Article
Multidisciplinary Sciences
J. Niskanen, A. Vladyka, J. Niemi, C. J. Sahle
Summary: In this study, we explore the sensitivity of several core-level spectroscopic methods to the atomistic structure using water molecule as a test system. We define a metric to measure the magnitude of spectral change as a function of structure, which enables us to identify structural regions with high spectral sensitivity. By employing machine-learning emulator-based decomposition of structural parameter space, we are able to recover more spectral variance and identify spectroscopically dominant degrees of freedom.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Chemistry, Physical
Daniel Tunega, Roland Solc, Peter Grancic, Martin H. Gerzabek, Marc-Oliver Goebel, Georg Guggenberger, Joerg Bachmann, Susanne K. Woche
Summary: This study examined the impact of different organic coatings on surface wettability by using dimethyl(DMS)-, aminopropyl(APS)-, and octadecyl(ODS)-siloxane coated glass slides. Molecular dynamics simulations were performed to investigate the factors determining surface wettability. The results showed that chain length, polarity of terminal group, and coating density are the main factors influencing surface wettability.
APPLIED SURFACE SCIENCE
(2023)
Article
Chemistry, Physical
Maxim K. Rabchinskii, Svyatoslav D. Saveliev, Dina Yu. Stolyarova, Maria Brzhezinskaya, Demid A. Kirilenko, Marina Baidakova, Sergei A. Ryzhkov, Vladimir V. Shnitov, Victor V. Sysoev, Pavel N. Brunkov
Summary: This study demonstrates the modulation of N species by tailoring the functionalization and atomic structure of graphene derivatives prior to chemical N-doping. Thermal annealing at moderate temperatures was shown to readjust the composition of N-species in graphene derivatives regardless of their chemistry, nanostructure, and the initial distribution of the N-species. The oxidation of the graphene layer governs the manifestation of pi* resonances and configuration of sigma* resonance.
Article
Materials Science, Ceramics
Zhichao Song, Jun Zhang, Yan Wang, Jianping Li
Summary: SnO2 nanomaterials and SnO2/Li2SnO3 composite nanomaterials doped with different Li contents were synthesized via a one-step thermal evaporation method. The increase of Li doping resulted in changes in the structure and properties, as observed in X-ray diffraction, Raman scattering, and X-ray photoelectron spectroscopy.
CERAMICS INTERNATIONAL
(2021)
Article
Chemistry, Physical
Ke Yuan, Nikhil Rampal, Paul Fenter, James D. Kubicki, Andrew G. Stack, Stephan Irle
Summary: The researchers used density functional tight-binding (DFTB) to simulate the structures of quartz surfaces with different types and densities of defects in water, revealing that the rotation of surface [SiO4] tetrahedra near Si vacancies can lead to outward displacements of Si atoms and inward relaxations of terminal oxygens.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Physical
Biswajyoti Mohanty, Anamitra Chattopadhyay, Jhasaketan Nayak
Summary: Combining PbS with CeO2 can reduce the band gap of CeO2 and enhance electrical conductivity. CeO2 PbS nanocomposites were synthesized at different concentrations of Pb precursor and characterized for morphology and structure, showing potential for optoelectronic devices and solar cell applications.
JOURNAL OF ALLOYS AND COMPOUNDS
(2021)
Article
Materials Science, Multidisciplinary
Jia Chen, Jianwei Xiao, Chang-Yu Hung, Wenbo Wang, Jing Zhao, F. Marc Michel, Chuang Deng, Wenjun Cai
Summary: The effects of alloying concentration on the aqueous corrosion behavior of aluminum-manganese-molybdenum (Al-Mn-Mo) alloys were investigated. The study showed that an increase in Mo concentration improved the corrosion resistance and resulted in the formation of a more compact and less defective passive film.
Article
Multidisciplinary Sciences
Norman Tran, Sathish Dasari, Sarah A. E. Barwell, Matthew J. Mcleod, Subha Kalyaanamoorthy, Todd Holyoak, Aravindhan Ganesan
Summary: This study reveals the conformational changes and inactivated state of the main protease Mpro of the novel coronavirus SARS-CoV-2 under oxidative stress, achieved through the mutation H163A, and elucidates the mechanistic details of this conformational change using atomistic simulations.
NATURE COMMUNICATIONS
(2023)
Article
Optics
Yu Wang, Peng Peng Zhang, Lan Luo, Xing Tao Chen, Rui Guo, Jing Yi Xu
Summary: This paper investigates the effects of Lu3+ ion doping on the structure and photoluminescent properties of Ba2SiO4:Eu2+ phosphors. It is found that Lu3+ ions can enhance the conversion of Eu3+ to Eu2+, leading to improved luminescence performance.
JOURNAL OF LUMINESCENCE
(2021)
Article
Chemistry, Multidisciplinary
Alberto Garcia-Fernandez, Sebastian Svanstrom, Cody M. Sterling, Abhijeet Gangan, Axel Erbing, Chinnathambi Kamal, Tamara Sloboda, Birgit Kammlander, Gabriel J. Man, Hakan Rensmo, Michael Odelius, Ute B. Cappel
Summary: This study investigates the surface properties and electronic structure of lead halide perovskite single crystals using synchrotron-based soft X-ray photoelectron spectroscopy, molecular dynamics simulations, and density functional theory. The results provide reference spectra for photoelectron spectroscopy investigations of polycrystalline thin films and can be used to optimize the design of device interfaces.
Article
Chemistry, Physical
Tomofumi Kato, Yasuhiro Yamada, Yasushi Nishikawa, Hiroki Ishikawa, Satoshi Sato
Summary: The carbonization mechanisms of PMDA-ODA-type polyimide heated at 1273 K or lower were studied, revealing the formation of isoimide and cyclic ether. Computational spectral analysis combined with molecular dynamics simulation (ReaxFF) was used to analyze carbon materials containing nitrogen, oxygen, pentagons, and heptagons. Experimental and calculated XPS and C-13 NMR spectra supported the findings, including the formation of pentagons and heptagons in polyimide heated between 833 and 1273 K.
Article
Chemistry, Physical
Teodor I. Milenov, Dimitar A. Dimov, Ivalina A. Avramova, Stefan K. Kolev, Dimitar V. Trifonov, Georgi V. Avdeev, Daniela B. Karashanova, Biliana C. Georgieva, Kamen V. Ivanov, Evgenia P. Valcheva
Summary: This study focuses on the evaluation of the influence of chemical treatment on the structure and morphology of carbon phases. The chemical interactions of two types of graphite and carbon black with acetone, toluene, and phenol were studied. Experimental and theoretical methods were used to determine the chemical and phase composition, as well as the morphology and structure. The findings suggest that the treatment of graphite powders and carbon black with acetone, toluene, or phenol can be an effective preliminary stage for their modification and conversion into graphene-like phases.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Jacob N. Vagott, Kathryn Bairley, Juanita Hidalgo, Carlo A. R. Perini, Andres-Felipe Castro-Mendez, Sarah Lombardo, Barry Lai, Lihua Zhang, Kim Kisslinger, Josh Kacher, Juan-Pablo Correa-Baena
Summary: Atomic layer deposition (ALD) allows precise control over the thickness, stoichiometry, and structural defects of materials. This study deposited lead iodide (PbI2) using a facile ALD process with readily accessible and low-cost precursors. The deposited PbI2 was characterized using various techniques and lays the foundation for further development of lead halide perovskite processes by ALD.
CHEMISTRY OF MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Delano P. Chong
Summary: The electron spectra of indole and four azaindoles were calculated using density functional theory after geometry optimization. Experimental data for indole and 7-azaindole were compared with the theoretical values, while predictions were provided for the other azaindoles to aid in interpreting experimental spectra.
Article
Electrochemistry
Aida Raauf, David Graf, Yakup Gonullu, Praveen K. Sekhar, Michael Frank, Sanjay Mathur
Summary: The nanostructured thin film of Nd2Sn2O7 pyrochlore obtained through solution processing shows unprecedented selectivity towards hydrogen sensing, with the highest sensitivity towards H-2 detected at 300 degrees Celsius. The high efficiency and reproducibility of the investigated sensor devices indicate the potential of Nd2Sn2O7 based sensors for hydrogen safety applications.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Vladimir Lipp, Victor Tkachenko, Michal Stransky, Balint Aradi, Thomas Frauenheim, Beata Ziaja
Summary: This article presents a dedicated computational approach developed to study X-ray induced transitions in a broad range of solid materials. The approach utilizes the versatile density functional tight binding code DFTB+ to track the band structure evolution in irradiated materials, and demonstrates outstanding performance through a comparative study of XUV induced graphitization in diamond.
SCIENTIFIC REPORTS
(2022)
Article
Physics, Multidisciplinary
Ichiro Inoue, Victor Tkachenko, Konrad J. Kapcia, Vladimir Lipp, Beata Ziaja, Yuichi Inubushi, Toru Hara, Makina Yabashi, Eiji Nishibori
Summary: By using an x-ray pump x-ray probe technique, the transient structural changes of Al2O3 on subatomic length scales following irradiation with an intense x-ray laser pulse have been investigated. The results show that electron excitation and relaxation modify the potential energy surface and drive directional atomic displacements. This implies that high-resolution x-ray structural analysis is feasible even with intense x-ray pulses.
PHYSICAL REVIEW LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Michal Stransky, Zoltan Jurek, Robin Santra, Adrian P. Mancuso, Beata Ziaja
Summary: In this work, tree-algorithm based solvers were incorporated into the molecular dynamics code XMDYN for the first time, improving its performance and enabling computationally efficient simulations of X-ray irradiated large atomic assemblies.
Article
Chemistry, Physical
Cecilia M. Casadei, Ahmad Hosseinizadeh, Spencer Bliven, Tobias Weinert, Jorg Standfuss, Russell Fung, Gebhard F. X. Schertler, Robin Santra
Summary: Low-pass spectral analysis (LPSA) is an effective algorithm for retrieving dynamics in model data affected by incompleteness and weighting errors. In this study, LPSA is applied to experimental time-resolved crystallography data and the parametric sensitivity is analyzed. The presence of high-frequency contamination in dynamical modes is investigated using synthetic data with various uncertainties and errors. A method is proposed to handle missing observations and improved dynamics retrieval is achieved.
STRUCTURAL DYNAMICS-US
(2023)
Article
Multidisciplinary Sciences
Zhong Yin, Yi-Ping Chang, Tadas Balciunas, Yashoj Shakya, Aleksa Djorovic, Geoffrey Gaulier, Giuseppe Fazio, Robin Santra, Ludger Inhester, Jean-Pierre Wolf, Hans Jakob Worner
Summary: Researchers have revealed the femtosecond proton-transfer dynamics in ionized urea dimers in aqueous solution using table-top water-window X-ray absorption spectroscopy. By combining quantum-mechanical and molecular-mechanics calculations, they were able to identify the subsequent rearrangement of the urea dimer and the associated change of the electronic structure with site selectivity. These findings highlight the potential of table-top X-ray absorption spectroscopy in elucidating ultrafast dynamics in biomolecular systems.
Review
Multidisciplinary Sciences
Beata Ziaja, John Jasper Bekx, Martin Masek, Nikita Medvedev, Vladimir Lipp, Vikrant Saxena, Michal Stransky
Summary: In this review, the application of Boltzmann kinetic equations in modelling warm dense matter and plasma formed after irradiation of solid materials with intense femtosecond X-ray pulses is described. The classical Boltzmann kinetic equations are derived from the reduced N-particle Liouville equations and include only single-particle densities of ions and free electrons present in the sample. The Boltzmann code was first completed in 2006 to model non-equilibrium evolution of X-ray-irradiated atomic systems, and it has been further adapted to study plasma created from X-ray-irradiated materials.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2023)
Article
Multidisciplinary Sciences
E. Juncheng, Michal Stransky, Zhou Shen, Zoltan Jurek, Carsten Fortmann-Grote, Richard Bean, Robin Santra, Beata Ziaja, Adrian P. Mancuso
Summary: This study investigates the impact of water layer thickness and radiation damage on orientation recovery from diffraction patterns of the nitrogenase iron protein. The 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.
SCIENTIFIC REPORTS
(2023)
Article
Optics
Vladimir Lipp, Ichiro Inoue, Beata Ziaja
Summary: We conducted a comparative theoretical study on silicon crystals irradiated with X-ray free-electron laser pulses of varying energies. Through simulations with our in-house hybrid code XTANT, we found that using higher photon energies would be advantageous for diffraction-before-destruction experiments, based on the comparison of coherently scattered signal strength and corresponding electronic radiation damage for three X-ray photon energies available at the SACLA free-electron laser facility.
Article
Optics
Yashoj Shakya, Ralph Welsch, Ludger Inhester, Robin Santra
Summary: Simulations of coupled electronic and nuclear dynamics in molecules are computationally challenging and limited to model systems or small molecules. The approach presented in this study combines Tully's fewest switches surface hopping (FSSH) with ring-polymer molecular dynamics (RPMD) to overcome the limitations of FSSH in describing electronic coherences and decoherence phenomena. By incorporating decoherence effects through an electronic density-matrix formulation, this method captures a crucial decoherence mechanism missing in FSSH and provides a superior description of electronic coherences compared to earlier attempts at combining RPMD and FSSH.
Article
Physics, Multidisciplinary
Arunangshu Debnath, Robin Santra
Summary: We present a theoretical formulation for interpreting high-energy x-ray diffraction measurements using synchrotron radiation sources. The formulation allows classification of physical resources contributing to the correlation signatures and provides a unique perspective for structural imaging studies. It also offers a framework necessary for theoretical developments of associated reconstruction algorithms.
PHYSICAL REVIEW RESEARCH
(2023)
Article
Optics
Laura Budewig, Sang-Kil Son, Robin Santra
Summary: We propose a theoretical framework to study the state-resolved ionization dynamics of neon atoms driven by ultraintense x-ray free-electron-laser pulses. By combining a state-resolved electronic-structure calculation with a Monte Carlo rate-equation method, we are able to investigate the dynamics based on time-dependent state populations. Our results show that both configuration-based and state-resolved calculations yield similar charge-state distributions, except when resonant excitations are involved. Furthermore, we analyze time-resolved spectra of ions, electrons, and photons to explore frustrated absorption during the ionization dynamics of neon atoms.
Article
Physics, Multidisciplinary
Niels Breckwoldt, Sang-Kil Son, Tommaso Mazza, Aljoscha Roerig, Rebecca Boll, Michael Meyer, Aaron C. LaForge, Debadarshini Mishra, Nora Berrah, Robin Santra
Summary: X-ray free-electron lasers (XFELs) bring new possibilities for probing and manipulating atomic and molecular dynamics with unprecedented resolution. However, accurately comparing experimental results with theoretical simulations requires precise characterization of the spatial and temporal profile of the X-ray pulses. In this study, we propose a calibration scheme based on Bayesian optimization to accurately determine the pulse duration and spatial fluence distribution profile of intense XFEL pulses. This method can serve as a comprehensive tool for characterizing ultraintense and ultrafast X-ray pulses.
PHYSICAL REVIEW RESEARCH
(2023)
Article
Materials Science, Multidisciplinary
Konrad J. Kapcia, Victor Tkachenko, Flavio Capotondi, Alexander Lichtenstein, Serguei Molodtsov, Leonard Mueller, Andre Philippi-Kobs, Przemyslaw Piekarz, Beata Ziaja
Summary: Magnetization dynamics induced by ultrashort laser pulses and intense x-ray pulses have been studied. The exact mechanisms of x-ray-induced demagnetization is still not fully understood and is the focus of ongoing research. In this study, a theoretical analysis of demagnetization in a Co multilayer system irradiated by x-ray pulses was presented, and it was found that electronic processes play a predominant role in demagnetization.
Article
Optics
Daria Kolbasova, Robin Santra
Summary: Building on a previous strategy, this study presents an efficient alternative approach for characterizing ultrashort low-frequency laser pulses in situ. By using quantum-mechanical calculations, the researchers simulate the ionization of rare-gas atoms in strong fields and generate autocorrelation patterns for femtosecond laser pulses. They investigate the nonperturbative and nonlinear dependence of these patterns on pulse characteristics and propose an analytical function to describe them. The function's parameters and supervised machine learning are then utilized to retrieve key pulse parameters from the autocorrelation patterns produced via strong-field ionization. This approach offers advantages for experimental data applications.
Article
Optics
Stanislaw Wirok-Stoletow, Rui Jin, Daria Kolbasova, Sang-Kil Son, Andrew Aquila, Robin Santra
Summary: We theoretically investigate the formation of highly charged ions in a germanium solid driven by intense X-ray pulses and its effect on the cross sections for nonsequential two-photon absorption. Our study finds that the formation of charged ions in germanium is quick under the given experimental conditions, but the cross sections for nonsequential two-photon absorption are insensitive to different charge states.