Laser-Induced Dissociation of an Energetic Polymer: A Spectroscopic Study of the Gaseous Products

Previous studies of GAP (glycidyl azido polymer) laser-induced decomposition (Propellants, ExplosiVes, Pyrotechnics 1996, 21, 258), revealed that the shock wave produced from a diluted polymer is more energetic than from the neat polymer. In this paper, direct measurement of the energy disposal into molecular products is reported using spectroscopic methods. Chemiluminescence probes electronically excited species, and laserinduced fluorescence, ground-state radicals. It is found that the initial velocity and internal energy content of small diatomic molecules is larger in some diluted polymers than in the neat one. This finding is in line with a simple model based on the assumption of a self-sustained reaction following initial laser excitation

Spatial Resolution of Double-Sided Silicon Microstrip Detectors for the PAMELA Apparatus

The PAMELA apparatus has been assembled and it is ready to be launched in a satellite mission to study mainly the antiparticle component of cosmic rays. In this paper the performances obtained for the silicon microstrip detectors used in the magnetic spectrometer are presented. This subdetector reconstructs the curvature of a charged particle in the magnetic field produced by a permanent magnet and consequently determines momentum and charge sign, thanks to a very good accuracy in the position measurements (better than 3 um in the bending coordinate). A complete simulation of the silicon microstrip detectors has been developed in order to investigate in great detail the sensor's characteristics. Simulated events have been then compared with data gathered from minimum ionizing particle (MIP) beams during the last years in order to tune free parameters of the simulation. Finally some either widely used or original position finding algorithms, designed for such kind of detectors, have been applied to events with different incidence angles. As a result of the analysis, a method of impact point reconstruction can be chosen, depending on both the particle's incidence angle and the cluster multiplicity, so as to maximize the capability of the spectrometer in antiparticle tagging.Comment: 28 pages, 18 figures, submitted to Nuclear Instruments and Methods in Physics Research

Stabilities of nanohydrated thymine radical cations: insights from multiphoton ionization experiments and ab initio calculations

Multi-photon ionization experiments have been carried out on thymine-water clusters in the gas phase. Metastable H2O loss from T+(H2O)n was observed at n ≥ 3 only. Ab initio quantum-chemical calculations of a large range of optimized T+(H2O)n conformers have been performed up to n = 4, enabling binding energies of water to be derived. These decrease smoothly with n, consistent with the general trend of increasing metastable H2O loss in the experimental data. The lowest-energy conformers of T+(H2O)3 and T+(H2O)4 feature intermolecular bonding via charge-dipole interactions, in contrast with the purely hydrogen-bonded neutrals. We found no evidence for a closed hydration shell at n = 4, also contrasting with studies of neutral clusters

Modularization of biochemical networks based on classification of Petri net t-invariants

<p>Abstract</p> <p>Background</p> <p>Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.</p> <p>With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system.</p> <p>Methods</p> <p>Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied.</p> <p>Results</p> <p>We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in <it>Saccharomyces cerevisiae</it>) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability.</p> <p>Conclusion</p> <p>We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis.</p

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species

Soft Ionization of Thermally Evaporated Hypergolic Ionic Liquid Aerosols

Isolated ion pairs of a conventional ionic liquid, 1-Ethyl-3-Methyl-Imidazolium Bis(trifluoromethylsulfonyl)imide ([Emim+][Tf2N?]), and a reactive hypergolic ionic liquid, 1-Butyl-3-Methyl-Imidazolium Dicyanamide ([Bmim+][Dca?]), are generated by vaporizing ionic liquid submicron aerosol particles for the first time; the vaporized species are investigated by dissociative ionization with tunable vacuum ultraviolet (VUV) light, exhibiting clear intact cations, Emim+ and Bmim+, presumably originating from intact ion pairs. Mass spectra of ion pair vapor from an effusive source of the hypergolic ionic liquid show substantial reactive decomposition due to the internal energy of the molecules emanating from the source. Photoionization efficiency curves in the near threshold ionization region of isolated ion pairs of [Emim+][Tf2N?]ionic liquid vapor are compared for an aerosol source and an effusive source, revealing changes in the appearance energy due to the amount of internal energy in the ion pairs. The aerosol source has a shift to higher threshold energy (~;;0.3 eV), attributed to reduced internal energy of the isolated ion pairs. The method of ionic liquid submicron aerosol particle vaporization, for reactive ionic liquids such as hypergolic species, is a convenient, thermally ?cooler? source of isolated intact ion pairs in the gas phase compared to effusive sources

Vacuum-Ultraviolet Photoionization and Mass Spectrometric Characterization of Lignin Monomers Coniferyl and Sinapyl Alcohols

The fragmentation mechanisms of monolignols under various energetic processes are studied with jet-cooled thermal desorption molecular beam (TDMB) mass spectrometry (MS), 25 keV Bi3+ secondary ion MS (SIMS), synchrotron vacuum-ultraviolet secondary neutral MS (VUV-SNMS) and theoretical methods. Experimental and calculated appearance energies of fragments observed in TDMB MS indicate that the coniferyl alcohol photoionization mass spectra contain the molecular parent and several dissociative photoionization products. Similar results obtained for sinapyl alcohol are also discussed briefly. Ionization energies of 7.60 eV ? 0.05 eV for coniferyl alcohol and<7.4 eV for both sinapyl and dihydrosinapyl alcohols are determined. The positive ion SIMS spectrum of coniferyl alcohol shares few characteristic peaks (m/z = 137 and 151) with the TDMB mass spectra, shows extensive fragmentation, and does not exhibit clear molecular parent signals. VUV-SNMS spectra, on the other hand, are dominated by the parent ion and main fragments also present in the TDMB spectra. Molecular fragmentation in VUV-SNMS spectra can be reduced by increasing the extraction delay time. Some features resembling the SIMS spectra are also observed in the desorbed neutral products. The monolignol VUV-SNMS peaks shared with the TDMB mass spectra suggest that dissociative photoionization of ion-sputtered neutral molecules predominate in the VUV-SNMS mass spectra, despite the extra internal energy imparted in the initial ion impact. The potential applications of these results to imaging mass spectrometry of bio-molecules are discussed