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2025 Summer Internship Application
Education 11 Oct 2016
We are now accepting applications for the 2025 BioXFEL Summer Internship Program that will occur May 29, 2025 - August 1, 2025.… buffalo.edu if you have any questions. Please be sure to complete the form in it's entirety and submit it by February 14, 2025, or your application will not be considered.……
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BioXFEL Publications 22 Mar 2025
https://doi.org/10.1080/07370652.2025.… R., Herman, M. J., Watkins, E. B., Yeager, J. D., Marquez, M. P., Long, A. M., Carver, D. T., Knepper, R., & Kuhl, T. L. (2025).… Journal of Energetic Materials, 1–24. https://doi.org/10.1080/07370652.2025.
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BioXFEL Publications 4 Mar 2025
https://doi.org/10.1016/j.jnoncrysol.2025.… R., Huber, R. C., Yu, P., Finney, T. J., Felvey, N., Chow, P., Xiao, Y., Kuhl, T. L., & Watkins, E. B. (2025).… Journal of Non-Crystalline Solids, 656, 123448. https://doi.org/10.1016/j.jnoncrysol.2025.
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Advances in uncovering the mechanisms of macromolecular conformational entropy
BioXFEL Publications 24 Apr 2025 Contributor(s): James Fraser
https://doi.org/10.1038/s41589-025-01879-3 journal-article Wankowicz, S. A., & Fraser, J. S. (2025).
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Advances in microfluidic mixers for time-resolved structural biology with X-rays
BioXFEL Publications 23 May 2025 Contributor(s): Kara Zielinski, Lois Pollack
https://doi.org/10.1007/s12551-025-01321-x journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zielinski, K. A., & Pollack, L. (2025).
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BPS2025 - Unraveling the catalytic mechanism of the SARS-CoV-2 macrodomain ADP-ribosylhydrolase
BioXFEL Publications 13 Feb 2025 Contributor(s): James Fraser
https://doi.org/10.1016/j.bpj.2024.11.2882 journal-article Mitra, R., Correy, G., & Fraser, J. (2025).
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BioXFEL Publications 13 Feb 2025 Contributor(s): Lois Pollack
https://doi.org/10.1016/j.bpj.2024.11.476 journal-article Wang, T., Hu, Q., Fronhofer, S., & Pollack, L. (2025).
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Where and how to house big data on small fragments
BioXFEL Publications 5 May 2025 Contributor(s): James Fraser
https://doi.org/10.1038/s41467-025-59233-z journal-article Erlanson, D. A., Burley, S. K., Fearon, D., Fraser, J. S., Kreitler, D., Nonato, M. C., Sakai, N., Wollenhaupt, J., & Weiss, M. S. (2025).
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BPS2025 - Molecular simulation with 3D-RISM: Using hybrid Monte Carlo for efficient sampling
BioXFEL Publications 13 Feb 2025 Contributor(s): David Case
https://doi.org/10.1016/j.bpj.2024.11.1742 journal-article Pishaki, N. C., Luchko, T., & Case, D. A. (2025).
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BPS2025 - Automated, efficient, and rigorous absolute binding free energy calculations
BioXFEL Publications 13 Feb 2025 Contributor(s): David Case
https://doi.org/10.1016/j.bpj.2024.11.1764 journal-article Ayoub, S., Luchko, T., Barton, M., & Case, D. A. (2025).
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BioXFEL Publications 13 Feb 2025 Contributor(s): David Case
https://doi.org/10.1016/j.bpj.2024.11.509 journal-article Van Elslande, T. Y., Carvalho, F. S., Case, D., Cavagnero, S., & Luchko, T. (2025).
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The impact of library size and scale of testing on virtual screening
BioXFEL Publications 3 Jan 2025 Contributor(s): James Fraser
https://doi.org/10.1038/s41589-024-01797-w journal-article Liu, F., Mailhot, O., Glenn, I. S., Vigneron, S. F., Bassim, V., Xu, X., Fonseca-Valencia, K., Smith, M. S., Radchenko, D. S., Fraser, J. S., Moroz, Y. S., Irwin, J. J., & Shoichet, B. K. (2025).
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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 Publications 10 Jan 2025 Contributor(s): Kara Zielinski, Lois Pollack
https://doi.org/10.1063/5.0218572 X-ray spectroscopies are uniquely poised to describe the geometric and electronic structure of metalloenzyme active sites under a wide variety of sample conditions. UV/Vis (ultraviolet/visible) spectroscopy is a similarly well-established technique that can identify and quantify catalytic intermediates. The work…
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BioXFEL Publications 10 Apr 2025 Contributor(s): James Fraser
https://doi.org/10.1063/4.0000388 Biomolecules exchange between multiple conformational states in their folded state, crucial for their function. Traditional structural biology methods, such as X-ray crystallography and cryogenic electron microscopy (cryo-EM), produce density maps that are ensemble averages, capturing molecules in various…
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Determining the Mechanism of DJ-1 Using Mix-and-Inject Synchrotron Serial Crystallography
BioXFEL Publications 10 Apr 2025 Contributor(s): Kara Zielinski, Lois Pollack
https://doi.org/10.1063/4.0000378 Determining the molecular basis of enzyme catalytic activity is a central challenge in biochemistry. Time-resolved serial X-ray crystallography using X-ray free electron (XFELs) and synchrotron sources allows enzyme reactions to be observed in real time in a crystalline environment (1-3). We used pink beam…
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Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization
BioXFEL Publications 22 Nov 2024 Contributor(s): Tek Narsingh Malla, SRINIVASAN MUNIYAPPAN, Emina Stojkovic, Shibom Basu, Marius Schmidt
https://doi.org/10.1107/s2052252524010868 The upgrade of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France to an Extremely Brilliant Source (EBS) is expected to enable time-resolved synchrotron serial crystallography (SSX) experiments with sub-millisecond time resolution. ID29 is a new beamline dedicated to SSX experiments at…
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BioXFEL Publications 10 Apr 2025 Contributor(s): Kara Zielinski, Lois Pollack
https://doi.org/10.1063/4.0000425 Mix-and-inject serial crystallography (MISC) is a well established technique at X-ray Free Electron Lasers (XFELs) to capture snapshots of the progress of a reaction, typically between a protein and a ligand. Key to this method are specialized diffusive mixers which efficiently mix small molecules into protein…
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BioXFEL Publications 1 May 2025 Contributor(s): SRINIVASAN MUNIYAPPAN, Shibom Basu, Peter Schwander, Tek Narsingh Malla, Emina Stojkovic, Marius Schmidt
https://doi.org/10.1063/4.0000301 Phytochromes are red-light photoreceptors first identified in plants, with homologs found in bacteria and fungi, that regulate a variety of critical physiological processes. They undergo a reversible photocycle between two distinct states: a red-light-absorbing Pr form and a far-red light-absorbing Pfr form. This…
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Filling data analysis gaps in time-resolved crystallography by machine learning
BioXFEL Publications 21 Jan 2025 Contributor(s): Russell Fung, Peter Schwander, Ahmad Hosseinizadeh
https://doi.org/10.1063/4.0000280 There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments. Time-resolved serial femtosecond crystallography (TR-SFX) with x-ray Free Electron Lasers allows the measurement of ultrafast structural changes in proteins. Nevertheless, this technique…
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BioXFEL Publications 28 May 2025 Contributor(s): James Fraser
https://doi.org/10.1126/sciadv.ads7187 The macrodomain of severe acute respiratory syndrome coronavirus 2 nonstructural protein 3 is required for viral pathogenesis and is an emerging antiviral target. We previously performed an x-ray crystallography–based fragment screen and found submicromolar inhibitors by fragment linking.…
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Time-resolved cryogenic electron tomography using mix-and-inject microfluidic devices
BioXFEL Publications 10 Apr 2025 Contributor(s): Kara Zielinski, Christopher Kupitz, Mark S. Hunter, Lois Pollack
https://doi.org/10.1063/4.0000362 Cryogenic electron tomography (cryo-ET) is the highest resolution three-dimensional imaging technique applicable to the life sciences, enabling sub-nanometer visualization of rapidly frozen biological specimens preserved in their near native states. The rapid freezing process lends itself to time-resolved studies,…
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BioXFEL Undergraduate Internships
Education 5 Nov 2013
BioXFEL is a National Science Foundation Science and Technology Center (STC) that focuses on promoting and advancing the study of Biological molecules using X-ray Free Electron Lasers (XFELs). A summer internship is the best way to get started in this new and exciting field. BioXFEL offers Summer Research Internships to highly qualified…
