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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1930-1942 
    ISSN: 0192-8651
    Keywords: molecular simulation ; periodic boundary conditions ; box shape ; lattice ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In molecular simulations with periodic boundary conditions the computational box may have five different shapes: triclinic; the hexagonal prism; two types of dodecahedrons; and the truncated octahedron. In this article, we show that every molecular simulation, formulated in one of these boxes, can be transformed into a simulation in one of the other ones. The transformation can be done in a preprocessing phase. The simulation in the new box is exactly identical to the simulation in the original one. This means that every molecular simulation may be done in the same type of box. Because the triclinic box is the easiest one to implement, we pay special attention to how to transform the other four box types into triclinic boxes. As a consequence, simulations in the often used truncated octahedron are superfluous; they may be done in a much simpler way in a triclinic box.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1930-1942, 1997
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1463-1472 
    ISSN: 0192-8651
    Keywords: constraints ; molecular dynamics ; Langevin dynamics ; SHAKE ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1463-1472, 1997
    Additional Material: 2 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Organic Magnetic Resonance 14 (1980), S. 337-343 
    ISSN: 0030-4921
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Paramagnetic NMR shift reagents, Eu(fod)3 and Pr(fod)3, have been applied to study the one-ene conformations of isomeric dienones. The results obtained using various complex formation models are analysed. The preferred model suggests participation of both carbonyl oxygen Ione pairs in binding with the shift reagents. Criteria for the estimation of errors in the determination of the structure parameters of the substrate-paramagnetic reagent complexes are suggested. The data obtained using NMR shift reagents are consistent with the existence of dienone α,β-cis-isomers as s-cis-conformers only, with the carbonyl group lying out of the plane of all the other atoms of the molecule. Both s-cis and s-trans conformers occur in dienone α,β-trans-isomers.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The activation energy parameters for the reaction of PdX42- (X=Cl-, Br-) in aqueous halide acid solution with thiourea (tu) and selenourea (seu) have been determined. High rates of reaction parallel low enthalpies and appreciable negative entropy of activation. The rate law in each case simplifies to kobs=k[L] where L=tu or seu, and only ligand-dependent rate constants are observed at 25°C. The ligand-dependent rate constants for the first identifiable step in the PdCl42- + X system is (9.1±0.1) × 103 M-1 sec-1 and (4.5±0.1) × 104 M-1 sec-1 for X=tu and seu, respectively, while for the PdBr42- + X system it is (2.0±0.1) × 104 M-1 sec-1 and (9.0±0.1) × 104 M-1 sec-1 for X=tu and seu, respectively.
    Additional Material: 4 Tab.
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  • 5
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Earth-Science Reviews 163 (2016): 323-348, doi:10.1016/j.earscirev.2016.10.013.
    Description: Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages have yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth’s ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies.
    Description: LJR gratefully acknowledges the support of a Vanier Canada Graduate Scholarship. Discovery Grants from the Natural Sciences and Engineering Research Council of Canada (NSERC) to CAP, BK, DSA, SAC, and KOK supported this work. This material is based upon work supported by the National Aeronautics and Space Administration through the NASA Astrobiology Institute under Cooperative Agreement No. NNA15BB03A issued through the Science Mission Directorate. NJP receives support from the Alternative Earths NASA Astrobiology Institute. Funding from the NASA Astrobiology Institute, and the NSF FESD and ELT programs to TWL, and the Region of Brittany and LabexMER funding to SVL are also gratefully acknowledged. AB thanks the Society of Independent Thinkers.
    Keywords: Iron formations ; Black shales ; Eukaryotes ; Prokaryotes ; Evolution ; Trace elements ; Biolimitation ; Precambrian
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 6
    Publication Date: 2024-03-20
    Description: During surveys in central Florida of the zombie-ant fungus Ophiocordyceps camponoti-floridani, which manipulates the behavior of the carpenter ant Camponotus floridanus, two distinct fungal morphotypes were discovered associated with and purportedly parasitic on O. camponoti-floridani. Based on a combination of unique morphology, ecology and phylogenetic placement, we discovered that these morphotypes comprise two novel lineages of fungi. Here, we propose two new genera, Niveomyces and Torrubiellomyces, each including a single species within the families Cordycipitaceae and Ophiocordycipitaceae, respectively. We generated de novo draft genomes for both new species and performed morphological and multi-loci phylogenetic analyses. The macromorphology and incidence of both new species, Niveomyces coronatus and Torrubiellomyces zombiae, suggest that these fungi are mycoparasites since their growth is observed exclusively on O. camponoti-floridani mycelium, stalks and ascomata, causing evident degradation of their fungal hosts. This work provides a starting point for more studies into fungal interactions between mycopathogens and entomopathogens, which have the potential to contribute towards efforts to battle the global rise of plant and animal mycoses.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Hypocreales ; behaviour manipulation ; entomopathogenic fungi ; genomics ; mycoparasites ; new taxa ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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