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Gao C, Li Y, Jin F, Zeng J, Yuan J. Transmissions of an x-ray free electron laser pulse through Al: Influence of nonequilibrium electron kinetics. Phys Rev E 2024; 110:015201. [PMID: 39160986 DOI: 10.1103/physreve.110.015201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/12/2024] [Indexed: 08/21/2024]
Abstract
A theoretical model for investigating the radiative transfer of an x-ray free electron laser (XFEL) pulse is developed based on a one-dimensional radiative transfer equation. The population dynamics of energy levels is obtained by rate equation approximation coupling with the Fokker-Planck equation, in which the electron energy distribution function (EEDF) is self-consistently determined. As an illustrative example, XFEL pulse propagation through a solid-density aluminum (Al) is investigated. The characteristics of the temporal evolution of the x-ray pulse shape, level population, and EEDF are demonstrated. The EEDF usually has two parts in XFEL-Al interactions: the near equilibrium part in the lower energy regions and the nonequilibrium part in the higher energy region. The deep gap between the two parts is quickly filled in the solid-density Al plasma. The pulse shape is distorted and the duration shortens as the x-ray pulse propagates through the Al sample. The x-ray transmission spectra were compared with experimental and other theoretical results, and good agreement was found. There are slight discrepancies between the transmission obtained by solving the Fokker-Planck equation and Maxwellian assumptions because nonequilibrium electrons in the higher energy region account for only a small fraction of the total electrons.
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Affiliation(s)
| | - Yongjun Li
- Graduate School of China Academy of Engineering Physics, Beijing 100193, People's Republic of China
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2
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Cardoch S, Trost F, Scott HA, Chapman HN, Caleman C, Timneanu N. Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions. Phys Rev E 2023; 107:015205. [PMID: 36797944 DOI: 10.1103/physreve.107.015205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/09/2022] [Indexed: 01/19/2023]
Abstract
Saturable absorption is a nonlinear effect where a material's ability to absorb light is frustrated due to a high influx of photons and the creation of electron vacancies. Experimentally induced saturable absorption in copper revealed a reduction in the temporal duration of transmitted x-ray laser pulses, but a detailed account of changes in opacity and emergence of resonances is still missing. In this computational work, we employ nonlocal thermodynamic equilibrium plasma simulations to study the interaction of femtosecond x rays and copper. Following the onset of frustrated absorption, we find that a K-M resonant transition occurring at highly charged states turns copper opaque again. The changes in absorption generate a transient transparent window responsible for the shortened transmission signal. We also propose using fluorescence induced by the incident beam as an alternative source to achieve shorter x-ray pulses. Intense femtosecond x rays are valuable to probe the structure and dynamics of biological samples or to reach extreme states of matter. Shortened pulses could be relevant for emerging imaging techniques.
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Affiliation(s)
- Sebastian Cardoch
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Fabian Trost
- Center for Free-Electron Laser Science CFEL, Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Howard A Scott
- Lawrence Livermore National Laboratory, L-18, P.O. Box 808, Livermore, California 94550, USA
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.,Center for Free-Electron Laser Science CFEL, Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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3
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Jin R, Jurek Z, Santra R, Son SK. Plasma environmental effects in the atomic structure for simulating x-ray free-electron-laser-heated solid-density matter. Phys Rev E 2022; 106:015206. [PMID: 35974549 DOI: 10.1103/physreve.106.015206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
High energy density (HED) matter exists extensively in the Universe, and it can be created with extreme conditions in laboratory facilities such as x-ray free-electron lasers (XFEL). In HED matter, the electronic structure of individual atomic ions is influenced by a dense plasma environment, and one of the most significant phenomena is the ionization potential depression (IPD). Incorporation of the IPD effects is of great importance in accurate modeling of dense plasmas. All theoretical treatments of IPD so far have been based on the assumption of local thermodynamic equilibrium, but its validity is questionable in ultrafast formation dynamics of dense plasmas, particularly when interacting with intense XFEL pulses. A treatment of transient IPD, based on an electronic-structure calculation of an atom in the presence of a plasma environment described by classical particles, has recently been proposed [Phys. Rev. E 103, 023203 (2021)2470-004510.1103/PhysRevE.103.023203], but its application to and impact on plasma dynamics simulations have not been investigated yet. In this work, we extend XMDYN, a hybrid quantum-classical approach combining Monte Carlo and molecular dynamics, by incorporating the proposed IPD treatment into plasma dynamics simulations. We demonstrate the importance of the IPD effects in theoretical modeling of aluminum dense plasmas by comparing two XMDYN simulations: one with electronic-structure calculations of isolated atoms (without IPD) and the other with those of atoms embedded in a plasma (with IPD). At equilibrium, the mean charge obtained in the plasma simulation with IPD is in good agreement with the full quantum-mechanical average-atom model. The present approach promises to be a reliable tool to simulate the creation and nonequilibrium evolution of dense plasmas induced by ultraintense and ultrashort XFEL pulses.
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Affiliation(s)
- Rui Jin
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Zoltan Jurek
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestrasse 9-11, 22607 Hamburg, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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4
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Jin R, Abdullah MM, Jurek Z, Santra R, Son SK. Transient ionization potential depression in nonthermal dense plasmas at high x-ray intensity. Phys Rev E 2021; 103:023203. [PMID: 33735970 DOI: 10.1103/physreve.103.023203] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/22/2021] [Indexed: 11/07/2022]
Abstract
The advent of x-ray free-electron lasers (XFELs), which provide intense ultrashort x-ray pulses, has brought a new way of creating and analyzing hot and warm dense plasmas in the laboratory. Because of the ultrashort pulse duration, the XFEL-produced plasma will be out of equilibrium at the beginning, and even the electronic subsystem may not reach thermal equilibrium while interacting with a femtosecond timescale pulse. In the dense plasma, the ionization potential depression (IPD) induced by the plasma environment plays a crucial role for understanding and modeling microscopic dynamical processes. However, all theoretical approaches for IPD have been based on local thermal equilibrium (LTE), and it has been controversial to use LTE IPD models for the nonthermal situation. In this work, we propose a non-LTE (NLTE) approach to calculate the IPD effect by combining a quantum-mechanical electronic-structure calculation and a classical molecular dynamics simulation. This hybrid approach enables us to investigate the time evolution of ionization potentials and IPDs during and after the interaction with XFEL pulses, without the limitation of the LTE assumption. In our NLTE approach, the transient IPD values are presented as distributions evolving with time, which cannot be captured by conventional LTE-based models. The time-integrated ionization potential values are in good agreement with benchmark experimental data on solid-density aluminum plasma and other theoretical predictions based on LTE. The present work is promising to provide critical insights into nonequilibrium dynamics of dense plasma formation and thermalization induced by XFEL pulses.
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Affiliation(s)
- Rui Jin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240 Shanghai, China
| | | | - Zoltan Jurek
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.,Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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5
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Kozlov A, Gureyev TE, Paganin DM, Martin AV, Caleman C, Quiney HM. Recovery of undamaged electron-density maps in the presence of damage-induced partial coherence in single-particle imaging. IUCRJ 2020; 7:1114-1123. [PMID: 33209322 PMCID: PMC7642773 DOI: 10.1107/s2052252520013019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Resolving the electronic structure of single biological molecules in their native state was among the primary motivations behind X-ray free-electron lasers. The ultra-short pulses they produce can outrun the atomic motion induced by radiation damage, but the electronic structure of the sample is still significantly modified from its original state. This paper explores the decoherence of the scattered signal induced by temporal evolution of the electronic structure in the sample molecule. It is shown that the undamaged electron density of a single-molecule sample can often be retrieved using only the two most occupied modes from the coherent mode decomposition of the partially coherent diffraction fluence.
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Affiliation(s)
- Alexander Kozlov
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Timur E. Gureyev
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
- Faculty of Health Sciences, University of Sydney, Sydney, NSW 2006, Australia
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - David M. Paganin
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - Andrew V. Martin
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
- School of Physics, RMIT University, Melbourne, Victoria 3000, Australia
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, PO Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, DE-22607 Hamburg, Germany
| | - Harry M. Quiney
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
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6
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Le HP, Sherlock M, Scott HA. Influence of atomic kinetics on inverse bremsstrahlung heating and nonlocal thermal transport. Phys Rev E 2019; 100:013202. [PMID: 31499790 DOI: 10.1103/physreve.100.013202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Indexed: 11/07/2022]
Abstract
This paper describes a computational model that self-consistently combines physics of kinetic electrons and atomic processes in a single framework. The formulation consists of a kinetic Vlasov-Boltzmann-Fokker-Planck equation for free electrons and a non-Maxwellian collisional-radiative model for atomic state populations. We utilize this model to examine the influence of atomic kinetics on inverse bremsstrahlung (IB) heating and nonlocal thermal transport. We show that atomic kinetics affects nonlinear IB absorption rates by further modifying the electron distribution in addition to laser heating. We also show that accurate modeling of nonlocal heat flow requires a self-consistent treatment of atomic kinetics, because the effective thermal conductivity strongly depends on the ionization balance of the plasma.
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Affiliation(s)
- Hai P Le
- Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Mark Sherlock
- Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Howard A Scott
- Lawrence Livermore National Laboratory, Livermore, California 94551, USA
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7
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Nass K. Radiation damage in protein crystallography at X-ray free-electron lasers. Acta Crystallogr D Struct Biol 2019; 75:211-218. [PMID: 30821709 PMCID: PMC6400258 DOI: 10.1107/s2059798319000317] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/07/2019] [Indexed: 01/17/2023] Open
Abstract
Radiation damage is still the most limiting factor in obtaining high-resolution structures of macromolecules in crystallographic experiments at synchrotrons. With the advent of X-ray free-electron lasers (XFELs) that produce ultrashort and highly intense X-ray pulses, it became possible to outrun most of the radiation-damage processes occurring in the sample during exposure to XFEL radiation. Although this is generally the case, several experimental and theoretical studies have indicated that structures from XFELs may not always be radiation-damage free. This is especially true when higher intensity pulses are used and protein molecules that contain heavy elements in their structures are studied. Here, the radiation-damage mechanisms that occur in samples exposed to XFEL pulses are summarized, results that show indications of radiation damage are reviewed and methods that can partially overcome it are discussed.
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Affiliation(s)
- Karol Nass
- Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
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8
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Hao Y, Inhester L, Hanasaki K, Son SK, Santra R. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041707. [PMID: 26798806 PMCID: PMC4711638 DOI: 10.1063/1.4919794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 04/24/2015] [Indexed: 05/16/2023]
Abstract
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
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9
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Abstract
Next-generation synchrotron radiation sources, such as X-ray free-electron lasers, energy recovery linacs, and ultra-low-emittance storage rings, are catalyzing novel methods of biomolecular microcrystallography and solution scattering. These methods are described and future trends are predicted. Importantly, there is a growing realization that serial microcrystallography and certain cutting-edge solution scattering experiments can be performed at existing storage ring sources by utilizing new technology. In this sense, next-generation sources are serving two distinct functions, namely, provision of new capabilities that require the newer sources and inspiration of new methods that can be performed at existing sources.
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10
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Hau-Riege SP, Bennion BJ. Reproducible radiation-damage processes in proteins irradiated by intense x-ray pulses. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022705. [PMID: 25768529 DOI: 10.1103/physreve.91.022705] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 06/04/2023]
Abstract
X-ray free-electron lasers have enabled femtosecond protein nanocrystallography, a novel method to determine the structure of proteins. It allows time-resolved imaging of nanocrystals that are too small for conventional crystallography. The short pulse duration helps in overcoming the detrimental effects of radiation damage because x rays are scattered before the sample has been significantly altered. It has been suggested that, fortuitously, the diffraction process self-terminates abruptly once radiation damage destroys the crystalline order. Our calculations show that high-intensity x-ray pulses indeed trigger a cascade of damage processes in ferredoxin crystals, a particular metalloprotein of interest. However, we found that the damage process is initially not completely random. Correlations exist among the protein monomers, so that Bragg diffraction still occurs in the damaged crystals, despite significant atomic displacements. Our results show that the damage process is reproducible to a certain degree, which is potentially beneficial for the orientation step in single-molecule imaging.
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Affiliation(s)
- Stefan P Hau-Riege
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Brian J Bennion
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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11
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Leonov A, Ksenzov D, Benediktovitch A, Feranchuk I, Pietsch U. Time dependence of X-ray polarizability of a crystal induced by an intense femtosecond X-ray pulse. IUCRJ 2014; 1:402-17. [PMID: 25485121 PMCID: PMC4224459 DOI: 10.1107/s2052252514018156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/07/2014] [Indexed: 06/01/2023]
Abstract
The time evolution of the electron density and the resulting time dependence of Fourier components of the X-ray polarizability of a crystal irradiated by highly intense femtosecond pulses of an X-ray free-electron laser (XFEL) is investigated theoretically on the basis of rate equations for bound electrons and the Boltzmann equation for the kinetics of the unbound electron gas. The photoionization, Auger process, electron-impact ionization, electron-electron scattering and three-body recombination have been implemented in the system of rate equations. An algorithm for the numerical solution of the rate equations was simplified by incorporating analytical expressions for the cross sections of all the electron configurations in ions within the framework of the effective charge model. Using this approach, the time dependence of the inner shell populations during the time of XFEL pulse propagation through the crystal was evaluated for photon energies between 4 and 12 keV and a pulse width of 40 fs considering a flux of 10(12) photons pulse(-1) (focusing on a spot size of ∼1 µm). This flux corresponds to a fluence ranging between 0.8 and 2.4 mJ µm(-2). The time evolution of the X-ray polarizability caused by the change of the atomic scattering factor during the pulse propagation is numerically analyzed for the case of a silicon crystal. The time-integrated polarizability drops dramatically if the fluence of the X-ray pulse exceeds 1.6 mJ µm(-2).
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Affiliation(s)
- A. Leonov
- Department of Theoretical Physics, Belarusian State University, 220030 Nezavisimosti Avenue 4, Minsk, Belarus
| | - D. Ksenzov
- Festkörperphysik, Universität Siegen, 57072 Walter-Flex-Straße 3, Siegen, Germany
| | - A. Benediktovitch
- Department of Theoretical Physics, Belarusian State University, 220030 Nezavisimosti Avenue 4, Minsk, Belarus
| | - I. Feranchuk
- Department of Theoretical Physics, Belarusian State University, 220030 Nezavisimosti Avenue 4, Minsk, Belarus
| | - U. Pietsch
- Festkörperphysik, Universität Siegen, 57072 Walter-Flex-Straße 3, Siegen, Germany
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