Characterization and performance evaluation of the XSPA-500k detector using synchrotron radiation.

Hybrid photon counting (HPC) detectors are widely used at both synchrotron facilities and in-house laboratories. The features of HPC detectors, such as no readout noise, high dynamic range, high frame rate, excellent point spread function, no blurring etc. along with fast data acquisition, provide a high-performance detector with a low detection limit and high sensitivity. Several HPC detector systems have been developed around the world. A number of them are commercially available and used in academia and industry. One of the important features of an HPC detector is a fast readout speed. Most HPC detectors can easily achieve over 1000 frames s-1, one or two orders of magnitude faster than conventional CCD detectors. Nevertheless, advanced scientific challenges require ever faster detectors in order to study dynamical phenomena in matter. The XSPA-500k detector can achieve 56 kframes s-1 continuously, without dead-time between frames. Using `burst mode', a special mode of the UFXC32k ASIC, the frame rate reaches 1 000 000 frames s-1. XSPA-500k was fully evaluated at the Metrology beamline at Synchrotron SOLEIL (France) and its readout speed was confirmed by tracking the synchrotron bunch time structure. The uniformity of response, modulation transfer function, linearity, energy resolution and other performance metrics were also verified either with fluorescence X-rays illuminating the full area of the detector or with the direct beam.

20†µs-resolved high-throughput X-ray photon correlation spectroscopy on a 500k pixel detector enabled by data-management workflow.

The performance of the new 52 kHz frame rate Rigaku XSPA-500k detector was characterized on beamline 8-ID-I at the Advanced Photon Source at Argonne for X-ray photon correlation spectroscopy (XPCS) applications. Due to the large data flow produced by this detector (0.2 PB of data per 24 h of continuous operation), a workflow system was deployed that uses the Advanced Photon Source data-management (DM) system and high-performance software to rapidly reduce area-detector data to multi-tau and two-time correlation functions in near real time, providing human-in-the-loop feedback to experimenters. The utility and performance of the workflow system are demonstrated via its application to a variety of small-angle XPCS measurements acquired from different detectors in different XPCS measurement modalities. The XSPA-500k detector, the software and the DM workflow system allow for the efficient acquisition and reduction of up to ∼109 area-detector data frames per day, facilitating the application of XPCS to measuring samples with weak scattering and fast dynamics.

Molecular Mechanism of Thymidylate Synthase Inhibition by N4-Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies.

Novel evidence is presented allowing further clarification of the mechanism of the slow-binding thymidylate synthase (TS) inhibition by N4-hydroxy-dCMP (N4-OH-dCMP). Spectrophotometric monitoring documented time- and temperature-, and N4-OH-dCMP-dependent TS-catalyzed dihydrofolate production, accompanying the mouse enzyme incubation with N4-OH-dCMP and N5,10-methylenetetrahydrofolate, known to inactivate the enzyme by the covalent binding of the inhibitor, suggesting the demonstrated reaction to be uncoupled from the pyrimidine C(5) methylation. The latter was in accord with the hypothesis based on the previously presented structure of mouse TS (cf. PDB ID: 4EZ8), and with conclusions based on the present structure of the parasitic nematode Trichinella spiralis, both co-crystallized with N4-OH-dCMP and N5,10-methylenetetrahdrofolate. The crystal structure of the mouse TS-N4-OH-dCMP complex soaked with N5,10-methylenetetrahydrofolate revealed the reaction to run via a unique imidazolidine ring opening, leaving the one-carbon group bound to the N(10) atom, thus too distant from the pyrimidine C(5) atom to enable the electrophilic attack and methylene group transfer.

Advanced Spectroscopy and APBS Modeling for Determination of the Role of His190 and Trp103 in Mouse Thymidylate Synthase Interaction with Selected dUMP Analogues.

A homo-dimeric enzyme, thymidylate synthase (TS), has been a long-standing molecular target in chemotherapy. To further elucidate properties and interactions with ligands of wild-type mouse thymidylate synthase (mTS) and its two single mutants, H190A and W103G, spectroscopic and theoretical investigations have been employed. In these mutants, histidine at position 190 and tryptophan at position 103 are substituted with alanine and glycine, respectively. Several emission-based spectroscopy methods used in the paper demonstrate an especially important role for Trp 103 in TS ligands binding. In addition, the Advanced Poisson-Boltzmann Solver (APBS) results show considerable differences in the distribution of electrostatic potential around Trp 103, as compared to distributions observed for all remaining Trp residues in the mTS family of structures. Together, spectroscopic and APBS results reveal a possible interplay between Trp 103 and His190, which contributes to a reduction in enzymatic activity in the case of H190A mutation. Comparison of electrostatic potential for mTS complexes, and their mutants, with the substrate, dUMP, and inhibitors, FdUMP and N4-OH-dCMP, suggests its weaker influence on the enzyme-ligand interactions in N4OH-dCMP-mTS compared to dUMP-mTS and FdUMP-mTS complexes. This difference may be crucial for the explanation of the "abortive reaction" inhibitory mechanism of N4OH-dCMP towards TS. In addition, based on structural analyses and the H190A mutant capacity to form a denaturation-resistant complex with N4-OH-dCMP in the mTHF-dependent reaction, His190 is apparently responsible for a strong preference of the enzyme active center for the anti rotamer of the imino inhibitor form.

First pump-probe-probe hard X-ray diffraction experiments with a 2D hybrid pixel detector developed at the SOLEIL synchrotron.

A new photon-counting camera based on hybrid pixel technology has been developed at the SOLEIL synchrotron, making it possible to implement pump-probe-probe hard X-ray diffraction experiments for the first time. This application relies on two specific advantages of the UFXC32k readout chip, namely its high frame rate (50 kHz) and its high linear count rate (2.6 × 106 photons s-1 pixel-1). The project involved the conception and realization of the chips and detector carrier board, the data acquisition system, the server with its specific software, as well as the mechanical and cooling systems. This article reports on in-laboratory validation tests of the new detector, as well as on tests performed at the CRISTAL beamline within the targeted experimental conditions. A benchmark experiment was successfully performed, showing the advantages of the pump-probe-probe scheme in correcting for drifts of the experimental conditions.

Alvaxanthone, a Thymidylate Synthase Inhibitor with Nematocidal and Tumoricidal Activities.

With the aim to identify novel inhibitors of parasitic nematode thymidylate synthase (TS), we screened in silico an in-house library of natural compounds, taking advantage of a model of nematode TS three-dimensional (3D) structure and choosing candidate compounds potentially capable of enzyme binding/inhibition. Selected compounds were tested as (i) inhibitors of the reaction catalyzed by TSs of different species, (ii) agents toxic to a nematode parasite model (C. elegans grown in vitro), (iii) inhibitors of normal human cell growth, and (iv) antitumor agents affecting human tumor cells grown in vitro. The results pointed to alvaxanthone as a relatively strong TS inhibitor that causes C. elegans population growth reduction with nematocidal potency similar to the anthelmintic drug mebendazole. Alvaxanthone also demonstrated an antiproliferative effect in tumor cells, associated with a selective toxicity against mitochondria observed in cancer cells compared to normal cells.

Thymidylate synthase-catalyzed, tetrahydrofolate-dependent self-inactivation by 5-FdUMP.

In view of previous crystallographic studies, N4-hydroxy-dCMP, a slow-binding thymidylate synthase inhibitor apparently caused "uncoupling" of the two thymidylate synthase-catalyzed reactions, including the N5,10-methylenetetrahydrofolate one-carbon group transfer and reduction, suggesting the enzyme's capacity to use tetrahydrofolate as a cofactor reducing the pyrimidine ring C(5) in the absence of the 5-methylene group. Testing the latter interpretation, a possibility was examined of a TS-catalyzed covalent self-modification/self-inactivation with certain pyrimidine deoxynucleotides, including 5-fluoro-dUMP and N4-hydroxy-dCMP, that would be promoted by tetrahydrofolate and accompanied with its parallel oxidation to dihydrofolate. Electrophoretic analysis showed mouse recombinant TS protein to form, in the presence of tetrahydrofolate, a covalently bound, electrophoretically separable 5-fluoro-dUMP-thymidylate synthase complex, similar to that produced in the presence of N5,10-methylenetetrahydrofolate. Further studies of the mouse enzyme binding with 5-fluoro-dUMP/N4-hydroxy-dCMP by TCA precipitation of the complex on filter paper showed it to be tetrahydrofolate-promoted, as well as to depend on both time in the range of minutes and the enzyme molecular activity, indicating thymidylate synthase-catalyzed reaction to be responsible for it. Furthermore, the tetrahydrofolate- and time-dependent, covalent binding by thymidylate synthase of each 5-fluoro-dUMP and N4-hydroxy-dCMP was shown to be accompanied by the enzyme inactivation, as well as spectrophotometrically confirmed dihydrofolate production, the latter demonstrated to depend on the reaction time, thymidylate synthase activity and temperature of the incubation mixture, further documenting its catalytic character.

Evolution of structure and dynamics of thermo-reversible nanoparticle gels-A combined XPCS and rheology study.

A combined X-ray photon correlation spectroscopy and rheology study is carried out to capture the evolution of structure, fast particle-scale dynamics, and moduli (elastic and loss) at early times of gel formation near the fluid-gel boundary of a suspension of nanoparticles. The system is comprised of moderately concentrated suspensions of octadecyl silica in decalin (ϕ = 0.2) undergoing thermoreversible gelation. Near the gel boundary, the rate of gel formation is very sensitive to changes in attraction strength. However, we find that at different attraction strengths, the system goes through identical intermediate states of microscopic and macroscopic behavior, even though the absolute time needed to form a gel varies by orders of magnitude. We identify a single dimensionless time parameter, tw/tg, where tw is the wait time following the quench and tg is the rheologically determined gel time, that captures the similarity in gel formation at a range of attraction strengths. Following a temperature quench below the gel boundary, the system is initially fluidlike and forms diffusive clusters (∼8.5 times the particle diameter). After a lag-time, tL, clusters aggregate to form a network like structure which is characterized by the onset of mechanical rigidity and a rapid growth in microscopic relaxation times. At tg, the Baxter parameter obtained from adhesive hard sphere fits of the structure factor attains a constant value corresponding to the theoretical percolation boundary, thus demonstrating that gelation is percolation driven.

Sub-microsecond-resolved multi-speckle X-ray photon correlation spectroscopy with a pixel array detector.

Small-angle X-ray photon correlation spectroscopy (XPCS) measurements spanning delay times from 826 ns to 52.8 s were performed using a photon-counting pixel array detector with a dynamic range of 0-3 (2 bits). Fine resolution and a wide dynamic range of time scales was achieved by combining two modes of operation of the detector: (i) continuous mode, where data acquisition and data readout are performed in parallel with a frame acquisition time of 19.36 µs, and (ii) burst mode, where 12 frames are acquired with frame integration times of either 2.56 µs frame-1 or 826 ns frame-1 followed by 3.49 ms or 1.16 ms, respectively, for readout. The applicability of the detector for performing multi-speckle XPCS was demonstrated by measuring the Brownian dynamics of 10 nm-radius gold and 57 nm-radius silica colloids in water at room temperature. In addition, the capability of the detector to faithfully record one- and two-photon counts was examined by comparing the statistical distribution of photon counts with expected probabilities from the negative binomial distribution. It was found that in burst mode the ratio of 2 s to 1 s is markedly smaller than predicted and that this is attributable to pixel-response dead-time.

Evaluation of the UFXC32k photon-counting detector for pump-probe experiments using synchrotron radiation.

This paper presents the performance of a single-photon-counting hybrid pixel X-ray detector with synchrotron radiation. The camera was evaluated with respect to time-resolved experiments, namely pump-probe-probe experiments held at SOLEIL. The UFXC camera shows very good energy resolution of around 1.5 keV and allows the minimum threshold setting to be as low as 3 keV keeping the high-count-rate capabilities. Measurements of a synchrotron characteristic filling mode prove the proper separation of an isolated bunch of photons and the usability of the detector in time-resolved experiments.

Dynamic Scaling of Colloidal Gel Formation at Intermediate Concentrations.

We have examined the formation and dissolution of gels composed of intermediate volume-fraction nanoparticles with temperature-dependent short-range attractions using small-angle x-ray scattering, x-ray photon correlation spectroscopy, and rheology to obtain nanoscale and macroscale sensitivity to structure and dynamics. Gel formation after temperature quenches to the vicinity of the rheologically determined gel temperature, T_{gel}, was characterized via the slowdown of dynamics and changes in microstructure observed in the intensity autocorrelation functions and structure factor, respectively, as a function of quench depth (ΔT=T_{quench}-T_{gel}), wave vector, and formation time t_{f}. We find the wave-vector-dependent dynamics, microstructure, and rheology at a particular ΔT and t_{f} map to those at other ΔTs and t_{f}s via an effective scaling temperature, T_{s}. A single T_{s} applies to a broad range of ΔT and t_{f} but does depend on the particle size. The rate of formation implied by the scaling is a far stronger function of ΔT than expected from the attraction strength between colloids. We interpret this strong temperature dependence in terms of cooperative bonding required to form stable gels via energetically favored, local structures.

Properties of phosphorylated thymidylate synthase.

Thymidylate synthase (TS) may undergo phosphorylation endogenously in mammalian cells, and as a recombinant protein expressed in bacterial cells, as indicated by the reaction of purified enzyme protein with Pro-Q® Diamond Phosphoprotein Gel Stain (PGS). With recombinant human, mouse, rat, Trichinella spiralis and Caenorhabditis elegans TSs, expressed in Escherichia coli, the phosphorylated, compared to non-phosphorylated recombinant enzyme forms, showed a decrease in Vmax(app), bound their cognate mRNA (only rat enzyme studied), and repressed translation of their own and several heterologous mRNAs (human, rat and mouse enzymes studied). However, attempts to determine the modification site(s), whether endogenously expressed in mammalian cells, or recombinant proteins, did not lead to unequivocal results. Comparative ESI-MS/analysis of IEF fractions of TS preparations from parental and FdUrd-resistant mouse leukemia L1210 cells, differing in sensitivity to inactivation by FdUMP, demonstrated phosphorylation of Ser(10) and Ser(16) in the resistant enzyme only, although PGS staining pointed to the modification of both L1210 TS proteins. The TS proteins phosphorylated in bacterial cells were shown by (31)P NMR to be modified only on histidine residues, like potassium phosphoramidate (KPA)-phosphorylated TS proteins. NanoLC-MS/MS, enabling the use of CID and ETD peptide fragmentation methods, identified several phosphohistidine residues, but certain phosphoserine and phosphothreonine residues were also implicated. Molecular dynamics studies, based on the mouse TS crystal structure, allowed one to assess potential of several phosphorylated histidine residues to affect catalytic activity, the effect being phosphorylation site dependent.

Submillisecond X-ray photon correlation spectroscopy from a pixel array detector with fast dual gating and no readout dead-time.

Small-angle scattering X-ray photon correlation spectroscopy (XPCS) studies were performed using a novel photon-counting pixel array detector with dual counters for each pixel. Each counter can be read out independently from the other to ensure there is no readout dead-time between the neighboring frames. A maximum frame rate of 11.8 kHz was achieved. Results on test samples show good agreement with simple diffusion. The potential of extending the time resolution of XPCS beyond the limit set by the detector frame rate using dual counters is also discussed.

First experimental feasibility study of VIPIC: a custom-made detector for X-ray speckle measurements.

The Vertically Integrated Photon Imaging Chip (VIPIC) was custom-designed for X-ray photon correlation spectroscopy, an application in which occupancy per pixel is low but high time resolution is needed. VIPIC operates in a sparsified streaming mode in which each detected photon is immediately read out as a time- and position-stamped event. This event stream can be fed directly to an autocorrelation engine or accumulated to form a conventional image. The detector only delivers non-zero data (sparsified readout), greatly reducing the communications overhead typical of conventional frame-oriented detectors such as charge-coupled devices or conventional hybrid pixel detectors. This feature allows continuous acquisition of data with timescales from microseconds to hours. In this work VIPIC has been used to measure X-ray photon correlation spectroscopy data on polystyrene latex nano-colliodal suspensions in glycerol and on colloidal suspensions of silica spheres in water. Relaxation times of the nano-colloids have been measured for different temperatures. These results demonstrate that VIPIC can operate continuously in the microsecond time frame, while at the same time probing longer timescales.

Thermodynamic parameters for binding of some halogenated inhibitors of human protein kinase CK2.

The interaction of human CK2α with a series of tetrabromobenzotriazole (TBBt) and tetrabromobenzimidazole (TBBz) analogs, in which one of the bromine atoms proximal to the triazole/imidazole ring is replaced by a methyl group, was studied by biochemical (IC50) and biophysical methods (thermal stability of protein-ligand complex monitored by DSC and fluorescence). Two newly synthesized tri-bromo derivatives display inhibitory activity comparable to that of the reference compounds, TBBt and TBBz, respectively. DSC analysis of the stability of protein-ligand complexes shows that the heat of ligand binding (Hbind) is driven by intermolecular electrostatic interactions involving the triazole/imidazole ring, as indicated by a strong correlation between Hbind and ligand pKa. Screening, based on fluorescence-monitored thermal unfolding of protein-ligand complexes, gave comparable results, clearly identifying ligands that most strongly bind to the protein. Overall results, additionally supported by molecular modeling, confirm that a balance of hydrophobic and electrostatic interactions contribute predominantly, relative to possible intermolecular halogen bonding, in binding of the ligands to the CK2α ATP-binding site.

Iron uptake pathway of Escherichia coli as an entry route for peptide nucleic acids conjugated with a siderophore mimic.

Bacteria secrete various iron-chelators (siderophores), which scavenge Fe3+ from the environment, bind it with high affinity, and retrieve it inside the cell. After the Fe3+ uptake, bacteria extract the soluble iron(II) from the siderophore. Ferric siderophores are transported inside the cell via the TonB-dependent receptor system. Importantly, siderophore uptake paths have been also used by sideromycins, natural antibiotics. Our goal is to hijack the transport system for hydroxamate-type siderophores to deliver peptide nucleic acid oligomers into Escherichia coli cells. As siderophore mimics we designed and synthesized linear and cyclic Nδ-acetyl-Nδ-hydroxy-l-ornithine based peptides. Using circular dichroism spectroscopy, we found that iron(III) is coordinated by the linear trimer with hydroxamate groups but not by the cyclic peptide. The internal flexibility of the linear siderophore oxygen atoms and their interactions with Fe3+ were confirmed by all-atom molecular dynamics simulations. Using flow cytometry we found that the designed hydroxamate trimer transports PNA oligomers inside the E. coli cells. Growth recovery assays on various E. coli mutants suggest the pathway of this transport through the FhuE outer-membrane receptor, which is responsible for the uptake of the natural iron chelator, ferric-coprogen. This pathway also involves the FhuD periplasmic binding protein. Docking of the siderophores to the FhuE and FhuD receptor structures showed that binding of the hydroxamate trimer is energetically favorable corroborating the experimentally suggested uptake path. Therefore, this siderophore mimic, as well as its conjugate with PNA, is most probably internalized through the hydroxamate pathway.

Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography.

Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.

The Influence of Vibro-Assisted Abrasive Processing on the Surface Roughness and Sub-Surface Microstructure of Inconel 939 Specimen Made by LPBF.

This paper presents the research results on the influence of vibration abrasive machining parameters on the surface layer integrity of elements made by LPBF technology from Inconel 939. The research was carried out on samples of various sizes on vibrating smoothing machines. The influence of the size of the processed elements, the type of abrasive shapes, the processing time, and the supporting fluid on the surface roughness and microstructure of the processed elements was analyzed. Tests have shown that as a result of using vibration processing, it is possible to reduce the surface roughness five times to the value of Ra = 1.1 µm. A significant influence of the type of abrasive shapes was found. There was no significant effect of the machining fluid on the process.

Impact of an Aluminization Process on the Microstructure and Texture of Samples of Haynes 282 Nickel Alloy Produced Using the Direct Metal Laser Sintering (DMLS) Technique.

In this study, we examined the effects of an aluminization process on the microstructure and texture of Haynes 282 nickel samples fabricated using the direct metal laser sintering technique. The aluminization process involved the use of chemical vapor deposition with AlCl3 vapors in a hydrogen atmosphere at a temperature of 1040 °C for 8 h. Following the 3D printing and aluminization steps, we analyzed the microstructure of the Haynes 282 nickel alloy samples using light microscopy and scanning electron microscopy. Additionally, we investigated the texture using X-ray diffractometry. A texture analysis revealed that after the process of direct laser sintering of metals, the texture of the Haynes 282 nickel alloy samples developed a texture typical of cast materials. Then, in the aluminization process, the texture was transformed-from foundry-type components to a texture characteristic of recrystallization.

Effect of Step Size on the Formability of Al/Cu Bimetallic Sheets in Single Point Incremental Sheet Forming.

Single Point Incremental Forming (SPIF) is an unconventional forming process that is suitable for prototype production and small lot production due to the economical tooling cost, short lead time, and the ability to create symmetrical and asymmetrical complex geometries without the use of expensive dies. This article presents the effect of the step size Δz of a forming tool made of 145Cr6 tool steel on the formability and maximum forming angle, mechanical properties, hardness, surface roughness, microstructure and texture of bimetallic Al/Cu sheets. Experiments were conducted at a constant rotational speed and feed rate, with the use of rapeseed oil as a lubricant. The tests were carried out with the use of a forming tool on both sides of the bimetallic sheet. The shape and dimensions of the formed elements are determined by non-contact optical 3D scanning. It has been proved that an increase in the step size Δz affects the deterioration of the surface quality of the specimens (an increase in the Ra parameter from 0.2 µm to approximately 3 µm for the step size of 1.2 mm), while a small step size down Δz favours the geometric stability of the samples. With increasing step size (at Δx = Δy = const.), the drawpiece wall continually thinned until the material fractured. Based on the results, it was shown that increasing the step size Δz over 1.1 mm causes cracking of the drawpieces. Furthermore, greater thinning of the Al/Cu sheet was observed in the range of step size Δz between 0.7 and 1.0 mm for aluminum side and step size Δz ≤ 0.6 mm and Δz ≥ 1.1 mm for copper side. It was also found that the mechanical properties of the bimetal sheet decreased as a result of incremental forming. The greatest decrease in strength and ductility was recorded for a pitch of 1.2 mm. Strength decreased from 230 MPa (for sheet in initial state) to approximately 80 MPa, elongation from 12% to approximately 8.5%, and hardness from 120 HV10 for Cu and 60 HV10 for Al to approximately 30 HV10 for both layers.