum compatible chambers in which various probes, analyzers, detectors and other facilities are housed. A toroidal electron energy analyzer will

Plastique: A synchrotron radiation beamline for time resolved fluorescence in the frequency domain

Science.gov (United States)

De Stasio, Gelsomina; Zema, N.; Antonangeli, F.; Savoia, A.; Parasassi, T.; Rosato, N.

1991-06-01

PLASTIQUE is the only synchrotron radiation beamline in the world that performs time resolved fluorescence experiments in frequency domain. These experiments are extremely valuable sources of information on the structure and dynamics of molecules. We describe the beamline and some initial data.

Characteristics and performance of the Los Alamos VUV beamline at the NSLS

International Nuclear Information System (INIS)

Bartlett, R.J.; Trela, W.J.; Michaud, F.D.; Southworth, S.H.; Alkire, R.W.; Roy, P.; Rothe, R.; Walsh, P.J.; Shinn, N.

1988-01-01

We describe the design and performance of the Los Alamos VUV synchrotron radiation beamline, U3C, on the VUV ring of the National Synchrotron Light Source at Brookhaven National Laboratory. The beamline uses separate function optics to collect and focus the horizontally and vertically diverging beam. The monochromator is a grazing incidence Rowland circle instrument of the extended grasshopper design (ERG). A postmonochromator refocusing mirror is used to focus or collimate the diverging beam from the monochromator. The beamline control and diagnostics systems are also discussed. Particular emphasis in the design has been placed on the reduction of stray and harmonic light. Higher order light is reduced by a grazing angle mirror low pass filter installed immediately downstream from the monochromator while stray light is reduced through the use of baffles and thin film filters. Also included in the line is a differential pumping section that permits gas phase and other experiments requiring pressures in the 10 -5 to 10 -4 Torr range to be coupled to the beamline. (orig.)

The Beginnings of X-ray Crystallography

Indian Academy of Sciences (India)

IAS Admin

significant change in his career came in 1904 when he gave a talk at Dunedin on ... In his personal reminiscences, W L Bragg talks about his school days in Australia. ... two Braggs on the occasion of the International Year of Crystallography .

Optimizing the Recognition of Surface Crystallography

Czech Academy of Sciences Publication Activity Database

Frank, Luděk; Mika, Filip; Müllerová, Ilona

2015-01-01

Roč. 21, S4 (2015), s. 124-129 ISSN 1431-9276 R&D Projects: GA MŠk(CZ) LO1212 Institutional support: RVO:68081731 Keywords : surface crystallography Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.730, year: 2015

The status of the first infrared beamline at Shanghai Synchrotron Radiation Facility

International Nuclear Information System (INIS)

Ji, Te; Tong, Yajun; Zhu, Huachun; Zhang, Zengyan; Peng, Weiwei; Chen, Min; Xiao, Tiqiao; Xu, Hongjie

2015-01-01

Construction of the first infrared beamline BL01B1 at Shanghai Synchrotron Radiation Facility (SSRF) was completed at the end of 2013. The IR beamline collects both edge radiation (ER) and bending magnet radiation (BMR) from a port, providing a solid angle of 40 mrad and 20 mrad in the horizontal and vertical directions, respectively. The optical layout of the infrared beamline and the design of the extraction mirror are described in this paper. A calculation of the beam propagation has been used to optimize the parameters of the optical components. The photon flux and spatial resolution have been measured at the end-station, and the experimental results are in good agreement with the theoretical calculation

The status of the first infrared beamline at Shanghai Synchrotron Radiation Facility

Energy Technology Data Exchange (ETDEWEB)

Ji, Te; Tong, Yajun; Zhu, Huachun; Zhang, Zengyan; Peng, Weiwei; Chen, Min, E-mail: chenmin@sinap.ac.cn; Xiao, Tiqiao; Xu, Hongjie

2015-07-11

Construction of the first infrared beamline BL01B1 at Shanghai Synchrotron Radiation Facility (SSRF) was completed at the end of 2013. The IR beamline collects both edge radiation (ER) and bending magnet radiation (BMR) from a port, providing a solid angle of 40 mrad and 20 mrad in the horizontal and vertical directions, respectively. The optical layout of the infrared beamline and the design of the extraction mirror are described in this paper. A calculation of the beam propagation has been used to optimize the parameters of the optical components. The photon flux and spatial resolution have been measured at the end-station, and the experimental results are in good agreement with the theoretical calculation.

The status of the first infrared beamline at Shanghai Synchrotron Radiation Facility

Science.gov (United States)

Ji, Te; Tong, Yajun; Zhu, Huachun; Zhang, Zengyan; Peng, Weiwei; Chen, Min; Xiao, Tiqiao; Xu, Hongjie

2015-07-01

Construction of the first infrared beamline BL01B1 at Shanghai Synchrotron Radiation Facility (SSRF) was completed at the end of 2013. The IR beamline collects both edge radiation (ER) and bending magnet radiation (BMR) from a port, providing a solid angle of 40 mrad and 20 mrad in the horizontal and vertical directions, respectively. The optical layout of the infrared beamline and the design of the extraction mirror are described in this paper. A calculation of the beam propagation has been used to optimize the parameters of the optical components. The photon flux and spatial resolution have been measured at the end-station, and the experimental results are in good agreement with the theoretical calculation.

PLASTIQUE: A synchrotron radiation beamline for time resolved fluorescence in the frequency domain

International Nuclear Information System (INIS)

De Stasio, G.; Zema, N.; Antonangeli, F.; Parasassi, T.; Rosato, N.

1991-01-01

PLASTIQUE is the only synchrotron radiation beamline in the world that performs time resolved fluorescence experiments in the frequency domain. These experiments are extremely valuable sources of informations on the structure and dynamics of molecules. The beamline and some examples of initial data are described

Structure studies of macromolecular systems

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich; Dohnálek, Jan; Skálová, Tereza; Dušková, Jarmila; Kolenko, Petr

2006-01-01

Roč. 13, č. 3 (2006), s. 136 ISSN 1211-5894. [Czech and Slovak Crystallographic Colloquium. 22.06.2006-24.06.2006, Grenoble] R&D Projects: GA AV ČR IAA4050811; GA MŠk 1K05008 Keywords : structure * X-ray diffraction * synchrotron Subject RIV: CD - Macromolecular Chemistry http://www. xray .cz/ms/default.htm

Control of Macromolecular Architectures for Renewable Polymers: Case Studies

Science.gov (United States)

Tang, Chuanbing

The development of sustainable polymers from nature biomass is growing, but facing fierce competition from existing petrochemical-based counterparts. Controlling macromolecular architectures to maximize the properties of renewable polymers is a desirable approach to gain advantages. Given the complexity of biomass, there needs special consideration other than traditional design. In the presentation, I will talk about a few case studies on how macromolecular architectures could tune the properties of sustainable bioplastics and elastomers from renewable biomass such as resin acids (natural rosin) and plant oils.

Hypoxic tumor environments exhibit disrupted collagen I fibers and low macromolecular transport.

Directory of Open Access Journals (Sweden)

Samata M Kakkad

Full Text Available Hypoxic tumor microenvironments result in an aggressive phenotype and resistance to therapy that lead to tumor progression, recurrence, and metastasis. While poor vascularization and the resultant inadequate drug delivery are known to contribute to drug resistance, the effect of hypoxia on molecular transport through the interstitium, and the role of the extracellular matrix (ECM in mediating this transport are unexplored. The dense mesh of fibers present in the ECM can especially influence the movement of macromolecules. Collagen 1 (Col1 fibers form a key component of the ECM in breast cancers. Here we characterized the influence of hypoxia on macromolecular transport in tumors, and the role of Col1 fibers in mediating this transport using an MDA-MB-231 breast cancer xenograft model engineered to express red fluorescent protein under hypoxia. Magnetic resonance imaging of macromolecular transport was combined with second harmonic generation microscopy of Col1 fibers. Hypoxic tumor regions displayed significantly decreased Col1 fiber density and volume, as well as significantly lower macromolecular draining and pooling rates, than normoxic regions. Regions adjacent to severely hypoxic areas revealed higher deposition of Col1 fibers and increased macromolecular transport. These data suggest that Col1 fibers may facilitate macromolecular transport in tumors, and their reduction in hypoxic regions may reduce this transport. Decreased macromolecular transport in hypoxic regions may also contribute to poor drug delivery and tumor recurrence in hypoxic regions. High Col1 fiber density observed around hypoxic regions may facilitate the escape of aggressive cancer cells from hypoxic regions.

Macromolecular target prediction by self-organizing feature maps.

Science.gov (United States)

Schneider, Gisbert; Schneider, Petra

2017-03-01

Rational drug discovery would greatly benefit from a more nuanced appreciation of the activity of pharmacologically active compounds against a diverse panel of macromolecular targets. Already, computational target-prediction models assist medicinal chemists in library screening, de novo molecular design, optimization of active chemical agents, drug re-purposing, in the spotting of potential undesired off-target activities, and in the 'de-orphaning' of phenotypic screening hits. The self-organizing map (SOM) algorithm has been employed successfully for these and other purposes. Areas covered: The authors recapitulate contemporary artificial neural network methods for macromolecular target prediction, and present the basic SOM algorithm at a conceptual level. Specifically, they highlight consensus target-scoring by the employment of multiple SOMs, and discuss the opportunities and limitations of this technique. Expert opinion: Self-organizing feature maps represent a straightforward approach to ligand clustering and classification. Some of the appeal lies in their conceptual simplicity and broad applicability domain. Despite known algorithmic shortcomings, this computational target prediction concept has been proven to work in prospective settings with high success rates. It represents a prototypic technique for future advances in the in silico identification of the modes of action and macromolecular targets of bioactive molecules.

Magnetic shielding tests for MFTF-B neutral beamlines

International Nuclear Information System (INIS)

Kerns, J.; Fabyan, J.; Wood, R.; Koger, P.

1983-01-01

A test program to determine the effectiveness of various magnetic shielding designs for MFTF-B beamlines was established at Lawrence Livermore National Laboratory (LLNL). The proposed one-tenth-scale shielding-design models were tested in a uniform field produced by a Helmholtz coil pair. A similar technique was used for the MFTF source-injector assemblies, and the model test results were confirmed during the Technology Demonstration in 1982. The results of these tests on shielding designs for MFTF-B had an impact on the beamline design for MFTF-B. The iron-core magnet and finger assembly originally proposed were replaced by a simple, air-core, race-track-coil, bending magnet. Only the source injector needs to be magnetically shielded from the fields of approximately 400 gauss

The Cambridge crystallography subroutine library

International Nuclear Information System (INIS)

Brown, P.J.; Matthewman, J.C.

1981-06-01

This manual is an amalgamation of the original Cambridge Crystallography Subroutine Library Mark II manual and its supplement No I. The original Mark II system, a set of FORTRAN Subroutines which can be used for standard crystallographic calculations, has been extended to include facilities for conventional least squares refinement. Several new routines have also been added. (U.K.)

High pressure XAFS experiments at the XAFS beamline, INDUS-2

International Nuclear Information System (INIS)

Ramanan, Nitya; Lahiri, Debdutta; Garg, Nandini; Sharma, Surinder M.; Bhattacharyya, D.; Jha, S.N.; Sahoo, N.K.

2011-01-01

The dispersive EXAFS beamline at the INDUS-2 synchrotron source, RRCAT, Indore uses a bent Si (111) crystal as a dispersive-cum-focusing element and a position sensitive CCD detector to enable instantaneous measurement of the whole EXAFS spectrum around the absorption edge of a particular atom. One of the proposed activities with this beamline is the characterization of amorphous materials under high pressure. Polychromator-based beamline is ideal for high pressure studies using Diamond Anvil Cell (DAC) with ∼ 50 μm sample size. Larger spot size would give rise to unwanted diffraction peaks from diamond, superimposed on the XAFS data. Micro-focusing by polychromator crystal and absence of its mechanical movement (unlike monochromator-based scanning-mode beamlines), during data collection, lead to required focal spot stability for DAC experiments. Currently, the theoretically determined spot size (Horizontal x vertical) varies between 17 x 137 μm and 37 x 142 μm for the X-ray energy range 5 keV-20 keV. To reduce the vertical spot size to <50 μm, we have designed an additional focusing mirror between the polychromator and sample position. The mirror, fabricated at SESO, France will be installed shortly. Meanwhile, we have carried out preliminary XAFS experiments on Sr-compounds at ∼16 keV, under ambient conditions and inside diamond anvil cell, in order to assess the signal intensity and quality. We have obtained reasonably good signal. (author)

Chemical Crystallography· From Inception to Maturity

Indian Academy of Sciences (India)

design, charge density ... did not readily accept this first chemical crystallography experi- .... graphics. The packages clearly illustrate the complexity involved in both molecu- ... interactive online programs help to search, match and analyze.

1993 CAT workshop on beamline optical designs

Energy Technology Data Exchange (ETDEWEB)

1993-11-01

An Advanced Photon Source (APS) Collaborative Access Team (CAT) Workshop on Beamline Optical Designs was held at Argonne National Laboratory on July 26--27, 1993. The goal of this workshop was to bring together experts from various synchrotron sources to provide status reports on crystal, reflecting, and polarizing optics as a baseline for discussions of issues facing optical designers for CAT beamlines at the APS. Speakers from the European Synchrotron Radiation Facility (ESRF), the University of Chicago, the National Synchrotron Light Source, and the University of Manchester (England) described single- and double-crystal monochromators, mirrors, glass capillaries, and polarizing optics. Following these presentations, the 90 participants divided into three working groups: Crystal Optics Design, Reflecting Optics, and Optics for Polarization Studies. This volume contains copies of the presentation materials from all speakers, summaries of the three working groups, and a ``catalog`` of various monochromator designs.

1993 CAT workshop on beamline optical designs

International Nuclear Information System (INIS)

1993-11-01

An Advanced Photon Source (APS) Collaborative Access Team (CAT) Workshop on Beamline Optical Designs was held at Argonne National Laboratory on July 26--27, 1993. The goal of this workshop was to bring together experts from various synchrotron sources to provide status reports on crystal, reflecting, and polarizing optics as a baseline for discussions of issues facing optical designers for CAT beamlines at the APS. Speakers from the European Synchrotron Radiation Facility (ESRF), the University of Chicago, the National Synchrotron Light Source, and the University of Manchester (England) described single- and double-crystal monochromators, mirrors, glass capillaries, and polarizing optics. Following these presentations, the 90 participants divided into three working groups: Crystal Optics Design, Reflecting Optics, and Optics for Polarization Studies. This volume contains copies of the presentation materials from all speakers, summaries of the three working groups, and a ''catalog'' of various monochromator designs

Crystallography and Interphase Boundary of Martensite and Bainite in Steels

Science.gov (United States)

Furuhara, Tadashi; Chiba, Tadachika; Kaneshita, Takeshi; Wu, Huidong; Miyamoto, Goro

2017-06-01

Grain refinements in lath martensite and bainite structures are crucial for strengthening and toughening of high-strength structural steels. Clearly, crystallography of transformation plays an important role in determining the "grain" sizes in these structures. In the present study, crystallography and intrinsic boundary structure of martensite and bainite are described. Furthermore, various extrinsic factors affecting variant selection and growth kinetics, such as elastic/plastic strain and alloying effects on interphase boundary migration, are discussed.

Rossendorf Beamline at ESRF (ROBL-CRG). Bi-annual report 2009/2010

International Nuclear Information System (INIS)

Scheinost, Andreas C.; Baehtz, Carsten

2011-01-01

The Rossendorf Beamline (ROBL) - located at BM20 of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France - is in operation since 1998. This 7th report covers the period from January 2009 to December 2010. In these two years, 67 peer- reviewed papers have been published based on experiments done at the beamline, more than in any biannual period before. Six highlight reports have been selected for this report to demonstrate the scientific strength and diversity of the experiments performed on the two end-stations of the beamline, dedicated to Radiochemistry (RCH) and Materials Research (MRH). The beamtime was more heavily overbooked than ever before, with an acceptance rate of only 25% experiments. We would like to thank our external proposal review members, Prof. Andre Maes (KU Leuven, Belgium), Prof. Laurent Charlet (UJF Grenoble, France), Dr. Andreas Leinweber (MPI Metallforschung, Stuttgart, Germany), Prof. David Rafaja (TU Bergakademie Freiberg, Germany), Prof. Dirk Meyer (TU Dresden, Germany), who evaluated the inhouse proposals in a thorough manner, thereby ensuring that beamtime was distributed according to scientific merit. The period was not only characterized by very successful science, but also by intense work on the optics upgrade. In spring 2009, a workshop was held at ROBL, assembling beamline experts from German, Spanish and Swiss synchrotrons, to evaluate the best setup for the new optics. These suggestions was used to prepare the call for tender published in July 2009. From the tender acceptance in November 2009 on, a series of design review meetings and factory acceptance tests followed. Already in July 2010, the first piece of equipment was delivered, the new double-crystal, double-multilayer monochromator. The disassembly of the old optics components started end of July, 2011, followed by the installation of the new components. As of December 2011, the new optics have seen the first test beam and thorough hot commissioning will

Rossendorf Beamline at ESRF (ROBL-CRG). Bi-annual report 2009/2010

Energy Technology Data Exchange (ETDEWEB)

Scheinost, Andreas C; Baehtz, Carsten [eds.

2011-07-01

The Rossendorf Beamline (ROBL) - located at BM20 of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France - is in operation since 1998. This 7th report covers the period from January 2009 to December 2010. In these two years, 67 peer- reviewed papers have been published based on experiments done at the beamline, more than in any biannual period before. Six highlight reports have been selected for this report to demonstrate the scientific strength and diversity of the experiments performed on the two end-stations of the beamline, dedicated to Radiochemistry (RCH) and Materials Research (MRH). The beamtime was more heavily overbooked than ever before, with an acceptance rate of only 25% experiments. We would like to thank our external proposal review members, Prof. Andre Maes (KU Leuven, Belgium), Prof. Laurent Charlet (UJF Grenoble, France), Dr. Andreas Leinweber (MPI Metallforschung, Stuttgart, Germany), Prof. David Rafaja (TU Bergakademie Freiberg, Germany), Prof. Dirk Meyer (TU Dresden, Germany), who evaluated the inhouse proposals in a thorough manner, thereby ensuring that beamtime was distributed according to scientific merit. The period was not only characterized by very successful science, but also by intense work on the optics upgrade. In spring 2009, a workshop was held at ROBL, assembling beamline experts from German, Spanish and Swiss synchrotrons, to evaluate the best setup for the new optics. These suggestions was used to prepare the call for tender published in July 2009. From the tender acceptance in November 2009 on, a series of design review meetings and factory acceptance tests followed. Already in July 2010, the first piece of equipment was delivered, the new double-crystal, double-multilayer monochromator. The disassembly of the old optics components started end of July, 2011, followed by the installation of the new components. As of December 2011, the new optics have seen the first test beam and thorough hot commissioning will

Stochastic reaction-diffusion algorithms for macromolecular crowding

Science.gov (United States)

Sturrock, Marc

2016-06-01

Compartment-based (lattice-based) reaction-diffusion algorithms are often used for studying complex stochastic spatio-temporal processes inside cells. In this paper the influence of macromolecular crowding on stochastic reaction-diffusion simulations is investigated. Reaction-diffusion processes are considered on two different kinds of compartmental lattice, a cubic lattice and a hexagonal close packed lattice, and solved using two different algorithms, the stochastic simulation algorithm and the spatiocyte algorithm (Arjunan and Tomita 2010 Syst. Synth. Biol. 4, 35-53). Obstacles (modelling macromolecular crowding) are shown to have substantial effects on the mean squared displacement and average number of molecules in the domain but the nature of these effects is dependent on the choice of lattice, with the cubic lattice being more susceptible to the effects of the obstacles. Finally, improvements for both algorithms are presented.

MARS, a new beamline for radioactive matter studies at SOLEIL

International Nuclear Information System (INIS)

Solari, Pier Lorenzo; Schlutig, Sandrine; Hermange, Herve; Sitaud, Bruno

2009-01-01

MARS (Multi Analyses on Radioactive Samples) beamline is the hard X-ray bending magnet beamline dedicated to the study of radioactive matter of the new French synchrotron SOLEIL. The beamline, which has been built thanks to a close partnership and support by the CEA, has been designed to provide X-rays in the energy range of 3.5 keV to 35 keV. This allows to encompass M and L absorption edges of actinides, as well as K edges of transition metals (that are present in alloys and fuel claddings) up to heavy halogens, rare gases and alkalis (fission products in nuclear fuels). The MARS project aims to extend the possibilities of synchrotron based X-ray characterizations towards a wider variety of radioactive elements and a wider variety of techniques than what is currently available at other facilities. Thus, its specific and innovative infrastructure has been optimized in order to carry out analyses on materials with activities up to 18.5 GBq per sample for α and β emitters and 2 GBq for γ and n emitters. So, today, more than 70 different elements and more than 350 different isotopes have been proposed for studies on the beamline by the involved user community. The arrangement of the different elements in the optics hutch is based on an original scheme which permits to have two alternative optical configurations (monochromatic or dispersive) depending on the nature of experiments to be performed. At least three main techniques are progressively being proposed on the three complementary end-stations located in the experimental hutch: transmission and high resolution powder diffraction (TXRD and HRXRD), standard and dispersive X-ray absorption spectroscopy (XAS and EDXAS) and X-ray fluorescence (XRF). In addition, by using the KB optics, a micro-focused beam will be available on the second station of the monochromatic branch. The beamline is currently under commissioning. The first two experimental stations, using the monochromatic branch, are scheduled to be

Vacuum ultraviolet beamline at the Swiss Light Source for chemical dynamics studies

International Nuclear Information System (INIS)

Johnson, Melanie; Bodi, Andras; Schulz, Lothar; Gerber, Thomas

2009-01-01

A bend-magnet vacuum ultraviolet (VUV) beamline, intended for chemical dynamics studies, was constructed and brought into operation at the Swiss Light Source (SLS) of the Paul Scherrer Institut. The beamline delivers synchrotron radiation in the 5-30 eV photon energy range with a photon flux of 10 11 photons/s at 10 eV and 10 12 photons/s at 20 eV with a resolving power of 2500. The resolving power increases to 10 4 at the cost of photon flux. An in-house designed rare gas filter is used to suppress higher harmonic radiation by a factor of >10 4 , yielding purely monochromatic light in the energy range of 5-21.6 eV. The filter is compact, easy to align, requires a total pumping power of less than 645 l/s and consumes only 3 normal l/h of filter gas. It is located at the end of the beamline, right in front of the experimental endstation. It is usually operated at a higher pressure than the endstation, which offers the additional benefit of protecting the beamline vacuum from sample contamination.

Current status of the hard x-ray nanoprobe beamline at the SSRF

Science.gov (United States)

Li, Aiguo; Jiang, Hui; Wang, Hua; Zhang, Zhaohong; He, Yan; Zhao, Gaofeng; Shu, Deming

2017-09-01

The hard X-ray nanoprobe beamline (HXN) designed at the Shanghai Synchrotron Radiation facility (SSRF) will be of capability to realize a focal spot size of 10 nm for hard X-rays to satisfy requirements in biology, environmental, material sciences and etc.. The beamline includes two modes of operation, high energy resolution mode and high flux mode respectively. High flux mode utilizes the multilayer KB system to obtain high-flux diffraction-limited focusing of 10nm. An ultra-high-precision figure fabrication for diffraction-limited focusing is required to meet the Rayleigh Criterion. An idea to overcome this problem is to introduce a phase compensator upstream of the KB system to compensate the wavefront errors in the beamline. At wavelength speckle-based method will be used to measure the wavefront error in the beamline and feedback to the phase compensator. Vibration measurements have been carried out at the secondary source and endstation hutch. The flexure hinge mechanisms and high-precision actuators ensure the KB system and sample manipulator working with high stability. The building of HXN has been designed and is under construction at present.

Australian synchrotron radiation science

International Nuclear Information System (INIS)

White, J.W.

1996-01-01

Full text: The Australian Synchrotron Radiation Program, ASRP, has been set up as a major national research facility to provide facilities for scientists and technologists in physics, chemistry, biology and materials science who need access to synchrotron radiation. Australia has a strong tradition in crystallography and structure determination covering small molecule crystallography, biological and protein crystallography, diffraction science and materials science and several strong groups are working in x-ray optics, soft x-ray and vacuum ultra-violet physics. A number of groups whose primary interest is in the structure and dynamics of surfaces, catalysts, polymer and surfactant science and colloid science are hoping to use scattering methods and, if experience in Europe, Japan and USA can be taken as a guide, many of these groups will need third generation synchrotron access. To provide for this growing community, the Australian National Beamline at the Photon Factory, Tsukuba, Japan, has been established since 1990 through a generous collaboration with Japanese colleagues, the beamline equipment being largely produced in Australia. This will be supplemented in 1997 with access to the world's most powerful synchrotron x-ray source at the Advanced Photon Source, Argonne National Laboratory, USA. Some recent experiments in surface science using neutrons as well as x-rays from the Australian National Beamline will be used to illustrate one of the challenges that synchrotron x-rays may meet

Why do We Trust X-ray Crystallography?

Indian Academy of Sciences (India)

IAS Admin

crystal X-ray diffraction pattern and good chemical sense that elevates X-ray crystallography to its position as the most trusted analytical technique. Suggested Reading. [1] William Clegg, Crystal Structure Determination, Oxford Chemistry Prim-.

Construction and characterization of a laser-driven proton beamline at GSI

OpenAIRE

Busold, Simon

2014-01-01

The thesis includes the first experiments with the new 100 TW laser beamline of the PHELIX laser facility at GSI Darmstadt to drive a TNSA (Target Normal Sheath Acceleration) proton source at GSI's Z6 experimental area. At consecutive stages a pulsed solenoid has been applied for beam transport and energy selection via chromatic focusing, as well as a radiofrequency cavity for energy compression of the bunch. This novel laser-driven proton beamline, representing a central experiment of the...

7-GeV advanced photon source beamline initiative: Conceptual design report

International Nuclear Information System (INIS)

1993-05-01

The DOE is building a new generation 6-7 GeV Synchrotron Radiation Source known as the Advanced Photon Source (APS) at Argonne National Laboratory. This facility, to be completed in FY 1996, can provide 70 x-ray sources of unprecedented brightness to meet the research needs of virtually all scientific disciplines and numerous technologies. The technological research capability of the APS in the areas of energy, communications and health will enable a new partnership between the DOE and US industry. Current funding for the APS will complete the current phase of construction so that scientists can begin their applications in FY 1996. Comprehensive utilization of the unique properties of APS beams will enable cutting-edge research not currently possible. It is now appropriate to plan to construct additional radiation sources and beamline standard components to meet the excess demands of the APS users. In this APS Beamline Initiative, 2.5-m-long insertion-device x-ray sources will be built on four straight sections of the APS storage ring, and an additional four bending-magnet sources will also be put in use. The front ends for these eight x-ray sources will be built to contain and safeguard access to these bright x-ray beams. In addition, funds will be provided to build standard beamline components to meet scientific and technological research demands of the Collaborative Access Teams. The Conceptual Design Report (CDR) for the APS Beamline Initiative describes the scope of all the above technical and conventional construction and provides a detailed cost and schedule for these activities. The document also describes the preconstruction R ampersand D plans for the Beamline Initiative activities and provides the cost estimates for the required R ampersand D

New developments at the INE-Beamline for actinide research at ANKA

Science.gov (United States)

Dardenne, K.; Brendebach, B.; Denecke, M. A.; Liu, X.; Rothe, J.; Vitova, T.

2009-11-01

The INE-Beamline for actinide research at the synchrotron source ANKA is operated by the Institut für Nukleare Entsorgung (INE) at the Forschungszentrum Karlsruhe. Experiments on radioactive samples with activities up to 106 times the limit of exemption inside a safe and flexible double containment concept are possible. One great advantage of the beamline is its close proximity to INE's active laboratories with its equipment for manipulation of actinide materials and state-of-the-art spectroscopic, analytical, and microscopic instrumentation. This constellation is unique in Europe. The INE-Beamline is built primarily to serve INE in-house research associated with safe disposal of high level nuclear waste such as actinide speciation or coordination-, redox-, and geo-chemistry of actinides. A wide energy range from around 2.1 keV to 25 keV covering the K-edges from P to Pd and the L3, L2, and L1 edges for actinides from Th to Cm can be used. The INE-Beamline is optimized for X-ray absorption spectroscopy techniques (XANES/EXAFS), but x-ray fluorescence (XRF) analysis and powder diffraction (XRD) are also possible, as well as surface sensitive measurements in grazing incidence geometry (GI-XAFS). Upgrades of instrumentation and extension of experimental capabilities at the INE-Beamline are driven by user needs. Two of the recent upgrades are presented: 1) installation of a microfocus option for spatially resolved studies (μ-XRF, μ-XANES, μ-XRD) and investigations of small volumes (e.g., heterogeneous natural samples and diamond anvil high pressure cells); 2) construction, and commissioning of a high resolution x-ray emission spectrometer (HRXES); 3) availability of an electrochemical cell for investigation of redox sensitive systems.

Highlights from e-EPS: New milestone for ELI Beamlines facility

CERN Multimedia

Jorge Rivero González, e-EPS News

2013-01-01

e-EPS News is a monthly addition to the CERN Bulletin line-up, showcasing articles from e-EPS – the European Physical Society newsletter – as part of a collaboration between the two publications.   On 16 September 2013, the Extreme Light Infrastructure (ELI) Beamlines facility awarded a contract worth approximately €34.5m to Lawrence Livermore National Security LLC (LLNS, California, USA) to develop and deliver a state-of-the-art laser system that will be at the heart of the ELI Beamlines user facility. Located in the village of Dolní Břežany, Czech Republic, the ELI Beamlines facility aims to pioneer work in a number of research fields using ultra-high intensity lasers. The facility will host a cutting-edge research laser, around 100 times more powerful than any other laser in operation today. In particular, it will focus on providing users with ultra-short energetic particle beams (10 GeV) and radiation beams (up to a few MeV), produced by...

National Synchrotron Light Source user's manual: Guide to the VUV and x-ray beamlines

International Nuclear Information System (INIS)

Gmuer, N.F.

1993-04-01

The success of the National Synchrotron Light Source is based, in large part, on the size of the user community and the diversity of the scientific and technical disciplines represented by these users. As evidence of this success, the VUV Ring has just celebrated its 10th anniversary and the X-ray Ring will do the same in 1995. In order to enhance this success, the NSLS User's Manual: Guide to the VUV and X-Ray Beamlines - Fifth Edition, is being published. This Manual presents to the scientific community-at-large the current and projected architecture, capabilities and research programs of the various VUV and X-ray beamlines. Also detailed is the research and computer equipment a General User can expect to find and use at each beamline when working at the NSLS. The Manual is updated periodically in order to keep pace with the constant changes on these beamlines

BEAMLINE-CONTROLLED STEERING OF SOURCE-POINT ANGLE AT THE ADVANCED PHOTON SOURCE

Energy Technology Data Exchange (ETDEWEB)

Emery, L.; Fystro, G.; Shang, H.; Smith, M.

2017-06-25

An EPICS-based steering software system has been implemented for beamline personnel to directly steer the angle of the synchrotron radiation sources at the Advanced Photon Source. A script running on a workstation monitors "start steering" beamline EPICS records, and effects a steering given by the value of the "angle request" EPICS record. The new system makes the steering process much faster than before, although the older steering protocols can still be used. The robustness features of the original steering remain. Feedback messages are provided to the beamlines and the accelerator operators. Underpinning this new steering protocol is the recent refinement of the global orbit feedback process whereby feedforward of dipole corrector set points and orbit set points are used to create a local steering bump in a rapid and seamless way.

Beam-line considerations for experiments with highly-charged ions

International Nuclear Information System (INIS)

Johnson, B.M.

1990-01-01

The APS offers exciting possibilities for a bright future in x-ray research. For example, measurements on the inner-shell photoionization of ions will be feasible using stored ions in ions traps or ion beams from an electron-cyclotron-resonance ion source, or perhaps even a heavy-ion storage ring. Such experiments with ionic targets are the focus for the discussion given here on the optimization of photon flux on a generic beamline at the APS. The performance of beam lines X26C, X26A, and X17 on the x-ray ring of the National Synchrotron Light Source will be discussed as specific examples of beam-line design considerations

Beam-line considerations for experiments with highly-charged ions

Energy Technology Data Exchange (ETDEWEB)

Johnson, B.M.

1990-01-01

The APS offers exciting possibilities for a bright future in x-ray research. For example, measurements on the inner-shell photoionization of ions will be feasible using stored ions in ions traps or ion beams from an electron-cyclotron-resonance ion source, or perhaps even a heavy-ion storage ring. Such experiments with ionic targets are the focus for the discussion given here on the optimization of photon flux on a generic beamline at the APS. The performance of beam lines X26C, X26A, and X17 on the x-ray ring of the National Synchrotron Light Source will be discussed as specific examples of beam-line design considerations.

Status of the Nanoscopium scanning nanoprobe beamline of Synchrotron Soleil

Science.gov (United States)

Somogyi, A.; Medjoubi, K.; Kewish, C. M.; Leroux, V.; Ribbens, M.; Baranton, G.; Polack, F.; Samama, J. P.

2013-09-01

The Nanoscopium 155 m-long scanning nanoprobe beamline of Synchrotron Soleil (St Aubin, France) is dedicated to quantitative multi-modal imaging. Dedicated experimental stations, working in consecutive operation mode, will provide coherent scatter imaging and spectro-microscopy techniques in the 5-20 keV energy range for various user communities. Next to fast scanning, cryogenic cooling will reduce the radiation damage of sensitive samples during the measurements. Nanoscopium is in the construction phase, the first user experiments are expected in 2014. The main characteristics of the beamline and an overview of its status are given in this contribution.

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography

International Nuclear Information System (INIS)

Nakane, Takanori; Song, Changyong; Suzuki, Mamoru; Nango, Eriko; Kobayashi, Jun; Masuda, Tetsuya; Inoue, Shigeyuki; Mizohata, Eiichi; Nakatsu, Toru; Tanaka, Tomoyuki; Tanaka, Rie; Shimamura, Tatsuro; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Iwata, So; Sugahara, Michihiro

2015-01-01

Sulfur SAD phasing facilitates the structure determination of diverse native proteins using femtosecond X-rays from free-electron lasers via serial femtosecond crystallography. Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures

Optical Design in Phase-Space for the I13L X-Ray Imaging and Coherence Beamline at Diamond using XPHASY

International Nuclear Information System (INIS)

Wagner, Ulrich H.; Rau, Christoph

2010-01-01

I13L is a 250 m long beamline for imaging and coherent diffraction currently under construction at the Diamond Light Source. For modeling the beamline optics the phase-space based ray-tracing code XPHASY was developed, as general ray-tracing codes for x-rays do not easily allow studying the propagation of coherence along the beamline. In contrast to computational intensive wave-front propagation codes, which fully describe the propagation of a photon-beam along a beamline but obscure the impact of individual optical components onto the beamline performance, this code allows to quickly calculate the photon-beam propagation along the beamline and estimate the impact of individual components.In this paper we will discuss the optical design of the I13L coherence branch from the perspective of phase-space by using XPHASY. We will demonstrate how the phase-space representation of a photon-beam allows estimating the coherence length at any given position along the beamline. The impact of optical components on the coherence length and the effect of vibrations on the beamline performance will be discussed. The paper will demonstrate how the phase-space representation of photon-beams allows a more detailed insight into the optical performance of a coherence beamline than ray-tracing in real space.

The design of an automatically-tuned beamline

International Nuclear Information System (INIS)

Ball, M.S.; Ellison, T.J.P.; Hamilton, B.J.; Jones, W.P.

1994-01-01

A new 30 m beamline (BL1C) is being assembled to connect the new High Intensity Polarized Ion Source (HIPIOS) to the IUCF cyclotrons. This line is being instrumented for complete automatic optimization of all transverse and longitudinal ion optical elements by providing a unique feedback signal for each controllable device. Transversely, steerers and 4-quadrant electrostatic pickups are located approximately 90 degree apart in betatron phase advance along the beamline. Each pickup is instrumented with a single-board, 4-layer op-amp circuit (BPM system) which measures the beam intensity, horizontal (H) and vertical (V) position, and H and V 10 Hz position modulation. The transverse beam ellipse parameters are first automatically determined at the entrance to the beamline by measuring the beam size using a wire scanner as a function of the strength of a quadrupole. The computer then programs the amplitude and phase of four 10 Hz modulators which vary the current in 4 steerers to move the beam centroid around this (reduced area) ellipse in 4-dimensional phase space. The BPM system then outputs voltages proportional to the beam intensity, centroid location, and envelope. Computer algorithms will then set the steerers and quadrupoles to correct the beam position, dispersion, and envelope. Longitudinally, hardware feedback loops, with a bandwidth adjustable from 10 Hz to 30 kHz, will phase-lock the beam to the two bunching systems; another hardware system will automatically vary the buncher amplitudes to compensate for the significant and varying space charge defocusing as the beam current fluctuates. The bunchers' quiescent phases and amplitudes will be optimized using software ''synchronous detectors.''

Special issue on Chemical Crystallography Editorial

Indian Academy of Sciences (India)

Virtually, every invitation that we extended has translated into an article. We sincerely believe and wish that the collection of articles in this issue sufficiently showcases the panorama of chemical science involving X-ray crystallography in India. We note with pride that Prof. Gautam R. Desiraju, an eminent scientist who has.

The first synchrotron infrared beamlines at the Advanced Light Source: Spectromicroscopy and fast timing

International Nuclear Information System (INIS)

Martin, Michael C.; McKinney, Wayne R.

1999-01-01

Two recently commissioned infrared beamlines on the 1.4 bending magnet port at the Advanced Light Source, LBNL, are described. Using a synchrotron as an IR source provides three primary advantages: increased brightness, very fast light pulses, and enhanced far-IR flux. The considerable brightness advantage manifests itself most beneficially when performing spectroscopy on a microscopic length scale. Beamline (BL) 1.4.3 is a dedicated FTIR spectromicroscopy beamline, where a diffraction-limited spot size using the synchrotron source is utilized. BL 1.4.2 consists of a vacuum FTIR bench with a wide spectral range and step-scan capability. This BL makes use of the pulsed nature of the synchrotron light as well as the far-IR flux. Fast timing is demonstrated by observing the pulses from the electron bunch storage pattern at the ALS. Results from several experiments from both IR beamlines will be presented as an overview of the IR research currently being done at the ALS

Phasing in crystallography a modern perspective

CERN Document Server

Giacovazzo, Carmelo

2014-01-01

Modern crystallographic methods originate from the synergy of two main research streams, the small-molecule and the macro-molecular streams. The first stream was able to definitively solve the phase problem for molecules up to 200 atoms in the asymmetric unit. The achievements obtained by the macromolecular stream are also impressive. A huge number of protein structures have been deposited in the Protein Data Bank. The solution of them is no longer reserved to an elite group of scientists, but may be attained in a large number of laboratories around the world, even by young scientists. New probabilistic approaches have been tailored to deal with larger structures, errors in the experimental data, and modest data resolution. Traditional phasing techniques like ab initio, molecular replacement, isomorphous replacement, and anomalous dispersion techniques have been revisited. The new approaches have been implemented in robust phasing programs, which have been organized in automatic pipelines usable even by non-e...

Optical design of an x-ray absorption spectroscopy beamline at Indus-2 synchrotron radiation source

International Nuclear Information System (INIS)

Das, N.C.; Jha, S.N.; Roy, A.P.

1999-10-01

Details of optical design of EXAFS beamline at Indus-2 SRS, under development at CAT, Indore, have been discussed in this report. This beamline will cover the photon energy range of 5 keV to 20 keV and will use a bent crystal of Si(111) having 2d value equal to 6.2709 A. It will accept a horizontal divergence of 1.5 mrad. The heart of the beamline is the bent crystal polychromator which will disperse and focus the synchrotron beam at the experimental sample position. The transmitted radiation from the sample will be, subsequently, detected by a position sensitive detector (CCD type). The detector length is 25 mm. Assuming a suitable value for the distance between the source and the crystal, we have computed several geometrical parameters of the beamline, such as, Bragg angle, crystal length, crystal radius, crystal to sample distance, sample to detector distance, etc. for three different photon energies, namely, 5 keV, 10 keV, and 20 keV. The band passes around these photon energies are 0.3 keV, 1 keV and 2 keV respectively. It has been found that computed geometrical parameters are well within acceptable limits. An extensive ray tracing work was done using the software program SHADOW to evaluate the imaging properties of the beamline. It was established that the image spot size at the sample position improved substantially when the crystal is changed from spherical cylinder shape to elliptic cylinder shape. From the ray intensity plots, the average resolution of the crystal bender was estimated to be 1 eV per channel. Finally based on the optical layout of the beamline, a schematic mechanical layout of the beamline has been prepared. (author)

[SUNY beamline facilities at the National Synchrotron Light Source

International Nuclear Information System (INIS)

Coppens, P.

1992-01-01

This report contains short discussions on the following topics which mainly deal with superconductors: crystallography; surface structure; scattering and EXAFS studies; small angle scattering of x-rays

Crowding-facilitated macromolecular transport in attractive micropost arrays.

Science.gov (United States)

Chien, Fan-Tso; Lin, Po-Keng; Chien, Wei; Hung, Cheng-Hsiang; Yu, Ming-Hung; Chou, Chia-Fu; Chen, Yeng-Long

2017-05-02

Our study of DNA dynamics in weakly attractive nanofabricated post arrays revealed crowding enhances polymer transport, contrary to hindered transport in repulsive medium. The coupling of DNA diffusion and adsorption to the microposts results in more frequent cross-post hopping and increased long-term diffusivity with increased crowding density. We performed Langevin dynamics simulations and found maximum long-term diffusivity in post arrays with gap sizes comparable to the polymer radius of gyration. We found that macromolecular transport in weakly attractive post arrays is faster than in non-attractive dense medium. Furthermore, we employed hidden Markov analysis to determine the transition of macromolecular adsorption-desorption on posts and hopping between posts. The apparent free energy barriers are comparable to theoretical estimates determined from polymer conformational fluctuations.

Super-resolution biomolecular crystallography with low-resolution data.

Science.gov (United States)

Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

2010-04-22

X-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X

The design of the beamline for magnetic circular dichroism study at HNSRL

CERN Document Server

ShengWeiFan; Li Da Shi; Yan Yong Lia

2000-01-01

A synchrotron radiation beamline for MCD study is being developed at Hefei National Synchrotron Radiation Laboratory (HNSRL) in the P. R. China. As a key component on the beamline, the varied line-spacing plane grating (VLSPG) monochromator is designed to cover a broad photon energy range from 100 to 1000 eV with a medium energy resolving power of 2000. The design is analyzed and optimized to meet the high requirements of MCD studying.

An unique synchrotron beamline for fine X ray characterizations of nuclear fuel cycle materials

Energy Technology Data Exchange (ETDEWEB)

Sitaud, B.; Lequien, S

2004-07-01

A beamline dedicated to the study of highly radioactive samples up to 18.5 GBq will be constructed on the new third generation synchrotron SOLEIL. Based on the use of X ray beam of very high flux, this beamline named MARS will give true opportunities for new studies of chemistry and physics on fuel cycle materials with the respect of safety conditions. Complementary investigations should be carried out on different experimental stations. The three main techniques will be the micro fluorescence, the micro absorption and the high resolution diffraction. The MARS beamline should be up and working for the international community by the beginning of 2007. (authors)

An unique synchrotron beamline for fine X ray characterizations of nuclear fuel cycle materials

International Nuclear Information System (INIS)

Sitaud, B.; Lequien, S.

2004-01-01

A beamline dedicated to the study of highly radioactive samples up to 18.5 GBq will be constructed on the new third generation synchrotron SOLEIL. Based on the use of X ray beam of very high flux, this beamline named MARS will give true opportunities for new studies of chemistry and physics on fuel cycle materials with the respect of safety conditions. Complementary investigations should be carried out on different experimental stations. The three main techniques will be the micro fluorescence, the micro absorption and the high resolution diffraction. The MARS beamline should be up and working for the international community by the beginning of 2007. (authors)

TREFF: Reflectometer and instrument component test beamline at MLZ

Directory of Open Access Journals (Sweden)

Peter Link

2017-11-01

Full Text Available TREFF is a high resolution polarized neutron reflectometer and instrument component test beamline resulting in a highly modular instrument providing a flexible beam line for various applications.

The story of crystallography

International Nuclear Information System (INIS)

Nigam, G.D.

1976-01-01

The historical development of the very important field of crystallography has been narrated. The important land marks such as the first determination of the crystal structure of NaCl by Sir Poragy and that of DNA by Watson et al., etc. are mentioned. The important role played by this field and its role in bringing broad fields such as physics, chemistry and biology very close to each other are emphasised. Some of the outstanding contributions made by eminent crystallographers in India and abroad are mentioned. (K.B.)

(SUNY beamline facilities at the National Synchrotron Light Source)

Energy Technology Data Exchange (ETDEWEB)

Coppens, P.

1992-01-01

This report contains short discussions on the following topics which mainly deal with superconductors: crystallography; surface structure; scattering and EXAFS studies; small angle scattering of x-rays. (LSP)

Intensity interferometry at the X13A undulator beamline

International Nuclear Information System (INIS)

Gluskin, E.; McNulty, I.; Yang, L.; Randall, K.J.; Johnson, E.D.

1993-01-01

We are constructing a soft x-ray intensity interferometer and an undulator based beamline to demonstrate intensity interferometry in the x-ray region. The 10-period soft x-ray undulator at the NSLS provides the necessary coherent flux; the X13A beamline is designed to preserve the spatial coherence of the bright x-ray beam and provide sufficient temporal coherence using a horizontally deflecting spherical grating monochromator. Using the interferometer, which consists of an array of small slits, a wedge-shaped beamsplitter and two fast microchannel plate detectors, we expect to measure the spatial coherence of the undulator beam and therefore the size of the source in the vertical plane. Details of the bean-dine design and the interferometer experiment are discussed

Functional description of APS beamline front ends

International Nuclear Information System (INIS)

Kuzay, T.

1993-02-01

Traditional synchrotron sources were designed to produce bending magnet radiation and have proven to be an essential scientific tool. Currently, a new generation of synchrotron sources is being built that will be able to accommodate a large number of insertion device (ID) and high quality bending magnet (BM) sources. One example is the 7-GeV Advanced Photon Source (APS) now under construction at Argonne National Laboratory. The research and development effort at the APS is designed to fully develop the potential of this new generation of synchrotron sources. Of the 40 straight sections in the APS storage ring, 34 will be available for IDs. The remaining six sections are reserved for the storage ring hardware and diagnostics. Although the ring incorporates 80 BMs, only 40 of them can be used to extract radiation. The accelerator hardware shadows five of these 40 bending magnets, so the maximum number of BM sources on the lattice is 35. Generally, a photon beamline consists of four functional sections. The first section is the ID or the BM, which provides the radiation source. The second section, which is immediately outside the storage ring but inside a concrete shielding tunnel, is the front end, which is designed to control, define, and/or confine the x-ray beam. In the case of the APS, the front ends are designed to confine the photon beam. The third section, just outside the concrete shielding tunnel and on the experimental floor, is the first optics enclosure, which contains optics to filter and monochromatize the photon beam. The fourth section of a beamline consists of beam transports, additional optics, and experiment stations to do the scientific investigations. This document describes only the front ends of the APS beamlines

The vacuum interlock system for the PETRA III beamlines

Energy Technology Data Exchange (ETDEWEB)

Degenhardt, Markus; Hahn, Ulrich; Hesse, Mathias; Schulte-Schrepping, Horst [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2008-07-01

The storage ring PETRA at DESY in Hamburg is being reconstructed into the third generation source for synchrotron radiation, PETRA III. The up to 100 m long beamlines are large UHV-systems that guide the synchrotron radiation from the storage ring to the experiments. Each beamline will be equipped with a vacuum interlock system to ensure the safe operation of the vacuum components. In particular the task of the vacuum interlock is to prevent faulty operations that can cause a ventilation of the vacuum system or a damage of vacuum components by the high power synchrotron radiation beam. The interlock system will be implemented as a PLC that is connected to a distributed input/output layer via a field bus system. As a specialty, the PLC will be realised as a soft-PLC running on a PC with a real time windows operating system. Another specialty is the visualisation and remote control of the vacuum interlock system by means of a website. At the beamline the interlock will be operated via a touch panel that displays the visualisation website. Additionally, the interlock can be remotely operated from any location by opening the visualisation website with a browser. The interlock is protected against unauthorised operation by a login page. All relevant interlock data will be fed into the existing network-based archive system.

Diagnostics Beamline for the SRF Gun Project

CERN Document Server

Kamps, T; Goldammer, K; Krämer, Dietrich; Kuske, P; Kuszynski, J; Lipka, D; Marhauser, F; Quast, T; Richter, R

2005-01-01

A superconducting rf photo electron injector (SRF gun) is currently under construction by a collaboration between BESSY, DESY, FZR and MBI. The project aims at the design and setup of an CW SRF gun including a diagnostics beamline for the ELBE FEL and to address R&D issues on low emittance injectors for future light sources such as the BESSY FEL. Of critical importance for the injector performance is the control of the electron beam parameters. For this reason a compact diagnostics beamline is under development serving a multitude of operation settings ranging from low-charge (77pC), low-emittance (1 pi mm mrad) mode to high-charge (2.5nC) operation of the gun. For these operation modes beam dynamics simulations are resulting in boundary conditions for the beam instrumentation. Proven and mature technology is projected wherever possible, for example for current and beam position monitoring. The layout of the beam profile and emittance measurement systems is described. For the bunch length, which varies be...

Muon Colliders: the Ultimate Neutrino Beamlines

International Nuclear Information System (INIS)

King, Bruce J.

1999-01-01

It is shown that muon decays in straight sections of muon collider rings will naturally produce highly collimated neutrino beams that can be several orders of magnitude stronger than the beams at existing accelerators. We discuss possible experimental setups and give a very brief overview of the physics potential from such beamlines. Formulae are given for the neutrino event rates at both short and long baseline neutrino experiments in these beams

Nomenclature of SLC Arc beamline components

International Nuclear Information System (INIS)

Silva, J.; Weng, W.T.

1986-01-01

This note defines I and C formal names for beamline components in the Arc as specified in the TRANSPORT decks ARCN FINAL and ARCS FINAL of June 5, 1985. The formal name consists of three fields: the primary name, the zone and the unit number. The general principles and guidelines are explained in Reference 1. The rationale and the final resolutions of the naming conventions for the Arc are explained

A high-pressure MWPC detector for crystallography

DEFF Research Database (Denmark)

Ortuno-Prados, F.; Bazzano, A.; Berry, A.

1999-01-01

The application of the Multi-Wire Proportional Counter (MWPC) as a potential detector for protein crystallography and other wide-angle diffraction experiments is presented. Electrostatic problems found with our large area MWPC when operated at high pressure are discussed. We suggest that a solution...

Crystallography of the Sb-Te-Ni system

Czech Academy of Sciences Publication Activity Database

Laufek, F.; Drábek, M.; Skála, Roman; Císařová, I.

2005-01-01

Roč. 12, č. 2 (2005), s. 153-154 ISSN 1211-5894 Grant - others:GAUK(CZ) 43-203391 Institutional research plan: CEZ:AV0Z30130516 Keywords : crystallography * antimony * tellurium Subject RIV: DB - Geology ; Mineralogy http:// xray .cz/ms/bul2005-2/student3.pdf

Toyota beamline (BL33XU) at SPring-8

Energy Technology Data Exchange (ETDEWEB)

Nonaka, T., E-mail: nonaka@mosk.tytlabs.co.jp; Dohmae, K.; Hayashi, Y.; Yamaguchi, S.; Nagai, Y.; Hirose, Y. [Toyota Central R& D Labs., Inc., 41-1 Nagakute Aichi 480-1192 Japan (Japan); Araki, T. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE UK (United Kingdom); Tanaka, T.; Kitamura, H. [RIKEN Harima Institute 1-1-1 Koto Sayo, Hyogo 679-5148 (Japan); Uruga, T.; Yamazaki, H.; Yumoto, H.; Ohashi, H.; Goto, S. [JASRI/SPring-8 1-1-1 Koto Sayo, Hyogo 679-5148 (Japan)

2016-07-27

The Toyota beamline (BL33XU) at SPring-8 is an undulator beamline developed to assist in the study of various automotive-related materials. The light source is a tapered in-vacuum undulator that provides a variable energy band width as well as a high brilliance X-ray beam. Two different optical arrangements are available: Optics 1 and Optics 2. Optics 1 is dedicated to time-resolved X-ray absorption spectroscopy (XAFS), and consists of two channel-cut crystal monochromators and four water-cooled flat Si mirrors. The Si(111) and Si(220) monochromator crystals cover an energy range of 4.0–46.0 keV and are driven by high-speed AC servo motors. These monochromators, in conjunction with the tapered undulator, enable high-quality XAFS data acquisition with a temporal resolution of 10 ms. Optics 2 is optimized for X-ray diffraction, scattering and imaging and includes a recently installed double crystal monochromator, two water-cooled flat Si mirrors and Kirkpatrick-Baez (KB) focusing mirrors. The monochromator incorporates parallel mounted Si(111) and Si(311) crystals and covers an energy range of 4.5–70 keV. The beamline provides two experimental stations: Exp. Hutch 2 and Exp. Hutch 3. The gas supply system and mass spectrometers installed in Exp. Hutch 2 allow in-operando measurements under various atmospheres. The scanning three-dimensional X-ray diffraction (scanning 3DXRD) microscopy instrumentation developed and installed in Exp. Hutch 3 enables non-destructive orientation and stress mapping of 1 mm-thick steel specimens using a high energy microbeam.

Toyota beamline (BL33XU) at SPring-8

International Nuclear Information System (INIS)

Nonaka, T.; Dohmae, K.; Hayashi, Y.; Yamaguchi, S.; Nagai, Y.; Hirose, Y.; Araki, T.; Tanaka, T.; Kitamura, H.; Uruga, T.; Yamazaki, H.; Yumoto, H.; Ohashi, H.; Goto, S.

2016-01-01

The Toyota beamline (BL33XU) at SPring-8 is an undulator beamline developed to assist in the study of various automotive-related materials. The light source is a tapered in-vacuum undulator that provides a variable energy band width as well as a high brilliance X-ray beam. Two different optical arrangements are available: Optics 1 and Optics 2. Optics 1 is dedicated to time-resolved X-ray absorption spectroscopy (XAFS), and consists of two channel-cut crystal monochromators and four water-cooled flat Si mirrors. The Si(111) and Si(220) monochromator crystals cover an energy range of 4.0–46.0 keV and are driven by high-speed AC servo motors. These monochromators, in conjunction with the tapered undulator, enable high-quality XAFS data acquisition with a temporal resolution of 10 ms. Optics 2 is optimized for X-ray diffraction, scattering and imaging and includes a recently installed double crystal monochromator, two water-cooled flat Si mirrors and Kirkpatrick-Baez (KB) focusing mirrors. The monochromator incorporates parallel mounted Si(111) and Si(311) crystals and covers an energy range of 4.5–70 keV. The beamline provides two experimental stations: Exp. Hutch 2 and Exp. Hutch 3. The gas supply system and mass spectrometers installed in Exp. Hutch 2 allow in-operando measurements under various atmospheres. The scanning three-dimensional X-ray diffraction (scanning 3DXRD) microscopy instrumentation developed and installed in Exp. Hutch 3 enables non-destructive orientation and stress mapping of 1 mm-thick steel specimens using a high energy microbeam.

A beamline systems model for Accelerator-Driven Transmutation Technology (ADTT) facilities

Energy Technology Data Exchange (ETDEWEB)

Todd, A.M.M.; Paulson, C.C.; Peacock, M.A. [Grumman Research and Development Center, Princeton, NJ (United States)] [and others

1995-10-01

A beamline systems code, that is being developed for Accelerator-Driven Transmutation Technology (ADTT) facility trade studies, is described. The overall program is a joint Grumman, G.H. Gillespie Associates (GHGA) and Los Alamos National Laboratory effort. The GHGA Accelerator Systems Model (ASM) has been adopted as the framework on which this effort is based. Relevant accelerator and beam transport models from earlier Grumman systems codes are being adapted to this framework. Preliminary physics and engineering models for each ADTT beamline component have been constructed. Examples noted include a Bridge Coupled Drift Tube Linac (BCDTL) and the accelerator thermal system. A decision has been made to confine the ASM framework principally to beamline modeling, while detailed target/blanket, balance-of-plant and facility costing analysis will be performed externally. An interfacing external balance-of-plant and facility costing model, which will permit the performance of iterative facility trade studies, is under separate development. An ABC (Accelerator Based Conversion) example is used to highlight the present models and capabilities.

X-ray optics simulation and beamline design for the APS upgrade

Science.gov (United States)

Shi, Xianbo; Reininger, Ruben; Harder, Ross; Haeffner, Dean

2017-08-01

The upgrade of the Advanced Photon Source (APS) to a Multi-Bend Achromat (MBA) will increase the brightness of the APS by between two and three orders of magnitude. The APS upgrade (APS-U) project includes a list of feature beamlines that will take full advantage of the new machine. Many of the existing beamlines will be also upgraded to profit from this significant machine enhancement. Optics simulations are essential in the design and optimization of these new and existing beamlines. In this contribution, the simulation tools used and developed at APS, ranging from analytical to numerical methods, are summarized. Three general optical layouts are compared in terms of their coherence control and focusing capabilities. The concept of zoom optics, where two sets of focusing elements (e.g., CRLs and KB mirrors) are used to provide variable beam sizes at a fixed focal plane, is optimized analytically. The effects of figure errors on the vertical spot size and on the local coherence along the vertical direction of the optimized design are investigated.

A beamline systems model for Accelerator-Driven Transmutation Technology (ADTT) facilities

International Nuclear Information System (INIS)

Todd, Alan M. M.; Paulson, C. C.; Peacock, M. A.; Reusch, M. F.

1995-01-01

A beamline systems code, that is being developed for Accelerator-Driven Transmutation Technology (ADTT) facility trade studies, is described. The overall program is a joint Grumman, G. H. Gillespie Associates (GHGA) and Los Alamos National Laboratory effort. The GHGA Accelerator Systems Model (ASM) has been adopted as the framework on which this effort is based. Relevant accelerator and beam transport models from earlier Grumman systems codes are being adapted to this framework. Preliminary physics and engineering models for each ADTT beamline component have been constructed. Examples noted include a Bridge Coupled Drift Tube Linac (BCDTL) and the accelerator thermal system. A decision has been made to confine the ASM framework principally to beamline modeling, while detailed target/blanket, balance-of-plant and facility costing analysis will be performed externally. An interfacing external balance-of-plant and facility costing model, which will permit the performance of iterative facility trade studies, is under separate development. An ABC (Accelerator Based Conversion) example is used to highlight the present models and capabilities

Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents

Directory of Open Access Journals (Sweden)

Arghya Chakravorty

2018-03-01

Full Text Available Conventional modeling techniques to model macromolecular solvation and its effect on binding in the framework of Poisson-Boltzmann based implicit solvent models make use of a geometrically defined surface to depict the separation of macromolecular interior (low dielectric constant from the solvent phase (high dielectric constant. Though this simplification saves time and computational resources without significantly compromising the accuracy of free energy calculations, it bypasses some of the key physio-chemical properties of the solute-solvent interface, e.g., the altered flexibility of water molecules and that of side chains at the interface, which results in dielectric properties different from both bulk water and macromolecular interior, respectively. Here we present a Gaussian-based smooth dielectric model, an inhomogeneous dielectric distribution model that mimics the effect of macromolecular flexibility and captures the altered properties of surface bound water molecules. Thus, the model delivers a smooth transition of dielectric properties from the macromolecular interior to the solvent phase, eliminating any unphysical surface separating the two phases. Using various examples of macromolecular binding, we demonstrate its utility and illustrate the comparison with the conventional 2-dielectric model. We also showcase some additional abilities of this model, viz. to account for the effect of electrolytes in the solution and to render the distribution profile of water across a lipid membrane.

General design of the layout for new undulator-only beamline front ends

International Nuclear Information System (INIS)

Shu Deming; Ramanathan, Mohan; Kuzay, Tuncer M.

2001-01-01

A great majority of the Advanced Photon Source (APS) users have chosen an undulator as the only source for their insertion device beamline. Compared with a wiggler source, the undulator source has a much smaller horizontal divergence, providing us with an opportunity to optimize the beamline front-end design further. In this paper, the particular designs and specifications, as well as the optical and bremsstrahlung ray-tracing analysis of the new APS front ends for undulator-only operation are presented

Conceptual design of NBI beamline for VEST plasma heating

Energy Technology Data Exchange (ETDEWEB)

Kim, T.S., E-mail: tskim@kaeri.re.kr; In, S.R.; Jeong, S.H.; Park, M.; Chang, D.H.; Jung, B.K.; Lee, K.W.

2016-11-01

Highlights: • VEST NBI injector is conceptually designed to support further VEST plasma experiment. • VEST NBI injector composed of 2 sets of 20 keV/25A magnetic cusp type bucket ion source, neutralizer ducts, electrostatic ion dumps, NB vessel with cryopump, and rotating calorimerter. • The vacuum vessel of the beamline is divided into two parts for high injection efficiency and different direction (co- and counter-current) of neutral beam injection. • An ion source for the VEST NBI system was also designed to deliver neutral hydrogen beams with a power of 0.3 MW. The plasma generator of the VEST NB ion source has modified TFTR bucket multi-cusp chamber. The plasma generator has twelve hair-pin shaped tungsten filaments used as a cathode and an arc chamber including a bucket and an electron dump which serve as anode. The accelerator system consists of three grids, each having extraction area of 100 mm × 320 mm and 64 shaped slits of 3 mm spacing. • The preliminary structure design and the layout of the main components of the injector have been completed. Simulation and calculation for optimization of the NB beamline design results prove that the parameters of ion source, neutralization efficiency (76%:95% equilibrium neutralization efficiency), and beam power transmission efficiency (higher than 90%) are in agreement with design targets of the VEST NB beamline. • This VEST NBI system will provide a neutral beam of ∼0.6 MW for both heating and current drive in torus plasma. - Abstract: A 10 m s-pulsed NBI (Neutral Beam Injection) system for VEST (Versatile Experiment Spherical Torus) plasma heating is designed to provide a beam power of more than 0.6 MW with 20 keV H° neutrals. The VEST NBI injector is composed of 2 sets of 20 keV/25A magnetic cusp type bucket ion source, neutralizer ducts, residual ion dump, NB vessel with a cryopump, and rotating calorimeter. The position and size of these beamline components are roughly determined with geometric

Conceptual design of NBI beamline for VEST plasma heating

International Nuclear Information System (INIS)

Kim, T.S.; In, S.R.; Jeong, S.H.; Park, M.; Chang, D.H.; Jung, B.K.; Lee, K.W.

2016-01-01

Highlights: • VEST NBI injector is conceptually designed to support further VEST plasma experiment. • VEST NBI injector composed of 2 sets of 20 keV/25A magnetic cusp type bucket ion source, neutralizer ducts, electrostatic ion dumps, NB vessel with cryopump, and rotating calorimerter. • The vacuum vessel of the beamline is divided into two parts for high injection efficiency and different direction (co- and counter-current) of neutral beam injection. • An ion source for the VEST NBI system was also designed to deliver neutral hydrogen beams with a power of 0.3 MW. The plasma generator of the VEST NB ion source has modified TFTR bucket multi-cusp chamber. The plasma generator has twelve hair-pin shaped tungsten filaments used as a cathode and an arc chamber including a bucket and an electron dump which serve as anode. The accelerator system consists of three grids, each having extraction area of 100 mm × 320 mm and 64 shaped slits of 3 mm spacing. • The preliminary structure design and the layout of the main components of the injector have been completed. Simulation and calculation for optimization of the NB beamline design results prove that the parameters of ion source, neutralization efficiency (76%:95% equilibrium neutralization efficiency), and beam power transmission efficiency (higher than 90%) are in agreement with design targets of the VEST NB beamline. • This VEST NBI system will provide a neutral beam of ∼0.6 MW for both heating and current drive in torus plasma. - Abstract: A 10 m s-pulsed NBI (Neutral Beam Injection) system for VEST (Versatile Experiment Spherical Torus) plasma heating is designed to provide a beam power of more than 0.6 MW with 20 keV H° neutrals. The VEST NBI injector is composed of 2 sets of 20 keV/25A magnetic cusp type bucket ion source, neutralizer ducts, residual ion dump, NB vessel with a cryopump, and rotating calorimeter. The position and size of these beamline components are roughly determined with geometric

Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA

Czech Academy of Sciences Publication Activity Database

Degtjarik, O.; Brynda, Jiří; Ettrichová, O.; Kutý, M.; Sinha, D.; Kutá Smatanová, I.; Carey, J.; Ettrich, R.; Řeha, D.

2016-01-01

Roč. 120, č. 22 (2016), s. 4867-4877 ISSN 1520-6106 Institutional support: RVO:61388963 Keywords : macromolecular crystallography * noncovalent interactions * molecular replacement Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.177, year: 2016

TOF technique for laser-driven proton beam diagnostics for the ELIMED beamline

International Nuclear Information System (INIS)

Milluzzo, G.; Scuderi, V.; Amico, A.G.; Cirrone, G.A.P.; Cuttone, G.; Larosa, G.; Leanza, R.; Petringa, G.; Pipek, J.; Romano, F.; Napoli, M. De; Dostal, J.; Margarone, D.; Schillaci, F.; Velyhan, A.

2017-01-01

The Time of Flight (TOF) method for laser-driven ion beam diagnostics has been extensively investigated so far for low energy ion diagnostics and several works, reported in literature [1,2], have shown its efficiency in the measurement of particle beam characteristics such as ion species, energy spectrum and current. Moreover, such technique allows obtaining a shot-to-shot on-line monitoring of optically accelerated particles, necessary to control the reproducibility of the accelerated beam and to deliver a beam suitable for any kind of applications. For this reason, the ELIMED beamline [3,4], which will be entirely developed at INFN-LNS and installed in 2017 within the ion beamline ELIMAIA (ELI Multidisciplinary Applications of laser-Ion Acceleration) experimental hall at ELI-Beamlines in Prague, will be equipped with an on-line diagnostics system composed by silicon carbide and diamond detectors, using the TOF technique. In this contribution, the procedure developed for TOF signal analysis will be briefly reported.

Blade-type X-ray beam position monitors for SPring-8 undulator beamlines

CERN Document Server

Aoyagi, H; Kitamura, H

2001-01-01

The X-ray beam position monitors had been designed and installed for SPring-8 insertion device beamlines. These monitors are being utilized for photon beam diagnostics. The beam from the standard undulator in SPring-8 has the total power of 11 kW and the power density of 470 kW/mrad sup 2 , typically. Each monitor has four CVD diamond blades coated with metal for detector heads. We have already introduced three styles of monitors to match various insertion devices in SPring-8. A standard style, or a fixed-blade style, is used mainly for a standard in-vacuum undulator beamlines. A horizontal-blade-drive style and a four-blade-drive style are used for beamlines of a wiggler and a twin helical undulator that have wide power distributions, and for figure-8 undulators that have asymmetric power distributions, respectively. This report describes the design and the structure of these monitors and the beam-tests for the photon beam diagnostics in detail.

Quantitative SRXRF analysis on the BL15U1 beamline at SSRF

International Nuclear Information System (INIS)

Zhang Yanle; Yu Xiaohan

2010-01-01

In this paper, we give an introduction first to two quantification methods for synchrotron radiation X-ray fluorescence analysis (SRXRF), namely fundamental parameters method and Monte-Carlo simulation method, for their application on the BL15U1 beamline (hard X-ray microprobe) at SSRF (Shanghai Synchrotron Radiation Facility). Effectiveness of the two methods is demonstrated and the XRF detection limits of the BL15U1 beamline are calculated. The results show that, quantitative analysis at the ppm level can be done using the two methods, with an accuracy of better than 10%. Although both the methods are valid for the SRXRF data analysis,the Monte Carlo method gives better analysis result, as it compares the simulated spectrum with the experiment spectrum, and this helps the determination of experiment parameters and thus minimizes the error caused by incorrect parameters. Finally, the detection limits shows that the BL15U1 beamline is capable of carrying out standard-of-the-art XRF experiment. (authors)

Sources, instrumentation and detectors for protein crystallography

CERN Document Server

Nave, C

2001-01-01

Some of the requirements for protein crystallography experiments on a synchrotron are described. Although data from different types of crystal are often collected without changing the X-ray beam properties, there are benefits if the incident beam is matched to a particular crystal and its diffraction pattern. These benefits are described with some examples. Radiation damage and other effects impose limits on the dose and dose rate on a protein crystal if the maximum amount of data is to be obtained. These limitations have possible consequences for the X-ray source required. Presently available commercial detector systems provide excellent data for protein crystallography but do not quite reach the specifications of the 'ideal' detector. In order to collect the most accurate data (e.g. for very weak anomalous scattering applications) detectors that produce near photon counting statistics over a wide dynamic range are required. It is possible that developments in 'pixel' detectors will allow these demanding exp...

Calibration and standards beamline 6.3.2 at the ALS

International Nuclear Information System (INIS)

Underwood, J.H.; Gullikson, E.M.; Koike, M.

1997-01-01

More sophisticated optics for the x-ray, soft x-ray and far ultraviolet spectral regions being developed for synchrotron radiation research and many other applications, require accurate calibration and standards facilities for measuring reflectivity of mirrors and multilayer coatings, transmission of thin films, bandpass of multilayers, efficiency of gratings or detectors, etc. For this purpose beamline 6.3.2 was built at the ALS. Its energy coverage, versatility, simplicity and convenience also make it useful for a wide range of other experiments. The paper describes the components of this beamline, consisting of: a four jaw aperture; a horizontal focusing mirror; a monochromator; exit slit; vertical focusing mirror; mechanical and vacuum system; reflectometer; filter wheels; and data acquisition system

Calibration and standards beamline 6.3.2 at the ALS

Energy Technology Data Exchange (ETDEWEB)

Underwood, J.H.; Gullikson, E.M.; Koike, M. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)] [and others

1997-04-01

More sophisticated optics for the x-ray, soft x-ray and far ultraviolet spectral regions being developed for synchrotron radiation research and many other applications, require accurate calibration and standards facilities for measuring reflectivity of mirrors and multilayer coatings, transmission of thin films, bandpass of multilayers, efficiency of gratings or detectors, etc. For this purpose beamline 6.3.2 was built at the ALS. Its energy coverage, versatility, simplicity and convenience also make it useful for a wide range of other experiments. The paper describes the components of this beamline, consisting of: a four jaw aperture; a horizontal focusing mirror; a monochromator; exit slit; vertical focusing mirror; mechanical and vacuum system; reflectometer; filter wheels; and data acquisition system.

Bremsstrahlung scattering calculations for the beam stops and collimators in the APS insertion-device beamlines

International Nuclear Information System (INIS)

Job, P.K.; Haeffner, D.R.; Shu, D.

1994-12-01

Bremsstrahlung is produced in the APS storage ring by the interaction of positrons with the residual gas molecules in the vacuum chamber of the storage ring. The bremsstrahlung production causes a serious challenge in shielding the insertion-device beamlines because the entire straight section (15 meters) is in the line of sight of the beamline. The radiation emerges in a narrow cone tangential to the beam path with the characteristic emission angle 1/γ, where γ is E/mc 2 which is the ratio of the kinetic energy to the rest mass for the positrons. This high-energy gamma radiation has an approximate 1/E spectrum with the maximum energy extending up to the particle energy (7 GeV for the APS). Bremsstrahlung, being high-energy photons, produces an electromagnetic shower when it encounters the beamline elements. A beamline element not thick enough to fully contain an electromagnetic shower can cause considerable scatter of the high-energy bremsstrahlung radiation. The low-energy component of the bremsstrahlung can also be scattered and create high dose rates in the first-optical and white-beam enclosures. The fully developed electromagnetic shower will have a photon spectrum almost independent of the material. The electromagnetic showers in the high-Z materials can also produce photoneutrons. This note reports the summary of EGS4 calculations performed on bremsstrahlung scattering from different beamline components in a typical APS insertion-device beamline. The related recommendations for shielding are also given. The shielding criterion adopted is a total dose rate of 2.5μSv/h (0.25 mrem/h) at 30 cm from the shield

Nanotomography endstation at the P05 beamline: Status and perspectives

Science.gov (United States)

Greving, I.; Ogurreck, M.; Marschall, F.; Last, A.; Wilde, F.; Dose, T.; Burmester, H.; Lottermoser, L.; Müller, M.; David, C.; Beckmann, F.

2017-06-01

The Imaging Beamline IBL/P05 at the DESY storage ring PETRA III, operated by the Helmholtz-Zentrum Geesthacht, has two dedicated endstations optimized for micro- and nanotomography experiments [1-3]. Here we present the status of the nanotomography endstation, highlight the latest instrumentation upgrades and present first experimental results. In particular in materials science, where structures with ceramics or metallic materials are of interest, X-ray energies of 15 keV and above are required even for sample sizes of several 10 μm in diameter. The P05 imaging beamline is dedicated to materials science and is designed to allow for imaging applications with X-ray energies of 10 to 50 keV. In addition to the full field X-ray microscopy setup, the layout of the nanotomography endstation allows switching to cone-beam configuration. Kinematics for X-ray optics like compound refractive lenses (CRLs), Fresnel zone plates (FZP) or beam-shaping optics are implemented and the installation of a Kirkpatrick Baez-mirror (KB mirror) system is foreseen at a later stage of the beamline development. Altogether this leads to a high flexibility of the nanotomography setup such that the instrument can be tailored to the specific experimental requirements of a range of sample systems.

Thermal, structural, and fabrication aspects of diamond windows for high power synchrotron x-ray beamlines

International Nuclear Information System (INIS)

Khounsary, A.M.; Phillips, W.

1992-01-01

Recent advances in chemical vapor deposition (CVD) technology have made it possible to produce thin free-standing diamond foils that can be used as the window material in high heat load, synchrotron beamlines. Numerical simulations suggest that these windows can offer an attractive and at times the only altemative to beryllium windows for use in third generation x-ray synchrotron radiation beamlines. Utilization, design, and fabrication aspects of diamond windows for high heat load x-ray beamlines are discussed, as are the microstructure characteristics bearing on diamond's performance in this role. Analytic and numerical results are also presented to provide a basis for the design and testing of such windows

The first synchrotron infrared beamlines at the Advanced Light Source: Microspectroscopy and fast timing

International Nuclear Information System (INIS)

Martin, M.C.; McKinney, W.R.

1998-05-01

A set of new infrared (IR) beamlines on the 1.4 bending magnet port at the Advanced Light Source, LBNL, are described. Using a synchrotron as an IR source provides considerable brightness advantages, which manifests itself most beneficially when performing spectroscopy on a microscopic length scale. Beamline (BL) 1.4.3 is a dedicated microspectroscopy beamline, where the much smaller focused spot size using the synchrotron source is utilized. This enables an entirely new set of experiments to be performed where spectroscopy on a truly microscopic scale is now possible. BL 1.4.2 consists of a vacuum FTIR bench with a wide spectral range and step-scan capabilities. The fast timing is demonstrated by observing the synchrotron electron storage pattern at the ALS

Optical design study of the PEARL beamline at SLS

Czech Academy of Sciences Publication Activity Database

Oberta, Peter; Flechsig, U.; Muntwiler, M.; Quitmann, C.

2011-01-01

Roč. 635, č. 1 (2011), s. 116-120 ISSN 0168-9002 Institutional research plan: CEZ:AV0Z10100522 Keywords : PGM * beamline design * photo-emision Subject RIV: BH - Optics, Masers, Lasers Impact factor: 1.207, year: 2011

A readout system for X-ray powder crystallography

CERN Document Server

Loukas, D; Pavlidis, A; Karvelas, E; Psycharis, K; Misiakos, V; Mousa, J; Dre, C

2000-01-01

A system for capturing and processing data, from radiation detectors, in the field of X-ray crystallography has been developed. The system includes a custom-made mixed analog-digital 16-channel VLSI circuit in 50 mu m pitch. Each channel comprises a charge amplifier, a shaper, a comparator and a 21-bit counter. The circuit can be scaled in a daisy chain configuration. Data acquisition is performed with a custom made PCI card while the control software is developed with Visual C++ under the MS Windows NT environment. Performance of a fully operational system, in terms of electronic noise, statistical variations and data capture speed is presented. The noise level permits counting of X-rays down to 8 keV while the counting capability is in excess of 200 kHz. The system is intended for X-ray crystallography with silicon detectors.

High resolution inner-shell spectroscopies of atoms and molecules in gas phase using the soft x-ray photochemistry beamline at SPring-8

International Nuclear Information System (INIS)

Ueda, Kiyoshi

2003-01-01

This article describes recent activities on inner-shell spectroscopies of atoms and molecules on beamline 27SU, nicknamed soft X-ray photochemistry beamline, at SPring-8, an 8-GeV synchrotron radiation facility in Japan. This beamline provides linearly polarized monochromatic soft X-rays at the resolution higher than 10,000. The end station is designed so that one can perform various kinds of excitation and de-excitation spectroscopies as well as coincidence spectroscopies. Following the description of the beamline and the end station, we present recent results for inner-shell spectroscopies on Ne, CO 2 , BF 3 , and CF 4 . Emphasis is given to illustrate the strategy of the research on this beamline and performance of the beamline and the end station. (author)

The charm of protein crystals--Structural biology at a glance in the International Year of Crystallography

International Nuclear Information System (INIS)

Su Xiaodong; Cao Qin

2014-01-01

Crystallography is a typical intellectual endeavor that has spanned human history for centuries. Through the persistent efforts of generations of scientists, crystallography has been transformed from a mathematical hypothesis to actual physical reality, mainly thanks to X-ray diffraction technology. 2014 is celebrated as the International Year of Crystallography (IYCr-2014), to commemorate that about 100 years ago, when Max von Laue in Germany and the father-and-son Braggs (William Henry Bragg and William Lawrence Bragg) in England pioneered the use of X-rays to determine the atomic structure of crystals; for this pioneering work they were awarded Nobel prizes for physics in the years of 1914 and 1915. This article is dedicated to the IYCr to describe the use of protein crystals, an application that has developed into protein crystallography and subsequently structural biology. In our overview of the history and future prospects of this field, we discuss in detail one example of caspase-6, to demonstrate how protein crystallography can help us understand the structure-function relationship of important proteins. (authors)

The X-ray microscopy beamline UE46-PGM2 at BESSY

International Nuclear Information System (INIS)

Follath, R.; Schmidt, J. S.; Weigand, M.; Fauth, K.

2010-01-01

The Max Planck Institute for Metal Physics in Stuttgart and the Helmholtz Center Berlin operate a soft X-ray microscopy beamline at the storage ring BESSY II. A collimated PGM serves as monochromator for a scanning X-ray microscope and a full field X-ray microscope at the helical undulator UE46. The selection between both instruments is accomplished via two switchable focusing mirrors. The scanning microscope (SM) is based on the ALS STXM microscope and fabricated by the ACCEL company. The full field microscope (FFM) is currently in operation at the U41-SGM beamline and will be relocated to its final location this year.

Motion control system of MAX IV Laboratory soft x-ray beamlines

International Nuclear Information System (INIS)

Sjöblom, Peter; Lindberg, Mirjam; Forsberg, Johan; Persson, Andreas G.; Urpelainen, Samuli; Såthe, Conny

2016-01-01

At the MAX IV Laboratory, five new soft x-ray beamlines are under development. The first is Species and it will be used to develop and set the standard of the control system, which will be common across the facility. All motion axes at MAX IV will be motorized using stepper motors steered by the IcePAP motion controller and a mixture of absolute and incremental encoders following a predefined coordinate system. The control system software is built in Tango and uses the Python-based Sardana framework. The user controls the entire beamline through a synoptic overview and Sardana is used to run the scans.

Motion control system of MAX IV Laboratory soft x-ray beamlines

Energy Technology Data Exchange (ETDEWEB)

Sjöblom, Peter, E-mail: peter.sjoblom@maxlab.lu.se; Lindberg, Mirjam, E-mail: mirjam.lindberg@maxlab.lu.se; Forsberg, Johan, E-mail: johan.forsberg@maxlab.lu.se; Persson, Andreas G., E-mail: andreas-g.persson@maxlab.lu.se; Urpelainen, Samuli, E-mail: samuli.urpelainen@maxlab.lu.se; Såthe, Conny, E-mail: conny.sathe@maxlab.lu.se [MAX IV Laboratory, Photongatan 2, 225 92 Lund (Sweden)

2016-07-27

At the MAX IV Laboratory, five new soft x-ray beamlines are under development. The first is Species and it will be used to develop and set the standard of the control system, which will be common across the facility. All motion axes at MAX IV will be motorized using stepper motors steered by the IcePAP motion controller and a mixture of absolute and incremental encoders following a predefined coordinate system. The control system software is built in Tango and uses the Python-based Sardana framework. The user controls the entire beamline through a synoptic overview and Sardana is used to run the scans.

Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules

Directory of Open Access Journals (Sweden)

Esko Oksanen

2017-04-01

Full Text Available Abstract: The hydrogen bond (H bond is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.

Murthy, Prof. Mathur Ramabhadrashastry Narasimha

Indian Academy of Sciences (India)

Specialization: Macromolecular Crystallography, Virus Structure & Assembly, Protein Structure & Function and X-ray Diffraction Address: Professor, Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, Karnataka Contact: Office: (080) 2293 2458. Residence: (080) 2293 3219. Mobile: 99003 13742

Macromolecular Networks Containing Fluorinated Cyclic Moieties

Science.gov (United States)

2015-12-12

Briefing Charts 3. DATES COVERED (From - To) 17 Nov 2015 – 12 Dec 2015 4. TITLE AND SUBTITLE Macromolecular Networks Containing Fluorinated Cyclic... FLUORINATED CYCLIC MOIETIES 12 December 2015 Andrew J. Guenthner,1 Scott T. Iacono,2 Cynthia A. Corley,2 Christopher M. Sahagun,3 Kevin R. Lamison,4...Reinforcements Good Flame, Smoke, & Toxicity Characteristics Low Water Uptake with Near Zero Coefficient of Hygroscopic Expansion ∆ DISTRIBUTION A

Design and application of a C++ macromolecular class library.

Science.gov (United States)

Chang, W; Shindyalov, I N; Pu, C; Bourne, P E

1994-01-01

PDBlib is an extensible object oriented class library written in C++ for representing the 3-dimensional structure of biological macromolecules. PDBlib forms the kernel of a larger software framework being developed for assiting in knowledge discovery from macromolecular structure data. The software design strategy used by PDBlib, how the library may be used and several prototype applications that use the library are summarized. PDBlib represents the structural features of proteins, DNA, RNA, and complexes thereof, at a level of detail on a par with that which can be parsed from a Protein Data Bank (PDB) entry. However, the memory resident representation of the macromolecule is independent of the PDB entry and can be obtained from other back-end data sources, for example, existing relational databases and our own object oriented database (OOPDB) built on top of the commercial object oriented database, ObjectStore. At the front-end are several prototype applications that use the library: Macromolecular Query Language (MMQL) is based on a separate class library (MMQLlib) for building complex queries pertaining to macromolecular structure; PDBtool is an interactive structure verification tool; and PDBview, is a structure rendering tool used either as a standalone tool or as part of another application. Each of these software components are described. All software is available via anonymous ftp from cuhhca.hhmi.columbia.edu.

Simulation of a high energy neutron irradiation facility at beamline 11 of the China Spallation Neutron Source

Energy Technology Data Exchange (ETDEWEB)

Tairan, Liang [School of Physics and Electronic Information Inner Mongolia University for the Nationalities, Tongliao 028043 (China); Zhiduo, Li [Dongguan Branch, Institute of High Energy Physics, CAS, Beijing 100049 (China); Wen, Yin, E-mail: wenyin@aphy.iphy.ac.cn [Dongguan Branch, Institute of High Energy Physics, CAS, Beijing 100049 (China); Institute of Physics, CAS, P.O. Box 603, Beijing 100190 (China); Fei, Shen [Dongguan Branch, Institute of High Energy Physics, CAS, Beijing 100049 (China); Quanzhi, Yu [Dongguan Branch, Institute of High Energy Physics, CAS, Beijing 100049 (China); Institute of Physics, CAS, P.O. Box 603, Beijing 100190 (China); Tianjiao, Liang [Dongguan Branch, Institute of High Energy Physics, CAS, Beijing 100049 (China)

2017-07-11

The China Spallation Neutron Source (CSNS) will accommodate 20 neutron beamlines at its first target station. These beamlines serve different purposes, and beamline 11 is designed to analyze the degraded models and damage mechanisms, such as Single Event Effects in electronic components and devices for aerospace electronic systems. This paper gives a preliminary discussion on the scheme of a high energy neutron irradiation experiment at the beamline 11 shutter based on the Monte Carlo simulation method. The neutron source term is generated by calculating the neutrons scattering into beamline 11 with a model that includes the target-moderator-reflector area. Then, the neutron spectrum at the sample position is obtained. The intensity of neutrons with energy of hundreds of MeV is approximately 1E8 neutron/cm{sup 2}/s, which is useful for experiments. The displacement production rate and gas productions are calculated for common materials such as tungsten, tantalum and SS316. The results indicate that the experiment can provide irradiation dose rate ranges from 1E-5 to 1E-4 dpa per operating year. The residual radioactivity is also calculated for regular maintenance work. These results give the basic reference for the experimental design.

Characterising the large coherence length at diamond’s beamline I13L

Energy Technology Data Exchange (ETDEWEB)

Wagner, U. H., E-mail: ulrich.wagner@diamond.ac.uk; Parsons, A. [Diamond Light Source Ltd, Didcot, UK, OX11 0DE (United Kingdom); Rahomaki, J.; Vogt, U. [KTH Royal Institute of Technology, Stockholm, Sweden, SE-100 44 (Sweden); Rau, C. [Diamond Light Source Ltd, Didcot, UK, OX11 0DE (United Kingdom); Northwestern University, Chicago, IL 60611-3008 (United States)

2016-07-27

I13 is a 250 m long hard x-ray beamline (6 keV to 35 keV) at the Diamond Light Source. The beamline comprises of two independent experimental endstations: one for imaging in direct space using x-ray microscopy and one for imaging in reciprocal space using coherent diffraction based imaging techniques [1]. An outstanding feature of the coherence branch, due to its length and a new generation of ultra-stable beamline instrumentation [2], is its capability of delivering a very large coherence length well beyond 200 μm, providing opportunities for unique x-ray optical experiments. In this paper we discuss the challenges of measuring a large coherence length and present quantitative measurement based on analyzing diffraction patterns from a boron fiber [3]. We also discuss the limitations of this classical method in respect to detector performance, very short and long coherence lengths. Furthermore we demonstrate how a Ronchi grating setup [4] can be used to quickly establish if the beam is coherent over a large area.

Characterising the large coherence length at diamond’s beamline I13L

International Nuclear Information System (INIS)

Wagner, U. H.; Parsons, A.; Rahomaki, J.; Vogt, U.; Rau, C.

2016-01-01

I13 is a 250 m long hard x-ray beamline (6 keV to 35 keV) at the Diamond Light Source. The beamline comprises of two independent experimental endstations: one for imaging in direct space using x-ray microscopy and one for imaging in reciprocal space using coherent diffraction based imaging techniques [1]. An outstanding feature of the coherence branch, due to its length and a new generation of ultra-stable beamline instrumentation [2], is its capability of delivering a very large coherence length well beyond 200 μm, providing opportunities for unique x-ray optical experiments. In this paper we discuss the challenges of measuring a large coherence length and present quantitative measurement based on analyzing diffraction patterns from a boron fiber [3]. We also discuss the limitations of this classical method in respect to detector performance, very short and long coherence lengths. Furthermore we demonstrate how a Ronchi grating setup [4] can be used to quickly establish if the beam is coherent over a large area.

Solutions to mitigate heat loads due to electrons on sensitive components of ITER HNB beamlines

Energy Technology Data Exchange (ETDEWEB)

Sartori, Emanuele, E-mail: emanuele.sartori@gmail.com [Consorzio RFX (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), C.so Stati Uniti 4, 35127 Padova (Italy); Veltri, Pierluigi; Dalla Palma, Mauro; Agostinetti, Piero [Consorzio RFX (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), C.so Stati Uniti 4, 35127 Padova (Italy); Hemsworth, Ronald; Singh, Mahendrajit [ITER Organization, Route de Vinon sur Verdon, 13115 Saint Paul Lez Durance (France); Serianni, Gianluigi [Consorzio RFX (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), C.so Stati Uniti 4, 35127 Padova (Italy)

2016-11-01

Highlights: • Energetic electrons leaking out of the ITER HNB accelerator are simulated. • Electrons generated along the ITER HNB beamline are simulated. • Heat loads and heat load maps on cryopumps are calculated for ITER HNB and test facility. • Protection solutions that will be installed are presented and their effect discussed. - Abstract: The operation of neutral beam injectors for plasma heating and current drive in a fusion device provides challenges in the thermal management of beamline components. Sensitive components such as the cryogenic pumps at beamline periphery shall be protected from the heat flux due to stray electrons. These are emitted by the negative ion accelerator or generated along the beamline by interaction of fast electrons, ions or atoms with background gas and surfaces. In this article the case of the ITER Heating Neutral Beam (HNB) and its test facility MITICA is discussed, for which the beam parameters and the required pulse length of one hour is a major leap forward with respect to the present experience with neutral beam systems. The engineering solutions adopted for effective cryopump protection against the heat load from electrons are described. The use of three-dimensional numerical simulations of particle trajectories in the complex geometry of the beamline was needed for the quantitative estimations of the heat loads. The presented solutions were optimized to minimize the impact on gas pumping and on the functionality of other components.

Design and optimization of a compact laser-driven proton beamline.

Science.gov (United States)

Scisciò, M; Migliorati, M; Palumbo, L; Antici, P

2018-04-19

Laser-accelerated protons, generated by irradiating a solid target with a short, energetic laser pulse at high intensity (I > 10 18  W·cm -2 ), represent a complementary if not outperforming source compared to conventional accelerators, due  to their intrinsic features, such as high beam charge and short bunch duration. However, the broadband energy spectrum of these proton sources is a bottleneck that precludes their use in applications requiring a more reduced energy spread. Consequently, in recent times strong effort has been put to overcome these limits and to develop laser-driven proton beamlines with low energy spread. In this paper, we report on beam dynamics simulations aiming at optimizing a laser-driven beamline - i.e. a laser-based proton source coupled to conventional magnetic beam manipulation devices - producing protons with a reduced energy spread, usable for applications. The energy range of investigation goes from 2 to 20 MeV, i.e. the typical proton energies that can be routinely obtained using commercial TW-power class laser systems. Our beamline design is capable of reducing the energy spread below 20%, still keeping the overall transmission efficiency around 1% and producing a proton spot-size in the range of 10 mm 2 . We briefly discuss the results in the context of applications in the domain of Cultural Heritage.

MONO: A program to calculate synchrotron beamline monochromator throughputs

International Nuclear Information System (INIS)

Chapman, D.

1989-01-01

A set of Fortran programs have been developed to calculate the expected throughput of x-ray monochromators with a filtered synchrotron source and is applicable to bending magnet and wiggler beamlines. These programs calculate the normalized throughput and filtered synchrotron spectrum passed by multiple element, flat un- focussed monochromator crystals of the Bragg or Laue type as a function of incident beam divergence, energy and polarization. The reflected and transmitted beam of each crystal is calculated using the dynamical theory of diffraction. Multiple crystal arrangements in the dispersive and non-dispersive mode are allowed as well as crystal asymmetry and energy or angle offsets. Filters or windows of arbitrary elemental composition may be used to filter the incident synchrotron beam. This program should be useful to predict the intensities available from many beamline configurations as well as assist in the design of new monochromator and analyzer systems. 6 refs., 3 figs

Using the particle beam optics lab. (PBO LABtm) for beamline design and analysis

International Nuclear Information System (INIS)

Gillespie, G.H.; Hill, B.W.; Martono, H.; Moore, J.M.; Lampel, M.C.; Brown, N.A.

1999-01-01

The Particle Beam Optics Interactive Computer Laboratory (PBO Lab) represents a new approach to providing software for particle beam optics modeling. The PBO Lab includes four key elements: a graphic user interface shell; a graphic beamline construction kit for users to interactively and visually construct optical beam lines; a knowledge database on the physics and technology of optical elements, and various charged particle optics computational engines. A first-order matrix code, including a space charge model, can be used to produce scaled images of beamlines together with overlays of single trajectories and beam envelopes. The qualitative results of graphically sliding beamline components, or adjusting bend angles, can be explored interactively. Quantitative computational engines currently include the third-order TRANSPORT code and the multi-particle ray tracing program TURTLE. The use of the PBO Lab for designing and analyzing a second order achromatic bend is illustrated with the Windows 95/NT version of the software. (authors)

Considerations for a soft x-ray spectromicroscopy beamline

International Nuclear Information System (INIS)

Winn, B.; Hao, X.; Jacobsen, C.

1996-01-01

The X-1A soft x-ray undulator at the NSLS is the source for the experimental programs in spectromicroscopy. The authors require both spatial and temporal coherence. Due to the relatively large horizontal divergence of the electron beam in the low β straight section of the x-ray storage ring, it has been possible to split the beam using a scraping mirror into two branches: X-1A used by the authors' program and X-1B used for high resolution spectroscopy. They are now rebuilding the X-1A beamline to provide improved resolving power and essentially linear trade-off between photon rate at the zone plate and resolving power for the soft x-ray spectromicroscopy experiments. This new beamline will exploit both additional floorspace due to the NSLS building expansion and increases in the brightness of the x-ray ring. The beam will be further split into two separate beamlines, both of which will use toroidal mirrors to focus the source on the monochromator entrance slits horizontally and to focus on the monochromator exit slits vertically. This separation comes at no loss of coherent flux and permits low thermal loading on the optics, since the authors need little more than the coherent fraction of the beam at the Fresnel zone plate for microfocusing. Because of the small angular acceptance for spatially coherent illumination of the zone plates and the use of an approximately satisfied Rowland condition, the monochromators have sufficient resolving power with fixed exit arms. Experiments can then be placed near the exit slits, with spatial coherence established by the exit slit size. Resolving power will be controlled by adjusting the entrance slit alone with no change of spatial coherence. The zone plates will be overfilled to be less sensitive to beam vibration and drift

ELIMED, MEDical and multidisciplinary applications at ELI-Beamlines

International Nuclear Information System (INIS)

Schillaci, F; Anzalone, A; Cirrone, G A P; Cuttone, G; Musumarra, A; Pisciotta, P; Romano, F; Romano, F P; Carpinelli, M; Cutroneo, M; De Martinis, C; Giove, D; Korn, G; Maggiore, M; Margarone, D; Manti, L; Perozziello, F M; Petrovic, I; Ristic-Fira, A; Renis, M

2014-01-01

ELI-Beamlines is one of the pillars of the pan-European project ELI (Extreme Light Infrastructure). It will be an ultra high-intensity, high repetition-rate, femtosecond laser facility whose main goal is generation and applications of high-brightness X-ray sources and accelerated charged particles in different fields. Particular care will be devoted to the potential applicability of laser-driven ion beams for medical treatments of tumors. Indeed, such kind of beams show very interesting peculiarities and, moreover, laser-driven based accelerators can really represent a competitive alternative to conventional machines since they are expected to be more compact in size and less expensive. The ELIMED project was launched thanks to a collaboration established between FZU-ASCR (ELI-Beamlines) and INFN-LNS researchers. Several European institutes have already shown a great interest in the project aiming to explore the possibility to use laser-driven ion (mostly proton) beams for several applications with a particular regard for medical ones. To reach the project goal several tasks need to be fulfilled, starting from the optimization of laser-target interaction to dosimetric studies at the irradiation point at the end of a proper designed transport beam-line. Researchers from LNS have already developed and successfully tested a high-dispersive power Thomson Parabola Spectrometer, which is the first prototype of a more performing device to be used within the ELIMED project. Also a Magnetic Selection System able to produce a small pencil beam out of a wide energy distribution of ions produced in laser-target interaction has been realized and some preliminary work for its testing and characterization is in progress. In this contribution the status of the project will be reported together with a short description of the of the features of device recently developed.

Nanoflow electrospinning serial femtosecond crystallography

Science.gov (United States)

Sierra, Raymond G.; Laksmono, Hartawan; Kern, Jan; Tran, Rosalie; Hattne, Johan; Alonso-Mori, Roberto; Lassalle-Kaiser, Benedikt; Glöckner, Carina; Hellmich, Julia; Schafer, Donald W.; Echols, Nathaniel; Gildea, Richard J.; Grosse-Kunstleve, Ralf W.; Sellberg, Jonas; McQueen, Trevor A.; Fry, Alan R.; Messerschmidt, Marc M.; Miahnahri, Alan; Seibert, M. Marvin; Hampton, Christina Y.; Starodub, Dmitri; Loh, N. Duane; Sokaras, Dimosthenis; Weng, Tsu-Chien; Zwart, Petrus H.; Glatzel, Pieter; Milathianaki, Despina; White, William E.; Adams, Paul D.; Williams, Garth J.; Boutet, Sébastien; Zouni, Athina; Messinger, Johannes; Sauter, Nicholas K.; Bergmann, Uwe; Yano, Junko; Yachandra, Vittal K.; Bogan, Michael J.

2012-01-01

An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14–3.1 µl min−1 to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min−1 and diffracted to beyond 4 Å resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption. PMID:23090408

Radiation field characterization and shielding studies for the ELI Beamlines facility

Energy Technology Data Exchange (ETDEWEB)

Ferrari, A., E-mail: a.ferrari@hzdr.de [Institute of Radiation Physics, Helmholtz-Zentrum Dresden-Rossendorf, PF 510119, 01314 Dresden (Germany); Amato, E. [Department of Radiological Sciences, Messina University (Italy); Margarone, D. [ELI Beamlines Project, Institute of Physics of the ASCR, Na Slovance 2, 18221 Prague (Czech Republic); PALS Centre, Za Slovankou, 18200 Prague (Czech Republic); Cowan, T. [Institute of Radiation Physics, Helmholtz-Zentrum Dresden-Rossendorf, PF 510119, 01314 Dresden (Germany); Korn, G. [ELI Beamlines Project, Institute of Physics of the ASCR, Na Slovance 2, 18221 Prague (Czech Republic)

2013-05-01

The ELI (Extreme Light Infrastructure) Beamlines facility in the Czech Republic, which is planned to complete the installation in 2015, is one of the four pillars of the ELI European project. Several laser beamlines with ultrahigh intensities and ultrashort pulses are foreseen, offering versatile radiation sources in an unprecedented energy range: laser-driven particle beams are expected to range between 1 and 50 GeV for electrons and from 100 MeV up to 3 GeV for protons. The number of particles delivered per laser shot is estimated to be 10{sup 9}–10{sup 10} for the electron beams and 10{sup 10}–10{sup 12} for the proton beams. The high energy and current values of the produced particles, together with the potentiality to operate at 10 Hz laser repetition rate, require an accurate study of the primary and secondary radiation fields to optimize appropriate shielding solutions: this is a key issue to minimize prompt and residual doses in order to protect the personnel, reduce the radiation damage of electronic devices and avoid strong limitations in the operational time. A general shielding study for the 10 PW (0.016 Hz) and 2 PW (10 Hz) laser beamlines is presented here. Starting from analytical calculations, as well as from dedicated simulations, the main electron and proton fields produced in the laser-matter interaction have been described and used to characterize the “source terms” in full simulations with the Monte Carlo code FLUKA. The secondary radiation fields have been then analyzed to assess a proper shielding. The results of this study and the proposed solutions for the beam dumps of the high energy beamlines, together with a cross-check analysis performed with the Monte Carlo code GEANT4, are presented.

Guide to beamline radiation shielding design at the Advanced Photon Source

International Nuclear Information System (INIS)

Ipe, N.; Haeffner, D.R.; Alp, E.E.; Davey, S.C.; Dejus, R.J.; Hahn, U.; Lai, B.; Randall, K.J.; Shu, D.

1993-11-01

This document is concerned with the general requirements for radiation shielding common to most Advanced Photon Source (APS) users. These include shielding specifications for hutches, transport, stops, and shutters for both white and monochromatic beams. For brevity, only the results of calculations are given in most cases. So-called open-quotes special situationsclose quotes are not covered. These include beamlines with white beam mirrors for low-pass energy filters (open-quotes pink beamsclose quotes), extremely wide band-pass monochromators (multilayers), or novel insertion devices. These topics are dependent on beamline layout and, as such, are not easily generalized. Also, many examples are given for open-quotes typicalclose quotes hutches or other beamline components. If a user has components that differ greatly from those described, particular care should be taken in following these guidelines. Users with questions on specific special situations should address them to the APS User Technical Interface. Also, this document does not cover specifics on hutch, transport, shutter, and stop designs. Issues such as how to join hutch panels, floor-wall interfaces, cable feed-throughs, and how to integrate shielding into transport are covered in the APS Beamline Standard Components Handbook. It is a open-quotes living documentclose quotes and as such reflects the improvements in component design that are ongoing. This document has the following content. First, the design criteria will be given. This includes descriptions of some of the pertinent DOE regulations and policies, as well as brief discussions of abnormal situations, interlocks, local shielding, and storage ring parameters. Then, the various sources of radiation on the experimental floor are discussed, and the methods used to calculate the shielding are explained (along with some sample calculations). Finally, the shielding recommendations for different situations are given and discussed

Material failures observed in Doublet III neutral beamlines

International Nuclear Information System (INIS)

Bailey, E.W.; Colleraine, A.; Doll, D.; Grunloh, H.; Kim, J.; Langhorn, A.; Thurgood, B.

1983-12-01

The Doublet III neutral beam injectors consist of three separable spools two meters in diameter by four meters long overall when assembled. Contained within these spools are the neutralizers, ion dumps, deflecting magnet, calorimeter dumps, cryogenic panels and beam scraping collimators 3,7. To date three beamlines are in operation on Doublet III, and the beams have accumulated operating time of approximately 32 months, with the oldest having been in operation for 18 months. During this time operation of DIII with the neutral beam sources has demonstrated the following: 7.8 MW injected neutrals from three beamlines (6 sources), high β (4.5%), and non-circular plasma shape. The sources have also exhibited a very reliable injected shot history 4, 5, 6, 8. Material failures encountered during the operation of DIII N.B. injectors and the solutions to these failures are described. Failures include cracking of the neutralizer exit collimator due to heating cycles, failure of cyropanel support rods due to cooling cycles, failure of the sliding drive of the moveable calorimeter due to friction

A study on radiation shielding and safety analysis for a synchrotron radiation beamline

International Nuclear Information System (INIS)

Asano, Yoshihiro

2001-03-01

Methods of shielding design and safety analysis are presented for a beam-line of synchrotron radiation. This paper consists of the shielding and safety study of synchrotron radiation with extremely intense and low energy photon below several hundreds keV, and the study for the behavior of remarkable high-energy photons up to 8 GeV, which can creep into beam-lines. A new shielding design code, STAC8 was developed to estimate the leakage dose outside the beam line hutch (an enclosure of the beam, optical elements or experimental instruments) easily and quickly with satisfactory accuracy. The code can calculate consistently from sources of synchrotron radiation to dose equivalent outside hutches with considering the build up effect and polarization effect. Validity of the code was verified by comparing its calculations with those of Monte Carlo simulations and measurement results of the doses inside the hutch of the BL14C of Photon Factory in the High Energy Accelerator Research Organization (KEK), showing good agreements. The shielding design calculations using STAC8 were carried out to apply to the practical beam-lines with the considering polarization effect and clarified the characteristics of the typical beam-line of the third generation synchrotron radiation facility, SPring-8. In addition, the shielding calculations were compared with the measurement outside the shield wall of the bending magnet beam-line of SPring-8, and showed fairly good agreement. The new shielding problems, which have usually been neglected in shielding designs for existing synchrotron radiation facilities, are clarified through the analysis of the beam-line shielding of SPring-8. The synchrotron radiation from the SPring-8 has such extremely high-intensity involving high energy photons that the scattered synchrotron radiation from the concrete floor of the hutch, the ground shine, causes a seriously high dose. The method of effective shielding is presented. For the estimation of the gas

A study on radiation shielding and safety analysis for a synchrotron radiation beamline

Energy Technology Data Exchange (ETDEWEB)

Asano, Yoshihiro [Japan Atomic Energy Research Inst., Kansai Research Establishment, Synchrotron Radiation Research Center, Mikazuhi, Hyogo (Japan)

2001-03-01

Methods of shielding design and safety analysis are presented for a beam-line of synchrotron radiation. This paper consists of the shielding and safety study of synchrotron radiation with extremely intense and low energy photon below several hundreds keV, and the study for the behavior of remarkable high-energy photons up to 8 GeV, which can creep into beam-lines. A new shielding design code, STAC8 was developed to estimate the leakage dose outside the beam line hutch (an enclosure of the beam, optical elements or experimental instruments) easily and quickly with satisfactory accuracy. The code can calculate consistently from sources of synchrotron radiation to dose equivalent outside hutches with considering the build up effect and polarization effect. Validity of the code was verified by comparing its calculations with those of Monte Carlo simulations and measurement results of the doses inside the hutch of the BL14C of Photon Factory in the High Energy Accelerator Research Organization (KEK), showing good agreements. The shielding design calculations using STAC8 were carried out to apply to the practical beam-lines with the considering polarization effect and clarified the characteristics of the typical beam-line of the third generation synchrotron radiation facility, SPring-8. In addition, the shielding calculations were compared with the measurement outside the shield wall of the bending magnet beam-line of SPring-8, and showed fairly good agreement. The new shielding problems, which have usually been neglected in shielding designs for existing synchrotron radiation facilities, are clarified through the analysis of the beam-line shielding of SPring-8. The synchrotron radiation from the SPring-8 has such extremely high-intensity involving high energy photons that the scattered synchrotron radiation from the concrete floor of the hutch, the ground shine, causes a seriously high dose. The method of effective shielding is presented. For the estimation of the gas

The ELIMED transport and dosimetry beamline for laser-driven ion beams

Czech Academy of Sciences Publication Activity Database

Romano, F.; Schillaci, F.; Cirrone, G.A.P.; Cuttone, G.; Scuderi, Valentina; Allegra, L.; Amato, A.; Amico, A.; Candiano, G.; De Luca, G.; Gallo, G.; Giordanengo, S.; Guarachi, L.F.; Korn, Georg; Larosa, G.; Leanza, R.; Manna, R.; Marchese, V.; Marchetto, F.; Margarone, Daniele; Milluzzo, G.; Petringa, G.; Pipek, J.; Pulvirenti, S.; Rizzo, D.; Sacchi, R.; Salamone, S.; Sedita, M.; Vignati, A.

2016-01-01

Roč. 829, Sep (2016), s. 153-158 ISSN 0168-9002 R&D Projects: GA MŠk LQ1606; GA MŠk EF15_008/0000162; GA MŠk EE2.3.30.0057; GA ČR(CZ) GA15-02964S; GA MŠk ED1.1.00/02.0061 Grant - others:ELI Beamlines(XE) CZ.02.1.01/0.0/0.0/15_008/0000162; OP VK 4 POSTDOK(XE) CZ.1.07/2.3.00/30.0057; ELI Beamlines(XE) CZ.1.05/1.1.00/02.0061 Institutional support: RVO:68378271 Keywords : laser-driven beams * beam handling Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 1.362, year: 2016

AILES: the infrared and THz beamline on SOLEIL synchrotron radiation source

International Nuclear Information System (INIS)

Roy, P.; Brubach, J.B.; Rouzieres, M.; Pirali, O.; Kwabia Tchana, F.; Manceron, L.

2008-01-01

The development of a new infrared beamline (ligne de lumiere AILES) at the third generation Synchrotron Radiation source SOLEIL is underway. This beamline utilizes infrared synchrotron radiation from both the edge emission and the constant field conventional source. The expected performances including flux, spatial distribution of the photons, spectral range and stability are calculated and discussed. The optical system, spectroscopic stations and workspace are described. The calculation in the near field approach and the simulation by ray tracing show that the source with its adapted optics offers high flux and brilliance for a variety of infrared experiments. We also review the main research themes and the articulation and developments of the infrared sources at SOLEIL. (authors)

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

Science.gov (United States)

Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

2016-04-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

Salunke, Dr Dinakar Mashnu

Indian Academy of Sciences (India)

Fellow Profile. Elected: 2001 Section: General Biology. Salunke, Dr Dinakar Mashnu Ph.D. (IISc), FNASc, FNA, FTWAS. Date of birth: 1 July 1955. Specialization: Structural Biology, Macromolecular Crystallography and Immunology Address: Director, International Centre for Genetic Engineering, & Biotechnology, Aruna Asaf ...

Aberration analysis calculations for synchrotron radiation beamline design

International Nuclear Information System (INIS)

McKinney, W.R.; Howells, M.; Padmore, H.A.

1997-09-01

The application of ray deviation calculations based on aberration coefficients for a single optical surface for the design of beamline optical systems is reviewed. A systematic development is presented which allows insight into which aberration may be causing the rays to deviate from perfect focus. A new development allowing analytical calculation of line shape is presented

Macromolecular diffusion in crowded media beyond the hard-sphere model.

Science.gov (United States)

Blanco, Pablo M; Garcés, Josep Lluís; Madurga, Sergio; Mas, Francesc

2018-04-25

The effect of macromolecular crowding on diffusion beyond the hard-core sphere model is studied. A new coarse-grained model is presented, the Chain Entanglement Softened Potential (CESP) model, which takes into account the macromolecular flexibility and chain entanglement. The CESP model uses a shoulder-shaped interaction potential that is implemented in the Brownian Dynamics (BD) computations. The interaction potential contains only one parameter associated with the chain entanglement energetic cost (Ur). The hydrodynamic interactions are included in the BD computations via Tokuyama mean-field equations. The model is used to analyze the diffusion of a streptavidin protein among different sized dextran obstacles. For this system, Ur is obtained by fitting the streptavidin experimental long-time diffusion coefficient Dlongversus the macromolecular concentration for D50 (indicating their molecular weight in kg mol-1) dextran obstacles. The obtained Dlong values show better quantitative agreement with experiments than those obtained with hard-core spheres. Moreover, once parametrized, the CESP model is also able to quantitatively predict Dlong and the anomalous exponent (α) for streptavidin diffusion among D10, D400 and D700 dextran obstacles. Dlong, the short-time diffusion coefficient (Dshort) and α are obtained from the BD simulations by using a new empirical expression, able to describe the full temporal evolution of the diffusion coefficient.

Gas delivery system and beamline studies for the test beam facility of the Collider Detector at Fermilab

International Nuclear Information System (INIS)

Franke, H.G. III.

1987-12-01

A fixed-target test beam facility has been designed and constructed at the Meson Test (MT) site to support studies of components of the Collider Detector at Fermi National Accelerator Laboratory (CDF). I assisted in the design and constuction of the test beam facility gas delivery system, and I conducted the initial studies to document the ability of the MT beamline to meet the needs of CDF. Analysis of the preliminary performance data on MT beamline components and beam tunes at required particle energies is presented. Preliminary studies show that the MT beamline has the necessary flexibility to satisfy most CDF requirements now

Design of a dedicated beamline for THz coherent synchrotron radiation at UVSOR-III

International Nuclear Information System (INIS)

Kimura, Shin-ichi; Nakamura, Eiken; Imura, Keiichiro; Katoh, Masahiro; Hosaka, Masahito; Takahashi, Toshiharu

2012-01-01

We report the design of a THz beamline for coherent synchrotron radiation (CSR) at the UVSOR-III very-low-emittance synchrotron radiation light source. The emitted THz-CSR is collected by a three-dimensional 'magic mirror', which is a perfect collecting mirror for bending-magnet radiation with an acceptance angle of 288 mrad (H) × 80 mrad (V). A quasi-monochromatic THz-CSR with an average flux of 104 μW/0.1 % b.w. and a peak power of 120 nJ/pulse/0.1 % b.w. is expected at the beamline.

A Remote and Virtual Synchrotron Beamline

Science.gov (United States)

Jackson, J. M.; Alp, E.; Sturhahn, W.

2012-12-01

National facilities offer one-of-a-kind opportunities to apply state-of-the-art experimental techniques to the pressing scientific problems of today. Yet, few students are able to experience research projects at national facilities due to limited accessibility caused in part by limited involvement in the local academic institution, constrained working areas at the experimental stations, and/or travel costs. We present a virtual and remote beam-line for Earth science studies using nuclear resonant and inelastic x-ray scattering methods at Sector 3 of the Advanced Photon Source at Argonne National Laboratory. Off-site students have the capability of controlling their measurements via secure internet connections and webcams. Students can access a 'view only mode' for ease of interaction and safety-control. More experienced users have exclusive control of the experiment and can remotely change variables within the experimental setup. Students may also access the virtual aspects these experiments by simulating certain conditions with our newly developed software. We evaluate such a tool by giving "before" and "after" assignments to students at different levels. These levels include high-school students from the Pasadena and greater Los Angeles area school districts, undergraduate students from Caltech's SURF/MURF program, and graduate students at Caltech. We specifically target underrepresented groups. Our results thus far show that the capabilities offered by our remote and virtual beamline show improved knowledge and understanding of applying experimental-based studies at the synchrotron to solve problems in the Earth sciences.

CARNAÚBA: The Coherent X-Ray Nanoprobe Beamline for the Brazilian Synchrotron SIRIUS/LNLS

Science.gov (United States)

Tolentino, Hélio C. N.; Soares, Márcio M.; Perez, Carlos A.; Vicentin, Flávio C.; Abdala, Dalton B.; Galante, Douglas; Teixeira, Verônica de C.; de Araújo, Douglas H. C.; Westfahl, Harry, Jr.

2017-06-01

The CARNAÚBA beamline is the tender-to-hard X-ray (2 - 15 keV) scanning nanoprobe planned for the 4th generation storage ring SIRIUS at the LNLS. CARNAÚBA uses an undulator source with vertical linear polarization in a low-beta straight section and grazing incidence-focusing mirrors to create a nanoprobe at 143 m from the source. The beamline optic is based on KB mirrors and provides high brilliance at an achromatic focal spot down to the diffraction limit diameter of ˜30 nm with a working distance of ˜6 cm. These characteristics are crucial for studying nanometric samples in experiments involving complex stages and environments. The CARNAÚBA beamline aims to perform raster scans using x-ray fluorescence, x-ray absorption spectroscopy, x-ray diffraction and coherent x-ray imaging techniques. Computed tomography will extend these methods to three dimensions.

Ultrabroadband terahertz source and beamline based on coherent transition radiation

Directory of Open Access Journals (Sweden)

S. Casalbuoni

2009-03-01

Full Text Available Coherent transition radiation (CTR in the THz regime is an important diagnostic tool for analyzing the temporal structure of the ultrashort electron bunches needed in ultraviolet and x-ray free-electron lasers. It is also a powerful source of such radiation, covering an exceptionally broad frequency range from about 200 GHz to 100 THz. At the soft x-ray free-electron laser FLASH we have installed a beam transport channel for transition radiation (TR with the intention to guide a large fraction of the radiation to a laboratory outside the accelerator tunnel. The radiation is produced on a screen inside the ultrahigh vacuum beam pipe of the linac, coupled out through a diamond window and transported to the laboratory through an evacuated tube equipped with five focusing and four plane mirrors. The design of the beamline has been based on a thorough analysis of the generation of TR on metallic screens of limited size. The optical propagation of the radiation has been computed taking into account the effects of near-field (Fresnel diffraction. The theoretical description of the TR source is presented in the first part of the paper, while the design principles and the technical layout of the beamline are described in the second part. First experimental results demonstrate that the CTR beamline covers the specified frequency range and preserves the narrow time structure of CTR pulses emitted by short electron bunches.

Ultra-high performance mirror systems for the imaging and coherence beamline I13 at the Diamond Light Source

Science.gov (United States)

Wagner, U. H.; Alcock, S.; Ludbrook, G.; Wiatryzk, J.; Rau, C.

2012-05-01

I13L is a 250m long hard x-ray beamline (6 keV to 35 keV) currently under construction at the Diamond Light Source. The beamline comprises of two independent experimental endstations: one for imaging in direct space using x-ray microscopy and one for imaging in reciprocal space using coherent diffraction based imaging techniques. To minimise the impact of thermal fluctuations and vibrations onto the beamline performance, we are developing a new generation of ultra-stable beamline instrumentation with highly repeatable adjustment mechanisms using low thermal expansion materials like granite and large piezo-driven flexure stages. For minimising the beam distortion we use very high quality optical components like large ion-beam polished mirrors. In this paper we present the first metrology results on a newly designed mirror system following this design philosophy.

G4beamline Simulations for H8

CERN Document Server

Thoresen, Freja

2015-01-01

Detailed simulations of the H8 beam line at the North Area, using the G4beamline software were performed in the framework of this study. The conventions used by the program are analysed. Having modelled precisely the beam line, several studies examining the beam transmission and composition were performed. The results were compared with measurements, where a satisfactory agreement was found. The muon production and transport is studied in details throughout the beam line.

Successful test of SPS-to-LHC beamline

CERN Multimedia

Maximilien Brice

2004-01-01

On 23 October there was great excitement in the Prevessin control room when, on the first attempt, a beam passed over 2.5 km down the new SPS-to-LHC transfer line, TI8, to within a few metres of the LHC tunnel. Members of the AB, AT and TS departments involved in the beamline and its test, celebrate their success with the Director General, Robert Aymar, and the LHC Project Leader, Lyn Evans.

Successful test of SPS-to-LHC beamline

CERN Multimedia

2004-01-01

On 23 October there was great excitement in the Prevessin control room when, on the first attempt, a beam passed over 2.5 km down the new SPS-to-LHC transfer line, TI8, to within a few metres of the LHC tunnel. Above: members of the AB, AT and TS departments involved in the beamline and its test, celebrate their success with the Director General, Robert Aymar, and the LHC Project Leader, Lyn Evans.

A simple quantitative model of macromolecular crowding effects on protein folding: Application to the murine prion protein(121-231)

Science.gov (United States)

Bergasa-Caceres, Fernando; Rabitz, Herschel A.

2013-06-01

A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.

NSLS 2007 Activity Report (National Synchrotron Light Source Activity Report 2007)

Energy Technology Data Exchange (ETDEWEB)

Miller ,L.; Nasta, K.

2008-05-01

The National Synchrotron Light Source is one of the world's most productive and cost-effective user facilities. With 2,219 individual users, about 100 more than last year, and a record-high 985 publications, 2007 was no exception. In addition to producing an impressive array of science highlights, which are included in this Activity Report, many NSLS users were honored this year for their scientific accomplishments. Throughout the year, there were major strides in the development of the scientific programs by strengthening strategic partnerships with major research resources and with the Center for Functional Nanomaterials (CFN). Of particular note, the Consortium for Materials Properties Research in Earth Sciences (COMPRES) received renewed funding for the next five years through the National Science Foundation. COMPRES operates four high-pressure NSLS beamlines--X17B2, X17B3, X17C, and U2A--and serves the earth science community as well as the rapidly expanding segment of researchers using high-pressure techniques in materials, chemical, and energy-related sciences. A joint appointment was made between the NSLS and Stony Brook University to further enhance interactions with COMPRES. There was major progress on two key beamline projects outlined in the Five-Year Strategic Plan: the X25 beamline upgrade and the construction of the X9 small angle scattering (SAXS) beamline. The X25 overhaul, which began with the installation of the in-vacuum mini-gap undulator (MGU) in January 2006, is now complete. X25 is once again the brightest beamline for macromolecular crystallography at the NSLS, and in tandem with the X29 undulator beamline, it will keep the NSLS at the cutting edge in this important area of research. Upgrade work associated with the new MGU and the front end for the X9 SAXS beamline--jointly developed by the NSLS and the CFN--also was completed. Beamline X9 will host the SAXS program that currently exists at beamline X21 and will provide new microbeam

Simultaneous X-ray diffraction from multiple single crystals of macromolecules

DEFF Research Database (Denmark)

Paithankar, Karthik S.; Sørensen, Henning Osholm; Wright, Jonathan P.

2011-01-01

The potential in macromolecular crystallography for using multiple crystals to collect X-ray diffraction data simultaneously from assemblies of up to seven crystals is explored. The basic features of the algorithms used to extract data and their practical implementation are described. The procedure...

A Superbend X-Ray Microdiffraction Beamline at the Advanced Light Source

Energy Technology Data Exchange (ETDEWEB)

Tamura, N.; Kunz, M.; Chen, K.; Celestre, R.S.; MacDowell, A.A.; Warwick, T.

2009-03-10

Beamline 12.3.2 at the Advanced Light Source is a newly commissioned beamline dedicated to x-ray microdiffraction. It operates in both monochromatic and polychromatic radiation mode. The facility uses a superconducting bending magnet source to deliver an X-ray spectrum ranging from 5 to 22 keV. The beam is focused down to {approx} 1 um size at the sample position using a pair of elliptically bent Kirkpatrick-Baez mirrors enclosed in a vacuum box. The sample placed on high precision stages can be raster-scanned under the microbeam while a diffraction pattern is taken at each step. The arrays of diffraction patterns are then analyzed to derive distribution maps of phases, strain/stress and/or plastic deformation inside the sample.

Macromolecular crystallographic results obtained using a 2048x2048 CCD detector at CHESS

International Nuclear Information System (INIS)

Thiel, D.J.; Ealick, S.E.; Tate, M.W.; Gruner, S.M.; Eikenberry, E.F.

1996-01-01

We present results of macromolecular crystallographic experiments performed at the Cornell High Energy Synchrotron Source (CHESS) with a new CCD-based detector. This detector, installed in January 1995, complements a 1024x1024 CCD detector that has been in continuous operation at CHESS since December 1993. The new detector is based on a 4-port, 2048x2048 pixel CCD that is directly coupled to a Gd 2 O 2 S:Tb phosphor by a 3:1 tapered fiber optic. The active area of the phosphor is a square 82 mm on an edge. The readout time is 7 seconds. In the standard mode of operation, the pixel size at the active area is 41 μm on the edge leading to the capability of resolving approximately 200 orders of diffraction across the detector face. The detector also operates in a 1024x1024 mode in which the pixel size is electronically increased by a factor of 4 in area resulting in smaller data files and faster detector readout but at the expense of spatial resolution. Most of the data that has been collected by this detector has been collected in this mode. Dozens of data sets have been collected by many experimenters using this detector at CHESS during the four month period from its installation until the start of the six-month down period of the storage ring. The capabilities of the detector will be illustrated with results from various crystallographic measurements including experiments in which the recorded diffraction patterns extend in resolution as far as 1 A. The results demonstrate that this detector is capable of collecting data of quality at least equal to that of imaging plates but, in many circumstances, with much greater beamline efficiency. copyright 1996 American Institute of Physics

Beamline standard component designs for the Advanced Photon Source

International Nuclear Information System (INIS)

Shu, D.; Barraza, J.; Brite, C.; Chang, J.; Sanchez, T.; Tcheskidov, V.; Kuzay, T.M.

1994-01-01

The Advanced Photon Source (APS) has initiated a design standardization and modularization activity for the APS synchrotron radiation beamline components. These standard components are included in components library, sub-components library and experimental station library. This paper briefly describes these standard components using both technical specifications and side view drawings

Description and calibration beamline SEM/Ion Chamber Current Digitizer

International Nuclear Information System (INIS)

Schoo, D.

1994-05-01

This report discusses the following on beamline SEM/ion chamber current digitizers: Module description; testing and calibration; common setup procedures; summary of fault indications and associated causes; summary of input and output connections; SEM conversion constant table; ion chamber conversion constant table; hexadecimal to decimal conversion table; and schematic diagram

The CAT-ACT Beamline at ANKA: A new high energy X-ray spectroscopy facility for CATalysis and ACTinide research

Science.gov (United States)

Zimina, A.; Dardenne, K.; Denecke, M. A.; Grunwaldt, J. D.; Huttel, E.; Lichtenberg, H.; Mangold, S.; Pruessmann, T.; Rothe, J.; Steininger, R.; Vitova, T.

2016-05-01

A new hard X-ray beamline for CATalysis and ACTinide research has been built at the synchrotron radiation facility ANKA. The beamline design is dedicated to X-ray spectroscopy, including ‘flux hungry’ photon-in/photon-out and correlative techniques with a special infrastructure for radionuclide and catalysis research. The CAT-ACT beamline will help serve the growing need for high flux/hard X-ray spectroscopy in these communities. The design, the first spectra and the current status of this project are reported.

Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

Science.gov (United States)

Wan, Qun; Parks, Jerry M.; Hanson, B. Leif; Fisher, Suzanne Zoe; Ostermann, Andreas; Schrader, Tobias E.; Graham, David E.; Coates, Leighton; Langan, Paul; Kovalevsky, Andrey

2015-01-01

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen. PMID:26392527

National synchrotron light source. Activity report, October 1, 1995--September 30, 1996

Energy Technology Data Exchange (ETDEWEB)

Rothman, E.Z.; Hastings, J.B. [eds.

1997-05-01

The hard work done by the synchrotron radiation community, in collaboration with all those using large-scale central facilities during 1995, paid off in FY 1996 through the DOE`s Presidential Scientific Facilities Initiative. In comparison with the other DOE synchrotron radiation facilities, the National Synchrotron Light Source benefited least in operating budgets because it was unable to increase running time beyond 100%-nevertheless, the number of station hours was maintained. The major thrust at Brookhaven came from a 15% increase in budget which allowed the recruitment of seven staff in the beamlines support group and permitted a step increment in the funding of the extremely long list of upgrades; both to the sources and to the beamlines. During the December 1995 shutdown, the VUV Ring quadrant around U10-U12 was totally reconstructed. New front ends, enabling apertures up to 90 mrad on U10 and U12, were installed. During the year new PRTs were in formation for the infrared beamlines, encouraged by the investment the lab was able to commit from the initiative funds and by awards from the Scientific Facilities Initiative. A new PRT, specifically for small and wide angle x-ray scattering from polymers, will start work on X27C in FY 1997 and existing PRTs on X26C and X9B working on macromolecular crystallography will be joined by new members. Plans to replace aging radio frequency cavities by an improved design, originally a painfully slow six or eight year project, were brought forward so that the first pair of cavities (half of the project for the X-Ray Ring) will now be installed in FY 1997. Current upgrades to 350 mA initially and to 438 mA later in the X-Ray Ring were set aside due to lack of funds for the necessary thermally robust beryllium windows. The Scientific Facilities Initiative allowed purchase of all 34 windows in FY 1996 so that the power upgrade will be achieved in FY 1997.

The Postgraduate Study of Macromolecular Sciences at the University of Zagreb (1971-1980

Directory of Open Access Journals (Sweden)

Kunst, B.

2008-07-01

Full Text Available The postgraduate study of macromolecular sciences (PSMS was established at the University of Zagreb in 1971 as a university study in the time of expressed interdisciplinary permeation of natural sciences - physics, chemistry and biology, and application of their achievements in technologicaldisciplines. PSMS was established by a group of prominent university professors from the schools of Science, Chemical Technology, Pharmacy and Medicine, as well as from the Institute of Biology. The study comprised basic fields of macromolecular sciences: organic chemistry of synthetic macromolecules, physical chemistry of macromolecules, physics of macromolecules, biological macromolecules and polymer engineering with polymer application and processing, and teaching was performed in 29 lecture courses lead by 30 professors with their collaborators. PSMS ceased to exist with the change of legislation in Croatia in 1980, when the attitude prevailed to render back postgraduate studies to the university schools. During 9 years of existence of PSMS the MSci grade was awarded to 37 macromolecular experts. It was assessed that the PSMS some thirty years ago was an important example of modern postgraduate education as compared with the international postgraduate development. In concordance with the recent introduction of similar interdisciplinary studies in macromolecular sciences elsewhere in the world, the establishment of a modern interdisciplinary study in the field would be of importance for further development of these sciences in Croatia.

Synthesis and characterization of macromolecular rhodamine tethers and their interactions with P-glycoprotein.

Science.gov (United States)

Crawford, Lindsey; Putnam, David

2014-08-20

Rhodamine dyes are well-known P-glycoprotein (P-gp) substrates that have played an important role in the detection of inhibitors and other substrates of P-gp, as well as in the understanding of P-gp function. Macromolecular conjugates of rhodamines could prove useful as tethers for further probing of P-gp structure and function. Two macromolecular derivatives of rhodamine, methoxypolyethylene glycol-rhodamine6G and methoxypolyethylene glycol-rhodamine123, were synthesized through the 2'-position of rhodamine6G and rhodamine123, thoroughly characterized, and then evaluated by inhibition with verapamil for their ability to interact with P-gp and to act as efflux substrates. To put the results into context, the P-gp interactions of the new conjugates were compared to the commercially available methoxypolyethylene glycol-rhodamineB. FACS analysis confirmed that macromolecular tethers of rhodamine6G, rhodamine123, and rhodamineB were accumulated in P-gp expressing cells 5.2 ± 0.3%, 26.2 ± 4%, and 64.2 ± 6%, respectively, compared to a sensitive cell line that does not overexpress P-gp. Along with confocal imaging, the efflux analysis confirmed that the macromolecular rhodamine tethers remain P-gp substrates. These results open potential avenues for new ways to probe the function of P-gp both in vitro and in vivo.

Investigation of collisional effects within the bending magnet region of a DIII-D neutral beamline

International Nuclear Information System (INIS)

Kessler, D.N.; Hong, R.; Kellman, D.H.

1993-10-01

The region between the pole faces of the DIII-D neutral beamline residual ion bending magnets is an area of transient high gas pressure which may cause beam defocusing and increased heating of beamline internal components due to collisional effects. An investigation of these effects helps in understanding residual ion trajectories and in providing information for studying in the beamline capability for operation with increased pulse duration. Examination of collisional effects, and of the possible existence of space charge blow-up, was carried out by injecting deuterium gas into the region between the magnet pole faces with rates varying from 0 to 18 torr-ell/sec. Thermocouple and waterflow calorimetry data were taken to measure the beamline component heating and beam powder deposition on the magnet pole shields, magnet louvers, ion dump, beam collimators, and calorimeter. Data was also taken at gas flow rates varying from 0 to 25 torr-ell/sec into the neutralizer cell and is compared with the magnet region gas injection data obtained. Results show that both collisional effects and space charge blow-up play a role in magnet region component heating and that neutralizer gas flow sufficiently reduces component heating without incurring unacceptable power losses through collisional effects

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

Science.gov (United States)

Borbulevych, Oleg Y; Plumley, Joshua A; Martin, Roger I; Merz, Kenneth M; Westerhoff, Lance M

2014-05-01

Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein-ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

High precision mirror alignment mechanism for use in synchrotron radiation beamlines

International Nuclear Information System (INIS)

Verma, Adu; Srivastava, P.K.; Das, Suraj; Nookaraju, Mogali

2009-01-01

The performance of a synchrotron radiation beamline is highly depends on parameters, crucially on the manufacturing accuracies of the optical elements and very good alignment of optical elements in the beam path. To develop a synchrotron beamline the misalignment effects have to be estimated and the mechanical components that hold optical elements have to be designed and developed within the specified tolerance limits. The translational inaccuracies result in shifting the image spot, which affect the flux throughput. The misorientation errors i.e. the rotation of optical elements about their mean position affects the image quality. The horizontal misorientation i.e. the rotation of an optical element about an axis passing through its centre and perpendicular to the plane containing the mirror has the most sever effect on the spectral resolution of the beamline, because of an increase in the dispersive spot size at the image plane. The design development and testing of a high precision mirror alignment mechanism is reported in this abstract. Though this mirror alignment mechanism is developed for the X-ray diffraction beamline on synchrotron radiation source Indus-2, 2.5 GeV, 300 mA, the design is general purpose and can be adapted for any other synchrotron facility or a similar ultra high vacuum environment. The mirror alignment mechanism is based on a constrained kinematic chain which provides the angular motions about three co-ordinate axes in the range of 0 to ±1° with the backlash free resolution of 1 arc second. The linear motions in three orthogonal directions are performed by other kinematic mounts in the range of 0 to ± 10 mm with a fine adjustment of 10 μm. The motions are transferred from air to ultra high vacuum through bellows. The ultra high vacuum chamber has been designed, fabricated and tested as per the ASME code. The rotational motions of the mirror alignment mechanism has been tested using a laser interferometer. (author)

MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

Directory of Open Access Journals (Sweden)

Anthony R Bradley

2017-06-01

Full Text Available Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis.

Design of integral shutters for the beamlines at the Advanced Photon Source

International Nuclear Information System (INIS)

Chang, J.; Shu, D.; Nian, H.L.; Kuzay, T.M.; Job, P.K.

1994-01-01

An integral shutter is a device that integrates a white-beam stop, monochromatic-beam (mono-beam) shutters, a safety stop, and a collimator into one assembly to save space in the photon beamline. Various integral shutters have been developed as standard components for the beamlines at the Advanced Photon Source. The integral shutters are designed to be operated in white-beam mode or mono-beam mode. With regard to safety, each mode of operation is secured by locking certain devices in their up or down positions. Some of the components of the integral shutters share designs similar to the front-end shutters or fixed masks. Design details of the integral shutters are presented

Diffusion accessibility as a method for visualizing macromolecular surface geometry.

Science.gov (United States)

Tsai, Yingssu; Holton, Thomas; Yeates, Todd O

2015-10-01

Important three-dimensional spatial features such as depth and surface concavity can be difficult to convey clearly in the context of two-dimensional images. In the area of macromolecular visualization, the computer graphics technique of ray-tracing can be helpful, but further techniques for emphasizing surface concavity can give clearer perceptions of depth. The notion of diffusion accessibility is well-suited for emphasizing such features of macromolecular surfaces, but a method for calculating diffusion accessibility has not been made widely available. Here we make available a web-based platform that performs the necessary calculation by solving the Laplace equation for steady state diffusion, and produces scripts for visualization that emphasize surface depth by coloring according to diffusion accessibility. The URL is http://services.mbi.ucla.edu/DiffAcc/. © 2015 The Protein Society.

Contribution of X-ray crystallography in energy related problems

International Nuclear Information System (INIS)

Majid, C.A.; Hussain, M.A.

1995-01-01

Crystallography is concerned with the study of the structure of matter at the atomic level in condensed state. The great practical importance of scientific knowledge of the structure of solid is self evident when consideration is given to the definition of desired physical and chemical properties. The strength of steel girders, the corrosion of alloys, the plasticity of lime, the wearing properties of case hardness steel, the dielectric capacity of materials, the lubricating properties of long chain paraffin's or of graphite, the stretching of rubber and innumerable other practical phenomena of every day life depend upon ultimate structure of these materials. To understand function to control, manipulate and best utilize their properties, and to produce materials with properties meeting a desired set of specification it is essential to understand thoroughly both the characteristics and origin of each property. Origins of materials properties lie in a combination of natural laws with the detailed structure and composition of materials, i.e. the choice, location, bonding, etc. of every atom in the material object. Therefore, to understand their various properties, it is important to explore the structure property relationship in materials. X-ray crystallography is not only helping to develop new materials having desired properties, but also in improving existing materials. Radiation effects, electrolytes, superconductors and catalysts etc. are just a few examples of many areas where crystallography is helping. With the invent of new radiation sources like synchrotron and new detectors materials and techniques, this almost 80 years old discipline continues to capture the interest of solid state physicists and chemists alike. (author)

Geometrical layout and optics modelling of the surface science beamline station at the SESAME synchrotron radiation facility.

Science.gov (United States)

Salah, Wa'el; Sanchez del Rio, Manuel

2011-05-01

The layout and the optical performance of the SGM branch of the D09 bending-magnet beamline, under construction at SESAME, are presented. The beamline is based on the Dragon-type design and delivers photons over the spectral range 15-250 eV. One fixed entrance slit and a movable exit slit are used. The performance of the beamline has been characterized by calculating the mirror reflectivities and the grating efficiencies. The flux and resolution were calculated by ray-tracing using SHADOW. The grating diffraction efficiencies were calculated using the GRADIF code. The results and the overall shapes of the predicted curves are in reasonable agreement with those obtained using an analytical formula.

Local analysis of strains and rotations for macromolecular electron microscopy maps

Energy Technology Data Exchange (ETDEWEB)

Martin-Ramos, A.; Prieto, F.; Melero, R.; Martin-Benito, J.; Jonic, S.; Navas-Calvente, J.; Vargas, J.; Oton, J.; Abrishami, V.; Rosa-Trevin, J.L. de la; Gomez-Blanco, J.; Vilas, J.L.; Marabini, R.; Carazo, R.; Sorzano, C.O.S.

2016-07-01

Macromolecular complexes can be considered as molecular nano-machines that must have mobile parts in order to perform their physiological functions. The reordering of their parts is essential to execute their task. These rearrangements induce local strains and rotations which, after analyzing them, may provide relevant information about how the proteins perform their function. In this project these deformations of the macromolecular complexes are characterized, translating into a “mathematical language” the conformational changes of the complexes when they perform their function. Electron Microscopy (EM) volumes are analyzed using a method that uses B-splines as its basis functions. It is shown that the results obtained are consistent with the conformational changes described in their corresponding reference publications. (Author)

The current status of small-angle x-ray scattering beamline at Diamond Light Source

International Nuclear Information System (INIS)

Inoue, Katsuaki; Doutch, James; Terrill, Nick

2013-01-01

The small-angle X-ray scattering (SAXS) covers the major disciplines of biology, chemistry and physics delivering structural and dynamic information in nanoscience, mesoscopic architectures, supramolecular structures, and nucleation/growth of crystals. SAXS is also proving to be important in archaeological, environmental, and conservation sciences, and has further indicated its ability to span wide-ranging scientific disciplines. Thus, strong needs for SAXS studies are increasing significantly in a broad range of scientific fields year by year. Based on such a background, the demand for high throughput SAXS experiments is increasing. At the synchrotron facility, Diamond Light Source, one SAXS beamline, Non-crystalline diffraction I22 is now operational and highly automated throughput small-angle X-ray scattering (HATSAXS) beamline B21 is now under construction. I22 is the Undulator beamline and wide varieties of experiments, including time-resolved experiments are attempted. Based on the concept of HATSAXS, the key feature of B21 will focuses on the automation of end-station equipment. A automated sample changer has been purchased for solution SAXS measurements on biomolecules. A robotic-arm-type automated sample changer that is capable of handling several kinds of samples in material science is also being constructed. B21 is expected to successfully provide all users highly automated throughput measurements with the highest possible reliability and accuracy. Construction of this beamline will end in the second half of 2012, and will be open for users in the early summer of 2013 after commissioning. (author)

[Macromolecular aromatic network characteristics of Chinese power coal analyzed by synchronous fluorescence and X-ray diffraction].

Science.gov (United States)

Ye, Cui-Ping; Feng, Jie; Li, Wen-Ying

2012-07-01

Coal structure, especially the macromolecular aromatic skeleton structure, has a strong influence on coke reactivity and coal gasification, so it is the key to grasp the macromolecular aromatic skeleton coal structure for getting the reasonable high efficiency utilization of coal. However, it is difficult to acquire their information due to the complex compositions and structure of coal. It has been found that the macromolecular aromatic network coal structure would be most isolated if small molecular of coal was first extracted. Then the macromolecular aromatic skeleton coal structure would be clearly analyzed by instruments, such as X-ray diffraction (XRD), fluorescence spectroscopy with synchronous mode (Syn-F), Gel permeation chromatography (GPC) etc. Based on the previous results, according to the stepwise fractional liquid extraction, two Chinese typical power coals, PS and HDG, were extracted by silica gel as stationary phase and acetonitrile, tetrahydrofuran (THF), pyridine and 1-methyl-2-pyrollidinone (NMP) as a solvent group for sequential elution. GPC, Syn-F and XRD were applied to investigate molecular mass distribution, condensed aromatic structure and crystal characteristics. The results showed that the size of aromatic layers (La) is small (3-3.95 nm) and the stacking heights (Lc) are 0.8-1.2 nm. The molecular mass distribution of the macromolecular aromatic network structure is between 400 and 1 130 amu, with condensed aromatic numbers of 3-7 in the structure units.

The quality assessment of radial and tangential neutron radiography beamlines of TRR

International Nuclear Information System (INIS)

Dastjerdi, M.H. Choopan; Movafeghi, A.; Khalafi, H.; Kasesaz, Y.

2017-01-01

To achieve a quality neutron radiographic image in a relatively short exposure time, the neutron radiography beam must be of good quality and relatively high neutron flux. Characterization of a neutron radiography beam, such as determination of the image quality and the neutron flux, is vital for producing quality radiographic images and also provides a means to compare the quality of different neutron radiography facilities. This paper provides a characterization of the radial and tangential neutron radiography beamlines at the Tehran research reactor. This work includes determination of the facilities category according to the American Society for Testing and Materials (ASTM) standards, and also uses the gold foils to determine the neutron beam flux. The radial neutron beam is a Category I neutron radiography facility, the highest possible quality level according to the ASTM. The tangential beam is a Category IV neutron radiography facility. Gold foil activation experiments show that the measured neutron flux for radial beamline with length-to-diameter ratio (L/D) =150 is 6.1× 10 6 n cm −2 s −1 and for tangential beamline with (L/D)=115 is 2.4× 10 4 n cm −2 s −1 .

CERN announces the fourth annual Beamline for Schools competition

CERN Multimedia

BL4S team

2016-01-01

CERN is pleased to announce the fourth annual Beamline for Schools (BL4S) competition. Once again, in 2017, a fully equipped beamline will be made available at CERN for students. As in previous years, two teams will be invited to the Laboratory to execute the experiments they proposed in their applications. The 2017 competition is being made possible thanks to support from the Alcoa Foundation for the second consecutive year.   The competition is open to teams of high-school students aged 16 or older who, if they win, are invited (with two supervisors) to CERN to carry out their experiment. Teams must have at least five students but there is no upper limit to a team’s size (although just nine students per winning team will be invited to CERN). Teams may be composed of pupils from a single school, or from a number of schools working together. As science-loving mega-celebrity Will.I.Am told us: “If you’re interested in science, technology, engineering or ...

In situ beamline analysis and correction of active optics.

Science.gov (United States)

Sutter, John; Alcock, Simon; Sawhney, Kawal

2012-11-01

At the Diamond Light Source, pencil-beam measurements have enabled long-wavelength slope errors on X-ray mirror surfaces to be examined under ultra-high vacuum and beamline mounting without the need to remove the mirror from the beamline. For an active mirror an automated procedure has been implemented to calculate the actuator settings that optimize its figure. More recently, this in situ pencil-beam method has been applied to additional uses for which ex situ measurements would be inconvenient or simply impossible. First, it has been used to check the stability of the slope errors of several bimorph mirrors at intervals of several weeks or months. Then, it also proved useful for the adjustment of bender and sag compensation actuators on mechanically bent mirrors. Fits to the bending of ideal beams have been performed on the slope errors of a mechanically bent mirror in order to distinguish curvatures introduced by the bending actuators from gravitational distortion. Application of the optimization procedure to another mechanically bent mirror led to an improvement of its sag compensation mechanism.

Material failures observed in the Doublet III neutral beamlines

International Nuclear Information System (INIS)

Bailey, E.W.; Colleraine, A.; Doll, D.; Grunloh, H.; Kim, J.; Langhorn, A.; Thurgood, B.

1983-01-01

The Doublet III neutral beam injectors consist of three separable spools two meters in diameter by four meters long overall when assembled. Contained within these spools are the neutralizers, ion dumps, deflecting magnet, calorimeter dumps, cryogenic panels and beam scraping collimators. To date three beamlines are in operation on Doublet III, and the beams have accumulated operating time of approximately 32 months, with the oldest having been in operation for 18 months. During this time operation of DIII with the neutral beam sources has demonstrated the following: 7.8 MW injected neutrals from three beamlines (6 sources), high β (4.5%), and non-circular plasma shape. The sources have also exibited a very reliable injected shot history. Material failures encountered during the operation of DIII N.B. injectors and the solutions to these failures are described. Failures include cracking of the neutralizer exit collimator due to heating cycles, failure of cyropanel support rods due to cooling cycles, failure of the sliding drive of the moveable calorimeter due to friction

Mirror and grating surface figure requirements for grazing incidence synchrotron radiation beamlines: Power loading effects

Energy Technology Data Exchange (ETDEWEB)

Hulbert, S.L.; Sharma, S.

1987-01-01

At present, grazing incidence mirrors are used almost exclusively as the first optical element in VUV and soft x-ray synchrotron radiation beamlines. The performance of these mirrors is determined by thermal and mechanical stress-induced figure errors as well as by figure errors remaining from the grinding and polishing process. With the advent of VUV and soft x-ray undulators and wigglers has come a new set of thermal stress problems related to both the magnitude and the spatial distribution of power from these devices. In many cases the power load on the entrance slits and gratings in these beamlines is no longer negligible. The dependence of thermally-induced front-end mirror figure errors on various storage ring and insertion device parameters (especially those at the National Synchrotron Light Source) and the effects of these figure errors on two classes of soft x-ray beamlines are presented.

Operation of the Australian Store.Synchrotron for macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Meyer, Grischa R. [Monash University, Clayton, Victoria 3800 (Australia); Aragão, David; Mudie, Nathan J.; Caradoc-Davies, Tom T. [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia); McGowan, Sheena; Bertling, Philip J.; Groenewegen, David; Quenette, Stevan M. [Monash University, Clayton, Victoria 3800 (Australia); Bond, Charles S. [The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia (Australia); Buckle, Ashley M. [Monash University, Clayton, Victoria 3800 (Australia); Androulakis, Steve, E-mail: steve.androulakis@monash.edu [Monash Bioinformatics Platform, Monash University, Clayton, Victoria 3800 (Australia)

2014-10-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

Operation of the Australian Store.Synchrotron for macromolecular crystallography

International Nuclear Information System (INIS)

Meyer, Grischa R.; Aragão, David; Mudie, Nathan J.; Caradoc-Davies, Tom T.; McGowan, Sheena; Bertling, Philip J.; Groenewegen, David; Quenette, Stevan M.; Bond, Charles S.; Buckle, Ashley M.; Androulakis, Steve

2014-01-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community

Operation of the Australian Store.Synchrotron for macromolecular crystallography.

Science.gov (United States)

Meyer, Grischa R; Aragão, David; Mudie, Nathan J; Caradoc-Davies, Tom T; McGowan, Sheena; Bertling, Philip J; Groenewegen, David; Quenette, Stevan M; Bond, Charles S; Buckle, Ashley M; Androulakis, Steve

2014-10-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

On R factors for dynamic structure crystallography

DEFF Research Database (Denmark)

Coppens, Philip; Kaminski, Radoslaw; Schmøkel, Mette Stokkebro

2010-01-01

In studies of dynamic changes in crystals in which induced metastable species may have lifetimes of microseconds or less, refinements are most sensitive if based on the changes induced in the measured intensities. Agreement factors appropriate for such refinements, based on the ratios of the inte...... of the intensities before and after the external perturbation is applied, are discussed and compared with R factors commonly applied in static structure crystallography....