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2. Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field

Author

D’Amore, Lorenzo, Hahn, David F, Dotson, David L, Horton, Joshua T, Anwar, Jamshed, Craig, Ian, Fox, Thomas, Gobbi, Alberto, Lakkaraju, Sirish Kaushik, Lucas, Xavier, Meier, Katharina, Mobley, David L, Narayanan, Arjun, Schindler, Christina EM, Swope, William C, Veld, Pieter J in ’t, Wagner, Jeffrey, Xue, Bai, and Tresadern, Gary

Subjects
Medicinal and Biomolecular Chemistry, Chemical Sciences, Generic health relevance, Thermodynamics, Ligands, Proteins, Physical Phenomena, Theoretical and Computational Chemistry, Computation Theory and Mathematics, Medicinal & Biomolecular Chemistry, Medicinal and biomolecular chemistry, Theoretical and computational chemistry
Abstract

Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small-molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small-molecule force field. In this report, industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4, and SMIRNOFF99Frosst. We analyzed force-field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a clear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.

Published
2022

6. Optimized lockdown strategies for curbing the spread of COVID-19: A South African case study

Author

Olivier, Laurentz E., Botha, Stefan, and Craig, Ian K.

Subjects
Quantitative Biology - Populations and Evolution, Physics - Physics and Society
Abstract

To curb the spread of COVID-19, many governments around the world have implemented tiered lockdowns with varying degrees of stringency. Lockdown levels are typically increased when the disease spreads and reduced when the disease abates. A predictive control approach is used to develop optimized lockdown strategies for curbing the spread of COVID-19. The strategies are then applied to South African data. The South African case is of interest as the South African government has defined five distinct levels of lockdown, which serves as a discrete control input. An epidemiological model for the spread of COVID-19 in South Africa was previously developed, and is used in conjunction with a hybrid model predictive controller to optimize lockdown management under different policy scenarios. Scenarios considered include how to flatten the curve to a level that the healthcare system can cope with, how to balance lives and livelihoods, and what impact the compliance of the population to the lockdown measures has on the spread of COVID-19. The main purpose of this paper is to show what the optimal lockdown level should be given the policy that is in place, as determined by the closed-loop feedback controller., Comment: 11 pages, 7 figures, 4 tables

Published
2020
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17. Whatever Happened to Educational Management? The Case for Reinstatement

Author

Craig, Ian

Abstract

'Leadership' has now become one of the most over-used terms in school organisation, so much so that it is now difficult to find mentions of 'management' and 'administration' in school organisation literature. Papers published in "Educational Management, Administration and Leadership" and "Management in Education" over the last few years confirm this view. This article argues that although there is a significant overlap between them, leadership, management and administration are different from each other and this should be recognised when talking and writing about school organisation and development, with not all three being subsumed under the banner of 'leadership'. In particular, the article argues for the re-establishment of management as a major element in the development and training of heads and prospective heads of schools and colleges.

Published
2021
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20. Seawater intake risers for Floating Liquefied Natural Gas (FLNG) vessels

Author

Craig, Ian

Subjects
665.7, Engineering
Abstract

As the world energy demand increases, and the desire for cleaner fuels strengthens, a number of major oil and gas companies are developing Floating Liquefied Natural Gas (FLNG) vessels to harvest natural gas ‘stranded’ in reservoirs that have previously been considered too uneconomic to develop. A key requirement for this new generation of vessels is a high volume of low temperature seawater for process cooling. The aim of this research is to investigate whether the concepts underpinning free hanging cantilever seawater intake risers used on Floating, Production, Storage and Offloading (FPSO) vessels can be extended to the design of seawater intake risers for FLNG vessels in order to reach and import colder seawater from depths greater than has so far been achieved with these systems. The research focusses on establishing the physical, mechanical and fatigue properties of a number of material elements under consideration for this application and then investigates a number of combinations to determine the optimum configuration for a hybrid deep seawater intake riser. To demonstrate the strength and fatigue capabilities of the hybrid riser, the selected configuration is then subject to a more detailed analysis with consideration of a number of key aspects such as vessel motion, marine growth, vortex induced vibration, stability due to internal flow and excursion due to external fluid. A number of sensitivities are also performed with respect to riser damping, riser length, vessel size and geographical location. Additionally, the flow characteristics in terms of pressure loss and temperature gain are examined and a number of sensitivities performed to show that the cold seawater can be imported effectively. Finally, using published data for FLNG vessels currently under construction, an economic argument is presented to highlight the potential cost advantage of reaching and importing colder seawater by means of a deep seawater intake riser. As a result of this research, the solution being presented offers a significant technological advantage for these systems in the field enabling high volumes of seawater to be imported from greater depths whilst accommodating the loads induced by the environmental conditions and minimising the loads induced into the hull of the vessel. Furthermore, the solution is based on the concepts of a field proven system, thereby limiting the risks associated with untested technological advancements. The findings of this research enable the process efficiencies of FLNG vessels to be greatly enhanced thus contributing to the more efficient extraction of a cleaner fuel which, in a world with ever increasing energy demands, is critical to the global economy. The novelty of the research is demonstrated by two successful patent applications, one in relation to the improved features of existing seawater intake riser systems and the other in relation to the use of multiple material elements for a hybrid seawater intake riser. Both patents have been examined and granted in five jurisdictions, namely, Europe, Japan, China. South Korea and the USA.

Published
2018

22. From Nobel Prize to clinical practice: An update on messenger RNA-based therapies for lipid disorders.

Author

HAMILTON-CRAIG, IAN R.

Subjects
*SMALL interfering RNA, *LIPOPROTEIN lipase, *INDIGENOUS Australians, *CLINICAL trials, *NUCLEIC acids, *DYSLIPIDEMIA
Abstract

This article provides an update on messenger RNA (mRNA)-based therapies for lipid disorders, specifically focusing on inclisiran, a medication used to lower LDL-cholesterol levels. It explains the biological mechanism of gene silencing by mRNA inhibition and how it has been used to develop therapies targeting specific proteins involved in lipid metabolism. The article highlights the potential of mRNA therapies in reducing cardiovascular events and provides information on clinical trials and the efficacy of inclisiran. It also discusses the advantages and contraindications of inclisiran, but notes that long-term outcomes and cost-effectiveness data are not yet available. Overall, mRNA-based therapies show promise in the treatment of lipid disorders, but further research is needed. [Extracted from the article]

Published
2024

23. Reversible Colorimetric Sensing of Volatile Analytes By Wicking in Close Proximity to A Photonic Film

Author

Timothy J. Palinski, Bin Guan, Bronwyn H. Bradshaw-Hajek, Michael A. Lienhard, Craig Ian Priest, and Félix A. Miranda

Subjects
Earth Resources and Remote Sensing
Abstract

Isolation of volatile analytes from environmental or biological fluids is a rate-determining step that can delay the response time for continuous sensing. In this paper, we demonstrate a colorimetric sensing system that enables the rapid detection of gas-phase analytes released from a flowing micro-volume fluid sample. The sensor platform is an analyte-responsive metal-insulator-metal (MIM) thin-film structure integrated with a large area quartz micropillar array. This allows precise planar alignment and microscale separation (310 μm) of the optical and fluidic structures. This configuration offers rapid and homogeneous color changes over large areas that permits detection by low-resolution optics or eye, which is well-suited to portable/wearable devices. For our proof-of-principle demonstration, we utilized a poly(methyl methacrylate) (PMMA) spacer and evaluated the sensor's response (color change) to ethanol vapor. We show that the RGB color value is quantitatively linked to the spacer swelling, which is reversible and repeatable. The optofluidic platform reduces the sensor response time from minutes to seconds compared with experiments using a conventional chamber. The sensor's concentration-dependent response was examined, confirming the potential of the reported sensing platform for continuous, compact, and quantitative colorimetric analysis of volatile analytes in low-volume samples, such as biofluids.

Published
2022
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24. Synopsis of an integrated guidance for enhancing the care of familial hypercholesterolaemia: an Australian perspective

Author

Ademi, Zanfina, Ardill, Justin J, Barnett, Wendy, Bates, Timothy R, Beilin, Lawrence J, Bishop, Warrick, Black, J Andrew, Brown, Alex, Burnett, John R, Bursill, Christina A, Colley, Alison, Clifton, Peter M, Ekinci, Elif I, Figtree, Gemma A, Forge, Brett H, Garton-Smith, Jacquie, Graham, Dorothy F, Hamilton-Craig, Ian, Hamilton-Craig, Christian R, Heal, Clare, Hespe, Charlotte M, Hooper, Amanda J, Howes, Laurence G, Ingles, Jodie, Janus, Edward D, Kangaharan, Nadarajah, Keech, Anthony C, Kirke, Andrew B, Kritharides, Leonard, Kyle, Campbell V, Lacaze, Paul, Li, Stephen CH, Maticevic, Stjepana, McQuillan, Brendan M, Mirzaee, Sam, Mori, Trevor A, Morton, Allison C, Colquhoun, David M, Moullin, Joanna C, Nestel, Paul J, Nowak, Kristen J, O'Brien, Richard C, Pachter, Nicholas, Page, Michael M, Psaltis, Peter J, Radford, Jan, Reid, Nicola J, Robertson, Elizabeth N, Ryan, Jacqueline DM, Sarkies, Mitchell N, Schultz, Carl J, Scott, Russell S, Semsarian, Christopher, Simons, Leon A, Spinks, Catherine, Tonkin, Andrew M, van Bockxmeer, Frank, Waddell-Smith, Kathryn E, Ward, Natalie C, White, Harvey D, Wilson, Andrew M, Winship, Ingrid, Woodward, Ann Marie, Nicholls, Stephen J, Brett, Peter, Elias, Luke, Malan, Wynand, Irvin, John, Lambert, Kirsten, Pedrotti, Annette, Watts, Gerald F., Sullivan, David R., Hare, David L., Kostner, Karam M., Horton, Ari E., Bell, Damon A., Brett, Tom, Trent, Ronald J., Poplawski, Nicola K., Martin, Andrew C., Srinivasan, Shubha, Justo, Robert N., Chow, Clara K., and Pang, Jing

Published
2021
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25. Integrated Guidance for Enhancing the Care of Familial Hypercholesterolaemia in Australia

Author

Ademi, Zanfina, Ardill, Justin J., Barnett, Wendy, Bates, Timothy R., Beilin, Lawrence J., Bishop, Warrick, Black, J. Andrew, Brett, Peter, Brown, Alex, Burnett, John R., Bursill, Christina A., Colley, Alison, Clifton, Peter M., Ekinci, Elif I., Elias, Luke, Figtree, Gemma A., Forge, Brett H., Garton-Smith, Jacquie, Graham, Dorothy F., Hamilton-Craig, Ian, Hamilton-Craig, Christian R., Heal, Clare, Hespe, Charlotte M., Hooper, Amanda J., Howes, Laurence G., Ingles, Jodie, Irvin, John, Janus, Edward D., Kangaharan, Nadarajah, Keech, Anthony C., Kirke, Andrew B., Kritharides, Leonard, Kyle, Campbell V., Lacaze, Paul, Lambert, Kirsten, Li, Stephen C.H., Malan, Wynand, Maticevic, Stjepana, McQuillan, Brendan M., Mirzaee, Sam, Mori, Trevor A., Morton, Allison C., Colquhoun, David M., Moullin, Joanna C., Nestel, Paul J., Nowak, Kristen J., O'Brien, Richard C., Pachter, Nicholas, Page, Michael M., Pedrotti, Annette, Psaltis, Peter J., Radford, Jan, Reid, Nicola J., Robertson, Elizabeth N., Ryan, Jacqueline D.M., Sarkies, Mitchell N., Schultz, Carl J., Scott, Russell S., Semsarian, Christopher, Simons, Leon A., Spinks, Catherine, Tonkin, Andrew M., van Bockxmeer, Frank, Waddell-Smith, Kathryn E., Ward, Natalie C., White, Harvey D., Wilson, Andrew M., Winship, Ingrid, Woodward, Ann Marie, Nicholls, Stephen J., Watts, Gerald F., Sullivan, David R., Hare, David L., Kostner, Karam M., Horton, Ari E., Bell, Damon A., Brett, Tom, Trent, Ronald J., Poplawski, Nicola K., Martin, Andrew C., Srinivasan, Shubha, Justo, Robert N., Chow, Clara K., and Pang, Jing

Published
2021
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33. Anonymous Sojourners: Mapping the Territory of Caribbean Experiences of Immersion for Language Learning

Author

Craig, Ian

Abstract

This paper presents findings of a pilot qualitative study of Caribbean students undertaking overseas immersion primarily for the purpose of perfecting their knowledge of a language and understanding of a culture other than their own. The participants were a group of eleven University of the West Indies (UWI), Cave Hill (Barbados) graduates, five in Colombia, six in France, all working as English-language assistants for eight to ten months during the 2007-2008 academic year. Three data collection instruments were used: (1) diaries kept by participants throughout the sojourn; (2) eleven semi-structured interviews averaging 56 minutes duration, with eight of these being after the sojourn and three during (after three months); and (3) a questionnaire administered six months after return. One of the principal functions of this study is to fill a gap in the research by assessing how the relative size and "recognizability" of the home and host states may affect the sojourner's experience. The results of this study are discussed. (Contains 1 note.)

Published
2010

35. Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

Author

O'Dushlaine, Colm, Rossin, Lizzy, Lee, Phil H, Duncan, Laramie, Parikshak, Neelroop N, Newhouse, Stephen, Ripke, Stephan, Neale, Benjamin M, Purcell, Shaun M, Posthuma, Danielle, Nurnberger, John I, Lee, S Hong, Faraone, Stephen V, Perlis, Roy H, Mowry, Bryan J, Thapar, Anita, Goddard, Michael E, Witte, John S, Absher, Devin, Agartz, Ingrid, Akil, Huda, Amin, Farooq, Andreassen, Ole A, Anjorin, Adebayo, Anney, Richard, Anttila, Verneri, Arking, Dan E, Asherson, Philip, Azevedo, Maria H, Backlund, Lena, Badner, Judith A, Bailey, Anthony J, Banaschewski, Tobias, Barchas, Jack D, Barnes, Michael R, Barrett, Thomas B, Bass, Nicholas, Battaglia, Agatino, Bauer, Michael, Bayes, Monica, Bellivier, Frank, Bergen, Sarah E, Berrettini, Wade, Betancur, Catalina, Bettecken, Thomas, Biederman, Joseph, Binder, Elisabeth B, Black, Donald W, Blackwood, Douglas HR, Bloss, Cinnamon S, Boehnke, Michael, Boomsma, Dorret I, Breuer, Rene, Bruggeman, Richard, Cormican, Paul, Buccola, Nancy G, Buitelaar, Jan K, Bunney, William E, Buxbaum, Joseph D, Byerley, William F, Byrne, Enda M, Caesar, Sian, Cahn, Wiepke, Cantor, Rita M, Casas, Miguel, Chakravarti, Aravinda, Chambert, Kimberly, Choudhury, Khalid, Cichon, Sven, Mattheisen, Manuel, Cloninger, C Robert, Collier, David A, Cook, Edwin H, Coon, Hilary, Cormand, Bru, Corvin, Aiden, Coryell, William H, Craig, David W, Craig, Ian W, Crosbie, Jennifer, Cuccaro, Michael L, Curtis, David, Czamara, Darina, Datta, Susmita, Dawson, Geraldine, Day, Richard, De Geus, Eco J, Degenhardt, Franziska, Djurovic, Srdjan, Donohoe, Gary J, Doyle, Alysa E, Duan, Jubao, Dudbridge, Frank, Duketis, Eftichia, Ebstein, Richard P, Edenberg, Howard J, Elia, Josephine, Ennis, Sean, Etain, Bruno, and Fanous, Ayman

Subjects
Human Genome, Brain Disorders, Serious Mental Illness, Schizophrenia, Genetics, Depression, Mental Health, Aetiology, 2.1 Biological and endogenous factors, Mental health, Good Health and Well Being, Brain, Databases, Genetic, Genetic Predisposition to Disease, Genome-Wide Association Study, Histones, Humans, Mental Disorders, Signal Transduction, Network and Pathway Analysis Subgroup of Psychiatric Genomics Consortium, Neurosciences, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

Genome-wide association studies (GWAS) of psychiatric disorders have identified multiple genetic associations with such disorders, but better methods are needed to derive the underlying biological mechanisms that these signals indicate. We sought to identify biological pathways in GWAS data from over 60,000 participants from the Psychiatric Genomics Consortium. We developed an analysis framework to rank pathways that requires only summary statistics. We combined this score across disorders to find common pathways across three adult psychiatric disorders: schizophrenia, major depression and bipolar disorder. Histone methylation processes showed the strongest association, and we also found statistically significant evidence for associations with multiple immune and neuronal signaling pathways and with the postsynaptic density. Our study indicates that risk variants for psychiatric disorders aggregate in particular biological pathways and that these pathways are frequently shared between disorders. Our results confirm known mechanisms and suggest several novel insights into the etiology of psychiatric disorders.

Published
2015

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