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  • 1
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    A community benchmark for viscoplastic thermal convection in a 2-D square box (2015)
    Wiley
    Details
    Publication Date: 2015-06-16
    Description: Numerical simulations of thermal convection in the Earth's mantle often employ a pseudo-plastic rheology in order to mimic the plate-like behavior of the lithosphere. Yet the benchmark tests available in the literature are largely based on simple linear rheologies in which the viscosity is either assumed to be constant or weakly dependent on temperature. Here we present a suite of simple tests based on non-linear rheologies featuring temperature-, pressure-, and strain rate dependent viscosity. Eleven different codes based on the finite volume, finite element, or spectral methods have been used to run five benchmark cases leading to stagnant lid, mobile lid, and periodic convection in a 2-D square box. For two of these cases, we also show resolution tests from all contributing codes. In addition, we present a bifurcation analysis, describing the transition from a mobile lid regime to a periodic regime, and from a periodic regime to a stagnant lid regime, as a function of the yield stress. At a resolution of around 100 cells or elements in both vertical and horizontal directions, all codes reproduce the required diagnostic quantities with a discrepancy of at most ∼ 3% in the presence of both linear and non-linear rheologies. Furthermore they consistently predict the critical value of the yield stress at which the transition between different regimes occurs. As the most recent mantle convection codes can handle a number of different geometries within a single solution framework, this benchmark will also prove useful when validating viscoplastic thermal convection simulations in such geometries. This article is protected by copyright. All rights reserved.
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    The mantle wedge's transient 3-D flow regime and thermal structure (2015)
    Wiley
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    Publication Date: 2015-12-19
    Description: Arc volcanism, volatile cycling, mineralisation and continental crust formation are likely regulated by the mantle wedge's flow regime and thermal structure. Wedge flow is often assumed to follow a regular corner-flow pattern. However, studies that incorporate a hydrated rheology and thermal buoyancy predict internal small-scale-convection (SSC). Here, we systematically explore mantle-wedge dynamics in 3-D simulations. We find that longitudinal ‘Richter-rolls’ of SSC (with trench-perpendicular axes) commonly occur if wedge hydration reduces viscosities to $\lesssim1\cdot10^{19}$Pa s, although transient transverse rolls (with trench-parallel axes) can dominate at viscosities of $\sim 5\cdot10^{18} - 1\cdot10^{19}$Pa s. Rolls below the arc and back-arc differ. Sub-arc rolls have similar trench-parallel and trench-perpendicular dimensions of 100–150 km and evolve on a 1–5 Myr time-scale. Sub-back-arc instabilities, on the other hand, coalesce into elongated sheets, usually with a preferential trench-perpendicular alignment, display a wavelength of 150–400 km and vary on a 5–10 Myr time-scale. The modulating influence of sub-back-arc ridges on the sub-arc system increases with stronger wedge hydration, higher subduction velocity and thicker upper plates. We find that trench-parallel averages of wedge velocities and temperature are consistent with those predicted in 2-D models. However, lithospheric thinning through SSC is somewhat enhanced in 3-D, thus expanding hydrous melting regions and shifting dehydration boundaries. Sub-arc Richter-rolls generate time-dependent trench-parallel temperature variations of up to $\sim150$K, which exceed the transient 50–100 K variations predicted in 2–D and may contribute to arc-volcano spacing and the variable seismic velocity structures imaged beneath some arcs. This article is protected by copyright. All rights reserved.
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    Interaction of subducted slabs with the mantle transition-zone: A regime diagram from 2-D thermomechanical models with a mobile trench and an overriding plate (2014)
    Wiley
    Details
    Publication Date: 2014-04-11
    Description: Transition zone slab deformation influences Earth's thermal, chemical and tectonic evolution. However, the mechanisms responsible for the wide-range of imaged slab morphologies remain debated. Here, we use 2-D thermo-mechanical models with a mobile trench, an overriding plate, a temperature- and stress-dependent rheology, and a 10, 30 or 100-fold increase in lower mantle viscosity, to investigate the effect of initial subducting- and overriding-plate ages on slab transition-zone interaction. Four subduction styles emerge: (i) a “vertical folding” mode, with a quasi-stationary trench, near-vertical subduction and buckling/folding at depth (VF); (ii) slabs that induce mild trench retreat, which are flattened/“horizontally deflected” and stagnate at the upper-lower mantle interface (HD); (iii) inclined slabs, which result from rapid sinking and strong trench retreat (ISR); (iv) a two-stage mode, displaying backward-bent and subsequently inclined slabs, with late trench retreat (BIR). Transitions from regime (i) to (iii) occur with increasing subducting-plate age (i.e. buoyancy and strength). Regime (iv) develops for old (strong) subducting and overriding plates. We find that the interplay between trench motion and slab deformation at depth dictate the subduction style, both being controlled by slab strength, which is consistent with predictions from previous compositional subduction models. However, due to feedbacks between deformation, sinking rate, temperature and slab strength, the subducting-plate buoyancy, overriding-plate strength and upper-lower mantle viscosity jump are also important controls in thermo-mechanical subduction. For intermediate upper-lower mantle viscosity jumps (×30), our regimes reproduce the diverse range of seismically imaged slab morphologies.
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    A systematic 2-D Investigation into the mantle wedge's transient flow regime and thermal structure: Complexities arising from a hydrated rheology and thermal buoyancy (2013)
    Wiley
    Details
    Publication Date: 2013-11-30
    Description: Arc volcanism at subduction zones is likely regulated by the mantle wedge's flow regime and thermal structure and, hence, numerous studies have attempted to quantify the principal controls on mantle wedge conditions. In this paper, we build on these previous studies by undertaking a systematic 2-D numerical investigation into how a hydrated rheology and thermal buoyancy influence the wedge's flow regime and associated thermal structure. We quantify the role of a range of plausible: (i) water contents (0-5000 H/10 6 Si); (ii) subduction velocities (2-10 cm/yr); and (iii) upper-plate ages (50-120 Myr), finding that small-scale convection (SSC), resulting from Rayleigh-Taylor instabilities, or drips, off the base of the overriding lithosphere, is a typical occurrence. The morphology of SSC varies with viscosity and subduction parameters, with drips at their most prominent when subduction velocities and wedge viscosities are low. Our results confirm that high subduction velocities and wedge viscosities promote a dominantly corner-flow regime, and strong upper-plate erosion below the arc region. By contrast, we find that back-arc upper-plate erosion by SSC is largely controlled by wedge viscosity, occurring when: (i) viscosities are 〈 5 10 18 Pa s; and (ii) the length of the upper plate, available for destabilisation, exceeds the characteristic wavelength of instabilities. Thus, if hydrous weakening of wedge rheology extends at least 100 - 150km from the trench, our 2-D models predict an unstable flow regime, resulting in temperature fluctuations of 50-100K, which are sufficient to influence melting and the stability of hydrous minerals.
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    Protein evolution. On the ancestry of barrels (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-09-19
    Description: Most proteins consist of several domains linked together in a single polypeptide chain, and many of these proteins have evolved by gene duplication and fusion. Miles and Davies discuss the study by Lang et al., who show that this type of protein evolution may also occur in b/a barrel proteins, a common single-domain protein fold. Other single domain proteins may have arisen from similar evolutionary mechanisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miles, E W -- Davies, D R -- New York, N.Y. -- Science. 2000 Sep 1;289(5484):1490.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NIH, Bethesda, MD 20892-0830, USA. edithm@intra.niddk.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10991737" target="_blank"〉PubMed〈/a〉
    Keywords: Aldose-Ketose Isomerases/*chemistry/genetics/metabolism ; Amino Acid Motifs ; Aminohydrolases/*chemistry/genetics/metabolism ; Catalysis ; Crystallography, X-Ray ; Dimerization ; *Evolution, Molecular ; Gene Duplication ; Models, Molecular ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Recombination, Genetic ; Thermotoga maritima/enzymology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Three-dimensional structure of the Tn5 synaptic complex transposition intermediate (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-07-07
    Description: Genomic evolution has been profoundly influenced by DNA transposition, a process whereby defined DNA segments move freely about the genome. Transposition is mediated by transposases, and similar events are catalyzed by retroviral integrases such as human immunodeficiency virus-1 (HIV-1) integrase. Understanding how these proteins interact with DNA is central to understanding the molecular basis of transposition. We report the three-dimensional structure of prokaryotic Tn5 transposase complexed with Tn5 transposon end DNA determined to 2.3 angstrom resolution. The molecular assembly is dimeric, where each double-stranded DNA molecule is bound by both protein subunits, orienting the transposon ends into the active sites. This structure provides a molecular framework for understanding many aspects of transposition, including the binding of transposon end DNA by one subunit and cleavage by a second, cleavage of two strands of DNA by a single active site via a hairpin intermediate, and strand transfer into target DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davies, D R -- Goryshin, I Y -- Reznikoff, W S -- Rayment, I -- AR35186/AR/NIAMS NIH HHS/ -- GM50692/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 7;289(5476):77-85.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10884228" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Catalysis ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA/*chemistry/*metabolism ; *DNA Transposable Elements ; Dimerization ; Manganese/metabolism ; Mutation ; Nucleic Acid Conformation ; Plasmids ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Transposases/*chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Triplex RNA (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rich, A -- Davies, D R -- Felsenfeld, G -- New York, N.Y. -- Science. 1991 Jul 5;253(5015):17.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1712122" target="_blank"〉PubMed〈/a〉
    Keywords: Molecular Structure ; RNA/*chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Crystal structure of transforming growth factor-beta 2: an unusual fold for the superfamily (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-17
    Description: The transforming growth factors-beta (TGF-beta 1 through -beta 5) are a family of homodimeric cytokines that regulate proliferation and function in many cell types. Family members have 66 to 80% sequence identity and nine strictly conserved cysteines. A crystal structure of a member of this family, TGF-beta 2, has been determined at 2.1 angstrom (A) resolution and refined to an R factor of 0.172. The monomer lacks a well-defined hydrophobic core and displays an unusual elongated nonglobular fold with dimensions of approximately 60 A by 20 A by 15 A. Eight cysteines form four intrachain disulfide bonds, which are clustered in a core region forming a network complementary to the network of hydrogen bonds. The dimer is stabilized by the ninth cysteine, which forms an interchain disulfide bond, and by two identical hydrophobic interfaces. Sequence profile analysis of other members of the TGF-beta superfamily, including the activins, inhibins, and several developmental factors, imply that they also adopt the TGF-beta fold.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Daopin, S -- Piez, K A -- Ogawa, Y -- Davies, D R -- New York, N.Y. -- Science. 1992 Jul 17;257(5068):369-73.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1631557" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography ; Drosophila ; Humans ; Mice ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Transforming Growth Factor beta/*chemistry ; Xenopus laevis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-08-14
    Description: Joint refinement of macromolecules against crystallographic and nuclear magnetic resonance (NMR) observations is presented as a way of combining experimental information from the two methods. The model of interleukin-1 beta derived by the joint x-ray and NMR refinement is shown to be consistent with the experimental observations of both methods and to have crystallographic R value and geometrical parameters that are of the same quality as or better than those of models obtained by conventional crystallographic studies. The few NMR observations that are violated by the model serve as an indicator for genuine differences between the crystal and solution structures. The joint x-ray-NMR refinement can resolve structural ambiguities encountered in studies of multidomain proteins, in which low- to medium-resolution diffraction data can be complemented by higher resolution NMR data obtained for the individual domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaanan, B -- Gronenborn, A M -- Cohen, G H -- Gilliland, G L -- Veerapandian, B -- Davies, D R -- Clore, G M -- New York, N.Y. -- Science. 1992 Aug 14;257(5072):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laborator of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1502561" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Interleukin-1/*chemistry ; Magnetic Resonance Spectroscopy/*methods ; Models, Molecular ; *Protein Conformation ; Proteins/*chemistry ; X-Ray Diffraction/*methods
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Structural basis of toll-like receptor 3 signaling with double-stranded RNA (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-19
    Description: Toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), a molecular signature of most viruses, and triggers inflammatory responses that prevent viral spread. TLR3 ectodomains (ECDs) dimerize on oligonucleotides of at least 40 to 50 base pairs in length, the minimal length required for signal transduction. To establish the molecular basis for ligand binding and signaling, we determined the crystal structure of a complex between two mouse TLR3-ECDs and dsRNA at 3.4 angstrom resolution. Each TLR3-ECD binds dsRNA at two sites located at opposite ends of the TLR3 horseshoe, and an intermolecular contact between the two TLR3-ECD C-terminal domains coordinates and stabilizes the dimer. This juxtaposition could mediate downstream signaling by dimerizing the cytoplasmic Toll interleukin-1 receptor (TIR) domains. The overall shape of the TLR3-ECD does not change upon binding to dsRNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761030/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761030/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Lin -- Botos, Istvan -- Wang, Yan -- Leonard, Joshua N -- Shiloach, Joseph -- Segal, David M -- Davies, David R -- Z01 BC009254-33/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 18;320(5874):379-81. doi: 10.1126/science.1155406.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18420935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Humans ; Ligands ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/metabolism ; NF-kappa B/metabolism ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Double-Stranded/*chemistry/*metabolism ; *Signal Transduction ; Toll-Like Receptor 3/*chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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