XMDYN and XATOM: versatile simulation tools for quantitative modeling of X-ray free-electron laser induced dynamics of matter
Abstract
Rapid development of X-ray free-electron laser (XFEL) science has taken place in recent years owing to the consecutive launch of large-scale XFEL instruments around the world. Research areas such as warm dense matter physics and coherent X-ray imaging take advantage of the unprecedentedly high intensities of XFELs. A single XFEL pulse can induce very complex dynamics within matter initiated by core-hole photoionization. Owing to this complexity, theoretical modeling revealing details of the excitation and relaxation of irradiated matter is important for the correct interpretation of the measurements and for proposing new experiments.XMDYN is a computer simulation tool developed for modeling dynamics of matter induced by high-intensity X-rays. It utilizes atomic data calculated by the ab initio XATOM toolkit. Here these tools are discussed in detail.
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For atoms, an experimentally well-tested approach to describing the electronic response to high-intensity x-rays is the model implemented within XATOM [2,112].
“For atoms, an experimentally well-tested approach to describing the electronic response to high-intensity x-rays is the model implemented within XATOM [2,112].”
From Roadmap of ultrafast x-ray atomic and molecular physics (2018) · cites this paper as [112]
An experimentally tested approach to addressing these challenges is the model implemented in XMDYN [112,113].
“An experimentally tested approach to addressing these challenges is the model implemented in XMDYN [112,113].”
From Roadmap of ultrafast x-ray atomic and molecular physics (2018) · cites this paper as [112]
Cites
A Simplification of the Hartree-Fock Method
Slater, J. C. (1951) · Physical Review · doi:10.1103/physrev.81.385 · Cited by 4,600 · see citing works
Swope, W. C., Andersen, H. C., Berens, P. H., & Wilson, K. R. (1982) · The Journal of Chemical Physics · doi:10.1063/1.442716 · Cited by 4,068 · see citing works
Brenner, D. W. (1990) · Physical review. B, Condensed matter · doi:10.1103/physrevb.42.9458 · Cited by 4,047 · see citing works
First lasing and operation of an ångstrom-wavelength free-electron laser
Emma, P., Akre, R., Arthur, J., Bionta, R., Bostedt, C., Bozek, J., Brachmann, A., Bucksbaum, P., Coffee, R., Decker, F.-J., et al. (2010) · Nature Photonics · doi:10.1038/nphoton.2010.176 · Cited by 3,167 · see citing works
A compact X-ray free-electron laser emitting in the sub-ångström region
Ishikawa, T., Aoyagi, H., Asaka, T., Asano, Y., Azumi, N., Bizen, T., Ego, H., Fukami, K., Fukui, T., Furukawa, Y., et al. (2012) · Nature Photonics · doi:10.1038/nphoton.2012.141 · Cited by 1,824 · see citing works
Operation of a free-electron laser from the extreme ultraviolet to the water window
Ackermann, W., Asova, G., Ayvazyan, V., Azima, A., Baboi, N., Bahr, J. W., Balandin, V., Beutner, B., Brandt, A., Bolzmann, A., et al. (2007) · Nature Photonics · doi:10.1038/nphoton.2007.76 · Cited by 1,644 · see citing works
Binary-encounter-dipole model for electron-impact ionization
Kim, Y., & Rudd, M. E. (1994) · Physical Review A · doi:10.1103/physreva.50.3954 · Cited by 1,027 · see citing works
Femtosecond electronic response of atoms to ultra-intense X-rays
Young, L., Kanter, E. P., Krässig, B., Li, Y., March, A. M., Pratt, S. T., Santra, R., Southworth, S. H., Rohringer, N., DiMauro, L. F., et al. (2010) · Nature · doi:10.1038/nature09177 · Cited by 792 · see citing works
Self-citationTong, X., & Chu, S. (1997) · Chemical Physics · doi:10.1016/s0301-0104(97)00063-3 · Cited by 422 · see citing works
Ultra-efficient ionization of heavy atoms by intense X-ray free-electron laser pulses
Rudek, B., Son, S.-K., Foucar, L., Epp, S. W., Erk, B., Hartmann, R., Adolph, M., Andritschke, R., Aquila, A., Berrah, N., et al. (2012) · Nature Photonics · doi:10.1038/nphoton.2012.261 · Cited by 261 · cited 3× · see citing works
“The coupled rate equations are solved by (i) direct time propagation (Son, Young & Santra, 2011), (ii) a Monte Carlo approach with a pre-calculated table of atomic data (Rudek et al., 2012; Son & Santra, 2012) or (iii) Monte Carlo on the fly (Fukuzawa et al., 2013).”
MethodSelf-citationNonlinear Atomic Response to Intense Ultrashort X Rays
Doumy, G., Roedig, C., Son, S.-K., Blaga, C. I., DiChiara, A. D., Santra, R., Berrah, N., Bostedt, C., Bozek, J. D., Bucksbaum, P. H., et al. (2011) · Physical Review Letters · doi:10.1103/physrevlett.106.083002 · Cited by 255 · see citing works
Self-citationDense plasmas, screened interactions, and atomic ionization
Murillo, M. S. (1998) · Physics Reports · doi:10.1016/s0370-1573(98)00017-9 · Cited by 241 · see citing works
Dynamics of biological molecules irradiated by short x-ray pulses
Hau‐Riege, S. P., London, R. A., & Szöke, A. (2004) · Physical Review E · doi:10.1103/physreve.69.051906 · Cited by 217 · see citing works
Impact of hollow-atom formation on coherent x-ray scattering at high intensity
Son, S.-K., Young, L., & Santra, R. (2011) · Physical Review A · doi:10.1103/physreva.83.033402 · Cited by 209 · see citing works
Self-citationX-ray nonlinear optical processes using a self-amplified spontaneous emission free-electron laser
Rohringer, N., & Santra, R. (2007) · Physical Review A · doi:10.1103/physreva.76.033416 · Cited by 175 · see citing works
Self-citationDeep Inner-Shell Multiphoton Ionization by Intense X-Ray Free-Electron Laser Pulses
Fukuzawa, H., Son, S.-K., Motomura, K., Mondal, S., Nagaya, K., Wada, S., Liu, X.-J., Feifel, R., Tachibana, T., Ito, Y., et al. (2013) · Physical Review Letters · doi:10.1103/physrevlett.110.173005 · Cited by 157 · see citing works
Self-citationMicroscopic Analysis of Large-Cluster Explosion in Intense Laser Fields
Jungreuthmayer, C., Geissler, M., Zanghellini, J., et al. (2004) · Physical Review Letters · doi:10.1103/physrevlett.92.133401 · Cited by 148 · see citing works
Femtosecond X-ray-induced explosion of C60 at extreme intensity
Murphy, B. F., Osipov, T., Jurek, Z., Fang, L., Son, S.-K., Mucke, M., Eland, J. H. D., Zhaunerchyk, V., Feifel, R., Avaldi, L., et al. (2014) · Nature Communications · doi:10.1038/ncomms5281 · Cited by 138 · see citing works
Self-citationGeneralized pseudospectral methods with mappings for bound and resonance state problems
Yao, G., & Chu, S. (1993) · Chemical Physics Letters · doi:10.1016/0009-2614(93)90025-v · Cited by 136 · see citing works
Dynamics in a cluster under the influence of intense femtosecond hard X-ray pulses
Jurek, Z., Faigel, G., & Tegze, M. (2004) · The European Physical Journal D · doi:10.1140/epjd/e2004-00033-3 · Cited by 134 · see citing works
Self-citationMultiwavelength Anomalous Diffraction at High X-Ray Intensity
Son, S.-K., Chapman, H. N., & Santra, R. (2011) · Physical Review Letters · doi:10.1103/physrevlett.107.218102 · Cited by 120 · see citing works
Self-citationSimulation of exploding clusters ionized by high-intensity femtosecond laser pulses
Ditmire, T. (1998) · Physical Review A · doi:10.1103/physreva.57.r4094 · Cited by 115 · see citing works
Theory of Multiphoton Multielectron Ionization of Xenon under Strong 93-eV Radiation
Makris, M. G., Lambropoulos, P., & Mihelič, A. (2009) · Physical Review Letters · doi:10.1103/physrevlett.102.033002 · Cited by 110 · see citing works
ATOMIC AND MOLECULAR DYNAMICS IN INTENSE OPTICAL FIELDS
Sheehy, B., & DiMauro, L. F. (1996) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.47.1.463 · Cited by 99 · see citing works
Synchrotron Light Sources and Free-Electron Lasers
Jaeschke, E., Khan, S., Schneider, J. R., et al. (2014) · Springer eBooks · doi:10.1007/978-3-319-04507-8 · Cited by 95 · see citing works
Son, S.-K., & Santra, R. (2012) · Physical Review A · doi:10.1103/physreva.85.063415 · Cited by 80 · see citing works
Self-citationElectron Release of Rare-Gas Atomic Clusters under an Intense Laser Pulse
Siedschlag, C., & Rost, J. M. (2002) · Physical Review Letters · doi:10.1103/physrevlett.89.173401 · Cited by 78 · see citing works
Nanoplasma Formation by High Intensity Hard X-rays
Tachibana, T., Jurek, Z., Fukuzawa, H., Motomura, K., Nagaya, K., Wada, S., Johnsson, P., Siano, M., Mondal, S., Ito, Y., et al. (2015) · Scientific Reports · doi:10.1038/srep10977 · Cited by 73 · see citing works
Self-citationResonance-enhanced multiple ionization of krypton at an x-ray free-electron laser
Rudek, B., Rolles, D., Son, S.-K., Foucar, L., Erk, B., Epp, S. W., Boll, R., Anielski, D., Bostedt, C., Schorb, S., et al. (2013) · Physical Review A · doi:10.1103/physreva.87.023413 · Cited by 71 · see citing works
Self-citationSantra, R. (2008) · Journal of Physics B Atomic Molecular and Optical Physics · doi:10.1088/0953-4075/42/2/023001 · Cited by 70 · see citing works
Self-citationModelling dynamics of samples exposed to free-electron-laser radiation with Boltzmann equations
Ziaja, B., Castro, A., Weckert, E., & Möller, T. B. (2006) · The European Physical Journal D · doi:10.1140/epjd/e2006-00240-x · Cited by 63 · see citing works
Self-citationEfficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
Hao, Y., Inhester, L., Hanasaki, K., Son, S.-K., & Santra, R. (2015) · Structural Dynamics · doi:10.1063/1.4919794 · Cited by 61 · see citing works
Self-citationMotomura, K., Fukuzawa, H., Son, S.-K., Mondal, S., Tachibana, T., Ito, Y., Kimura, M., Nagaya, K., Sakai, T., Matsunami, K., et al. (2013) · Journal of Physics B Atomic Molecular and Optical Physics · doi:10.1088/0953-4075/46/16/164024 · Cited by 53 · see citing works
Self-citationQian, X., & Schlick, T. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1458542 · Cited by 51 · see citing works
Yoon, C. H., Yurkov, M. V., Schneidmiller, E. A., Samoylova, L., Buzmakov, A., Jurek, Z., Ziaja, B., Santra, R., Loh, N. D., Tschentscher, T., et al. (2016) · Scientific Reports · doi:10.1038/srep24791 · Cited by 51 · see citing works
Self-citationGeorgescu, I., Saalmann, U., & Rost, J. M. (2007) · Physical Review A · doi:10.1103/physreva.76.043203 · Cited by 47 · see citing works
Incoherent x-ray scattering in single molecule imaging
Slowik, J. M., Son, S.-K., Dixit, G., Jurek, Z., & Santra, R. (2014) · New Journal of Physics · doi:10.1088/1367-2630/16/7/073042 · Cited by 40 · see citing works
Self-citationFully microscopic analysis of laser-driven finite plasmas using the example of clusters
Peltz, C., Varin, C., Brabec, T., & Fennel, T. (2012) · New Journal of Physics · doi:10.1088/1367-2630/14/6/065011 · Cited by 31 · see citing works
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms
Barash, D., Yang, L., Qian, X., et al. (2002) · Journal of Computational Chemistry · doi:10.1002/jcc.10196 · Cited by 31 · see citing works
Determination of multiwavelength anomalous diffraction coefficients at high x-ray intensity
Son, S.-K., Chapman, H. N., & Santra, R. (2013) · Journal of Physics B Atomic Molecular and Optical Physics · doi:10.1088/0953-4075/46/16/164015 · Cited by 30 · see citing works
Self-citationTowards RIP using free-electron laser SFX data
Galli, L., Son, S.-K., White, T. A., et al. (2015) · Journal of Synchrotron Radiation · doi:10.1107/s1600577514027854 · Cited by 29 · see citing works
Self-citationTowards phasing using high X-ray intensity
Galli, L., Son, S.-K., Barends, T. R. M., White, T. A., Barty, A., Botha, S., Boutet, S., Caleman, C., Doak, R. B., Nanao, M., et al. (2015) · IUCrJ · doi:10.1107/s2052252515014049 · Cited by 28 · see citing works
Self-citationThiele, R., Son, S.-K., Ziaja, B., et al. (2012) · Physical Review A · doi:10.1103/physreva.86.033411 · Cited by 26 · see citing works
Self-citationModeling quantum processes in classical molecular dynamics simulations of dense plasmas
Hau‐Riege, S. P., Weisheit, J. C., Castor, J., et al. (2013) · New Journal of Physics · doi:10.1088/1367-2630/15/1/015011 · Cited by 25 · see citing works
Galli, L., Son, S.-K., Klinge, M., Bajt, S., Barty, A., Bean, R., Betzel, C., Beyerlein, K. R., Caleman, C., Doak, R. B., et al. (2015) · Structural Dynamics · doi:10.1063/1.4919398 · Cited by 23 · see citing works
Self-citationDynamics of photo-activated Coulomb complexes
Gnodtke, C., Saalmann, U., & Rost, J.-M. (2011) · New Journal of Physics · doi:10.1088/1367-2630/13/1/013028 · Cited by 19 · see citing works
Applicability of the classical molecular dynamics method to study x-ray irradiated molecular systems
Jurek, Z., Ziaja, B., & Santra, R. (2014) · Journal of Physics B Atomic Molecular and Optical Physics · doi:10.1088/0953-4075/47/12/124036 · Cited by 15 · see citing works
Self-citationDynamics of photo-activated Coulomb complexesPreprint
Gnodtke, C., Saalmann, U., & Rost, J. M. (2011) · Cited by 11 · see citing works
Hydrodynamic model for picosecond propagation of laser-created nanoplasmas
Saxena, V., Jurek, Z., Ziaja, B., & Santra, R. (2015) · High Energy Density Physics · doi:10.1016/j.hedp.2015.04.002 · Cited by 4 · see citing works
Self-citationHydrodynamic model for picosecond propagation of laser-created nanoplasmas
Saxena, V., Jurek, Z., Ziaja, B., & Santra, R. (2015) · Desy publication database (The Deutsches Elektronen-Synchrotron) · Cited by 4 · see citing works
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Roadmap of ultrafast x-ray atomic and molecular physics
Young, L., Ueda, K., Gühr, M., Bucksbaum, P. H., Simon, M., Mukamel, S., Rohringer, N., Prince, K. C., Masciovecchio, C., Meyer, M., et al. (2018) · Journal of Physics B: Atomic, Molecular and Optical Physics · doi:10.1088/1361-6455/aa9735 · Cited by 337 · see citing works
Self-citationFemtosecond response of polyatomic molecules to ultra-intense hard X-rays
Rudenko, A., Inhester, L., Hanasaki, K., Li, X., Robatjazi, S. J., Erk, B., Boll, R., Toyota, K., Hao, Y., Vendrell, O., et al. (2017) · Nature · doi:10.1038/nature22373 · Cited by 175 · see citing works
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- Authors
- Jurek, Z., Son, S.-K., Ziaja, B., & Santra, R.
- Affiliations
- Deutsches Elektronen-Synchrotron DESY (DE)
- Universität Hamburg (DE)
- Venue
- Journal of Applied Crystallography
- Published
- 2016-04-22
- Volume
- 49
- Issue
- 3
- Pages
- 1048-1056
- ISSN
- 0021-8898 (ISSN-L)
- 1600-5767
- OpenAlex
- W2336407495
- Cited by
- 103
- References
- 50
- Citations by year
- 2026: 4 · 2025: 11 · 2024: 11 · 2023: 12 · 2022: 11 · 2021: 7 · 2020: 12 · 2019: 9 · 2018: 8 · 2017: 14 · 2016: 4
- FWCI
- 13.07
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Journal of Applied Crystallography (publishedVersion)
- Desy publication database (The Deutsches Elektronen-Synchrotron) (submittedVersion)
- Topics
- Physical Sciences › Physics and Astronomy › Radiation › X-ray Spectroscopy and Fluorescence Analysis
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Laser-Matter Interactions and Applications
- Physical Sciences › Physics and Astronomy › Radiation › Advanced X-ray Imaging Techniques
- Keywords
- X-ray free-electron laser, warm dense matter, coherent X-ray imaging, atomic data
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