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  • 1
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    Permafrost Carbon: Progress on Understanding Stocks and Fluxes Across Northern Terrestrial Ecosystems (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Biogeosciences, American Geophysical Union (AGU), 129(3), ISSN: 2169-8953
    Details
    Publication Date: 2024-02-27
    Description: Significant progress in permafrost carbon science made over the past decades include the identification of vast permafrost carbon stocks, the development of new pan‐Arctic permafrost maps, an increase in terrestrial measurement sites for CO〈jats:sub〉2〈/jats:sub〉 and methane fluxes, and important factors affecting carbon cycling, including vegetation changes, periods of soil freezing and thawing, wildfire, and other disturbance events. Process‐based modeling studies now include key elements of permafrost carbon cycling and advances in statistical modeling and inverse modeling enhance understanding of permafrost region C budgets. By combining existing data syntheses and model outputs, the permafrost region is likely a wetland methane source and small terrestrial ecosystem CO〈jats:sub〉2〈/jats:sub〉 sink with lower net CO〈jats:sub〉2〈/jats:sub〉 uptake toward higher latitudes, excluding wildfire emissions. For 2002–2014, the strongest CO〈jats:sub〉2〈/jats:sub〉 sink was located in western Canada (median: −52 g C m〈jats:sup〉−2〈/jats:sup〉 y〈jats:sup〉−1〈/jats:sup〉) and smallest sinks in Alaska, Canadian tundra, and Siberian tundra (medians: −5 to −9 g C m〈jats:sup〉−2〈/jats:sup〉 y〈jats:sup〉−1〈/jats:sup〉). Eurasian regions had the largest median wetland methane fluxes (16–18 g CH〈jats:sub〉4〈/jats:sub〉 m〈jats:sup〉−2〈/jats:sup〉 y〈jats:sup〉−1〈/jats:sup〉). Quantifying the regional scale carbon balance remains challenging because of high spatial and temporal variability and relatively low density of observations. More accurate permafrost region carbon fluxes require: (a) the development of better maps characterizing wetlands and dynamics of vegetation and disturbances, including abrupt permafrost thaw; (b) the establishment of new year‐round CO〈jats:sub〉2〈/jats:sub〉 and methane flux sites in underrepresented areas; and (c) improved models that better represent important permafrost carbon cycle dynamics, including non‐growing season emissions and disturbance effects.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 2
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    Tectono‐Stratigraphic Evolution of the Kerguelen Large Igneous Province: The Conjugate William’s Ridge‐Broken Ridge Rifted Margins (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Solid Earth, American Geophysical Union (AGU), 129(3), ISSN: 2169-9313
    Details
    Publication Date: 2024-03-04
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Extensive investigation of continental rift systems has been fundamental for advancing the understanding of extensional tectonics and modes of formation of new ocean basins. However, current rift classification schemes do not account for conjugate end members formed by Large Igneous Province crust, referring to thick mafic crust, sometimes including continental fragments. Here, we investigate the rifting of William's Ridge (Kerguelen Plateau) and Broken Ridge, components of the Kerguelen Large Igneous Province now situated in the Southeast Indian Ocean, and incorporate these end members into the deformation migration concept for rifted margins. We use multichannel seismic reflection profiles and data from scientific drill cores acquired on both conjugate margins to propose, for the first time, a combined tectono‐stratigraphic framework. We interpret seismic patterns, tectonic features, and magnetic anomaly picks to determine an across‐strike structural domain classification. This interpretation considers the rift system overall to be “magma‐poor” despite being located proximal to the Kerguelen plume but suggests that syn‐rift interaction between the Kerguelen mantle plume and the lithospheric structure of William's Ridge and Broken Ridge has controlled the along‐strike segmentation of both conjugates. We integrate seismic reflection and bathymetric data to test the hypothesis of predominantly transform motion, between the Australian and Antarctic plates, in Late Cretaceous and Paleogene time.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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    Tectono‐Stratigraphic Evolution of the Kerguelen Large Igneous Province: The Conjugate William’s Ridge‐Broken Ridge Rifted Margins (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Solid Earth, American Geophysical Union (AGU), 129(3), ISSN: 2169-9313
    Details
    Publication Date: 2024-03-04
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Extensive investigation of continental rift systems has been fundamental for advancing the understanding of extensional tectonics and modes of formation of new ocean basins. However, current rift classification schemes do not account for conjugate end members formed by Large Igneous Province crust, referring to thick mafic crust, sometimes including continental fragments. Here, we investigate the rifting of William's Ridge (Kerguelen Plateau) and Broken Ridge, components of the Kerguelen Large Igneous Province now situated in the Southeast Indian Ocean, and incorporate these end members into the deformation migration concept for rifted margins. We use multichannel seismic reflection profiles and data from scientific drill cores acquired on both conjugate margins to propose, for the first time, a combined tectono‐stratigraphic framework. We interpret seismic patterns, tectonic features, and magnetic anomaly picks to determine an across‐strike structural domain classification. This interpretation considers the rift system overall to be “magma‐poor” despite being located proximal to the Kerguelen plume but suggests that syn‐rift interaction between the Kerguelen mantle plume and the lithospheric structure of William's Ridge and Broken Ridge has controlled the along‐strike segmentation of both conjugates. We integrate seismic reflection and bathymetric data to test the hypothesis of predominantly transform motion, between the Australian and Antarctic plates, in Late Cretaceous and Paleogene time.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Late Holocene Dust Deposition Fluxes Over the Entire South Atlantic Ocean (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Geochemistry Geophysics Geosystems, American Geophysical Union (AGU), 25(1), ISSN: 1525-2027
    Details
    Publication Date: 2024-03-04
    Description: Mineral dust accumulated on the ocean floor is an important archive for reconstructing past atmospheric circulation changes and climatological conditions in the source areas. Dust emitted from Southern Hemisphere dust sources is widely deposited over the oceans. However, there are few records of dust deposition over the open ocean, and a large need for extended geographical coverage exists. We present a large data set (134 surface sediment samples) of Late Holocene dust deposition from seafloor surface sediments covering the entire South Atlantic Ocean. Polymodal grain-size distributions of the lithogenic fraction indicate that the sediments are composed of multiple sediment components. By using end-member modeling, we attempt to disentangle the dust signal from non-aeolian sediments. Combined with 230Th-normalized lithogenic fluxes, we quantified the specific deposition fluxes for mineral dust, crrent-sorted sediments and ice-rafted debris (IRD). Although the method could not completely separate the different components in every region, it shows that dust deposition off the most prominent dust source for the South Atlantic Ocean—southern South America—amounts up to approximately 0.7 g cm−2 Kyr−1 and decreases downwind. Bottom-current-sorted sediments and IRD are mostly concentrated around the continental margins. The ratio of the coarse to fine dust end members reveals input from north African dust sources to the South Atlantic. The majority of the observations are in good agreement with new model simulations. This extensive and relevant data set of dust grain size and deposition fluxes to the South Atlantic could be used to calibrate and validate further model simulations.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Tectono‐Stratigraphic Evolution of the Kerguelen Large Igneous Province: The Conjugate William’s Ridge‐Broken Ridge Rifted Margins (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Solid Earth, American Geophysical Union (AGU), 129(3), ISSN: 2169-9313
    Details
    Publication Date: 2024-03-04
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Extensive investigation of continental rift systems has been fundamental for advancing the understanding of extensional tectonics and modes of formation of new ocean basins. However, current rift classification schemes do not account for conjugate end members formed by Large Igneous Province crust, referring to thick mafic crust, sometimes including continental fragments. Here, we investigate the rifting of William's Ridge (Kerguelen Plateau) and Broken Ridge, components of the Kerguelen Large Igneous Province now situated in the Southeast Indian Ocean, and incorporate these end members into the deformation migration concept for rifted margins. We use multichannel seismic reflection profiles and data from scientific drill cores acquired on both conjugate margins to propose, for the first time, a combined tectono‐stratigraphic framework. We interpret seismic patterns, tectonic features, and magnetic anomaly picks to determine an across‐strike structural domain classification. This interpretation considers the rift system overall to be “magma‐poor” despite being located proximal to the Kerguelen plume but suggests that syn‐rift interaction between the Kerguelen mantle plume and the lithospheric structure of William's Ridge and Broken Ridge has controlled the along‐strike segmentation of both conjugates. We integrate seismic reflection and bathymetric data to test the hypothesis of predominantly transform motion, between the Australian and Antarctic plates, in Late Cretaceous and Paleogene time.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
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    The Role of Coastal Yedoma Deposits and Continental Shelf Sediments in the Arctic Ocean Silicon Cycle (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Global Biogeochemical Cycles, American Geophysical Union (AGU), 38(1), ISSN: 0886-6236
    Details
    Publication Date: 2024-02-13
    Description: The availability of silicon (Si) in the ocean plays an important role in regulating biogeochemical and ecological processes. The Si budget of the Arctic Ocean appears balanced, with inputs equivalent to outputs, though it is unclear how a changing climate might aggravate this balance. In this study, we focus on Si cycling in Arctic coastal areas and continental shelf sediments to better constrain the Arctic Ocean Si budget. We provide the first estimate of amorphous Si (ASi) loading from erosion of coastal Yedoma deposits (30–90 Gmol yr−1), demonstrating comparable rates to particulate Si loading from rivers (10–90 Gmol yr−1). We found a positive relationship between surface sediment ASi and organic matter content on continental shelves. Combining these values with published Arctic shelf sediment properties and burial rates we estimate 70 Gmol Si yr−1 is buried on Arctic continental shelves, equivalent to 4.5% of all Si inputs to the Arctic Ocean. Sediment dissolved Si fluxes increased with distance from river mouths along cruise transects of shelf regions influenced by major rivers in the Laptev and East Siberian seas. On an annual basis, we estimate that Arctic shelf sediments recycle approximately up to twice as much DSi (680 Gmol Si) as is loaded from rivers (340–500 Gmol Si).
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
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    A Synthesis of Global Coastal Ocean Greenhouse Gas Fluxes (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Global Biogeochemical Cycles, American Geophysical Union (AGU), 38(1), ISSN: 0886-6236
    Details
    Publication Date: 2024-02-13
    Description: The coastal ocean contributes to regulating atmospheric greenhouse gas concentrations by taking up carbon dioxide (CO2) and releasing nitrous oxide (N2O) and methane (CH4). In this second phase of the Regional Carbon Cycle Assessment and Processes (RECCAP2), we quantify global coastal ocean fluxes of CO2, N2O and CH4 using an ensemble of global gap-filled observation-based products and ocean biogeochemical models. The global coastal ocean is a net sink of CO2 in both observational products and models, but the magnitude of the median net global coastal uptake is ∼60% larger in models (−0.72 vs. −0.44 PgC year−1, 1998–2018, coastal ocean extending to 300 km offshore or 1,000 m isobath with area of 77 million km2). We attribute most of this model-product difference to the seasonality in sea surface CO2 partial pressure at mid- and high-latitudes, where models simulate stronger winter CO2 uptake. The coastal ocean CO2 sink has increased in the past decades but the available time-resolving observation-based products and models show large discrepancies in the magnitude of this increase. The global coastal ocean is a major source of N2O (+0.70 PgCO2-e year−1 in observational product and +0.54 PgCO2-e year−1 in model median) and CH4 (+0.21 PgCO2-e year−1 in observational product), which offsets a substantial proportion of the coastal CO2 uptake in the net radiative balance (30%–60% in CO2-equivalents), highlighting the importance of considering the three greenhouse gases when examining the influence of the coastal ocean on climate.
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
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    Selective Sorting and Degradation of Permafrost Organic Matter in the Nearshore Zone of Herschel Island (Yukon, Canada) (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Biogeosciences, American Geophysical Union (AGU), 129(1), ISSN: 2169-8953
    Details
    Publication Date: 2024-01-26
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Erosion of permafrost coasts due to climate warming releases large quantities of organic carbon (OC) into the Arctic Ocean. While burial of permafrost OC in marine sediments potentially limits degradation, resuspension of sediments in the nearshore zone potentially enhances degradation and greenhouse gas production, adding to the “permafrost carbon feedback.” Recent studies, focusing on bulk sediments, suggest that permafrost OC derived from coastal erosion is predominantly deposited close to shore. However, bulk approaches disregard sorting processes in the coastal zone, which strongly influence the OC distribution and fate. We studied soils and sediments along a transect from the fast‐eroding shoreline of Herschel Island—〈jats:italic〉Qikiqtaruk〈/jats:italic〉 (Yukon, Canada) to a depositional basin offshore. Sample material was fractionated by density (1.8 g cm〈jats:sup〉−3〈/jats:sup〉) and size (63 μm), separating loose OC from mineral‐associated OC. Each fraction was analyzed for element content (TOC, TN), carbon isotopes (δ〈jats:sup〉13〈/jats:sup〉C, Δ〈jats:sup〉14〈/jats:sup〉C), molecular biomarkers (〈jats:italic〉n〈/jats:italic〉‐alkanes, 〈jats:italic〉n〈/jats:italic〉‐alkanoic acids, lignin phenols, cutin acids), and mineral surface area. The OC partitioning between fractions changes considerably along the transect, highlighting the importance of hydrodynamic sorting in the nearshore zone. Additionally, OC and biomarker loadings decrease along the land‐ocean transect, indicating significant loss of OC during transport. However, molecular proxies for degradation show contrasting trends, suggesting that OC losses are not always well reflected in its degradation state. This study, using fraction partitioning that crosses land‐ocean boundaries in a way not done before, aids to disentangle sorting processes from degradation patterns, and provides quantitative insight into losses of thawed and eroded permafrost OC.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 9
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    Seismic Risk Communication in Europe: Lessons Learned and Future Perspectives (2024)
    American Geophysical Union (AGU)
    Details
    Publication Date: 2024-03-13
    Description: Since the 1980s various international directives and frameworks have acknowledged the potential of risk communication to foster community empowerment. However, to achieve empowerment, communication has to be effective. When it comes to natural disasters, such as earthquakes, science communication requires the involvement of communities as a whole, promoting bottom-up strategies and proactive engagement. In this light, we conducted a scoping review of scientific publications on seismic risk communication in Europe published between 2000 and 2022. We focused on how seismic risk communication has changed in that time span, looking for targeted approaches, tools, recipients and channels. Here we provide an overview of the results obtained from the analysis of 109 selected publications, also highlighting the importance of scientific communication as a transnational problem, due to the mobility of modern society. Our study reveals that seismic risk communication in Europe is becoming increasingly proactive, focusing on a bottom-up strategy that relies on youth to build the resilience of future generations. The potential for the community empowerment has been primarily addressed with seismic risk communication during the pre-crisis phase of the disaster, when risk awareness can be effectively raised. Social media are increasingly used to provide timely and actionable information in times of crisis, to engage citizens within a two-way risk communication model, in the pre-crisis time, and to provide scientific data for post-disaster processing. The future agenda of seismic risk communication in Europe should focus on building trust with the public, moving towards a three-way model of seismic risk communication and, even more importantly, taking action to curb the spread of fake news and their negative impact on disaster management. Last but not least, more efforts should be made to link practice and theory and explicitly build seismic risk communication on theoretical models.
    Description: Published
    Description: San Francisco, California, USA
    Description: OS: Terza missione
    Keywords: Seismic risk ; communication ; Europe ; scoping review ; 04.06. Seismology ; 05.08. Risk ; 05.09
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Oral presentation
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  • 10
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    Volcano-Tectonic seismicity during the unrest phase on the island of Vulcano (Italy) from mid-September 2021 to December 2022 (2024)
    American Geophysical Union (AGU)
    Details
    Publication Date: 2024-03-13
    Description: In mid-September 2021 there was a rapid increase in geophysical and geochemical parameters on the island of Vulcano, Italy, reaching alarming values. This phase of unrest aroused serious concern among Civil Protection, local authorities and the scientific community due to the risk of phreatomagmatic activity, with potentially serious repercussions on the inhabitants of the island and on visiting tourists. The beginning of the unrest was marked by a high occurrence rate of local micro-seismicity related to fluid dynamics within the shallower hydrothermal system (mainly Long Period and Very Long Period events); Volcano-Tectonic (VT) earthquakes increased in late October after most of the monitored parameters reached their climax. Afterwards, major episodes of VT activity were also recorded from March to April and at the end of the year 2022, when an earthquake of ML 4.6 occurred on December 4, SW of the island of Vulcano. Here, we analyze the VT earthquakes from January 2020 to December 2022, in terms of space-time distribution, energy release and focal mechanisms in the framework of the regional geodynamic context and in the light of the main characteristics of the seismic activity recorded in the Vulcano area over the past 36 years.
    Description: Published
    Description: San Francisco, California, USA
    Description: OST3 Vicino alla faglia
    Keywords: earthquakes ; monitoring ; volcano unrest ; Vulcano ; 04.06. Seismology ; 04.07. Tectonophysics ; 04.08. Volcanology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Oral presentation
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  • 11
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    Sediment Freeze‐On and Transport Near the Onset of a Fast‐Flowing Glacier in East Antarctica (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 51(6), ISSN: 0094-8276
    Details
    Publication Date: 2024-03-18
    Description: Understanding the material properties and physical conditions of basal ice is crucial for a comprehensive understanding of Antarctic ice‐sheet dynamics. Yet, direct data are sparse and difficult to acquire. Here, we employ ultra‐wideband radar to map high‐backscatter zones near the glacier bed within East Antarctica's Jutulstraumen drainage basin. Our backscatter analysis reveals that the basal ice in an area of ∼10,000 km² is composed of along‐flow oriented sediment‐laden basal ice units connected to the basal substrate, extending up to several hundred meters thick. Three‐dimensional thermomechanical modeling supports that these units form via basal freeze‐on of subglacial water that originated from further upstream. Our findings suggest that basal freeze‐on, and the entrainment and transport of subglacial material play a significant role in an accurate representation of material, physical, and rheological properties of the Antarctic ice sheet's basal ice, ultimately enhancing the accuracy and reliability of ice‐sheet modeling.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
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    Sediment Freeze‐On and Transport Near the Onset of a Fast‐Flowing Glacier in East Antarctica (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 51(6), ISSN: 0094-8276
    Details
    Publication Date: 2024-03-18
    Description: Understanding the material properties and physical conditions of basal ice is crucial for a comprehensive understanding of Antarctic ice‐sheet dynamics. Yet, direct data are sparse and difficult to acquire. Here, we employ ultra‐wideband radar to map high‐backscatter zones near the glacier bed within East Antarctica's Jutulstraumen drainage basin. Our backscatter analysis reveals that the basal ice in an area of ∼10,000 km² is composed of along‐flow oriented sediment‐laden basal ice units connected to the basal substrate, extending up to several hundred meters thick. Three‐dimensional thermomechanical modeling supports that these units form via basal freeze‐on of subglacial water that originated from further upstream. Our findings suggest that basal freeze‐on, and the entrainment and transport of subglacial material play a significant role in an accurate representation of material, physical, and rheological properties of the Antarctic ice sheet's basal ice, ultimately enhancing the accuracy and reliability of ice‐sheet modeling.
    Repository Name: EPIC Alfred Wegener Institut
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  • 13
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    Sediment Freeze‐On and Transport Near the Onset of a Fast‐Flowing Glacier in East Antarctica (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 51(6), ISSN: 0094-8276
    Details
    Publication Date: 2024-03-18
    Description: Understanding the material properties and physical conditions of basal ice is crucial for a comprehensive understanding of Antarctic ice‐sheet dynamics. Yet, direct data are sparse and difficult to acquire. Here, we employ ultra‐wideband radar to map high‐backscatter zones near the glacier bed within East Antarctica's Jutulstraumen drainage basin. Our backscatter analysis reveals that the basal ice in an area of ∼10,000 km² is composed of along‐flow oriented sediment‐laden basal ice units connected to the basal substrate, extending up to several hundred meters thick. Three‐dimensional thermomechanical modeling supports that these units form via basal freeze‐on of subglacial water that originated from further upstream. Our findings suggest that basal freeze‐on, and the entrainment and transport of subglacial material play a significant role in an accurate representation of material, physical, and rheological properties of the Antarctic ice sheet's basal ice, ultimately enhancing the accuracy and reliability of ice‐sheet modeling.
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
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    Anthropogenic Influence on Tropospheric Reactive Bromine Since the Pre‐industrial: Implications for Arctic Ice‐Core Bromine Trends (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 51(5), ISSN: 0094-8276
    Details
    Publication Date: 2024-03-21
    Description: Tropospheric reactive bromine (Bry) influences the oxidation capacity of the atmosphere by acting as a sink for ozone and nitrogen oxides. Aerosol acidity plays a crucial role in Bry abundances through acid-catalyzed debromination from sea-salt-aerosol, the largest global source. Bromine concentrations in a Russian Arctic ice-core, Akademii Nauk, show a 3.5-fold increase from pre-industrial (PI) to the 1970s (peak acidity, PA), and decreased by half to 1999 (present day, PD). Ice-core acidity mirrors this trend, showing robust correlation with bromine, especially after 1940 (r = 0.9). Model simulations considering anthropogenic emission changes alone show that atmospheric acidity is the main driver of Bry changes, consistent with the observed relationship between acidity and bromine. The influence of atmospheric acidity on Bry should be considered in interpretation of ice-core bromine trends.
    Repository Name: EPIC Alfred Wegener Institut
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  • 15
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    The Chemical Effect of Increased Water Vapor From the Hunga Tonga‐Hunga Ha'apai Eruption on the Antarctic Ozone Hole (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 51(4), ISSN: 0094-8276
    Details
    Publication Date: 2024-03-27
    Description: The eruption of the Hunga Tonga‐Hunga Ha'apai volcano on 15 January 2022 was one of the most explosive eruptions of the last decades. The amount of water vapor injected into the stratosphere was unprecedented in the observational record, increasing the stratospheric water vapor burden by about 10%. Using model runs from the ATLAS chemistry and transport model and Microwave Limb Sounder (MLS) satellite observations, we show that while 20%–40% more water vapor than usual was entrained into the Antarctic polar vortex in 2023 as it formed, the direct chemical effect of the increased water vapor on Antarctic ozone depletion in June through October was minor (less than 4 DU). This is because low temperatures in the vortex, as occur every year in the Antarctic, limit water vapor to the saturation pressure and thus reset any anomalies through the process of dehydration before they can affect ozone loss.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    Tectono‐Stratigraphic Evolution of the Kerguelen Large Igneous Province: The Conjugate William’s Ridge‐Broken Ridge Rifted Margins (2024)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Solid Earth, American Geophysical Union (AGU), 129(3), ISSN: 2169-9313
    Details
    Publication Date: 2024-04-05
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Extensive investigation of continental rift systems has been fundamental for advancing the understanding of extensional tectonics and modes of formation of new ocean basins. However, current rift classification schemes do not account for conjugate end members formed by Large Igneous Province crust, referring to thick mafic crust, sometimes including continental fragments. Here, we investigate the rifting of William's Ridge (Kerguelen Plateau) and Broken Ridge, components of the Kerguelen Large Igneous Province now situated in the Southeast Indian Ocean, and incorporate these end members into the deformation migration concept for rifted margins. We use multichannel seismic reflection profiles and data from scientific drill cores acquired on both conjugate margins to propose, for the first time, a combined tectono‐stratigraphic framework. We interpret seismic patterns, tectonic features, and magnetic anomaly picks to determine an across‐strike structural domain classification. This interpretation considers the rift system overall to be “magma‐poor” despite being located proximal to the Kerguelen plume but suggests that syn‐rift interaction between the Kerguelen mantle plume and the lithospheric structure of William's Ridge and Broken Ridge has controlled the along‐strike segmentation of both conjugates. We integrate seismic reflection and bathymetric data to test the hypothesis of predominantly transform motion, between the Australian and Antarctic plates, in Late Cretaceous and Paleogene time.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Future Arctic Climate Change in CMIP6 Strikingly Intensified by NEMO‐Family Climate Models (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(4), ISSN: 0094-8276
    Details
    Publication Date: 2023-06-23
    Description: Climate change in the Arctic has substantial impacts on human life and ecosystems both within and beyond the Arctic. Our analysis of CMIP6 simulations shows that some climate models project much larger Arctic climate change than other models, including changes in sea ice, ocean mixed layer, air-sea heat flux, and surface air temperature in wintertime. In particular, dramatic enhancement of Arctic Ocean convection down to a few hundred meters is projected in these models but not in others. Interestingly, these models employ the same ocean model family (NEMO) while the choice of models for the atmosphere and sea ice varies. The magnitude of Arctic climate change is proportional to the strength of the increase in poleward ocean heat transport, which is considerably higher in this group of models. Establishing the plausibility of this group of models with high Arctic climate sensitivity to anthropogenic forcing is imperative given the implied ramifications.
    Repository Name: EPIC Alfred Wegener Institut
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    Turbulent heat exchange over polar leads revisited: A large eddy simulation study (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Atmospheres, American Geophysical Union (AGU), ISSN: 2169-897X
    Details
    Publication Date: 2023-06-23
    Description: Sea ice leads play an important role in energy exchange between the ocean and atmosphere in polar regions, and therefore must be considered in weather and climate models. As sea ice leads are not explicitly resolved in such models, lead-averaged surface heat flux is of considerable interest for the parameterization of energy exchange. Measurements and numerical studies have established that the lead-averaged surface heat flux depends not only on meteorological parameters, but also on lead width. Nonetheless, few studies to date have investigated the dependency of surface heat flux on lead width. Most findings on that dependency are based on observations with lead widths smaller than a few hundred meters, but leads can have widths from a few meters to several kilometers. In this parameter study, we present the results of three series of large-eddy simulations of turbulent exchange processes above leads. We varied the lead width and air temperature, as well as the roughness length. As this study focused on conditions without background wind, ice-breeze circulation occurred, and was the main driver of the adjustment of surface heat flux. A previous large-eddy simulation study with uncommonly large roughness length found that lead-averaged surface heat flux exhibited a distinct maximum at lead widths of about 3 km, while our results show the largest heat fluxes for the smallest leads simulated (lead width of 50 m). At more realistic roughness lengths, we observed monotonously increasing heat fluxes with increasing lead width. Further, new scaling laws for the ice-breeze circulation are proposed.
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    Impact of Cyclonic Wind Anomalies Caused by Massive Winter Sea Ice Retreat in the Barents Sea on Atlantic Water Transport Toward the Arctic: A Model Study (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research - Oceans, American Geophysical Union (AGU), 128(3), ISSN: 2169-9275
    Details
    Publication Date: 2023-06-23
    Description: The Arctic is warming much faster than the global average. This is known as Arctic Amplification and is caused by feedbacks in the local climate system. In this study, we explore a previously proposed hypothesis that an associated wind feedback in the Barents Sea could play an important role by increasing the warm water inflow into the Barents Sea. We find that the strong recent decrease in Barents Sea winter sea ice cover causes enhanced ocean-atmosphere heat flux and a local air temperature increase, thus a reduction in sea level pressure and a local cyclonic wind anomaly with eastward winds in the Barents Sea Opening. By investigating various reanalysis products and performing high-resolution perturbation experiments with the ocean and sea ice model FESOM2.1, we studied the impact of cyclonic atmospheric circulation changes on the warm Atlantic Water import into the Arctic via the Barents Sea and Fram Strait. We found that the observed wind changes do not significantly affect the warm water transport into the Barents Sea, which rejects the wind-feedback hypothesis. At the same time, the cyclonic wind anomalies in the Barents Sea increase the amount of Atlantic Water recirculating westwards in Fram Strait by a downslope shift of the West Spitsbergen Current, and thus reduce Atlantic Water reaching the Arctic basin via Fram Strait. The resulting warm-water anomaly in the Greenland Sea Gyre drives a local anticyclonic circulation anomaly.
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  • 20
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    The Impacts of Optimizing Model‐Dependent Parameters on the Antarctic Sea Ice Data Assimilation (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(22), ISSN: 0094-8276
    Details
    Publication Date: 2023-11-25
    Description: Given the role played by the historical and extensive coverage of sea ice concentration (SIC) observations in reconstructing the long‐term variability of Antarctic sea ice, and the limited attention given to model‐dependent parameters in current sea ice data assimilation studies, this study focuses on enhancing the performance of the Data Assimilation System for the Southern Ocean in assimilating SIC through optimizing the localization and observation error estimate, and two assimilation experiments were conducted from 1979 to 2018. By comparing the results with the sea ice extent of the Southern Ocean and the sea ice thickness in the Weddell Sea, it becomes evident that the experiment with optimizations outperforms that without optimizations due to achieving more reasonable error estimates. Investigating uncertainties of the sea ice volume anomaly modeling reveals the importance of the sea ice‐ocean interaction in the SIC assimilation, implying the necessity of assimilating more oceanic and sea‐ice observations.
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  • 21
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    Snow‐Atmosphere Humidity Exchange at the Ice Sheet Surface Alters Annual Mean Climate Signals in Ice Core Records (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(20), ISSN: 0094-8276
    Details
    Publication Date: 2023-11-20
    Description: Surface processes alter the water stable isotope signal of the surface snow after deposition. However, it remains an open question to which extent surface post-depositional processes should be considered when inferring past climate information from ice core records. Here, we present simulations for the Greenland Ice Sheet, combining outputs from two climate models with an isotope-enabled snowpack model. We show that surface vapor exchange and associated fractionation imprint a climate signal into the firn, resulting in an increase in the annual mean value of δ18O by +2.3‰ and a reduction in d-excess by −6.3‰. Further, implementing isotopic fractionation during surface vapor exchange improves the representation of the observed seasonal amplitude in δ18O from 65.0% to 100.2%. Our results stress that surface vapor exchange is important in the climate proxy signal formation and needs consideration when interpreting ice core climate records.
    Repository Name: EPIC Alfred Wegener Institut
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  • 22
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    Preconditioning of Summer Melt Ponds From Winter Sea Ice Surface Temperature (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(4), ISSN: 0094-8276
    Details
    Publication Date: 2023-02-23
    Description: Comparing helicopter-borne surface temperature maps in winter and optical orthomosaics in summer from the year-long Multidisciplinary drifting Observatory for the Study of Arctic Climate expedition, we find a strong geometric correlation between warm anomalies in winter and melt pond location the following summer. Warm anomalies are associated with thinner snow and ice, that is, surface depression and refrozen leads, that allow for water accumulation during melt. Warm surface temperature anomalies in January were 0.3–2.5 K warmer on sea ice that later formed melt ponds. A one-dimensional steady-state thermodynamic model shows that the observed surface temperature differences are in line with the observed ice thickness and snow depth. We demonstrate the potential of seasonal prediction of summer melt pond location and coverage from winter surface temperature observations. A threshold-based classification achieves a correct classification for 41% of the melt ponds.
    Repository Name: EPIC Alfred Wegener Institut
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  • 23
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    Atmospheric CO2 concentration based on boron isotopes versus simulations of the global carbon cycle during the Plio‐Pleistocene (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union (AGU), 38, 22 p., pp. e2022PA004439-e2022PA004439, ISSN: 2572-4517
    Details
    Publication Date: 2023-08-30
    Description: Atmospheric carbon dioxide concentrations (pCO2) beyond ice core records have been reconstructed from δ11B derived from planktic foraminifera found in equatorial sediment cores. Here, I applied a carbon cycle model over the Plio-Pleistocene to evaluate the assumptions leading to these numbers. During glacials times, simulated atmospheric pCO2 was unequilibrated with pCO2 in the equatorial surface ocean by up to 35 ppm while the δ11B-based approaches assume unchanged (quasi)equilibrium between both. In the Pliocene, δ11B-based estimates of surface ocean pH are lower in the Pacific than in the Atlantic resulting in higher calculated pCO2. This offset in pH between ocean basins is not supported by models. To calculate pCO2 in surface waters out of the δ11B-based pH some assumptions on either total alkalinity or dissolved inorganic carbon are necessary. However, the assumed values of these under-constrained variables were according to my results partly inconsistent with chemically possible combinations within the marine carbonate system. The model results show glacial/interglacial variability in total alkalinity of the order of 100 μmol/kg, which is rarely applied to proxy reconstructions. Simulated atmospheric pCO2 is tightly (r2 〉 0.9) related to equatorial surface-ocean pH, which can be used for consistency checks. Long-term trends in volcanic CO2 outgassing and the strength of the continental weathering fluxes are still unconstrained, allowing for a wide range of possible atmospheric pCO2 across the Plio-Pleistocene. Nevertheless, this carbon cycle analysis suggests that reported atmospheric pCO2 above 500 ppm in the Pliocene might, for various reasons, need to be revised to smaller numbers.
    Repository Name: EPIC Alfred Wegener Institut
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  • 24
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    Stable Carbon Isotope Signature of Methane Released From Phytoplankton (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(12), ISSN: 0094-8276
    Details
    Publication Date: 2023-09-01
    Description: Aquatic ecosystems play an important role in global methane cycling and many field studies have reported methane supersaturation in the oxic surface mixed layer (SML) of the ocean and in the epilimnion of lakes. The origin of methane formed under oxic condition is hotly debated and several pathways have recently been offered to explain the “methane paradox.” In this context, stable isotope measurements have been applied to constrain methane sources in supersaturated oxygenated waters. Here we present stable carbon isotope signatures for six widespread marine phytoplankton species, three haptophyte algae and three cyanobacteria, incubated under laboratory conditions. The observed isotopic patterns implicate that methane formed by phytoplankton might be clearly distinguished from methane produced by methanogenic archaea. Comparing results from phytoplankton experiments with isotopic data from field measurements, suggests that algal and cyanobacterial populations may contribute substantially to methane formation observed in the SML of oceans and lakes.
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  • 25
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    Teardrop and Parabolic Lens Yield Curves for Viscous‐Plastic Sea Ice Models: New Constitutive Equations and Failure Angles (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Advances in Modeling Earth Systems, American Geophysical Union (AGU), 15(9), ISSN: 1942-2466
    Details
    Publication Date: 2023-09-04
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Most viscous‐plastic sea ice models use the elliptical yield curve. This yield curve has a fundamental flaw: it excludes acute angles between deformation features at high resolution. Conceptually, the teardrop (TD) and parabolic lens (PL) yield curves offer an attractive alternative. These yield curves feature a non‐symmetrical shape, a Coulombic behavior for the low‐medium compressive stress, and a continuous transition to the ridging‐dominant mode, but their published formulation leads to negative or zero bulk and shear viscosities and, consequently, poor numerical convergence with stress states at times outside the yield curve. These issues are a consequence of the original assumption that the constitutive equations of the commonly used elliptical yield curve are also applicable to non‐symmetrical yield curves and yield curves with tensile strength. We derive a corrected formulation for the constitutive relations of the TD and PL yield curves. Results from simple uni‐axial loading experiments show that with the new formulation the numerical convergence of the solver improves and much smaller nonlinear residuals after a smaller number of total solver iterations can be reached, resulting in significant improvements in numerical efficiency and representation of the stress and deformation fields. The TD and PL yield curves lead to smaller angles of failure that better agree with observations. They are promising candidates to replace the elliptical yield curve in high‐resolution pan‐Arctic sea ice simulations.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 26
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    Antarctic Sedimentary Basins and Their Influence on Ice‐Sheet Dynamics (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Reviews of Geophysics, American Geophysical Union (AGU), 61(3), ISSN: 8755-1209
    Details
    Publication Date: 2023-10-09
    Description: Knowledge of Antarctica's sedimentary basins builds our understanding of the coupled evolution of tectonics, ice, ocean, and climate. Sedimentary basins have properties distinct from basement-dominated regions that impact ice-sheet dynamics, potentially influencing future ice-sheet change. Despite their importance, our knowledge of Antarctic sedimentary basins is restricted. Remoteness, the harsh environment, the overlying ice sheet, ice shelves, and sea ice all make fieldwork challenging. Nonetheless, in the past decade the geophysics community has made great progress in internationally coordinated data collection and compilation with parallel advances in data processing and analysis supporting a new insight into Antarctica's subglacial environment. Here, we summarize recent progress in understanding Antarctica's sedimentary basins. We review advances in the technical capability of radar, potential fields, seismic, and electromagnetic techniques to detect and characterize basins beneath ice and advances in integrated multi-data interpretation including machine-learning approaches. These new capabilities permit a continent-wide mapping of Antarctica's sedimentary basins and their characteristics, aiding definition of the tectonic development of the continent. Crucially, Antarctica's sedimentary basins interact with the overlying ice sheet through dynamic feedbacks that have the potential to contribute to rapid ice-sheet change. Looking ahead, future research directions include techniques to increase data coverage within logistical constraints, and resolving major knowledge gaps, including insufficient sampling of the ice-sheet bed and poor definition of subglacial basin structure and stratigraphy. Translating the knowledge of sedimentary basin processes into ice-sheet modeling studies is critical to underpin better capacity to predict future change.
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  • 27
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    Structure and Seasonal Variability of the Arctic Boundary Current North of Severnaya Zemlya (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research - Oceans, American Geophysical Union (AGU), 128(1), ISSN: 2169-9275
    Details
    Publication Date: 2023-05-10
    Description: We assessed the spatial and temporal variability of the Arctic Boundary Current (ABC) using seven oceanographic moorings, deployed across the continental slope north of Severnaya Zemlya in 2015–2018. Transports and individual water masses were quantified based on temperature and salinity recorders and current profilers. Our results were compared with observations from the northeast Svalbard and the central Laptev Sea continental slopes to evaluate the hydrographic transformation along the ABC pathway. The highest velocities (〉0.30 m s−1) of the ABC occurred at the upper continental slope and decreased offshore to below 0.03 m s−1 in the deep basin. The ABC showed seasonal variability with velocities two times higher in winter than in summer. Compared to upstream conditions in Svalbard, water mass distribution changed significantly within 20 km of the shelf edge due to mixing with- and intrusion of shelf waters. The ABC transported 4.15 ± 0.3 Sv in the depth range 50–1,000 m, where 0.88 ± 0.1, 1.5 ± 0.2, 0.61 ± 0.1 and 1.0 ± 0.15 Sv corresponded to Atlantic Water (AW), Dense Atlantic Water (DAW), Barents Sea Branch Water (BSBW) and Transformed Atlantic Water (TAW). 62–70% of transport was constrained to within 30–40 km of the shelf edge, and beyond 84 km, transport increases were estimated to be 0.54 Sv. Seasonality of TAW derived from local shelf-processes and advection of seasonal-variable Fram Strait waters, while BSBW transport variability was dominated by temperature changes with maximum transport coinciding with minimum temperatures. Further Barents Sea warming will likely reduce TAW and BSBW transport leading to warmer conditions along the ABC pathway.
    Repository Name: EPIC Alfred Wegener Institut
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  • 28
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    Stable Barium Isotope Fractionation in Pore Waters of Estuarine Sediments (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Geochemistry, Geophysics, Geosystems, American Geophysical Union (AGU), 24(6), ISSN: 1525-2027
    Details
    Publication Date: 2023-06-01
    Repository Name: EPIC Alfred Wegener Institut
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  • 29
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    The Impact of Different Atmospheric CO2 Concentrations on Large Scale Miocene Temperature Signatures (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union (AGU), ISSN: 2572-4517
    Details
    Publication Date: 2023-02-03
    Repository Name: EPIC Alfred Wegener Institut
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  • 30
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    Moisture Sources and Pathways Determine Stable Isotope Signature of Himalayan Waters in Nepal (2023)
    American Geophysical Union (AGU)
    In:  EPIC3AGU Advances, American Geophysical Union (AGU), 4(1), ISSN: 2576-604X
    Details
    Publication Date: 2024-03-01
    Description: The Himalayan mountain range produces one of the steepest and largest rainfall gradients on Earth, with 〉3 m/yr rainfall difference over a ∼100 km distance. The Indian Summer Monsoon (ISM) contributes more than 80% to the annual precipitation budget of the central Himalayas. The remaining 20% falls mainly during pre-ISM season. Understanding the seasonal cycle and the transfer pathways of moisture from precipitation to the rivers is crucial for constraining water availability in a warming climate. However, the partitioning of moisture into the different storage systems such as snow, glacier, and groundwater and their relative contribution to river discharge throughout the year remains under-constrained. Here, we present novel field data from the Kali Gandaki, a trans-Himalayan river, and use 4-year time series of river and rain water stable isotope composition (δ18O and δ2H values) as well as river discharge, satellite Global Precipitation Measurement amounts, and moisture source trajectories to constrain hydrological variability. We find that rainfall before the onset of the ISM is isotopically distinct and that ISM rain and groundwater have similar isotopic values. Our study lays the groundwork for using isotopic measurements to track changes in precipitation sources during the pre-ISM to ISM transition in this key region of orographic precipitation. Specifically, we highlight the role of pre-ISM precipitation, derived from the Gangetic plain, to define the seasonal river isotopic variability across the central Himalayas. Lastly, isotopic values across the catchment document the importance of a large well-mixed groundwater reservoir supplying river discharge, especially during the non-ISM season.
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  • 31
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    Moisture Sources and Pathways Determine Stable Isotope Signature of Himalayan Waters in Nepal (2023)
    American Geophysical Union (AGU)
    In:  EPIC3AGU Advances, American Geophysical Union (AGU), 4(1), ISSN: 2576-604X
    Details
    Publication Date: 2024-03-01
    Description: The Himalayan mountain range produces one of the steepest and largest rainfall gradients on Earth, with 〉3 m/yr rainfall difference over a ∼100 km distance. The Indian Summer Monsoon (ISM) contributes more than 80% to the annual precipitation budget of the central Himalayas. The remaining 20% falls mainly during pre-ISM season. Understanding the seasonal cycle and the transfer pathways of moisture from precipitation to the rivers is crucial for constraining water availability in a warming climate. However, the partitioning of moisture into the different storage systems such as snow, glacier, and groundwater and their relative contribution to river discharge throughout the year remains under-constrained. Here, we present novel field data from the Kali Gandaki, a trans-Himalayan river, and use 4-year time series of river and rain water stable isotope composition (δ18O and δ2H values) as well as river discharge, satellite Global Precipitation Measurement amounts, and moisture source trajectories to constrain hydrological variability. We find that rainfall before the onset of the ISM is isotopically distinct and that ISM rain and groundwater have similar isotopic values. Our study lays the groundwork for using isotopic measurements to track changes in precipitation sources during the pre-ISM to ISM transition in this key region of orographic precipitation. Specifically, we highlight the role of pre-ISM precipitation, derived from the Gangetic plain, to define the seasonal river isotopic variability across the central Himalayas. Lastly, isotopic values across the catchment document the importance of a large well-mixed groundwater reservoir supplying river discharge, especially during the non-ISM season.
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  • 32
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    Quantifying Sub\xe2\x80\x90Seasonal Growth Rate Changes in Fossil Giant Clams Using Wavelet Transformation of Daily Mg/Ca Cycles (2023)
    American Geophysical Union (AGU)
    In:  Geochemistry, Geophysics, Geosystems vol. 24 no. 10
    Details
    Publication Date: 2024-02-08
    Description: Shells of the giant clam Tridacna can provide decade-long records of past environmental conditions via their geochemical composition and structurally through growth banding. Counting the daily bands can give an accurate internal age model with high temporal resolution, but daily banding is not always visually retrievable, especially in fossil specimens. We show that daily geochemical cycles (e.g., Mg/Ca) are resolvable via highly spatially resolved laser-ablation inductively coupled plasma mass spectrometry (LA-ICPMS; 3 \xc3\x97 33 \xce\xbcm laser slit) in our Miocene (\xe2\x88\xbc10 Ma) specimen, even in areas where daily banding is not visually discernible. By applying wavelet transformation on the measured daily geochemical cycles, we quantify varying daily growth rates throughout the shell. These growth rates are thus used to build an internal age model independent of optical daily band countability. Such an age model can be used to convert the measured elemental ratios from a function of distance to a function of time, which helps evaluate paleoenvironmental proxy data, for example, regarding the timing of sub-seasonal events. Furthermore, the quantification of daily growth rates across the shell facilitates the evaluation of (co)dependencies between growth rates and corresponding elemental compositions.
    Keywords: Tridacna
    Repository Name: National Museum of Natural History, Netherlands
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    Postdepositional Behavior of Molybdenum in Deep Sediments and Implications for Paleoredox Reconstruction (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(21), ISSN: 0094-8276
    Details
    Publication Date: 2023-11-01
    Description: Molybdenum (Mo) is a trace element sensitive to oceanic redox conditions. The fidelity of sedimentary Mo as a paleoredox proxy of coeval seawater depends on the extent of Mo remobilization during postdepositional processes. Here we present the Mo content and isotope profiles for deep sediments from the Nankai Trough, Japan. The Mo signature suggests that these sediments have experienced extensive early diagenesis and hydrothermal alteration at depth. Iron (Fe)‐manganese (Mn) (oxyhydr)oxide alteration combined with Mo thiolation leads to a more than twenty‐fold enrichment of Mo within the sulfate reduction zone. Hydrothermal fluids and Mo adsorption onto Fe‐Mn (oxyhydr)oxides cause extremely negative Mo‐isotope values at the underthrust zone. These postdepositional Mo signals might be misinterpreted as expanded anoxia in the water column. Our findings highlight the importance of constraining postdepositional effects on Mo‐based proxies during paleoredox reconstruction.
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    Cyclone Impacts on Sea Ice Concentration in the Atlantic Arctic Ocean: Annual Cycle and Recent Changes (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(17), ISSN: 0094-8276
    Details
    Publication Date: 2023-09-08
    Description: We quantify sea ice concentration (SIC) changes related to synoptic cyclones separately for each month of the year in the Greenland, Barents and Kara Seas for 1979–2018. We find that these SIC changes can be statistically significant throughout the year. However, their strength varies from region to region and month to month, and their sign strongly depends on the considered time scale (before/during vs. after cyclone passages). Our results show that the annual cycle of cyclone impacts on SIC is related to varying cyclone intensity and traversed sea ice conditions. We further show that significant changes in these cyclone impacts have manifested in the last 40 years, with the strongest changes occurring in October and November. For these months, SIC decreases before/during cyclones have more than doubled in magnitude in the Barents and Kara Seas, while SIC increases following cyclones have weakened (intensified) in the Barents Sea (Kara Sea).
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    An Assessment of CO2 Uptake in the Arctic Ocean From 1985 to 2018 (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Global Biogeochemical Cycles, American Geophysical Union (AGU), 37(11), ISSN: 0886-6236
    Details
    Publication Date: 2023-12-19
    Description: As a contribution to the Regional Carbon Cycle Assessment and Processes phase 2 (RECCAP2) project, we present synthesized estimates of Arctic Ocean sea-air CO2 fluxes and their uncertainties from surface ocean pCO2-observation products, ocean biogeochemical hindcast and data assimilation models, and atmospheric inversions. For the period of 1985–2018, the Arctic Ocean was a net sink of CO2 of 116 ± 4 TgC yr−1 in the pCO2 products, 92 ± 30 TgC yr−1 in the models, and 91 ± 21 TgC yr−1 in the atmospheric inversions. The CO2 uptake peaks in late summer and early autumn, and is low in winter when sea ice inhibits sea-air fluxes. The long-term mean CO2 uptake in the Arctic Ocean is primarily caused by steady-state fluxes of natural carbon (70% ± 15%), and enhanced by the atmospheric CO2 increase (19% ± 5%) and climate change (11% ± 18%). The annual mean CO2 uptake increased from 1985 to 2018 at a rate of 31 ± 13 TgC yr−1 dec−1 in the pCO2 products, 10 ± 4 TgC yr−1 dec−1 in the models, and 32 ± 16 TgC yr−1 dec−1 in the atmospheric inversions. Moreover, 77% ± 38% of the trend in the net CO2 uptake over time is caused by climate change, primarily due to rapid sea ice loss in recent years. Furthermore, true uncertainties may be larger than the given ensemble standard deviations due to common structural biases across all individual estimates.
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    Seasonal Variability of the Surface Ocean Carbon Cycle: A Synthesis (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Global Biogeochemical Cycles, American Geophysical Union (AGU), 37(9), ISSN: 0886-6236
    Details
    Publication Date: 2024-01-06
    Description: The seasonal cycle is the dominant mode of variability in the air-sea CO2 flux in most regions of the global ocean, yet discrepancies between different seasonality estimates are rather large. As part of the Regional Carbon Cycle Assessment and Processes Phase 2 project (RECCAP2), we synthesize surface ocean pCO2 and air-sea CO2 flux seasonality from models and observation-based estimates, focusing on both a present-day climatology and decadal changes between the 1980s and 2010s. Four main findings emerge: First, global ocean biogeochemistry models (GOBMs) and observation-based estimates (pCO2 products) of surface pCO2 seasonality disagree in amplitude and phase, primarily due to discrepancies in the seasonal variability in surface DIC. Second, the seasonal cycle in pCO2 has increased in amplitude over the last three decades in both pCO2 products and GOBMs. Third, decadal increases in pCO2 seasonal cycle amplitudes in subtropical biomes for both pCO2 products and GOBMs are driven by increasing DIC concentrations stemming from the uptake of anthropogenic CO2 (Cant). In subpolar and Southern Ocean biomes, however, the seasonality change for GOBMs is dominated by Cant invasion, whereas for pCO2 products an indeterminate combination of Cant invasion and climate change modulates the changes. Fourth, biome-aggregated decadal changes in the amplitude of pCO2 seasonal variability are largely detectable against both mapping uncertainty (reducible) and natural variability uncertainty (irreducible), but not at the gridpoint scale over much of the northern subpolar oceans and over the Southern Ocean, underscoring the importance of sustained high-quality seasonally resolved measurements over these regions.
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  • 37
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    Magnitude, Trends, and Variability of the Global Ocean Carbon Sink From 1985 to 2018 (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Global Biogeochemical Cycles, American Geophysical Union (AGU), 37(10), ISSN: 0886-6236
    Details
    Publication Date: 2024-01-06
    Description: This contribution to the RECCAP2 (REgional Carbon Cycle Assessment and Processes) assessment analyzes the processes that determine the global ocean carbon sink, and its trends and variability over the period 1985–2018, using a combination of models and observation-based products. The mean sea-air CO2 flux from 1985 to 2018 is −1.6 ± 0.2 PgC yr−1 based on an ensemble of reconstructions of the history of sea surface pCO2 (pCO2 products). Models indicate that the dominant component of this flux is the net oceanic uptake of anthropogenic CO2, which is estimated at −2.1 ± 0.3 PgC yr−1 by an ensemble of ocean biogeochemical models, and −2.4 ± 0.1 PgC yr−1 by two ocean circulation inverse models. The ocean also degasses about 0.65 ± 0.3 PgC yr−1 of terrestrially derived CO2, but this process is not fully resolved by any of the models used here. From 2001 to 2018, the pCO2 products reconstruct a trend in the ocean carbon sink of −0.61 ± 0.12 PgC yr−1 decade−1, while biogeochemical models and inverse models diagnose an anthropogenic CO2-driven trend of −0.34 ± 0.06 and −0.41 ± 0.03 PgC yr−1 decade−1, respectively. This implies a climate-forced acceleration of the ocean carbon sink in recent decades, but there are still large uncertainties on the magnitude and cause of this trend. The interannual to decadal variability of the global carbon sink is mainly driven by climate variability, with the climate-driven variability exceeding the CO2-forced variability by 2–3 times. These results suggest that anthropogenic CO2 dominates the ocean CO2 sink, while climate-driven variability is potentially large but highly uncertain and not consistently captured across different methods.
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  • 38
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    The Southern Ocean Carbon Cycle 1985–2018: Mean, Seasonal Cycle, Trends, and Storage (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Global Biogeochemical Cycles, American Geophysical Union (AGU), 37(11), ISSN: 0886-6236
    Details
    Publication Date: 2023-12-20
    Description: We assess the Southern Ocean CO2 uptake (1985–2018) using data sets gathered in the REgional Carbon Cycle Assessment and Processes Project Phase 2. The Southern Ocean acted as a sink for CO2 with close agreement between simulation results from global ocean biogeochemistry models (GOBMs, 0.75 ± 0.28 PgC yr−1) and pCO2-observation-based products (0.73 ± 0.07 PgC yr−1). This sink is only half that reported by RECCAP1 for the same region and timeframe. The present-day net uptake is to first order a response to rising atmospheric CO2, driving large amounts of anthropogenic CO2 (Cant) into the ocean, thereby overcompensating the loss of natural CO2 to the atmosphere. An apparent knowledge gap is the increase of the sink since 2000, with pCO2-products suggesting a growth that is more than twice as strong and uncertain as that of GOBMs (0.26 ± 0.06 and 0.11 ± 0.03 Pg C yr−1 decade−1, respectively). This is despite nearly identical pCO2 trends in GOBMs and pCO2-products when both products are compared only at the locations where pCO2 was measured. Seasonal analyses revealed agreement in driving processes in winter with uncertainty in the magnitude of outgassing, whereas discrepancies are more fundamental in summer, when GOBMs exhibit difficulties in simulating the effects of the non-thermal processes of biology and mixing/circulation. Ocean interior accumulation of Cant points to an underestimate of Cant uptake and storage in GOBMs. Future work needs to link surface fluxes and interior ocean transport, build long overdue systematic observation networks and push toward better process understanding of drivers of the carbon cycle.
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  • 39
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    Structure and Seasonal Variability of the Arctic Boundary Current North of Severnaya Zemlya (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research - Oceans, American Geophysical Union (AGU), 128(1), ISSN: 2169-9275
    Details
    Publication Date: 2024-01-31
    Description: We assessed the spatial and temporal variability of the Arctic Boundary Current (ABC) using seven oceanographic moorings, deployed across the continental slope north of Severnaya Zemlya in 2015–2018. Transports and individual water masses were quantified based on temperature and salinity recorders and current profilers. Our results were compared with observations from the northeast Svalbard and the central Laptev Sea continental slopes to evaluate the hydrographic transformation along the ABC pathway. The highest velocities (〉0.30 m s−1) of the ABC occurred at the upper continental slope and decreased offshore to below 0.03 m s−1 in the deep basin. The ABC showed seasonal variability with velocities two times higher in winter than in summer. Compared to upstream conditions in Svalbard, water mass distribution changed significantly within 20 km of the shelf edge due to mixing with- and intrusion of shelf waters. The ABC transported 4.15 ± 0.3 Sv in the depth range 50–1,000 m, where 0.88 ± 0.1, 1.5 ± 0.2, 0.61 ± 0.1 and 1.0 ± 0.15 Sv corresponded to Atlantic Water (AW), Dense Atlantic Water (DAW), Barents Sea Branch Water (BSBW) and Transformed Atlantic Water (TAW). 62–70% of transport was constrained to within 30–40 km of the shelf edge, and beyond 84 km, transport increases were estimated to be 0.54 Sv. Seasonality of TAW derived from local shelf-processes and advection of seasonal-variable Fram Strait waters, while BSBW transport variability was dominated by temperature changes with maximum transport coinciding with minimum temperatures. Further Barents Sea warming will likely reduce TAW and BSBW transport leading to warmer conditions along the ABC pathway.
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  • 40
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    On the polar bias in ice core 10Be data (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Atmospheres, American Geophysical Union (AGU), ISSN: 2169-897X
    Details
    Publication Date: 2024-01-22
    Repository Name: EPIC Alfred Wegener Institut
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  • 41
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    Local Seismicity and Sediment Deformation in the West Svalbard Margin: Implications of Neotectonics for Seafloor Seepage (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Geochemistry Geophysics Geosystems, American Geophysical Union (AGU), 24(12), ISSN: 1525-2027
    Details
    Publication Date: 2024-01-22
    Description: In the Fram Strait, mid-ocean ridge spreading is represented by the ultra-slow system of the Molloy Ridge, the Molloy Transform Fault and the Knipovich Ridge. Sediments on oceanic and continental crust are gas charged and there are several locations with documented seafloor seepage. Sedimentary faulting shows recent stress release in the sub-surface, but the drivers of stress change and its influence on fluid flow are not entirely understood. We present here the results of an 11-month-long ocean bottom seismometer survey conducted over the highly faulted sediment drift northwards from the Knipovich Ridge to monitor seismicity and infer the regional state of stress. We obtain a detailed earthquake catalog that improves the spatial resolution of mid-ocean ridge seismicity compared with published data. Seismicity at the Molloy Transform Fault is occurring southwards from the bathymetric imprint of the fault, as supported by a seismic profile. Earthquakes in the northern termination of the Knipovich Ridge extend eastwards from the ridge valley, which together with syn-rift faulting identified in seismic reflection data, suggests that a portion of the currently active spreading center is buried under sediments away from the bathymetric expression of the rift valley. This hints at the direct link between crustal rifting processes and faulting in shallow sediments. Two earthquakes occur close to the seepage system of the Vestnesa Ridge further north from the network. We suggest that deeper rift structures, reactivated by gravity and/or post-glacial subsidence, may lead to accommodation of stress through shallow extensional faults, therefore impacting seepage dynamics.
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  • 42
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    Assessing Seasonal and Inter‐Annual Marine Sediment Climate Proxy Data (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union (AGU), 38(10), ISSN: 2572-4517
    Details
    Publication Date: 2024-03-13
    Description: Three recently published papers including Napier et al. (2022, https://doi.org/10.1029/2021PA004355) utilize novel microanalytical approaches with varved marine sediments to demonstrate the potential to reconstruct seasonal and inter-annual climate variability. Obtaining paleoclimate data at a resolution akin to the observational record is vitally important for improving our understanding of climate phenomena such as monsoons and modes of variability such as the El Niño Southern Oscillation, for which appraisals of past inter-annual variability is critical. The ability to generate seasonal and inter annual resolution sea surface temperature proxy time series spanning a thousand years or more is revolutionary and has the potential to fill gaps in our knowledge of climate variability. Although generally limited to sediments from regions with oxygen depleted bottom waters, there is great potential to integrate shorter seasonal resolution climate “snap shots” from other archives such as annually banded corals into composite time series. But as paleoceanographic data are used more by the observational and modeling fields, we make the case for conducting a thorough case-by-case assessment of the processes that influence the climate signal recovered from proxies, using careful replication to validate new approaches. Understanding or exploring the potential influence of processes which effectively filter the climate signal will lead to more quantitative paleoceanographic data that will better serve the broader climate science community.
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  • 43
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    Implications of Snowpack Reactive Bromine Production for Arctic Ice Core Bromine Preservation (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Atmospheres, American Geophysical Union (AGU), 128(20), ISSN: 2169-897X
    Details
    Publication Date: 2024-03-21
    Description: Snowpack emissions are recognized as an important source of gas-phase reactive bromine in the Arctic and are necessary to explain ozone depletion events in spring caused by the catalytic destruction of ozone by halogen radicals. Quantifying bromine emissions from snowpack is essential for interpretation of ice-core bromine. We present ice-core bromine records since the pre-industrial (1750 CE) from six Arctic locations and examine potential post-depositional loss of snowpack bromine using a global chemical transport model. Trend analysis of the ice-core records shows that only the high-latitude coastal Akademii Nauk (AN) ice core from the Russian Arctic preserves significant trends since pre-industrial times that are consistent with trends in sea ice extent and anthropogenic emissions from source regions. Model simulations suggest that recycling of reactive bromine on the snow skin layer (top 1 mm) results in 9–17% loss of deposited bromine across all six ice-core locations. Reactive bromine production from below the snow skin layer and within the snow photic zone is potentially more important, but the magnitude of this source is uncertain. Model simulations suggest that the AN core is most likely to preserve an atmospheric signal compared to five Greenland ice cores due to its high latitude location combined with a relatively high snow accumulation rate. Understanding the sources and amount of photochemically reactive snow bromide in the snow photic zone throughout the sunlit period in the high Arctic is essential for interpreting ice-core bromine, and warrants further lab studies and field observations at inland locations.
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  • 44
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    The Subglacial Lake That Wasn't There: Improved Interpretation From Seismic Data Reveals a Sediment Bedform at Isunnguata Sermia (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Earth Surface, American Geophysical Union (AGU), 128(10), ISSN: 2169-9003
    Details
    Publication Date: 2024-03-14
    Description: Radio Echo Sounding (RES) surveys conducted in May 2010 and April 2011 revealed a 2 km2 flat area with increased bed reflectivity at the base of Isunnguata Sermia at the western margin of the Greenland Ice Sheet. This flat reflector was located within a localized subglacial hydraulic potential (hydropotential) minimum, as part of a complex and elongated trough system. By analogy with comparable features in Antarctica, the initial interpretation of such a feature was a potential subglacial lake. In September 2013 a co-located seismic survey revealed a 1,750 m by 540 and 37 m thick stratified lens-shaped bedform at the base of a subglacial trough system. Amplitude Versus Angle (AVA) analysis yields a derived reflection coefficient R = 0.09 ± 0.14 indicative of consolidated sediments possibly overlain by dilatant till. The bed and flank on the northern side of the trough consist of unconsolidated, possibly water-bearing sediments with R = −0.10 ± 0.08, whereas on the southern side it consists of more consolidated material. We interpret the trough as a key component of the wider subglacial drainage network, for which the sediments on its northern side act as a localized water-storage reservoir. Given the observation of seasonally forming and rapidly draining supraglacial meltwater lakes in this area, we interpret the lens-shaped bedform as deposited by episodically ponding meltwater within the subglacial trough system. Our results highlight the importance of transient subglacial hydrological and sedimentological processes such as drainage events for the interaction of ice sheets and their substrates, to understand ice dynamics in a warming climate.
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  • 45
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    Nitrous Oxide Fluxes in Permafrost Peatlands Remain Negligible After Wildfire and Thermokarst Disturbance (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Biogeosciences, American Geophysical Union (AGU), 128(4), ISSN: 2169-8953
    Details
    Publication Date: 2024-04-19
    Description: The greenhouse gas (GHG) balance of boreal peatlands in permafrost regions will be affected by climate change through disturbances such as permafrost thaw and wildfire. Although the future GHG balance of boreal peatlands including ponds is dominated by the exchange of both carbon dioxide (CO2) and methane (CH4), disturbance impacts on fluxes of the potent GHG nitrous oxide (N2O) could contribute to shifts in the net radiative balance. Here, we measured monthly (April to October) fluxes of N2O, CH4, and CO2 from three sites located across the sporadic and discontinuous permafrost zones of western Canada. Undisturbed permafrost peat plateaus acted as N2O sinks (−0.025 mg N2O m−2 d−1), but N2O uptake was lower from burned plateaus (−0.003 mg N2O m−2 d−1) and higher following permafrost thaw in the thermokarst bogs (−0.054 mg N2O m−2 d−1). The thermokarst bogs had below-ambient N2O soil gas concentrations, suggesting that denitrification consumed atmospheric N2O during reduction to dinitrogen. Atmospheric uptake of N2O in peat plateaus and thermokarst bogs increased with soil temperature and soil moisture, suggesting sensitivity of N2O consumption to further climate change. Four of five peatland ponds acted as N2O sinks (−0.018 mg N2O m−2 d−1), with no influence of thermokarst expansion. One pond with high nitrate concentrations had high N2O emissions (0.30 mg N2O m−2 d−1). Overall, our study suggests that the future net radiative balance of boreal peatlands will be dominated by impacts of wildfire and permafrost thaw on CH4 and CO2 fluxes, while the influence from N2O is minor.
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  • 46
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    Anthropogenic Perturbations Change the Quality and Quantity of Terrestrial Carbon Flux to the Coastal Ocean (2023)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Biogeosciences, American Geophysical Union (AGU), 128(10), ISSN: 2169-8953
    Details
    Publication Date: 2024-04-11
    Description: Human activities have increasingly changed terrestrial particulate organic carbon (POC) export to the coastal ocean since the Industrial Age (19th century). However, the influence of human perturbations on the composition and flux of terrestrial biospheric and petrogenic POC sub-pools remains poorly constrained. Here, we examined 13C and 14C compositions of bulk POC and source-specific biomarkers (fatty acids, FA) from two nearshore sediment cores collected in the Pearl River-derived mudbelt, to determine the impacts of human perturbations of the Pearl River watershed on the burial of terrestrial POC in the coastal ocean over the last century. Our results show that although agricultural practices and deforestation during the 1930s–1950s increased C4 plant coverage in the watershed, the export fluxes of terrestrial biospheric and petrogenic POC remained rather unchanged; however, added perturbations since 1974, including increasing coal consumption, embankment and dam constructions caused massive export of both petrogenic POC and relatively fresh terrestrial biospheric POC from the river delta. Our data reveal that human activities substantially enhance the transfer of petrogenic POC and fresh biospheric POC to the coastal ocean after ca. 1974, with the latter process acting as an important sink for anthropogenic CO2.
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  • 47
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    Arctic Ocean Freshwater in CMIP6 Coupled Models (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Earth's Future, American Geophysical Union (AGU), 10(9), ISSN: 2328-4277
    Details
    Publication Date: 2022-11-06
    Description: In this study we assessed the representation of the sea surface salinity (SSS) and liquid freshwater content (LFWC) of the Arctic Ocean in the historical simulation of 31 CMIP6 models with comparison to 39 Coupled Model Intercomparison Project phase 5 (CMIP5) models, and investigated the projected changes in Arctic liquid and solid freshwater content and freshwater budget in scenarios with two different shared socioeconomic pathways (SSP2-4.5 and SSP5-8.5). No significant improvement was found in the SSS and LFWC simulation from CMIP5 to CMIP6, given the large model spreads in both CMIP phases. The overestimation of LFWC continues to be a common bias in CMIP6. In the historical simulation, the multi-model mean river runoff, net precipitation, Bering Strait and Barents Sea Opening (BSO) freshwater transports are 2,928 ± 1,068, 1,839 ± 3,424, 2,538 ± 1,009, and −636 ± 553 km3/year, respectively. In the last decade of the 21st century, CMIP6 MMM projects these budget terms to rise to 4,346 ± 1,484 km3/year (3,678 ± 1,255 km3/year), 3,866 ± 2,935 km3/year (3,145 ± 2,651 km3/year), 2,631 ± 1,119 km3/year (2,649 ± 1,141 km3/year) and 1,033 ± 1,496 km3/year (449 ± 1,222 km3/year) under SSP5-8.5 (SSP2-4.5). Arctic sea ice is expected to continue declining in the future, and sea ice meltwater flux is likely to decrease to about zero in the mid-21st century under both SSP2-4.5 and SSP5-8.5 scenarios. Liquid freshwater exiting Fram and Davis straits will be higher in the future, and the Fram Strait export will remain larger. The Arctic Ocean is projected to hold a total of 160,300 ± 62,330 km3 (141,590 ± 50,310 km3) liquid freshwater under SSP5-8.5 (SSP2-4.5) by 2100, about 60% (40%) more than its historical climatology.
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  • 48
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    The Role of Zooplankton Grazing and Nutrient Recycling for Global Ocean Biogeochemistry and Phytoplankton Phenology (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Biogeosciences, American Geophysical Union (AGU), 127(10), ISSN: 2169-8953
    Details
    Publication Date: 2023-06-21
    Description: Zooplankton plays a notable role in ocean biogeochemical cycles. However, it is often simulated as one generic group and top closure term in ocean biogeochemical models. This study presents the description of three zooplankton functional types (zPFTs, micro-, meso- and macrozooplankton) in the ocean biogeochemical model FESOM-REcoM. In the presented model, microzooplankton is a fast-growing herbivore group, mesozooplankton is another major consumer of phytoplankton, and macrozooplankton is a slow-growing group with a low temperature optimum. Meso- and macrozooplankton produce fast-sinking fecal pellets. With three zPFTs, the annual mean zooplankton biomass increases threefold to 210 Tg C. The new food web structure leads to a 25% increase in net primary production and a 10% decrease in export production globally. Consequently, the export ratio decreases from 17% to 12% in the model. The description of three zPFTs reduces model mismatches with observed dissolved inorganic nitrogen and chlorophyll concentrations in the South Pacific and the Arctic Ocean, respectively. Representation of three zPFTs also strongly affects phytoplankton phenology: Fast nutrient recycling by zooplankton sustains higher chlorophyll concentrations in summer and autumn. Additional zooplankton grazing delays the start of the phytoplankton bloom by 3 weeks and controls the magnitude of the bloom peak in the Southern Ocean. As a result, the system switches from a light-controlled Sverdrup system to a dilution-controlled Behrenfeld system. Overall, the results suggest that representation of multiple zPFTs is important to capture underlying processes that may shape the response of ecosystems and ecosystem services to on-going and future environmental change in model projections.
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  • 49
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    Sea‐Ice Forecasts With an Upgraded AWI Coupled Prediction System (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Advances in Modeling Earth Systems, American Geophysical Union (AGU), 14(12), ISSN: 1942-2466
    Details
    Publication Date: 2023-06-23
    Description: A new version of the AWI Coupled Prediction System is developed based on the Alfred Wegener Institute Climate Model v3.0. Both the ocean and the atmosphere models are upgraded or replaced, reducing the computation time by a factor of 5 at a given resolution. This allowed us to increase the ensemble size from 12 to 30, maintaining a similar resolution in both model components. The online coupled data assimilation scheme now additionally utilizes sea-surface salinity and sea-level anomaly as well as temperature and salinity profile observations. Results from the data assimilation demonstrate that the sea-ice and ocean states are reasonably constrained. In particular, the temperature and salinity profile assimilation has mitigated systematic errors in the deeper ocean, although issues remain over polar regions where strong atmosphere-ocean-ice interaction occurs. One-year-long sea-ice forecasts initialized on 1 January, 1 April, 1 July and 1 October from 2003 to 2019 are described. To correct systematic forecast errors, sea-ice concentration from 2011 to 2019 is calibrated by trend-adjusted quantile mapping using the preceding forecasts from 2003 to 2010. The sea-ice edge raw forecast skill is within the range of operational global subseasonal-to-seasonal forecast systems, outperforming a climatological benchmark for about 2 weeks in the Arctic and about 3 weeks in the Antarctic. The calibration is much more effective in the Arctic: Calibrated sea-ice edge forecasts outperform climatology for about 45 days in the Arctic but only 27 days in the Antarctic. Both the raw and the calibrated forecast skill exhibit strong seasonal variations.
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  • 50
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    New Insights Into Cyclone Impacts on Sea Ice in the Atlantic Sector of the Arctic Ocean in Winter (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 49(22), ISSN: 0094-8276
    Details
    Publication Date: 2023-06-21
    Description: Based on the ERA5 reanalysis, we report on statistically significant impacts of transient cyclones on sea ice concentration (SIC) in the Atlantic sector of the Arctic Ocean in winter under “New Arctic” conditions (2000–2020). This includes a pattern of reduced SIC prior to and during cyclones for the whole study domain, while a regional difference between increased SIC in the Barents Sea and reduced SIC in the Greenland Sea is found as the net effect from 3 days prior to 5 days after the cyclone passage. Generally, locally low to medium SIC conditions combined with intense cyclones drive highest SIC changes. There are indications that both thermodynamic and dynamic effects contribute to the SIC changes, but a detailed quantification is required in future research. We provide evidence that cyclone impacts on SIC have amplified compared to the “Old Arctic” (1979–1999), particularly in the Barents Sea.
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  • 51
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    A Modeling Perspective on the Lingering Glacial Sea Surface Temperature Conundrum (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 49(23), ISSN: 0094-8276
    Details
    Publication Date: 2023-09-19
    Description: The strong cooling during the Last Glacial Maximum (LGM, 21 ka BP) provides a rigorous test of climate models' ability to simulate past and future climate changes. We force an atmospheric general circulation model with two recent global LGM sea surface temperature (SST) reconstructions, one suggesting a weak and the other a more pronounced cooling, and compare the simulated land surface temperatures (LSTs) to reconstructed data. Our results do not confirm either SST reconstruction. The cold SST data set leads to good agreement between simulated and observed LSTs at low latitudes, but is systematically too cold at mid-latitudes. The opposite is true for the warm SST data set. Differences between the simulated LSTs are caused by varying land surface albedos, which is lower for the warmer SST reconstruction. The inconsistency between reconstructed and simulated climate points to a potentially significant bias in the proxy reconstructions and/or the climate sensitivity of current climate models.
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  • 52
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    Isotopic Characterization of Water Masses in the Southeast Pacific Region: Paleoceanographic Implications (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research - Oceans, American Geophysical Union (AGU), 127(1), ISSN: 2169-9275
    Details
    Publication Date: 2024-01-31
    Description: In this study, we used stable isotopes of oxygen (δ18O), deuterium (δD), and dissolved inorganic carbon (δ13CDIC) in combination with temperature, salinity, oxygen, and nutrient concentrations to characterize the coastal (71°–78°W) and an oceanic (82°–98°W) water masses (SAAW—Subantarctic Surface Water; STW—Subtropical Water; ESSW—Equatorial Subsurface water; AAIW—Antarctic Intermediate Water; PDW—Pacific Deep Water) of the Southeast Pacific (SEP). The results show that δ18O and δD can be used to differentiate between SAAW-STW, SAAW-ESSW, and ESSW-AAIW. δ13CDIC signatures can be used to differentiate between STW-ESSW (oceanic section), SAAW-ESSW, ESSW-AAIW, and AAIW-PDW. Compared with the oceanic section, our new coastal section highlights differences in both the chemistry and geometry of water masses above 1,000 m. Previous paleoceanographic studies using marine sediments from the SEP continental margin used the present-day hydrological oceanic transect to compare against, as the coastal section was not sufficiently characterized. We suggest that our new results of the coastal section should be used for past characterizations of the SEP water masses that are usually based on continental margin sediment samples.
    Repository Name: EPIC Alfred Wegener Institut
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    Intensification of the East Australian Current After ∼1400 CE (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 49(24), ISSN: 0094-8276
    Details
    Publication Date: 2024-03-13
    Description: The East Australian Current (EAC) is the western boundary current of the South Pacific Subtropical Gyre that transports warm tropical waters to higher southern latitudes and significantly impacts the climate of Australia and New Zealand. Modern observations show that the EAC has strengthened with rising global temperatures. However, little is known about the pre-industrial variability of the EAC and the forcing mechanisms. Planktic foraminifera Globigerinoides ruber (white) Mg/Ca-based sea surface temperature reconstructions offshore northeastern Australia between 15° and 26°S reveal an increase by ∼1.2°C after ∼1400 CE. We infer that the increase in temperature is related to a stronger EAC heat transport that is likely driven by a strengthening of the Southern Hemisphere subtropical gyre circulation due to a progressive shift of the Southern annular mode toward its positive phase and of El Niño-Southern Oscillation toward more El Niño-like conditions.
    Repository Name: EPIC Alfred Wegener Institut
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    Presence, Sources and Transport of Polycyclic Aromatic Hydrocarbons in the Arctic Ocean (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 50(1), ISSN: 0094-8276
    Details
    Publication Date: 2024-03-28
    Repository Name: EPIC Alfred Wegener Institut
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    Atmosphere‐Snow Exchange Explains Surface Snow Isotope Variability (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 49(20), pp. e2022gl099529-e2022gl099529, ISSN: 0094-8276
    Details
    Publication Date: 2024-03-14
    Description: The climate signal imprinted in the snow isotopic composition allows to infer past climate variability from ice core stable water isotope records. The concurrent evolution of vapor and surface snow isotopic composition between precipitation events indicates that post-depositional atmosphere-snow humidity exchange influences the snow and hence the ice core isotope signal. To date, however, this is not accounted for in paeleoclimate reconstructions from isotope records. Here we show that vapor-snow exchange explains 36% of the summertime day-to-day δ18O variability of the surface snow between precipitation events, and 53% of the δD variability. Through observations from the Greenland Ice Sheet and accompanying modeling we demonstrate that vapor-snow exchange introduces a warm bias on the summertime snow isotope value relevant for ice core records. In case of long-term variability in atmosphere-snow exchange the relevance for the ice core signal is also variable and thus paleoclimate reconstructions from isotope records should be revisited.
    Repository Name: EPIC Alfred Wegener Institut
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    Interdecadal Pacific Oscillation in Northern Greenland Dust Concentration Variability During the Last 400 Years (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 49(24), ISSN: 0094-8276
    Details
    Publication Date: 2024-04-22
    Description: Statistical analysis of reanalysis and observed data reveals that high dust surface mass concentration in northern Greenland is associated with a Pacific Decadal Oscillation like pattern in its negative phase in the North Pacific as well as with La Niña conditions in the tropical Pacific region. The sea surface temperature anomalies in the Pacific realm resemble the Interdecadal Pacific Oscillation (IPO). The associated atmospheric circulation pattern, in the form of a wave-train from the North Pacific to the Eurasian continent, favors enhanced dust uptake and transport toward the northern Greenland. Similar patterns are associated with a low-resolution stacked record of five Ca2+ ice cores, that is, ngt03C93.2 (B16), ngt14C93.2 (B18), ngt27C94.2 (B21), GISP2−B, and NEEM-2011-S1, from northern Greenland, a proxy for regional dust concentration, during the last 400 years. We argue that northern Greenland ice core dust records could be used as proxies for the IPO and related teleconnections.
    Repository Name: EPIC Alfred Wegener Institut
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    Reversals in Temperature‐Precipitation Correlations in the Northern Hemisphere Extratropics During the Holocene (2022)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 49(22), ISSN: 0094-8276
    Details
    Publication Date: 2024-04-23
    Description: Future precipitation levels remain uncertain because climate models have struggled to reproduce observed variations in temperature-precipitation correlations. Our analyses of Holocene proxy-based temperature-precipitation correlations and hydrological sensitivities from 2,237 Northern Hemisphere extratropical pollen records reveal a significant latitudinal dependence and temporal variations among the early, middle, and late Holocene. These proxy-based variations are largely consistent with patterns obtained from transient climate simulations (TraCE21k). While high latitudes and subtropical monsoon areas show mainly stable positive correlations throughout the Holocene, the mid-latitude pattern is temporally and spatially more variable. In particular, we identified a reversal from positive to negative temperature-precipitation correlations in the eastern North American and European mid-latitudes from the early to mid-Holocene that mainly related to slowed down westerlies and a switch to moisture-limited convection under a warm climate. Our palaeoevidence of past temperature-precipitation correlation shifts identifies those regions where simulating past and future precipitation levels might be particularly challenging.
    Repository Name: EPIC Alfred Wegener Institut
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    On the Damping Time Scale of EVP Sea Ice Dynamics (2021)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Advances in Modeling Earth Systems, American Geophysical Union (AGU), 13(10), ISSN: 1942-2466
    Details
    Publication Date: 2023-06-21
    Description: We propose to make the damping time scale, which governs the decay of pseudo-elastic waves in the Elastic Viscous Plastic (EVP) sea-ice solvers, independent of the external time step and large enough to warrant numerical stability for a moderate number of internal time steps. A necessary condition is that the forcing on sea ice varies slowly on the damping time scale, in which case an EVP solution may still approach a Viscous Plastic one, but on a time scale longer than a single external time step. In this case, the EVP method becomes very close to the recently proposed modified EVP (mEVP) method in terms of stability and simulated behavior. In a simple test case dealing with sea ice breaking under the forcing of a moving cyclone, the EVP method with an enlarged damping time scale can simulate linear kinematic features which are very similar to those from the traditional EVP implementation, although a much smaller number of internal time steps is used. There is more difference in sea-ice thickness and linear kinematic features simulated in a realistic Arctic configuration between using the traditional and our suggested choices of EVP damping time scales, but it is minor considering model uncertainties associated with choices of many other parameters in sea-ice models.
    Repository Name: EPIC Alfred Wegener Institut
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    Counteracting Contributions of the Upper and Lower Meridional Overturning Limbs to the North Atlantic Nutrient Budgets: Enhanced Imbalance in 2010 (2021)
    American Geophysical Union (AGU)
    In:  EPIC3Global Biogeochemical Cycles, American Geophysical Union (AGU), 35(6), ISSN: 0886-6236
    Details
    Publication Date: 2024-01-18
    Description: The North Atlantic Basin is a major sink for atmospheric carbon dioxide (CO2) due in part to the extensive plankton blooms which form there supported by nutrients supplied by the three-dimensional ocean circulation. Hence, changes in ocean circulation and/or stratification may influence primary production and biological carbon export. In this study, we assess this possibility by evaluating inorganic nutrient budgets for 2004 and 2010 in the North Atlantic based on observations from the transatlantic A05-24.5°N and the Greenland-Portugal OVIDE hydrographic sections, to which we applied a box inverse model to solve the circulation and estimate the across-section nutrient transports. Full water column nutrient budgets were split into upper and lower meridional overturning circulation (MOC) limbs. According to our results, anomalous circulation in early 2010, linked to extreme negative NAO conditions, led to an enhanced northward advection of more nutrient-rich waters by the upper overturning limb, which resulted in a significant nitrate and phosphate convergence north of 24.5°N. Combined with heaving of the isopycnals, this anomalous circulation event in 2010 favored an enhancement of the nutrient consumption (5.7 ± 4.1 kmol-P s−1) and associated biological CO2 uptake (0.25 ± 0.18 Pg-C yr−1, upper-bound estimate), which represents a 50% of the mean annual sea–air CO2 flux in the region. Our results also suggest a transient state of deep silicate divergence in both years. Both results are indicative of a MOC-driven modulation of the biological carbon uptake (by the upper MOC limb) and nutrient inventories (by the lower MOC limb) in the North Atlantic.
    Repository Name: EPIC Alfred Wegener Institut
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    Clouds and Radiation Processes in Regional Climate Models Evaluated Using Observations Over the Ice‐free Arctic Ocean (2021)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Atmospheres, American Geophysical Union (AGU), 126(1), ISSN: 2169-897X
    Details
    Publication Date: 2024-03-14
    Description: The presence of clouds in the Arctic regulates the surface energy budget (SEB) over the sea-ice surface and the ice-free ocean. Following several previous field campaigns, the cloud-radiation relationship, including cloud vertical structure and phase, has been elucidated; however, modeling of this relationship has matured slowly. In recognition of the recent decline in the Arctic sea-ice extent, representation of the cloud system in numerical models should consider the effects of areas covered by sea ice and ice-free areas. Using an in situ stationary meteorological observation data set obtained over the ice-free Arctic Ocean by the Japanese Research Vessel Mirai (September 2014), coordinated evaluation of six regional climate models (RCMs) with nine model runs was performed by focusing on clouds and the SEB. The most remarkable findings were as follows: (1) reduced occurrence of unstable stratification with low-level cloud water in all models in comparison to the observations, (2) significant differences in cloud water representations between single- and double-moment cloud schemes, (3) extensive differences in partitioning of hydrometeors including solid/liquid precipitation, and (4) pronounced lower-tropospheric air temperature biases. These issues are considered as the main sources of SEB uncertainty over ice-free areas of the Arctic Ocean. The results from a coupled RCM imply that the SEB is constrained by both the atmosphere and the ocean (and sea ice) with considerable feedback. Coordinated improvement of both stand-alone atmospheric and coupled RCMs would promote a more comprehensive and improved understanding of the Arctic air-ice-sea coupled system.
    Repository Name: EPIC Alfred Wegener Institut
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    Bedforms of Thwaites Glacier, West Antarctica: Character and Origin (2021)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Earth Surface, American Geophysical Union (AGU), 126(12), ISSN: 2169-9003
    Details
    Publication Date: 2024-03-14
    Description: Bedforms of Thwaites Glacier, West Antarctica both record and affect ice flow, as shown by geophysical data and simple models. Thwaites Glacier flows across the tectonic fabric of the West Antarctic rift system with its bedrock highs and sedimentary basins. Swath radar and seismic surveys of the glacier bed have revealed soft-sediment flutes 100 m or more high extending 15 km or more across basins downglacier from bedrock highs. Flutes end at prominent hard-bedded moats on stoss sides of the next topographic highs. We use simple models to show that ice flow against topography increases pressure between ice and till upglacier along the bed over a distance that scales with the topography. In this basal zone of high pressure, ice-contact water would be excluded, thus increasing basal drag by increasing ice-till coupling and till flux, removing till to allow bedrock erosion that creates moats. Till carried across highlands would then be deposited in lee-side positions forming bedforms that prograde downglacier over time, and that remain soft on top through feedbacks that match till-deformational fluxes from well upglacier of the topography. The bedforms of the part of Thwaites surveyed here are prominent because ice flow has persisted over a long time on this geological setting, not because ice flow is anomalous. Bedform development likely has caused evolution of ice flow over time as till and lubricating water were redistributed, moats were eroded and bedforms grew.
    Repository Name: EPIC Alfred Wegener Institut
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    A Kinematic Kinetic Energy Backscatter Parametrization: From Implementation to Global Ocean Simulations (2020)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Advances in Modeling Earth Systems, American Geophysical Union (AGU), 12(12), ISSN: 1942-2466
    Details
    Publication Date: 2023-06-21
    Description: Ocean models at eddy-permitting resolution are generally overdissipative, damping the intensity of the mesoscale eddy field. To reduce overdissipation, we propose a simplified, kinematic energy backscatter parametrization built into the viscosity operator in conjunction with a new flow-dependent coefficient of viscosity based on nearest neighbor velocity differences. The new scheme mitigates excessive dissipation of energy and improves global ocean simulations at eddy-permitting resolution. We find that kinematic backscatter substantially raises simulated eddy kinetic energy, similar to an alternative, previously proposed dynamic backscatter parametrization. While dynamic backscatter is scale aware and energetically more consistent, its implementation is more complex. Furthermore, it turns out to be computationally more expensive, as it applies, among other things, an additional prognostic subgrid energy equation. The kinematic backscatter proposed here, by contrast, comes at no additional computational cost, following the principle of simplicity. Our primary focus is the discretization on triangular unstructured meshes with cell placement of velocities (an analog of B-grids), as employed by the Finite-volumE Sea ice-Ocean Model (FESOM2). The kinematic backscatter scheme with the new viscosity coefficient is implemented in FESOM2 and tested in the simplified geometry of a zonally reentrant channel as well as in a global ocean simulation on a 1/4° mesh. This first version of the new kinematic backscatter needs to be tuned to the specific resolution regime of the simulation. However, the tuning relies on a single parameter, emphasizing the overall practicality of the approach.
    Repository Name: EPIC Alfred Wegener Institut
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    Spatial Variability of Dissolved Organic Carbon, Solutes, and Suspended Sediment in Disturbed Low Arctic Coastal Watersheds (2020)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Biogeosciences, American Geophysical Union (AGU), 125(2), ISSN: 2169-8953
    Details
    Publication Date: 2024-01-30
    Description: Climate change in the Arctic leads to permafrost degradation and to associated changes infreshwater geochemistry. There is a limited understanding of how disturbances such as active layerdetachments or retrogressive thaw slumps impact water quality on a catchment scale. This study investigateshow permafrost degradation affects concentrations of dissolved organic carbon (DOC), total dissolvedsolids (TDS), suspended sediment, and stable water isotopes in adjacent Low Arctic watersheds. Weincorporated data on disturbance between 1952 and 2015, as well as sporadic runoff and geochemistry dataof streams nearby. Our results show that the total disturbed area decreased by 41% between 1952 and 2015,whereas the total number of disturbances increased by 66% in all six catchments. The spatial variabilityof hydrochemical parameters is linked to catchment properties and not necessarily reflected at the outflow.Degrading ice‐wedge polygons were found to increase DOC concentrations upstream in Ice Creek West,whereas hydrologically connected disturbances were linked to increases in TDS and suspended sediment.Although we found a great spatial variability of hydrochemical concentrations along the paired watershed,there was a linear relationship between catchment size and daily DOC, total dissolved nitrogen, and TDSfluxes for all six streams. Suspended sedimentflux on the contrary did not show a clear relationship as onehydrologically connected retrogressive thaw slump impacted the overallflux in one of the streams.Understanding the spatial variability of water quality will help to model the lateral geochemicalfluxes fromArctic catchments
    Repository Name: EPIC Alfred Wegener Institut
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    Ventilation of the Deep Ocean Carbon Reservoir During the Last Deglaciation: Results From the Southeast Pacific (2019)
    American Geophysical Union (AGU)
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union (AGU), 34(12), pp. 2080-2097, ISSN: 2572-4517
    Details
    Publication Date: 2023-03-31
    Description: Coeval changes in atmospheric CO2 and 14C contents during the last deglaciation are often attributed to ocean circulation changes that released carbon stored in the deep ocean during the Last Glacial Maximum (LGM). Work is being done to generate records that allow for the identification of the exact mechanisms leading to the accumulation and release of carbon from the oceanic reservoir, but these mechanisms are still the subject of debate. Here we present foraminifera 14C data from five cores in a transect across the Chilean continental margin between ~540 and ~3,100 m depth spanning the last 20,000 years. Our data reveal that during the LGM, waters at ~2,000 m were 50% to 80% more depleted in Δ14C than waters at ~1,500 m when compared to modern values, consistent with the hypothesis of a glacial deep ocean carbon reservoir that was isolated from the atmosphere. During the deglaciation, our intermediate water records reveal homogenization in the Δ14C values between ~800 and ~1,500 m from ~16.5–14.5 ka cal BP to ~14–12 ka cal BP, which we interpret as deeper penetration of Antarctic Intermediate Water. While many questions still remain, this process could aid the ventilation of the deep ocean at the beginning of the deglaciation, contributing to the observed ~40 ppm rise in atmospheric pCO2.
    Repository Name: EPIC Alfred Wegener Institut
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    Retrieval of Wintertime Sea Ice Production in Arctic Polynyas Using Thermal Infrared and Passive Microwave Remote Sensing Data (2019)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Oceans, American Geophysical Union (AGU), 124(8), pp. 5503-5528, ISSN: 2169-9275
    Details
    Publication Date: 2022-11-02
    Repository Name: EPIC Alfred Wegener Institut
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    Concentrations and Water Mass Transport of Legacy POPs in the Arctic Ocean (2018)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 45(23), pp. 12972-12981, ISSN: 0094-8276
    Details
    Publication Date: 2023-01-30
    Description: The Arctic Ocean is known to be contaminated by various persistent organic pollutants (POPs). The Fram Strait, the only deepwater passage to the Arctic Ocean (from the Atlantic Ocean), represents an unquantified gateway for POPs fluxes into and out of the Arctic. Polyethylene passive samplers were deployed in vertical profiles in the Fram Strait and in air and surface water in the Canadian Archipelago to determine the concentrations, profiles, and mass fluxes of dissolved polychlorinated biphenyls (PCBs) and organochlorine pesticides. In the Fram Strait, higher concentrations of ΣPCBs (1.3–3.6 pg/L) and dichlorodiphenyltrichloroethanes (ΣDDTs, 5.2–9.1 pg/L) were observed in the deepwater masses (below 1,000 m), similar to nutrient-like vertical profiles. There was net southward transport of hexachlorobenzene and hexachlorocyclohexanes (ΣHCHs) of 0.70 and 14 Mg/year but a net northward transport of ΣPCBs at 0.16 Mg/year through the Fram Strait.
    Repository Name: EPIC Alfred Wegener Institut
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    Framework disorder and its effect on selective hysteretic sorption of a T-shaped azole-based metal–organic framework (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-12-08
    Description: Metal–organic frameworks with highly ordered porosity have been studied extensively. In this paper, the effect of framework (pore) disorder on the gas sorption of azole-based isoreticular Cu(II) MOFs with rtl topology and characteristic 1D tubular pore channels is investigated for the first time. In contrast to other isoreticular rtl metal–organic frameworks, the Cu(II) metal–organic framework based on 5-(1H-imidazol-1-yl)isophthalate acid has a crystallographically identifiable disordered framework without open N-donor sites. The framework provides a unique example for investigating the effect of pore disorder on gas sorption that can be systematically evaluated. It exhibits remarkable temperature-dependent hysteretic CO2 sorption up to room temperature, and shows selectivity of CO2 over H2, CH4 and N2 at ambient temperature. The unique property of the framework is its disordered structure featuring distorted 1D tubular channels and DMF-guest-remediated defects. The results imply that structural disorder (defects) may play an important role in the modification of the performance of the material.
    Keywords: metal–organic frameworksT-shaped ligandsdisorderMOFssolid propertieschannel structuresgas separation
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-12-08
    Description: SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns (`stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012), J. Appl. Cryst. 45, 335–341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
    Keywords: serial crystallographyX-ray free-electron lasersXFELelectron diffractiondiffract-then-destroydynamical studiesauto-indexing algorithmsBragg peaks
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    The hydrocarbon-bearing clathrasil chibaite and its host–guest structure at low temperature (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-08-09
    Description: The natural sII-type clathrasil chibaite [chemical formula SiO2·(M12,M16), where Mx denotes a guest molecule] was investigated using single-crystal X-ray diffraction and Raman spectroscopy in the temperature range from 273 to 83 K. The O atoms of the structure at room temperature, which globally conforms to space group Fd{\overline 3}m [V = 7348.9 (17) Å3, a = 19.4420 (15) Å], have anomalous anisotropic displacement parameters indicating a static or dynamic disorder. With decreasing temperature, the crystal structure shows a continuous symmetry-lowering transformation accompanied by twinning. The intensities of weak superstructure reflections increase as temperature decreases. A monoclinic twinned superstructure was derived at 100 K [A2/n, V = 7251.0 (17) Å3, a′ = 23.7054 (2), b′ = 13.6861 (11), c′ = 23.7051 (2) Å, β′ = 109.47°]. The transformation matrix from the cubic to the monoclinic system is ai′ = (½ 1 ½ / ½ 0 −½ / ½ −1 ½). The A2/n host framework has Si—O bond lengths and Si—O—Si angles that are much closer to known values for stable silicate-framework structures compared with the averaged Fd{\overline 3}m model. As suggested from band splitting observed in the Raman spectra, the [512]-type cages (one crystallographically unique in Fd{\overline 3}m, four different in A2/n) entrap the hydrocarbon species (CH4, C2H6, C3H8, i-C4H10). The [51264]-type cage was found to be unique in both structure types. It contains the larger hydrocarbon molecules C2H6, C3H8 and i-C4H10.
    Keywords: chibaiteclathrasilshydrocarbonsRaman spectroscopyX-ray diffractionlow temperature
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-08-09
    Description: Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein–nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases.
    Keywords: class II CPD photolyasesDNA repairDNA distortioncyclobutane pyrimidine dimercrystal structure
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    De novo protein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-08-09
    Description: During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.
    Keywords: serial crystallographySIRAS phasinglipidic cubic phaseheavy-atom soakingde novo protein structure determination
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Conformational aspects of polymorphs and phases of 2-propyl-1H-benzimidazole (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-09-15
    Description: This paper reports on the polymorphism of 2-propyl-1H-benzimidazole (2PrBzIm) induced by temperature change. Upon heating, an irreversible reconstructive-type phase transition at T = 384 K from the ordered form I (P212121) to a new polymorph, form IIHT (Pcam), was observed. The structural transformation between forms I and II involves significant changes in the crystal packing, as well as a key conformational variation around the propyl chain of the molecule. After the first irreversible phase transition, the IIHT form undergoes two further (reversible) phase transitions upon cooling at 361 K (IIRT) and 181 K (IILT). All three phases (forms IIHT, IIRT and IILT) have almost identical crystal packing and, given the reversibility of the conversions as a function of temperature, they are referred to as form II temperature phases. They differ, however, with respect to conformational variations around the propyl chain of 2PrBzIm. Energy calculations of the gas-phase conformational energy landscape of this compound about its flexible bonds allowed us to classify the observed conformational variations of all forms into changes and adjustments of conformers. This reveals that forms I and II are related by conformational change, and that two of the form II phases (HT and RT) are related by conformational adjustment, whilst the other two (RT and LT) are related by conformational change. We introduce the term `conformational phases' for different crystal phases with almost identical packing but showing changes in conformation.
    Keywords: molecular crystalspolymorphismphase transitionsconformational changesenergy minimization
    Electronic ISSN: 2052-2525
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    Signal-to-noise, spatial resolution and information capacity of coherent diffraction imaging (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-09-15
    Description: It is shown that the average signal-to-noise ratio (SNR) in the three-dimensional electron-density distribution of a sample reconstructed by coherent diffractive imaging cannot exceed twice the square root of the ratio of the mean total number of scattered photons detected during the scan and the number of spatially resolved voxels in the reconstructed volume. This result leads to an upper bound on Shannon's information capacity of this imaging method by specifying the maximum number of distinguishable density distributions within the reconstructed volume when the radiation dose delivered to the sample and the spatial resolution are both fixed. If the spatially averaged SNR in the reconstructed electron density is fixed instead, the radiation dose is shown to be proportional to the third or fourth power of the spatial resolution, depending on the sampling of the three-dimensional diffraction space and the scattering power of the sample.
    Keywords: coherent diffractive imagingsignal-to-noise ratiospatial resolutioninformation capacity
    Electronic ISSN: 2052-2525
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    Three-beam convergent-beam electron diffraction for measuring crystallographic phases (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-09
    Description: Under almost all circumstances, electron diffraction patterns contain information about the phases of structure factors, a consequence of the short wavelength of an electron and its strong Coulombic interaction with matter. However, extracting this information remains a challenge and no generic method exists. In this work, a set of simple analytical expressions is derived for the intensity distribution in convergent-beam electron diffraction (CBED) patterns recorded under three-beam conditions. It is shown that these expressions can be used to identify features in three-beam CBED patterns from which three-phase invariants can be extracted directly, without any iterative refinement processes. The octant, in which the three-phase invariant lies, can be determined simply by inspection of the indexed CBED patterns (i.e. the uncertainty of the phase measurement is ±22.5°). This approach is demonstrated with the experimental measurement of three-phase invariants in two simple test cases: centrosymmetric Si and non-centrosymmetric GaAs. This method may complement existing structure determination methods by providing direct measurements of three-phase invariants to replace `guessed' invariants in ab initio phasing methods and hence provide more stringent constraints to the structure solution.
    Keywords: crystallographic phase problemthree-phase invariantsconvergent-beam electron diffractionstructure determinationenantiomorph ambiguitynanocrystalsdynamical studiesmultiple scattering
    Electronic ISSN: 2052-2525
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    Unwarping GISAXS data (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-09
    Description: Grazing-incidence small-angle X-ray scattering (GISAXS) is a powerful technique for measuring the nanostructure of coatings and thin films. However, GISAXS data are plagued by distortions that complicate data analysis. The detector image is a warped representation of reciprocal space because of refraction, and overlapping scattering patterns appear because of reflection. A method is presented to unwarp GISAXS data, recovering an estimate of the true undistorted scattering pattern. The method consists of first generating a guess for the structure of the reciprocal-space scattering by solving for a mutually consistent prediction from the transmission and reflection sub-components. This initial guess is then iteratively refined by fitting experimental GISAXS images at multiple incident angles, using the distorted-wave Born approximation (DWBA) to convert between reciprocal space and detector space. This method converges to a high-quality reconstruction for the undistorted scattering, as validated by comparing with grazing-transmission scattering data. This new method for unwarping GISAXS images will broaden the applicability of grazing-incidence techniques, allowing experimenters to inspect undistorted visualizations of their data and allowing a broader range of analysis methods to be applied to GI data.
    Keywords: X-ray scatteringGISAXSGTSAXSimage healingreconstructiondistorted-wave Born approximation
    Electronic ISSN: 2052-2525
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    Deformation pathway and defect generation in crystals: a combined group theory and graph theory description (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-12-19
    Description: The generation and motion of crystalline defects during plastic deformation are critical processes that determine the mechanical properties of a crystal. The types of defect generated are not only related to the symmetry of a crystal but also associated with the symmetry-breaking process during deformation. Proposed here is a new mathematical framework to capture the intrinsic coupling between crystal symmetry and deformation-induced symmetry breaking. Using a combination of group theory and graph theory, a general approach is demonstrated for the systematic determination of the types of crystalline defect induced by plastic deformation, through the construction of a crystal deformation group and a deformation pathway graph. The types of defect generated in the deformation of a face-centered cubic crystal are analyzed through the deformation pathway graph and compared with experimental observations.
    Keywords: crystal deformationcrystalline defectsgroup theoryCayley graph
    Electronic ISSN: 2052-2525
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    Incommensurate structures of the [CH3NH3][Co(COOH)3] compound (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-12-19
    Description: The present article is devoted to the characterization of the structural phase transitions of the [CH3NH3][Co(COOH)3] (1) perovskite-like metal–organic compound through variable-temperature single-crystal neutron diffraction. At room temperature, compound 1 crystallizes in the orthorhombic space group Pnma (phase I). A decrease in temperature gives rise to a first phase transition from the space group Pnma to an incommensurate phase (phase II) at approximately 128 K. At about 96 K, this incommensurate phase evolves into a second phase with a sharp change in the modulation vector (phase III). At lower temperatures (ca 78 K), the crystal structure again becomes commensurate and can be described in the monoclinic space group P21/n (phase IV). Although phases I and IV have been reported previously [Boča et al. (2004). Acta Cryst. C60, m631–m633; Gómez-Aguirre et al. (2016). J. Am. Chem. Soc. 138, 1122–1125; Mazzuca et al. (2018). Chem. Eur. J. 24, 388–399], phases III and IV corresponding to the Pnma(00γ)0s0 space group have not yet been described. These phase transitions involve not only the occurrence of small distortions in the three-dimensional anionic [Co(HCOO)3]− framework, but also the reorganization of the [CH3NH3]+ counter-ions in the cavities of the structure, which gives rise to an alteration of the hydrogen-bonded network, modifying the electrical properties of compound 1.
    Keywords: phase transitionsincommensurate structuresformate ligandmultiferroic materialsaperiodic structuresmaterials scienceinorganic chemistryphase transitionsMOFs
    Electronic ISSN: 2052-2525
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    Structure model of γ-Al2O3 based on planar defects (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-12-19
    Description: The defect structure of γ-Al2O3 derived from boehmite was investigated using a combination of selected-area electron diffraction (SAED) and powder X-ray diffraction (XRD). Both methods confirmed a strong dependence of the diffraction line broadening on the diffraction indices known from literature. The analysis of the SAED patterns revealed that the dominant structure defects in the spinel-type γ-Al2O3 are antiphase boundaries located on the lattice planes (00l), which produce the sublattice shifts {{1}\over{4}}\langle 10{\overline 1}\rangle. Quantitative information about the defect structure of γ-Al2O3 was obtained from the powder XRD patterns. This includes mainly the size of γ-Al2O3 crystallites and the density of planar defects. The correlation between the density of the planar defects and the presence of structural vacancies, which maintain the stoichiometry of the spinel-type γ-Al2O3, is discussed. A computer routine running on a fast graphical processing unit was written for simulation of the XRD patterns. This routine calculates the atomic positions for a given kind and density of planar defect, and simulates the diffracted intensities with the aid of the Debye scattering equation.
    Keywords: γ-aluminamicrostructure defectsantiphase boundariesrotational boundariesselected-area electron diffractionpowder X-ray diffractionDebye equationanisotropic broadening
    Electronic ISSN: 2052-2525
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    Tailoring structural and magnetic properties of Mn3−xFexGa alloys towards multifunctional applications (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-18
    Description: This study investigated the structural and magnetic properties of Mn3−xFexGa alloys (x = 0, 0.2, 0.4, 0.6, 0.8, 1) under different heat-treatment conditions. A tetragonal structure was observed in samples that were heat treated at 623 K for three days followed by quenching in ice water. These tetragonal alloys present large coercive fields in the range 0.8–5 kOe and low saturation magnetization, and have great potential for application in spin-transfer torque-based devices. A hexagonal structure was observed in samples subjected to heat treatment at 883 K for three days following quenching in ice water. A moderate decrease in the coercive field has been observed for the hexagonal alloys compared with those with a tetragonal structure. However, the Mn3−xFexGa alloys with a hexagonal structure exhibit other attractive magnetic properties, including collinear and non-collinear magnetic properties, holding high promise for technological applications. A face-centred-cubic (f.c.c.) structure was observed when subjected to annealing at 1073 K for three days followed by quenching in ice water. In contrast to the tetragonal and hexagonal structures, all f.c.c. alloys exhibit antiferromagnetic behaviour. This versatile material can display a wide range of multi-functionalities attributed to its tuneable crystal structure. This investigation will guide the design of multiple structures of these materials in order to utilise the wide functionalities for practical applications.
    Keywords: Mn–Fe–Ga alloystetragonal Heusler alloysmultiple structural materials
    Electronic ISSN: 2052-2525
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    Structure-based mechanism of action of a viral poly(ADP-ribose) polymerase 1-interacting protein facilitating virus replication (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-01
    Description: Poly(ADP-ribose) polymerase 1 (PARP-1), an enzyme that modifies nuclear proteins by poly(ADP-ribosyl)ation, regulates various cellular activities and restricts the lytic replication of oncogenic gammaherpesviruses by inhibiting the function of replication and transcription activator (RTA), a key switch molecule of the viral life cycle. A viral PARP-1-interacting protein (vPIP) encoded by murine gammaherpesvirus 68 (MHV-68) orf49 facilitates lytic replication by disrupting interactions between PARP-1 and RTA. Here, the structure of MHV-68 vPIP was determined at 2.2 Å resolution. The structure consists of 12 α-helices with characteristic N-terminal β-strands (Nβ) and forms a V-shaped-twist dimer in the asymmetric unit. Structure-based mutagenesis revealed that Nβ and the α1 helix (residues 2–26) are essential for the nuclear localization and function of vPIP; three residues were then identified (Phe5, Ser12 and Thr16) that were critical for the function of vPIP and its interaction with PARP-1. A recombinant MHV-68 harboring mutations of these three residues showed severely attenuated viral replication both in vitro and in vivo. Moreover, ORF49 of Kaposi's sarcoma-associated herpesvirus also directly interacted with PARP-1, indicating a conserved mechanism of action of vPIPs. The results elucidate the novel molecular mechanisms by which oncogenic gammaherpesviruses overcome repression by PARP-1 using vPIPs.
    Keywords: viral PARP-1-interacting proteinopen reading frame 49poly(ADP-ribose) polymerase 1murine gammaherpesvirus 68Kaposi's sarcoma-associated herpesvirusstructure determinationX-ray crystallography
    Electronic ISSN: 2052-2525
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    A corrective prescription for GISAXS (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-01
    Keywords: X-ray scatteringGISAXSimage healingreconstructiondistorted-wave Born approximation
    Electronic ISSN: 2052-2525
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    K-paracelsian (KAlSi3O8·H2O) and identification of a simple building scheme of dense double-crankshaft zeolite topologies (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-12-05
    Description: During screening of the phase space using KOH and 1-methyl-4-aza-1-azoniabicyclo[2.2.2]octane hydroxide (1-methyl-DABCO) under hydrothermal zeolite synthesis conditions, K-paracelsian was synthesized. Scanning electron microscopy, energy dispersive X-ray spectroscopy and ex situ powder X-ray diffraction analysis revealed a material that is compositionally closely related to the mineral microcline and structurally closely related to the mineral paracelsian, both of which are feldspars. In contrast to the feldspars, K-paracelsian contains intrazeolitic water corresponding to one molecule per cage. In the case of K-paracelsian it might be useful to consider it a link between feldspars and zeolites. It was also shown that K-paracelsian can be described as the simplest endmember of a family of dense double-crankshaft zeolite topologies. By applying the identified building principle, a number of known zeolite topologies can be constructed. Furthermore, it facilitates the construction of a range of hypothetical small-pore structures that are crystallo-chemically healthy, but which have not yet been realized experimentally.
    Keywords: K-paracelsiandense double-crankshaft zeolite topologiesstructure refinementcrystal engineeringinorganic porous solidsmicroporous materials
    Electronic ISSN: 2052-2525
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    Determination of chemical ordering in the complex perovskite Pb(Cd1/3Nb2/3)O3 (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-25
    Description: Pure-phase Pb(Cd1/3Nb2/3)O3 (PCN) single crystals and ceramics with a complex perovskite structure are synthesized for the first time. The local chemical ordering in PCN has been investigated by X-ray diffraction (including diffuse scattering) and Cs-corrected transmission electron microscopy experiments. It is concluded that the PCN samples have large coherent chemical ordering regions that even extend to the long range, and the ordering model is consistent with β-type chemical ordered regions. The antiphase domain boundaries were also observed. Two dielectric anomaly peaks were found in these two types of samples, one of which indicates possible relaxor behaviour. The novel structure of the completely ordered regions and its relationship with the electrical properties make PCN a unique material for the fundamental understanding of chemically substituted perovskites.
    Keywords: chemical orderingdiffuse scatteringelectron microscopyatomic resolution EDSperovskitesdielectric permittivityrelaxors
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    Crystal engineering, crystals and crystallography (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-30
    Keywords: crystal engineeringcrystalscrystallography
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    Committee machine that votes for similarity between materials (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-30
    Description: A method has been developed to measure the similarity between materials, focusing on specific physical properties. The information obtained can be utilized to understand the underlying mechanisms and support the prediction of the physical properties of materials. The method consists of three steps: variable evaluation based on nonlinear regression, regression-based clustering, and similarity measurement with a committee machine constructed from the clustering results. Three data sets of well characterized crystalline materials represented by critical atomic predicting variables are used as test beds. Herein, the focus is on the formation energy, lattice parameter and Curie temperature of the examined materials. Based on the information obtained on the similarities between the materials, a hierarchical clustering technique is applied to learn the cluster structures of the materials that facilitate interpretation of the mechanism, and an improvement in the regression models is introduced to predict the physical properties of the materials. The experiments show that rational and meaningful group structures can be obtained and that the prediction accuracy of the materials' physical properties can be significantly increased, confirming the rationality of the proposed similarity measure.
    Keywords: data miningmaterials informaticsfirst-principles calculationsphysical properties of materialsmachine learningsimilarity
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    Self-adapted clustering of solute atoms into a confined two-dimensional prismatic platelet with an ellipse-like quasi-unit cell (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-30
    Description: This paper reports a new structured prismatic platelet, self-assembled by an ellipse-like quasi-unit cell, precipitated in Mg–In–Yb and Mg–In–Ca ternary alloys and aged isothermally at 200°C using aberration-corrected high-angle annular dark-field scanning transmission electron microscopy combined with density functional theory computations. The ordered stacking of solute atoms along the [0001]α direction based on elliptically shaped self-adapted clustering leads to the generation of the quasi-unit cell. The bonding of these ellipse-like quasi-unit-cell rods by the Mg atomic columns along the 〈11{\overline 2}0〉α directions formed a two-dimensional planar structure, which has three variants with a {10{\overline 1}0}α habit plane and full coherence with the α-Mg matrix. This finding is important for understanding the clustering and stacking behaviors of solute atoms in condensed matter, and is expected to guide the future design of novel high-strength Mg alloys strengthened by such high-density prismatic platelets.
    Keywords: magnesium alloysprecipitationprismatic plateletsquasi-unit-cellsDFTHAADF-STEM
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    Crystal structure, interaction energies and experimental electron density of the popular drug ketoprophen (2018)
    International Union of Crystallography (IUCr)
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    Publication Date: 2018-10-30
    Description: The crystal and molecular structure of the pure (S)-enantiomer of the popular analgesic and anti-inflammatory drug ketoprophen (α-ket) is reported. A detailed aspherical charge-density model based on high-resolution X-ray diffraction data has been refined, yielding a high-precision geometric description and classification of the O—H...O interactions as medium strength hydrogen bonds. The crystal structure of the racemic form of ketoprophen (β-ket) was also redetermined at 100 K, at 0.5 Å resolution. A previously unreported disorder (10% occupancy) was discovered. In contrast to the racemic β-ket case, the (S)-enantiomer crystallizes with two independent molecules in the asymmetric unit with two distinct conformations. The major difference between the β-ket and α-ket crystal forms lies in the formation of distinct hydrogen-bonded motifs: a closed ring motif in β-ket versus infinite chains of hydrogen bonds in the chiral α-ket structure. However, the overall crystal packing of both forms is surprisingly similar, with close-packed layers of antiparallel-oriented benzophenone moieties bound by C—H...π interactions. Notably, the most important stabilizing term in the total lattice energies in both instances proved to be the dispersion related to these interactions. Both forms of the title compound (α- and β-ket) were additionally characterized by differential scanning calorimetry and thermogravimetric analysis.
    Keywords: ketoprophencharge densitycrystal structurespharmaceuticalsbioinversion
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    Deep Consensus, a deep learning-based approach for particle pruning in cryo-electron microscopy (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-30
    Description: Single-particle cryo-electron microscopy (cryo-EM) has recently become a mainstream technique for the structural determination of macromolecules. Typical cryo-EM workflows collect hundreds of thousands of single-particle projections from thousands of micrographs using particle-picking algorithms. However, the number of false positives selected by these algorithms is large, so that a number of different `cleaning steps' are necessary to decrease the false-positive ratio. Most commonly employed techniques for the pruning of false-positive particles are time-consuming and require user intervention. In order to overcome these limitations, a deep learning-based algorithm named Deep Consensus is presented in this work. Deep Consensus works by computing a smart consensus over the output of different particle-picking algorithms, resulting in a set of particles with a lower false-positive ratio than the initial set obtained by the pickers. Deep Consensus is based on a deep convolutional neural network that is trained on a semi-automatically generated data set. The performance of Deep Consensus has been assessed on two well known experimental data sets, virtually eliminating user intervention for pruning, and enhances the reproducibility and objectivity of the whole process while achieving precision and recall figures above 90%.
    Keywords: cryo-EMdeep learningimage processingparticle pruningthree-dimensional reconstruction
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    Thresholding of cryo-EM density maps by false discovery rate control (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-09
    Description: Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task owing to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control has been developed. In this way, three-dimensional confidence maps contain signal separated from background noise in the form of local detection rates of EM density values. It is demonstrated that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures owing to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and is particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions in the structure.
    Keywords: electron cryo-microscopysignal detectionfalse discovery ratecryo-EM densitysubtomogram averaginglocal resolutionligand binding
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    A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-09
    Description: A new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The motion within the sample is modelled through the use of Gaussian process regression. This allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. This formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized. Since the smoothness prior requires three parameters that describe the statistics of the observed motion, an efficient stochastic method to estimate these parameters is also proposed. Finally, a practical algorithm is proposed that estimates the average amount of cumulative radiation damage as a function of radiation dose and spatial frequency, and then fits relative B factors to that damage in a robust way. The method is evaluated on three publicly available data sets, and its usefulness is illustrated by comparison with state-of-the-art methods and previously published results. The new method has been implemented as Bayesian polishing in RELION-3, where it replaces the existing particle-polishing method, as it outperforms the latter in all tests conducted.
    Keywords: Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy
    Electronic ISSN: 2052-2525
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    Homology-based loop modeling yields more complete crystallographic protein structures (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-08-09
    Description: Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and `graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects.
    Keywords: loop buildingstructural re-buildingPDB-REDOmodel completioncrystallography
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-08-30
    Description: Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.
    Keywords: phytochromesphotoreceptorsphotosynthetic bacteriamyxobacteriaabsorption spectra
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    Bond orders for intermolecular interactions in crystals: charge transfer, ionicity and the effect on intramolecular bonds (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-08-30
    Description: The question of whether intermolecular interactions in crystals originate from localized atom...atom interactions or as a result of holistic molecule...molecule close packing is a matter of continuing debate. In this context, the newly introduced Roby–Gould bond indices are reported for intermolecular `σ-hole' interactions, such as halogen bonding and chalcogen bonding, and compared with those for hydrogen bonds. A series of 97 crystal systems exhibiting these interaction motifs obtained from the Cambridge Structural Database (CSD) has been analysed. In contrast with conventional bond-order estimations, the new method separately estimates the ionic and covalent bond indices for atom...atom and molecule...molecule bond orders, which shed light on the nature of these interactions. A consistent trend in charge transfer from halogen/chalcogen bond-acceptor to bond-donor groups has been found in these intermolecular interaction regions via Hirshfeld atomic partitioning of the electron populations. These results, along with the `conservation of bond orders' tested in the interaction regions, establish the significant role of localized atom...atom interactions in the formation of these intermolecular binding motifs.
    Keywords: intermolecular interactionsbond orderionicityhydrogen bondinghalogen bondingcrystal engineeringcomputational modellingmolecular crystals
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Atomic level three-dimensional structure of individual particles with XFELs (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-09-06
    Keywords: single-particle three-dimensional imagingX-ray free electron lasersimaging virus particlesimage analysisthree-dimensional reconstructionatomic scale structure
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 95
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    Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-09-06
    Description: Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.
    Keywords: XFELsMelbourneviruscoherent diffractive imagingLCLSimage reconstruction
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    Exploring the simultaneous σ-hole/π-hole bonding characteristics of a Br...π interaction in an ebselen derivative via experimental and theoretical electron-density analysis (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-09-06
    Description: In this study, the nature and characteristics of a short Br...π interaction observed in an ebselen derivative, 2-(2-bromophenyl)benzo[d][1,2]selenazol-3(2H)-one, has been explored. The electronic nature of this Br...π interaction was investigated via high-resolution X-ray diffraction and periodic density functional theory calculations using atoms-in-molecules (AIM) analysis. This study unravels the simultaneous presence of σ-hole and π-hole bonding characteristics in the same interaction. The dual characteristics of this unique Br...π interaction are further established via molecular electrostatic potentials (MESPs) and natural bond orbitals (NBOs).
    Keywords: σ-hole bondingπ-hole bondingebselenelectron densitymolecular electrostatic potentialscrystal engineeringcharge, spin and momentum densitiescomputational modellingmolecular crystals
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-09-12
    Description: Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver 70–2000 nm particles into the XFEL beam efficiently and at low noise. Improving the technique of aerosol sample delivery and extending it to single proteins necessitates quantitative aerosol diagnostics. Here a lab-based technique is introduced for Rayleigh-scattering microscopy allowing us to track and size aerosolized particles down to 40 nm in diameter as they exit the injector. This technique was used to characterize the `Uppsala injector', which is a pioneering and frequently used aerosol sample injector for XFEL single-particle imaging. The particle-beam focus, particle velocities, particle density and injection yield were measured at different operating conditions. It is also shown how high particle densities and good injection yields can be reached for large particles (100–500 nm). It is found that with decreasing particle size, particle densities and injection yields deteriorate, indicating the need for different injection strategies to extend XFEL imaging to smaller targets, such as single proteins. This work demonstrates the power of Rayleigh-scattering microscopy for studying focused aerosol beams quantitatively. It lays the foundation for lab-based injector development and online injection diagnostics for XFEL research. In the future, the technique may also find application in other fields that employ focused aerosol beams, such as mass spectrometry, particle deposition, fuel injection and three-dimensional printing techniques.
    Keywords: Rayleigh scatteringXFELsaerosol injectionUppsala injectorsnanoparticles
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 98
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    Photocage-initiated time-resolved solution X-ray scattering investigation of protein dimerization (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-09-13
    Description: This work demonstrates a new method for investigating time-resolved structural changes in protein conformation and oligomerization via photocage-initiated time-resolved X-ray solution scattering by observing the ATP-driven dimerization of the MsbA nucleotide-binding domain. Photocaged small molecules allow the observation of single-turnover reactions of non-naturally photoactivatable proteins. The kinetics of the reaction can be derived from changes in X-ray scattering associated with ATP-binding and subsequent dimerization. This method can be expanded to any small-molecule-driven protein reaction with conformational changes traceable by X-ray scattering where the small molecule can be photocaged.
    Keywords: biophysicsX-ray solution scatteringphotocagingstructural biology
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 99
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    Towards the theoretical limitations of X-ray nanocrystallography at high intensity: the validity of the effective-form-factor description (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-09-15
    Description: X-ray free-electron lasers (XFELs) broaden horizons in X-ray crystallography. Facilitated by the unprecedented high intensity and ultrashort duration of the XFEL pulses, they enable us to investigate the structure and dynamics of macromolecules with nano-sized crystals. A limitation is the extent of radiation damage in the nanocrystal target. A large degree of ionization initiated by the incident high-intensity XFEL pulse alters the scattering properties of the atoms leading to perturbed measured patterns. In this article, the effective-form-factor approximation applied to capture this phenomenon is discussed. Additionally, the importance of temporal configurational fluctuations at high intensities, shaping these quantities besides the average electron loss, is shown. An analysis regarding the applicability of the approach to targets consisting of several atomic species is made, both theoretically and via realistic radiation-damage simulations. It is concluded that, up to intensities relevant for XFEL-based nanocrystallography, the effective-form-factor description is sufficiently accurate. This work justifies treating measured scattering patterns using conventional structure-reconstruction algorithms.
    Keywords: XFELsX-ray nanocrystallographyeffective form factorionizationradiation damage
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    Single-particle imaging without symmetry constraints at an X-ray free-electron laser (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-09-19
    Description: The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.
    Keywords: single-particle imagingthree-dimensional virus reconstructionsXFELs
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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