36 results on '"Fortmann-Grote C"'
Search Results
2. SIMEX: Simulation of Experiments at Advanced Light Sources
- Author
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Fortmann-Grote, C, Andreev, A A, Briggs, R, Bussmann, M, Buzmakov, A, Garten, M, Grund, A, Hübl, A, Hauff, S, Joy, A, Jurek, Z, Loh, N D, Rüter, T, Samoylova, L, Santra, R, Schneidmiller, E A, Sharma, A, Wing, M, Yakubov, S, Yoon, C H, Yurkov, M V, Ziaja, B, and Mancuso, A P
- Subjects
Physics - Computational Physics ,Physics - Instrumentation and Detectors - Abstract
Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these experiments investigating ever more complex physical systems, e.g. biomolecules, complex materials, and ultra-short lived states of highly excited matter. Traditional photon science modelling takes into account only isolated aspects of an experiment, such as the beam propagation, the photon-matter interaction, or the scattering process, making idealized assumptions about the remaining parts, e.g.\ the source spectrum, temporal structure and coherence properties of the photon beam, or the detector response. In SIMEX, we have implemented a platform for complete start-to-end simulations, following the radiation from the source, through the beam transport optics to the sample or target under investigation, its interaction with and scattering from the sample, and its registration in a photon detector, including a realistic model of the detector response to the radiation. Data analysis tools can be hooked up to the modelling pipeline easily. This allows researchers and facility operators to simulate their experiments and instruments in real life scenarios, identify promising and unattainable regions of the parameter space and ultimately make better use of valuable beamtime. This work is licensed under the Creative Commons Attribution 3.0 Unported License: http://creativecommons.org/licenses/by/3.0/., Comment: Presented at the 11th NOBUGS conference, Copenhagen, on Oct. 17th 2016. 7 pages, 3 figures, 29 references
- Published
- 2016
3. NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and Bioimage Analysis
- Author
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Moore, J., Kunis, S., Grüning, B., Blank-Burian, M., Mallm, J.-P., Stöter, T., Zuschratter, W., Figge, M.T., Kreshuk, A., Tischer, C., Haase, R., Zobel, T., Bauer, P., Svensson, C.-M., Gerst, R., Hanne, J., Schmidt, C., Becker, M.M., Bocklitz, T., Bumberger, Jan, Chalopin, C., Chen, J., Czodrowski, P., Dickscheid, T., Fortmann-Grote, C., Huisken, J., Lohmann, J., Schauss, A., Baumann, M., Beretta, C., Burel, J.-M., Heuveline, V., Kuner, R., Landwehr, M., Leibfried, A., Nitschke, R., Mittal, D., von Suchodoletz, H., Valencia-Schneider, M., Zentis, P., Brilhaus, D., Hartley, M., Hülsmann, B., Dunker, Susanne, Keppler, A., Mathur, A., Meesters, C., Möbius, W., Nahnsen, S., Pfander, C., Rehwald, S., Serrano-Solano, B., Vilardell Scholten, L., Vogl, R., Becks, L., Ferrando-May, E., Weidtkamp-Peters, S., Moore, J., Kunis, S., Grüning, B., Blank-Burian, M., Mallm, J.-P., Stöter, T., Zuschratter, W., Figge, M.T., Kreshuk, A., Tischer, C., Haase, R., Zobel, T., Bauer, P., Svensson, C.-M., Gerst, R., Hanne, J., Schmidt, C., Becker, M.M., Bocklitz, T., Bumberger, Jan, Chalopin, C., Chen, J., Czodrowski, P., Dickscheid, T., Fortmann-Grote, C., Huisken, J., Lohmann, J., Schauss, A., Baumann, M., Beretta, C., Burel, J.-M., Heuveline, V., Kuner, R., Landwehr, M., Leibfried, A., Nitschke, R., Mittal, D., von Suchodoletz, H., Valencia-Schneider, M., Zentis, P., Brilhaus, D., Hartley, M., Hülsmann, B., Dunker, Susanne, Keppler, A., Mathur, A., Meesters, C., Möbius, W., Nahnsen, S., Pfander, C., Rehwald, S., Serrano-Solano, B., Vilardell Scholten, L., Vogl, R., Becks, L., Ferrando-May, E., and Weidtkamp-Peters, S.
- Abstract
Bioimaging refers to a collection of methods to visualize the internal structures and mechanisms of living organisms. The fundamental tool, the microscope, has enabled seminal discoveries like that of the cell as the smallest unit of life, and continues to expand our understanding of biological processes. Today, we can follow the interaction of single molecules within nanoseconds in a living cell, and the development of complete small organisms like fish and flies over several days starting from the fertilized egg. Each image pixel encodes multiple spatiotemporal and spectral dimensions, compounding the massive volume and complexity of bioimage data. Proper handling of this data is indispensable for analysis and its lack has become a growing hindrance for the many disciplines of the life and biomedical sciences relying on bioimaging. No single domain has the expertise to tackle this bottleneck alone. As a method-specific consortium, NFDI4BIOMAGE seeks to address these issues, enabling bioimaging data to be shared and re-used like they are acquired, i.e., independently of disciplinary boundaries. We will provide solutions for exploiting the full information content of bioimage data and enable new discoveries through sharing and re-analysis. Our RDM strategy is based on a robust needs analysis that derives not only from a community survey but also from over a decade of experience in German BioImaging, the German Society for Microscopy and Image Analysis. It considers the entire lifecycle of bioimaging data, from acquisition to archiving, including analysis and enabling re-use. A foundational element of this strategy is the definition of a common, cloud-compatible, and interoperable digital object that bundles binary images with their descriptive and provenance metadata. With members from plant biology to neuroscience, NFDI4BIOIMAGE will champion the standardization of bioimage data to create a framework that answers discipline-specific needs while ensuring communicati
- Published
- 2024
4. Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties
- Author
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E, Juncheng, primary, Kim, Y., additional, Bielecki, J., additional, Sikorski, M., additional, de Wijn, R., additional, Fortmann-Grote, C., additional, Sztuk-Dambietz, J., additional, Koliyadu, J. C. P., additional, Letrun, R., additional, Kirkwood, H. J., additional, Sato, T., additional, Bean, R., additional, Mancuso, A. P., additional, and Kim, C., additional
- Published
- 2022
- Full Text
- View/download PDF
5. SIMEX test data
- Author
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Fortmann-Grote, C.
- Published
- 2020
- Full Text
- View/download PDF
6. Measurements of the momentum-dependence of plasmonic excitations in matter around 1 Mbar using an X-ray free electron laser
- Author
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Preston, T. R., primary, Appel, K., additional, Brambrink, E., additional, Chen, B., additional, Fletcher, L. B., additional, Fortmann-Grote, C., additional, Glenzer, S. H., additional, Granados, E., additional, Göde, S., additional, Konôpková, Z., additional, Lee, H. J., additional, Marquardt, H., additional, McBride, E. E., additional, Nagler, B., additional, Nakatsutsumi, M., additional, Sperling, P., additional, Witte, B. B. L., additional, and Zastrau, U., additional
- Published
- 2019
- Full Text
- View/download PDF
7. Modeling Multiple Coherent and Incoherent Photon Scattering in Solid-Density Plasmas with Particle-In-Cell Simulations
- Author
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Garten, M., Grund, A., Hübl, A., Burau, H., Widera, R., Pausch, R., Debus, A., Kluge, T., Fortmann-Grote, C., Schramm, U., Cowan, T., and Bussmann, M.
- Subjects
XFEL ,HPC ,PIConGPU ,X-Ray ,SAXS ,particle-in-cell ,simulation ,ParaTAXIS - Abstract
Laser-driven solid density plasmas can be used to generate highly energetic electrons and ions. Diagnosing properties within those plasmas at nm length scales and down to fs timescales is crucial in understanding the involved processes. This has recently become feasible through the advent of X-Ray Free Electron Lasers (XFELs). For instance, XFELs allow imaging the electron density distribution within plasmas via Small Angle X-Ray Scattering (SAXS). We present a scalable GPU-based software framework for simulating photon scattering processes of X-ray beams in matter using Monte-Carlo methods. These simulations enable us to produce synthetic SAXS signals from the interaction of a modeled X-ray pulse with an arbitrarily complex, 3D electron density distribution obtained e.g. from detailed particle-in-cell simulations. Additionally, we present radiation transport methods in our 3D3V fully-relativistic PIC code PIConGPU. These methods enhance modeling of self-imaging of solid-density plasmas and lay the foundation for in-situ simulations of pump-probe experiments. Our new framework allows for single and multiple scattering and is extendable to include complex physics processes like ionization, atomic excitation and de-excitation along the photon path to further enhance its predictive capability.
- Published
- 2017
8. Start-to-end simulations for photon interaction in ultra-high intensity short pulse laser experiments with solids
- Author
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Kluge, T., Burau, H., Garten, M., Grund, A., Huebl, A., Matthes, A., Jung, F., Widera, R., Zacharias, M., Fortmann-Grote, C., and Bussmann, M.
- Subjects
ComputingMilieux_GENERAL ,ComputingMethodologies_GENERAL ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,ComputingMilieux_MISCELLANEOUS - Abstract
EUCALL annual meeting poster
- Published
- 2017
9. Simulations of ultrafast X-ray laser experiments
- Author
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Fortmann-Grote, C., Andreev, A. A., Appel, K., Branco, J., Briggs, R., Bussmann, M., Buzmakov, A., Garten, M., Grund, A., Huebl, A., Jurek, Z., Loh, N. D., Nakatsutsumi, M., Samoylova, L., Santra, R., Schneidmiller, E. A., Sharma, A., Steiniger, K., Yakubov, S., Yoon, C., Yurkov, M. V., Zastrau, U., Ziaja-Motyka, B., and Mancuso, A. P.
- Subjects
X-ray ,warm dense matter ,ultrafast ,XFEL ,scattering ,imaging ,simulation ,biomolecules - Abstract
Simulations of experiments at modern light sources, such as optical laser laboratories, synchrotrons, and free electron lasers, become increasingly important for the successful preparation, execution, and analysis of these experiments investigating ever more complex physical systems, e.g. biomolecules, complex materials, and ultra-short lived states of matter at extreme conditions. We have implemented a platform for complete start-to-end simulations of various types of photon science experiments, tracking the radiation from the source through the beam transport optics to the sample or target under investigation, its interaction with and scattering from the sample, and registration in a photon detector. This tool allows researchers and facility operators to simulate their experiments and instruments under real life conditions, identify promising and unattainable regions of the parameter space and ultimately make better use of valuable beamtime. In this paper, we present an overview about status and future development of the simulation platform and discuss three applications: 1.) Single-particle imaging of biomolecules using x-ray free electron lasers and optimization of x-ray pulse properties, 2.) x-ray scattering diagnostics of hot dense plasmas in high power laser-matter interaction and identification of plasma instabilities, and 3.) x-ray absorption spectroscopy in warm dense matter created by high energy laser-matter interaction and pulse shape optimization for low-isentrope dynamic compression.
- Published
- 2017
10. Scalable, multi-GPU photon tracing for in-situ X-ray radiation transport in solid density plasmas
- Author
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Garten, M., Grund, A., Huebl, A., Burau, H., Widera, R., Kluge, T., Fortmann-Grote, C., and Bussmann, M.
- Subjects
radiation transport ,plasma physics ,PIConGPU ,atomic processes ,ParaTAXIS - Abstract
We present our scientific roadmap towards in-situ modeling of non-LTE interactions of XFEL type X-rays with solid density plasmas using a symbiosis of our performance portable, open source, 3D3V particle-in-cell (PIC) code PIConGPU and its X-ray tracing prototype ParaTAXIS. Treating radiation transport via various atomic processes will enable us to synthesize detector signals and gain predictive capabilities for upcoming pump-probe experiments at the European XFEL. With the world’s fastest particle-in-cell code PIConGPU and the raw computational power of the largest high performance computers we open up the possibility for large-scale case studies of unprecedented repeatability.
- Published
- 2017
11. PIConGPU Particle-in-Cell Simulations of Transient High Energy Density Plasmas
- Author
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Huebl, A., Kluge, T., Garten, M., Grund, A., Pausch, R., Widera, R., Matthes, A., Debus, A., Vorberger, J., Fortmann-Grote, C., Chung, H.-K., and Bussmann, M.
- Subjects
PIConGPU EUCALL non-LTE HPC I/O transient plasma processes - Abstract
This talk shows the progress of PIConGPU on modeling transient high-energy density plasmas for the EUCALL annual workshop. We report on new features in PIConGPU, challenges in HPC-scale I/O for PIC simulations and how we interact with simex_platform and our approach for collisional-radiative non-LTE modeling within the scope of particle-in-cell.
- Published
- 2017
12. Predicting SAXS images beyond single scattering
- Author
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Garten, M., Grund, A., Huebl, A., Burau, H., Widera, R., Kluge, T., Fortmann-Grote, C., and Bussmann, M.
- Subjects
pump-probe ,XFEL ,scattering ,HPC ,GPU ,SAXS ,simulation - Abstract
We present a scalable GPU-based software framework for simulating photon scattering processes of X-ray beams in matter using Monte-Carlo methods. These simulations enable us to predict SAXS signals for experiments at upcoming superlative research facilities like the European XFEL. Often the expected outcome of SAXS experiments is produced by a Fourier Transform of a static 2D electron density distribution. Our new framework provides the opportunity to simulate the probing of femtosecond timescale 3D3V electron dynamics with single and multiple scattering and is extendable by more complex physics processes like laser absorption, atomic excitation and de-excitation to further enhance its predictive capability. As a foundation we use libPMacc, a powerful particle-mesh accelerator library that is also used by PIConGPU, the reportedly fastest fully-relativistic 3D3V particle-in-cell code in the world.
- Published
- 2017
13. The need for detailed scattering simulations for Small Angle X-Ray Scattering on laser driven solids
- Author
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Thomas Kluge, Burau, H., Garten, M., Grund, A., Huebl, A., Matthes, A., Jung, F., Widera, R., Zacharias, M., Fortmann-Grote, C., and Bussmann, M.
- Abstract
SIMEX progress report June 2017
- Published
- 2017
14. Predicting SAXS images beyond single scattering
- Author
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(0000-0001-6994-2475) Garten, M., Grund, A., Huebl, A., Burau, H., Widera, R., Kluge, T., Fortmann-Grote, C., Bussmann, M., (0000-0001-6994-2475) Garten, M., Grund, A., Huebl, A., Burau, H., Widera, R., Kluge, T., Fortmann-Grote, C., and Bussmann, M.
- Abstract
We present a scalable GPU-based software framework for simulating photon scattering processes of X-ray beams in matter using Monte-Carlo methods. These simulations enable us to predict SAXS signals for experiments at upcoming superlative research facilities like the European XFEL. Often the expected outcome of SAXS experiments is produced by a Fourier Transform of a static 2D electron density distribution. Our new framework provides the opportunity to simulate the probing of femtosecond timescale 3D3V electron dynamics with single and multiple scattering and is extendable by more complex physics processes like laser absorption, atomic excitation and de-excitation to further enhance its predictive capability. As a foundation we use libPMacc, a powerful particle-mesh accelerator library that is also used by PIConGPU, the reportedly fastest fully-relativistic 3D3V particle-in-cell code in the world.
- Published
- 2017
15. Scalable, multi-GPU photon tracing for in-situ X-ray radiation transport in solid density plasmas
- Author
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(0000-0001-6994-2475) Garten, M., Grund, A., Huebl, A., Burau, H., Widera, R., Kluge, T., Fortmann-Grote, C., Bussmann, M., (0000-0001-6994-2475) Garten, M., Grund, A., Huebl, A., Burau, H., Widera, R., Kluge, T., Fortmann-Grote, C., and Bussmann, M.
- Abstract
We present our scientific roadmap towards in-situ modeling of non-LTE interactions of XFEL type X-rays with solid density plasmas using a symbiosis of our performance portable, open source, 3D3V particle-in-cell (PIC) code PIConGPU and its X-ray tracing prototype ParaTAXIS. Treating radiation transport via various atomic processes will enable us to synthesize detector signals and gain predictive capabilities for upcoming pump-probe experiments at the European XFEL. With the world’s fastest particle-in-cell code PIConGPU and the raw computational power of the largest high performance computers we open up the possibility for large-scale case studies of unprecedented repeatability.
- Published
- 2017
16. PIConGPU Particle-in-Cell Simulations of Transient High Energy Density Plasmas
- Author
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(0000-0003-1943-7141) Huebl, A., Kluge, T., Garten, M., Grund, A., Pausch, R., (0000-0003-1642-0459) Widera, R., (0000-0002-6702-2015) Matthes, A., Debus, A., Vorberger, J., (0000-0002-2579-5546) Fortmann-Grote, C., Chung, H.-K., (0000-0002-8258-3881) Bussmann, M., (0000-0003-1943-7141) Huebl, A., Kluge, T., Garten, M., Grund, A., Pausch, R., (0000-0003-1642-0459) Widera, R., (0000-0002-6702-2015) Matthes, A., Debus, A., Vorberger, J., (0000-0002-2579-5546) Fortmann-Grote, C., Chung, H.-K., and (0000-0002-8258-3881) Bussmann, M.
- Abstract
This talk shows the progress of PIConGPU on modeling transient high-energy density plasmas for the EUCALL annual workshop. We report on new features in PIConGPU, challenges in HPC-scale I/O for PIC simulations and how we interact with simex_platform and our approach for collisional-radiative non-LTE modeling within the scope of particle-in-cell.
- Published
- 2017
17. Modeling Multiple Coherent and Incoherent Photon Scattering in Solid-Density Plasmas with Particle-In-Cell Simulations
- Author
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(0000-0001-6994-2475) Garten, M., (0000-0002-7196-8452) Grund, A., (0000-0003-1943-7141) Hübl, A., Burau, H., (0000-0003-1642-0459) Widera, R., (0000-0001-7990-9564) Pausch, R., (0000-0002-3844-3697) Debus, A., (0000-0003-4861-5584) Kluge, T., (0000-0002-2579-5546) Fortmann-Grote, C., (0000-0003-0390-7671) Schramm, U., (0000-0002-5845-000X) Cowan, T., (0000-0002-8258-3881) Bussmann, M., (0000-0001-6994-2475) Garten, M., (0000-0002-7196-8452) Grund, A., (0000-0003-1943-7141) Hübl, A., Burau, H., (0000-0003-1642-0459) Widera, R., (0000-0001-7990-9564) Pausch, R., (0000-0002-3844-3697) Debus, A., (0000-0003-4861-5584) Kluge, T., (0000-0002-2579-5546) Fortmann-Grote, C., (0000-0003-0390-7671) Schramm, U., (0000-0002-5845-000X) Cowan, T., and (0000-0002-8258-3881) Bussmann, M.
- Abstract
Laser-driven solid density plasmas can be used to generate highly energetic electrons and ions. Diagnosing properties within those plasmas at nm length scales and down to fs timescales is crucial in understanding the involved processes. This has recently become feasible through the advent of X-Ray Free Electron Lasers (XFELs). For instance, XFELs allow imaging the electron density distribution within plasmas via Small Angle X-Ray Scattering (SAXS). We present a scalable GPU-based software framework for simulating photon scattering processes of X-ray beams in matter using Monte-Carlo methods. These simulations enable us to produce synthetic SAXS signals from the interaction of a modeled X-ray pulse with an arbitrarily complex, 3D electron density distribution obtained e.g. from detailed particle-in-cell simulations. Additionally, we present radiation transport methods in our 3D3V fully-relativistic PIC code PIConGPU. These methods enhance modeling of self-imaging of solid-density plasmas and lay the foundation for in-situ simulations of pump-probe experiments. Our new framework allows for single and multiple scattering and is extendable to include complex physics processes like ionization, atomic excitation and de-excitation along the photon path to further enhance its predictive capability.
- Published
- 2017
18. The need for detailed scattering simulations for Small Angle X-Ray Scattering on laser driven solids
- Author
-
(0000-0003-4861-5584) Kluge, T., Burau, H., Garten, M., Grund, A., Huebl, A., (0000-0002-6702-2015) Matthes, A., Jung, F., (0000-0003-1642-0459) Widera, R., Zacharias, M., Fortmann-Grote, C., (0000-0002-8258-3881) Bussmann, M., (0000-0003-4861-5584) Kluge, T., Burau, H., Garten, M., Grund, A., Huebl, A., (0000-0002-6702-2015) Matthes, A., Jung, F., (0000-0003-1642-0459) Widera, R., Zacharias, M., Fortmann-Grote, C., and (0000-0002-8258-3881) Bussmann, M.
- Abstract
SIMEX progress report June 2017
- Published
- 2017
19. Scalable, multi-GPU photon tracing for the interaction of X-Rays with solid density plasmas
- Author
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Grund, A., Huebl, A., Kluge, T., Widera, R., Fortmann-Grote, C., and Bussmann, M.
- Subjects
photon beamline ,SIMEX ,EUCALL ,XFEL ,PIConGPU ,GPU ,x-ray scattering ,ParaTAXIS - Abstract
We present the scientific workflow using our performance portable, open source, 3D3V particle-in-cell (PIC) code PIConGPU and its X-Ray tracing prototype ParaTAXIS to model the interaction of XFEL type X-Rays with solid density plasmas. With an open and modern software environment, our infrastructure is already suited for the largest available supercomputers today and key numerical and methodical challenges have been solved towards first simulations of upcoming pump-probe experiments at the European XFEL.
- Published
- 2016
20. Plasmas, Photons, Open Standards: PIConGPU meets simex_platform through openPMD
- Author
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Huebl, A., Kluge, T., Grund, A., Fortmann-Grote, C., Widera, R., and Bussmann, M.
- Subjects
SIMEX ,openPMD ,EUCALL ,XFEL ,PIConGPU ,GPU - Abstract
Technische Aspekte des Datenaustauschs SIMEX XFEL Wavefronts -> XRT/PIConGPU via openPMD, die wir zusammen erstellt haben und aktueller Stand der Photon-Plasma Streuung der dann anschließenden HPC Simulation auf unserer Seite. Topics: - SIMEX Platform: Short intro functional parts, PIConGPU = interaction - SIMEX Platform: Wavefronts to Photon Picture - openPMD: why, what, how - status XRT (PIConGPU photon scattering code prototype) - typical HPC size of a PIConGPU simulation for dense targets - continuous integration (simex platform & PIConGPU) - maybe some future ideas such as successful docker-ization of PIConGPU for our "relatively fixed" beamline
- Published
- 2016
21. Electrostatic fluctuations in collisional plasmas
- Author
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Rozmus, W., primary, Brantov, A., additional, Fortmann-Grote, C., additional, Bychenkov, V. Yu., additional, and Glenzer, S., additional
- Published
- 2017
- Full Text
- View/download PDF
22. Simulations of ultrafast x–ray laser experiments
- Author
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Fortmann-Grote, C., additional, Andreev, A. A., additional, Appel, K., additional, Branco, J., additional, Briggs, R., additional, Bussmann, M., additional, Buzmakov, A., additional, Garten, M., additional, Grund, A., additional, Huebl, A., additional, Jurek, Z., additional, Loh, N. D., additional, Nakatsutsumi, M., additional, Samoylova, L., additional, Santra, R., additional, Schneidmiller, E. A., additional, Sharma, A., additional, Steiniger, K., additional, Yakubov, S., additional, Yoon, C. H., additional, Yurkov, M. V., additional, Zastrau, U., additional, Ziaja-Motyka, B., additional, and Mancuso, A. P., additional
- Published
- 2017
- Full Text
- View/download PDF
23. VINYL: The VIrtual Neutron and x-raY Laboratory and its applications
- Author
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Chubar, Oleg, Sawhney, Kawal, E., J. C., Hafner, A., Kluyver, T., Bertelsen, M., Upadhyay Kahaly, M., Lecz, Z., Nourbakhsh, S., Mancuso, A. P., and Fortmann-Grote, C.
- Published
- 2020
- Full Text
- View/download PDF
24. Parallel performance of "Synchrotron Radiation Workshop" code: partially coherent calculations for storage rings and time-dependent calculations for XFELs
- Author
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Chubar, Oleg, Sawhney, Kawal, He, A., Chubar, O., Rakitin, M., Samoylova, L., Fortmann-Grote, C., Yakubov, S., and Buzmakov, A.
- Published
- 2020
- Full Text
- View/download PDF
25. SIMEX: Simulation of Experiments at Advanced Light Sources
- Author
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Fortmann-Grote, C., Andreev, A. A., Briggs, R., Bussmann, M., Buzmakov, A., Garten, M., Grund, A., (0000-0003-1943-7141) Huebl, A., Hauff, S., Joy, A., Jurek, Z., Loh, N. D., Rüter, T., Samoylova, L., Santra, R., Schneidmiller, E. A., Sharma, A., Wing, M., Yakubov, S., Yoon, C. H., Yurkov, M. V., Ziaja, B., Mancuso, A. P., Fortmann-Grote, C., Andreev, A. A., Briggs, R., Bussmann, M., Buzmakov, A., Garten, M., Grund, A., (0000-0003-1943-7141) Huebl, A., Hauff, S., Joy, A., Jurek, Z., Loh, N. D., Rüter, T., Samoylova, L., Santra, R., Schneidmiller, E. A., Sharma, A., Wing, M., Yakubov, S., Yoon, C. H., Yurkov, M. V., Ziaja, B., and Mancuso, A. P.
- Abstract
Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these experiments investigating ever more complex physical systems, e.g. biomolecules, complex materials, and ultra--short lived states of highly excited matter. Traditional photon science modelling takes into account only isolated aspects of an experiment, such as the beam propagation, the photon-matter interaction, or the scattering process, making idealized assumptions about the remaining parts, e.g. the source spectrum, temporal structure and coherence properties of the photon beam, or the detector response. In SIMEX, we have implemented a platform for complete start-to-end simulations, following the radiation from the source, through the beam transport optics to the sample or target under investigation, its interaction with and scattering from the sample, and its registration in a photon detector, including a realistic model of the detector response to the radiation. Data analysis tools can be hooked up to the modelling pipeline easily. This allows researchers and facility operators to simulate their experiments and instruments in real life scenarios, identify promising and unattainable regions of the parameter space and ultimately make better use of valuable beamtime.
- Published
- 2016
26. Plasmas, Photons, Open Standards: PIConGPU meets simex_platform through openPMD
- Author
-
(0000-0003-1943-7141) Huebl, A., Kluge, T., Grund, A., Fortmann-Grote, C., Widera, R., Bussmann, M., (0000-0003-1943-7141) Huebl, A., Kluge, T., Grund, A., Fortmann-Grote, C., Widera, R., and Bussmann, M.
- Abstract
Technische Aspekte des Datenaustauschs SIMEX XFEL Wavefronts -> XRT/PIConGPU via openPMD, die wir zusammen erstellt haben und aktueller Stand der Photon-Plasma Streuung der dann anschließenden HPC Simulation auf unserer Seite. Topics: - SIMEX Platform: Short intro functional parts, PIConGPU = interaction - SIMEX Platform: Wavefronts to Photon Picture - openPMD: why, what, how - status XRT (PIConGPU photon scattering code prototype) - typical HPC size of a PIConGPU simulation for dense targets - continuous integration (simex platform & PIConGPU) - maybe some future ideas such as successful docker-ization of PIConGPU for our "relatively fixed" beamline
- Published
- 2016
27. Simulations of single--particle imaging of hydrated proteins with x-ray free-electron lasers.
- Author
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Fortmann-Grote, C., Bielecki, J., Jurek, Z., Santra, R., Ziaja-Motyk, B., and Mancuso, A. P.
- Published
- 2017
- Full Text
- View/download PDF
28. Ultrafast electron kinetics in short pulse laser-driven dense hydrogen
- Author
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Zastrau, U, primary, Sperling, P, additional, Fortmann-Grote, C, additional, Becker, A, additional, Bornath, T, additional, Bredow, R, additional, Döppner, T, additional, Fennel, T, additional, Fletcher, L B, additional, Förster, E, additional, Göde, S, additional, Gregori, G, additional, Harmand, M, additional, Hilbert, V, additional, Laarmann, T, additional, Lee, H J, additional, Ma, T, additional, Meiwes-Broer, K H, additional, Mithen, J P, additional, Murphy, C D, additional, Nakatsutsumi, M, additional, Neumayer, P, additional, Przystawik, A, additional, Skruszewicz, S, additional, Tiggesbäumker, J, additional, Toleikis, S, additional, White, T G, additional, Glenzer, S H, additional, Redmer, R, additional, and Tschentscher, T, additional
- Published
- 2015
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29. Simulations of single-particle imaging of hydrated proteins with x-ray free-electron lasers
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Chubar, Oleg, Sawhney, Kawal, Fortmann-Grote, C., Bielecki, J., Jurek, Z., Santra, R., Ziaja-Motyka, B., and Mancuso, A. P.
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- 2017
- Full Text
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30. Simulations of ultrafast x–ray laser experiments
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Tschentscher, Thomas, Patthey, Luc, Fortmann-Grote, C., Andreev, A. A., Appel, K., Branco, J., Briggs, R., Bussmann, M., Buzmakov, A., Garten, M., Grund, A., Huebl, A., Jurek, Z., Loh, N. D., Nakatsutsumi, M., Samoylova, L., Santra, R., Schneidmiller, E. A., Sharma, A., Steiniger, K., Yakubov, S., Yoon, C. H., Yurkov, M. V., Zastrau, U., Ziaja-Motyka, B., and Mancuso, A. P.
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- 2017
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31. SIMEX: Simulation of Experiments at Advanced Light Sources
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Rüter, T, Samoylova, L, Santra, R, Grund, A, Garten, M, Buzmakov, A, Bussmann, M, Schneidmiller, E, Briggs, R, Sharma, A, Wing, M, Andreev, A, Yakubov, S, Yoon, C, Yurkov, M, Ziaja, B, Joy, A, Hübl, A, Jurek, Z, Loh, N, Mancuso, A, Fortmann-Grote, C, and Hauff, S
- Subjects
Physics - Instrumentation and Detectors ,bepress|Physical Sciences and Mathematics|Physics ,FOS: Physical sciences ,Instrumentation and Detectors (physics.ins-det) ,Computational Physics (physics.comp-ph) ,Physics - Computational Physics - Abstract
Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these experiments investigating ever more complex physical systems, e.g. biomolecules, complex materials, and ultra-short lived states of highly excited matter. Traditional photon science modelling takes into account only isolated aspects of an experiment, such as the beam propagation, the photon-matter interaction, or the scattering process, making idealized assumptions about the remaining parts, e.g.\ the source spectrum, temporal structure and coherence properties of the photon beam, or the detector response. In SIMEX, we have implemented a platform for complete start-to-end simulations, following the radiation from the source, through the beam transport optics to the sample or target under investigation, its interaction with and scattering from the sample, and its registration in a photon detector, including a realistic model of the detector response to the radiation. Data analysis tools can be hooked up to the modelling pipeline easily. This allows researchers and facility operators to simulate their experiments and instruments in real life scenarios, identify promising and unattainable regions of the parameter space and ultimately make better use of valuable beamtime. This work is licensed under the Creative Commons Attribution 3.0 Unported License: http://creativecommons.org/licenses/by/3.0/., Comment: Presented at the 11th NOBUGS conference, Copenhagen, on Oct. 17th 2016. 7 pages, 3 figures, 29 references
32. Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses.
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Round A, Jungcheng E, Fortmann-Grote C, Giewekemeyer K, Graceffa R, Kim C, Kirkwood H, Mills G, Round E, Sato T, Pascarelli S, and Mancuso A
- Subjects
- Crystallography, X-Ray, X-Rays, Lasers, Electrons, Proteins chemistry
- Abstract
The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability., (© 2024. The Author(s), under exclusive license to Springer Nature Switzerland AG.)
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- 2024
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33. Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser.
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E J, Stransky M, Shen Z, Jurek Z, Fortmann-Grote C, Bean R, Santra R, Ziaja B, and Mancuso AP
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- X-Ray Diffraction, X-Rays, Lasers, Solvents, Electrons, Water
- Abstract
The noise caused by sample heterogeneity (including sample solvent) has been identified as one of the determinant factors for a successful X-ray single-particle imaging experiment. It influences both the radiation damage process that occurs during illumination as well as the scattering patterns captured by the detector. Here, we investigate the impact of water layer thickness and radiation damage on orientation recovery from diffraction patterns of the nitrogenase iron protein. Orientation recovery is a critical step for single-particle imaging. It enables to sort a set of diffraction patterns scattered by identical particles placed at unknown orientations and assemble them into a 3D reciprocal space volume. The recovery quality is characterized by a "disconcurrence" metric. Our results show that while a water layer mitigates protein damage, the noise generated by the scattering from it can introduce challenges for orientation recovery and is anticipated to cause problems in the phase retrieval process to extract the desired protein structure. Compared to these disadvantageous effects due to the thick water layer, the effects of radiation damage on the orientation recovery are relatively small. Therefore, minimizing the amount of residual sample solvent should be considered a crucial step in improving the fidelity and resolution of X-ray single-particle imaging experiments., (© 2023. Springer Nature Limited.)
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- 2023
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34. Genome Update for Pseudomonas fluorescens Isolate SBW25.
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Fortmann-Grote C, Hugoson E, Summers J, Theodosiou L, and Rainey PB
- Abstract
We report a genome update for Pseudomonas fluorescens isolate SBW25. The updated genome assembly, which was derived from the original isolate, is based on PacBio long-read sequence data. It shows three minor differences, compared with the previously published genome sequence. Original annotations were merged with recent automated annotations to preserve information.
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- 2023
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35. Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser.
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E J, Stransky M, Jurek Z, Fortmann-Grote C, Juha L, Santra R, Ziaja B, and Mancuso AP
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- Electrons, Photons, Lasers, Molecular Dynamics Simulation, Molecular Imaging methods, Oxidoreductases chemistry, Oxidoreductases radiation effects, Water chemistry, X-Ray Diffraction instrumentation, X-Ray Diffraction methods, X-Rays adverse effects
- Abstract
We present a computational case study of X-ray single-particle imaging of hydrated proteins on an example of 2-Nitrogenase-Iron protein covered with water layers of various thickness, using a start-to-end simulation platform and experimental parameters of the SPB/SFX instrument at the European X-ray Free-Electron Laser facility. The simulations identify an optimal thickness of the water layer at which the effective resolution for imaging the hydrated sample becomes significantly higher than for the non-hydrated sample. This effect is lost when the water layer becomes too thick. Even though the detailed results presented pertain to the specific sample studied, the trends which we identify should also hold in a general case. We expect these findings will guide future single-particle imaging experiments using hydrated proteins., (© 2021. The Author(s).)
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- 2021
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36. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser.
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Fortmann-Grote C, Buzmakov A, Jurek Z, Loh ND, Samoylova L, Santra R, Schneidmiller EA, Tschentscher T, Yakubov S, Yoon CH, Yurkov MV, Ziaja-Motyka B, and Mancuso AP
- Abstract
Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.
- Published
- 2017
- Full Text
- View/download PDF
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