Computational and Theoretical Chemistry

2023

A machine learning emulator for Lagrangian particle dispersion model footprints: a case study using NAME

Fillola, E., Santos-Rodriguez, R., Manning, A., O'Doherty, S. & Rigby, M., 12 Apr 2023, In: Geoscientific Model Development. 16, 7, p. 1997-2009 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

A quasi-one-dimensional model for ion-aerosol interactions and aerosol charge state downwind of corona-producing alternating current (AC) HVPL under stable atmospheric conditions

Wright, M. D., Matthews, J. C. & Shallcross, D. E., 15 Aug 2023, In: Environmental Research. 231, Pt 1, 11 p., 115908.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

Bioisosteric Design Identifies Inhibitors of Mycobacterium tuberculosis DNA Gyrase ATPase Activity

Kamsri, B., Pakamwong, B., Thongdee, P., Phusi, N., Kamsri, P., Punkvang, A., Ketrat, S., Saparpakorn, P., Hannongbua, S., Sangswan, J., Suttisintong, K., Sureram, S., Kittakoop, P., Hongmanee, P., Santanirand, P., Leanpolchareanchai, J., Goudar, K. E., Spencer, J., Mulholland, A. J. & Pungpo, P., 8 May 2023, In: Journal of Chemical Information and Modeling. 63, 9, p. 2707-2718 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Controlling kinetic pathways in demixing microgel-micelle mixtures

Fussell, S. L., Royall, C. P. & Van Duijneveldt, J. S., 9 Jan 2023, (E-pub ahead of print) In: Langmuir. 39, 3, 9 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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Dynamics and interactions of Quincke roller clusters: From orbits and flips to excited states

Mauleon Amieva, A., Allen, M. P., Liverpool, T. B. & Royall, C. P., 17 May 2023, In: Science Advances. 9, 20, p. eadf5144

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

Gas-phase kinetics, POCPs and an investigation of the contributions of VOCs to urban ozone production in the U.K.

Holland, R. E. T., Khan, M. A. H., Derwent, R., Lynch, J., Ahmed, F., Grace, S., Bacak, A. & Shallcross, D. E., 20 Mar 2023, (E-pub ahead of print) In: International Journal of Chemical Kinetics. 55, 7, p. 350-364 15 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

Global increase of ozone-depleting chlorofluorocarbons from 2010 to 2020

Western, L. M., Vollmer, M. K., Krummel, P. B., Adcock, K. E., Fraser, P. J., Harth, C. M., Langenfelds, R. L., Montzka, S. A., Mühle, J., O'Doherty, S., Oram, D. E., Reimann, S., Rigby, M. L., Vimont, I., Weiss, R. F., Young, T. D. S. & C. Laube, J., 3 Apr 2023, In: Nature Geoscience. 16, 4, p. 309-313 5 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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1 Citation (Scopus)

119 Downloads (Pure)

In Situ Observations of Halogenated Gases at the Shangdianzi Background Station and Emission Estimates for Northern China

Yi, L., An, M., Yu, H., Ma, Z., Xu, L., O'Doherty, S., Rigby, M. L., Western, L. M., Ganesan, A. L., Zhou, L., Shi, Q., Hu, Y., Hu, J., Xu, W. & Yao, B., 26 Apr 2023, (E-pub ahead of print) In: Environmental Science & Technology. 57, 18, p. 7217-7229 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Investigating the role of organic compounds in intercontinental ozone transport: Reactivity scales and Global Warming Potentials (GWPs)

Derwent, R. G., Utembe, S. R., Jenkin, M. E., Khan, M. A. H. & Shallcross, D. E., 5 May 2023, In: Atmospheric Environment. 306, 119817.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Off-setting climate change through formation flying of aircraft, a feasibility study reliant on high fidelity gas-phase chemical kinetic data

Khan, M. A. H., Tait, K. N., Derwent, R. G., Roome, S. B., Bacak, A., Bullock, S., Lowenberg, M. H. & Shallcross, D. E., 5 Apr 2023, (E-pub ahead of print) In: International Journal of Chemical Kinetics. 55, 7, p. 402-412 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

Overhead AC powerlines and rain can alter the electric charge distribution on airborne particles: implications for aerosol dispersion and lung deposition

Wright, M. D., Buckley, A. J., Matthews, J. C., Shallcross, D. E. & Henshaw, D. L., 1 Jul 2023, In: Environmental Research. 228, 13 p., 115834.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

Particle number concentration measurements on public transport in Bangkok, Thailand

Matthews, J. C., Chompoobut, C., Navasumrit, P., Khan, M. A. H., Wright, M. D., Ruchirawat, M. & Shallcross, D. E., 29 Mar 2023, In: International Journal of Environmental Research and Public Health. 20, 7, 5316.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

Pyrazolones Potentiate Colistin Activity against MCR-1-Producing Resistant Bacteria: Computational and Microbiological Study

Hanpaibool, C., Ngamwongsatit, N., Ounjai, P., Yotphan, S., Wolschann, P., Mulholland, A. J., Spencer, J. & Rungrotmongkol, T., 7 Mar 2023, In: ACS Omega. 8, 9, p. 8366-8376 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

Tautomer-Specific Deacylation and Ω-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 β-Lactamase

Tooke, C. L., Hinchliffe, P., Beer, M., Zinovjev, K., Colenso, C. K., Schofield, C. J., Mulholland, A. J. & Spencer, J., 5 Apr 2023, In: Journal of the American Chemical Society. 145, 13, p. 7166-7180 15 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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Towards emulated Lagrangian particle dispersion model footprints for satellite observations

Fillola, E., Santos-Rodriguez, R. & Rigby, M., 26 Feb 2023

Research output: Other contribution

2022

Ab initio study of negative electron affinity on the scandium-terminated diamond (100) surface for electron emission devices

Zulkharnay, R., Allan, N. L. & May, P. W., 30 Aug 2022, In: Carbon. 196, p. 176-185 10 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

2 Citations (Scopus)

Ab initio study of structural, elastic and thermodynamic properties of Fe₃S at high pressure: implications for planetary cores

Valencia, K., De Moya, A., Morard, G., Allan, N. L. & Pinilla, C., 1 Feb 2022, (E-pub ahead of print) In: American Mineralogist. 107, 2, p. 248-256 9 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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Acyclic halogenated monoterpenes from marine macroalgae: Estimated atmospheric lifetimes, potential degradation products, and their atmospheric impacts

Khan, M. A. H., Shallcross, D. E., Harrison, T. G., Booth, A. M., Bacak, A., Percival, C. J., Beukes, D. R. & Davies-Coleman, M. T., 3 Mar 2022, In: Transactions of the Royal Society of South Africa. 77, 1, p. 73-88 16 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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22 Downloads (Pure)

Aerosol mass and size‑resolved metal content in urban Bangkok, Thailand

Matthews, J. C., Navasumrit, P., Wright, M. D., Chaisatra, K., Chompoobut, C., Arbon, R. E., Khan, M. A. H., Ruchirawat, M. & Shallcross, D. E., 15 Jun 2022, In: Environmental Science and Pollution Research. 29, 52, p. 79025-79040 16 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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A Functional Interaction Between Y674-R685 Region of the SARS-CoV-2 Spike Protein and the Human α7 Nicotinic Receptor

Chrestia, J. F., Oliveira, A., Mulholland, A. J., Gallagher, T., Bermudez, I. & Bouzat, C., 20 Jul 2022, In: Molecular Neurobiology. 59, 10, p. 6076-6090 15 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Aircraft Emissions, Their Plume-Scale Effects, and the Spatio-Temporal Sensitivity of the Atmospheric Response: A Review

Tait, K. N., Khan, M. A. H., Bullock, S., Lowenberg, M. H. & Shallcross, D. E., 4 Jul 2022, In: Aerospace. 9, 7, 47 p., 355.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors

Gervasoni, S., Spencer, J., Hinchliffe, P., Pedretti, A., Vairoletti, F., Mahler, G. & Mulholland, A. J., Feb 2022, In: Proteins: Structure, Function, and Bioinformatics. 90, 2, p. 372-384 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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2 Citations (Scopus)

38 Downloads (Pure)

A renewed rise in global HCFC-141b emissions between 2017-2021

Western, L. M., Redington, A. L., Manning, A. J., Trudinger, C. M., Hu, L., Henne, S., Fang, X., Kuijpers, L. J. M., Theodoridi, C., Godwin, D. S., Arduini, J., Dunse, B. L., Engel, A., Fraser, P. J., Harth, C. M., Krummel, P. B., Maione, M., Mühle, J., O'Doherty, S., Park, H., & 15 othersPark, S., Reimann, S., Salameh, P. K., Say, D., Schmidt, R., Schuck, T., Siso, C., Stanley, K. M., Vimont, I., Vollmer, M. K., Young, T. D. S., Prinn, R. G., Weiss, R. F., Montzka, S. A. & Rigby, M. L., 28 Jul 2022, In: Atmospheric Chemistry and Physics. 22, 14, p. 9601–9616 16 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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1 Citation (Scopus)

22 Downloads (Pure)

Carbon Dioxide Fixation in RuBisCO Is Protonation-State-Dependent and Irreversible

Douglas-Gallardo, O. A., Murillo-López, J. A., Oller, J., Mulholland, A. J. & Vöhringer-Martinez, E., 5 Aug 2022, In: ACS Catalysis. 12, 15, p. 9418-9429 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

2 Citations (Scopus)

Discovery of novel and potent InhA inhibitors by an in silico screening and pharmacokinetic prediction

Hanwarinroj, C., Phusi, N., Kamsri, B., Kamsri, P., Punkvang, A., Ketrat, S., Saparpakorn, P., Hannongbua, S., Suttisintong, K., Kittakoop, P., Spencer, J., Mulholland, A. J. & Pungpo, P., 1 May 2022, In: Future Medicinal Chemistry. 14, 10, p. 717-729 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of De Novo Designed Glu/Lys Peptides

Lang, E. J. M., Baker, E. G., Woolfson, D. N. & Mulholland, A. J., 10 Jun 2022, (E-pub ahead of print) In: Journal of Chemical Theory and Computation. 18, 7, p. 4070−4076 7 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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4 Citations (Scopus)

28 Downloads (Pure)

Global emissions of perfluorocyclobutane (PFC-318, c-C4F8) resulting from the use of hydrochlorofluorocarbon-22 (HCFC-22) feedstock to produce polytetrafluoroethylene (PTFE) and related fluorochemicals

Mühle, J., Kuijpers, L. J. M., Stanley, K. M., Rigby, M. L., Western, L. M., Kim, J., Park, S., Harth, C. M., Krummel, P. B., Fraser, P. J., O'Doherty, S., Salameh, P. K., Schmidt, R., Young, T. D. S., Prinn, R. G., Wang, R. H. J. & Weiss, R. F., 14 Mar 2022, In: Atmospheric Chemistry and Physics. 22, 5, p. 3371-3378 8 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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Identification of potent DNA Gyrase inhibitors active against mycobacterium tuberculosis

Pakamwong, B., Thongdee, P., Spencer, J., Kamsri, B., Mulholland, A. J. & Pungpo, P., 29 Mar 2022, (E-pub ahead of print) In: Journal of Chemical Information and Modeling. 62, 7, p. 1680-1690 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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5 Citations (Scopus)

5 Downloads (Pure)

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M pro Explored by QM/MM Simulations.

Martí, S., Arafet, K., Lodola, A., Mulholland, A. J., Świderek, K. & Moliner, V., 7 Jan 2022, In: ACS Catalysis. 12, 1, p. 698-708 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

10 Citations (Scopus)

In silico design of novel quinazoline-based compounds as potential Mycobacterium tuberculosis PknB inhibitors through 2D and 3D-QSAR, molecular dynamics simulations combined with pharmacokinetic predictions

Hanwarinroj, C., Thongdee, P., Sukchit, D., Taveepanich, S., Punkvang, A., Kamsri, P., Saparpakorn, P., Ketrat, S. K., Hannongbua, S., Suttisintong, K., Kittakoop, P., Spencer, J., Mulholland, A. J. & Pungpo, P., 3 Jun 2022, In: Journal of Molecular Graphics and Modelling. 115, 19 p., 108231.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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Interactivity: the missing link between virtual reality technology and drug discovery pipelines

Walters, R. K., Gale, E. M., Barnoud, J., Glowacki, D. R. & Mulholland, A. J., 8 Feb 2022.

Research output: Working paper › Preprint

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Investigating the Variation of Benzene and 1,3-Butadiene in the UK during 2000–2020

Holland, R. E. T., Khan, M. A. H., Matthews, J. C., Bonifacio, S., Walters, R., Koria, P., Clowes, J., Rodgers, K., Jones, T., Patel, L., Cross, R., Sandberg, F. & Shallcross, D. E., 21 Sept 2022, In: International Journal of Environmental Research and Public Health. 19, 19, 17 p., 11904.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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Lattice dynamics and thermodynamic peropties of Y₃Al₅O1₂ (YAG)

Poulos, M., Giaremis, S., Arvanitidis, J., Christofilos, D., Ves, S., Hehlen, M., Allan, N. L., Mohn, C. & Papagelis, K., 1 Mar 2022, In: Journal of Physics and Chemistry of Solids. 162, 10 p., 110512.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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Mechanistic Insights into the Ligand-Induced Unfolding of an RNA G-Quadruplex

Haldar, S., Zhang, Y., Xia, Y., Islam, B., Liu, S., Gervasio, F. L., Mulholland, A. J., Waller, Z. A. E., Wei, D. & Haider, S., 19 Jan 2022, In: Journal of the American Chemical Society. 144, 2, p. 935-950 16 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

Modelling the growth of atmospheric nitrous oxide using a global hierarchical inversion

Stell, A. C., Bertolacci, M., Zammit-Mangion, A., Rigby, M. L., Fraser, P., Harth, C., Krummel, P., Lan, X., Manizza, M., Mühle, J., O'Doherty, S., Prinn, R., Weiss, R., Young, T. D. S. & Ganesan, A. L., 10 Oct 2022, In: Atmospheric Chemistry and Physics. 22, 19, p. 12945–12960 16 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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7 Downloads (Pure)

Molecular dynamics of spike variants in the locked conformation: RBD interfaces, fatty acid binding and furin cleavage sites

Shoemark, D. K., Oliveira, A. S. F., Davidson, A. D., Berger, I., Schaffitzel, C. & Mulholland, A. J., 8 May 2022

Research output: Other contribution

Multiscale simulations identify origins of differential carbapenem hydrolysis by the OXA-48 β-lactamase

Hirvonen, V. H. A., Weizmann, T., Mulholland, A. J., Spencer, J. & Van der Kamp, M. W., 3 Apr 2022, In: ACS Catalysis. 12, 8, p. 4534–4544 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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3 Citations (Scopus)

2 Downloads (Pure)

Oxidative degradation of triblock-copolymer surfactant and its effects on self-assembly

Fussell, S. L., King, S. M., Royall, C. P. & Van Duijneveldt, J. S., 15 Jan 2022, In: Journal of Colloid and Interface Science. 606, p. 953-960 8 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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1 Citation (Scopus)

52 Downloads (Pure)

Projections of hydrofluorocarbon (HFC) emissions and the resulting global warming based on recent trends in observed abundances and current policies: Atmospheric Chemistry and Physics

Velders, G. J. M., Daniel, J. S., Montzka, S. A., Vimont, I., Rigby, M., Krummel, P. B., Muhle, J., O'Doherty, S., Prinn, R. G., Weiss, R. F. & Young, D., 10 May 2022, In: Atmospheric Chemistry and Physics. 22, 9, p. 6087-6101 15 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

QM/MM Molecular Modeling Reveals Mechanism Insights into Flavin Peroxide Formation in Bacterial Luciferase

Lawan, N., Tinikul, R., Surawatanawong, P., Mulholland, A. J. & Chaiyen, P., 24 Jan 2022, In: Journal of Chemical Information and Modeling. 62, 2, p. 399-411 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-lactamases

Chudyk, E. I., Beer, M., Limb, M. A. L., Jones, C., Spencer, J., Van der Kamp, M. W. & Mulholland, A. J., 12 Aug 2022, In: ACS Infectious Diseases. 8, 8, p. 1521-1532 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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Quantifying fossil fuel methane emissions using observations of atmospheric ethane and an uncertain emission ratio

Ramsden, A., Ganesan, A. L., Western, L. M., Rigby, M. L., Manning, A. J., Foulds, A., France, J. L., Barker, P., Levy, P., Say, D., Wisher, A. C., Arnold, T., Rennick, C., Stanley, K. M., Young, T. D. S. & O'Doherty, S., 25 Mar 2022, In: Atmospheric Chemistry and Physics. 22, 6, p. 3911-3929 19 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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SARS-CoV-2 spike variants differ in their allosteric response to linoleic acid

Oliveira, A. S. F., Shoemark, D. K., Davidson, A. D., Berger, I., Schaffitzel, C. & Mulholland, A. J., 22 Apr 2022, bioRxiv.org.

Research output: Other contribution

Structural and temporal basis for agonism in the α4β2 nicotinic acetylcholine receptor

Oliveira, A. S. F., Bermudez, I., Gallagher, T., Wonnacott, S., Ciccotti, G., Sessions, R. B. & Mulholland, A. J., 24 Feb 2022, bioRxiv.org.

Research output: Other contribution

Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2

Gupta, K., Toelzer, C., Kavanagh Williamson, M., Shoemark, D. K., Oliveira, A., Davidson, A. D., Almuqrin, A. M., Staufer, O., Yadav Kadapalakere, S., Borucu, U., Garzoni, F., Fitzgerald, D. J., Spatz, J. P., Mulholland, A. J., Davidson, A. D., Berger-Schaffitzel, C. H. & Berger, I., 11 Jan 2022, In: Nature Communications. 13, 1, 12 p., 222.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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9 Citations (Scopus)

46 Downloads (Pure)

The emerging potential of interactive virtual reality in drug discovery

Walters, R. K., Gale, E. M., Barnoud, J., Glowacki, D. R. & Mulholland, A. J., 31 May 2022, (E-pub ahead of print) In: Expert Opinion on Drug Discovery. 17, 7, p. 685-698 14 p.

Research output: Contribution to journal › Review article (Academic Journal) › peer-review

Open Access

3 Citations (Scopus)

40 Downloads (Pure)

The Emissions of Water Vapour and NOx from Modelled Hydrogen-Fuelled Aircraft and the Impact of NOx Reduction on Climate Compared with Kerosene-Fuelled Aircraft

Khan, M. A. H., Brierley, J., Tait, K. N., Bullock, S., Shallcross, D. E. & Lowenberg, M. H., 12 Oct 2022, In: Atmosphere. 13, 10, 12 p., 1660.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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Virtual Screening Identifies Novel and Potent Inhibitors of Mycobacterium tuberculosis PknB with Antibacterial Activity

Thongdee, P., Hanwarinroj, C., Pakamwong, B., Kamsri, P., Punkvang, A., Leanpolchareanchai, J., Ketrat, S., Saparpakorn, P., Hannongbua, S., Ariyachaokun, K., Suttisintong, K., Sureram, S., Kittakoop, P., Hongmanee, P., Santanirand, P., Mukamolova, G. V., Blood, R. A., Takebayashi, Y., Spencer, J., Mulholland, A. J., & 1 othersPungpo, P., 22 Aug 2022, (E-pub ahead of print) In: Journal of Chemical Information and Modeling. 62, 24, 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

WOMBAT v1.0: A fully Bayesian global flux-inversion framework

Zammit-Mangion, A., Bertolacci, M., Fisher, J., Stavert, A., Rigby, M., Cao, Y. & Cressie, N., 6 Jan 2022, In: Geoscientific Model Development. 15, 1, p. 45-73 29 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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4 Citations (Scopus)

39 Downloads (Pure)

2021

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

Dommer, A., Casalino, L., Kearns, F., Rosenfeld, M., Wauer, N., Ahn, S-H., Russo, J., Oliveira, S., Morris, C., Bogetti, A., Trifan, A., Brace, A., Sztain, T., Clyde, A., Ma, H., Chennubhotla, C., Lee, H., Turilli, M., Khalid, S., Tamayo-Mendoza, T., & 32 othersWelborn, M., Christensen, A., Smith, D. G. A., Qiao, Z., Sirumalla, S. K., O'Connor, M., Manby, F., Anandkumar, A., Hardy, D., Phillips, J., Stern, A., Romero, J., Clark, D., Dorrell, M., Maiden, T., Huang, L., McCalpin, J., Woods, C., Gray, A., Williams, M., Barker, B., Rajapaksha, H., Pitts, R., Gibbs, T., Stone, J., Zuckerman, D., Mulholland, A., Miller, T., Jha, S., Ramanathan, A., Chong, L. & Amaro, R., 15 Nov 2021, International Journal of High Performance Computing Applications, (bioRxiv).

Research output: Working paper

Open Access

Computational and Theoretical Chemistry

Research output

Search results