Yields Of Fragments Research Articles

Exclusive studies of 130–270 MeVHe3- and 200-MeV proton-induced reactions onAl27,Agnat, andAu197

Exclusive light-charged-particle and IMF spectra have been measured with the ISiS detector array for bombardments of $^{27}\mathrm{Al}$, $^{\mathrm{nat}}\mathrm{Ag}$, and $^{197}\mathrm{Au}$ nuclei with 130--270-MeV $^{3}\mathrm{He}$ and 200-MeV protons. The results are consistent with previous interpretations based on inclusive data that describe the global yield of complex fragments in terms of a time-dependent process. The emission mechanism for energetic nonequilibrium fragments observed at forward angles with momenta up to twice the beam momentum is also investigated. This poorly understood mechanism, for which the angular distributions indicate formation on a time scale comparable to the nuclear transit time, are accompanied primarily by thermal-like emissions. The data are most consistent with a schematic picture in which nonequilibrium fragments are formed in a localized region of the target nucleus at an early stage in the energy-dissipation process, where the combined effects of high energy density and Fermi motion produce the observed suprathermal spectra.

Measurement of azimuthal asymmetries in inclusive production of hadron pairs ine+e−annihilation ats=10.58 GeV

The Collins effect connects transverse quark spin with a measurable azimuthal asymmetry in the yield of hadronic fragments around the quark's momentum vector. Using two different reconstruction methods we measure statistically significant azimuthal asymmetries for charged pion pairs in e+e- annihilation at center-of-mass energies of 10.52 GeV and 10.58 GeV, which can be attributed to the fragmentation of primordial quarks with transverse spin components. The measurement was performed using a data set of 547fb-1 collected by the Belle detector at KEKB improving the statistics of the previously published results by nearly a factor of 20. © 2008 The American Physical Society.

An Improved Method for the Isolation of Free‐Circulating Plasma DNA and Cell‐Free DNA from Other Body Fluids

Cell-free DNA is of increasing interest in different fields, such as cancer research, prenatal diagnosis, and the diagnosis of nonmalignant diseases. The quantity of free-circulating DNA in plasma, serum, and other body fluids is usually low and its isolation is still a challenge. Here we evaluate the application of the new commercially available NucleoSpin Plasma XS Kit for the isolation of cell-free DNA from plasma, serum, and cell-free bronchial lavage samples. The NucleoSpin columns proved superior to the QIAamp system in terms of DNA yield, purity, and retrieval of small DNA fragments. The procedure is fast and easy to standardize and might be valuable for laboratories working in the field of CNAPS.

Cluster primary ions: Spikes, sputtering yields, secondary ion yields, and interrelationships for secondary molecular ions for static secondary ion mass spectrometry

A framework is provided to describe the enhanced sputtering yields and secondary ion yields of molecular fragments, from molecules on substrates, achieved when using cluster primary ions. Analysis of published sputtering yield measurements shows that one particular model of sputtering, which includes the thermal spike, is an excellent quantitative description of the yields for a wide range of monatomic and polyatomic primary ions. The model is valid for describing clusters of up to more than ten atoms over three orders of magnitude in sputtering yield. Using data from one primary ion, extremely good descriptions of measurements reported with other primary ions are achieved. This is then used to evaluate the important molecular ion yield behavior for static secondary ion mass spectrometry based on data for Irganox 1010. Universal dependences for the deprotonated molecular ion yields, valid for all the primary ions studied, both single atom and cluster, over five decades of emission intensity are obtained. This permits the prediction of the (M−H)− secondary ion yield for different, or new, cluster primary ions, e.g., Bin+ and C70+, for the analysis of organic materials. Optimal primary ion sources are predicted and discussed. For analyzing materials, raising the molecular secondary ion yield is extremely helpful but it is the ratio of this yield to the disappearance cross section that is critical for obtaining the maximum useful molecular yield and/or the best spatial resolution for molecular signals from molecular monolayers. Data are evaluated and a description is given to show how this ratio varies with the cluster to provide further universal dependences.

WE-C-AUD B-09: Evaluation of Radiobiological Effects of Carbon Ion Beams: Mixed Particle Fields and Fragmentation

Purpose: The purpose of this report is to investigate the effects on the Relative Biological Effectiveness (RBE) due to nuclear fragmentation during irradiation with therapeuticcarbonion beams, by using biological model calculations. Method and Materials: In order to disentangle the biological effects of the mixed particle fields, we evaluated the RBE originated by primary carbon ions and by fragments together and separately. The radiobiological efficiency of charged particles is mainly characterized by their high local ionization density which can be directly correlated to the local density of DNA damage. We developed a code based on the Local Effect Model (LEM) for the calculation of the cell survival after irradiation with carbon ions. As input we use particle distributions sampled at different depths in a water volume, for different energies of the primary ions (between 150 and 400 MeV/u), generated by Monte Carlo simulations using the package GEANT4. The computational effort was performed using the distributed INFN (Istituto Nazionale di Fisica Nucleare) Grid computing resources. Results: For carbon ions, high RBE values were found in the high‐LET region (Bragg peak), as well as in the low‐dose region, the distal region after the Bragg peak, where the contribution to the RBE is mainly due to fragments. We show that the global biological effect can be well reconstructed by a weighted combination of the alpha and beta parameters of the Linear‐Quadratic Model (LQM) evaluated separately for primary ions and fragments. The analysis provided also an estimate of the RBE sensitivity to the uncertainties present in the experimental data of fragment yield. Conclusion: Our work estimated the impact of the fragments in hadrontherapy using carbonion beams. Due to the high RBE values found, the resulting biological dose can be important in regions outside the irradiated target, in presence of organs at risk.

Photofragmentation of 2‐Deoxy‐D‐Ribose Molecules in the Gas Phase

We have measured the synchrotron-induced photofragmentation of isolated 2-deoxy-D-ribose molecules (C(5)H(10)O(4)) at four photon energies, namely, 23.0, 15.7, 14.6, and 13.8 eV. At all photon energies above the molecule's ionization threshold we observe the formation of a large variety of molecular cation fragments, including CH(3) (+), OH(+), H(3)O(+), C(2)H(3) (+), C(2)H(4) (+), CH(x)O(+) (x=1,2,3), C(2)H(x)O(+) (x=1-5), C(3)H(x)O(+) (x=3-5), C(2)H(4)O(2) (+), C(3)H(x)O(2) (+) (x=1,2,4-6), C(4)H(5)O(2) (+), C(4)H(x)O(3) (+) (x=6,7), C(5)H(7)O(3) (+), and C(5)H(8)O(3) (+). The formation of these fragments shows a strong propensity of the DNA sugar to dissociate upon absorption of vacuum ultraviolet photons. The yields of particular fragments at various excitation photon energies in the range between 10 and 28 eV are also measured and their appearance thresholds determined. At all photon energies, the most intense relative yield is recorded for the m/q=57 fragment (C(3)H(5)O(+)), whereas a general intensity decrease is observed for all other fragments- relative to the m/q=57 fragment-with decreasing excitation energy. Thus, bond cleavage depends on the photon energy deposited in the molecule. All fragments up to m/q=75 are observed at all photon energies above their respective threshold values. Most notably, several fragmentation products, for example, CH(3) (+), H(3)O(+), C(2)H(4) (+), CH(3)O(+), and C(2)H(5)O(+), involve significant bond rearrangements and nuclear motion during the dissociation time. Multibond fragmentation of the sugar moiety in the sugar-phosphate backbone of DNA results in complex strand lesions and, most likely, in subsequent reactions of the neutral or charged fragments with the surrounding DNA molecules.

Control of Molecular Fragmentation Using Shaped Femtosecond Pulses

The possibility that chemical reactions may be controlled by tailored femtosecond laser pulses has inspired recent studies that take advantage of their short pulse duration, comparable to intramolecular dynamics, and high peak intensity to fragment and ionize molecules. In this article, we present an experimental quest to control the chemical reactions that take place when isolated molecules interact with shaped near-infrared laser pulses with peak intensities ranging from 1013 to 1016 W/cm2. Through the exhaustive evaluation of hundreds of thousands of experiments, we methodically evaluated the molecular response of 16 compounds, including isomers, to the tailored light fields, as monitored by time-of-flight mass spectrometry. Analysis of the experimental data, taking into account its statistical significance, leads us to uncover important trends regarding the interaction of isolated molecules with an intense laser field. Despite the energetics involved in fragmentation and ionization, the integrated second-harmonic generation of a given laser pulse (ISHG), which was recorded as an independent diagnostic parameter, was found to be linearly proportional to the total ion yield (IMS) generated by that pulse in all of our pulse shaping measurements. Order of magnitude laser control over the relative yields of different fragment ions was observed for most of the molecules studied; the fragmentation yields were found to vary monotonically with IMS and/or ISHG. When the extensive changes in fragmentation yields as a function of IMS were compared for different phase functions, we found essentially identical results. This observation implies that fragmentation depends on a parameter that is responsible for IMS and independent from the particular time-frequency structure of the shaped laser pulse. With additional experiments, we found that individual ion yields depend only on the average pulse duration, implying that coherence does not play a role in the observed changes in yield as a function of pulse shaping. These findings were consistently observed for all molecules studied (p-, m-, o-nitrotoluene, 2,4-dinitrotoluene, benzene, toluene, naphthalene, azulene, acetone, acetyl chloride, acetophenone, p-chrolobenzonitrile, N,N-dimethylformamide, dimethyl phosphate, 2-chloroethyl ethyl sulfide, and tricarbonyl-[eta5-1-methyl-2,4-cyclopentadien-1-yl]-manganese). The exception to our conclusion is that the yield of small singly-charged fragments resulting from a multiple ionization process in a subset of molecules, were found to be highly sensitive to the phase structure of the intense pulses. This coherent process plays a minimal role in photofragmentation; therefore, we consider it an exception rather than a rule. Changes in the fragmentation process are dependent on molecular structure, as evidenced in a number of isomers, therefore femtosecond laser fragmentation could provide a practical dimension to analytical chemistry techniques.

SIMAC (Sequential Elution from IMAC), a Phosphoproteomics Strategy for the Rapid Separation of Monophosphorylated from Multiply Phosphorylated Peptides

The complete analysis of phosphoproteomes has been hampered by the lack of methods for efficient purification, detection, and characterization of phosphorylated peptides from complex biological samples. Despite several strategies for affinity enrichment of phosphorylated peptides prior to mass spectrometric analysis, such as immobilized metal affinity chromatography or titanium dioxide, the coverage of the phosphoproteome of a given sample is limited. Here we report a simple and rapid strategy, SIMAC (sequential elution from IMAC), for sequential separation of monophosphorylated peptides and multiply phosphorylated peptides from highly complex biological samples. This allows individual analysis of the two pools of phosphorylated peptides using mass spectrometric parameters differentially optimized for their unique properties. We compared the phosphoproteome identified from 120 mug of human mesenchymal stem cells using SIMAC and an optimized titanium dioxide chromatographic method. More than double the total number of identified phosphorylation sites was obtained with SIMAC, primarily from a 3-fold increase in recovery of multiply phosphorylated peptides.

A step-wise approach significantly enhances protein yield of a rationally-designed agonist antibody fragment in E. coli

Fab59 is a rationally-designed antibody fragment (Fab) that mimics the activity of the cytokine thrombopoietin (TPO). Fab59 activity was initially detected directly from bacterial supernatants in a cell-based assay and was subsequently estimated to be equipotent to TPO using purified material. However, the expression of Fab59 was insufficient to support in vivo characterization of the Fab due to extremely low expression levels from its initial phage display expression vector. To boost expression, a new expression vector was designed and constructed, and Fab59 light chain codons were optimized for bacterial expression. However, from this a new challenge arose, in that the codon-optimized Fab59 was more toxic to Escherichia coli cells than parental Fab59. Co-expression of the bacterial chaperon protein Skp alleviated this toxicity. A two-step purification method was used to isolate monomeric Fab59 from the periplasm. Although Fab59 was prone to form aggregates during the purification process, buffer modification efficiently eliminated this problem. Overall, optimization of Fab59 expression and purification achieved a 100-fold increase in Fab59 production in E. coli relative to the starting yield. The yield of purified monomeric Fab59 from a shake flask reached up to 3.5mg/L, which was sufficient to support testing of the agonist activity of purified monomeric Fab59 in vivo. Even higher yields may be achieved by purification of Fab present in the culture media, as Skp most significantly increased accumulation of Fab59 in that location.

Stability and dissociation pathways of doped AunX+clusters (X = Y, Er, Nb)

Size dependent stabilities, fragmentation pathways and dissociation energies of a series of gas phase cationic doped gold clusters, Au(n)X+ (3 < or = n < or = 20; X = Y, Er and Nb), and pure Au(n)+ clusters were investigated in photofragmentation experiments. Size dependent stability patterns were obtained and the branching between monomer and dimer evaporation was studied. For bare gold, the competing neutral monomer and dimer evaporation channels were found to be in agreement with earlier studies. For doped clusters, monomer evaporation is the most likely fragmentation channel with the exception of Au18Y+ and Au20Y+ for which gold dimer evaporation is also observed. Relations between the evaporative activation energies and both the experimental abundances and the fragment yield were derived based on unimolecular rate constants. The dissociation energies from this analysis show an odd-even staggering and enhanced stabilities for certain cluster sizes, in agreement with simple electronic shell model predictions.

FISSION FRAGMENT PROPERTIES AT SCISSION WITH THE GOGNY FORCE

Two-dimensional Hartree-Fock-Bogoliubov (HFB) calculations have been performed from spherical shapes to large deformations with constraints on axial quadrupole and octupole deformations in 238 U , 256–260 Fm and 226 Th actinides. Scission configurations have then been identified in this subspace of collective coordinates and many nuclear properties of the nascent fragments have been derived, such as deformation, deformation energy or prompt neutron multiplicity. The HFB states have then served as basis states for time-dependent collective calculations based on the Time-Dependent Generator Coordinate Method and the Gaussian Overlap Approximation to derive fission fragment yields.

An apparatus for the study of high temperature water radiolysis in a nuclear reactor: Calibration of dose in a mixed neutron/gamma radiation field

The cooling water of nuclear reactors undergoes radiolytic decomposition induced by gamma, fast electron, and neutron radiation in the core. To model the process, recombination reaction rates and radiolytic yields for the water radical fragments need to be measured at high temperature and pressure. Yields for the action of neutron radiation are particularly hard to determine independently because of the beta/gamma field also present in any reactor. In this paper we report the design of an apparatus intended to measure neutron radiolysis yields as a function of temperature and pressure. A new methodology for separation of neutron and beta/gamma radiolysis yields in a mixed radiation field is proposed and demonstrated.

Production of single chain Fab (scFab) fragments in Bacillus megaterium

BackgroundThe demand on antigen binding reagents in research, diagnostics and therapy raises questions for novel antibody formats as well as appropriate production systems. Recently, the novel single chain Fab (scFab) antibody format combining properties of single chain Fv (scFv) and Fab fragments was produced in the Gram-negative bacterium Escherichia coli. In this study we evaluated the Gram-positive bacterium Bacillus megaterium for the recombinant production of scFab and scFvs in comparison to E. coli.ResultsThe lysozyme specific D1.3 scFab was produced in B. megaterium and E. coli. The total yield of the scFab after purification obtained from the periplasmic fraction and culture supernatant of E. coli was slightly higher than that obtained from culture supernatant of B. megaterium. However, the yield of functional scFab determined by analyzing the antigen binding activity was equally in both production systems. Furthermore, a scFv fragment with specificity for the human C reactive protein was produced in B. megaterium. The total yield of the anti-CRP scFv produced in B. megaterium was slightly lower compared to E. coli, whereas the specific activity of the purified scFvs produced in B. megaterium was higher compared to E. coli.ConclusionB. megaterium allows the secretory production of antibody fragments including the novel scFab antibody format. The yield and quality of functional antibody fragment is comparable to the periplasmic production in E. coli.

Characterization of fragment emission inNe20(7–10 MeV/nucleon)+C12reactions

The inclusive energy distributions of the complex fragments (3{<=}Z{<=}7) emitted from the bombardment of {sup 12}C by {sup 20}Ne beams with incident energies between 145 and 200 MeV have been measured in the angular range 10 deg.{<=}{theta}{sub lab}{<=}50 deg. Damped fragment yields in all the cases have been found to have the characteristic of emission from fully energy equilibrated composites. The binary fragment yields are compared with the standard statistical model predictions. Whereas Li and Be fragments yields are in agreement with statistical-model calculations, enhanced yields of entrance channel fragments (5{<=}Z{<=}7) indicate the survival of orbiting-like process in {sup 20}Ne+{sup 12}C system at these energies.

The Initial Stages of Radiation Damage in Ionic Liquids and Ionic Liquid-Based Extraction Systems

Radical intermediates generated in radiolysis and photoionization of ionic liquids (ILs) composed of ammonium, phosphonium, pyrrolidinium, and imidazolium cations and bis(triflyl)amide, dicyanamide, and bis(oxalato)borate anions have been studied using magnetic resonance spectroscopy. Large yields of terminal and penultimate C-centered radicals are observed in the aliphatic chains of the phosphonium, ammonium, and pyrrolidinium cations, but not for imidazolium cation. This pattern is indicative of efficient deprotonation of a hole trapped on the parent cation (the radical dication) that competes with rapid electron transfer from a nearby anion. This charge transfer leads to the formation of stable N- or O-centered radicals; the dissociation of parent anions is a minor pathway. Addition of 10-40 wt % of trialkyl phosphate (a common extraction agent) has relatively little effect on the fragmentation of the ILs. The yield of the alkyl radical fragment generated by dissociative electron attachment to the trialkyl phosphate is <4% of the yield of the radical fragments derived from the IL solvent. The import of these observations for radiation stability of the prospective nuclear cycle extraction systems based upon the ILs is discussed.

Ionization, evaporation and fragmentation of C60 in collisions with highly charged C, O and F ions—effect of projectile charge state.

We study the various inelastic processes such ionization, fragmentation and evaporation of C60 molecule in collisions with fast heavy ions. We have used 2.33 MeV/u C, O and F projectile ion beams. Various ionization and fragmentation products were detected using time-of-flight mass spectrometer. The multiply charged C60r+ ions were detected for maximum r = 4. The projectile charge state (qp) dependence of the single and double ionization cross sections is well reproduced by a model based on the giant dipole plasmon resonance (GDPR). The qp-dependence of the fragmentation yields, was found to be linear. Variation of relative yields of the evaporation products of C602+ (i.e. C582+, C562+ etc) and C603+ (i.e. C583+, C563+ etc) with qp has also been investigated for various projectiles.

Study of dissipative collisions ofNe20(≈7−11MeV/nucleon)+Al27

The inclusive energy distributions of complex fragments ($3\ensuremath{\leqslant}9$) emitted in the reactions $^{20}\mathrm{Ne}$ (145, 158, 200, 218 MeV) $+$ $^{27}\mathrm{Al}$ have been measured in the angular range ${10}^{\ifmmode^\circ\else\textdegree\fi{}}\text{\ensuremath{-}}{50}^{\ifmmode^\circ\else\textdegree\fi{}}$. The fusion-fission and the deep-inelastic components of the fragment yield have been extracted using multiple Gaussian functions from the experimental fragment energy spectra. The elemental yields of the fusion-fission component have been found to be fairly well explained in the framework of the standard statistical model. It is found that strong competition occurs between the fusion-fission and the deep-inelastic processes at these energies. The time scale of the deep-inelastic process was estimated to be typically in the range of $~{10}^{\ensuremath{-}21}$--${10}^{\ensuremath{-}22}$ s, and it was found to decrease with increasing fragment mass. The angular momentum dissipations in the fully energy damped deep-inelastic process have been estimated from the average energies of the deep-inelastic components of the fragment energy spectra. The estimated angular momentum dissipations, for lighter fragments in particular, are found to be greater than those predicted by the empirical sticking limit.

Energy‐variable collision‐induced dissociation study of 1,3,5‐trisubstituted 2‐pyrazolines by electrospray mass spectrometry

The pathways of the ([M+H](+)) ions generated from electrosprayed solutions of nine 1,3,5-trisubstituted 2-pyrazoline derivatives were studied using energy-variable collision-induced dissociation (CID) and pseudo-MS(3) (in-source CID combined with MS/MS) methods. It was shown that under CID conditions several structurally important product ions such as the 2,4-substituted azete and 1,2-substituted aziridine ions were formed. The compositions of the product ions were unambiguously supported by accurate mass measurement (mass accuracy was within +/- 8 ppm). The fragmentation pathways of 1,3,5-trisubstituted 2-pyrazolines were established by means of pseudo-MS(3). It was found that a substituent at the N-1 position greatly affects the fragmentation pathways of the 2-pyrazoline derivatives. The 1-acetyl- and 1-propionyl-2-pyrazoline derivatives dissociate mainly through formation of a pyrazolium cation, while in the case of 1-phenyl-2-pyrazoline derivatives product ions arising from the consecutive fragmentation of 2,4-substituted azete and 1,2-substituted aziridine ions dominate. Another interesting finding is the formation of a radical cation from the 2,4-substituted azete by loss of a methyl radical. The fragmentation yield as a function of the collision energy for each of the 1,3,5-trisubstituted 2-pyrazolines was determined. Based on the fragmentation yield versus collision energy curves the relative fragmentation stabilities for the 1,3,5-trisubstituted 2-pyrazoline derivatives were also evaluated.

Probing the Sub-microsecond Photodissociation Dynamics in Gas-Phase Retinal Chromophores

The photoinduced fragmentation of a retinal model chromophore (all-trans-n-butyl protonated Schiff-base retinal) was studied in vacuo using a new experimental technique. The apparatus is able to record the photodissociation yield of gas-phase biomolecular ions in the first microseconds after absorption. Together with the existing ion storage ring ELISA, which operates on the millisecond to second time scale, the complete decay dynamics of such molecules can now be followed. In the case of retinal, the time-dependent fragmentation yield observed after irradiation with a 410 nm laser pulse exhibits contributions from one- and two-photon absorption, which decay non-exponentially with lifetimes on the order of 1 ms and 1 micros, respectively. The decay can be simulated using a statistical model, yielding good agreement with the experimental findings on both the millisecond and the microsecond time scales. No indication for nonstatistical processes is found for this molecule, the upper limit for a possible direct rate being a factor of 10(4) below the observed statistical dissociation rate.

Analysis of cluster ion sputtering yields: correlation with the thermal spike model and implications for static secondary ion mass spectrometry

AbstractAn assessment is made of the behaviours in ion sputtering and static secondary ion mass spectrometry to provide a framework to understand the enhanced secondary ion yield of molecular fragments, from molecules on defined substrates, achieved by using primary ion clusters. First, an analysis is made of the published ion sputtering yield data for mono‐elemental solids sputtered by mono‐elemental primary ion clusters, mainly of the type Aun+. These are evaluated using Sigmund and Claussen's thermal spike model. That theory is shown to be consistent with, and an excellent description of, the published ion sputtering yields for elemental targets over a wide energy range for primary ion cluster sizes from 1 to 13 for gold primary ion clusters and for a number of different primary ion species. This theory is then used to evaluate the molecular ion yield behaviour of interest in static secondary ion mass spectrometry (SIMS). This is done for measurements on Irganox 1010. The thermal spike sputtering yield is first related to the total secondary ion yield. The secondary ion yield of the molecular ion, whether protonated or de‐protonated, is then shown to be proportional to the square of the total secondary ion yield and hence to the square of the sputtering yield. This rule is valid for all primary ions, both single atom and cluster, over 5 decades of emission intensity, largely independent of the chemical identity of the primary ions for those data. This enables recommendations for future sources of higher efficiency for the analysis of organic materials. © Crown copyright 2007. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley &amp; Sons, Ltd.