Web-based Tools for the Analysis of DNA Microarrays

End of project reportDNA microarrays are widely used for gene expression profiling. Raw data resulting from microarray experiments, however, tends to be very noisy and there are many sources of technical variation and bias. This raw data needs to be quality assessed and interactively preprocessed to minimise variation before statistical analysis in order to achieve meaningful result. Therefore microarray analysis requires a combination of visualisation and statistical tools, which vary depending on what microarray platform or experimental design is used.Bioconductor is an existing open source software project that attempts to facilitate analysis of genomic data. It is a collection of packages for the statistical programming language R. Bioconductor is particularly useful in analyzing microarray experiments. The problem is that the R programming language’s command line interface is intimidating to many users who do not have a strong background in computing. This often leads to a situation where biologists will resort to using commercial software which often uses antiquated and much less effective statistical techniques, as well as being expensively priced. This project aims to bridge this gap by providing a user friendly web-based interface to the cutting edge statistical techniques of Bioconductor

Suppression of complete fusion due to breakup in the reactions 10,11^{10,11}B + 209^{209}Bi

Above-barrier cross sections of $\alpha$-active heavy reaction products, as well as fission, were measured for the reactions of $^{10,11}$B with $^{209}$Bi. Detailed analysis showed that the heavy products include components from incomplete fusion as well as complete fusion (CF), but fission originates almost exclusively from CF. Compared with fusion calculations without breakup, the CF cross sections are suppressed by 15% for $^{10}$B and 7% for $^{11}$B. A consistent and systematic variation of the suppression of CF for reactions of the weakly bound nuclei $^{6,7}$Li, $^{9}$Be, $^{10,11}$B on targets of $^{208}$Pb and $^{209}$Bi is found as a function of the breakup threshold energy

Influence of entrance-channel magicity and isospin on quasi-fission

The role of spherical quantum shells in the competition between fusion and quasi-fission is studied for reactions forming heavy elements. Measurements of fission fragment mass distributions for different reactions leading to similar compound nuclei have been made near the fusion barrier. In general, more quasi-fission is observed for reactions with non-magic nuclei. However, the $^{40}$Ca+$^{208}$Pb reaction is an exception, showing strong evidence for quasi-fission, though both nuclei are doubly magic. Time-dependent Hartree-Fock calculations predict fast equilibration of $N/Z$ in the two fragments early in the collision. This transfer of nucleons breaks the shell effect, causing this reaction to behave more like a non-magic one in the competition between fusion and quasi-fission. Future measurements of fission in reactions with exotic beams should be able to test this idea with larger $N/Z$ asymmetries.Comment: accepted for publication in Physics Letters

Relating breakup and incomplete fusion of weakly-bound nuclei through a classical trajectory model with stochastic breakup

A classical dynamical model that treats break-up stochastically is presented for low energy reactions of weakly-bound nuclei. The three-dimensional model allows a consistent calculation of breakup, incomplete and complete fusion cross sections. The model is assessed by comparing the breakup observables with CDCC quantum mechanical predictions, which are found to be in reasonable agreement. Through the model, it is demonstrated that the breakup probability of the projectile as a function of its distance from the target is of primary importance for understanding complete and incomplete fusion at energies near the Coulomb barrier.Comment: Accepted in Physical Review Letter

Microscopic study of the effect of intrinsic degrees of freedom on fusion

Fusion cross-sections are computed for the $^{40}$Ca$+^{40}$Ca system over a wide energy range with two microscopic approaches where the only phenomenological input is the Skyrme energy density functional. The first method is based on the coupled-channels formalism, using the bare nucleus-nucleus potential calculated with the frozen Hartree-Fock technique and the deformation parameters of vibrational states computed with the time-dependent Hartree-Fock (TDHF) approach. The second method is based on the density-constrained TDHF method to generate nucleus-nucleus potentials from TDHF evolution. Both approaches incorporate the effect of couplings to internal degrees of freedoms in different ways. The predictions are in relatively good agreement with experimental data.Comment: 6 pages, 11 figures. Invited talk to FUSION1

Dissipative quantum dynamics in low-energy collisions of complex nuclei

Model calculations that include the effects of irreversible, environmental couplings on top of a coupled-channels dynamical description of the collision of two complex nuclei are presented. The Liouville-von Neumann equation for the time-evolution of the density matrix of a dissipative system is solved numerically providing a consistent transition from coherent to decoherent (and dissipative) dynamics during the collision. Quantum decoherence and dissipation are clearly manifested in the model calculations. Energy dissipation, due to the irreversible decay of giant-dipole vibrational states of the colliding nuclei, is shown to result in a hindrance of quantum tunneling and fusion.Comment: Accepted in Physical Review

Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions

Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H_2, CH) and triatomic (H_3, CH_2) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or linear dependence of its explicitly antisymmetrized form, the convergence of the apparently disparate atomic-product and explicitly antisymmetrized atomic-product forms to a common invariant subspace, and the nature of a chemical bonding descriptor provided by the atomic-product compositions of molecular eigenstates. Concluding remarks indicate additional studies in progress and the prognosis for performing atomic spectral-product calculations more generally and efficiently

Importance of Non-Linear Couplings in Fusion Barrier Distributions and Mean Angular Momenta

The effects of higher order coupling of surface vibrations to the relative motion on heavy-ion fusion reactions at near-barrier energies are investigated. The coupled channels equations are solved to all orders, and also in the linear and the quadratic coupling approximations. It is shown that the shape of fusion barrier distributions and the energy dependence of the average angular momentum of the compound nucleus can significantly change when the higher order couplings are included. The role of octupole vibrational excitation of ^{16}O in the ^{16}O + ^{144}Sm fusion reaction is also discussed using the all order coupled-channels equations.Comment: 8 pages, 6 figures, To be published in the Proceedings of the FUSION 97 Conference, South Durras, Australia, March 1997 (J. Phys. G

Effect of Pauli repulsion and transfer on fusion

The effect of the Pauli exclusion principle on the nucleus-nucleus bare potential is studied using a new density-constrained extension of the Frozen-Hartree-Fock (DCFHF) technique. The resulting potentials exhibit a repulsion at short distance. The charge product dependence of this Pauli repulsion is investigated. Dynamical effects are then included in the potential with the density-constrained time-dependent Hartree-Fock (DCTDHF) method. In particular, isovector contributions to this potential are used to investigate the role of transfer on fusion, resulting in a lowering of the inner part of the potential for systems with positive Q-value transfer channels.Comment: Proceedings of an invited talk given at FUSION17, Hobart, Tasmania, AU (20-24 February, 2017