Reaction mechanisms of pair transfer

The mechanisms of nuclear transfer reactions are described for the transfer of two nucleons from one nucleus to another. Two-nucleon overlap functions are defined in various coordinate systems, and their transformation coefficients given between coordinate systems. Post and prior couplings are defined for sequential transfer mechanisms, and it is demonstrated that the combination of `prior-post' couplings avoids non-orthogonality terms, but does not avoid couplings that do not have good zero-range approximations. The simultaneous and sequential mechanisms are demonstrated for the $^{124}$Sn(p,t)$^{122}$Sn reaction at 25 MeV using shell-model overlap functions. The interference between the various simultaneous and sequential amplitudes is shown.Comment: 14 pages, 3 figures, chapter 34 in "50 Years of Nuclear BCS", edited by R. A. Broglia and V. Zelevinsky: ISBN 978-981-4412-48-3 Uses WS macros (included). Corrected text and calculations as in the published versio

Reaction Mechanisms with Exotic Nuclei

This talk examines a number of reaction mechanisms for scattering initiated by an exotic projectile. Comparisons are made with recent experimental data, in order to extract information on the peculiarity of the nuclear structure under extreme conditions and to test the accuracy of the available theoretical methods. Predictions for future experiments are also made.Comment: 13 Latex pages, 2 table, 2 ps figures. Invited talk given at the Symposium on Nuclear Clusters, Rauischholzhausen, Germany, 5-9 August 200

Heuristics-Guided Exploration of Reaction Mechanisms

For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive species are involved that might cause a myriad of side reactions. Without automation, a complete investigation of complex reaction mechanisms is tedious and possibly unfeasible. Therefore, only the expected dominant reaction paths of a chemical reaction network (e.g., a catalytic cycle or an enzymatic cascade) are usually explored in practice. Here, we present a computational protocol that constructs such networks in a parallelized and automated manner. Molecular structures of reactive complexes are generated based on heuristic rules derived from conceptual electronic-structure theory and subsequently optimized by quantum chemical methods to produce stable intermediates of an emerging reaction network. Pairs of intermediates in this network that might be related by an elementary reaction according to some structural similarity measure are then automatically detected and subjected to an automated search for the connecting transition state. The results are visualized as an automatically generated network graph, from which a comprehensive picture of the mechanism of a complex chemical process can be obtained that greatly facilitates the analysis of the whole network. We apply our protocol to the Schrock dinitrogen-fixation catalyst to study alternative pathways of catalytic ammonia production.Comment: 27 pages, 9 figure

Reaction mechanisms in the 6Li+59Co system

The reactions induced by the weakly bound 6Li projectile interacting with the intermediate mass target 59Co were investigated. Light charged particles singles and $\alpha$-$d$ coincidence measurements were performed at the near barrier energies E_lab = 17.4, 21.5, 25.5 and 29.6 MeV. The main contributions of the different competing mechanisms are discussed. A statistical model analysis, Continuum-Discretized Coupled-Channels calculations and two-body kinematics were used as tools to provide information to disentangle the main components of these mechanisms. A significant contribution of the direct breakup was observed through the difference between the experimental sequential breakup cross section and the CDCC prediction for the non-capture breakup cross section.Comment: 30 pages, 8 figure

MACiE: a database of enzyme reaction mechanisms.

SUMMARY: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/.EPSRC (G.L.H. and J.B.O.M.), the BBSRC (G.J.B. and J.M.T.—CASE studentship in association with Roche Products Ltd; N.M.O.B. and J.B.O.M.—grant BB/C51320X/1), the Chilean Government’s Ministerio de Planificacio´n y Cooperacio´n and Cambridge Overseas Trust (D.E.A.) for funding and Unilever for supporting the Centre for Molecular Science Informatics.application note restricted to 2 printed pages web site: http://www-mitchell.ch.cam.ac.uk/macie

Reaction mechanisms in 24Mg+12C and 32S+24Mg

The occurence of "exotic" shapes in light N=Z alpha-like nuclei is investigated for 24Mg+12C and 32S+24Mg. Various approaches of superdeformed and hyperdeformed bands associated with quasimolecular resonant structures with low spin are presented. For both reactions, exclusive data were collected with the Binary Reaction Spectrometer in coincidence with EUROBALL IV installed at the VIVITRON Tandem facility of Strasbourg. Specific structures with large deformation were selectively populated in binary reactions and their associated $\gamma$-decays studied. The analysis of the binary and ternary reaction channels is discussed.Comment: 7 pages, 4 figures, Paper presented at the Fusion08 International Conference on New Aspects of Heavy Ion Collisions Near the Coulomb Barrier, Chicago. Proceedings to be published by AIP Conference Proceedings Illinois, USA, September 22-26, 200

BlenX-based compositional modeling of complex reaction mechanisms

Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality

Application of hpDGFEM to mechanisms at channel microband electrodes

We extend our earlier work (Harriman et al., Oxford University Computing Laboratory Technical Report NA04/19) on hp-DGFEM for disc electrodes to the case of reaction mechanisms to the increasingly popular channel microband electrode configuration. We present results for the simple E reaction mechanism (convection-diffusion equation), for the ECE and EC2E reaction mechanisms (linear and nonlinear systems of reaction-convection- diffusion equations, respectively) and for the DISP1 and DISP2 reaction mechanisms (linear and nonlinear coupled systems of reaction-convection-diffusion equations, respectively). In all cases we demonstrate excellent agreement with previous results using relatively coarse meshes and without the need for streamline-diffusion stabilisation, even at high flow rates

Organic reaction mechanisms

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