Sizes of pure and doped helium droplets from single shot x-ray imaging.

Advancements in x-ray free-electron lasers on producing ultrashort, ultrabright, and coherent x-ray pulses enable single-shot imaging of fragile nanostructures, such as superfluid helium droplets. This imaging technique gives unique access to the sizes and shapes of individual droplets. In the past, such droplet characteristics have only been indirectly inferred by ensemble averaging techniques. Here, we report on the size distributions of both pure and doped droplets collected from single-shot x-ray imaging and produced from the free-jet expansion of helium through a 5 µm diameter nozzle at 20 bars and nozzle temperatures ranging from 4.2 to 9 K. This work extends the measurement of large helium nanodroplets containing 109-1011 atoms, which are shown to follow an exponential size distribution. Additionally, we demonstrate that the size distributions of the doped droplets follow those of the pure droplets at the same stagnation condition but with smaller average sizes.

Replacing gamma knife beam-profiles on film with point-detector scans.

PURPOSE: Detector arrays and profile-scans have widely replaced film-measurements for quality assurance (QA) on linear accelerators. Film is still used for relative output factor (ROF) measurements, positioning, and dose-profile verification for annual Leksell Gamma Knife (LGK) QA. This study shows that small-field active detector measurements can be performed in the easily accessed clinical mode and that they are an effective replacement to time-consuming and exacting film measurements. METHODS: Beam profiles and positioning scans for 4-mm, 8-mm, and 16-mm-collimated fields were collected along the x-, y-, and z-axes. The Exradin W2-scintillator and the PTW microdiamond-detector were placed in custom inserts centered in the Elekta solid-water phantom for these scans. GafChromic EBT3-film was irradiated with single uniformly collimated exposures as the clinical-standard reference, using the same solid-water phantom for profile tests and the Elekta film holder for radiation focal point (RFP)/patient-positioning system (PPS) coincidence. All experimental data were compared to the tissue-maximum-ratio-based (TMR10) dose calculation. RESULTS: The detector-measured beam profiles and film-based profiles showed excellent agreement with TMR10-predicted full-width, half-maximum (FWHM) values. Absolute differences between the measured FWHM and FWHM from the treatment-planning system were on average 0.13 mm, 0.08 mm, and 0.04 mm for film, microdiamond, and scintillator, respectively. The coincidence between the RFP and the PPS was measured to be ≤0.5 mm with microdiamond, ≤0.41 mm with the W2-1 × 1 scintillator, and ≤0.22 mm using the film-technique. CONCLUSIONS: Small-volume field detectors, used in conjunction with a clinically available phantom, an electrometer with data-logging, and treatment plans created in clinical mode offer an efficient and viable alternative for film-based profile tests. Position verification can be accurately performed when CBCT-imaging is available to correct for residual detector-position uncertainty. Scans are easily set up within the treatment-planning-system and, when coupled with an automated analysis, can provide accurate measurements within minutes.

Automatic couch position calculation using eclipse scripting for external beam radiotherapy.

PURPOSE: The treatment couch position of a patient in external beam radiation therapy (EBRT) is usually acquired during initial treatment setup. This procedure has shown potential failure modes leading to near misses and adverse events in radiation treatment. This study aims to develop a method to automatically determine the couch position before setting up a patient for initial treatment. METHODS: The Qfix couch-tops (kVue and DoseMax) have embedded reference marks (BBs) indicating its index levels and couch centerline. With the ESAPI, a C# script was programmed to automatically find the couch-top and embedded BBs in the planning CT and derive the treatment couch position according to treatment isocenter of a plan. Couch positions of EBRT plans with the kVue couch-top and SBRT plans using the DoseMax were calculated using the script. The calculation was evaluated by comparing calculated positions with couch coordinates captured during the initial treatment setup after image guidance. The calculations were further compared with daily treatment couch positions post image-guided adjustment for each treatment fraction. RESULTS: For plans using the kVue couch-top for various treatment sites, the median (5-95 percentiles) differences between calculated and captured couch positions were 0.1 (-0.2 - 0.9), 0.5 (-1.1-2.0), 0.10 (-1.3-1.3) cm in the vertical, longitudinal, and lateral direction respectively. For the DoseMax couch-top, the median differences were 0.1 (-0.2-0.7), 0.2 (-0.3-1.1), and 0.2 (-0.7-0.9) cm in respective direction. The calculated positions were within 1 and 2 cm from the mean fraction positions for 95% patients on DoseMax and kVue couch-top respectively. CONCLUSIONS: A method that automatically and accurately calculates treatment couch position from simulation CT was implemented in Varian Eclipse for Qfix couch-tops. This technique increases the efficiency of patient setup and enhances patient safety by reducing the risks of positioning errors.

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

The xcalib toolkit has been developed 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. 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. Theoretical CSDs are obtained using 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. The optimization procedure employing the reinforcement learning 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.

Unexpected reversal of stability in strained systems containing one-electron bonds.

Ring strain energy is a very well documented feature of neutral cycloalkanes, and influences their structural, thermochemical and reactivity properties. In this work, we apply density functional theory and high-level coupled cluster calculations to describe the geometry and relative stability of C6H12+˙ radical cations, whose cyclic isomers are prototypes of singly-charged cycloalkanes. Molecular ions with the mentioned stoichiometry were produced via electron impact experiments using a gaseous cyclohexane sample (20-2000 eV). From our calculations, in addition to structures that resemble linear and branched alkenes as well as distinct conformers of cyclohexane, we have found low-lying species containing three-, four- and five-membered rings with the presence of an elongated C-C bond. Remarkably, the stability trend of these ring-bearing radical cations is anomalous, and the three-membered species are up to 11.3 kcal mol-1 more stable than the six-membered chair structure. Generalized Valence Bond calculations and the Spin Coupled theory with N electrons and M orbitals were used in conjunction with the Generalized Product Function Energy Partitioning (GPF-EP) method and Interference Energy Analysis (IEA) to describe the chemical bonding in such moieties. Our results confirm that these elongated C-C motifs are one-electron sigma bonds. Our calculations also reveal the effects that drive thermochemical preference of strained systems over their strained-free isomers, and the origin of the unusual stability trend observed for cycloalkane radical cations.

Doubly and Triply Charged Species Formed from Chlorobenzene Reveal Unusual C-Cl Multiple Bonding.

In free-radical halogenation of aromatics, singly charged ions are usually formed as intermediates. These stable species can be easily observed by time-of-flight mass spectrometry (TOF-MS). Here we used electron and proton beams to ionize chlorobenzene (C6H5Cl) and investigate the ions stability by TOF-MS. Additionally to the singly charged parent ion and its fragments, we find a significant yield of doubly and triply charged parent ions not previously reported. In order to characterize these species, we used high-level theoretical methods based on density functional theory (DFT), coupled-cluster (CC), and generalized valence bond (GVB) to calculate the structure, relative stabilities, and bonding of these dications and trications. The most stable isomers exhibit unusual carbon-chlorine multiple bonding: a terminal C═Cl double bond in a formyl-like CHCl moiety (1, rC-Cl = 1.621 Å) and a ketene-like C═C═Cl cumulated species (2, rC-Cl = 1.542 Å). The calculations suggest that an excited state of 2 has a nitrile-like C≡Cl triple bond structure.

Fragment and cluster ions from gaseous and condensed pyridine produced under electron impact.

We report on direct measurement of all major ion-fragments and cluster-ions formed during high-energy electron impact of 2 keV on gaseous and condensed-phase pyridine. The ion-fragments of the parent pyridine cation are discussed in groups according to the number of atoms from the aromatic ring. The ion yield distributions within these groups show significant shifts towards higher masses for condensed pyridine compared to gaseous pyridine due to hydrogen migration. A wide spectrum of desorbed hydrogenated fragment-ions and ionic clusters with masses up to 320 u are observed for pyridine. The ion yields for the protonated parent molecule (C5H5NH+), the dehydrogenated dimer (C10H9N2+) and the dehydrogenated trimer (C15H12N3+) depend on the mass of the desorbing ionic clusters. The strongest cluster signals are assigned to binding between the parent cation and subunits of the pyridine molecule. Quantum-chemical calculations reveal that the formation of a bond between the pyridine molecules and a carbenium ion is crucial for the stability of selected cluster ions.

Femtosecond X-ray protein nanocrystallography.

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 µm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

Double differential cross sections for proton induced electron emission from molecular analogues of DNA constituents for energies in the Bragg peak region.

For track structure simulations in the Bragg peak region, measured electron emission cross sections of DNA constituents are required as input for developing parameterized model functions representing the scattering probabilities. In the present work, double differential cross sections were measured for the electron emission from vapor-phase pyrimidine, tetrahydrofuran, and trimethyl phosphate that are structural analogues to the base, the sugar, and the phosphate residue of the DNA, respectively. The range of proton energies was from 75 keV to 135 keV, the angles ranged from 15° to 135°, and the electron energies were measured from 10 eV to 200 eV. Single differential and total electron emission cross sections are derived by integration over angle and electron energy and compared to the semi-empirical Hansen-Kocbach-Stolterfoht (HKS) model and a quantum mechanical calculation employing the first Born approximation with corrected boundary conditions (CB1). The CB1 provides the best prediction of double and single differential cross section, while total cross sections can be fitted with semi-empirical models. The cross sections of the three samples are proportional to their total number of valence electrons.

Lipidic phase membrane protein serial femtosecond crystallography.

X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.

In vivo protein crystallization opens new routes in structural biology.

Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

Automated identification and classification of single particle serial femtosecond X-ray diffraction data.

The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even though the sample is ultimately destroyed by the deposited X-ray energy. Single particle X-ray diffraction experiments generate data at the FEL repetition rate, resulting in more than 400,000 detector readouts in an hour, the data stream during an experiment contains blank frames mixed with hits on single particles, clusters and contaminants. The diffraction signal is generally weak and it is superimposed on a low but continually fluctuating background signal, originating from photon noise in the beam line and electronic noise from the detector. Meanwhile, explosion of the sample creates fragments with a characteristic signature. Here, we describe methods based on rapid image analysis combined with ion Time-of-Flight (ToF) spectroscopy of the fragments to achieve an efficient, automated and unsupervised sorting of diffraction data. The studies described here form a basis for the development of real-time frame rejection methods, e.g. for the European XFEL, which is expected to produce 100 million pulses per hour.

Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser.

X-ray free-electron lasers (FELs) enable crystallographic data collection using extremely bright femtosecond pulses from microscopic crystals beyond the limitations of conventional radiation damage. This diffraction-before-destruction approach requires a new crystal for each FEL shot and, since the crystals cannot be rotated during the X-ray pulse, data collection requires averaging over many different crystals and a Monte Carlo integration of the diffraction intensities, making the accurate determination of structure factors challenging. To investigate whether sufficient accuracy can be attained for the measurement of anomalous signal, a large data set was collected from lysozyme microcrystals at the newly established `multi-purpose spectroscopy/imaging instrument' of the SPring-8 Ångstrom Compact Free-Electron Laser (SACLA) at RIKEN Harima. Anomalous difference density maps calculated from these data demonstrate that serial femtosecond crystallography using a free-electron laser is sufficiently accurate to measure even the very weak anomalous signal of naturally occurring S atoms in a protein at a photon energy of 7.3 keV.

Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers.

Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.

Sensing the wavefront of x-ray free-electron lasers using aerosol spheres.

Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.

Femtosecond free-electron laser x-ray diffraction data sets for algorithm development.

We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.

Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering.

Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.

Roadmap for metal nanoparticles in radiation therapy: current status, translational challenges, and future directions.

This roadmap outlines the potential roles of metallic nanoparticles (MNPs) in the field of radiation therapy. MNPs made up of a wide range of materials (from Titanium, Z = 22, to Bismuth, Z = 83) and a similarly wide spectrum of potential clinical applications, including diagnostic, therapeutic (radiation dose enhancers, hyperthermia inducers, drug delivery vehicles, vaccine adjuvants, photosensitizers, enhancers of immunotherapy) and theranostic (combining both diagnostic and therapeutic), are being fabricated and evaluated. This roadmap covers contributions from experts in these topics summarizing their view of the current status and challenges, as well as expected advancements in technology to address these challenges.

Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams.

Gold nanoparticle (GNP) radio-enhancement is a promising technique to increase the dose deposition in a tumor while sparing neighboring healthy tissue. Previous experimental studies showed effects on cell survival and tumor control for keV x-rays but surprisingly also for MV-photons, proton and carbon-ion beams. In a systematic study, we use the Monte Carlo simulation tool TOPAS-nBio to model the GNP radio-enhancement within a cell as a function of GNP concentration, size and clustering for a wide range of energies for photons, protons and, for the first time, carbon-ions. Moreover, we include water radiolysis, which has been recognized as a major pathway of GNP mediated radio-enhancement. At a GNP concentration of 0.5% and a GNP diameter of 10 nm, the dose enhancement ratio was highest for 50 keV x-rays (1.36) and decreased in the orthovoltage (1.04 at 250 keV) and megavoltage range (1.01 at 1 MeV). The dose enhancement linearly increased with GNP concentration and decreased with GNP size and degree of clustering for all radiation modalities. While the highest physical dose enhancement at 5% concentrations was only 1.003 for 10 MeV protons and 1.004 for 100 MeV carbon-ions, we find the number of hydroxyl ([Formula: see text]) altered by 23% and 3% after 1 [Formula: see text]s at low, clinically-relevant concentrations. For the same concentration and proton-impact, the G-value is most sensitive to the nanoparticle size with 46 times more radical interactions at GNPs for 2 nm than for 50 nm GNP diameter within 1 [Formula: see text]s. Nanoparticle clustering was found to decrease the number of interactions at GNPs, e.g. for a cluster of 25 GNPs by a factor of 3.4. The changes in G-value correlate to the average distance between the chemical species and the GNPs. While the radiochemistry of GNP-loaded water has yet to be fully understood, this work offers a first relative quantification of radiolysis products for a broad parameter-set.

Relativistic and resonant effects in the ionization of heavy atoms by ultra-intense hard X-rays.

An accurate description of the interaction of intense hard X-ray pulses with heavy atoms, which is crucial for many applications of free-electron lasers, represents a hitherto unresolved challenge for theory because of the enormous number of electronic configurations and relativistic effects, which need to be taken into account. Here we report results on multiple ionization of xenon atoms by ultra-intense (about 1019 W/cm2) femtosecond X-ray pulses at photon energies from 5.5 to 8.3 keV and present a theoretical model capable of reproducing the experimental data in the entire energy range. Our analysis shows that the interplay of resonant and relativistic effects results in strongly structured charge state distributions, which reflect resonant positions of relativistically shifted electronic levels of highly charged ions created during the X-ray pulse. The theoretical approach described here provides a basis for accurate modeling of radiation damage in hard X-ray imaging experiments on targets with high-Z constituents.