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  • 1
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    In:  J. Geophys. Res., New York, August, vol. 99/B7, no. 3, pp. 13655-13665, pp. B05S05, (ISSN: 1340-4202)
    Publication Date: 1994
    Keywords: AnisotropyS ; China ; Seismology ; earth mantle ; JGR
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  • 2
    Publication Date: 2014-05-30
    Description: The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an outstanding challenge. Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137318/" 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/PMC4137318/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Neil P -- Bale, Jacob B -- Sheffler, William -- McNamara, Dan E -- Gonen, Shane -- Gonen, Tamir -- Yeates, Todd O -- Baker, David -- T32 GM067555/GM/NIGMS NIH HHS/ -- T32GM067555/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Jun 5;510(7503):103-8. doi: 10.1038/nature13404. Epub 2014 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA [3]. ; 1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, USA [3]. ; 1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2]. ; UCLA Department of Chemistry and Biochemistry, Los Angeles, California 90095, USA. ; 1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA. ; Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA. ; 1] UCLA Department of Chemistry and Biochemistry, Los Angeles, California 90095, USA [2] UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, USA [3] UCLA Molecular Biology Institute, Los Angeles, California 90095, USA. ; 1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA [3] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24870237" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; Crystallography, X-Ray ; Drug Design ; Models, Molecular ; Nanostructures/*chemistry/ultrastructure ; Protein Subunits/chemistry ; Proteins/*chemistry/ultrastructure
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2016-12-15
    Description: The September 3, 2016, Mw 5.8 Pawnee earthquake was the largest recorded earthquake in the state of Oklahoma. Seismic and geodetic observations of the Pawnee sequence, including precise hypocenter locations and moment tensor modeling, shows the Pawnee earthquake occurred on a previously unknown left-lateral strike-slip basement fault that intersects the mapped right-lateral Labette fault zone. The Pawnee earthquake is part of an unprecedented increase in the earthquake rate in Oklahoma that is largely considered the result of the deep injection of waste fluids from oil and gas production. If this is, indeed, the case for the M5.8 Pawnee earthquake, then this would be the largest event to have been induced by fluid injection. Since 2015, Oklahoma has undergone wide scale mitigation efforts primarily aimed at reducing injection volumes. Thus far in 2016, the rate of M3 and greater earthquakes has decreased as compared to 2015 while the cumulative moment—or energy released from earthquakes—has increased. This highlights the difficulty in earthquake hazard mitigation efforts given the poorly understood long-term diffusive effects of wastewater injection and their connection to seismicity.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
    Publication Date: 2016-09-28
    Description: The Mw 5.1 Fairview, Oklahoma, earthquake on February 13, 2016, and its associated seismicity produced the largest moment release in the central and eastern U.S. since the 2011 Mw 5.6 Prague, Oklahoma, earthquake sequence and is one of the largest earthquakes potentially linked to wastewater injection. This energetic sequence has produced five earthquakes with Mw 4.4 or larger. Almost all of these earthquakes occur in Precambrian basement on a partially unmapped 14-km-long fault. Regional injection into the Arbuckle formation increased approximately 7-fold in the 36 months prior to the start of the sequence (January, 2015). We suggest far-field pressurization from clustered, high-rate wells greater than 12 km from this sequence induced these earthquakes. As compared to the Fairview sequence, seismicity is diffuse near high-rate wells, where pressure changes are expected to be largest. This points to the critical role that pre-existing faults play in the occurrence of large induced earthquakes.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
    Publication Date: 2015-10-01
    Description: Natural systems dominated by sediment transport are notoriously difficult to forecast. This is particularly true along the ocean coastline, a region that draws considerable human attention as economic investment and infrastructure are threatened by both persistent, long-term and acute, event driven processes (i.e., sea level rise and storm damage, respectively). Forecasting the coastline's evolution over intermediate time (daily) and space (tens of meters) scales is hindered by the complexity of sediment transport and hydrodynamics, and limited access to the detailed local forcing that drives fast scale processes. Modern remote sensing systems provide an efficient, economical means to collect data within these regions. A solar-powered digital camera installation is used to capture the coast's evolution, and machine learning algorithms are implemented to extract the shoreline and estimate the daily mean intertidal coastal profile. Methods in nonlinear time series forecasting and genetic programming applied to these data corroborate that coastal morphology at these scales is predominately driven by nonlinear internal dynamics, which partially mask external forcing signatures. Results indicate that these forecasting techniques achieve nontrivial predictive skill for spatiotemporal forecast of the upper coastline profile (as much as 43% of variance in data explained for one day predictions). This analysis provides evidence that societally relevant coastline forecasts can be achieved without knowing the forcing environment or the underlying dynamical equations that govern coastline evolution.
    Print ISSN: 1054-1500
    Electronic ISSN: 1089-7682
    Topics: Physics
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  • 6
    Publication Date: 2015-01-28
    Description: The sharp increase in seismicity over a broad region of central Oklahoma has raised concern regarding the source of the activity and its potential hazard to local communities and energy industry infrastructure. Since early 2010, numerous organizations have deployed temporary portable seismic stations in central Oklahoma in order to record the evolving seismicity. In this study, we apply a multiple-event relocation method to produce a catalog of 3,639 central Oklahoma earthquakes from late 2009 through 2014. RMT source parameters were determined for 195 of the largest and best-recorded earthquakes. Combining RMT results with relocated seismicity enabled us to determine the length, depth and style-of-faulting occurring on reactivated subsurface fault systems. Results show that the majority of earthquakes occur on near vertical, optimally oriented (NE-SW and NW-SE), strike-slip faults in the shallow crystalline basement. These are necessary first order observations required to assess the potential hazards of individual faults in Oklahoma.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
    Publication Date: 2011-04-21
    Description: A large portion of the seismic noise spectrum is dominated by water wave energy coupled into the solid Earth. Distinct mechanisms of water wave induced ground motions are distinguished by their spectral content. For example, cultural noise is generally
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
    Publication Date: 2017-03-23
    Description: We estimate stress drops for earthquakes in and near the continental United States using the method of spectral ratios. The ratio of acceleration spectra between collocated earthquakes recorded at a given station removes the effects of path and recording site and yields source parameters including corner frequency for, and the ratio of seismic moment between, the two earthquakes. We determine stress drop from these parameters for 1121 earthquakes greater than M ~3 in 60 earthquake clusters. We find that the average Brune stress drop for the few eastern United States (EUS) tectonic mainshocks studied (2.6–36 MPa) is about three times greater than that of tectonic mainshocks in the western United States (WUS, 1.0–7.9 MPa) and five times greater than mainshocks potentially induced by wastewater injection in the central United States (CUS, 0.6–5.6 MPa). EUS events tend to be deeper thrusting events, whereas WUS events tend to be shallower but have a wide range of focal mechanisms. CUS events tend to be shallow with strike-slip to normal-faulting mechanisms. With the possible exception of CUS aftershocks, we find that differences in stress drop among all events can be taken into account, within one standard deviation of significance, by differences in the shear failure stress as outlined by Mohr–Coulomb theory. The shear failure stress is a function of vertical stress (or depth), the fault style (normal, strike slip, or reverse), and coefficient of friction (estimated here to be, on average, 0.64). After accounting for faulting style and depth dependence, we find that the average Brune stress drop is about 3% of the failure stress. These results suggest that high-frequency shaking hazard (〉~1 Hz) from shallow induced events and aftershocks is reduced to some extent by lower stress drop. However, the shallow hypocenters will increase hazard within several kilometers of the source. Electronic Supplement: Earthquake catalog.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
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  • 9
    Publication Date: 2016-07-01
    Description: Herbivores play an important role in marine communities. On coral reefs, the diversity and unique feeding behaviours found within this functional group can have a comparably diverse set of impacts in structuring the benthic community. Here, using a spatially explicit model of herbivore foraging, we explore how the spatial pattern of grazing behaviours impacts the recovery of a reef ecosystem, considering movements at two temporal scales—short term (e.g. daily foraging patterns) and longer term (e.g. monthly movements across the landscape). Model simulations suggest that more spatially constrained herbivores are more effective at conferring recovery capability by providing a favourable environment to coral recruitment and growth. Results also show that the composition of food available to the herbivore community is linked directly to the pattern of space use by herbivores. To date, most studies of variability among the impacts of herbivore species have considered the diversity of feeding modes and mouthparts. Our work provides a complementary view of spatial patterns of foraging, revealing that variation in movement behaviours alone can affect patterns of benthic change, and thus broadens our view of realized links between herbivore diversity and reef recovery.
    Keywords: mathematical modelling, theoretical biology, ecology
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 10
    Publication Date: 2015-09-11
    Print ISSN: 0895-0695
    Electronic ISSN: 1938-2057
    Topics: Geosciences
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