A segment-swapping approach for executing trapped computations

We consider the problem of supporting goal-level, independent andparallelism (IAP) in the presence of non-determinism. IAP is exploited when two or more goals which will not interfere at run time are scheduled for simultaneous execution. Backtracking over non-deterministic parallel goals runs into the wellknown trapped goal and garbage slot problems. The proposed solutions for these problems generally require complex low-level machinery which makes systems difficult to maintain and extend, and in some cases can even affect sequential execution performance. In this paper we propose a novel solution to the problem of trapped nondeterministic goals and garbage slots which is based on a single stack reordering operation and offers several advantages over previous proposals. While the implementation of this operation itself is not simple, in return it does not impose constraints on the scheduler. As a result, the scheduler and the rest of the run-time machinery can safely ignore the trapped goal and garbage slot problems and their implementation is greatly simplified. Also, standard sequential execution remains unaffected. In addition to describing the solution we report on an implementation and provide performance results. We also suggest other possible applications of the proposed approach beyond parallel execution.

Kinetics of amorphization induced by swift heavy ions in α-quartz

The kinetics of amorphization in crystalline SiO2 (α-quartz) under irradiation with swift heavy ions (O+1 at 4 MeV, O+4 at 13 MeV, F+2 at 5 MeV, F+4 at 15 MeV, Cl+3 at 10 MeV, Cl+4 at 20 MeV, Br+5 at 15 and 25 MeV and Br+8 at 40 MeV) has been analyzed in this work with an Avrami-type law and also with a recently developed cumulative approach (track-overlap model). This latter model assumes a track morphology consisting of an amorphous core (area σ) and a surrounding defective halo (area h), both being axially symmetric. The parameters of the two approaches which provide the best fit to the experimental data have been obtained as a function of the electronic stopping power Se. The extrapolation of the σ(Se) dependence yields a threshold value for amorphization, Sth ≈ 2.1 keV/nm; a second threshold is also observed around 4.1 keV/nm. We believe that this double-threshold effect could be related to the appearance of discontinuous tracks in the region between 2.1 and 4.1 keV/nm. For stopping power values around or below the lower threshold, where the ratio h/σ is large, the track-overlap model provides a much better fit than the Avrami function. Therefore, the data show that a right modeling of the amorphization kinetics needs to take into account the contribution of the defective track halo. Finally, a short comparative discussion with the kinetic laws obtained for elastic collision damage is given.

Ionoluminescence induced by swift heavy ions in silica and quartz: a comparative analysis

Ionoluminescence (IL) of the two SiO2 phases, amorphous silica and crystalline quartz, has been comparatively investigated in this work, in order to learn about the structural defects generated by means of ion irradiation and the role of crystalline order on the damage processes. Irradiations have been performed with Cl at 10 MeV and Br at 15 MeV, corresponding to the electronic stopping regime (i.e., where the electronic stopping power Se is dominant) and well above the amorphization threshold. The light-emission kinetics for the two main emission bands, located at 1.9 eV (652 nm) and 2.7 eV (459 nm), has been measured under the same ion irradiation conditions as a function of fluence for both, silica and quartz. The role of electronic stopping power has been also investigated and discussed within current views for electronic damage. Our experiments provide a rich phenomenological background that should help to elucidate the mechanisms responsible for light emission and defect creation.

Ultraintense lasers applied to laser fusion material testing: production of ions, X rays and neutrons

Due to the particular characteristics of the fusion products, i.e. very short pulses (less than a few μs long for ions when arriving to the walls; less than 1 ns long for X-rays), very high fluences ( 10 13 particles/cm 2 for both ions and X rays photons) and broad particle energy spectra (up to 10 MeV ions and 100 keV photons), the laser fusion community lacks of facilities to accurately test plasma facing materials under those conditions. In the present work, the ability of ultraintese lasers to create short pulses of energetic particles and high fluences is addressed as a solution to reproduce those ion and X-ray bursts. Based on those parameters, a comparison between fusion ion and laser driven ion beams is presented and discussed, describing a possible experimental set-up to generate with lasers the appropriate ion pulses. At the same time, the possibility of generating X-ray or neutron beams which simulate those of laser fusion environments is also indicated and assessed under current laser intensities. It is concluded that ultraintense lasers should play a relevant role in the validation of materials for laser fusion facilities.

Tailoring the Optical Properties of Silica Irradiated with Swift Heavy Ions

Irradiation with swift heavy ions (SHI), roughly defined as those having atomic masses larger than 15 and energies exceeding 1 MeV/amu, may lead to significant modification of the irradiated material in a nanometric region around the (straight) ion trajectory (i.e., latent tracks). In the case of amorphous silica it has been reported that SHI irradiation originates nano-tracks of either higher density than the virgin material (for low electronic stopping powers, Se < 7 keV/nm) [1] or having a low-density core and a dense shell (Se > 12 keV/nm) [2]. The intermediate region has not been studied in detail but we will show in this work that essentially no changes in density occur in this zone. An interesting effect of the compaction is that the refractive index is increased with respect to that of the surroundings. In the first Se region it is clear that track overlapping leads to continuous amorphous layers that present a significant contrast with respect to the pristine substrate and this has been used to produce optical waveguides. The optical effects of intermediate and high stopping powers, on the other hand, are largely unknown so far. In this work we have studied theoretically (molecular dynamics and optical simulations) and experimentally (irradiation with SHI and optical characterization) the dependence of the macroscopic optical properties (i.e., the refractive index of the effective medium, n_EMA) on the electronic stopping power of the incoming ions. Our results show that the refractive index of the irradiated silica is not increased in the intermediate region, as expected; however, the core-shell tracks of the high-Se region produce a quite effective enhancement of n_EMA that could prove attractive for the fabrication of optical waveguides at ultralow fluences (as low as 1E11 cm^-2). 1. J. Manzano, J. Olivares, F. Agulló-López, M. L. Crespillo, A. Moroño, and E. Hodgson, "Optical waveguides obtained by swift-ion irradiation on silica (a-SiO2)," Nucl. Instrum. Meth. B 268, 3147-3150 (2010). 2. P. Kluth, C. S. Schnohr, O. H. Pakarinen, F. Djurabekova, D. J. Sprouster, R. Giulian, M. C. Ridgway, A. P. Byrne, C. Trautmann, D. J. Cookson, K. Nordlund, and M. Toulemonde, "Fine structure in swift heavy ion tracks in amorphous SiO2," Phys. Rev. Lett. 101, 175503 (2008).

Three metal ions at the active site of the Tetrahymena group I ribozyme

Metal ions are critical for catalysis by many RNA and protein enzymes. To understand how these enzymes use metal ions for catalysis, it is crucial to determine how many metal ions are positioned at the active site. We report here an approach, combining atomic mutagenesis with quantitative determination of metal ion affinities, that allows individual metal ions to be distinguished. Using this approach, we show that at the active site of the Tetrahymena group I ribozyme the previously identified metal ion interactions with three substrate atoms, the 3′-oxygen of the oligonucleotide substrate and the 3′- and 2′-moieties of the guanosine nucleophile, are mediated by three distinct metal ions. This approach provides a general tool for distinguishing active site metal ions and allows the properties and roles of individual metal ions to be probed, even within the sea of metal ions bound to RNA.

Conversion of agonist site to metal-ion chelator site in the β2-adrenergic receptor

Previously metal-ion sites have been used as structural and functional probes in seven transmembrane receptors (7TM), but as yet all the engineered sites have been inactivating. Based on presumed agonist interaction points in transmembrane III (TM-III) and -VII of the β2-adrenergic receptor, in this paper we construct an activating metal-ion site between the amine-binding Asp-113 in TM-III—or a His residue introduced at this position—and a Cys residue substituted for Asn-312 in TM-VII. No increase in constitutive activity was observed in the mutant receptors. Signal transduction was activated in the mutant receptors not by normal catecholamine ligands but instead either by free zinc ions or by zinc or copper ions in complex with small hydrophobic metal-ion chelators. Chelation of the metal ions by small hydrophobic chelators such as phenanthroline or bipyridine protected the cells from the toxic effect of, for example Cu2+, and in several cases increased the affinity of the ions for the agonistic site. Wash-out experiments and structure–activity analysis indicated, that the high-affinity chelators and the metal ions bind and activate the mutant receptor as metal ion guided ligand complexes. Because of the well-understood binding geometry of the small metal ions, an important distance constraint has here been imposed between TM-III and -VII in the active, signaling conformation of 7TM receptors. It is suggested that atoxic metal-ion chelator complexes could possibly in the future be used as generic, pharmacologic tools to switch 7TM receptors with engineered metal-ion sites on or off at will.

Biosynthesis of terpenoids: 4-Diphosphocytidyl-2-C-methyl-d-erythritol kinase from tomato

The putative catalytic domain (residues 81–401) of a predicted tomato protein with similarity to 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase of Escherichia coli was expressed in a recombinant E. coli strain. The protein was purified to homogeneity and was shown to catalyze the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2-C-methyl-d-erythritol at a rate of 33 μmol⋅mg−1⋅min−1. The structure of the reaction product, 4-diphosphocytidyl-2-C-methyl-d-erythritol 2-phosphate, was established by NMR spectroscopy. Divalent metal ions, preferably Mg2+, are required for activity. Neither the tomato enzyme nor the E. coli ortholog catalyzes the phosphorylation of isopentenyl monophosphate.

Flexibility of the Kir6.2 inward rectifier K+ channel pore

Interactions of sulfhydryl reagents with introduced cysteines in the pore-forming (Kir6.2) subunits of the KATP channel were examined. 2-Aminoethyl methanethiosulfonate (MTSEA+) failed to modify Cd2+-insensitive control-Kir6.2 channels, but rapidly and irreversibly modified Kir6.2[L164C] (L164C) channels. Although a single Cd2+ ion is coordinated by L164C, four MTSEA+ “hits” can occur, each sequentially reducing the single-channel current. A dimeric fusion of control-Kir6.2 and L164C subunits generates Cd2+-insensitive channels, confirming that at least three cysteines are required for coordination, but MTSEA+ modification of the dimer occurs in two hits. L164C channels were not modified by bromotrimethyl ammoniumbimane (qBBr+), even though qBBr+ caused voltage-dependent block (as opposed to modification) that was comparable to that of MTSEA+ or 3-(triethylammonium)propyl methanethiosulfonate (MTSPTrEA+), implying that qBBr+ can also enter the inner cavity but does not modify L164C residues. The Kir channel pore structure was modeled by homology with the KcsA crystal structure. A stable conformation optimally places the four L164C side chains for coordination of a single Cd2+ ion. Modification of these cysteines by up to four MTSEA+ (or three MTSPTrEA+, or two qBBr+) does not require widening of the cavity to accommodate the derivatives within it. However, like the KcsA crystal structure, the energy-minimized model shows a narrowing at the inner entrance, and in the Kir6.2 model this narrowing excludes all ions. To allow entry of ions as large as MTSPTrEA+ or qBBr+, the entrance must widen to >8 Å, but this widening is readily accomplished by minimal M2 helix motion and side-chain rearrangement.

Synthesis and spectroscopic characterization of site-specific 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine oligodeoxyribonucleotide adducts

The aim of the present study is to determine the chemical structure and conformation of DNA adducts formed by incubation of the bioactive form of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), N-acetoxy-PhIP, with a single-stranded 11mer oligodeoxyribonucleotide. Using conditions optimized to give the C8-dG-PhIP adduct as the major product, sufficient material was synthesized for NMR solution structure determination. The NMR data indicate that in duplex DNA this adduct exists in equilibrium between two different conformational states. In the main conformer, the covalently bound PhIP molecule intercalates in the helix, whilst in the minor conformation the PhIP ligand is probably solvent exposed. In addition to the C8-dG-PhIP adduct, at least eight polar adducts are found after reaction of N-acetoxy-PhIP with the oligonucleotide. Three of these were purified for further characterization and shown to exhibit lowest energy UV absorption bands in the range 342–347 nm, confirming the presence of PhIP or PhIP derivative. Accurate mass determination of two of the polar adducts by negative ion MALDI-TOF MS revealed ions consistent with a spirobisguanidino-PhIP derivative and a ring-opened adduct. The third adduct, which has the same mass as the C8-dG-PhIP oligonucleotide adduct, may contain PhIP bound to the N2 position of guanine.

Up-regulation of pressure-activated Ca(2+)-permeable cation channel in intact vascular endothelium of hypertensive rats.

In endothelial cells, stretch-activated cation channels have been proposed to act as mechanosensors for changes in hemodynamic forces. We have identified a novel mechanosensitive pressure-activated channel in intact endothelium from rat aorta and mesenteric artery. The 18-pS cation channel responded with a multifold increase in channel activity when positive pressure was applied to the luminal cell surface with the patch pipette and inactivated at negative pipette pressure. Channel permeability ratio for K+, Na+, and Ca2+ ions was 1:0.98:0.23. Ca2+ influx through the channel was sufficient to activate a neighboring Ca2(+)-dependent K+ channel. Hemodynamic forces are chronically disturbed in arterial hypertension. Endothelial cell dysfunction has been implicated in the pathogenesis of arterial hypertension. In two comparative studies, density of the pressure-activated channel was found to be significantly higher in spontaneously hypertensive rats and renovascular hypertensive rats compared with their respective normotensive controls. Channel activity presumably leads to mechanosensitive Ca2+ influx and induces cell hyperpolarization by K+ channel activity. Both Ca2+ influx and hyperpolarization are known to induce a vasodilatory endothelial response by stimulating endothelial nitric oxide (NO) production. Up-regulation of channel density in hypertension could, therefore, represent a counterregulatory mechanism of vascular endothelium.

Ribonuclease P (RNase P) RNA is converted to a Cd(2+)-ribozyme by a single Rp-phosphorothioate modification in the precursor tRNA at the RNase P cleavage site.

To study the cleavage mechanism of bacterial Nase P RNA, we have synthesized precursor tRNA substrates carrying a single Rp- or Sp-phosphorothioate modification at the RNase P cleavage site. Both the Sp- and the Rp-diastereomer reduced the rate of processing by Escherichia coli RNase P RNA at least 1000-fold under conditions where the chemical step is rate-limiting. The Rp-modification had no effect and the Sp-modification had a moderate effect on precursor tRNA ground state binding to RNase P RNA. Processing of the Rp-diastereomeric substrate was largely restored in the presence of the "thiophilic" Cd2+ as the only divalent metal ion, demonstrating direct metal ion coordination to the (pro)-Rp substituent at the cleavage site and arguing against a specific role for Mg(2+)-ions at the pro-Sp oxygen. For the Rp-diastereomeric substrate, Hill plot analysis revealed a cooperative dependence upon [Cd2+] of nH = 1.8, consistent with a two-metal ion mechanism. In the presence of the Sp-modification, neither Mn2+ nor Cd2+ was able to restore detectable cleavage at the canonical site. Instead, the ribozyme promotes cleavage at the neighboring unmodified phosphodiester with low efficiency. Dramatic inhibition of the chemical step by both the Rp- and Sp-phosphorothioate modification is unprecedented among known ribozymes and points to unique features of transition state geometry in the RNase P RNA-catalyzed reaction.