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  • 1
    Electronic Resource
    Electronic Resource
    Benchmark variational coupled cluster doubles results (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 8873-8879 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present the first application of the Rayleigh–Ritz variational procedure to the coupled cluster doubles trial function. The variational approach is applied to the potential surface of H4, the double dissociation of water and the dissociation of N2, and the results are compared to standard coupled cluster doubles calculations. It is found that the variational approach gives a greatly improved description of strongly correlated systems, where the standard approach is known to fail. Some examination of the basis set dependence of the results is presented. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1319643
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  • 2
    Electronic Resource
    Electronic Resource
    A nonorthogonal approach to perfect pairing (2000)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 5633-5638 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present an alternative formulation of perfect pairing (PP) aimed at giving a more faithful representation of the valence correlation energy of an arbitrary molecule. In the new theory, the occupied and virtual orbitals are nonorthogonal amongst themselves but orthogonal to each other. Whereas for the fully orthogonal version of PP one has the number of pairs equal to the number of occupied orbitals, the current formulation allows for an arbitrary number of pairs built from redundant orbitals. We propose setting the number of pairs equal to the number of valence orbitals in the molecule. Preliminary results indicate that the redundant formulation gives qualitatively improved results for delocalized systems such as benzene, while maintaining the attractive features of PP for localized systems. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.481138
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  • 3
    Electronic Resource
    Electronic Resource
    A novel form for the exchange-correlation energy functional (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 400-410 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new approximate form for the exchange-correlation energy functional is developed. The form is based on the density matrix expansion (DME) for the exchange functional [R. M. Koehl, G. K. Odom, and G. E. Scuseria, Mol. Phys. 87, 835 (1996)]. The nonlocal portion of the correlation energy is assumed to have the same general form as that derived for exchange, while the local portion is taken to be that of the uniform electron gas. The resulting formula does not resort to the use of exact-exchange mixing. A Kohn-Sham implementation of this functional is constructed and the parameters within the functional are adjusted to minimize the difference between the theoretical and the experimental data for a large set of atomic and molecular systems. The results are found to compare favorably with existing functionals, even those which include exact-exchange mixing. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476577
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  • 4
    Electronic Resource
    Electronic Resource
    Two-body coupled cluster expansions (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 5033-5040 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We show that the exact ground state wave function for an arbitrary two-body Hamiltonian can be exactly represented by a single reference coupled cluster wave function employing a general two-particle cluster operator. This can be used to construct a set of approximate methods that converge to the exact result and are in some sense complementary to the standard approach of including successively double, triple, quadruple, ..., excitations. We present exploratory variational results for the neon atom and the dissociation of N2 to demonstrate the strengths and weaknesses of these generalized coupled cluster approximations. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1390516
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  • 5
    Electronic Resource
    Electronic Resource
    Connections between coupled cluster and generalized valence bond theories (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 7814-7821 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We explore the fundamental connections between certain approximate coupled cluster (CC) and generalized valence bond (GVB) wave functions. We show that the GVB restricted configuration interaction (GVB-RCI) wave function can be associated with a compact CC expansion in the valence space. However, careful analysis reveals that a standard CC expansion contains terms that are not contained in the GVB-RCI wave function. The offending terms violate an effective pairwise exclusion principle (PEP) that is present in the RCI expansion, but is not enforced in the CC analog. These terms do not affect the size separability of either method. Variational calculations show noticeable improvements to the CC wave function when the PEP is enforced, with the most significant improvements coming near the dissociation limit. We modify the standard CC amplitude equations by removing the PEP violating terms and demonstrate remarkably improved results for the dissociation of N2 and the double dissociation of H2O. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1406536
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  • 6
    Electronic Resource
    Electronic Resource
    Gene conversion: a mechanism for generation of heterogeneity in the tprK gene of Treponema pallidum during infection (2004)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 52 (2004), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The tprK gene sequence of Treponema pallidum subspecies pallidum (T. pallidum) is heterogeneous within and among isolates. Heterogeneity in the tprK open reading frame is localized in seven discrete variable (V) regions, and variability results from apparent base changes, insertions or deletions. The TprK V regions are the focus of anti-TprK antibodies arising during infection. To test our hypothesis that V region sequences change during infection and passage, we developed a clonal isolate from the Chicago strain of T. pallidum and confirmed V region diversification during passage of this isolate. We describe the sequence anatomy of the seven V regions of tprK and the identification of putative donor sites for new V region sequences, and we propose a model for generation of new V regions by segmental gene conversion. These findings suggest that antigenic variation of TprK occurs in T. pallidum and may be important in immune evasion and persistence.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.2004.04086.x
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  • 7
    Electronic Resource
    Electronic Resource
    Identification of the Treponema pallidum subsp. pallidum glycerophosphodiester phosphodiesterase homologue (1997)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 154 (1997), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: To identify potential opsonic targets of Treponema pallidum subsp. pallidum, a treponemal genomic expression library was constructed and differentially screened with opsonic and non-opsonic T. pallidum antisera. This method identified an immunoreactive clone containing an open reading frame encoding a 356 residue protein. Nucleotide sequence analysis demonstrated the translated protein to be a homologue of glycerophosphodiester phosphodiesterase, a glycerol metabolizing enzyme previously identified in Haemophilus influenzae, Escherichia coli, Bacillus subtilis and Borrelia hermsii. Sequence alignment analyses revealed the T. pallidum and H. influenzae enzymes share a high degree of amino acid sequence similarity (72%), suggesting that in T. pallidum this molecule may be surface exposed and involved in IgD binding as is the case with its counterpart in H. influenzae.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1997.tb12660.x
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  • 8
    Electronic Resource
    Electronic Resource
    Two 16S-23S ribosomal DNA intergenic regions in different Treponema pallidum subspecies contain tRNA genes (1996)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 143 (1996), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract The 16S-23S intergenic spacers of Treponema pallidum subspecies pallidum, Nichols strain, and Treponema pallidum subspecies pertenue, Gauthier strain, have been cloned, characterized and sequenced. Isoleucine and alanine tRNA genes have been identified within the 16S-23S intergenic regions on separate alleles of 293 and 303 bases, respectively. The two alleles are present in both T.p. pallidum and T.p. pertenue, and show no sequence differences between the bacterial subspecies. The ile-tRNA and ala-tRNA genes show 65% and 84% sequence identity, respectively, with the homologous genes of the related spirochete, Borrelia burgdorferi.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1996.tb08486.x
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  • 9
    Electronic Resource
    Electronic Resource
    The estuarine character of the Gulf of Nicoya, an embayment on the Pacific coast of Central America (1983)
    Springer
    Hydrobiologia 99 (1983), S. 225-237 
    Details
    ISSN: 1573-5117
    Keywords: hydrography ; circulation ; estuary ; tropical
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Hydrography and exchange processes in a tropical estuary, the Gulf of Nicoya, Costa Rica, are described from data collected in 1979 and 1980. The measurements and analyses were made in both the dry season and wet season and include temperature, salinity, and density at twenty locations in the gulf and currents (over a semi-diurnal tidal cycle) at five locations. These new results enlarge on the early study by Peterson (1958). Circulation in the lower gulf shows a marked east-west asymmetry due to the predominant runoff along its eastern shore from Rio Barranca and Tarcoles. The freshened surface water from the upper gulf combines with the runoff from these rivers and flows southward along the eastern side of the lower gulf. This flow is compensated by a northward flow of more saline water on the western side at all depths and on the eastern side along the bottom. The boundary between the southward and northward surface flow is marked by a strong salinity front in the rainy season. There is a rapid increase in tidal energy density toward the shoaling northern reaches of the lower gulf, between San Lucas Island and Puntarenas Peninsula. Enhanced mixing must accompany this increase, and direct measurements in the constriction between San Lucas and Puntaneras show that tidal mixing is dominant in transporting salt into the upper gulf against the freshwater runoff.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00008774
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  • 10
    Electronic Resource
    Electronic Resource
    A relaxation method for nonconvex quadratically constrained quadratic programs (1995)
    Springer
    Journal of global optimization 6 (1995), S. 215-230 
    Details
    ISSN: 1573-2916
    Keywords: Quadratic constraints ; quadratic programming ; relaxation linearization technique ; branch and bound ; global optimization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract We present an algorithm for finding approximate global solutions to quadratically constrained quadratic programming problems. The method is based on outer approximation (linearization) and branch and bound with linear programming subproblems. When the feasible set is non-convex, the infinite process can be terminated with an approximate (possibly infeasible) optimal solution. We provide error bounds that can be used to ensure stopping within a prespecified feasibility tolerance. A numerical example illustrates the procedure. Computational experiments with an implementation of the procedure are reported on bilinearly constrained test problems with up to sixteen decision variables and eight constraints.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01099462
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