arXiv subjects

Zoltan Jurek

Publications and source records attributed to Zoltan Jurek.

16 recordsLinked to original sources

arXiv2024

Distinct transient structural rearrangement of ionized water revealed by XFEL X-ray pump X-ray probe experiment

Using X-ray free electron laser (XFEL) radiation to conduct an X-ray pump X-ray probe experiment, we studied strongly ionized water as part of our ongoing work on radiation damage. After irradiance with a pump pulse with a nominal fluence of ~$5 \times 10^5$ J/cm$^2$, we observed for pump-probe delays of 75 fs and longer an unexpected structural rearrangement, exhibiting a characteristic length scale of ~9 Å. Simulations suggest that the experiment probes a superposition of ionized water in two distinct regimes. In the first, fluences expected at the X-ray focus create nearly completely ionized water, which as a result becomes effectively transparent to the probe. In the second regime, out of focus pump radiation produces O$^{1+}$ and O$^{2+}$ ions, which rearrange due to Coulombic repulsion over 10s of fs. Importantly, structural changes in the low fluence regime have implications for the design of two-pulse X-ray experiments that aim to study unperturbed liquid samples. Our simulations account for two key observations in the experimental data: the decrease in ambient water signal and an increase in low-angle X-ray scattering. They cannot, however, account for the experimentally observed 9 Å feature. A satisfactory account of this feature presents a new challenge for theory.

physics.plasm-ph↗

arXiv2023

Femtosecond reduction of atomic scattering factors triggered by intense x-ray pulse

X-ray diffraction of silicon irradiated with tightly focused femtosecond x-ray pulses (photon energy: 11.5 keV, pulse duration: 6 fs) was measured at various x-ray intensities up to $4.6\times10^{19}$ W/cm$^2$. The measurement reveals that the diffraction intensity is highly suppressed when the x-ray intensity reaches of the order of $10^{19}$ W/cm$^2$. With a dedicated simulation, we confirm the observed reduction of the diffraction intensity is attributed to the femtosecond change in individual atomic scattering factors due to the ultrafast creation of highly ionized atoms through photoionization, Auger decay, and subsequent collisional ionization. We anticipate that this ultrafast reduction of atomic scattering factor will be a basis for new x-ray nonlinear techniques, such as pulse shortening and contrast variation x-ray scattering.

physics.atom-ph↗

arXiv2021

Transient ionization potential depression in nonthermal dense plasmas at high x-ray intensity

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 time-scale 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.

physics.plasm-ph↗

arXiv2018

XCALIB: a focal spot calibrator for intense X-ray free-electron laser pulses based on the charge state distributions of light atoms

We develop the XCALIB toolkit to calibrate the beam profile of an X-ray free-electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Accurate characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. To obtain theoretical CSDs, we use XATOM, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. We have implemented an optimization procedure employing the reinforcement learning technique. The technique can automatize and organize calibration procedures which, before, had been performed manually. XCALIB has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with XATOM, XCALIB serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region.

physics.app-ph↗

arXiv2017

A molecular-dynamics approach for studying the non-equilibrium behavior of x-ray-heated solid-density matter

When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e., warm or hot dense matter. The resulting system consists of atoms in various electronic configurations, thermalizing on sub-picosecond to picosecond timescales after photoexcitation. We present a simulation study of x-ray-heated solid-density matter. For this we use XMDYN, a Monte-Carlo molecular-dynamics-based code with periodic boundary conditions, which allows one to investigate non-equilibrium dynamics. XMDYN is capable of treating systems containing light and heavy atomic species with full electronic configuration space and 3D spatial inhomogeneity. For the validation of our approach we compare for a model system the electron temperatures and the ion charge-state distribution from XMDYN to results for the thermalized system based on the average-atom model implemented in XATOM, an ab-initio x-ray atomic physics toolkit extended to include a plasma environment. Further, we also compare the average charge evolution of diamond with the predictions of a Boltzmann continuum approach. We demonstrate that XMDYN results are in good quantitative agreement with the above mentioned approaches, suggesting that the current implementation of XMDYN is a viable approach to simulate the dynamics of x-ray-driven non-equilibrium dynamics in solids. In order to illustrate the potential of XMDYN for treating complex systems we present calculations on the triiodo benzene derivative 5-amino-2,4,6-triiodoisophthalic acid (I3C), a compound of relevance of biomolecular imaging, consisting of heavy and light atomic species.

physics.atm-clus↗

arXiv2016

Calculation of x-ray scattering patterns from nanocrystals at high x-ray intensity

We present a generalized method to describe the x-ray scattering intensity of the Bragg spots in a diffraction pattern from nanocrystals exposed to intense x-ray pulses. Our method involves the subdivision of a crystal into smaller units. In order to calculate the dynamics within every unit we employ a Monte-Carlo (MC)-molecular dynamics (MD)-ab-initio hybrid framework using real space periodic boundary conditions. By combining all the units we simulate the diffraction pattern of a crystal larger than the transverse x-ray beam profile, a situation commonly encountered in femtosecond nanocrystallography experiments with focused x-ray free-electron laser radiation. Radiation damage is not spatially uniform and depends on the fluence associated with each specific region inside the crystal. To investigate the effects of uniform and non-uniform fluence distribution we have used two different spatial beam profiles, gaussian and flattop.

physics.atm-clus↗

arXiv2015

Hydrodynamic model for picosecond propagation of laser-created nanoplasmas

The interaction of a free-electron-laser pulse with a moderate or large size cluster is known to create a quasi-neutral nanoplasma, which then expands on hydrodynamic timescale, i.e., $>1$ ps. To have a better understanding of ion and electron data from experiments derived from laser-irradiated clusters, one needs to simulate cluster dynamics on such long timescales for which the molecular dynamics approach becomes inefficient. We therefore propose a two-step Molecular Dynamics-Hydrodynamic scheme. In the first step we use molecular dynamics code to follow the dynamics of an irradiated cluster until all the photo-excitation and corresponding relaxation processes are finished and a nanoplasma, consisting of ground-state ions and thermalized electrons, is formed. In the second step we perform long-timescale propagation of this nanoplasma with a computationally efficient hydrodynamic approach. In the present paper we examine the feasibility of a hydrodynamic two-fluid approach to follow the expansion of spherically symmetric nanoplasma, without accounting for the impact ionization and three-body recombination processes at this stage. We compare our results with the corresponding molecular dynamics simulations. We show that all relevant information about the nanoplasma propagation can be extracted from hydrodynamic simulations at a significantly lower computational cost when compared to a molecular dynamics approach. Finally, we comment on the accuracy and limitations of our present model and discuss possible future developments of the two-step strategy.

physics.plasm-ph↗

arXiv2014

Incoherent x-ray scattering in single molecule imaging

Imaging of the structure of single proteins or other biomolecules with atomic resolution would be enormously beneficial to structural biology. X-ray free-electron lasers generate highly intense and ultrashort x-ray pulses, providing a route towards imaging of single molecules with atomic resolution. The information on molecular structure is encoded in the coherent x-ray scattering signal. In contrast to crystallography there are no Bragg reflections in single molecule imaging, which means the coherent scattering is not enhanced. Consequently, a background signal from incoherent scattering deteriorates the quality of the coherent scattering signal. This background signal cannot be easily eliminated because the spectrum of incoherently scattered photons cannot be resolved by usual scattering detectors. We present an ab initio study of incoherent x-ray scattering from individual carbon atoms, including the electronic radiation damage caused by a highly intense x-ray pulse. We find that the coherent scattering pattern suffers from a significant incoherent background signal at high resolution. For high x-ray fluence the background signal becomes even dominating. Finally, based on the atomic scattering patterns, we present an estimation for the average photon count in single molecule imaging at high resolution. By varying the photon energy from 3.5 keV to 15 keV, we find that imaging at higher photon energies may improve the coherent scattering signal quality.

physics.atom-ph↗

arXiv2014

Quantum-mechanical calculation of ionization potential lowering in dense plasmas

The charged environment within a dense plasma leads to the phenomenon of ionization potential depression (IPD) for ions embedded in the plasma. Accurate predictions of the IPD effect are of crucial importance for modeling atomic processes occurring within dense plasmas. Several theoretical models have been developed to describe the IPD effect, with frequently discrepant predictions. Only recently, first experiments on IPD in Al plasma have been performed with an x-ray free-electron laser (XFEL), where their results were found to be in disagreement with the widely-used IPD model by Stewart and Pyatt. Another experiment on Al, at the Orion laser, showed disagreement with the model by Ecker and Kröll. This controversy shows a strong need for a rigorous and consistent theoretical approach to calculate the IPD effect. Here we propose such an approach: a two-step Hartree-Fock-Slater model. With this parameter-free model we can accurately and efficiently describe the experimental Al data and validate the accuracy of standard IPD models. Our model can be a useful tool for calculating atomic properties within dense plasmas with wide-ranging applications to studies on warm dense matter, shock experiments, planetary science, inertial confinement fusion and studies of non-equilibrium plasmas created with XFELs.

physics.plasm-ph↗

arXiv2012

Post-orientation free single molecule imaging by XFELs

Single molecule imaging is one of the main target areas of X-ray free electron lasers. It relies on the possibility of orienting the large number of low counting statistics 2D diffraction patterns taken at random orientations of identical replicas of the sample. This is a difficult process and the low statistics limits the usability of orientation methods and ultimately it could prevent single molecule imaging. We suggest a new approach, which avoids the orientation process from the diffraction patterns. In our schema one measures the orientation of the sample together with the diffraction pattern by detecting some fragments of the Coulomb explosion. We show by molecular dynamics simulations that from the angular distribution of the fragments one can obtain the orientation of the samples.

physics.atm-clus↗

arXiv2012

Effect of two-particle correlations on x-ray coherent diffractive imaging studies performed with continuum models

Coherent diffraction imaging (CDI) of single molecules at atomic resolution is a major goal for the x-ray free electron lasers (XFELs). However, during an imaging pulse, the fast laser-induced ionization may strongly affect the recorded diffraction pattern of the irradiated sample. The radiation tolerance of the imaged molecule should then be investigated 'a priori' with a dedicated simulation tool. The continuum approach is a powerful tool for modeling the evolution of irradiated large systems consisting of more than a few hundred thousand atoms. However, this method follows the evolution of average single-particle densities, and the experimentally recorded intensities reflect the spatial two-particle correlations. The information on these correlations is then inherently not accessible within the continuum approach. In this paper we analyze this limitation of continuum models and discuss the applicability of continuum models for imaging studies. We propose a formula to calculate scattered intensities (including both elastic and inelastic scattering) from the estimates obtained with a single-particle continuum model. We derive this formula for systems under conditions typical for CDI studies with XFELs.

cond-mat.mes-hall↗

arXiv2009

The effect of inhomogenities on single molecule imaging by hard XFEL pulses

We study the local distortion of the atomic structure in small biological samples illuminated by x-ray free electron laser (XFEL) pulses. We concentrate on the effect of inhomogenities: heavy atoms in a light matrix and non-homogeneous spatial distribution of atoms. In biological systems we find both. Using molecular-dynamics type modeling it is shown that the local distortions about heavy atoms are larger than the average distortion in the light matrix. Further it is also shown that the large spatial density fluctuations also significantly alter the time evolution of atomic displacements as compared to samples with uniform density. This fact has serious consequences on single particle imaging. This is discussed and the possibility of a correction is envisaged.

physics.atm-clus↗

arXiv2008

The effect of tamper layer on the explosion dynamics of atom clusters

The behavior of small samples in very short and intense hard x-ray pulses is studied by molecular dynamics type calculations. The main emphasis is put on the effect of various tamper layers about the sample. This is discussed from the point of view of structural imaging of single particles, including not only the distortion of the structure but also the background conditions. A detailed picture is given about the Coulomb explosion, with explanation of the tampering mechanism. It is shown that a thin water layer is efficient in slowing down the distortion of the atomic structure, but it gives a significant contribution to the background.

physics.atm-clus↗

arXiv2003

Imaging atom-clusters by hard x-ray free electron lasers

The ingenious idea of single molecule imaging by hard x-ray Free Electron Laser (X-FEL) pulses was recently proposed by Neutze et al. [Nature,406,752(2000)]. However, in their numerical modelling of the Coulomb explosion several interactions were neglected and no reconstruction of the atomic structure was given. In this work we carried out improved molecular dynamics calculations including all quantum processes which affect the explosion. Based on this time evolution we generated composite elastic scattering patterns, and by using Fienup's algorithm successfully reconstructed the original atomic structure. The critical evaluation of these results gives guidelines and sets important conditions for future experiments aiming single molecule structure solution.

cond-mat↗

arXiv2003

Phase field theory of crystal nucleation in hard sphere liquid

The phase field theory of crystal nucleation described in [L. Granasy, T. Borzsonyi, T. Pusztai, Phys. Rev. Lett. 88, 206105 (2002)] is applied for nucleation in hard--sphere liquids. The exact thermodynamics from molecular dynamics is used. The interface thickness for phase field is evaluated from the cross--interfacial variation of the height of the singlet density peaks. The model parameters are fixed in equilibrium so that the free energy and thickness of the (111), (110), and (100) interfaces from molecular dynamics are recovered. The density profiles predicted without adjustable parameters are in a good agreement with the filtered densities from the simulations. Assuming spherical symmetry, we evaluate the height of the nucleation barrier and the Tolman length without adjustable parameters. The barrier heights calculated with the properties of the (111) and (110) interfaces envelope the Monte Carlo results, while those obtained with the average interface properties fall very close to the exact values. In contrast, the classical sharp interface model considerably underestimates the height of the nucleation barrier. We find that the Tolman length is positive for small clusters and decreases with increasing size, a trend consistent with computer simulations.

cond-mat.stat-mech↗

arXiv2003

Dynamics in a cluster under the influence of intense femtosecond hard x-ray pulses

In this paper we examine the behavior of small cluster of atoms in a short (10-50 fs) very intense hard x-ray (10 keV) pulse. We use numerical modeling based on the non-relativistic classical equation of motion. Quantum processes are taken into account by the respective cross sections. We show that there is a Coulomb explosion, which has a different dynamics than one finds in classical laser driven cluster explosions. We discuss the consequences of our results to single molecule imaging by the free electron laser pulses.

physics.atm-clus↗