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1. Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

Author

Croci, M. and Wells, G. N.

Subjects
Mathematics - Numerical Analysis, Computer Science - Hardware Architecture, Computer Science - Mathematical Software
Abstract

In this paper we develop the first fine-grained rounding error analysis of finite element (FE) cell kernels and assembly. The theory includes mixed-precision implementations and accounts for hardware-acceleration via matrix multiplication units, thus providing theoretical guidance for designing reduced- and mixed-precision FE algorithms on CPUs and GPUs. Guided by this analysis, we introduce hardware-accelerated mixed-precision implementation strategies which are provably robust to low-precision computations. Indeed, these algorithms are accurate to the lower-precision unit roundoff with an error constant that is independent from: the conditioning of FE basis function evaluations, the ill-posedness of the cell, the polynomial degree, and the number of quadrature nodes. Consequently, we present the first AMX-accelerated FE kernel implementations on Intel Sapphire Rapids CPUs. Numerical experiments demonstrate that the proposed mixed- (single/half-) precision algorithms are up to 60 times faster than their double precision equivalent while being orders of magnitude more accurate than their fully half-precision counterparts., Comment: Keywords: Mixed precision, finite element method, finite element kernel and assembly, rounding error analysis, hardware acceleration, matrix units, Intel AMX

Published
2024

2. Physical properties of the trans-Neptunian object (38628) Huya from a multi-chord stellar occultation

Author

Santos-Sanz, P., Ortiz, J. L., Sicardy, B., Popescu, M., Benedetti-Rossi, G., Morales, N., Vara-Lubiano, M., Camargo, J. I. B., Pereira, C. L., Rommel, F. L., Assafin, M., Desmars, J., Braga-Ribas, F., Duffard, R., Oliveira, J. Marques, Vieira-Martins, R., Fernández-Valenzuela, E., Morgado, B. E., Acar, M., Anghel, S., Atalay, E., Ateş, A., Bakış, H., Bakış, V., Eker, Z., Erece, O., Kaspi, S., Kayhan, C., Kilic, S. E., Kilic, Y., Manulis, I., Nedelcu, D. A., Niaei, M. S., Nir, G., Ofek, E., Ozisik, T., Petrescu, E., Satir, O., Solmaz, A., Sonka, A., Tekes, M., Unsalan, O., Yesilyaprak, C., Anghel, R., Berteşteanu, D., Curelaru, L., Danescu, C., Dumitrescu, V., Gherase, R., Hudin, L., Stoian, A-M., Tercu, J. O., Truta, R., Turcu, V., Vantdevara, C., Belskaya, I., Dementiev, T. O., Gazeas, K., Karampotsiou, S., Kashuba, V., Kiss, Cs., Koshkin, N., Kozhukhov, O. M., Krugly, Y., Lecacheux, J., Pal, A., Püsküllü, Ç., Szakats, R., Zhukov, V., Bamberger, D., Mondon, B., Perelló, C., Pratt, A., Schnabel, C., Selva, A., Teng, J. P., Tigani, K., Tsamis, V., Weber, C., Wells, G., Kalkan, S., Kudak, V., Marciniak, A., Ogloza, W., Ozdemir, T., Pakstiene, E., Perig, V., and Zejmo, M.

Subjects
Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics
Abstract

Within our international program to obtain accurate physical properties of trans-Neptunian objects (TNOs) we predicted a stellar occultation by the TNO (38628) Huya of the star Gaia DR2 4352760586390566400 (mG = 11.5 mag.) for March 18, 2019. After an extensive observational campaign, we updated the prediction and it turned out to be favorable to central Europe. Therefore, we mobilized half a hundred professional and amateur astronomers, and the occultation was finally detected from 21 telescopes located at 18 sites. This makes the Huya event one of the best ever observed stellar occultation by a TNO in terms of the number of chords. We determine accurate size, shape, and geometric albedo, and we also provide constraints on the density and other internal properties of this TNO. The 21 positive detections of the occultation by Huya allowed us to obtain well-separated chords which permitted us to fit an ellipse for the limb of the body at the moment of the occultation (i.e., the instantaneous limb) with kilometric accuracy. The projected semi-major and minor axes of the best ellipse fit obtained using the occultation data are (a', b') = (217.6 $\pm$ 3.5 km, 194.1 $\pm$ 6.1 km) with a position angle of the minor axis P' = 55.2 $\pm$ 9.1 degrees. From this fit, the projected area-equivalent diameter is 411.0 $\pm$ 7.3 km. This diameter is compatible with the equivalent diameter for Huya obtained from radiometric techniques (D = 406 $\pm$ 16 km). From this instantaneous limb, we obtained the geometric albedo for Huya (p$\rm_V$ = 0.079 $\pm$ 0.004) and we explored possible 3D shapes and constraints to the mass density for this TNO. We did not detect the satellite of Huya through this occultation, but the presence of rings or debris around Huya is constrained using the occultation data. We also derived an upper limit for a putative Pluto-like global atmosphere of about p$_{\rm surf}$ = 10 nbar., Comment: Accepted for publication in Astronomy & Astrophysics (30-April-2022). 19 pages, 7 figures

Published
2022
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5. Congenital heart disease in the ESC EORP Registry of Pregnancy and Cardiac disease (ROPAC)

Author

Hall, Roger, Roos-Hesselink, Jolien, Stein, Joerg, Parsonage, William Anthony, Budts, Werner, De Backer, Julie, Grewal, Jasmin, Marelli, Ariane, Kaemmerer, Harald, Jondeau, Guillaume, Johnson, Mark, Maggioni, Aldo P., Tavazzi, Luigi, Thilen, Ulf, Elkayam, Uri, Otto, Catherine, Sliwa, Karen, Aquieri, A., Saad, A., Vega, H. Ruda, Hojman, J., Caparros, J.M., Blanco, M. Vazquez, Arstall, M., Chung, C.M., Mahadavan, G., Aldridge, E., Wittwer, M., Chow, Y.Y., Parsonage, W.A., Lust, K., Collins, N., Warner, G., Hatton, R., Gordon, A., Nyman, E., Stein, J., Donhauser, E., Gabriel, H., Bahshaliyev, A., Guliyev, F., Hasanova, I., Jahangirov, T., Gasimov, Z., Salim, A., Ahmed, C.M., Begum, F., Hoque, M.H., Mahmood, M., Islam, M.N., Haque, P.P., Banerjee, S.K., Parveen, T., Morissens, M., De Backer, J., Demulier, L., de Hosson, M., Budts, W., Beckx, M., Kozic, M., Lovric, M., Kovacevic-Preradovic, T., Chilingirova, N., Kratunkov, P., Wahab, N., McLean, S., Gordon, E., Walter, L., Marelli, A., Montesclaros, A.R., Monsalve, G., Rodriguez, C., Balthazar, F., Quintero, V., Palacio, W., Cadavid, L.A. Mejía, Ortiz, E. Munoz, Hoyos, F. Fortich, Guerrero, E. Arevalo, Ricardo, J. Gandara, Penagos, J. Velasquez, Vavera, Z., Prague, Popelova, J., Vejlstrup, N., Grønbeck, L., Johansen, M., Ersboll, A., Elrakshy, Y., Eltamawy, K., Abd-El Aziz, M. Gamal, El Nagar, A., Ebaid, H., Elenin, H. Abo, Saed, M., Farag, S., Makled, W., Sorour, K., Ashour, Z., El-Sayed, G., Meguid Mahdy, M. Abdel, Taha, N., Dardeer, A., Shabaan, M., Ali, M., Moceri, P., Duthoit, G., Gouton, M., Nizard, J., Baris, L., Cohen, S., Ladouceur, M., Khimoud, D., Iung, B., Berger, F., Olsson, A., Gembruch, U., Merz, W.M., Reinert, E., Clade, S., Kliesch, Y., Wald, C., Sinning, C., Kozlik-Feldmann, R., Blankenberg, S., Zengin-Sahm, E., Mueller, G., Hillebrand, M., Hauck, P., von Kodolitsch, Y., Zarniko, N., Baumgartner, Muenster H., Schmidt, R., Hellige, A., Tutarel, O., Kaemmerer, H., Kuschel, B., Nagdyman, N., Motz, R., Maisuradze, D., Frogoudaki, A., Iliodromitis, E., Anastasiou-Nana, M., Marousi, Triantafyllis, D., Bekiaris, G., Karvounis, H., Giannakoulas, G., Ntiloudi, D., Mouratoglou, S.A., Temesvari, A., Balint, H., Kohalmi, D., Merkely, B., Liptai, C., Nemes, A., Forster, T., Kalapos, A., Berek, K., Havasi, K., Ambrus, N., Shelke, A., Kawade, R., Patil, S., Martanto, E., Aprami, T.M., Purnomowati, A., Cool, C.J., Hasan, M., Akbar, R., Hidayat, S., Dewi, T.I., Permadi, W., Soedarsono, D.A., Ansari-Ramandi, M.M., Samiei, N., Tabib, A., Kashfi, F., Ansari-Ramandi, S., Rezaei, S., Farhan, H. Ali, Al-Hussein, A., Al-Saedi, G., Mahmood, G., Yaseen, I.F., Al-Yousuf, L., AlBayati, M., Mahmood, S., Raheem, S., AlHaidari, T., Dakhil, Z., Thornton, P., Donnelly, J., Bowen, M., Blatt, A., Elbaz-Greener, G., Shotan, A., Yalonetsky, S., Goland, S., Biener, M., Assenza, G. Egidy, Bonvicini, M., Donti, A., Bulgarelli, A., Prandstraller, D., Romeo, C., Crepaz, R., Sciatti, E., Metra, M., Orabona, R., Ali, L. Ait, Festa, P., Fesslova, V., Bonanomi, C., Calcagnino, M., Lombardi, F., Colli, A.M., Ossola, M.W., Gobbi, C., Gherbesi, E., Tondi, L., Schiavone, M., Squillace, M., Carmina, M.G., Maina, A., Macchi, C., Gollo, E., Comoglio, F.M., Montali, N., Re, P., Bordese, R., Todros, T., Donvito, V., Marra, W. Grosso, Sinagra, G., D'Agata Mottolese, B., Bobbo, M., Gesuete, V., Rakar, S., Ramani, F., Niwa, K., Mekebekova, D., Mussagaliyeva, A., Lee, T., Mirrakhimov, E., Abilova, S., Bektasheva, E., Neronova, K., Lunegova, O., Žaliūnas, R., Jonkaitienė, R., Petrauskaitė, J., Laucevicius, A., Jancauskaite, D., Lauciuviene, L., Gumbiene, L., Lankutiene, L., Glaveckaite, S., Laukyte, M., Solovjova, S., Rudiene, V., Chee, K.H., Yim, C.C.-W., Ang, H.L., Kuppusamy, R., Watson, T., Caruana, M., Estensen, M.-E., Kayani, M.G.A. Mahmood, Munir, R., Tomaszuk-Kazberuk, A., Sobkowicz, B., Przepiesc, J., Lesniak-Sobelga, A., Tomkiewicz-Pajak, L., Komar, M., Olszowska, M., Podolec, P., Wisniowska-Smialek, S., Lelonek, M., Faflik, U., Cichocka-Radwan, A., Plaskota, K., Trojnarska, O., Guerra, N., de Sousa, L., Cruz, C., Ribeiro, V., Jovanova, S., Petrescu, V., Jurcut, R., Ginghina, C., Coman, I. Mircea, Musteata, M., Osipova, O., Golivets, T., Khamnagadaev, I., Golovchenko, O., Nagibina, A., Ropatko, I., Gaisin, I.R., Shilina, L. Valeryevna, Sharashkina, N., Shlyakhto, E., Irtyuga, O., Moiseeva, O., Karelkina, E., Zazerskaya, I., Kozlenok, A., Sukhova, I., Jovovic, L., Prokšelj, K., Koželj, M., Askar, A.O., Abdilaahi, A.A., Mohamed, M.H., Dirir, A.M., Sliwa, K., Manga, P., Pijuan-Domenech, A., Galian-Gay, L., Tornos, P., Subirana, M.T., T, M., Subirana, Oliver, J.M., Garcia-Aranda Dominguez, B., Gonzalez, I. Hernandez, Jimenez, J.F. Delgado, Subias, P. Escribano, Murga, N., Elbushi, A., Suliman, A., Jazzar, K., Murtada, M., Ahamed, N., Dellborg, M., Furenas, E., Jinesjo, M., Skoglund, K., Eriksson, P., Gilljam, T., Thilen, U., Tobler, D., Wustmann, K., Schwitz, F., Schwerzmann, M., Rutz, T., Bouchardy, J., Greutmann, M., Lopes, B.M. Santos, Meier, L., Arrigo, M., de Boer, K., Konings, T., Wajon, E., Wagenaar, L.J., Polak, P., Pieper, E.P.G., Roos-Hesselink, J., van Hagen, I., Duvekot, H., Cornette, J.M.J., De Groot, C., van Oppen, C., Sarac, L., Esen, O. Batukan, Enar, S. Catirli, Mondo, C., Ingabire, P., Nalwanga, B., Semu, T., Salih, B.T., Almahmeed, W.A.R., Wani, S., Farook, F.S. Mohamed, Ain, Al, Gerges, F., Komaranchath, A.M., Al bakshi, F., Al Mulla, A., Yusufali, A.H., Al Hatou, E.I., Bazargani, N., Hussain, F., Hudsmith, L., Thompson, P., Thorne, S., Bowater, S., Money-Kyrle, A., Clifford, P., Ramrakha, P., Firoozan, S., Chaplin, J., Bowers, N., Adamson, D., Schroeder, F., Wendler, R., Hammond, S., Nihoyannopoulos, P., Norfolk, Norwich, Hall, R., Freeman, L., Veldtman, G., Kerr, J., Tellett, L., Scott, N., Bhatt, A.B., DeFaria Yeh, D., Youniss, M.A., Wood, M., Sarma, A.A., Tsiaras, S., Stefanescu, A., Duran, J.M., Stone, L., Majdalany, D.S., Chapa, J., Chintala, K., Gupta, P., Botti, J., Ting, J., Davidson, W.R., Wells, G., Sparks, D., Paruchuri, V., Marzo, K., Patel, D., Wagner, W., Ahanya, S.N., Colicchia, L., Jentink, T., Han, K., Loichinger, M., Parker, M., Longtin, C., Yetman, A., Erickson, K., Cramer, J., Tsai, S., Fletcher, B., Warta, S., Cohen, C., Lindblade, C., Puntel, R., Nagaran, K., Croft, N., Gurvitz, M., Otto, C., Talluto, C., Murphy, D., Perlroth, M.G., Ramlakhan, Karishma P., Johnson, Mark R., Lelonek, Malgorzata, Saad, Aly, Gasimov, Zaur, Sharashkina, Natalia V., Thornton, Patrick, Arstall, Margaret, and Roos-Hesselink, Jolien W.

Published
2021
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9. Stated Preferences for Attributes of a CYP2C19 Pharmacogenetic Test Among the General Population Presented with a Hypothetical Acute Coronary Syndrome Scenario

Author

Bereza BG, Coyle D, So DY, Kadziola Z, Wells G, Grootendorst P, and Papadimitropoulos EA

Subjects
discrete choice experiment, pharmacogenetic test, patient preference, starting point bias, Medicine (General), R5-920, Therapeutics. Pharmacology, RM1-950
Abstract

Basil G Bereza, 1 Doug Coyle, 2 Derek Y So, 3 Zbigniew Kadziola, 4 George Wells, 2 Paul Grootendorst, 1 Emmanuel A Papadimitropoulos 1, 4 1University of Toronto Leslie Dan Faculty of Pharmacy, Toronto, ON, Canada; 2University of Ottawa School of Epidemiology and Public Health, Toronto, ON, Canada; 3University of Ottawa Heart Institute, Ottawa, ON, Canada; 4Eli Lilly & Company, Toronto, ON, CanadaCorrespondence: Basil G BerezaLeslie Dan Faculty of Pharmacy, 144 College Street, Toronto, ON M5S 3M2, CanadaTel +1 416-978-6989Email bgbereza@gmail.comBackground: Pharmacogenetic (PGx) testing identifies pharmacotherapeutic risks to permit personalized therapy. Identifying the genetic profile of patients with acute coronary syndrome (ACS) who are considered for therapy with clopidogrel (P2Y 12 receptor blockers) and acetylsalicylic acid (ASA) contributes to the treatment paradigm. Patient preferences would inform a collaborative framework and by extension inform healthcare policy formulation.Purpose: To quantify stated preferences (willingness to pay) for attributes of a novel point-of-care PGx (CYP2C19) test using a discrete choice experiment (DCE) from the general public in Ontario, Canada, and to identify starting point bias of the cost attribute.Methods: A web survey was created and included a questionnaire, decision board, and a DCE. DCE choice sets include the following attributes (levels): sample collection (blood, finger prick, and cheek swab), turnaround time for results (1 hr, 3 days, and 1 week), and cost in additional insurance premiums. The presence of starting point bias (cost attribute levels of $0, $1, $5 or $0, $2, $10) in the estimation of willingness to pay (WTP) was tested.Results: Estimates for turnaround time and cost attributes were statistically significant. Coefficients related to the starting point bias were also significant. Approximately 67% of survey participants chose the PGx test compared to status quo treatment options. WTP for a 1 hr turnaround time compared to a 1-week turnaround time was $10.77 (95% CI 9.58 -12.25).Conclusion: This translational study shows preference for a point of care PGx test.Keywords: discrete choice experiment, pharmacogenetic test, patient preference, startingpoint bias

Published
2020

10. Applying Multi-Domain Effects to Operation Inherent Resolve

Author

Murphy, Benjamin and Wells, G. Damon

Subjects
United States. Army, Military and naval science
Abstract

'Out of intense complexities, intense simplicities emerge.' --Sir Winston Churchill (1) Multi-domain operations (MDO) are the U.S. Department of Defense's most recent solution to the complex, multifaceted problem of state [...]

Published
2021

12. Integrated modeling of nature’s role in human well-being: A research agenda

Author

Chaplin-Kramer, R., Polasky, S., Alkemade, R., Burgess, N., Cheung, W., Fetzer, I., Harfoot, M., Hertel, T., Hill, S., Andrew Johnson, J., Janse, J., José v. Jeetze, P., Kim, H., Kuiper, J., Lonsdorf, E., Leclere, D., Mulligan, M., Peterson, G., Popp, A., Roe, S., Schipper, A., Snäll, T., van Soesbergen, A., Soterroni, A., Stehfest, E., van Vuuren, D., Visconti, P., Wang-Erlandsson, L., Wells, G., Pereira, H., Chaplin-Kramer, R., Polasky, S., Alkemade, R., Burgess, N., Cheung, W., Fetzer, I., Harfoot, M., Hertel, T., Hill, S., Andrew Johnson, J., Janse, J., José v. Jeetze, P., Kim, H., Kuiper, J., Lonsdorf, E., Leclere, D., Mulligan, M., Peterson, G., Popp, A., Roe, S., Schipper, A., Snäll, T., van Soesbergen, A., Soterroni, A., Stehfest, E., van Vuuren, D., Visconti, P., Wang-Erlandsson, L., Wells, G., and Pereira, H.

Abstract

Integrated assessment models that incorporate biodiversity and ecosystem services could be an important tool for improving our understanding of interconnected social-economic-ecological systems, and for analyzing how policy alternatives can shift future trajectories towards more sustainable development. Despite recent scientific and technological advances, key gaps remain in the scientific community’s ability to deliver information to decision-makers at the pace and scale needed to address sustainability challenges. We identify five research frontiers for integrated social-economic-ecological modeling (primarily focused on terrestrial systems) to incorporate biodiversity and ecosystem services: 1) downscaling impacts of direct and indirect drivers on ecosystems; 2) incorporating feedbacks in ecosystems; 3) linking ecological impacts to human well-being, 4) disaggregating outcomes for distributional equity considerations, and 5) incorporating dynamic feedbacks of ecosystem services on the social-economic system. We discuss progress and challenges along each of these five frontiers and the science-policy linkages needed to move new research and information into action.

Published
2024
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13. Protein Encapsulation of Experimental Anticancer Agents 5F 203 and Phortress: Towards Precision Drug Delivery

Author

Breen AF, Scurr D, Cassioli ML, Wells G, Thomas NR, Zhang J, Turyanska L, and Bradshaw TD

Subjects
benzothiazole, apoferritin, transferrin receptor, anticancer activity, drug delivery, Medicine (General), R5-920
Abstract

Alastair F Breen,1 David Scurr,1 Maria Letizia Cassioli,1 Geoffrey Wells,2 Neil R Thomas,3 Jihong Zhang,4 Lyudmila Turyanska,5 Tracey D Bradshaw1 1Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; 2UCL School of Pharmacy, University College London, London, UK; 3Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK; 4Medical School, Kunming University of Science and Technology, Kunming, People’s Republic of China; 5Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UKCorrespondences: Tracey D BradshawCentre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UKTel +44 115 9515033Email Tracey.Bradshaw@nottingham.ac.ukLyudmila TuryanskaFaculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UKTel +44 115 9515151Email Lyudmila.Turyanska@nottingham.ac.ukIntroduction: Advancement of novel anticancer drugs into clinical use is frequently halted by their lack of solubility, reduced stability under physiological conditions, and non-specific uptake by normal tissues, causing systemic toxicity. Their progress to use in the clinic could be accelerated by the development of new formulations employing suitable and complementary drug delivery vehicles.Methods: A robust method for apoferritin (AFt)-encapsulation of antitumour benzothiazoles has been developed for enhanced activity against and drug delivery to benzothiazole-sensitive cancers.Results: More than 70 molecules of benzothiazole 5F 203 were encapsulated per AFt cage. Post-encapsulation, the size and integrity of the protein cages were retained as evidenced by dynamic light scattering. ToF-SIMS depth profiling using an argon cluster beam confirmed 5F 203 exclusively within the AFt cavity. Improved encapsulation of benzothiazole lysyl-amide prodrugs was achieved (∼130 molecules of Phortress per AFt cage). Transferrin receptor 1, TfR1, was detected in lysates prepared from most cancer cell lines studied, contributing to enhanced anticancer potency of the AFt-encapsulated benzothiazoles (5F 203, Phortress, GW 610, GW 608-Lys). Nanomolar activity was demonstrated by AFt-formulations in breast, ovarian, renal and gastric carcinoma cell lines, whereas GI50 >50 μM was observed in non-tumourigenic MRC-5 fibroblasts. Intracellular 5F 203, a potent aryl hydrocarbon receptor (AhR) ligand, and inducible expression of cytochrome P450 (CYP) 1A1 were detected following exposure of sensitive cells to AFt-5F 203, confirming that the activity of benzothiazoles was not compromised following encapsulation.Conclusion: Our results show enhanced potency and selectivity of AFt-encapsulated 5F 203 against carcinomas derived from breast, ovarian, renal, colorectal as well as gastric cancer models, and offer realistic prospects for potential refinement of tumour-targeting and treatment, and merit further in vivo investigations.Keywords: benzothiazole, apoferritin, transferrin receptor, anticancer activity, drug delivery

Published
2019

14. Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

Author

Birkholtz, L. -M., Bastien, O., Wells, G., Grando, D., Joubert, F., Kasam, V., Zimmermann, M., Ortet, P., Jacq, N., Roy, S., Hoffmann-Apitius, M., Breton, V., Louw, A. I., and Maréchal, E.

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Distributed, Parallel, and Cluster Computing, Quantitative Biology - Genomics
Abstract

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed., Comment: 43 pages, 4 figures, to appear in Malaria Journal

Published
2006
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16. A discontinuous Galerkin method for strain gradient-dependent damage: Study of interpolations, convergence and two dimensional problems

Author

Molari, L., Wells, G. N., Garikipati, K., and Ubertini, F.

Subjects
Physics - Computational Physics, Physics - General Physics
Abstract

A discontinuous Galerkin method has been developed for strain gradient-dependent damage. The strength of this method lies in the fact that it allows the use of $C^0$ interpolation functions for continuum theories involving higher-order derivatives, while in a conventional framework at least $C^1$ interpolations are required. The discontinuous Galerkin formulation thereby offers significant potential for engineering computations with strain gradient-dependent models. When using basis functions with a low degree of continuity, jump conditions arise at element edges which are incorporated in the weak form. In addition to the formulation itself, a detailed study of the convergence properties of the method for various element types is presented, an error analysis is undertaken, and the method is also shown to work in two dimensions., Comment: LaTeX2e, 16 figures

Published
2004

17. A discontinuous Galerkin formulation for a strain gradient-dependent damage model

Author

Wells, G. N., Garikipati, K., and Molari, L.

Subjects
Mathematics - Numerical Analysis, 65L60, 65M60
Abstract

The numerical solution of strain gradient-dependent continuum problems has been dogged by continuity demands on the basis functions. For most commonly accepted models, solutions using the finite element method demand $C^{1}$ continuity of the shape functions. Here, recent development in discontinuous Galerkin methods are explored and exploited for the solution of a prototype nonlinear strain gradient dependent continuum model. A formulation is developed that allows the rigorous solution of a strain gradient damage model using standard $C^{0}$ shape functions. The formulation is tested in one-dimension for the simplest possible finite element formulation: piecewise linear displacement and constant (on elements) internal variable. Numerical results are shown to compare excellently with a benchmark solution. The results are remarkable given the simplicity of the proposed formulation., Comment: 22 pages, 7 figures, submitted, corrected to eliminate multiple appearance of pdf file

Published
2003
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18. Towards a standard for PET raw data

Author

Thielemans, K., primary, Kesner, A., additional, Asma, E., additional, Cabello, J., additional, Cook, M., additional, Hansen, M., additional, Jones, J., additional, Karakatsanis, N. A., additional, Leung, E. K. S., additional, Markiewicz, P., additional, Prevrhal, S., additional, Rahmim, A., additional, Saboury, B., additional, Stairs, J., additional, Stute, S., additional, Tashima, H., additional, and Wells, G., additional

Published
2023
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25. Discontinuous modelling of strain localisation and failure

Author

Wells, G. N., de Borst, Rene, and Sluys, Lambertus J

Subjects
620.1
Abstract

The computational simulation of failure in solids poses many challenges. A proper understanding of how structures respond under loading, both before and past the peak load, is important for safe and economical constructions. This requires numerical models for failure which are both faithful to the physical reality and mathematically well founded. A serious computational issue is that of objectivity with respect to the spatial discretisation of a problem. This requires that upon refinement of the spatial discretisation of a problem, a unique, physically meaningful result is approached. One approach to ensure objectivity with respect to spatial discretisation when simulating failure in solids is to allow displacement discontinuities in the solution. In this work, different techniques, of varying complexity, are developed to simulate displacement discontinuities which are independent of the spatial discretisation using finite elements. The different techniques are then critically evaluated. The first model examined involves adding only the effect of a displacement discontinuity to a finite element as an incompatible strain mode. This allows a traction-separation relationship to be applied at an interface and can be implemented simply in a standard finite element code. It is however shown that this type of model can be cast in an equivalent continuum format, a form which is known to be sensitive to the spatial discretisation. The second approach developed involves the addition of the Heaviside function to the underlying finite element interpolation basis. This method is based on the partition of unity concept, and allows the Heaviside function to be added locally to a finite element mesh to simulate a propagating displacement discontinuity. The approach is formulated for geometrically linear, geometrically nonlinear, quasi-static and dynamic problems. It is shown to be completely independent of the spatial discretisation. The partition of unity-based model is used also to simulate failure using a regularised strain softening model. When a critical level of inelastic deformation is reached, a displacement discontinuity is inserted. This model is better suited to modelling the entire failure process than a continuum or discontinuous model alone. Through numerical examples, it is shown that the inclusion of a displacement discontinuity during the failure process can lead to a different failure mode than for a continuum-only model.

Published
2001
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27. Effect of High-dose Folic Acid Supplementation in Pregnancy on Preeclampsia (FACT): Double-blind, Phase III, Randomized Controlled, International, Multicenter Trial

Author

Wen, S.W., White, R.R., Rybak, N., Gaudet, L.M., Robson, S., Hague, W., Simms-Stewart, D., Carroli, G., Smith, G., Fraser, W.D., Wells, G., Davidge, S.T., Kingdom, J., Coyle, D., Fergusson, D., Corsi, D.J., Champagne, J., Sabri, E., Ramsay, T., Mol, B.W.J., Oudijk, M.A., and Walker, M.C.

Published
2019
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