[ { "id": "authors:czj7n-6et27", "collection": "authors", "collection_id": "czj7n-6et27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230104-586485300.11", "type": "article", "title": "Novel device to collect deep-sea porewater in situ: A focus on benthic carbonate chemistry", "author": [ { "family_name": "Cetiner", "given_name": "Jaclyn E. P.", "orcid": "0000-0001-7879-059X", "clpid": "Cetiner-Jaclyn-E-P" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" }, { "family_name": "Rollins", "given_name": "Nick E.", "clpid": "Rollins-Nick-E" }, { "family_name": "Barnhart", "given_name": "Holly A.", "orcid": "0000-0002-0842-9464", "clpid": "Barnhart-Holly-A" }, { "family_name": "Liu", "given_name": "Xuewu", "orcid": "0000-0003-2896-3063", "clpid": "Liu-Xuewu" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Byrne", "given_name": "Robert H.", "orcid": "0000-0003-0726-0131", "clpid": "Byrne-Robert-H" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "abstract": "We have designed, built, tested, and deployed a novel device to extract porewater from deep-sea sediments in situ, constructed to work with a standard multicorer. Despite the importance of porewater measurements for numerous applications, many sampling artifacts can bias data and interpretation during traditional porewater processing from shipboard-processed cores. A well-documented artifact occurs in deep-sea porewater when carbonate precipitates during core recovery as a function of temperature and pressure changes, while porewater is in contact with sediment grains before filtration, thereby lowering porewater alkalinity and dissolved inorganic carbon (DIC). Here, we present a novel device built to obviate these sampling artifacts by filtering porewater in situ on the seafloor, with a focus near the sediment\u2013water interface on cm-scale resolution, to obtain accurate porewater profiles. We document 1\u201310% alkalinity loss in shipboard-processed sediment cores compared to porewater filtered in situ, at depths of 1600\u20133200\u2009m. We also show that alkalinity loss is a function of both weight % sedimentary CaCO\u2083 and water column depth. The average ratio of alkalinity loss to DIC loss in shipboard-processed sediment cores relative to in situ porewater is 2.2, consistent with the signal expected from carbonate precipitation. In addition to collecting porewater for defining natural profiles, we also conducted the first in situ dissolution experiments within the sediment column using isotopically labeled calcite. We present evidence of successful deployments of this device on and adjacent to the Cocos Ridge in the Eastern Equatorial Pacific across a range of depths and calcite saturation states.", "doi": "10.1002/lom3.10530", "issn": "1541-5856", "publisher": "American Society for Limnology and Oceanography", "publication": "Limnology and Oceanography: Methods", "publication_date": "2023-02", "series_number": "2", "volume": "21", "issue": "2", "pages": "82-97" }, { "id": "authors:6tvxf-m4c41", "collection": "authors", "collection_id": "6tvxf-m4c41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230307-205876300.15", "type": "article", "title": "Global Trends in the Distribution of Biogenic Minerals in the Ocean", "author": [ { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-Adam-V" }, { "family_name": "Pavia", "given_name": "Frank J.", "orcid": "0000-0003-3627-0179", "clpid": "Pavia-Frank-J" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Lam", "given_name": "Phoebe J.", "orcid": "0000-0001-6609-698X", "clpid": "Lam-Phoebe-J" } ], "abstract": "The cycling of marine particulate matter is critical for sequestering carbon in the deep ocean and in marine sediments. Biogenic minerals such as calcium carbonate (CaCO\u2083) and opal add density to more buoyant organic material, facilitating particle sinking and export. Here, we compile and analyze a global data set of particulate organic carbon (POC), particulate inorganic carbon (PIC, or CaCO\u2083), and biogenic silica (bSi, or opal) concentrations collected using large volume pumps (LVPs). We analyze the distribution of all three biogenic phases in the small (1\u201353 \u03bcm) and large (>53 \u03bcm) size classes. Over the entire water column 76% of POC exists in the small size fraction. Similarly, the small size class contains 82% of PIC, indicating the importance of small-sized coccolithophores to the PIC budget of the ocean. In contrast, 50% of bSi exists in the large size fraction, reflecting the larger size of diatoms and radiolarians compared with coccolithophores. We use PIC:POC and bSi:POC ratios in the upper ocean to document a consistent signal of shallow mineral dissolution, likely linked to biologically mediated processes. Sediment trap PIC:POC and bSi:POC are elevated with respect to LVP samples and increase strongly with depth, indicating the concentration of mineral phases and/or a deficit of POC in large sinking particles. We suggest that future sampling campaigns pair LVPs with sediment traps to capture the full particulate field, especially the large aggregates that contribute to mineral-rich deep ocean fluxes, and may be missed by LVPs.", "doi": "10.1029/2022jc019470", "issn": "2169-9275", "publisher": "American Geophysical Union", "publication": "Journal of Geophysical Research. Oceans", "publication_date": "2023-02", "series_number": "2", "volume": "128", "issue": "2", "pages": "Art. No. e2022JC019470" }, { "id": "authors:72g0f-4dq42", "collection": "authors", "collection_id": "72g0f-4dq42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230314-844891400.6", "type": "article", "title": "Constraining CaCO\u2083 Export and Dissolution With an Ocean Alkalinity Inverse Model", "author": [ { "family_name": "Liang", "given_name": "Hengdi", "orcid": "0000-0001-8975-4201", "clpid": "Liang-Hengdi" }, { "family_name": "Lunstrum", "given_name": "Abby M.", "orcid": "0000-0002-6176-3445", "clpid": "Lunstrum-Abby-M" }, { "family_name": "Dong", "given_name": "Sijia S.", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" }, { "family_name": "John", "given_name": "Seth G.", "orcid": "0000-0002-8257-626X", "clpid": "John-Seth-G" } ], "abstract": "Ocean alkalinity plays a fundamental role in the apportionment of CO\u2082 between the atmosphere and the ocean. The primary driver of the ocean's vertical alkalinity distribution is the formation of calcium carbonate (CaCO\u2083) by organisms at the ocean surface and its dissolution at depth. This so-called \"CaCO\u2083 counterpump\" is poorly constrained, however, both in terms of how much CaCO\u2083 is exported from the surface ocean, and at what depth it dissolves. Here, we created a steady-state model of global ocean alkalinity using Ocean Circulation Inverse Model transport, biogeochemical cycling, and field-tested calcite and aragonite dissolution kinetics. We find that limiting CaCO\u2083 dissolution to below the aragonite and calcite saturation horizons cannot explain excess alkalinity in the upper ocean, and that models allowing dissolution above the saturation horizons best match observations. Linking dissolution to organic matter respiration, or imposing a constant dissolution rate both produce good model fits. Our best performing models require export between 1.1 and 1.8 Gt PIC y\u207b\u00b9 (from 73 m), but all converge to 1.0 Gt PIC y\u207b\u00b9 export at 279 m, indicating that both high- and low-export scenarios can match observations, as long as high export is coupled to high dissolution in the upper ocean. These results demonstrate that dissolution is not a simple function of seawater CaCO\u2083 saturation (\u03a9) and calcite or aragonite solubility, and that other mechanisms, likely related to the biology and ecology of calcifiers, must drive significant dissolution throughout the water column.", "doi": "10.1029/2022gb007535", "issn": "0886-6236", "publisher": "American Geophysical Union", "publication": "Global Biogeochemical Cycles", "publication_date": "2023-02", "series_number": "2", "volume": "37", "issue": "2", "pages": "Art. No. e2022GB007535" }, { "id": "authors:ahk3v-fd659", "collection": "authors", "collection_id": "ahk3v-fd659", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221215-431170800.2", "type": "article", "title": "Authigenic Formation of Clay Minerals in the Abyssal North Pacific", "author": [ { "family_name": "Steiner", "given_name": "Zvi", "orcid": "0000-0002-9584-4956", "clpid": "Steiner-Zvi" }, { "family_name": "Rae", "given_name": "James W. B.", "orcid": "0000-0003-3904-2526", "clpid": "Rae-James-W-B" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Hou", "given_name": "Yi", "orcid": "0000-0002-0846-8615", "clpid": "Hou-Yi" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Lampronti", "given_name": "Giulio I.", "orcid": "0000-0002-1430-3446", "clpid": "Lampronti-Giulio-I" }, { "family_name": "Liu", "given_name": "Xuewu", "orcid": "0000-0003-2896-3063", "clpid": "Liu-Xuewu" }, { "family_name": "Achterberg", "given_name": "Eric P.", "orcid": "0000-0002-3061-2767", "clpid": "Achterberg-Eric-P" }, { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-Adam-V" }, { "family_name": "Turchyn", "given_name": "Alexandra V.", "orcid": "0000-0002-9298-2173", "clpid": "Turchyn-Alexandra-V" } ], "abstract": "Present estimates of the biogeochemical cycles of calcium, strontium, and potassium in the ocean reveal large imbalances between known input and output fluxes. Using pore fluid, incubation, and solid sediment data from North Pacific multi-corer cores we show that, contrary to the common paradigm, the top centimeters of abyssal sediments can be an active site of authigenic precipitation of clay minerals. In this region, clay authigenesis is the dominant sink for potassium and strontium and consumes nearly all calcium released from benthic dissolution of calcium carbonates. These observations support the idea that clay authigenesis occurring over broad regions of the world ocean may be a major buffer for ocean chemistry on the time scale of the ocean overturning circulation, and key to the long-term stability of Earth's climate.", "doi": "10.1029/2021gb007270", "issn": "0886-6236", "publisher": "American Geophysical Union", "publication": "Global Biogeochemical Cycles", "publication_date": "2022-11", "series_number": "11", "volume": "36", "issue": "11", "pages": "Art. No. e2021GB007270" }, { "id": "authors:0a2jd-z8886", "collection": "authors", "collection_id": "0a2jd-z8886", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230321-821389800.54", "type": "article", "title": "Authigenic Formation of Clay Minerals in the Abyssal North Pacific", "author": [ { "family_name": "Steiner", "given_name": "Zvi", "orcid": "0000-0002-9584-4956", "clpid": "Steiner-Zvi" }, { "family_name": "Rae", "given_name": "James W. B.", "orcid": "0000-0003-3904-2526", "clpid": "Rae-James-W-B" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Hou", "given_name": "Yi", "orcid": "0000-0002-0846-8615", "clpid": "Hou-Yi" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Lampronti", "given_name": "Giulio I.", "orcid": "0000-0002-1430-3446", "clpid": "Lampronti-Giulio-I" }, { "family_name": "Liu", "given_name": "Xuewu", "orcid": "0000-0003-2896-3063", "clpid": "Liu-Xuewu" }, { "family_name": "Achterberg", "given_name": "Eric P.", "orcid": "0000-0002-3061-2767", "clpid": "Achterberg-Eric-P" }, { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-Adam-V" }, { "family_name": "Turchyn", "given_name": "Alexandra V.", "orcid": "0000-0002-9298-2173", "clpid": "Turchyn-Alexandra-V" } ], "abstract": "Present estimates of the biogeochemical cycles of calcium, strontium, and potassium in the ocean reveal large imbalances between known input and output fluxes. Using pore fluid, incubation, and solid sediment data from North Pacific multi-corer cores we show that, contrary to the common paradigm, the top centimeters of abyssal sediments can be an active site of authigenic precipitation of clay minerals. In this region, clay authigenesis is the dominant sink for potassium and strontium and consumes nearly all calcium released from benthic dissolution of calcium carbonates. These observations support the idea that clay authigenesis occurring over broad regions of the world ocean may be a major buffer for ocean chemistry on the time scale of the ocean overturning circulation, and key to the long-term stability of Earth's climate.", "doi": "10.1029/2021gb007270", "issn": "0886-6236", "publisher": "American Geophysical Union", "publication": "Global Biogeochemical Cycles", "publication_date": "2022-11", "series_number": "11", "volume": "36", "issue": "11", "pages": "Art. No. e2021GB007270" }, { "id": "authors:9b972-53863", "collection": "authors", "collection_id": "9b972-53863", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220609-300102500", "type": "article", "title": "Shallow Calcium Carbonate Cycling in the North Pacific Ocean", "author": [ { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-A-V" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Naviaux", "given_name": "John D.", "orcid": "0000-0002-0681-3163", "clpid": "Naviaux-John-D" }, { "family_name": "Rollins", "given_name": "Nick E.", "clpid": "Rollins-Nick-E" }, { "family_name": "Ziveri", "given_name": "Patrizia", "orcid": "0000-0002-5576-0301", "clpid": "Ziveri-Patrizia" }, { "family_name": "Gray", "given_name": "William", "orcid": "0000-0001-5608-7836", "clpid": "Gray-William" }, { "family_name": "Rae", "given_name": "James W. B.", "orcid": "0000-0003-3904-2526", "clpid": "Rae-James-W-B" }, { "family_name": "Liu", "given_name": "Xuewu", "orcid": "0000-0003-2896-3063", "clpid": "Liu-Xuewu" }, { "family_name": "Byrne", "given_name": "Robert H.", "orcid": "0000-0003-0726-0131", "clpid": "Byrne-Robert-H" }, { "family_name": "Chen", "given_name": "Sang", "orcid": "0000-0001-8941-0791", "clpid": "Chen-Sang" }, { "family_name": "Moore", "given_name": "Christopher", "orcid": "0000-0003-3210-4878", "clpid": "Moore-Christopher" }, { "family_name": "Martell\u2010Bonet", "given_name": "Loraine", "orcid": "0000-0002-8546-8061", "clpid": "Martell\u2010Bonet-Loraine" }, { "family_name": "Steiner", "given_name": "Zvi", "orcid": "0000-0002-9584-4956", "clpid": "Steiner-Zvi" }, { "family_name": "Antler", "given_name": "Gilad", "orcid": "0000-0002-6865-5412", "clpid": "Antler-Gilad" }, { "family_name": "Hu", "given_name": "Huanting", "orcid": "0000-0003-4662-5375", "clpid": "Hu-Huanting" }, { "family_name": "Lunstrum", "given_name": "Abby", "orcid": "0000-0002-6176-3445", "clpid": "Lunstrum-Abby" }, { "family_name": "Hou", "given_name": "Yi", "orcid": "0000-0002-0846-8615", "clpid": "Hou-Yi" }, { "family_name": "Kemnitz", "given_name": "Nathaniel", "clpid": "Kemnitz-Nathaniel" }, { "family_name": "Stutsman", "given_name": "Johnny", "orcid": "0000-0002-1177-9393", "clpid": "Stutsman-Johnny" }, { "family_name": "Pallacks", "given_name": "Sven", "orcid": "0000-0002-8215-0007", "clpid": "Pallacks-Sven" }, { "family_name": "Dugenne", "given_name": "Mathilde", "orcid": "0000-0002-9316-1473", "clpid": "Dugenne-Mathilde" }, { "family_name": "Quay", "given_name": "Paul D.", "orcid": "0000-0001-5147-0289", "clpid": "Quay-Paul-D" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "abstract": "The cycling of biologically produced calcium carbonate (CaCO\u2083) in the ocean is a fundamental component of the global carbon cycle. Here, we present experimental determinations of in situ coccolith and foraminiferal calcite dissolution rates. We combine these rates with solid phase fluxes, dissolved tracers, and historical data to constrain the alkalinity cycle in the shallow North Pacific Ocean. The in situ dissolution rates of coccolithophores demonstrate a nonlinear dependence on saturation state. Dissolution rates of all three major calcifying groups (coccoliths, foraminifera, and aragonitic pteropods) are too slow to explain the patterns of both CaCO\u2083 sinking flux and alkalinity regeneration in the North Pacific. Using a combination of dissolved and solid-phase tracers, we document a significant dissolution signal in seawater supersaturated for calcite. Driving CaCO\u2083 dissolution with a combination of ambient saturation state and oxygen consumption simultaneously explains solid-phase CaCO\u2083 flux profiles and patterns of alkalinity regeneration across the entire N. Pacific basin. We do not need to invoke the presence of carbonate phases with higher solubilities. Instead, biomineralization and metabolic processes intimately associate the acid (CO\u2082) and the base (CaCO\u2083) in the same particles, driving the coupled shallow remineralization of organic carbon and CaCO\u2083. The linkage of these processes likely occurs through a combination of dissolution due to zooplankton grazing and microbial aerobic respiration within degrading particle aggregates. The coupling of these cycles acts as a major filter on the export of both organic and inorganic carbon to the deep ocean.", "doi": "10.1029/2022gb007388", "issn": "0886-6236", "publisher": "American Geophysical Union", "publication": "Global Biogeochemical Cycles", "publication_date": "2022-05", "series_number": "5", "volume": "36", "issue": "5", "pages": "Art. No. e2022GB007388" }, { "id": "authors:kmzvm-hrg45", "collection": "authors", "collection_id": "kmzvm-hrg45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211214-16662000", "type": "article", "title": "Depth profiles of suspended carbon and nitrogen along a North Pacific transect: Concentrations, isotopes, and ratios", "author": [ { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Wang", "given_name": "Xingchen Tony", "orcid": "0000-0001-5316-789X", "clpid": "Wang-Xingchen-Tony" }, { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-Adam-V" }, { "family_name": "Pavia", "given_name": "Frank J.", "orcid": "0000-0003-3627-0179", "clpid": "Pavia-Frank-J" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" } ], "abstract": "We present concentrations of total particulate carbon (PC), carbonate (PIC), total particulate nitrogen (PN), \u03b4\u00b9\u00b3C and \u03b4\u00b9\u2075N of suspended particles along a North Pacific transect. In the upper 400\u2009m, suspended PIC to particulate organic carbon (POC) ratios generally follow published sinking PIC/POC ratios. Below 600\u2009m, suspended PIC/POC become significantly lower than sinking PIC/POC, likely indicating PIC dissolution within the suspended load. In three out of the five stations, suspended PN \u03b4\u00b9\u2075N increase with depth from the euphotic zone to the thermocline, consistent with previous observations in many ocean regions (e.g.,BATS and HOT). However, in the other two stations where phytoplankton blooms were encountered, high suspended PN \u03b4\u00b9\u2075N (up to 12\u2030) were observed in the euphotic zone, which was likely caused by the export of low-\u03b4\u00b9\u2075N PN during the phytoplankton blooms. Average C_(org) : N ratio of suspended particles along the transect is 5.1 \u00b1 0.2, with the value in the subtropical gyre (5.8 \u00b1 0.3) slightly higher than the subarctic gyre (4.6 \u00b1 0.2).", "doi": "10.1002/lno.11989", "issn": "0024-3590", "publisher": "American Society of Limnology and Oceanography", "publication": "Limnology and Oceanography", "publication_date": "2022-01", "series_number": "1", "volume": "67", "issue": "1", "pages": "247-260" }, { "id": "authors:a1csm-3yn27", "collection": "authors", "collection_id": "a1csm-3yn27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210401-080618288", "type": "article", "title": "Microbially Induced Magnesium Carbonate Precipitation and its Potential Application in Combating Desertification", "author": [ { "family_name": "Zhang", "given_name": "Menglong", "orcid": "0000-0001-6345-9781", "clpid": "Zhang-Menglong" }, { "family_name": "Zhao", "given_name": "Liang", "clpid": "Zhao-Liang" }, { "family_name": "Li", "given_name": "Gen K.", "orcid": "0000-0002-6300-3570", "clpid": "Li-Gen-K" }, { "family_name": "Zhu", "given_name": "Chen", "clpid": "Zhu-Chen" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Li", "given_name": "Zibo", "orcid": "0000-0002-1234-2230", "clpid": "Li-Zibo" }, { "family_name": "Tang", "given_name": "Chaosheng", "clpid": "Tang-Chaosheng" }, { "family_name": "Ji", "given_name": "Junfeng", "clpid": "Ji-Junfeng" }, { "family_name": "Chen", "given_name": "Jun", "clpid": "Chen-Jun" } ], "abstract": "This study investigated the reaction processes of microbially induced magnesium carbonate precipitation (MIMP) with Sporosarcina pasteurii (ATCC 11859) and evaluated its feasibility for controlling desertification in the desert areas in Northwest China. We explored systematically bacterial growth curves, mineralogy of precipitates, and relative chemical conversion efficiencies of the reaction using magnesium carbonate and bacterial urea hydrolysis with Sporosarcina pasteurii. We also compared the results of MIMP with the previously, well-studied microbially induced calcium carbonate precipitation (MICP). Our results indicate that excess Mg\u00b2\u207a motivated bacterial growth slightly. Magnesium carbonate precipitates appeared as nesquehonite, Mg-amorphous calcium carbonate, and Mg-rich calcite. The relative chemical conversion efficiency was higher in Mg medium than in Ca medium. We next evaluated the potential of using MIMP to mitigate desertification. We validated our results using the Mg-rich solution obtained by dissolving abandoned Mg salts that formed from the potassium salt plants nearby salt lakes. MIMP could potentially overcome shortcomings of traditional sand fixing methods, and was particularly suitable for controlling desertification in desert areas in Northwest China where there are abundant Mg resources. If MIMP works at field scales, this approach would further benefit ecosystem reconstruction because MIMP has main products of organic nutrients and ammonia, which would facilitate the development of biomass and soils. Overall, this work provides new insights into MIMP and its geoengineering potential in controlling desertification.", "doi": "10.1080/01490451.2021.1900461", "issn": "0149-0451", "publisher": "Taylor & Francis", "publication": "Geomicrobiology Journal", "publication_date": "2021-03-22", "series_number": "6", "volume": "38", "issue": "6", "pages": "549-560" }, { "id": "authors:fsv35-yjz60", "collection": "authors", "collection_id": "fsv35-yjz60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200922-074257620", "type": "article", "title": "The Dissolution Rate of CaCO\u2083 in the Ocean", "author": [ { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Naviaux", "given_name": "John D.", "orcid": "0000-0002-0681-3163", "clpid": "Naviaux-John-D" }, { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-Adam-V" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" } ], "abstract": "The dissolution of CaCO\u2083 minerals in the ocean is a fundamental part of the marine alkalinity and carbon cycles. While there have been decades of work aimed at deriving the relationship between dissolution rate and mineral saturation state (a so-called rate law), no real consensus has been reached. There are disagreements between laboratory- and field-based studies and differences in rates for inorganic and biogenic materials. Rates based on measurements on suspended particles do not always agree with rates inferred from measurements made near the sediment\u2013water interface of the actual ocean. By contrast, the freshwater dissolution rate of calcite has been well described by bulk rate measurements from a number of different laboratories, fit by basic kinetic theory, and well studied by atomic force microscopy and vertical scanning interferometry to document the processes at the atomic scale. In this review, we try to better unify our understanding of carbonate dissolution in the ocean via a relatively new, highly sensitive method we have developed combined with a theoretical framework guided by the success of the freshwater studies. We show that empirical curve fits of seawater data as a function of saturation state do not agree, largely because the curvature is itself a function of the thermodynamics. Instead, we show that models that consider both surface energetic theory and the complicated speciation of seawater and calcite surfaces in seawater are able to explain most of the most recent data. This new framework can also explain features of the historical data that have not been previously explained. The existence of a kink in the relationship between rate and saturation state, reflecting a change in dissolution mechanism, may be playing an important role in accelerating CaCO\u2083 dissolution in key sedimentary environments.", "doi": "10.1146/annurev-marine-041720-092514", "issn": "1941-1405", "publisher": "Annual Reviews", "publication": "Annual Review of Marine Science", "publication_date": "2021-01", "volume": "13", "pages": "57-80" }, { "id": "authors:bx757-ays38", "collection": "authors", "collection_id": "bx757-ays38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200925-135425366", "type": "article", "title": "A Mechanistic Study of Carbonic Anhydrase Enhanced Calcite Dissolution", "author": [ { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Berelson", "given_name": "William M.", "clpid": "Berelson-William-M" }, { "family_name": "Teng", "given_name": "H. Henry", "clpid": "Teng-H-Henry" }, { "family_name": "Rollins", "given_name": "Nick E.", "clpid": "Rollins-Nick-E" }, { "family_name": "Pirbadian", "given_name": "Sahand", "clpid": "Pirbadian-Sahand" }, { "family_name": "El\u2010Naggar", "given_name": "Mohamed Y.", "clpid": "El\u2010Naggar-Mohamed-Y" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "abstract": "Carbonic anhydrase (CA) has been shown to promote calcite dissolution (Liu, 2001, https://doi.org/10.1111/j.1755-6724.2001.tb00531.x; Subhas et al., 2017, https://doi.org/10.1073/pnas.1703604114), and understanding the catalytic mechanism will facilitate our understanding of the oceanic alkalinity cycle. We use atomic force microscopy (AFM) to directly observe calcite dissolution in CA\u2010bearing solution. CA is found to etch the calcite surface only when in extreme proximity (~1 nm) to the mineral. Subsequently, the CA\u2010induced etch pits create step edges that serve as active dissolution sites. The possible catalytic mechanism is through the adsorption of CA on the calcite surface, followed by proton transfer from the CA catalytic center to the calcite surface during CO2 hydration. This study shows that the accessibility of CA to particulate inorganic carbon (PIC) in the ocean is critical in properly estimating oceanic CaCO3 and alkalinity cycles.", "doi": "10.1029/2020gl089244", "issn": "0094-8276", "publisher": "American Geophysical Union", "publication": "Geophysical Research Letters", "publication_date": "2020-10-16", "series_number": "19", "volume": "47", "issue": "19", "pages": "Art. No. e2020GL089244" }, { "id": "authors:32j94-fx282", "collection": "authors", "collection_id": "32j94-fx282", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200609-071637828", "type": "article", "title": "An Atomic Force Microscopy Study of Calcite Dissolution in Seawater", "author": [ { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Berelson", "given_name": "William M.", "clpid": "Berelson-W-M" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Rollins", "given_name": "Nick E.", "clpid": "Rollins-N-E" }, { "family_name": "Naviaux", "given_name": "John D.", "clpid": "Naviaux-J-D" }, { "family_name": "Pirbadian", "given_name": "Sahand", "clpid": "Pirbadian-Sahand" }, { "family_name": "El-Naggar", "given_name": "Mohamed Y.", "clpid": "El-Naggar-M-Y" }, { "family_name": "Teng", "given_name": "H. Henry", "clpid": "Teng-H-Henry" } ], "abstract": "We present the first examination of calcite dissolution in seawater using Atomic Force Microscopy (AFM). We quantify step retreat velocity and etch pit density to compare dissolution in seawater to low ionic strength water, and also to compare calcite dissolution under AFM conditions to those conducted in bulk solution experiments (e.g. Subhas et al., 2015, Dong et al., 2018). Bulk dissolution rates and step retreat velocities are slower at high and mid-saturation state (\u03a9) values and become comparable to low ionic strength water rates at low \u03a9. The onset of defect-assisted etch pit formation in seawater is at \u03a9\u202f\u223c\u202f0.85 (defined as \u03a9_(critical)), higher than in low ionic strength water (\u03a9\u202f\u223c\u202f0.54). There is an abrupt increase in etch pit density (from \u223c10\u2076 cm\u207b\u00b2 to \u223c10\u2078 cm\u207b\u00b2) occurring when \u03a9 falls below 0.7 in seawater, compared to \u03a9\u202f\u223c\u202f0.1 in low ionic strength water, suggesting a transition from defect-assisted dissolution to homogeneous dissolution much closer to equilibrium in seawater. The step retreat velocity (v) does not scale linearly with undersaturation (1-\u03a9) across an \u03a9 range of 0.4 to 0.9 in seawater, potentially indicating a high order correlation between kink rate and \u03a9 for non-Kossel crystals such as calcite, or surface complexation processes during calcite dissolution in seawater.", "doi": "10.1016/j.gca.2020.05.031", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2020-08-15", "volume": "283", "pages": "40-53" }, { "id": "authors:gy205-z0r22", "collection": "authors", "collection_id": "gy205-z0r22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191024-091357425", "type": "article", "title": "The carbonic anhydrase activity of sinking and suspended particles in the North Pacific Ocean", "author": [ { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-A-V" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Rollins", "given_name": "Nick E.", "clpid": "Rollins-N-E" }, { "family_name": "Berelson", "given_name": "William M.", "clpid": "Berelson-W-M" } ], "abstract": "The enzyme carbonic anhydrase (CA) is crucial to many physiological processes involving CO\u2082, from photosynthesis and respiration, to calcification and CaCO\u2083 dissolution. We present new measurements of CA activity along a North Pacific transect, on samples from in situ pumps, sediment traps, discreet plankton samples from the ship's underway seawater line, plankton tows, and surface sediment samples from multicores. CA activity is highest in the surface ocean and decreases with depth, both in suspended and sinking particles. Subpolar gyre surface particles exhibit 10\u00d7 higher CA activity per liter of seawater compared to subtropical gyre surface particles. Activity persists to 4700\u2009m in the subpolar gyre, but only to 1000\u2009m in the subtropics. All sinking CA activity normalized to particulate organic carbon (POC) follows a single relationship (CA/POC = 1.9\u2009\u00b1\u20090.2\u2009\u00d7\u200910\u207b\u2077 mol\u2009mol\u207b\u00b9). This relationship is consistent with CA/POC values in subpolar plankton tow material, suspended particles, and core top sediments. We hypothesize that most subpolar CA activity is associated with rapidly sinking diatom blooms, consistent with a large mat of diatomaceous material identified on the seafloor. Compared to the basin\u2010wide sinking CA/POC relationship, a lower subtropical CA/POC suggests that the inventory of subtropical biomass is different in composition from exported material. Pteropods also demonstrate substantial CA activity. Scaled to the volume within pteropod shells, first\u2010order CO\u2082 hydration rate constants are elevated \u2265\u20091000\u00d7 above background. This kinetic enhancement is large enough to catalyze carbonate dissolution within microenvironments, providing observational evidence for CA\u2010catalyzed, respiration\u2010driven CaCO\u2083 dissolution in the shallow North Pacific.", "doi": "10.1002/lno.11332", "issn": "0024-3590", "publisher": "American Society of Limnology and Oceanography", "publication": "Limnology and Oceanography", "publication_date": "2020-03", "series_number": "3", "volume": "65", "issue": "3", "pages": "637-651" }, { "id": "authors:n3bvq-3eb35", "collection": "authors", "collection_id": "n3bvq-3eb35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-142418170", "type": "article", "title": "Aragonite dissolution kinetics and calcite/aragonite ratios in sinking and suspended particles in the North Pacific", "author": [ { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" }, { "family_name": "Rollins", "given_name": "Nick E.", "clpid": "Rollins-Nick-E" }, { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-Adam-V" }, { "family_name": "Naviaux", "given_name": "John D.", "orcid": "0000-0002-0681-3163", "clpid": "Naviaux-John-D" }, { "family_name": "Celestian", "given_name": "Aaron J.", "orcid": "0000-0003-0775-6380", "clpid": "Celestian-Aaron-J" }, { "family_name": "Liu", "given_name": "Xuewu", "clpid": "Liu-Xuewu" }, { "family_name": "Turaga", "given_name": "Nitya", "clpid": "Turaga-Nitya" }, { "family_name": "Kemnitz", "given_name": "Nathaniel J.", "clpid": "Kemnitz-Nathaniel-J" }, { "family_name": "Byrne", "given_name": "Robert H.", "orcid": "0000-0003-0726-0131", "clpid": "Byrne-Robert-H" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "abstract": "The lack of consensus on CaCO\u2083 dissolution rates and calcite to aragonite production and export ratios in the ocean poses a significant barrier for the construction of global carbon budgets. We present here a comparison of aragonite dissolution rates measured in the lab vs. in situ along a transect between Hawaii and Alaska using a \u00b9\u00b3C labeling technique. Our results show a general agreement of aragonite dissolution rates in the lab versus in the field, and demonstrate that aragonite, like calcite, shows a non-linear response of dissolution rate as a function of saturation state (\u03a9). Total carbon fluxes along the N. Pacific transect in August 2017, as determined using sediment traps, account for 11\u223c23 weight % of total mass fluxes in the upper 200 m, with a PIC (particulate inorganic carbon)/POC (particulate organic carbon) mole ratio of 0.2\u223c0.6. A comparison of fluxes at depths of 100 m and 200 m indicates that 30\u223c60% PIC dissolves between these depths with 20\u223c70% attenuation in POC fluxes. The molar ratio of PIC to POC loss is 0.29. The simultaneous loss of PIC and POC in the upper 200 m potentially indicates PIC dissolution driven by organic matter respiration, or metazoan/zooplankton consumption. The calcite/aragonite ratio in trap material is significantly lower in the subtropical gyre than in the subarctic gyre. Aragonite fluxes vary from 0.07 to 0.38 mmol m\u207b\u00b2 day\u207b\u00b9 at 100 m, and 0.06 to 0.24 mmol m\u207b\u00b2 day\u207b\u00b9 at 200 m along the North Pacific transect, with no specific trend over latitude. The identification of suspended PIC mineral phases by Raman spectroscopy shows the presence of aragonite below 3000 m in the subtropical gyre, but none in the subpolar gyre. These multiple lines of evidence suggest that predictions based on a strictly thermodynamic view of aragonite dissolution, combined with measured aragonite fluxes, underestimate observed alkalinity excess and measured PIC attenuation in sinking particles. Our measured aragonite flux combined with our inorganic dissolution rate only account for 9% and 0.2% of the excess alkalinity observed in the North Pacific (Feely et al., 2004), assuming aragonite sinking rates of 1 m day\u207b\u00b9 and 100 m day\u207b\u00b9, respectively. However, respiration-driven dissolution or metazoan/zooplankton consumption, indicated by the simultaneous attenuation of PIC and POC in sediment traps, is able to generate the magnitude of dissolution suggested by observed excess alkalinity.", "doi": "10.1016/j.epsl.2019.03.016", "issn": "0012-821X", "publisher": "Elsevier", "publication": "Earth and Planetary Science Letters", "publication_date": "2019-06-01", "volume": "515", "pages": "1-12" }, { "id": "authors:tb3v8-fkw52", "collection": "authors", "collection_id": "tb3v8-fkw52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181205-100011581", "type": "article", "title": "Temperature Dependence of Calcite Dissolution Kinetics in Seawater", "author": [ { "family_name": "Naviaux", "given_name": "John D.", "clpid": "Naviaux-J-D" }, { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-A-V" }, { "family_name": "Rollins", "given_name": "Nick E.", "clpid": "Rollins-N-E" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Berelson", "given_name": "William M.", "clpid": "Berelson-W-M" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "abstract": "Knowledge of calcite dissolution kinetics in seawater is a critical component of our understanding of the changing global carbon budget. Towards this goal, we provide the first measurements of the temperature dependence of calcite dissolution kinetics in seawater. We measured the dissolution rates of ^(13)C-labeled calcite in seawater at 5, 12, 21, and 37\u00b0C across the full range of saturation states (0 < \u03a9 = Ca^(2+)[CO_3^(2-)/Ksp'< 1). We show that the dissolution rate is non-linearly dependent on \u03a9 and that the degree of non-linearity both increases with temperature, and changes abruptly at \"critical\" saturation states (\u03a9_(crit_). The traditional exponential rate law most often utilized in the oceanographic community, R=k(1-\u03a9)^n, requires different fits to k and n depending upon the degree of undersaturation. Though we calculate a similar activation energy to other studies far from equilibrium (25\u00b12 kJ/mol), the exponential rate law could not be used to mechanistically explain our near equilibrium results. We turn to an alternative framework, derived from crystal nucleation theory, and find that our results are consistent with calcite dissolution kinetics in seawater being set by the retreat of pre-existing edges/steps from \u03a9=1-0.9, defect-assisted etch pit formation from \u03a9=0.9-0.75, and finally homogenous etch pit formation from \u03a9=0.75-0. The \u03a9_(crit) s for each mechanism are shifted significantly closer to equilibrium than they occur in dilute solutions, such that ocean acidification may cause marine carbonates to enter faster dissolution regimes more readily than would be expected from previous studies. We use the observed temperature dependence for each dissolution mechanism to calculate step kinetic coefficients (\u03b2, cm/s), densities of active nucleation sites (n_s, sites/m^2), and step edge free energies (\u03b1, mJ/m^2). Homogenous dissolution is well explained within the surface nucleation framework, but defect-assisted dissolution is not. Dissolution is initiated via step-propagation at all temperatures, but the defect-assisted mechanism is skipped over at 5\u00b0C, potentially due to a lack of nucleation sites. The surface nucleation framework enhances our understanding of calcite dissolution in seawater, but our results suggest that a complete theory will also need to incorporate the role of solution/surface speciation and complexation.", "doi": "10.1016/j.gca.2018.11.037", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2019-02-01", "volume": "246", "pages": "363-384" }, { "id": "authors:6ew10-f8b97", "collection": "authors", "collection_id": "6ew10-f8b97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180720-100933524", "type": "article", "title": "A Kinetic Pressure Effect on Calcite Dissolution in Seawater", "author": [ { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-Adam-V" }, { "family_name": "Rollins", "given_name": "Nick E.", "clpid": "Rollins-Nick-E" }, { "family_name": "Naviaux", "given_name": "John D.", "orcid": "0000-0002-0681-3163", "clpid": "Naviaux-John-D" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" } ], "abstract": "This study provides laboratory data of calcite dissolution rate as a function of seawater undersaturation state (1-\u03a9) under variable pressure. \u00b9\u00b3C-labeled calcite was dissolved in unlabeled seawater and the evolving \u03b4\u00b9\u00b3C composition of the fluid was monitored over time to evaluate the dissolution rate. Results show that dissolution rates are enhanced by a factor of 2-4 at 700 dbar compared to dissolution at the same \u03a9 under ambient pressure (10 dbar). This dissolution rate enhancement under pressure applies over an \u03a9 range of 0.65 to 1 between 10 dbar and 700 dbar. Above 700 dbar (up to 2500 dbar), dissolution rates become independent of pressure. The observed enhancement is well beyond the uncertainty associated with the thermodynamic properties of calcite under pressure (partial molar volume \u0394V), and thus should be interpreted as a kinetic pressure effect on calcite dissolution. Dissolution at ambient pressure and higher pressures yield non-linear dissolution kinetics, the pressure effect does not significantly change the reaction order n in Rate = k(1-\u03a9^)n, which is shown to vary from 3.1 \u00b1 0.3 to 3.8 \u00b1 0.5 from 10 dbar to 700 dbar over \u03a9 = 0.65 to 0.9. Furthermore, two different dissolution mechanisms are indicated by a discontinuity in the rate-undersaturation relationship, and seen at both ambient and higher pressures. The discontinuity, \u03a9_(critical) = 0.87 \u00b1 0.05 and 0.90 \u00b1 0.03 at 10 dbar and 1050 dbar respectively, are similar within error. The reaction order, n, at \u03a9 > 0.9 is 0.47 \u00b1 0.27 and 0.46 \u00b1 0.15 at 10 dbar and 700 dbar respectively. This \u03a9_(critical) is considered to be the threshold between step retreat dissolution and defect-assisted dissolution. The kinetic enhancement of dissolution rate at higher pressures is related to a decrease in the interfacial energy barrier at dissolution sites. The impact of pressure on the calcite dissolution kinetics implies that sinking particles would dissolve at shallower depth than previously thought.", "doi": "10.1016/j.gca.2018.07.015", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2018-10-01", "volume": "238", "pages": "411-423" }, { "id": "authors:z4bm0-xpv39", "collection": "authors", "collection_id": "z4bm0-xpv39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160622-080207374", "type": "article", "title": "Conformational and Thermodynamic Landscape of GPCR Activation from Theory and Computation", "author": [ { "family_name": "Dong", "given_name": "Sijia S.", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" } ], "abstract": "We present a hybrid computational methodology to predict multiple energetically accessible conformations for G protein-coupled receptors (GPCRs) that might play a role in binding to ligands and different signaling partners. To our knowledge, this method, termed ActiveGEnSeMBLE, enables the first quantitative energy profile for GPCR activation that is consistent with the qualitative profile deduced from experiments. ActiveGEnSeMBLE starts with a systematic coarse grid sampling of helix tilts/rotations (\u223c13 trillion transmembrane-domain conformations) and selects the conformational landscape based on energy. This profile identifies multiple potential active-state energy wells, with the TM3\u2013TM6 intracellular distance as an approximate activation coordinate. These energy wells are then sampled locally using a finer grid to find locally minimized conformation in each energy well. We validate this strategy using the inactive and active experimental structures of \u03b2_2 adrenergic receptor (h\u03b2_2AR) and M2 muscarinic acetylcholine receptor. Structures of membrane-embedded h\u03b2_2AR along its activation coordinate are subjected to molecular-dynamics simulations for relaxation and interaction energy analysis to generate a quantitative energy landscape for h\u03b2_2AR activation. This landscape reveals several metastable states along this coordinate, indicating that for h\u03b2_2AR, the agonist alone is not enough to stabilize the active state and that the G protein is necessary, consistent with experimental observations. The method's application to somatostatin receptor SSTR5 (no experimental structure available) shows that to predict an active conformation it is better to start from an inactive structure template based on a close homolog than to start from an active template based on a distant homolog. The energy landscape for hSSTR5 activation is consistent with h\u03b2_2AR in the role of the G protein. These results demonstrate the utility of the ActiveGEnSeMBLE method for predicting multiple conformations along the pathways for activating GPCRs and the corresponding energy landscapes, thereby providing detailed structural insights into the initial molecular events of GPCR function that are not easily accessible by experiments.", "doi": "10.1016/j.bpj.2016.04.028", "pmcid": "PMC4919603", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2016-06-21", "series_number": "12", "volume": "110", "issue": "12", "pages": "2618-2629" }, { "id": "authors:bzbdj-tkk57", "collection": "authors", "collection_id": "bzbdj-tkk57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150914-094735715", "type": "article", "title": "A novel determination of calcite dissolution kinetics in seawater", "author": [ { "family_name": "Subhas", "given_name": "Adam V.", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-A-V" }, { "family_name": "Rollins", "given_name": "Nick E.", "clpid": "Rollins-N-E" }, { "family_name": "Berelson", "given_name": "William M.", "clpid": "Berelson-W-M" }, { "family_name": "Dong", "given_name": "Sijia", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Erez", "given_name": "Jonathan", "clpid": "Erez-J" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "abstract": "We present a novel determination of the dissolution kinetics of inorganic calcite in seawater. We dissolved ^(13)C-labeled calcite in unlabeled seawater, and traced the evolving \u03b4^(13)C composition of the fluid over time to establish dissolution rates. This method provides sensitive determinations of dissolution rate, which we couple with tight constraints on both seawater saturation state and surface area of the dissolving minerals. We have determined dissolution rates for two different abiotic calcite materials and three different grain sizes. Near-equilibrium dissolution rates are highly nonlinear, and are well normalized by geometric surface area, giving an empirical dissolution rate dependence on saturation state (\u03a9) of:\n\nRate (g/cm^2/day) = 7.2 \u00b1 0.6 \u00b7 10^(-4) (1-\u03a9)^(3.9\u00b10.1).\n \nThis result substantiates the non-linear response of calcite dissolution to undersaturation. The bulk dissolution rate constant calculated here is in excellent agreement with those determined in far from equilibrium and dilute solution experiments. Plots of dissolution versus undersaturation indicates the presence of at least two dissolution mechanisms, implying a criticality in the calcite-seawater system. Finally, our new rate determination has implications for modeling of pelagic and seafloor dissolution. Nonlinear dissolution kinetics in a simple 1-D lysocline model indicate a possible transition from kinetic to diffusive control with increasing water depth, and also confirm the importance of respiration-driven dissolution in setting the shape of the calcite lysocline.", "doi": "10.1016/j.gca.2015.08.011", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2015-12-01", "volume": "170", "pages": "51-68" }, { "id": "authors:afxhv-mxj11", "collection": "authors", "collection_id": "afxhv-mxj11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150812-101036401", "type": "article", "title": "Computational predictions of corroles as a class of Hsp90 inhibitors", "author": [ { "family_name": "Teo", "given_name": "Ruijie D.", "clpid": "Teo-R-D" }, { "family_name": "Dong", "given_name": "Sijia S.", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Gross", "given_name": "Zeev", "clpid": "Gross-Z" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Corroles have been shown experimentally to cause cell cycle arrest, and there is some evidence that this might be attributed to an inhibitory effect of corroles on Heat shock protein 90 (Hsp90), which is known to play a vital role in cancer cell proliferation. In this study, we used molecular dynamics to examine the interaction of gallium corroles with Hsp90, and found that they can bind preferentially to the ATP-binding N-terminal site. We also found that structural variations of the corrole ring can influence the binding energies and affinities of the corrole to Hsp90. We predict that both the biscarboxylated corrole (4-Ga) and a proposed 3,17-bis-sulfonated corrole (7-Ga) are promising alternatives to Ga(III) 5,10,15-tris(pentafluorophenyl)-2,17-bis(sulfonic acid)-corrole (1-Ga) as anti-cancer agents.", "doi": "10.1039/c5mb00352k", "issn": "1742-206X", "publisher": "Royal Society of Chemistry", "publication": "Molecular BioSystems", "publication_date": "2015-11", "series_number": "11", "volume": "11", "issue": "11", "pages": "2907-2914" }, { "id": "authors:pkx7z-vrq29", "collection": "authors", "collection_id": "pkx7z-vrq29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150323-093730177", "type": "article", "title": "The Predicted Ensemble of Low-Energy Conformations of Human Somatostatin Receptor Subtype 5 and the Binding of Antagonists", "author": [ { "family_name": "Dong", "given_name": "Sijia S.", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Human somatostatin receptor subtype\u20055 (hSSTR5) regulates cell proliferation and hormone secretion. However, the identification of effective therapeutic small-molecule ligands is impeded because experimental structures are not available for any SSTR subtypes. Here, we predict the ensemble of low-energy 3D structures of hSSTR5 using a modified GPCR Ensemble of Structures in Membrane BiLayer Environment (GEnSeMBLE) complete sampling computational method. We find that this conformational ensemble displays most interhelical interactions conserved in class\u2005A G\u2005protein-coupled receptors (GPCRs) plus seven additional interactions (e.g., Y2.43\u2013D3.49, T3.38\u2013S4.53, K5.64\u2013Y3.51) likely conserved among SSTRs. We then predicted the binding sites for a series of five known antagonists, leading to predicted binding energies consistent with experimental results reported in the literature. Molecular dynamics (MD) simulation of 50\u2005ns in explicit water and lipid retained the predicted ligand-bound structure and formed new interaction patterns (e.g. R3.50\u2013T6.34) consistent with the inactive \u03bc-opioid receptor X-ray structure. We suggest more than six mutations for experimental validation of our prediction. The final predicted receptor conformations and antagonist binding sites provide valuable insights for designing new small-molecule drugs targeting SSTRs.", "doi": "10.1002/cmdc.201500023", "issn": "1860-7179", "publisher": "Wiley-Blackwell", "publication": "ChemMedChem", "publication_date": "2015-04", "series_number": "4", "volume": "10", "issue": "4", "pages": "650-661" }, { "id": "authors:c1d32-ehd80", "collection": "authors", "collection_id": "c1d32-ehd80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140710-092918920", "type": "article", "title": "Computational Prediction of the Class a GPCR Active State Conformations", "author": [ { "family_name": "Dong", "given_name": "Sijia S.", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "There has been a great need for computational prediction of G-protein coupled receptor (GPCR) structures, especially those in their active states, in order to assist drug discovery. However, the active state conformation prediction is challenging not only because of the lack of homology templates derived from the existing active state X-ray structures, but also because of the high energy nature of the active conformations. In addition, experimental evidence suggests that a GPCR can have many different active states, but the existing several crystal structures usually only capture one of those states for each GPCR. Here we present a method to make the GPCR active state structural prediction possible, and our method can discover a number of active states for each GPCR. Instead of the traditional homology modeling, we used a template from mixed sources and sampled a discrete set of orientations of the seven transmembrane helices of the GPCR to locate structures that are likely to be in the active-state valley on the energy surface. Next, we did a local conformational sampling to find structures at the local minima of the active-state potential energy valleys. We have benchmarked the method with human \u03b2_2 adrenergic receptor, which has both its active and inactive state structures crystalized. Then we applied the method on a GPCR with unknown structure, the human somatostatin receptor subtype 5 (hSSTR5). Docking of agonists and antagonists to the predicted active and inactive state structures of hSSTR5 gave the expected result that antagonists favor the inactive state structures, while the agonists could not distinguish the inactive and active state structures without the presence of G proteins. In the end, we were able to build a model picture of hSSTR5 function consistent with experimental findings.", "doi": "10.1016/j.bpj.2013.11.1786", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2014-01-28", "series_number": "2", "volume": "106", "issue": "2", "pages": "308A" }, { "id": "authors:0vcvf-sx493", "collection": "authors", "collection_id": "0vcvf-sx493", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110404-100258063", "type": "article", "title": "Electronic Structures of Group 9 Metallocorroles with Axial Ammines", "author": [ { "family_name": "Dong", "given_name": "Sijia S.", "orcid": "0000-0002-5811-9333", "clpid": "Dong-Sijia-S" }, { "family_name": "Nielsen", "given_name": "Robert J.", "orcid": "0000-0002-7962-0186", "clpid": "Nielsen-R-J" }, { "family_name": "Palmer", "given_name": "Joshua H.", "clpid": "Palmer-J-H" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Gross", "given_name": "Zeev", "clpid": "Gross-Z" }, { "family_name": "Dasgupta", "given_name": "Siddharth", "orcid": "0000-0002-9161-7457", "clpid": "Dasgupta-S" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "The electronic structures of metallocorroles (tpfc)M(NH_3)_2 and (tfc)M(NH_3)_2 (tpfc is the trianion of 5,10,15-(tris)pentafluorophenylcorrole, tfc is the trianion of 5,10,15-trifluorocorrole, and M = Co, Rh, Ir) have been computed using first principles quantum mechanics [B3LYP flavor of Density Functional Theory (DFT) with Poisson\u2212Boltzmann continuum solvation]. The geometry was optimized for both the neutral systems (formal M^(III) oxidation state) and the one-electron oxidized systems (formally M^(IV)). As expected, the M^(III) systems have a closed shell d^6 configuration; for all three metals, the one-electron oxidation was calculated to occur from a ligand-based orbital (highest occupied molecular orbital (HOMO) of B_1 symmetry). The ground state of the formal M^(IV) system has M^(III)-C\u03c0 character, indicating that the metal remains d^6, with the hole in the corrole \u03c0 system. As a result the calculated M^(IV/III) reduction potentials are quite similar (0.64, 0.67, and 0.56 V vs SCE for M = Ir, Rh and Co, respectively), whereas the differences would have been large for purely metal-based oxidations. Vertically excited states with substantial metal character are well separated from the ground state in one-electron-oxidized cobalt (0.27 eV) and rhodium (0.24 eV) corroles, but become closer in energy in the iridium (0.15 eV) analogues. The exact splittings depend on the chosen functional and basis set combination and vary by ~0.1 eV.", "doi": "10.1021/ic1005902", "issn": "0020-1669", "publisher": "American Chemical Society", "publication": "Inorganic Chemistry", "publication_date": "2011-02-07", "series_number": "3", "volume": "50", "issue": "3", "pages": "764-770" } ]