Non-Maxwellian electron distributions in time-dependent simulations of low-Z materials illuminated by a high-intensity X-ray laser

The interaction of high intensity X-ray lasers with matter is modeled. A collisional-radiative timedependent module is implemented to study radiation transport in matter from ultrashort and ultraintense X-ray bursts. Inverse bremsstrahlung absorption by free electrons, electron conduction or hydrodynamic effects are not considered. The collisional-radiative system is coupled with the electron distribution evolution treated with a Fokker-Planck approach with additional inelastic terms. The model includes spontaneous emission, resonant photoabsorption, collisional excitation and de-excitation, radiative recombination, photoionization, collisional ionization, three-body recombination, autoionization and dielectronic capture. It is found that for high densities, but still below solid, collisions play an important role and thermalization times are not short enough to ensure a thermal electron distribution. At these densities Maxwellian and non-Maxwellian electron distribution models yield substantial differences in collisional rates, modifying the atomic population dynamics.

The N-terminal domain of PsaF: Precise recognition site for binding and fast electron transfer from cytochrome c6 and plastocyanin to photosystem I of Chlamydomonas reinhardtii

The PsaF-deficient mutant 3bF of Chlamydomonas reinhardtii was used to modify PsaF by nuclear transformation and site-directed mutagenesis. Four lysine residues in the N-terminal domain of PsaF, which have been postulated to form the positively charged face of a putative amphipathic α-helical structure were altered to K12P, K16Q, K23Q, and K30Q. The interactions between plastocyanin (pc) or cytochrome c6 (cyt c6) and photosystem I (PSI) isolated from wild type and the different mutants were analyzed using crosslinking techniques and flash absorption spectroscopy. The K23Q change drastically affected crosslinking of pc to PSI and electron transfer from pc and cyt c6 to PSI. The corresponding second order rate constants for binding of pc and cyt c6 were reduced by a factor of 13 and 7, respectively. Smaller effects were observed for mutations K16Q and K30Q, whereas in K12P the binding was not changed relative to wild type. None of the mutations affected the half-life of the microsecond electron transfer performed within the intermolecular complex between the donors and PSI. The fact that these single amino acid changes within the N-terminal domain of PsaF have different effects on the electron transfer rate constants and dissociation constants for both electron donors suggests the existence of a rather precise recognition site for pc and cyt c6 that leads to the stabilization of the final electron transfer complex through electrostatic interactions.

Kinetic coupling between electron and proton transfer in cytochrome c oxidase: simultaneous measurements of conductance and absorbance changes.

Bovine heart cytochrome c oxidase is an electron-current driven proton pump. To investigate the mechanism by which this pump operates it is important to study individual electron- and proton-transfer reactions in the enzyme, and key reactions in which they are kinetically and thermodynamically coupled. In this work, we have simultaneously measured absorbance changes associated with electron-transfer reactions and conductance changes associated with protonation reactions following pulsed illumination of the photolabile complex of partly reduced bovine cytochrome c oxidase and carbon monoxide. Following CO dissociation, several kinetic phases in the absorbance changes were observed with time constants ranging from approximately 3 microseconds to several milliseconds, reflecting internal electron-transfer reactions within the enzyme. The data show that the rate of one of these electron-transfer reactions, from cytochrome a3 to a on a millisecond time scale, is controlled by a proton-transfer reaction. These results are discussed in terms of a model in which cytochrome a3 interacts electrostatically with a protonatable group, L, in the vicinity of the binuclear center, in equilibrium with the bulk through a proton-conducting pathway, which determines the rate of proton transfer (and indirectly also of electron transfer). The interaction energy of cytochrome a3 with L was determined independently from the pH dependence of the extent of the millisecond-electron transfer and the number of protons released, as determined from the conductance measurements. The magnitude of the interaction energy, 70 meV (1 eV = 1.602 x 10(-19) J), is consistent with a distance of 5-10 A between cytochrome a3 and L. Based on the recently determined high-resolution x-ray structures of bovine and a bacterial cytochrome c oxidase, possible candidates for L and a physiological role for L are discussed.

Kinetics of photo-induced electron transfer from high-potential iron-sulfur protein to the photosynthetic reaction center of the purple phototroph Rhodoferax fermentans.

The kinetics of photo-induced electrontransfer from high-potential iron-sulfur protein (HiPIP) to the photosynthetic reaction center (RC) of the purple phototroph Rhodoferarfermentans were studied. The rapid photooxidation of heme c-556 belonging to RC is followed, in the presence of HiPIP, by a slower reduction having a second-order rate constant of 4.8 x 10(7) M(-1) x s(-1). The limiting value of kobs at high HiPIP concentration is 95 s(-1). The amplitude of this slow process decreases with increasing HiPIP concentration. The amplitude of a faster phase, observed at 556 and 425 nm and involving heme c-556 reduction, increases proportionately. The rate constant of this fast phase, determined at 425 and 556 nm, is approximately 3 x 10(5) s(-1). This value is not dependent on HiPIP concentration, indicating that it is related to a first-order process. These observations are interpreted as evidence for the formation of a HiPIP-RC complex prior to the excitation flash, having a dissociation constant of -2.5 microM. The fast phase is absent at high ionic strength, indicating that the complex involves mainly electrostatic interactions. The ionic strength dependence of kobs for the slow phase yields a second-order rate constant at infinite ionic strength of 5.4 x 10(6) M(-1) x s(-1) and an electrostatic interaction energy of -2.1 kcal/mol (1 cal = 4.184 J). We conclude that Rhodoferar fermentans HiPIP is a very effective electron donor to the photosynthetic RC.

Structure and conformational changes of DNA topoisomerase II visualized by electron microscopy.

Type II DNA topoisomerases, which create a transient gate in duplex DNA and transfer a second duplex DNA through this gate, are essential for topological transformations of DNA in prokaryotic and eukaryotic cells and are of interest not only from a mechanistic perspective but also because they are targets of agents for anticancer and antimicrobial chemotherapy. Here we describe the structure of the molecule of human topoisomerase II [DNA topoisomerase (ATP-hydrolyzing), EC 5.99.1.3] as seen by scanning transmission electron microscopy. A globular approximately 90-angstrom diameter core is connected by linkers to two approximately 50-angstrom domains, which were shown by comparison with genetically truncated Saccharomyces cerevisiae topoisomerase II to contain the N-terminal region of the approximately 170-kDa subunits and that are seen in different orientations. When the ATP-binding site is occupied by a nonhydrolyzable ATP analog, a quite different structure is seen that results from a major conformational change and consists of two domains approximately 90 angstrom and approximately 60 angstrom in diameter connected by a linker, and in which the N-terminal domains have interacted. About two-thirds of the molecules show an approximately 25 A tunnel in the apical part of the large domain, and the remainder contain an internal cavity approximately 30 A wide in the large domain close to the linker region. We propose that structural rearrangements lead to this displacement of an internal tunnel. The tunnel is likely to represent the channel through which one DNA duplex, after capture in the clamp formed by the N-terminal domains, is transferred across the interface between the enzyme's subunits. These images are consistent with biochemical observations and provide a structural basis for understanding the reaction of topoisomerase II.

Functionals for TDDFT description of electron transport in nanostructures

La Teoria di Densità Funzionale (DFT) e la sua versione dipendente dal tempo (TDDFT) sono strumenti largamente usati per simulare e calcolare le proprietà statiche e dinamiche di sistemi con elettroni interagenti. La precisione del metodo si basa su una serie di approssimazioni degli effetti di exchange correlation fra gli elettroni, descritti da un funzionale della sola densità di carica. Nella presente tesi viene testata l'affidabilità del funzionale Mixed Localization Potential (MLP), una media pesata fra Single Orbital Approximation (SOA) e un potenziale di riferimento, ad esempio Local Density Approximation (LDA). I risultati mostrano capacità simulative superiori a LDA per i sistemi statici (curando anche un limite di LDA noto in letteratura come fractional dissociation) e dei progressi per sistemi dinamici quando si sviluppano correnti di carica. Il livello di localizzazione del sistema, inteso come la capacità di un elettrone di tenere lontani da sé altri elettroni, è descritto dalla funzione Electron Localization Function (ELF). Viene studiato il suo ruolo come guida nella costruzione e ottimizzazione del funzionale MLP.

Mercury capture on a supported chlorocuprate(II) ionic liquid adsorbent studied using operando synchrotron X-ray absorption spectroscopy

Mercury scrubbing from gas streams using a supported 1-butyl-3-methylimidazolium chlorocuprate(II) ionic liquid ([C4mim]2[Cu2Cl6]) has been studied using operando EXAFS. Initial oxidative capture as [HgCl3]– anions was confirmed, this was then followed by the unanticipated generation of mercury(I) chloride through comproportionation with additional mercury from the gas stream. Combining these two mechanisms leads to net one electron oxidative extraction of mercury from the gas with increased potential capacity and efficiency for supported ionic liquid mercury scrubbers.

Quality controls for the Mu2e electromagnetic calorimeter and R&D studies for the muon capture rate determination

According to the SM, while Lepton Flavour Violation is allowed in the neutral sector, Charged Lepton Flavour Violation (CLFV) processes are forbidden. The Mu2e Experiment at Fermilab will search for the CLFV process of neutrinoless conversion of a muon into an electron within the field of an Al nucleus. The Mu2e detectors and its state-of-the-art superconducting magnetic system are presented, with special focus put to the electromagnetic crystal calorimeter. The calorimeter is composed by two annular disks, each one hosting pure CsI crystals read-out by custom silicon photomultipliers (SiPMs). The SiPMs are amplified by custom electronics (FEE) and are glued to copper holders in group of 2 SiPMs and 2 FEE boards thus forming a crystal Readout Unit. These Readout Units are being tested at the Quality Control (QC) Station, whose design, realization and operations are presented in this work. The QC Station allows to determine the gain, the response and the photon detection efficiency of each unit and to evaluate the dependence of these parameters from the supply voltage and temperature. The station is powered by two remotely-controlled power supplies and monitored thanks to a Slow Control system which is also illustrated in this work. In this thesis, we also demonstrated that the calorimeter can perform its own measurement of the Mu2e normalization factor, i.e. the counting of the 1.8 MeV photon line produced in nuclear muon captures. A specific calorimeter sub-system called CAPHRI, composed by four LYSO crystals with SiPM readout, has been designed and tested. We simulated the capability of this system on performing this task showing that it can get a faster and more reliable measurement of the muon capture rates with respect to the current Mu2e detector dedicated to this measurement. The characterization of energy resolution and response uniformity of the four procured LYSO crystals are llustrated.

Efficacy Of Ethylene-diamine-tetra-acetic Acid Associated With Chlorhexidine On Intracanal Medication Removal: A Scanning Electron Microscopy Study.

The aim of this study was to evaluate the effectiveness of 17% ethylene-diamine-tetra-acetic acid (EDTA) used alone or associated with 2% chlorhexidine gel (CHX) on intracanal medications (ICM) removal. Sixty single-rooted human teeth with fully formed apex were selected. The cervical and middle thirds of each canal were prepared with Gates Glidden drills and rotary files. The apical third was shaped with hand files. The specimens were randomly divided into two groups depending on the ICM used after instrumentation: calcium hydroxide Ca(OH)(2) +CHX or Ca(OH)(2) +sterile saline (SS). After seven days, each group was divided into subgroups according to the protocol used for ICM removal: instrumentation and irrigation either with EDTA, CHX+EDTA, or SS (control groups). All specimens were sectioned and processed for observation of the apical thirds by using scanning electron microscopy. Two calibrated evaluators attributed scores to each specimen. The differences between the protocols for ICM removal were analyzed with Kruskal-Wallis and Mann-Whitney U tests. Friedman and Wilcoxon signed rank tests were used for comparison between the score of debris obtained in each root canal third. Remains of Ca(OH)(2) were found in all specimens independently of the protocol and ICM used (P > 0.05). Seventeen percent EDTA showed the best results in removing ICM when used alone (P < 0.05), particularly in those associated with CHX. It was concluded that the chelating agent 17% EDTA significantly improved the removal of ICM when used alone. Furthermore, the type of the vehicle associated with Ca(OH)(2) also plays a role in the ICM removal.

Improvement Of The Physical Performance Is Associated With Activation Of No/pgc-1α/mttfa Signaling Pathway And Increased Protein Expressions Of Electron Transport Chain In Gastrocnemius Muscle From Rats Supplemented With L-arginine.

To examine the influence of l-arginine supplementation in combination with physical training on mitochondrial biomarkers from gastrocnemius muscle and its relationship with physical performance. Male Wistar rats were divided into four groups: control sedentary (SD), sedentary supplemented with l-arginine (SDLA), trained (TR) and trained supplemented with l-arginine (TRLA). Supplementation of l-arginine was administered by gavage (62.5mg/ml/day/rat). Physical training consisted of 60min/day, 5days/week, 0% grade, speed of 1.2km/h. The study lasted 8weeks. Skeletal muscle mitochondrial enriched fraction as well as cytoplasmic fractions were obtained for Western blotting and biochemical analyses. Protein expressions of transcriptor coactivator (PGC-1α), transcriptor factors (mtTFA), ATP synthase subunit c, cytochrome oxidase (COXIV), constitutive nitric oxide synthases (eNOS and nNOS), Cu/Zn-superoxide dismutase (SOD) and manganese-SOD (Mn-SOD) were evaluated. We also assessed in plasma: lipid profile, glycemia and malondialdehyde (MDA) levels. The nitrite/nitrate (NOx(-)) levels were measured in both plasma and cytosol fraction of the gastrocnemius muscle. 8-week l-arginine supplementation associated with physical training was effective in promoting greater tolerance to exercise that was accompanied by up-regulation of the protein expressions of mtTFA, PGC-1α, ATP synthase subunit c, COXIV, Cu/Zn-SOD and Mn-SOD. The upstream pathway was associated with improvement of NO bioavailability, but not in NO production since no changes in nNOS or eNOS protein expressions were observed. This combination would be an alternative approach for preventing cardiometabolic diseases given that in overt diseases a profound impairment in the physical performance of the patients is observed.

Megalencephalic Leukoencephalopathy With Subcortical Cysts (mlc) - A Case With Clinical And Magnetic Resonance Imaging (mri) Dissociation.

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Scanning electron microscopic study of the in situ effect of salivary stimulation on erosion and abrasion in human and bovine enamel

This in situ study investigated, using scanning electron microscopy, the effect of stimulated saliva on the enamel surface of bovine and human substrates submitted to erosion followed by brushing abrasion immediately or after one hour. During 2 experimental 7-day crossover phases, 9 previously selected volunteers wore intraoral palatal devices, with 12 enamel specimens (6 human and 6 bovine). In the first phase, the volunteers immersed the device for 5 minutes in 150 ml of a cola drink, 4 times a day (8h00, 12h00, 16h00 and 20h00). Immediately after the immersions, no treatment was performed in 4 specimens (ERO), 4 other specimens were immediately brushed (0 min) using a fluoride dentifrice and the device was replaced into the mouth. After 60 min, the other 4 specimens were brushed. In the second phase, the procedures were repeated but, after the immersions, the volunteers stimulated the salivary flow rate by chewing a sugar-free gum for 30 min. Enamel superficial alterations of all specimens were then evaluated using a scanning electron microscope. Enamel prism core dissolution was seen on the surfaces submitted to erosion, while on those submitted to erosion and to abrasion (both at 0 and 60 min) a more homogeneous enamel surface was observed, probably due to the removal of the altered superficial prism layer. For all the other variables - enamel substrate and salivary stimulation -, the microscopic pattern of the enamel specimens was similar.

Comparison among four commonly used demineralizing agents for root conditioning: a scanning electron microscopy

Dental roots that have been exposed to the oral cavity and periodontal pocket environment present superficial changes, which can prevent connective tissue reattachment. Demineralizing agents have been used as an adjunct to the periodontal treatment aiming at restoring the biocompatibility of roots. OBJECTIVE: This study compared four commonly used demineralizing agents for their capacity of removing smear layer and opening dentin tubules. METHODS: Fifty fragments of human dental roots previously exposed to periodontal disease were scaled and randomly divided into the following groups of treatment: 1) CA: demineralization with citric acid for 3 min; 2) TC-HCl: demineralization with tetracycline-HCl for 3 min; 3) EDTA: demineralization with EDTA for 3 min; 4) PA: demineralization with 37% phosphoric acid for 3 min; 5) Control: rubbing of saline solution for 3 min. Scanning electron microscopy was used to check for the presence of residual smear layer and for measuring the number and area of exposed dentin tubules. RESULTS: Smear layer was present in 100% of the specimens from the groups PA and control; in 80% from EDTA group; in 33.3% from TC-HCl group and 0% from CA group. The mean numbers of exposed dentin tubules in a standardized area were: TC-HCl=43.8±25.2; CA=39.3±37; PA=12.1±16.3; EDTA=4.4±7.5 and Control=2.3±5.7. The comparison showed significant differences between the following pairs of groups: TC-HCl and Control; TC-HCl and EDTA; CA and Control; and CA and EDTA. The mean percentages of area occupied by exposed dentin tubules were: CA=0.12±0.17%; TC-HCl=0.08±0.06%; PA=0.03±0.05%; EDTA=0.01±0.01% and Control=0±0%. The CA group differed significantly from the others except for the TC-HCl group. CONCLUSION: There was a decreasing ability for smear layer removal and dentin tubule widening as follows: AC>TC-HCl>PA>EDTA. This information can be of value as an extra parameter for choosing one of them for root conditioning.

Evaluation of the maxillary premolar roots dissociation using radiographic holders with conventional and digital radiography

This in vivo study evaluated the dissociation quality of maxillary premolar roots combining variations of vertical and horizontal angulations by using X-ray holders (Rinn -XCP), and made a comparison between two types of intraoral radiography systems - conventional film (Kodak Insight, Rochester, USA) and digital radiography (Kodak RVG 6100, Kodak, Rochester, USA). The study sample was comprised of 20 patients with a total of 20 maxillary premolars that were radiographed, using the paralleling angle technique (GP), with a 20º variation of the horizontal angle (GM) and 25º variation of the horizontal angle combined with 15º vertical angle (GMV). Each image was independently analyzed by two experienced examiners. These examiners assigned a score to the diagnostic capability of root dissociation and the measurement of the distance between the apexes. Statistical data was derived using the Wilcoxon Signed Rank test, Friedman and T test. The means of the measured distances between buccal and lingual root apexes were greater for the GMV, which ranged from 2.3 mm to 3.3 mm. A statistically significant difference was found between GM and GMV when compared to GP with p < 0.01. An established best diagnostic dissociation roots image was found in the GMV. These results support the use of the anterior X-ray holders which offer a better combined deviation (GMV) to dissociate maxillary premolar roots in both radiography systems.