Avian mass immunization for infectious bronchitis and Newcastle disease, Station Bulletin, no.416

The Bulletin is a publication of the New Hampshire Agricultural Experiment Station, College of Life Sciences and Agriculture, University of New Hampshire, Durham, New Hampshire

Correlation effects in ionic crystals: I. The cohesive energy of MgO

High-level quantum-chemical calculations, using the coupled-cluster approach and extended one-particle basis sets, have been performed for (Mg2+)n (O2-)m clusters embedded in a Madelung potential. The results of these calculations are used for setting up an incremental expansion for the correlation energy of bulk MgO. This way, 96% of the experimental cohesive energy of the MgO crystal is recovered. It is shown that only 60% of the correlation contribution to the cohesive energy is of intra-ionic origin, the remaining part being caused by van der Waals-like inter-ionic excitations.Comment: LaTeX, 20 pages, no figure

Raman scattering in C_{60} and C_{48}N_{12} aza-fullerene: First-principles study

We carry out large scale {\sl ab initio} calculations of Raman scattering activities and Raman-active frequencies (RAFs) in ${\rm C}_{48}{\rm N}_{12}$ aza-fullerene. The results are compared with those of ${\rm C}_{60}$. Twenty-nine non-degenerate polarized and 29 doubly-degenerate unpolarized RAFs are predicted for ${\rm C}_{48}{\rm N}_{12}$. The RAF of the strongest Raman signal in the low- and high-frequency regions and the lowest and highest RAFs for ${\rm C}_{48}{\rm N}_{12}$ are almost the same as those of ${\rm C}_{60}$. The study of ${\rm C}_{60}$ reveals the importance of electron correlations and the choice of basis sets in the {\sl ab initio} calculations. Our best calculated results for ${\rm C}_{60}$ with the B3LYP hybrid density functional theory are in excellent agreement with experiment and demonstrate the desirable efficiency and accuracy of this theory for obtaining quantitative information on the vibrational properties of these molecules.Comment: submitted to Phys.Rev.

Electron affinities of the first- and second- row atoms: benchmark ab initio and density functional calculations

A benchmark ab initio and density functional (DFT) study has been carried out on the electron affinities of the first- and second-row atoms. The ab initio study involves basis sets of $spdfgh$ and $spdfghi$ quality, extrapolations to the 1-particle basis set limit, and a combination of the CCSD(T), CCSDT, and full CI electron correlation methods. Scalar relativistic and spin-orbit coupling effects were taken into account. On average, the best ab initio results agree to better than 0.001 eV with the most recent experimental results. Correcting for imperfections in the CCSD(T) method improves the mean absolute error by an order of magnitude, while for accurate results on the second-row atoms inclusion of relativistic corrections is essential. The latter are significantly overestimated at the SCF level; for accurate spin-orbit splitting constants of second-row atoms inclusion of (2s,2p) correlation is essential. In the DFT calculations it is found that results for the 1st-row atoms are very sensitive to the exchange functional, while those for second-row atoms are rather more sensitive to the correlation functional. While the LYP correlation functional works best for first-row atoms, its PW91 counterpart appears to be preferable for second-row atoms. Among ``pure DFT'' (nonhybrid) functionals, G96PW91 (Gill 1996 exchange combined with Perdew-Wang 1991 correlation) puts in the best overall performance. The best results overall are obtained with the 1-parameter hybrid modified Perdew-Wang (mPW1) exchange functionals of Adamo and Barone [J. Chem. Phys. {\bf 108}, 664 (1998)], with mPW1LYP yielding the best results for first-row, and mPW1PW91 for second-row atoms. Indications exist that a hybrid of the type $a$ mPW1LYP + $(1-a)$ mPW1PW91 yields better results than either of the constituent functionals.Comment: Phys. Rev. A, in press (revised version, review of issues concerning DFT and electron affinities added

A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package

Estimating genomic instability mediated by Alu retroelements in breast cancer

Alu-PCR is a relatively simple technique that can be used to investigate genomic instability in cancer. This technique allows identification of the loss, gain or amplification of gene sequences based on the analysis of segments between two Alu elements coupled with quantitative and qualitative analyses of the profiles obtained from tumor samples, surgical margins and blood. In this work, we used Alu-PCR to identify gene alterations in ten patients with invasive ductal breast cancer. Several deletions and insertions were identified, indicating genomic instability in the tumor and adjacent normal tissue. Although not associated with specific genes, the alterations, which involved chromosomal bands 1p36.23, 1q41, 11q14.3, 13q14.2, occurred in areas of well-known genomic instability in breast and other types of cancer. These results indicate the potential usefulness of Alu-PCR in identifying altered gene sequences in breast cancer. However, caution is required in its application since the Alu primer can produce non-specific amplification

Modelling fast forms of visual neural plasticity using a modified second-order motion energy model

The Adelson-Bergen motion energy sensor is well established as the leading model of low-level visual motion sensing in human vision. However, the standard model cannot predict adaptation effects in motion perception. A previous paper Pavan et al.(Journal of Vision 10:1-17, 2013) presented an extension to the model which uses a first-order RC gain-control circuit (leaky integrator) to implement adaptation effects which can span many seconds, and showed that the extended model's output is consistent with psychophysical data on the classic motion after-effect. Recent psychophysical research has reported adaptation over much shorter time periods, spanning just a few hundred milliseconds. The present paper further extends the sensor model to implement rapid adaptation, by adding a second-order RC circuit which causes the sensor to require a finite amount of time to react to a sudden change in stimulation. The output of the new sensor accounts accurately for psychophysical data on rapid forms of facilitation (rapid visual motion priming, rVMP) and suppression (rapid motion after-effect, rMAE). Changes in natural scene content occur over multiple time scales, and multi-stage leaky integrators of the kind proposed here offer a computational scheme for modelling adaptation over multiple time scales. © 2014 Springer Science+Business Media New York

RAD59 and RAD1 cooperate in translocation formation by single-strand annealing in Saccharomyces cerevisiae

Studies in the budding yeast, Saccharomyces cerevisiae, have demonstrated that a substantial fraction of double-strand break repair following acute radiation exposure involves homologous recombination between repetitive genomic elements. We have previously described an assay in S. cerevisiae that allows us to model how repair of multiple breaks leads to the formation of chromosomal translocations by single-strand annealing (SSA) and found that Rad59, a paralog of the single-stranded DNA annealing protein Rad52, is critically important in this process. We have constructed several rad59 missense alleles to study its function more closely. Characterization of these mutants revealed proportional defects in both translocation formation and spontaneous direct-repeat recombination, which is also thought to occur by SSA. Combining the rad59 missense alleles with a null allele of RAD1, which encodes a subunit of a nuclease required for the removal of non-homologous tails from annealed intermediates, substantially suppressed the low frequency of translocations observed in rad1-null single mutants. These data suggest that at least one role of Rad59 in translocation formation by SSA is supporting the machinery required for cleavage of non-homologous tails

Combined Experimental and Computational Studies on the Nature of Aromatic C−H Activation by Octahedral Ruthenium(II) Complexes: Evidence for σ-Bond Metathesis from Hammett Studies

Octahedral ruthenium complexes of the type TpRu(L)(NCMe)R [Tp = hydridotris(pyrazolyl)borate; R = alkyl or aryl; L = CO or PMe3] have been shown previously to initiate the C-H activation of aromatic substrates. In order to probe the nature of the C-H activation step, reaction rates have been theoretically obtained for the conversion of TpRu(L)(η2-C, C-C6H5X)Me to TpRu(L)(P-C6H4X) and CH4 where X is varied among Br, Cl, CN, F, H, NH2, NO 2, and OMe. A linear Hammett correlation is calculated with a positive p value of 2.6 for L = CO and 3.2 for L = PMe3. Calculated kinetic data for the aromatic C-H activations indicate that an electrophilic aromatic substitution mechanism is unlikely. While experiments cannot fully replicate the entire range of calculated Hammett plots, reactivity trends are consistent with the calculations that suggest activation barriers to overall metal-mediated arene C-H bond cleavage are reduced by the presence of electron-withdrawing groups in the position para to the site of activation. Previous mechanistic studies, as well as the structure and imaginary vibrational modes of the present transition states, validate that the C-H activation for this family of TpRu complexes occurs through a σ-bond metathesis-type pathway. © 2007 American Chemical Society