Computational study of diffraction image formation from XFEL irradiated single ribosome molecule.

Single particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-ray free-electron lasers. Such a capability would create great opportunity within the biological sciences, as high-resolution structural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we report on a comprehensive computational study of diffraction image formation during single particle imaging of a macromolecule, containing over one hundred thousand non-hydrogen atoms.

Microscopic nonlinear optical response: Analysis and calculations with the Floquet-Bloch formalism.

We analyze microscopic nonlinear optical response of periodic structures within the Floquet-Bloch formalism. The analysis is focused on the real-space distributions of optically induced charge and electron current density within the unit cell of a crystal. We demonstrate that the time-reversal symmetry of a crystal determines the phases of the temporal oscillations of these distributions.

Attosecond-pump attosecond-probe x-ray spectroscopy of liquid water.

Attosecond-pump/attosecond-probe experiments have long been sought as the most straightforward method for observing electron dynamics in real time. Although there has been much success with overlapped near-infrared femtosecond and extreme ultraviolet attosecond pulses combined with theory, true attosecond-pump/attosecond-probe experiments have been limited. We used a synchronized attosecond x-ray pulse pair from an x-ray free-electron laser to study the electronic response to valence ionization in liquid water through all x-ray attosecond transient absorption spectroscopy (AX-ATAS).

Tracking Cavity Formation in Electron Solvation: Insights from X-ray Spectroscopy and Theory.

We present time-resolved X-ray absorption spectra of ionized liquid water and demonstrate that OH radicals, HO ions, and solvated electrons all leave distinct X-ray-spectroscopic signatures. Particularly, this allows us to characterize the electron solvation process through a tool that focuses on the electronic response of oxygen atoms in the immediate vicinity of a solvated electron. Our experimental results, supported by ab initio calculations, confirm the formation of a cavity in which the solvated electron is trapped.

Isotope effects in dynamics of water isotopologues induced by core ionization at an x-ray free-electron laser.

Dynamical response of water exposed to x-rays is of utmost importance in a wealth of science areas. We exposed isolated water isotopologues to short x-ray pulses from a free-electron laser and detected momenta of all produced ions in coincidence. By combining experimental results and theoretical modeling, we identify significant structural dynamics with characteristic isotope effects in HO, DO, and HDO, such as asymmetric bond elongation and bond-angle opening, leading to two-body or three-body fragmentation on a timescale of a few femtoseconds.

Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser.

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.

Multiple-core-hole resonance spectroscopy with ultraintense X-ray pulses.

Understanding the interaction of intense, femtosecond X-ray pulses with heavy atoms is crucial for gaining insights into the structure and dynamics of matter. One key aspect of nonlinear light-matter interaction was, so far, not studied systematically at free-electron lasers-its dependence on the photon energy. Here, we use resonant ion spectroscopy to map out the transient electronic structures occurring during the complex charge-up pathways of xenon.

Femtosecond proton transfer in urea solutions probed by X-ray spectroscopy.

Proton transfer is one of the most fundamental events in aqueous-phase chemistry and an emblematic case of coupled ultrafast electronic and structural dynamics. Disentangling electronic and nuclear dynamics on the femtosecond timescales remains a formidable challenge, especially in the liquid phase, the natural environment of biochemical processes. Here we exploit the unique features of table-top water-window X-ray absorption spectroscopy to reveal femtosecond proton-transfer dynamics in ionized urea dimers in aqueous solution.

Low-pass spectral analysis of time-resolved serial femtosecond crystallography data.

Low-pass spectral analysis (LPSA) is a recently developed dynamics retrieval algorithm showing excellent retrieval properties when applied to model data affected by extreme incompleteness and stochastic weighting. In this work, we apply LPSA to an experimental time-resolved serial femtosecond crystallography (TR-SFX) dataset from the membrane protein bacteriorhodopsin (bR) and analyze its parametric sensitivity. While most dynamical modes are contaminated by nonphysical high-frequency features, we identify two dominant modes, which are little affected by spurious frequencies.

Clinical, laboratory and high-resolution computed tomography (HRCT) thorax profile of reverse transcription polymerase chain reaction (RT-PCR) negative COVID-19 suspects with moderate to severe disease.

Background: Diagnostic dilemma arises when patients with clinical suspicion of COVID-19 disease having moderate-to-severe respiratory symptoms yield negative result for COVID-19 in reverse transcription polymerase chain reaction (RT-PCR). This study evaluated the clinical, laboratory and HRCT thorax findings among RT-PCR-negative COVID-19 suspects with moderate-to-severe disease.

Materials And Methods: A hospital-based retrospective observational study was conducted between July 2021 to December 2021, among 60 moderate and severe symptomatic COVID-19 suspects admitted in the severe acute respiratory illness (SARI) ward and intensive care unit (ICU), who were negative for COVID-19 in RT-PCR.

Chemical effects on the dynamics of organic molecules irradiated with high intensity x rays.

The interaction of a high intensity x-ray pulse with matter causes ionization of the constituent atoms through various atomic processes, and the system eventually goes through a complex structural dynamics. Understanding this whole process is important from the perspective of structure determination of molecules using single particle imaging. XMDYN, which is a classical molecular dynamics-Monte Carlo based hybrid approach, has been successful in simulating the dynamical evolution of various systems under intense irradiation over the past years.

Dynamics retrieval from stochastically weighted incomplete data by low-pass spectral analysis.

Time-resolved serial femtosecond crystallography (TR-SFX) provides access to protein dynamics on sub-picosecond timescales, and with atomic resolution. Due to the nature of the experiment, these datasets are often highly incomplete and the measured diffracted intensities are affected by partiality. To tackle these issues, one established procedure is that of splitting the data into time bins, and averaging the multiple measurements of equivalent reflections within each bin.

Plasma environmental effects in the atomic structure for simulating x-ray free-electron-laser-heated solid-density matter.

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.

Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN.

In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for computational single-particle imaging studies at the SPB/SFX instrument of the European XFEL facility.

Erratum: Transient ionization potential depression in nonthermal dense plasmas at high x-ray intensity [Phys. Rev. E 103, 023203 (2021)].

This corrects the article DOI: 10.1103/PhysRevE.103.

In Situ Reactivity of Electrochemically Generated Nitro Radical Anion on Tinidazole and Its Monomeric and Dimeric Cu Complexes on Model Biological Targets with Relative Manifestation of Preventing Bacterial Biofilm Formation.

Formation of nitro radical anion (-NO ) and other reduction products of 5-nitroimidazoles, although important for antimicrobial activity, makes the drugs neurotoxic. Hence, an appropriate generation and their role in the free radical pathway needs proper realization. This was attempted by studying the action of tinidazole and its Cu complexes on model targets (nucleic acid bases and calf thymus DNA).

Resonance-Enhanced Multiphoton Ionization in the X-Ray Regime.

Here, we report on the nonlinear ionization of argon atoms in the short wavelength regime using ultraintense x rays from the European XFEL. After sequential multiphoton ionization, high charge states are obtained. For photon energies that are insufficient to directly ionize a 1s electron, a different mechanism is required to obtain ionization to Ar^{17+}.

Few-fs resolution of a photoactive protein traversing a conical intersection.

The structural dynamics of a molecule are determined by the underlying potential energy landscape. Conical intersections are funnels connecting otherwise separate potential energy surfaces. Posited almost a century ago, conical intersections remain the subject of intense scientific interest.

Pulse Energy and Pulse Duration Effects in the Ionization and Fragmentation of Iodomethane by Ultraintense Hard X Rays.

The interaction of intense femtosecond x-ray pulses with molecules sensitively depends on the interplay between multiple photoabsorptions, Auger decay, charge rearrangement, and nuclear motion. Here, we report on a combined experimental and theoretical study of the ionization and fragmentation of iodomethane (CH_{3}I) by ultraintense (∼10^{19}  W/cm^{2}) x-ray pulses at 8.3 keV, demonstrating how these dynamics depend on the x-ray pulse energy and duration.

Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser.

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.

Ultrafast time-resolved x-ray absorption spectroscopy of ionized urea and its dimer through nonadiabatic dynamics.

Investigating the early dynamics of chemical systems following ionization is essential for our understanding of radiation damage. However, experimental as well as theoretical investigations are very challenging due to the complex nature of these processes. Time-resolved x-ray absorption spectroscopy on a femtosecond timescale, in combination with appropriate simulations, is able to provide crucial insights into the ultrafast processes that occur upon ionization due to its element-specific probing nature.

Erratum: Molecular-dynamics approach for studying the nonequilibrium behavior of x-ray-heated solid-density matter [Phys. Rev. E 96, 023205 (2017)].

This corrects the article DOI: 10.1103/PhysRevE.96.

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 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.

Electron-ion coincidence measurements of molecular dynamics with intense X-ray pulses.

Molecules can sequentially absorb multiple photons when irradiated by an intense X-ray pulse from a free-electron laser. If the time delay between two photoabsorption events can be determined, this enables pump-probe experiments with a single X-ray pulse, where the absorption of the first photon induces electronic and nuclear dynamics that are probed by the absorption of the second photon. Here we show a realization of such a single-pulse X-ray pump-probe scheme on N[Formula: see text] molecules, using the X-ray induced dissociation process as an internal clock that is read out via coincident detection of photoelectrons and fragment ions.

Simulation of time-resolved x-ray absorption spectroscopy of ultrafast dynamics in particle-hole-excited 4-(2-thienyl)-2,1,3-benzothiadiazole.

To date, alternating co-polymers based on electron-rich and electron-poor units are the most attractive materials to control functionality of organic semiconductor layers in which ultrafast excited-state processes play a key role. We present a computational study of the photoinduced excited-state dynamics of the 4-(2-thienyl)-2,1,3-benzothiadiazole (BT-1T) molecule, which is a common building block in the backbone of -conjugated polymers used for organic electronics. In contrast to homo-polymer materials, such as oligothiophene, BT-1T has two non-identical units, namely, thiophene and benzothiadiazole, making it attractive for intramolecular charge transfer studies.