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2. Transfer Learning for Protein Structure Classification at Low Resolution

Author

Hudson, Alexander and Gong, Shaogang

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Quantitative Biology - Biomolecules, I.2, I.4
Abstract

Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive, time-consuming analytical methods to visualise detailed protein conformation. In this study, we demonstrate that it is possible to make accurate ($\geq$80%) predictions of protein class and architecture from structures determined at low ($>$3A) resolution, using a deep convolutional neural network trained on high-resolution ($\leq$3A) structures represented as 2D matrices. Thus, we provide proof of concept for high-speed, low-cost protein structure classification at low resolution, and a basis for extension to prediction of function. We investigate the impact of the input representation on classification performance, showing that side-chain information may not be necessary for fine-grained structure predictions. Finally, we confirm that high-resolution, low-resolution and NMR-determined structures inhabit a common feature space, and thus provide a theoretical foundation for boosting with single-image super-resolution., Comment: 9 pages excluding references and appendices

Published
2020

3. Magnitude and pacing of Early Jurassic palaeoclimate change : chemostratigraphy and cyclostratigraphy of the British Lower Jurassic (Sinemurian-Pliensbachian)

Author

Hudson, Alexander Joseph Leslie, Hesselbo, S., Littler, K., and Riding, J.

Subjects
Geology, Geoscience, Palaeoclimate, Paleoclimate, Climate, Sedimentology, Cyclostratigraphy, Stratigraphy, Chemostratigraphy, Jurassic, Sinemurian, XRF, Burton Row, Mochras, Mercury Analysis, Astrochronology, Pliensbachian, Somerset
Abstract

Palaeoclimate research in the Early Jurassic (201.4-174.1 million years ago) has historically focussed on geologically short, large-magnitude climatic events such as the Triassic-Jurassic (T-J) boundary mass extinction and the Toarcian Oceanic Anoxic Event (T-OAE). However, the climate system in the remaining ~18 myr of the Early Jurassic is significantly under studied; particularly given the identification of several smaller magnitude and crucially, less well understood carbon-cycle perturbations. In this thesis, I examine the Sinemurian-Early Pliensbachian from three sites: two archived British Geological Survey (BGS) boreholes (Mochras Borehole Cardigan Bay, Wales and Burton Row Borehole, Somerset, England) as-well-as the Robin Hood's Bay coastal exposure, Yorkshire, England. I present new, high-resolution multiple-proxy chemostratigraphy (hand-held X-ray fluorescence, stable isotope (δ13Cbulk-org & wood), Rock Eval pyrolysis and Mercury concentration data) through the interval, in order to elucidate the climate and carbon cycle evolution. I demonstrate the reproducibility of two negative carbon cycle excursions of ~4 ‰ δ13Corg associated with enhanced organic burial, marine flooding surfaces and shallow marine dysoxia; the first across the obtusum-oxynotum zone and the second at the Sinemurian-Pliensbachian boundary (raricostatum-jamesoni Zones). Mercury analysis of samples from the Burton Row borehole suggest LIP volcanism did not force climatic change in the Sinemurian and Early Pliensbachian with largely background values of Hg/TOC and no correlation of Mercury enrichment with intervals of isotopically light carbon (or dates of late phase CAMP). Spectral analysis of the high-resolution chemostratigraphy reveals evidence of Milankovitch cyclicity embedded within all studied records and proxies. This finding allows the generation of a robust orbitally tuned age model for the Sinemurian providing an estimate of 7.18 myr for the stage duration. The astronomically tuned age model suggests approximately 0.6-0.8 myr for the obtusum-oxynotum zone CIE and 1.8 myr for the SPBE. The events coincide precisely with the 2.4 myr long eccentricity maxima alluding to an orbital eccentricity control on the carbon cycle and climate. A novel methodology for quantifying the amount of time held within cryptic hiatuses is presented based upon integrating sequence stratigraphy and astrochronology. This method allows the quantification of at least 200-400 kyr of missing time held within several levels in the Robin Hoods bay Sinemurian record. To this end, the results of this thesis provide a compelling insight into an interval of time seldom studied. The analysis of the competing effects of large igneous province volcanism and orbital forcing gives strong evidence for the latter as the primary driver of palaeoclimate change in the Sinemurian and raises intriguing questions about the context of the larger- magnitude Early Jurassic OAEs. Geochemical data from multiple sites provides the means to generate a robust astrochronology for the Sinemurian that has implications for the apportioned time in the Early Jurassic.

Published
2021

5. On the nature of the glass transition in atomistic models of glass formers

Author

Hudson, Alexander and Mandadapu, Kranthi K.

Subjects
Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter
Abstract

We study the nature of the glass transition by cooling model atomistic glass formers at constant rate from a temperature above the onset of glassy dynamics to $T=0$. Motivated by the East model, a kinetically constrained lattice model with hierarchical relaxation, we make several predictions about the behavior of the supercooled liquid as it passes through the glass transition. We then compare those predictions to the results of our atomistic simulations. Consistent with our predictions, our results show that the relaxation time $\tau$ of the material undergoes a crossover from super-Arrhenius to Arrhenius behavior at a cooling-rate-dependent glass transition temperature $T_\text{g}$. The slope of $\ln\tau$ with respect to inverse temperature exhibits a peak near $T_\text{g}$ that grows more pronounced with slower cooling, matching our expectations qualitatively. Additionally, the limiting value of this slope at low temperature shows remarkable quantitative agreement with our predictions. Our results also show that the rate of short-time particle displacements deviates from the equilibrium linear scaling around $T_\text{g}$, asymptotically approaching a different linear scaling. To our surprise, these short-time displacements, the dynamic indicators of the underlying excitations responsible for structural relaxation, show no spatial correlations beyond a few particle diameters, both above and below $T_\text{g}$. This final result is contrary to our expectation, based on previous results for East model glasses formed by cooling, that inter-excitation correlations should emerge as the liquid vitrifies., Comment: Supplemental Material was added in this version and can be found under "Ancillary files"

Published
2018

14. Rough interfaces, accurate predictions: The necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation

Author

Vaikuntanathan, Suriyanarayanan, Rotskoff, Grant M, Hudson, Alexander, and Geissler, Phillip

Subjects
Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter, Physics - Chemical Physics
Abstract

Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing in particular the importance of interfaces that emerge in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here we show that a coarse-grained lattice model in the spirit of those pioneered by Chandler and coworkers, when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many standard deviations from the mean, and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, as the model is fully specified by well-known properties of liquid water. As illustrative examples of its utility, we characterize the free energy profile for a solute crossing the air-water interface, and compute the thermodynamic cost of evacuating the space between extended nanoscale surfaces. Together, these calculations suggest that a highly reduced model for aqueous solvation can serve as the basis for efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces., Comment: 14 pages, 7 figures

Published
2015
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17. Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation

Author

Vaikuntanathan, Suriyanarayanan, Rotskoff, Grant, Hudson, Alexander, and Geissler, Phillip L

Subjects
Physical Sciences, Classical Physics, Hydrophobic and Hydrophilic Interactions, Models, Chemical, Thermodynamics, hydrophobic effect, self-assembly, coarse-grained model, lattice models, cond-mat.stat-mech, cond-mat.soft, physics.chem-ph
Abstract

Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing the importance of interfaces in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here, we show that a coarse-grained lattice model like that of Chandler [Chandler D (2005)Nature437(7059):640-647], when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many SDs from the mean and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, because the model is fully specified by well-known properties of liquid water. As examples of its utility, we compute the free-energy profile for a solute crossing the air-water interface, as well as the thermodynamic cost of evacuating the space between extended nanoscale surfaces. These calculations suggest that a highly reduced model for aqueous solvation can enable efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces.

Published
2016

19. Efforts towards the total synthesis of labelled CCL2 proteins and dipeptide chemotaxis inhibitors

Author

Hudson, Alexander Stephen

Subjects
540
Abstract

Chemokines such as CCL2 are small proteins with molecular weights between 8-10 kDa. They promote chemotaxis and play a vital role in the recruitment of leukocytes to the site of inflammation. Given their key biological functions, understanding their mechanism of action and inhibiting their action has therapeutic potential in a range of diseases. Selective inhibitors of CCL2 induced chemotaxis based on the diketopiperazine (DKP) natural product, cyclo(13,15-dichloro-L-Pro-L-Tyr) were recently reported by the Cobb group. In order to develop this work further and to produce an expanded library, we optimised an on-resin DKP synthesis. In collaboration with researchers at Newcastle Medical School, chemotaxis assays were performed in an attempted to define the structural features (required for inhibition) of the DKPs. To faciliate the aforementioned work, facile synthetic routes to a number of novel heteraromatic and proline derivatives were developed. The posttranslational nitration of CCL2 is used as a mechanism to a modulate CCL2. However, in all previous studies nitrated CCL2 was utilised as a heterogeneous mix of protein. Having access to single site nitrated CCL2 will enable the mechanism of abrogration to be pinpointed to a specific residue. Therefore, the total chemical synthesis of both native CCL2 and site-specifically nitrated CCL2 via solid phase peptide synthesis (SPPS) was undertaken. The work focused on the potential application of microwave assisted SPPS as a means to rapidly access the target proteins.

Published
2015

20. The Cyclostratigraphy Intercomparison Project (CIP): consistency, merits and pitfalls

Author

Sinnesael, Matthias, De Vleeschouwer, David, Zeeden, Christian, Batenburg, Sietske J., Da Silva, Anne-Christine, de Winter, Niels J., Dinarès-Turell, Jaume, Drury, Anna Joy, Gambacorta, Gabriele, Hilgen, Frederik J., Hinnov, Linda A., Hudson, Alexander J.L., Kemp, David B., Lantink, Margriet L., Laurin, Jiří, Li, Mingsong, Liebrand, Diederik, Ma, Chao, Meyers, Stephen R., Monkenbusch, Johannes, Montanari, Alessandro, Nohl, Theresa, Pälike, Heiko, Pas, Damien, Ruhl, Micha, Thibault, Nicolas, Vahlenkamp, Maximilian, Valero, Luis, Wouters, Sébastien, Wu, Huaichun, and Claeys, Philippe

Published
2019
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21. Initial results of coring at Prees, Cheshire Basin, UK (ICDP JET project): towards an integrated stratigraphy, timescale, and Earth system understanding for the Early Jurassic

Author

Hesselbo, Stephen P., primary, Al-Suwaidi, Aisha, additional, Baker, Sarah J., additional, Ballabio, Giorgia, additional, Belcher, Claire M., additional, Bond, Andrew, additional, Boomer, Ian, additional, Bos, Remco, additional, Bjerrum, Christian J., additional, Bogus, Kara, additional, Boyle, Richard, additional, Browning, James V., additional, Butcher, Alan R., additional, Condon, Daniel J., additional, Copestake, Philip, additional, Daines, Stuart, additional, Dalby, Christopher, additional, Damaschke, Magret, additional, Damborenea, Susana E., additional, Deconinck, Jean-Francois, additional, Dickson, Alexander J., additional, Fendley, Isabel M., additional, Fox, Calum P., additional, Fraguas, Angela, additional, Frieling, Joost, additional, Gibson, Thomas A., additional, He, Tianchen, additional, Hickey, Kat, additional, Hinnov, Linda A., additional, Hollaar, Teuntje P., additional, Huang, Chunju, additional, Hudson, Alexander J. L., additional, Jenkyns, Hugh C., additional, Idiz, Erdem, additional, Jiang, Mengjie, additional, Krijgsman, Wout, additional, Korte, Christoph, additional, Leng, Melanie J., additional, Lenton, Timothy M., additional, Leu, Katharina, additional, Little, Crispin T. S., additional, MacNiocaill, Conall, additional, Manceñido, Miguel O., additional, Mather, Tamsin A., additional, Mattioli, Emanuela, additional, Miller, Kenneth G., additional, Newton, Robert J., additional, Page, Kevin N., additional, Pálfy, József, additional, Pieńkowski, Gregory, additional, Porter, Richard J., additional, Poulton, Simon W., additional, Riccardi, Alberto C., additional, Riding, James B., additional, Roper, Ailsa, additional, Ruhl, Micha, additional, Silva, Ricardo L., additional, Storm, Marisa S., additional, Suan, Guillaume, additional, Szűcs, Dominika, additional, Thibault, Nicolas, additional, Uchman, Alfred, additional, Stanley, James N., additional, Ullmann, Clemens V., additional, van de Schootbrugge, Bas, additional, Vickers, Madeleine L., additional, Wadas, Sonja, additional, Whiteside, Jessica H., additional, Wignall, Paul B., additional, Wonik, Thomas, additional, Xu, Weimu, additional, Zeeden, Christian, additional, and Zhao, Ke, additional

Published
2023
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24. Remarkably low affinity of CD4/peptide-major histocompatibility complex class II protein interactions

Author

Jönsson, Peter, Southcombe, Jennifer H., Santos, Ana Mafalda, Huo, Jiandong, Fernandes, Ricardo A., McColl, James, Lever, Melissa, Evans, Edward J., Hudson, Alexander, Chang, Veronica T., Hanke, Tomáš, Godkin, Andrew, Dunne, Paul D., Horrocks, Mathew H., Palayret, Matthieu, Screaton, Gavin R., Petersen, Jan, Rossjohn, Jamie, Fugger, Lars, Dushek, Omer, Xu, Xiao-Ning, Davis, Simon J., and Klenerman, David

Published
2016

27. Initial results of coring at Prees, Cheshire Basin, UK (ICDP JET project): Towards an integrated stratigraphy, timescale, and Earth system understanding for the Early Jurassic

Author

Hesselbo, Stephen P., Al-Suwaidi, Aisha, Baker, Sarah J., Ballabio, Giorgia, Belcher, Claire M., Bond, Andrew, Boomer, Ian, Bos, Remco, Bjerrum, Christian J., Bogus, Kara, Boyle, Richard, Browning, James V., Butcher, Alan R., Condon, Daniel J., Copestake, Philip, Daines, Stuart, Dalby, Christopher, Damaschke, Magret, Damborenea, Susana E., Deconinck, Jean Francois, Dickson, Alexander J., Fendley, Isabel M., Fox, Calum P., Fraguas, Angela, Frieling, Joost, Gibson, Thomas A., He, Tianchen, Hickey, Kat, Hinnov, Linda A., Hollaar, Teuntje P., Huang, Chunju, Hudson, Alexander J.L., Jenkyns, Hugh C., Idiz, Erdem, Jiang, Mengjie, Krijgsman, Wout, Korte, Christoph, Leng, Melanie J., Lenton, Timothy M., Leu, Katharina, Little, Crispin T.S., Macniocaill, Conall, Manceñido, Miguel O., Mather, Tamsin A., Mattioli, Emanuela, Miller, Kenneth G., Newton, Robert J., Page, Kevin N., Pálfy, József, Pieńkowski, Gregory, Porter, Richard J., Poulton, Simon W., Riccardi, Alberto C., Riding, James B., Roper, Ailsa, Ruhl, Micha, Silva, Ricardo L., Storm, Marisa S., Suan, Guillaume, Szűcs, Dominika, Thibault, Nicolas, Uchman, Alfred, Stanley, James N., Ullmann, Clemens V., Van De Schootbrugge, Bas, Vickers, Madeleine L., Wadas, Sonja, Whiteside, Jessica H., Wignall, Paul B., Wonik, Thomas, Xu, Weimu, Zeeden, Christian, Zhao, Ke, Hesselbo, Stephen P., Al-Suwaidi, Aisha, Baker, Sarah J., Ballabio, Giorgia, Belcher, Claire M., Bond, Andrew, Boomer, Ian, Bos, Remco, Bjerrum, Christian J., Bogus, Kara, Boyle, Richard, Browning, James V., Butcher, Alan R., Condon, Daniel J., Copestake, Philip, Daines, Stuart, Dalby, Christopher, Damaschke, Magret, Damborenea, Susana E., Deconinck, Jean Francois, Dickson, Alexander J., Fendley, Isabel M., Fox, Calum P., Fraguas, Angela, Frieling, Joost, Gibson, Thomas A., He, Tianchen, Hickey, Kat, Hinnov, Linda A., Hollaar, Teuntje P., Huang, Chunju, Hudson, Alexander J.L., Jenkyns, Hugh C., Idiz, Erdem, Jiang, Mengjie, Krijgsman, Wout, Korte, Christoph, Leng, Melanie J., Lenton, Timothy M., Leu, Katharina, Little, Crispin T.S., Macniocaill, Conall, Manceñido, Miguel O., Mather, Tamsin A., Mattioli, Emanuela, Miller, Kenneth G., Newton, Robert J., Page, Kevin N., Pálfy, József, Pieńkowski, Gregory, Porter, Richard J., Poulton, Simon W., Riccardi, Alberto C., Riding, James B., Roper, Ailsa, Ruhl, Micha, Silva, Ricardo L., Storm, Marisa S., Suan, Guillaume, Szűcs, Dominika, Thibault, Nicolas, Uchman, Alfred, Stanley, James N., Ullmann, Clemens V., Van De Schootbrugge, Bas, Vickers, Madeleine L., Wadas, Sonja, Whiteside, Jessica H., Wignall, Paul B., Wonik, Thomas, Xu, Weimu, Zeeden, Christian, and Zhao, Ke

Abstract

Drilling for the International Continental Scientific Drilling Program (ICDP) Early Jurassic Earth System and Timescale project (JET) was undertaken between October 2020 and January 2021. The drill site is situated in a small-scale synformal basin of the latest Triassic to Early Jurassic age that formed above the major Permian-Triassic half-graben system of the Cheshire Basin. The borehole is located to recover an expanded and complete succession to complement the legacy core from the Llanbedr (Mochras Farm) borehole drilled through 1967-1969 on the edge of the Cardigan Bay Basin, North Wales. The overall aim of the project is to construct an astronomically calibrated integrated timescale for the Early Jurassic and to provide insights into the operation of the Early Jurassic Earth system. Core of Quaternary age cover and Early Jurassic mudstone was obtained from two shallow partially cored geotechnical holes (Prees 2A to 32.2g¯m below surface (mg¯b.s.) and Prees 2B to 37.0g¯mg¯b.s.) together with Early Jurassic and Late Triassic mudstone from the principal hole, Prees 2C, which was cored from 32.92 to 651.32g¯m (corrected core depth scale). Core recovery was 99.7g¯% for Prees 2C. The ages of the recovered stratigraphy range from the Late Triassic (probably Rhaetian) to the Early Jurassic, Early Pliensbachian (Ibex Ammonoid Chronozone). All ammonoid chronozones have been identified for the drilled Early Jurassic strata. The full lithological succession comprises the Branscombe Mudstone and Blue Anchor formations of the Mercia Mudstone Group, the Westbury and Lilstock formations of the Penarth Group, and the Redcar Mudstone Formation of the Lias Group. A distinct interval of siltstone is recognized within the Late Sinemurian of the Redcar Mudstone Formation, and the name "Prees Siltstone Member"is proposed. Depositional environments range from playa lake in the Late Triassic to distal offshore marine in the Early Jurassic. Initial datasets compiled from the core in

Published
2023

28. Initial results of coring at Prees, Cheshire Basin, UK (ICDP JET project): Towards an integrated stratigraphy, timescale, and Earth system understanding for the Early Jurassic

Author

Marine palynology and palaeoceanography, Paleomagnetism, Marine Palynology, Hesselbo, Stephen P., Al-Suwaidi, Aisha, Baker, Sarah J., Ballabio, Giorgia, Belcher, Claire M., Bond, Andrew, Boomer, Ian, Bos, Remco, Bjerrum, Christian J., Bogus, Kara, Boyle, Richard, Browning, James V., Butcher, Alan R., Condon, Daniel J., Copestake, Philip, Daines, Stuart, Dalby, Christopher, Damaschke, Magret, Damborenea, Susana E., Deconinck, Jean Francois, Dickson, Alexander J., Fendley, Isabel M., Fox, Calum P., Fraguas, Angela, Frieling, Joost, Gibson, Thomas A., He, Tianchen, Hickey, Kat, Hinnov, Linda A., Hollaar, Teuntje P., Huang, Chunju, Hudson, Alexander J.L., Jenkyns, Hugh C., Idiz, Erdem, Jiang, Mengjie, Krijgsman, Wout, Korte, Christoph, Leng, Melanie J., Lenton, Timothy M., Leu, Katharina, Little, Crispin T.S., Macniocaill, Conall, Manceñido, Miguel O., Mather, Tamsin A., Mattioli, Emanuela, Miller, Kenneth G., Newton, Robert J., Page, Kevin N., Pálfy, József, Pieńkowski, Gregory, Porter, Richard J., Poulton, Simon W., Riccardi, Alberto C., Riding, James B., Roper, Ailsa, Ruhl, Micha, Silva, Ricardo L., Storm, Marisa S., Suan, Guillaume, Szűcs, Dominika, Thibault, Nicolas, Uchman, Alfred, Stanley, James N., Ullmann, Clemens V., Van De Schootbrugge, Bas, Vickers, Madeleine L., Wadas, Sonja, Whiteside, Jessica H., Wignall, Paul B., Wonik, Thomas, Xu, Weimu, Zeeden, Christian, Zhao, Ke, Marine palynology and palaeoceanography, Paleomagnetism, Marine Palynology, Hesselbo, Stephen P., Al-Suwaidi, Aisha, Baker, Sarah J., Ballabio, Giorgia, Belcher, Claire M., Bond, Andrew, Boomer, Ian, Bos, Remco, Bjerrum, Christian J., Bogus, Kara, Boyle, Richard, Browning, James V., Butcher, Alan R., Condon, Daniel J., Copestake, Philip, Daines, Stuart, Dalby, Christopher, Damaschke, Magret, Damborenea, Susana E., Deconinck, Jean Francois, Dickson, Alexander J., Fendley, Isabel M., Fox, Calum P., Fraguas, Angela, Frieling, Joost, Gibson, Thomas A., He, Tianchen, Hickey, Kat, Hinnov, Linda A., Hollaar, Teuntje P., Huang, Chunju, Hudson, Alexander J.L., Jenkyns, Hugh C., Idiz, Erdem, Jiang, Mengjie, Krijgsman, Wout, Korte, Christoph, Leng, Melanie J., Lenton, Timothy M., Leu, Katharina, Little, Crispin T.S., Macniocaill, Conall, Manceñido, Miguel O., Mather, Tamsin A., Mattioli, Emanuela, Miller, Kenneth G., Newton, Robert J., Page, Kevin N., Pálfy, József, Pieńkowski, Gregory, Porter, Richard J., Poulton, Simon W., Riccardi, Alberto C., Riding, James B., Roper, Ailsa, Ruhl, Micha, Silva, Ricardo L., Storm, Marisa S., Suan, Guillaume, Szűcs, Dominika, Thibault, Nicolas, Uchman, Alfred, Stanley, James N., Ullmann, Clemens V., Van De Schootbrugge, Bas, Vickers, Madeleine L., Wadas, Sonja, Whiteside, Jessica H., Wignall, Paul B., Wonik, Thomas, Xu, Weimu, Zeeden, Christian, and Zhao, Ke

Published
2023

29. Initial results of coring at Prees, Cheshire Basin, UK (ICDP JET project):Towards an integrated stratigraphy, timescale, and Earth system understanding for the Early Jurassic

Author

Hesselbo, Stephen P., Al-Suwaidi, Aisha, Baker, Sarah J., Ballabio, Giorgia, Belcher, Claire M., Bond, Andrew, Boomer, Ian, Bos, Remco, Bjerrum, Christian J., Bogus, Kara, Boyle, Richard, Browning, James V., Butcher, Alan R., Condon, Daniel J., Copestake, Philip, Daines, Stuart, Dalby, Christopher, Damaschke, Magret, Damborenea, Susana E., Deconinck, Jean Francois, Dickson, Alexander J., Fendley, Isabel M., Fox, Calum P., Fraguas, Angela, Frieling, Joost, Gibson, Thomas A., He, Tianchen, Hickey, Kat, Hinnov, Linda A., Hollaar, Teuntje P., Huang, Chunju, Hudson, Alexander J. L., Jenkyns, Hugh C., Idiz, Erdem, Jiang, Mengjie, Krijgsman, Wout, Korte, Christoph, Leng, Melanie J., Lenton, Timothy M., Leu, Katharina, Little, Crispin T.S., Macniocaill, Conall, Manceñido, Miguel O., Mather, Tamsin A., Mattioli, Emanuela, Miller, Kenneth G., Newton, Robert J., Page, Kevin N., Pálfy, József, Pieńkowski, Gregory, Porter, Richard J., Poulton, Simon W., Riccardi, Alberto C., Riding, James B., Roper, Ailsa, Ruhl, Micha, Silva, Ricardo L., Storm, Marisa S., Suan, Guillaume, Szúcs, Dominika, Thibault, Nicolas, Uchman, Alfred, Stanley, James N., Ullmann, Clemens V., Van De Schootbrugge, Bas, Vickers, Madeleine L., Wadas, Sonja, Whiteside, Jessica H., Wignall, Paul B., Wonik, Thomas, Xu, Weimu, Zeeden, Christian, Zhao, Ke, Hesselbo, Stephen P., Al-Suwaidi, Aisha, Baker, Sarah J., Ballabio, Giorgia, Belcher, Claire M., Bond, Andrew, Boomer, Ian, Bos, Remco, Bjerrum, Christian J., Bogus, Kara, Boyle, Richard, Browning, James V., Butcher, Alan R., Condon, Daniel J., Copestake, Philip, Daines, Stuart, Dalby, Christopher, Damaschke, Magret, Damborenea, Susana E., Deconinck, Jean Francois, Dickson, Alexander J., Fendley, Isabel M., Fox, Calum P., Fraguas, Angela, Frieling, Joost, Gibson, Thomas A., He, Tianchen, Hickey, Kat, Hinnov, Linda A., Hollaar, Teuntje P., Huang, Chunju, Hudson, Alexander J. L., Jenkyns, Hugh C., Idiz, Erdem, Jiang, Mengjie, Krijgsman, Wout, Korte, Christoph, Leng, Melanie J., Lenton, Timothy M., Leu, Katharina, Little, Crispin T.S., Macniocaill, Conall, Manceñido, Miguel O., Mather, Tamsin A., Mattioli, Emanuela, Miller, Kenneth G., Newton, Robert J., Page, Kevin N., Pálfy, József, Pieńkowski, Gregory, Porter, Richard J., Poulton, Simon W., Riccardi, Alberto C., Riding, James B., Roper, Ailsa, Ruhl, Micha, Silva, Ricardo L., Storm, Marisa S., Suan, Guillaume, Szúcs, Dominika, Thibault, Nicolas, Uchman, Alfred, Stanley, James N., Ullmann, Clemens V., Van De Schootbrugge, Bas, Vickers, Madeleine L., Wadas, Sonja, Whiteside, Jessica H., Wignall, Paul B., Wonik, Thomas, Xu, Weimu, Zeeden, Christian, and Zhao, Ke

Abstract

Drilling for the International Continental Scientific Drilling Program (ICDP) Early Jurassic Earth System and Timescale project (JET) was undertaken between October 2020 and January 2021. The drill site is situated in a small-scale synformal basin of the latest Triassic to Early Jurassic age that formed above the major Permian-Triassic half-graben system of the Cheshire Basin. The borehole is located to recover an expanded and complete succession to complement the legacy core from the Llanbedr (Mochras Farm) borehole drilled through 1967-1969 on the edge of the Cardigan Bay Basin, North Wales. The overall aim of the project is to construct an astronomically calibrated integrated timescale for the Early Jurassic and to provide insights into the operation of the Early Jurassic Earth system. Core of Quaternary age cover and Early Jurassic mudstone was obtained from two shallow partially cored geotechnical holes (Prees 2A to 32.2g¯m below surface (mg¯b.s.) and Prees 2B to 37.0g¯mg¯b.s.) together with Early Jurassic and Late Triassic mudstone from the principal hole, Prees 2C, which was cored from 32.92 to 651.32g¯m (corrected core depth scale). Core recovery was 99.7g¯% for Prees 2C. The ages of the recovered stratigraphy range from the Late Triassic (probably Rhaetian) to the Early Jurassic, Early Pliensbachian (Ibex Ammonoid Chronozone). All ammonoid chronozones have been identified for the drilled Early Jurassic strata. The full lithological succession comprises the Branscombe Mudstone and Blue Anchor formations of the Mercia Mudstone Group, the Westbury and Lilstock formations of the Penarth Group, and the Redcar Mudstone Formation of the Lias Group. A distinct interval of siltstone is recognized within the Late Sinemurian of the Redcar Mudstone Formation, and the name "Prees Siltstone Member"is proposed. Depositional environments range from playa lake in the Late Triassic to distal offshore marine in the Early Jurassic. Initial datasets compiled from the core in

Published
2023

33. Statistical Mechanics and Dynamics of Liquids in and out of Equilibrium

Author

Hudson, Alexander

Subjects
Physical chemistry, glass, hydrophobicity, liquid, ribosome, water
Abstract

Liquids display an astonishing array of phenomena that, at first glance, seem to have little in common. In this thesis, we study two of these phenomena. The first is the hydrophobic effect, the well-known tendency of oil and water to demix and the driving force for biological assembly. The second is the glass transition, the process by which liquids cooled to very low temperatures become increasingly viscous until succumbing to structural arrest and displaying the rigidity of a solid with none of its microscopic ordering.In the first part of this thesis, we expand upon our prior understanding of the hydrophobic effect. We study the behavior of water in the confined volume created by a pair of RNA helices at the inter-subunit interface of the bacterial ribosome, which provides an opportunity to apply our contemporary understanding of the hydrophobic effect, first detailed by Lum, Chandler, and Weeks almost twenty years ago, to a context that is less idealized than previously studied. We also discuss and improve upon computational models of hydrophobic solvation, expanding their applicability to more complicated solute geometries.In the second part of this thesis, we study the glass transition from the perspective of the East model, a kinetically constrained lattice model of glass formers. We review and derive a number of results for East model glasses that we expect to emerge in more realistic, atomistic models of glass formers. We choose one such model and drive it out of equilibrium by cooling, forming a glass. We then check whether our East model predictions are correct. Of particular interest to us is whether inter-excitation correlations emerge out of equilibrium, a key prediction of the East model. Our atomistic results suggest that they do not, forcing us to reconsider our conceptual mapping between the highly abstract East model and more realistic models of glass formers.The common thread in these seemingly disparate parts of the thesis is the importance of collective fluctuations in liquid-state phenomena. The hydrophobic effect is a physical consequence of liquid-vapor interfacial fluctuations near extended hydrophobic surfaces, while dynamics in supercooled liquids, the precursors to glasses, are dominated by small, collective motions of particles in an otherwise jammed material. The importance of fluctuations in these and other liquid-state phenomena make the tools of statistical mechanics particularly suitable to their study. In this thesis, we employ these tools in the service of furthering our understanding of the liquid state.

Published
2016

34. TMQuery: a database of precomputed template modeling scores for assessment of protein structural similarity

Author

Price, Stephen, primary, Tombeur, Stéphane, additional, Hudson, Alexander, additional, Sathiyamoorthy, Nanda Kumar, additional, Smyth, Paul, additional, Singh, Anjana, additional, Peccianti, Mara, additional, Baroncelli, Elisa, additional, Essaghir, Ahmed, additional, Ferlenghi, Ilaria, additional, Phogat, Sanjay Kumar, additional, and Singh, Gurpreet, additional

Published
2022
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35. Costs and benefits of accepting presidential term limits

Author

Fruhstorfer, Anna (Dr.) and Hudson, Alexander

Subjects
ddc:330, Sozialwissenschaften, ddc:300
Abstract

As presidents approach the end of their constitutionally defined term in office, they face a number of difficulties, most importantly the deprivation of sources of power, personal enrichment, and protection from prosecution. This leads many of them to attempt to circumvent their term limits. Recent studies explain both the reasons for the extension or full abolition of term limits, and failed attempts to do so. Key explanations include electoral competition and the post-term fate of previous post holders. What we do not know yet is how compliance with term limits may be tied to the current president's expectations for their post-term fate. In particular, we do not know whether leaders who attempt to remove term limits and fail to do so jeopardize their post-term career as a result, and conversely, whether leaders who comply will have better outcomes in terms of security, prestige, and economic gain. Hence, we ask how the decision of a leader to comply or not comply with term limits is conditioned by the expectation of their post-term fate. To address this question, this article introduces new data on the career trajectories of term-limited presidents and its systematic effect on term limit compliance.

Published
2021

36. sj-pdf-1-prq-10.1177_1065912920984246 ��� Supplemental material for Majorities for Minorities: Participatory Constitution Making and the Protection of Minority Rights

Author

Fruhstorfer, Anna and Hudson, Alexander

Subjects
FOS: Political science, 160607 International Relations
Abstract

Supplemental material, sj-pdf-1-prq-10.1177_1065912920984246 for Majorities for Minorities: Participatory Constitution Making and the Protection of Minority Rights by Anna Fruhstorfer and Alexander Hudson in Political Research Quarterly

Published
2021
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40. Approaches to the Rational Design of Molecularly Imprinted Polymers Developed for the Selective Extraction or Detection of Antibiotics in Environmental and Food Samples

Author

Jamieson, Oliver, primary, Mecozzi, Francesco, additional, Crapnell, Robert D., additional, Battell, William, additional, Hudson, Alexander, additional, Novakovic, Katarina, additional, Sachdeva, Ashwin, additional, Canfarotta, Francesco, additional, Herdes, Carmelo, additional, Banks, Craig E., additional, Snyder, Helena, additional, and Peeters, Marloes, additional

Published
2021
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