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  • 1
    ISSN: 1432-0983
    Keywords: Asexual reproduction ; Clonality ; Group-I intron ; Mitochondrial small subunit ribosomal RNA gene Sclerotinia sclerotiorum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A 1 380-bp intervening sequence within the mitochondrial small subunit ribosomal RNA (mt SSU rRNA) gene of the fungus Sclerotinia sclerotiorum has been sequenced and identified as a group-I intron. This is the first report of an intron in the mt SSU rRNA gene. The intron shows close similarity in secondary structure to the subgroup-IC2 introns from Podospora (ND3i1, ND5i2, and COIi5) and Neurospora (ND5i1). The intron has an open reading frame (ORF) that encodes a putative protein of 420 amino acids which contains two copies of the LAGLI-DADG motif. The ORF belongs to a family of ORFs identified in Podospora (ND3i1, ND4Li1, ND4Li2, ND5i2, and COIi5) and Neurospora (ND5i1). The putative 420-aa polypeptide is also similar to a site-specific endonuclease in the chloroplast large subunit ribosomal RNA (LSU rRNA) gene of the green alga Chlamydomonas eugametos. In each clone of S. sclerotiorum examined, including several clones which were sampled over a 3-year period from geographically separated sites, all isolates either had the intron or lacked the intron within the mt SSU rRNA gene. Screening by means of Southern hybridization and PCR amplification detected the intron in the mt SSU rRNA genes of S. minor, S. trifoliorum and Sclerotium cepivorum, but not in other members of the Sclerotiniaceae, such as Botrytis anamorphs of Botryotinia spp., or in other ascomycetous and basidiomycetous fungi.
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  • 2
    ISSN: 1432-0983
    Keywords: Agaricus ; Plasmid-like DNAs ; Mitochondrial DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Two unique plasmid-like DNA components were localized in isolated mitochondria of the commercially important mushroom genus Agaricus: pEM (7.35 ± 0.15 kilobases) and pMPJ (3.65 ± 0.15 kilobases). These DNA moieties were linear; pEM possessed regions of terminal inverted repeated sequences. No homology was detected between pEM or pMPJ DNA and the nuclear or mitochondrial genomes. No homology existed between pEM and pMPJ. This suggests independent replication of pEM and pMPJ. Restriction endonuclease digests indicated that pEM consisted of two components (pEM1 and pEM2) with uniquely different restriction sites and copy number.
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 86 (1987), S. 7237-7239 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 3657-3664 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have calculated the ground state energy of the hydrogen molecule using the quantum Monte Carlo (QMC) method of solving the Schrödinger equation, without the use of the Born–Oppenheimer or any other adiabatic approximations. The wave function sampling was carried out in the full 12-dimensional configuration space of the four particles (two electrons and two protons). Two different methods were employed: the diffusion quantum Monte Carlo (DQMC) method and the Green's function quantum Monte Carlo (GFQMC) method. This computation is very demanding because the configurations must be evolved on the time scale of the electronic motion, whereas the finite nuclear mass effects are resolved accurately only after equilibration on the much slower time scale of the nuclear motion. Thus, a very large number of iterations is required. The calculations were performed on the CM-2 Connection Machine computer, a massively parallel supercomputer. The enormous speedup afforded by the massive parallelism allowed us to complete the computation in a reasonable amount of time. The total energy from the DQMC calculations is −1.163 97±0.000 05 a.u. A more accurate result was obtained from the GFQMC calculations of −1.164 024±0.000 009 a.u. Expressed as a dissociation energy, the GFQMC result is 36 117.9±2.0 cm−1, including the corrections for relativistic and radiative effects. This result is in close agreement with accurate nonadiabatic-relativistic dissociation energies from variational calculations (corrected for radiative effects) in the range of 36 117.9–36 118.1 cm−1 and with the best experimentally determined dissociation energy of McCormack and Eyler 36 118.1±0.2 cm−1.
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 86 (1987), S. 2839-2843 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new procedure for sampling molecular wave functions in quantum Monte Carlo calculations is used to determine energies for a number of configurations of the molecular ion H+3. With the Green's function fixed by use of a trial energy and with no drift terms required for importance sampling the procedure is both simple and efficient. For the equilibrium configuration of H+3 the energy is found to be −1.343 76±0.000 03 a.u. (i.e., ±0.02 kcal/mol).
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 82 (1985), S. 2662-2663 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Two extensions of the fixed-node random walk method of solving the Schrödinger equation are described. A simple iterative procedure is found to reduce time-step error and the use of two trial wave functions in place of one for importance sampling is found to reduce computation effort. In combination the two modifications reduce computation effort for a fixed accuracy by a factor of about 10.
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 9699-9702 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We report an improved Monte Carlo method for calculating the difference δ between a true wave function Ψ and an analytic trial wave function Ψ0. The method also produces a correction to the expectation value of the energy for the trial function. The nodes of the trial function are not corrected and the energy is corrected to the fixed-node energy of the trial function. Applications to several sample problems as well as to the water molecule are described. © 2000 American Institute of Physics.
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 4546-4548 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We report "exact" ab initio calculations with reduced statistical error for the potential energy of interaction of two helium atoms. For the equilibrium internuclear distance of 5.6 bohr, the calculated electronic energy is −5.807 483 53±0.000 000 06 hartrees and the corresponding well depth is (ε/k) 10.98±0.02 K. © 2001 American Institute of Physics.
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  • 9
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 8999-9001 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The interaction potential of three helium atoms in symmetric linear configurations is calculated under the Born–Oppenheimer approximation using an "exact'' Green's function quantum Monte Carlo method. The results are compared with those of "exact'' quantum Monte Carlo calculations for the helium dimer and the Axilrod–Teller triple-dipole energy expression. For nearest neighbor separations of 5.6 bohrs, the equilibrium distance for a helium dimer, the corresponding trimer energy is −21.5±1.9 K, compared to −22.3±0.2 K, calculated for pairwise additive behavior. For all internuclear separations in the neighborhood of the van der Waals well (∼5.6 bohrs), the nonadditive contribution is found to be very small.
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  • 10
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 2802-2805 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We report an improved Green's function quantum Monte Carlo calculation of the nonrelativistic ground-state energy of the hydrogen molecule, without the use of the Born–Oppenheimer or any other adiabatic approximations. A more accurate trial function for importance sampling and the use of the exact cancellation method combine to yield an energy which is a factor of 10 more accurate than that of previous quantum Monte Carlo calculations. The energy is less accurate than that of recently improved analytic variational calculations. The calculated energy is −1.164 0239 ±0.000 0009 hartree. Expressed as the dissociation energy and corrected for relativistic and radiative effects, the result is 36 117.84±0.20 cm−1, a value in agreement with the most recent experimental value 36 118.11±0.08 cm−1 obtained by Balakrishnan et al. © 1995 American Institute of Physics.
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