Abstract:
We suggest a local wave function based ab initio correlation method for infinite periodic systems, which can describe both the near range as well as the long range correlation effects coherently in the same scheme. Specifically, this work introduces a formalism which allows to describe the long range polarization cloud around a quasi particle in a solid explicitly in the formalism of local wave function based ab initio descriptions. To this end we reformulate the infinite lattice summation underlying the quantum chemistry formula to second order in a closed analytic form employing the elliptic theta function of the third kind. All formulas and manipulations are developed explicitely in full detail and a first numeric example demonstrates the principle idea. Good results for the long range polarization effects in LiH and LiF are found in agreement with earlier estimates.

Abstract:
The frequency dependence of the self energy of a general many--body problem is identified as a main obstacle in correlation calculations based on local approaches. A frequency independent formulation is proposed instead and proven to yield exactly the same numerical results as the original common scheme. Our approach is embedded in a general local-orbital based ab initio frame to obtain the Green's function for large heterogenous systems. First a Green's function formalism is introduced. Then the self energy is constructed from an incremental scheme. Subsequently we apply the proposed frequency independent formulation. The theory is applied to para-ditholbenzene as a realistic system and the numerical accuracy of the correlation contributions obtained from our frequency independent access are carefully tested against the exact frequency dependent results. Perfect agreement is reached and a speed--up of a factor 50 is established for the incremental scheme.

Abstract:
We present a study of the charge transmission behavior of a series of dithiol polyenes in the context of molecular junctions. Using the Landauer theory and zero voltage approximation the Green's functions of the inserted molecules are calculated from a fully ab initio wave function based procedure. Various possibilities in approximating the correlation space are explored and quantitatively evaluated. Our results show that the transmission behavior of a molecular junction is not a monotonic function of the length of the employed molecule. Moreover we introduce the analytic solution of a suitable model system to countercheck the ab initio results and find a remarkable degree of correspondence.

Abstract:
We describe an algorithm to compute Gr\"obner bases which combines F4-style reduction with the F5 criteria. Both F4 and F5 originate in the work of Jean-Charles Faug\`ere, who has successfully computed many Gr\"obner bases that were previously considered intractable. Another description of a similar algorithm already exists in Gwenole Ars' dissertation; unfortunately, this is only available in French, and although an implementation exists, it is not made available for study. We not only describe the algorithm, we also direct the reader to a study implementation for the free and open source Sage computer algebra system. We conclude with a short discussion of how the approach described here compares and contrasts with that of Ars' dissertation.

Abstract:
In this work, we present the M4RIE library which implements efficient algorithms for linear algebra with dense matrices over GF(2^e) for 2 <= 2 <= 10. As the name of the library indicates, it makes heavy use of the M4RI library both directly (i.e., by calling it) and indirectly (i.e., by using its concepts). We provide an open-source GPLv2+ C library for efficient linear algebra over GF(2^e) for e small. In this library we implemented an idea due to Bradshaw and Boothby which reduces matrix multiplication over GF(p^k) to a series of matrix multiplications over GF(p). Furthermore, we propose a caching technique - Newton-John tables - to avoid finite field multiplications which is inspired by Kronrod's method ("M4RM") for matrix multiplication over GF(2). Using these two techniques we provide asymptotically fast triangular solving with matrices (TRSM) and PLE-based Gaussian elimination. As a result, we are able to significantly improve upon the state of the art in dense linear algebra over GF(2^e) with 2 <= e <= 10.

Abstract:
Background Post-copulatory sexual selection has been shown to shape morphology of male gametes. Both directional and stabilizing selection on sperm phenotype have been documented in vertebrates in response to sexual promiscuity. Methodology Here we investigated the degree of variance in apical hook length and tail length in six taxa of murine rodents. Conclusions Tail sperm length and apical hook length were positively associated with relative testis mass, our proxy for levels of sperm competition, thus indicating directional post-copulatory selection on sperm phenotypes. Moreover, our study shows that increased levels of sperm competition lead to the reduction of variance in the hook length, indicating stabilizing selection. Hence, the higher risk of sperm competition affects increasing hook length together with decreasing variance in the hook length. Species-specific post-copulatory sexual selection likely optimizes sperm morphology.

Abstract:
We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wave function based description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green's function formalism. In addition we present an extension so as to include effects of the two-particle propagator. Our procedure is demonstrated for a dithiolbenzene molecule between silver electrodes. The full current-voltage characteristic is calculated. Specific conclusions for the contribution of correlation and two-particle effects are derived. The latter are found to contribute about 5% to the current. The order of magnitude of the current coincides with experiments.

Abstract:
We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wave function based full ab initio description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green's function formalism. Our procedure is demonstrated for a dithiolethine molecule between silver electrodes. The main conducting channel is identified and the full current-voltage characteristic is calculated.

Abstract:
Correlated ab-initio ground-state calculations, using relativistic energy-consistent pseudopotentials, are performed for six II-VI semiconductors. Valence ($ns,np$) correlations are evaluated using the coupled cluster approach with single and double excitations. An incremental scheme is applied based on correlation contributions of localized bond orbitals and of pairs and triples of such bonds. In view of the high polarity of the bonds in II-VI compounds, we examine both, ionic and covalent embedding schemes for the calculation of individual bond increments. Also, a partitioning of the correlation energy according to local ionic increments is tested. Core-valence ($nsp,(n-1)d$) correlation effects are taken into account via a core-polarization potential. Combining the results at the correlated level with corresponding Hartree-Fock data we recover about 94% of the experimental cohesive energies; lattice constants are accurate to \sim 1%; bulk moduli are on average 10% too large compared with experiment.

Abstract:
In this work we describe an efficient implementation of a hierarchy of algorithms for the decomposition of dense matrices over the field with two elements (GF(2)). Matrix decomposition is an essential building block for solving dense systems of linear and non-linear equations and thus much research has been devoted to improve the asymptotic complexity of such algorithms. In this work we discuss an implementation of both well-known and improved algorithms in the M4RI library. The focus of our discussion is on a new variant of the M4RI algorithm - denoted MMPF in this work -- which allows for considerable performance gains in practice when compared to the previously fastest implementation. We provide performance figures on x86_64 CPUs to demonstrate the viability of our approach.