Multidisciplinary Applications and Perspectives

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The following specific topics will be included:

• Fundamentals of Synchrotron & FEL Radiation
• X-ray Absorption, Scattering, and Diffraction with Synchrotrons & FELs;
and Applications
• Soft and hard X-ray Photoemission with Synchrotrons & FELs;
and Applications
• X-ray Microscopy and Imaging with Synchrotrons & FELs;
and Applications
• Multicolor Experiments, Transient States of Matter under Extreme Conditions and Ultrafast Dynamics

Invited Speakers

• Ian K. Robinson (Imperial College London, UK)
• Marcus C. Newton (University of Southampton, UK)
• Oleg Shpyrko (University of California San Diego, USA)
• Ross Harder (Argonne National Laboratory/APS, USA)
• Virginie Chamard (Aix-Marseille University, France)
• Yukio Takahashi (Osaka University, Japan)

Recently the National Synchrotron Radiation Research Center (NSRRC) has successfully constructed Taiwan Photon Source (TPS), a low-emittance 3 GeV synchrotron light source. The 7 phase-I beamlines at the TPS will soon be available to users and be able to demonstrate their wide variety of applications. Three of them, Coherent X-ray Scattering, Soft X-ray Scattering beamline and X-ray Nanoprobe beamlines, are designed for X-ray coherent experiments. Bragg Coherent Diffractive Imaging (CDI) has become an emerging tool for the forefront research of nano-scaled science owing to the advances of high-brilliance synchrotron sources and X-ray free-electron laser techniques. For example, many scientific results such as probes of static defects and operando dislocation imaging have been successfully demonstrated. The two-day scientific program of 2016 International Workshop on Bragg CDI will focus on the basics and latest applications of coherent X-ray on materials analysis. We also hope that the workshop will facilitate ample discussion for the new scientific opportunities at the TPS.

We are happy to announce VI-th National Crystallographic Symposium (NCS2016) that will be held on October 05-07, 2016, Sofia, Bulgaria.

As you may have already recognized this is will be the sixth "NCS" of the series started in 2009.

We have already started the preparation of the next issue of the conference (submitted manuscripts will be published in the journal “Bulgarian Chemical Communications”, a special issues due April 2017).NCS16 papers will also be online available in full text via the present platform.  You are warmly invited to come and join us!

NCS2016 is held under the auspices of BCS and is the major event on Crystallography, crystal growth, structure analyses and related techniques in Bulgaria. The Symposium aims at the applications of different crystallographic techniques in combination with other methods in the fields of materials sciences, mineralogy, biology, environmental engineering, computational methods etc. Bringing together researchers from different areas NCS16 will provide them with a high-qualified platform for them to share their latest studies and to assist further findings and collaboration.

With passionate participants from the world, NCS2016 Â would be perfect for you to present your research and find collaboration for your future work.

This is a Workshop of the 66th Annual Meeting of the American Crystallographic Association.

Description:

Time resolved pump-probe SFX studies additionally benefit from the use of tiny crystals because they are smaller than the extinction length of a pump laser, while in current state-of-the-art pump-probe experiments at synchrotrons, typically only 10-40% of molecules in a fixed sample are photoactivated. Non-photoactive molecules with reactions initiated by chemical/physical changes such as temperature, pH, or reactants (e.g. introduced via a mixing jet) also benefit from using microcrystals because of higher diffusion rates in nano- and microcrystals. In SFX, nano/microcrystals are delivered to the pulsed X-ray beam by either a micron-thick liquid jet (most commonly), a recently invented lipidic cubic phase (LCP) jet, electrospray, or by raster scanning fixed target supports. At LCLS, the X-ray pulses arrive at 120 Hz (with much higher rates planned for future XFELs), resulting in huge data sets that need to be efficiently filtered and cleaned. Each diffraction pattern is corrected, cleaned and indexed independently, before the data set is merged. Thousands of diffraction patterns, and hence, crystals, are needed for a full data set.

For time resolved studies, thousands of randomly oriented patterns are needed for each time point. Indeed, a single experiment can result in over 100 terabytes of raw data. These high data collection rates and large data sets have necessitated the development of novel high-throughput, parallelizable data analysis software for "live" feedback during an SFX experiment, as well as for further processing of the clean diffraction patterns. Since the diffraction patterns consist almost entirely of partial reflections, complicated post-refinement/scaling procedures are necessary to reduce the amount of data required to obtain accurate structure factors. A number of post refinement methods are being developed in SFX analysis software, and will be discussed during the workshop.

Synchrotrons and future XFELs - rapidly growing SFX user base.

Technological advances at synchrotron sources, producing smaller, brighter beams, coupled with new detectors (e.g. pixel array detectors running in shutterless mode) and novel crystal delivery devices have enabled the collection of SFX data from microcrystals at synchrotrons. Synchrotron SFX experiments include studies of in vivo grown needle-shaped crystals (helically scanned to avoid radiation damage) and

LCP-SFX of membrane protein crystals in room temperature, in air. Initial LCP-SFX studies at LCLS yielded the first room temperature GPCR structure (from a few hundred micrograms of purified protein), but the recently demonstrated synchrotron based LCP-SFX (still at room temperature) is an even more exciting result for these biomedically important proteins in large part because of the availability of high end MX synchrotron beamlines.

In summary, SFX has yielded several major and unique advances in structural biology previously unattainable with conventional technologies, including the potential for sub-picosecond time-resolved crystallographic studies, probing cyclic or even non-cyclic reactions. With the construction of more than a dozen new XFELs currently under way, and the growing use of serial crystallography at synchrotrons, the potential user base is growing significantly. The development and appropriate use of new software to tackle the unique problems of SFX data analysis is vital to making SFX practicable. It is our desire and responsibility to share the knowledge and experience from early SFX experiments, and train a new generation of scientists in SFX data analysis to make this exciting new technique even more accessible to the crystallographic community. We anticipate that the impact of SFX on (dynamical) structural biology will ultimately be immense.

The workshop will start with an introductory seminar, followed by most of the day dedicated to detailed hands-on tutorials with data sets collected at LCLS using the software suites Cheetah and CrystFEL, two of the most commonly used packages for SFX analysis. All the concepts unique to SFX that we will be discussing are software independent.

The workshop outline is as follows:

1. An introduction to serial femtosecond crystallography and how the data differ from conventional crystallography data.

2. Cheetah tutorial: From raw data to useful diffraction patterns.

The first tutorial session will focus on Cheetah (www.desy.de/~barty/cheetah), and will involve the initial analysis and reduction of raw data to a set of clean, usable diffraction patterns in a facility-independent format (HDF5) for further analysis.

In addition to running the software, a major focus will be optimizing this process to retain the best data. Several data sets (of varying quality) collected at LCLS will be used to detail the steps from data collection to data analysis. Relevant details about LCLS data storage formats and procedures will be described. Detector considerations (geometry calibration and signal corrections) will be discussed and students will be shown how to accurately determine detector geometry, a critical component of successful indexing. Spot finding algorithms will be described and students will have the opportunity to experiment with various parameters to learn the best practices for optimization. Tips and tricks for analyzing and for evaluating the success of a set of parameters will be explained.

We will discuss and demonstrate how to generate virtual powder patterns, radial stacks, histograms of various hit finding statistics, extract the spectrum of each XFEL shot, record pump laser profiles and other pertinent metadata.

Cheetah is open-source and has been released under the GNU GPL v3 license. Though designed for XFEL experiments (both for SFX and single particle / solution scattering), Cheetah can be readily adapted for use where parallelized diffraction data reduction and detector correction is necessary. Its modular, facility-independent library makes Cheetah portable and expandable to use with new detectors, and data type and formats.

3. CrystFEL tutorial: Indexing, integrating, merging, post-refinement and evaluation of serial crystallography data.

The second tutorial session will focus on indexing, integrating and merging the cleaned SFX data using CrystFEL, a software suite created for SFX data analysis (and simulation). The development of CrystFEL is lead by Thomas White (CFEL, DESY), who will be the main instructor for this tutorial, with hands-on support for students from the workshop organizers experienced with CrystFEL: Grant and Zatsepin. The suite is written in C with supporting Perl and shell scripts, and is available as source code under version 3 or later of the GNU General Public License.

At the core of CrystFEL is an automated, high throughput processing pipeline which indexes and integrates each diffraction pattern in a serial crystallography data set. Merging the results yields diffraction data which can be imported into standard crystallographic processing packages for further analysis.

We will describe in what way indexing algorithms differ from conventional crystallography for snapshots from randomly oriented microcrystals, and show students how to optimize indexing parameters to extract the most accurate structure factors from the data. We will show how variations in physical crystal features such as size and unit cell parameters may affect spot shape and intensity and how that influences integration routines. We will discuss how the XFEL spectrum affects SFX data, and how to optimize integration parameters. Methods of evaluating successful integration will also be shown. Detailed descriptions of proper merging procedures will be discussed, as well as how to deal with influencing factors such as scaling, partiality of reflections, detector saturation and more. We will also show students how to determine and evaluate multiple parameters for measuring the quality of the merged data, including signal to noise and multiplicity, and internal consistency quantified by Rsplit and CC1/2.

XFEL pulses generated by self amplified spontaneous emission (SASE) differ in spectrum and intensity from shot to shot. Meanwhile, each crystals, arriving in a random orientation and position relative to the X-ray pulse, may differ in size and shape. Accurate structure factors can be obtained from merging diffraction data from thousands of snapshots collected in this manner by Monte Carlo integration (which we will discuss in the workshop), with accuracy increasing with 1/sqrt(number of patterns). Much development is now dedicated from multiple SFX data analysis developers to post refinement methods that move SFX analysis "beyond Monte Carlo" to a regime where more accurate structures can be obtained from much smaller data sets (significantly reducing sample consumption) by modeling and refining the experimental parameters that fluctuate from shot to shot.

Anomalous signals for de novo phasing (single or multi-wavelength anomalous diffraction) can be enhanced by combining data sets from multiple crystals. De novo SAD phasing from SFX data has also been demonstrated (though not optimized). We will touch upon these topics in the discussions on data quality, post refinement and heterogeneity.

Additional time will be spent discussing how to deal with SFX analysis problems such as resolving the indexing ambiguity arising from the uncorrelated orientations of diffraction snapshots for particular space groups, considering heterogeneity between crystals, dealing with weak diffraction and indexing multiple lattices. Finally, students will be shown how to import their results into standard crystallographic processing packages for further analysis. At each stage students will be encouraged to ask questions and instructors will be available for help.

Computational resources and workshop preparation for students

SFX data reduction and analysis requires high-performance computational resources. Fortunately, SLAC's computational infrastructure has been designed for high-throughput data analysis with the Cheetah and CrystFEL pre-installed. Students will be expected to bring laptops with appropriate software preinstalled for connecting to SLAC via SSH. Students will be sent detailed information prior to the workshop to request access to SLAC computational resources and other instructions for testing software installations and connections. This format worked well for our previous workshop and students were able to quickly connect and use SLAC's computing resources without any appreciable delay. A website will be set up prior to the workshop with useful instructions and publications for workshop preparation. On-site network connectivity will be provided as part of the course. The data used in the workshops will be SFX data collected at LCLS that is publicly available on the Coherent X-ray Imaging Data Bank (cxidb.org). All of the data will be stored and analysis performed on SLAC computers; only text and images will be sent over the network. X-window forwarding will be required to interact with software GUIs, which will require a moderate network connection. Our previous workshop provided ethernet connectivity for individuals to provide the necessary bandwidth for the network traffic, with some students using WiFi, and proved to be sufficient.

Participants will be presumed to have some basic knowledge of conventional crystallographic data analysis such as what indexing, integration, and merging are and will instead focus on the specific features of SFX analysis, as described above.

The workshop will begin at 9:00am and end at approx. 5:00pm. Lunch will be provided. Preregistration and payment is required.

Fees:

• Students and postdocs - $100
• Academics others - $150
• Corporate - $250

This workshop is organized by the BioXFEL Science and Technology Center established by the National Science Foundation in 2013, committed to the development of XFEL science for the analysis of biological systems.

Contact:

Tom Grant
tgrant@hwi.buffalo.edu
716-898-8675
Hauptman-Woodward Institute, 700 Ellicott Street, Buffalo, NY 14203

Nadia Zatsepin
nadia.zatsepin@asu.edu
480-727-6364
Arizona State University, Physics Department, Center for Biological Physics, Tempe, AZ 85287-1504

9th annual CCP4 USA Crystallography School organized jointly with the National Institute of General Medical Sciences and National Cancer Institute Structural Biology Facility at the Advanced Photon Source (GM/CA@APS).

Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used.
Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections â€" lectures, tutorials, and hands-on, interactive trouble-shooting.
There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions.

Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 21.

Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses.

UXSS 2016 is a four day program hosted by Stanford University's PULSE Institute at SLAC National Accelerator Laboratory. UXSS 2016 is organized in collaboration with the Center for Free-Electron Laser Science at DESY in Hamburg, Germany.

The goal of UXSS 2016 is to disseminate information and train students and post-docs on new opportunities in ultrafast science, particularly using X-ray Free Electron Lasers. Lectures will be presented by expert scientists in this exciting new field. The attendees will be expected to participate in the discussions and will prepare a mock beamtime proposal poster with input from the instrument scientist for the Linac Coherent Light Source.

Speaker List

• Steve Johnson (ETH Zurich)
• Matthias Fuchs (University of Nebraska, Lincoln)
• Nora Berrah (University of Connecticut)
• Louis Di Mauro (Ohio State University)
• Sigfried Glenzer (SLAC National Accelerator Laboratory)
• Agostino Marinelli (SLAC National Accelerator Laboratory)
• Philippe Wernet (Helmholtz Zentrum Berlin)
• Ian Robinson (University College London)

This workshop is the successor to four previous successful workshops, which took place in 2007, 2009, 2011 and 2013. It is sponsored by the German Society for Crystallography (DGK) and organised in cooperation with the DGK Working Group 1 (Biological Structures).

The workshop comprises a series of basic lectures on the topic and two
extended practical sessions. It is aimed at PhD students in Biological Crystallography with little or no experience in diffraction data collection at a synchrotron. The practical sessions will take place at the MX beamlines located at the electron storage ring BESSY II.

The workshop fee is 80 EUR for DGK-members and 100 EUR for non-members. This fee covers all conference material as well as board and lodging for two nights on the campus in Berlin-Adlershof.

Registration is now open. Since the number of students will have to belimited to 20 in order to ensure that the practical sessions run efficiently, we expect that the workshop will fill up quickly. Participants are also expected to present a poster on their own work. As previously, the best poster will be awarded with an attractive prize.

We are organizing, for the fifth consecutive year, a science summer school to attract more undergraduate students in science especially in subjects related to large scale facilities.

This school will take place in Grenoble-France within the Université Grenoble Alpes (previously Université Joseph Fourier)

The program is six weeks long, with a 45 hours French course including cultural visits and a 60 hours scientific course taught in English.

Three scientific courses are available among which ''Introduction to large scale facilities: probing matter with synchrotron and neutron radiation''.Â

This course will consist of lectures, tutorials and practicals, as well as visits of ILL and ESRF. Students are welcome to participate.

For partner universities, the tuition fees are only 500 €.

Grants associated with a research institute in Grenoble may also be available for the best students willing to spend a couple of weeks until the end of July in a research environment.

Application deadline: 16th of March

The school will be held at the Centre for Free-Electron Laser Science at DESY

Prof. Carmelo Giacovazzo will give a full week of lectures on the basics
of crystallography and modern phasing methods in protein crystallography.
The course will cover mathematical understanding of crystallographic point
and space groups, systematic absences, diffraction experiments, structure
factor calculations, and other related topics. Besides the lectures, there
will be talks on applications of protein crystallography using advanced
light sources, such as 3rd generation synchrotron and X-ray Free Electron
Lasers (FELs). The course is aimed at PhD students working in the field of
crystallography, but exceptions can be made for motivated PostDocs and MSc
students. This will NOT be a workshop covering protein crystallographic
programs.

Speakers: Prof. Carmelo Giacovazzo (University of Bari), Prof. Henry Chapman (CFEL / DESY, University of Hamburg), Prof. Arwen Pearson (CUI, University of Hamburg), Dr Thomas White (CFEL / DESY), Dr Adrian Mancuso (XFEL.eu), Dr Thomas Schneider (EMBL), Gleb Bourenkov (EMBL), more TBA

Besides the lessons there will be guided tours of PETRAIII/European XFEL, a BBQ and a harbor boat trip scheduled.

The registration fee is 100 EUR per person, and includes coffee breaks and
lunch.

Applicants must(!) provide a motivation letter and a CV, directly to the
organizer Max Wiedorn (max.wiedorn@cfel.de). The number of participants is
limited to 35. Accommodations can be made at the DESY Guest House: 70 EUR per person for 7 nights (28.05 - 04.06.2016).

This scattering workshop is for those with an interest in soft condensed matter as found in biology, polymer science, the colloidal domain and interfacial science.

The workshop has some leading experimentalists giving tutorials on light scattering, small-angle scattering, grazing incidence scattering, pulsed field gradient NMR and reflectivity.

We will also host a small number of science talks but the primary focus of the meeting is to introduce researchers to a range of scattering techniques, with emphasis on their application to research in soft matter.

The workshop will be held at RMIT University's Melbourne city campus from the 11th to the 12th of Feb. Attendance is free but registration is necessary. There is some support available for students to attend the meeting from Australia and New Zealand.

Organisers: Dr Chris Garvey (cjg@ansto.gov.au) or Prof Gary Bryant (gary.bryant@rmit.edu.au)

The European XFEL Users' Meeting is an annual opportunity to strengthen the interaction between the European XFEL project and the scientific user community. The scope of this meeting includes:

• Progress and current status of the European XFEL
• Instrument design developments & advances
• Selected science applications
• Current developments in the field of XFEL facilities

Satellite meetings/workshops

Sample Environments for Biology at XFELs: 26th January 2016

From Picoseconds to Femtosecond X-Ray Experiments: 26th January 2016

4th Satellite Workshop on Photon Beam Diagnostics: 28th January 2016

Status and Science at HED instrument and of the HIBEF UC: 28th January 2016

USER-DEDICATED MICROSYMPOSIA (UDM) on Wednesday 10 February

• UDM1. Nanoscience: X-ray diffraction and coherence
• UDM2. Dynamics of complex systems
• UDM3. The future of (time resolved) room temperature protein X-ray crystallography

Scientific programme

Methods and techniques:

• High resolution diffraction and topography
• X-ray reflectometry and small-angle scattering
• Microdiffraction and nanodiffraction
• Coherent diffraction imaging
• Absorption and phase contrast imaging and tomography
• Resonant (anomalous) scattering
• Fluorescence imaging
• Time resolved methods
• Theory and simulations of X-ray scattering

Applications:

• Material science (from 0D to 3D objects)
• Nanomaterials and nanoscience
• Life and environmental sciences
• Non-destructive testing (including industrial needs and cultural heritage)

Instrumentation:

• X-ray optics and instrumentation
• Advances in laboratory instrumentation and applications
• Advances in synchrotron instrumentation and applications
• Experiments at X-ray free-electron lasers

• Interactions of X-rays with matter and fundamental parameters
• XRS Instrumentation (X-ray sources, optics and detectors)
• Quantification methodology and metrology
• TXRF, GIXRF and related techniques
• Microbeam techniques, confocal XRF and X-Ray imaging
• Mobile and portable XRF
• Synchrotron XRS, XAFS, high resolution XES, and RIXS
• PIXE instrumentation and applications
• Electron induced XRS
• WDXRS
• X-ray diffraction (XRD)
• XRS in Art and Cultural Heritage
• XRS in Advanced Materials and Nanoscience
• XRS in Earth and Environment sciences
• XRS in Industrial Quality and Process Control
• XRS in Life Sciences and Forensics
• Recent Scientific Developments by XRS Instrumentation Manufacturers (reserved to exhibitors)

Plenary speakers

• Susumu Yamamoto - Inst. for Solid State Phys. - Univ. of Tokyo (Japan)
  "Probing carriers and molecules on oxide surfaces by X-ray"
• Emmanuelle Schmitt - Polytechnique (France)
  "Structural and functional studies of the translation initiation factor e/alF2"
• Serena DeBeer - Max Planck Institute (Germany)
  "X-ray spectroscopic studies of Biological Dinitrogen Reduction"

Topics

• Biology / Health
• Chemistry and Physico-chemistry â€" in situ reactivity â€" Soft matter
• Electronic and magnetic property of matter â€" Surfaces and Interfaces
• Diluted Matter
• Matter & material properties: Structure, Organisation Characterisation, Elaboration
• Cultural heritage, archaeology, environment, geosciences

• Temporal resolution and dynamics
• Spatial resolution
• Multi beamline Measurements

A satellite workshop will be held on Tuesday 19th and Wednesday 20th of January, 2016 at SOLEIL:

HI-SPEARÂ (HIgh resolution SPEctroscopies for Applied Research)

Exploring All Facets of the Inorganic Chemistry of Life