171 research outputs found
Some calculations on the ground and lowest-triplet state of the helium isoelectronic sequence with the nucleus in motion
The method described in the preceding paper for the solution of two-electron atoms, which was used to calculate the 1 1S and 2 3S states of helium and heliumlike atoms within the fixed-nucleus approximation, has been applied to the case where all three particles are in relative motion. The solutions in the present case automatically include the effects of the mass polarization term and are compared with the results obtained for the term by using first-order perturbation theory with the fixed-nucleus wave functions. The input data for a particular atom consist of the atomic number, as before, but now the corresponding mass of the nucleus must be given also. Nonrelativistic energies with the nuclear mass included in the calculation have been obtained for the 1 1S and 2 3S states for Z ranging from 1 to 10. The energy with the nucleus in motion can be expressed only to eight significant figures (SF's) given the accuracy with which the relevant physical constants are known at present. All the results given here are computed as if these constants were known to ten SF's so that errors not incurred due to rounding. Convergence of the energies to ten SF's for both the singlet and triplet state was reached with a matrix of size 444 for Z values from 2 to 10. Convergence for the H- ion was a little slower
On Factorization of Molecular Wavefunctions
Recently there has been a renewed interest in the chemical physics literature
of factorization of the position representation eigenfunctions \{\} of
the molecular Schr\"odinger equation as originally proposed by Hunter in the
1970s. The idea is to represent in the form where
is \textit{purely} a function of the nuclear coordinates, while must
depend on both electron and nuclear position variables in the problem. This is
a generalization of the approximate factorization originally proposed by Born
and Oppenheimer, the hope being that an `exact' representation of can be
achieved in this form with and interpretable as `electronic'
and `nuclear' wavefunctions respectively. We offer a mathematical analysis of
these proposals that identifies ambiguities stemming mainly from the
singularities in the Coulomb potential energy.Comment: Manuscript submitted to Journal of Physics A: Mathematical and
Theoretical, May 2015. Accepted for Publication August 24 201
Comment on `On the Quantum Theory of Molecules' [J. Chem.Phys. {\bf 137}, 22A544 (2012)]
In our previous paper [J. Chem.Phys. {\bf 137}, 22A544 (2012)] we argued that
the Born-Oppenheimer approximation could not be based on an exact
transformation of the molecular Schr\"{o}dinger equation. In this Comment we
suggest that the fundamental reason for the approximate nature of the
Born-Oppenheimer model is the lack of a complete set of functions for the
electronic space, and the need to describe the continuous spectrum using
spectral projection.Comment: 2 page
On the Quantum Theory of Molecules
Transition state theory was introduced in the 1930s to account for chemical
reactions. Central to this theory is the idea of a potential energy surface
(PES). It was assumed that such a surface could be constructed using
eigensolutions of the Schr\"{o}dinger equation for the molecular (Coulomb)
Hamiltonian but at that time such calculations were not possible. Nowadays
quantum mechanical ab-initio electronic structure calculations are routine and
from their results PESs can be constructed which are believed to approximate
those assumed derivable from the eigensolutions. It is argued here that this
belief is unfounded. It is suggested that the potential energy surface
construction is more appropriately regarded as a legitimate and effective
modification of quantum mechanics for chemical purpose
SeqCode: a nomenclatural code for prokaryotes described from sequence data
Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.Funding was provided by the US National Science Foundation (DEB 1841658, DEB 1557042 and EAR 1516680) to B.H., A.-L.R. and A.M.; the US National Institute of General Medical Sciences (GM103440) from the National Institutes of Health to B.H.; the Spanish Ministry of Science, Innovation and Universities (PGC2018-096956-B-C41 and PID2021-126114NB-C42) to R.R.; the Australian Research Council (FL150100038) to P.H.; the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, SFB 1439/1 2021—426547801) and European Regional Development Funds (FEDER) to A.P.; and the International Society for Microbial Ecology (ISME) to all authors
Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.Funding was provided by the US National Science Foundation (DEB 1841658 and EAR 1516680), the US National Institute of General Medical Sciences (P20 GM103440) from the National Institutes of Health, the Spanish Ministry of Science, Innovation and Universities (PID2021-126114NB-C42), the Australian Research Council (FL150100038), the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, SFB 1439/1 2021 – 426547801) also supported with European Regional Development Funds (FEDER), and the International Society for Microbial Ecology (ISME
A genome-wide scan for common alleles affecting risk for autism
Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C
Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes
SeqCode: a nomenclatural code for prokaryotes described from sequence data
Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines
Phencyclidine (PCP)-Induced Disruption in Cognitive Performance is Gender-Specific and Associated with a Reduction in Brain-Derived Neurotrophic Factor (BDNF) in Specific Regions of the Female Rat Brain
Phencyclidine (PCP), used to mimic certain aspects of schizophrenia, induces sexually dimorphic, cognitive deficits in rats. In this study, the effects of sub-chronic PCP on expression of brain-derived neurotrophic factor (BDNF), a neurotrophic factor implicated in the pathogenesis of schizophrenia, have been evaluated in male and female rats. Male and female hooded-Lister rats received vehicle or PCP (n = 8 per group; 2 mg/kg i.p. twice daily for 7 days) and were tested in the attentional set shifting task prior to being sacrificed (6 weeks post-treatment). Levels of BDNF mRNA were measured in specific brain regions using in situ hybridisation. Male rats were less sensitive to PCP-induced deficits in the extra-dimensional shift stage of the attentional set shifting task compared to female rats. Quantitative analysis of brain regions demonstrated reduced BDNF levels in the medial prefrontal cortex (p < 0.05), motor cortex (p < 0.01), orbital cortex (p < 0.01), olfactory bulb (p < 0.05), retrosplenial cortex (p < 0.001), frontal cortex (p < 0.01), parietal cortex (p < 0.01), CA1 (p < 0.05) and polymorphic layer of dentate gyrus (p < 0.05) of the hippocampus and the central (p < 0.01), lateral (p < 0.05) and basolateral (p < 0.05) regions of the amygdaloid nucleus in female PCP-treated rats compared with controls. In contrast, BDNF was significantly reduced only in the orbital cortex and central amygdaloid region of male rats (p < 0.05). Results suggest that blockade of NMDA receptors by sub-chronic PCP administration has a long-lasting down-regulatory effect on BDNF mRNA expression in the female rat brain which may underlie some of the behavioural deficits observed post PCP administration
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