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BioXFEL Publications 31 Jul 2023 Contributor(s): Hasan Demirci
http://dx.doi.org/10.21203/rs.3.rs-3173078/v1 Abstract The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway.… Nmar_0206 catalyzes the conversion of 4-hydroxybutyrate (4HB) and Coenzyme-A (CoA) to…
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Education 7 Oct 2019
Grant Writers' Seminars and Workshops (GWSW) and BioXFEL are hosting a one-day grant writing workshop prior to the 2020 BioXFEL Annual International Conference on Monday, January 27th.… Robertson, PhD from GWSW will present "Write Winning Grant Proposals" to attendees interested in learning more about submitting proposals to…
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9th Annual BioXFEL International Conference
Events 8 Feb 2022
Feb 08 2022
The National Science Foundation BioXFEL Science and Technology Center is pleased to announce that it will be hosting its ninth annual international conference virtually February 8-10, 2022.… The annual International BioXFEL Conference brings together experts in a variety of fields (structural biology, physics, biochemistry, and…
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7th Annual BioXFEL International Conference
Events 28 Jan 2020
Jan 28 2020
The National Science Foundation BioXFEL Science and Technology Center is pleased to announce that it will be hosting its sixth annual international conference in San Juan, Puerto Rico January 28-30, 2020.… Click Here to Register! Conference Co-Chairs: … Dr. Marius Schmidt (UWM) & Dr. Emina Stojkovic…
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21st National School on Neutron and X-ray Scattering
Events 5 Mar 2019
Mar 05 2019
Graduate students at North American universities are invited to apply to the 21st National School on Neutron and X-ray Scattering, which will be held at Argonne and Oak Ridge National Labs from July 16 - July 20, 2019. This school is designed to introduce students to the capabilities available at U.S. neutron and x-ray user facilities and pays…
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10th Annual BioXFEL International Conference
Events 16 May 2023
May 16 2023
Click here for Conference Agenda … Click here for Welcome Packet The National Science Foundation BioXFEL Science and Technology Center is pleased to announce that it will be hosting its 10th Annual International Conference May 16 - 18, 2023.… From Time-Resolved Structure Factor Amplitudes to Structure and…
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SwissFEL Beamtime Applications DUE
Events 15 Sep 2019
Sep 15 2019
SwissFEL Calls for Proposals The PSI User Office invites user proposals for the first user run at SwissFEL. SwissFEL is being continuously developed but the proposals must be based on the parameters outlined below on this page After the submission deadline the proposals are evaluated in terms of safety and technical feasibility. Then they…
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News 21 Feb 2017
Molecules vibrate and resonate. These vibrations enable life to function, they are believed to play a role in photosynthesis in plants and protein folding in general. BioXFEL participant and University at Buffalo physicist Andrea Markelz has recently been awarded $1.35 million in grants, from the Department of Energy and National Science…
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Events 7 Feb 2022
Feb 07 2022
BioXFEL 2022 Conference Workshop: Diversity, Equity, and Inclusion in Science: Guidelines for Research Teams … February, 7th 2022 1:00PM to 5:00PM (EST) Speaker and Moderator - Sarah Holder - Diversity, Equity & Inclusion Program Manager at SLAC National Accelerator Laboratory Register for this event when registering for the…
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Education 9 Sep 2016
Research Opportunities for UNLV Students X-ray free electron lasers (XFELs) present unique capabilities that have the potential to revolutionize structural biology and its ability to probe the biological world. BioXFEL is a NSF Science and Technology Center that is focused on developing new techniques, educating the general public and generating…
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DOE Early Career Research Award
Events 1 Jan 2019
Jan 01 2019
Department of Energy Announces Early Career Research Program for FY 2019 … Awards Will Support University and National Laboratory Scientists WASHINGTON, D.C. — The U.S. Department of Energy (DOE) announced today it is accepting proposals for the tenth year of the DOE Office of Science Early Career Research Program to…
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Education 9 Oct 2018
BioXFEL Fellows are tasked with creating new education and outreach initiatives that will have a lasting impact on their local communities. They have all created new programs that will broaden the impact of BioXFEL and will add to the Center's legacy. Their thoughtful and insightful planning and organization of these events and groups is already…
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Education 1 Nov 2016
BioXFEL scholars are defined as Graduate students or postdoctoral associates that are working in a lab funded in part by BioXFEL. The scholar does not need to be directly supported by the Center, but should be working on a project related to XFEL science. BioXFEL Graduate Students and Postdocs must submit an application and complete the necessary…
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Seminars 21 Jul 2015
Dr. Marc Messerschmidt discusses the design and operation of the X-ray free electron laser at the LCLS. Be sure to grab the attached MP3 audio file to follow along. Topics discussed include: - XFEL fundamentals - LCLS machine capabilities and energy spectrum - Beamlines and instrumentation for crystallography - CSPAD detectors - Sample delivery and…
https://www.bioxfel.org/resources/crystallography-with-an-xfel
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Rescue of Conformational Dynamics in Enzyme Catalysis by Directed Evolution
BioXFEL Publications 6 Sep 2017 Contributor(s): James Fraser
http://dx.doi.org/10.1101/185009 Rational design and directed evolution have proved to be successful approaches to increase catalytic efficiencies of both natural and artificial enzymes. However, a comprehensive understanding of how evolution shapes the energy landscape of catalysis remains a fundamental challenge.… Here, we used…
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Nature Conference: Functional dynamics – visualizing molecules in action
Events 6 Nov 2019
Nov 06 2019
The Biodesign Institute at Arizona State University, Nature, Nature Chemistry, Nature Communications, Nature Methods, and Nature Physics are pleased to present: Functional dynamics – visualizing molecules in action https://www.nature.com/natureconferences/fd19/index.… The abstract submission deadline is August 12,…
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6th Annual BioXFEL International Conference
Events 12 Feb 2019
Feb 12 2019
The National Science Foundation BioXFEL Science and Technology Center is pleased to announce that it will be hosting its sixth annual international conference in San Diego, CA February 12th - 14th, 2019.… Click Here to Register! Conference Co-Chairs: … Dr. Brenda Hogue (ASU) & Dr. Nadia Zatsepin…
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BioXFEL STC 4th Annual International Conference
Events 10 Jan 2017
Jan 10 2017
Sponsored in part by: Thank You for Your Attendance and Sponsorship of the 4th BioXFEL Conference and Single Particle Sample Delivery Workshop … We would like to thank you for your attendance of the SP Workshop and 4th Annual Conference.… We’d also like to thank our vendors and…
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News 10 Jan 2023
Click here for Conference Agenda … Click here for Welcome Packet The National Science Foundation BioXFEL Science and Technology Center is pleased to announce that it will be hosting its 10th Annual International Conference May 16 - 18, 2023.… From Time-Resolved Structure Factor Amplitudes to…
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Members
Marius Schmidt is using physical methods to investigate biological molecules. He is concentrating mainly on static and time-resolved macromolecular crystallography to investigate the structure, dynamics and kinetics of proteins. Dr. Schmidt is also developing new, sophisticated software for the analysis of the time-resolved (4-dimensional) X-ray…
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Publications 10 Feb 2014 Contributor(s): Henry Chapman
The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even…
https://www.bioxfel.org/resources/Automated-identification-and-classification-of
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X-ray two-photon absorption with high fluence XFEL pulses
BioXFEL Publications 7 Sep 2015
http://dx.doi.org/10.1088/1742-6596/635/10/102009 J Hoszowska and J Szlachetko and J-Cl Dousse and W Błachucki and Y Kayser and Ch Milne and M Pajek and S Boutet and M Messerschmidt and G Williams and C T Chantler Hoszowska, J. et al., 2015. X-ray two-photon absorption with high fluence XFEL pulses. Journal of Physics: Conference Series, 635(10),…
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Experience with the CSPAD during dedicated detector runs at LCLS
BioXFEL Publications 31 Mar 2014
http://dx.doi.org/10.1088/1742-6596/493/1/012011 journal-article Carini, G.A. et al., 2014. Experience with the CSPAD during dedicated detector runs at LCLS. Journal of Physics: Conference Series, 493, p.
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Performance of silicon drift detectors at LCLS
BioXFEL Publications 25 Oct 2017
http://dx.doi.org/10.1109/nssmic.2016.8069827 proceedings-article Blaj, G. et al., 2016. Performance of silicon drift detectors at LCLS. 2016 IEEE Nuclear Science Symposium, Medical Imaging Conference and Room-Temperature Semiconductor Detector Workshop (NSS/MIC/RTSD).
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Members
Dr. Weierstall received his Ph.D., in Physics from the University of Tübingen, Germany in 1994 and then joined Arizona State University (ASU), as a postdoctoral fellow. He was employed as a Research Scientist at ASU from 1998 to 2008, where he designed a wide variety of new instrumentation, such as the Scanning Tunneling Atom Probe, which…
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BioXFEL Online Seminar - Abbas Ourmazd
Events 3 Aug 2016
Aug 03 2016
The BioXFEL August Seminar will be given by Dr. Abbas Ourmazd of the University of Wisconsin Milwaukee. Machine learning is guided by the intrinsic properties of the data, rather than user-directed notions. It is thus possible to determine the structure, conformations, energy landscapes, and dynamics of biological machines in equilibrium, or in the…
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BioXFEL Scientific Director John Spence passes away
News 13 Jul 2021
John Spence, the Scientific Director of BioXFEL, died peacefully Monday morning, June 28, in Boston. John was BioXFEL, he was a visionary in building the team and establishing the resulting community. He strongly impacted all faces of BioXFEL. He was on top of all the STC’s scientific activities. He attended many beamline sessions just to keep…
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Diffraction Methods in Structural Biology Gordon Research Seminar
Events 23 Jul 2022
Jul 23 2022
The Gordon Research Seminar on Diffraction Methods in Structural Biology is a unique forum for graduate students, post-docs, and other scientists with comparable levels of experience and education to present and exchange new data and cutting-edge ideas.… Macromolecular crystallography is experiencing a revolution in the rate of…
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BioXFEL Publications 7 Feb 2020 Contributor(s): Hasan Demirci
http://dx.doi.org/10.1101/2020.02.05.935528 AbstractAutotrophic microorganisms that convert inorganic carbon into organic matter were key players in the evolution of life on Earth. As the early atmosphere became oxygenated, microorganisms needed to develop mechanisms for oxygen protection, especially those relying on enzymes containing…
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Reconstruction of Objects from Their Averaged Finite Crystal Diffraction Intensity
BioXFEL Publications 26 Aug 2019
http://dx.doi.org/10.1109/icip.2019.8804468 proceedings-article Chen, J.P.J. et al., 2019. Reconstruction of Objects from Their Averaged Finite Crystal Diffraction Intensity. 2019 IEEE International Conference on Image Processing (ICIP).
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BioXFEL Graduate Student Cross-Training Scholarship
Teaching Materials 11 Nov 2015
BioXFEL is committed to providing our students with opportunities to diversify their skill sets and integrate themselves into our highly multidisciplinary Center. In addition to the workshops, conferences and online courses, we will now be offering our students the opportunity to train in another technique in another laboratory within the Center.
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Functional Dynamics Conference Early Registration and Abstract Submission Deadline
Events 12 Sep 2019
Sep 12 2019
The BioDesign Institute at Arizona State University, Nature, Nature Chemistry, Nature Communications, Nature Methods, and Nature Physics are pleased to present: Functional dynamics – visualizing molecules in actionNovember 6-8, 2019Arizona State University, Tempe, Arizona, USA The abstract submission deadline is September 12, 2019 at…
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Few-fs resolution of a photoactive protein traversing a conical intersection
News 4 Nov 2021
The structural dynamics of a molecule are determined by the underlying potential energy landscape.… Posited almost a century ago, conical intersections remain the subject of intense scientific interest. In biology, they have a pivotal role in vision, photosynthesis and DNA stability6. Accurate theoretical methods for examining…
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Simultaneous retrieval of coherently illuminated defocused objects
BioXFEL Publications 5 Jul 2018 Contributor(s): Joe Chen, Richard Kirian
http://dx.doi.org/10.1109/ivcnz.2017.8402481 proceedings-article Chen, J.P.J. & Kirian, R.A., 2017. Simultaneous retrieval of coherently illuminated defocused objects. 2017 International Conference on Image and Vision Computing New Zealand (IVCNZ).
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Orientation and analysis of XFEL serial diffraction patterns from fibrous molecular assemblies
BioXFEL Publications 5 Jul 2018 Contributor(s): Henry Chapman
http://dx.doi.org/10.1109/ivcnz.2017.8402508 proceedings-article Wojtas, D.H. et al., 2017. Orientation and analysis of XFEL serial diffraction patterns from fibrous molecular assemblies. 2017 International Conference on Image and Vision Computing New Zealand (IVCNZ).
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Graduate Students and Postdocs
Education 27 Apr 2017
Graduate Students Graduate studies with BioXFEL are available at some of the best research universities in the country.… Pursuing a Graduate degree with one of our partner institutions provides a comprehensive, interdisciplinary, and cutting-edge experience. Our Center is committed to advancing our research, and our graduate…
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Towards phasing using high X-ray intensity
BioXFEL Publications 29 Sep 2015 Contributor(s): Henry Chapman
X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during…
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BioXFEL Publications 22 Mar 2013
http://dx.doi.org/10.1088/1742-6596/425/19/192011 journal-article Shapiro, D. et al., 2013. Development of coherent scattering and diffractive imaging and the COSMIC facility at the Advanced Light Source. Journal of Physics: Conference Series, 425(19), p.
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Petra Fromme at Molecular Basis of Life
Events 24 Sep 2017
Sep 24 2017
The German Society for Biochemistry and Molecular Biology (GBM) will host the international conference Molecular Basis of Life in Bochum, Germany.… Conference Topics:
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Events 29 Sep 2015
Sep 29 2015
How do you make a movie of a single particle jiggling and wiggling with atomic resolution and ultra-fast temporal resolution? How do you calculate the energy landscape or the kinetics/dynamics of a sequence of conformational changes?… How can I use symmetry to my advantage? We will answer all these questions and more. The BioXFEL…
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News 2 Dec 2019
The European XFEL marks in a new age of protein movie-making that enables enzymes involved in disease to be observed in real time. To study the swiftness of biology – the protein chemistry behind every life function – scientists have need to see molecules changing and interacting in unimaginably rapid time increments – trillionths of a…
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BioXFEL at 2017 LCLS Users' Meeting
News 2 Nov 2017
BioXFEL was well represented at the LCLS/SSRL Users' Meeting with Henry Chapman giving a plenary talk on Serial Femtosecond Crystallography: Past, Present, and Future featuring snippets from data as recent as 24 hours before the talk. David Bushnell, moderated a session that included the LCLS young investigator award and Linda Horton, Director of…
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Mapping the decay of double core hole states of atoms and molecules
BioXFEL Publications 10 Apr 2014
journal-article http://dx.doi.org/10.1088/1742-6596/488/3/032021 Mucke, M. et al., 2014. Mapping the decay of double core hole states of atoms and molecules. Journal of Physics: Conference Series, 488(3), p.
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Events 17 Dec 2018
Dec 17 2018
Call for proposals The European X-Ray Free-Electron Laser Facility (European XFEL, http://www.xfel.eu) encourages the scientific community worldwide to submit proposals for Early User Experiments via the User Portal to the European XFEL (UPEX) until Monday 17 December 2018 14:00 (local Hamburg / Schenefeld time - UTC +1) Beamtime will be…
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Accurate positioning of functional residues with robotics-inspired computational protein design
BioXFEL Publications 7 Mar 2022 Contributor(s): Michael Thompson, James Fraser
http://dx.doi.org/10.1073/pnas.2115480119 Significance Computational protein design promises to advance applications in medicine and biotechnology by creating proteins with many new and useful functions. However, new functions require the design of specific and often irregular atom-level geometries, which remains a major challenge. Here,…
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Events 4 May 2017
May 04 2017
This is a call for proposals for experiments at LCLS using the AMO, SXR, XPP, CXI, MFX, XCS, and MEC Experimental Stations for the period November, 2017 – June, 2018 (“Run 16”). The DEADLINE is 4 pm PACIFIC on May 4, 2017 . For full details of the call, see: …
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BioXFEL STC 3rd Annual International Conference
Events 13 Jan 2016
Jan 13 2016
REGISTRATION DEADLINE EXTENDED TO DECEMBER 18TH The BioXFEL National Science Foundation Science and Technology Center is pleased to announce that it will be hosting its third annual international conference in San Juan, Puerto Rico January 13th - 15th, 2016.… #BioXFEL3 Conference Co-Chairs: Dr.… George…
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BioXFEL Scholar Education Programs
Education 22 Oct 2018
BioXFEL Scholar Programs BioXFEL generates and manages a customized set of educational programming that is is designed to supplement the existing curriculum at our participating Universities. The education program includes several scientific and professional development initiatives that have been designed by our Scholars and the BioXFEL Education…
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Workshop: Scientific opportunities at ASU Compact X-ray Free Electron Laser
Events 6 Apr 2018
Apr 06 2018
Dynamics, Structure, and Function in Biological Systems Scientific opportunities at ASU Compact X-ray Free Electron Laser Arizona State University Biodesign Institute, Center for Applied Structural Discovery Tempe, AZ April 6-8, 2018 More information and registration can be found here. Friday April 6 12:30 Light lunch in Biodesign Atrium,…
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Events 28 Sep 2020
Sep 28 2020
September 28 to October 9, 2020 Register online HERE The joint Stanford Synchrotron Radiation Lightsource (SSRL) and the Linac Coherent Light Source (LCLS) users' conference will be held VIRTUALLY!… So, save the dates September 28-October 9, 2020. Check back later for more program and registration details. Invited Talks &…
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FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
BioXFEL Publications 22 Feb 2018 Contributor(s): Henry Chapman
http://dx.doi.org/10.1016/j.hedp.2018.02.004 journal-article Jönsson, H.O. et al., 2018. FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography. High Energy Density Physics.
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U.S. Crystal Growing Competition celebrates 5th anniversary
News 3 Oct 2018
The contest — founded by a UB chemist — reaches thousands of children around the country each year
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Transient lattice contraction in the solid-to-plasma transition
BioXFEL Publications 30 Jan 2016 Contributor(s): Marc Messerschmidt
http://dx.doi.org/10.1126/sciadv.1500837 Ken R. Ferguson and Maximilian Bucher and Tais Gorkhover and Sébastien Boutet and Hironobu Fukuzawa and Jason E. Koglin and Yoshiaki Kumagai and Alberto Lutman and Agostino Marinelli and Marc Messerschmidt and Kiyonobu Nagaya and Jim Turner and Kiyoshi Ueda and Garth J. Williams and Philip H. Bucksbaum and…
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Wiki 22 May 2014
What is Wiki? A wiki is a collaborative software program that allows users to add or edit content on a Web page without having to know HMTL or programming languages. Most commonly, the term wiki refers to a Web page that can be revised by anyone.Creating and editing wikis are very simple; all that is required is Internet access and a browser.…
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Arizona State University Biophysics Seminar - Monarin Uervirojnangkoorn
Events 1 Oct 2014
Oct 01 2014
Prime: Post-Refinement and Merging Program for XFEL Data Abstract An X-ray free-electron laser (XFEL) delivers a micron-size beam with high brilliance femtosecond pulses. It has been shown that XFEL crystallography can produce diffraction data without radiation damage. Moreover, XFELs may enable data collection on crystals too small for current…
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Wiki 22 May 2014
A macro inserts dynamic HTML data in any context supporting . Using Macros Macro calls are enclosed in two ''square brackets''. Examples Display:Display:Display:To add a footnote to text you use the footnote macro. You use the same macro but with no text to display the accumulated list of footnotes. For example:Display:To add a footnote to text…
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Events 7 Aug 2017
Aug 07 2017
BioXFEL scientist, Abbas Ourmazd (UWM), will present at the International Workshop of Advanced Image Processing of Cryo-Electron Microscopy in Beijing China. Dr. Ourmazd will be presenting a lecture, “Dealing with macromolecular dynamics in cryoEM: an overview and perspective” and tutorial, “Conformational mapping of biological…
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Opacity effects in a solid-density aluminium plasma created by photo-excitation with an X-ray laser
BioXFEL Publications 15 Mar 2014
http://dx.doi.org/10.1016/j.hedp.2014.02.003 journal-article Rackstraw, D.S. et al., 2014. Opacity effects in a solid-density aluminium plasma created by photo-excitation with an X-ray laser. High Energy Density Physics, 11, pp.
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Single Particle Sample Delivery Workshop
Events 9 Jan 2017
Jan 09 2017
BioXFEL is pleased to announce it will be hosting a Single Particle Sample Delivery Workshop in conjunction with the 4th Annual Conference.… XFEL-based single-particle imaging techniques hold the potential to reveal the high-resolution structures of non-crystalline bioparticles such as proteins and viruses, including dynamical…
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Knowledge Transfer 12 May 2014
The NSF BioXFEL STC has partnered with museums to grow public knowledge and understanding of XFEL science. Our collaborative programs reach students, educators and the general public. Through our combined efforts we offer lectures, workshops and soon, a rotating exhibit. The Arizona Science Center has hosted the BioXFEL Center for one of it…
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American Crystallography Association Conference 2022
Events 29 Jul 2022
Jul 29 2022
The American Crystallographic Association is returning to an in-person gathering for the 72nd annual meeting. Scientists interested in biological, chemical, and material structures will travel to the heart of Portland, Oregon, July 29 - August 3, 2022. In an effort to remain flexible in this dynamic time, the ACA plans to offer a selection of the…
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High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle
BioXFEL Publications 17 Sep 2020 Contributor(s): Melissa Carrillo, suraj pandey, Ishwor Poudyal, Tek Narsingh Malla, Emina Stojkovic, Marius Schmidt
http://dx.doi.org/10.1101/2020.09.16.298463 AbstractPhytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting (dark) Pr state and the light activated Pfr state, in which light signals are received and transduced as…
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BioXFEL Publications 19 Nov 2020 Contributor(s): Reza Nazari, Brian Abbey, Henry Chapman, Alice Contreras, Hasan Demirci, Matthias Frank, Brenda Hogue, Ahmad Hosseinizadeh, Mark S. Hunter, Richard Kirian, Abbas Ourmazd, Peter Schwander
http://dx.doi.org/10.1038/s41597-020-00745-2 AbstractSingle Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772…
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SLAC's Electron Hub Gets New 'Metro Map' for World's Most Powerful X-Ray Laser
News 7 Jul 2017
The central hub for powerful electron beams at the Department of Energy’s SLAC National Accelerator Laboratory is getting a makeover to prepare for the installation of LCLS-II – a major upgrade to the Linac Coherent Light Source (LCLS), the world’s first hard X-ray free-electron laser.… The hub, called the Beam Switch…
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Members
Dr. Saldin’s research covers all aspects of the use of radiation to study matter, and diffraction and scattering phenomena. His particular interests center around holography, tomography, and x-ray scattering from biomolecules. He obtained his B.A in 1971 and his Ph.D. in Materials in 1975, both from the University of Oxford. From 1976 to 1981,…
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Education 12 Sep 2013
Postdoctoral positions are a key component of our program and are available at nearly all of our participating institutions. Our program encompasses a full mentorship program, participation in Center conferences and prepares each person for a successful, independent research career.
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BioXFEL Lecture Series - Single Particle Imaging
Events 1 Jul 2015
Jul 01 2015
Dr. Saldin’s research covers all aspects of the use of radiation to study matter, and diffraction and scattering phenomena. His particular interests center around holography, tomography, and x-ray scattering from biomolecules. He obtained his B.A in 1971 and his Ph.D. in Materials in 1975, both from the University of Oxford. From 1976 to 1981, he…
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Synchronous RNA conformational changes trigger ordered phase transitions in crystals
BioXFEL Publications 19 Mar 2021 Contributor(s): Chelsie E Conrad, Max Oliver Wiedorn, Chufeng Li, Mark S. Hunter, Nadia Zatsepin, suraj pandey, Marius Schmidt, John Spence, Henry Chapman
http://dx.doi.org/10.1038/s41467-021-21838-5 AbstractTime-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice.… Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal…
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Published 5 Nov 2013
Welcome to the ABYS* Founded at the 2014 SLAC/LCLS Users’ Meeting and Workshops, ABYS exists to foster the growth of the immediate next generation of XFEL scientists. ABYS provides a forum for BioXFEL Scholar education and plays a key role in determining how the Center’s education program operates. ABYS membership is open to the general…
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EducationM 12 Jul 2017
Welcome to the ABYS Founded at the 2014 SLAC/LCLS Users’ Meeting and Workshops, ABYS exists to foster the growth of the immediate next generation of XFEL scientists. ABYS provides a forum for BioXFEL Scholar education and plays a key role in determining how the Center’s education program operates. ABYS membership is open to the general public.…
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BioXFEL Protein Production and Purification Workshop at UPR-RP
Events 12 Oct 2017
Oct 12 2017
BioXFEL Protein Production and Purification Workshop As you may have guessed, this Workshop has been cancelled. It seems inappropriate to offer this at a time when Puerto Rico needs so much more than a protein workshop. The workshop will be rescheduled for another time in the spring. In the meantime, please stay safe and know that we are…
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Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel
Teaching Materials 9 Oct 2015
Traditional macroscale protein crystallization is accomplished nontrivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time-consuming and resource-intensive, hindering protein structure determination. Even more difficulties arise when crystallizing large…
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Biography 21 May 2013
Edward Snell Department of Structural BiologySUNY Buffalo Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203esnell@hwi.buffalo.edu (716) 898-8631Edward Snell, Ph.D., is a Senior Scientist at the Hauptman-Woodward Medical Research Institute and faculty member at the University at Buffalo in the Department of…
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Characterizing single-stranded RNA using SAXS and single-molecule FRET
BioXFEL Publications 10 Apr 2025 Contributor(s): Lois Pollack
https://doi.org/10.1063/4.0000644 Single-stranded RNA molecules play many important roles in biology, including in the formation of biomolecular condensates through liquid-liquid phase separation [1]. The flexibility of these molecules is critical, allowing them to take on a variety of conformations. However, their highly flexible nature makes the…
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BioXFEL Seminar Series - Peter Schwander UWM
Events 2 Nov 2017
Nov 02 2017
Join us Thursday, November 2nd, as BioXFEL member and UWM Associate Professor, Peter Schwander discusses his recent accomplishments in Single Particle Imaging. This presentation will be recorded and posted to our website. The seminar takes place at 3PM EDT (2PM CDT, 1PM MDT, 12PM PDT/MST) TitleSingle-Particle diffraction with the X-Ray…
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Ultrafast X-ray Summer School in Hamburg: 12-15 June 2017 Registration Deadline 3/31
Events 31 Mar 2017
Mar 31 2017
The Ultrafast X-ray Summer School (UXSS) is an annual event jointly organized by the Center for Free-Electron Laser Science (CFEL) at DESY and the PULSE institute at SLAC National Accelerator Laboratory. As you can see from the list of speakers below, the program will be highly interdisciplinary, with topics ranging from accelerator…
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BioXFEL Jazz Trio Performed Live at Caesar’s Palace
News 31 Jan 2017
The BioXFEL Jazz Trio headlined the 4th Annual BioXFEL International Conference at Caesar’s Palace featuring John C.
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Jobs at Lawrence Berkeley National Laboratory
Opportunities 8 Sep 2021
Two new positions are available in the group of Aaron Brewster at Lawrence Berkeley National Laboratory. Computational Project Scientist - https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=93507 Computational Postdoctoral Scholar - https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=93506 In these exciting roles, you will work in…
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Tips 25 Mar 2010
To change your dashboard page, simply click the Personalize button located in the upper-right corner of that page.… When you're done, click the finish button and all your changes will be saved.
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News 25 Mar 2021
Many organisms use sunlight to fuel cellular functions. But exactly how does this conversion of solar energy into chemical energy unfold?… In a recent experiment, an international team of scientists, including several research groups from the BioXFEL Science and Technology Center, used time-resolved serial femtosecond…
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BioXFEL Publications 23 Dec 2020 Contributor(s): James Fraser
http://dx.doi.org/10.1073/pnas.2011350117 How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites,…
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BioXFEL Publications 17 Nov 2020 Contributor(s): Edward Snell
http://dx.doi.org/10.1371/journal.pone.0239702 A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been…
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Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam
BioXFEL Publications 7 Sep 2023 Contributor(s): Tek Narsingh Malla, Kara Zielinski, Mark S. Hunter, Christopher Kupitz, suraj pandey, Ishwor Poudyal, Abbas Ourmazd, Petra Fromme, Peter Schwander, Henry Chapman, Emina Stojkovic, George Phillips, Lois Pollack, Marius Schmidt
http://dx.doi.org/10.1038/s41467-023-41246-1 AbstractFor decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach,…
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Opportunities 24 Feb 2021
LCLS has new postings out to fill positions to work on X-ray spectroscopy as well as sample environment and delivery. Positions are available in spectroscopy as well as sample environment and delivery. Posting ID (Job ID 4330) Project Scientist for X-ray Spectroscopy at LCLSInquiries can be sent to Roberto Alonso-Mori…
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Alternative Scientific Careers Panel
Events 13 Feb 2018
Feb 13 2018
While BioXFEL strives to retain students and postdocs within the Center, we also realize that this is not for everyone. The academic pipeline does not allow for 100% retention, so we would like to help you explore your options. During the first day of our 2018 conference, Tuesday, Feb 13th from 1:45-3:00 PM, we will host a panel of experts that…
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Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots
BioXFEL Publications 31 Mar 2018 Contributor(s): Ghoncheh Mashayekhi, Peter Schwander, Abbas Ourmazd
http://dx.doi.org/10.1101/291922 We present a new approach to determining the conformational changes associated with biological function, and demonstrate its capabilities in the context of experimental single-particle cryo-EM snapshots of ryanodine receptor (RyR1), a Ca2+-channel involved in skeletal muscle excitation/contraction coupling.
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Measure by measure: X-rays show viral transformation
News 7 Feb 2017
Viral multiplication A new insight into how viruses replicated based on X-ray crystallography work by a team at Thomas Jefferson University could ultimately lead to new antiviral drugs to treat pathogenic DNA viruses. When a virus infects a host it takes genetic control of the host cells in order to generate myriad self-assembling copies of its…
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BioXFEL Publications 10 Aug 2021 Contributor(s): Edward Snell
http://dx.doi.org/10.1107/s1600577521004045 X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a successful mitigation strategy but also has its…
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BioXFEL Publications 24 Nov 2021 Contributor(s): Hasan Demirci
http://dx.doi.org/10.1038/s41598-021-02180-8 AbstractThe ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far.
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Tips 25 Mar 2010
Rating a resource is quick and easy.Every resource has two sets of stars: the average rating and your rating. If you haven't rated a resource, you're rating will show up as a set of slightly grayed out stars.To rate the resource, hover over your rating stars. The stars will change to red depending on where your cursor is.… You…
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Cheetah documentation - all keywords
Series 21 Jul 2015 Contributor(s): Nadia Zatsepin
The official Cheetah website is http://www.desy.de/~barty/cheetah/ These pages will not reproduce all the content from the Cheetah site, but are meant as an addendum. Complete listing of keywords for Cheetah's configuration files Many of these are power user settings designed for turning on or off features in testing. Detector…
https://www.bioxfel.org/resources/cheetah_documentation_keywords
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Registration 25 Mar 2010
Don't panic! We can reset your password and send instructions to the e-mail address that you have on file with us. Then, you can follow the instructions, log in to the site, and change your password to anything you like.
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News 31 Jan 2017
The Science New electronic devices and energy solutions depend on scientists clearly seeing atoms and molecules at work.… To produce stable, organized pulses, scientists demonstrated a new scheme called echo-enabled harmonic generation (EEHG) at the SLAC National Accelerator Laboratory in California. They used conventional lasers…
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News 23 May 2017
Burrowed deep under the foothills near Palo Alto, Calif., scientists scurried through an underground laboratory, making final preparations for a series of explosions. THEIR PLAN: blow up tiny crystals of proteins that could reveal one of nature's best-kept secrets—how plant photosynthesis turns light into chemical energy.… It…
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Area Detectors for XFELs - Challenges and Developments
Events 17 Nov 2014
Nov 17 2014
ARIZONA STATE UNIVERSITY CENTER FOR BIOLOGICAL PHYSICS SPECIAL SEMINAR Monday, November 17, 2014 2:30 PM 487 Goldwater Center Cornelia “Trixi” Wunderer DESY Photon Science Detector Group Host: John Spence Area Detectors for XFELs - Challenges and Developments Abstract With the increased brilliance of state-of-the-art Synchrotron…
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Nora Berrah Named 2018 AAAS Fellow
News 13 Dec 2018
Professor Nora Berrah of the Department of Physics in the College of Liberal Arts and Sciences at University of Connecticut has been named a 2018 Fellow of the American Association for the Advancement of Science (AAAS).… Berrah, who was head of the physics department from 2014-2018, has been recognized for her distinguished…
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BioXFEL Publications 19 Oct 2016 Contributor(s): Michael Thompson, James Fraser
http://dx.doi.org/10.1101/081646 Although protein design has been used to introduce new functions, designed variants generally only function as well as natural proteins after rounds of laboratory evolution. One possibility for this pattern is that designed mutants frequently sample nonfunctional conformations. To test this idea, we exploited…
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Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase
News 1 Aug 2017
BioXFEL scientist Vadim Cherezov, along with others, publishes research article in ScienceDirect. Abstract: The nicotinamide nucleotide transhydrogenase (TH) is an integral membrane enzyme that uses the proton-motive force to drive hydride transfer from NADH to NADP+ in bacteria and eukaryotes. Here we solved a 2.2-Å crystal structure of the TH…
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News 5 Jul 2017
Riboswitches are structurally dynamic RNA molecules, undergoing changes in shape as they perform their regulatory functions.… Thus far, structures have been obtained for the aptamer domains, but the motions caused by ligand binding have been tricky to observe by crystallography: crystals typically freeze molecules in one shape,…
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News 25 Mar 2021
Phytochromes are the molecular eyes of plants and bacteria that regulate cellular response to light, an essential environmental signal. Upon light absorption, the phytochromes change their structures substantially from a conformation that absorbs in the red-light called Pr to another conformation that absorbs in the far-red light called Pfr,…
