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9. Persistence and modularity in PROLOG

Author

Moffatt, D. S.

Subjects
005.3
Abstract

Persistence is a feature of computer systems that makes data movement between primary and secondary memory transparent, allowing dynamically created objects to persist on disk, maintaining their referential structure, and able to be accessed in subsequent sessions. The research entailed the design and development of a persistent Prolog and of evaluating the final system. The development of a module system adequate for persistent applications soon became an integral part of the research. There are three main aspects to the thesis - a review of the issues of modularity and a description of the module scheme implemented for Persistent Prolog; the database view of Prolog and how persistent databases are integrated into it; and finally, external call-outs from Prolog and how to best use the persistent programming language PS-algol. Modules partition the program name space but also provide scope for updates to Prolog's internal database which makes them suitable models of the persistent partitions of the file store. In order to support exploratory updates to the Prolog database, modules can be committed independently allowing selected changes to be preserved. An atom based model of visibility was chosen for the modules because it simplified meta-level programming, allowed hiding of local data and supported independent modular commitment through separate module representations. The interface to PS-algol is a backtrackable one that allows tight coupling to externally supported databases and to algorithmic applications. The system's performance is an order of magnitudeslower than complete reads of dumped states but because of its incremental, shared and secure access to databases, it can be used for problems that defy the use of monolithic images.

Published
1988

13. A database of chlorophyll a in Australian waters

Author

Davies, CH, Ajani, P, Armbrecht, L, Atkins, N, Baird, ME, Beard, J, Bonham, P, Burford, M, Clementson, L, Coad, P, Crawford, C, Dela-Cruz, J, Doblin, MA, Edgar, S, Eriksen, R, Everett, JD, Furnas, M, Harrison, DP, Hassler, C, Henschke, N, Hoenner, X, Ingleton, T, Jameson, I, Keesing, J, Leterme, SC, James McLaughlin, M, Miller, M, Moffatt, D, Moss, A, Nayar, S, Patten, NL, Patten, R, Pausina, SA, Proctor, R, Raes, E, Robb, M, Rothlisberg, P, Saeck, EA, Scanes, P, Suthers, IM, Swadling, KM, Talbot, S, Thompson, P, Thomson, PG, Uribe-Palomino, J, Van Ruth, P, Waite, AM, Wright, S, Richardson, AJ, Davies, CH, Ajani, P, Armbrecht, L, Atkins, N, Baird, ME, Beard, J, Bonham, P, Burford, M, Clementson, L, Coad, P, Crawford, C, Dela-Cruz, J, Doblin, MA, Edgar, S, Eriksen, R, Everett, JD, Furnas, M, Harrison, DP, Hassler, C, Henschke, N, Hoenner, X, Ingleton, T, Jameson, I, Keesing, J, Leterme, SC, James McLaughlin, M, Miller, M, Moffatt, D, Moss, A, Nayar, S, Patten, NL, Patten, R, Pausina, SA, Proctor, R, Raes, E, Robb, M, Rothlisberg, P, Saeck, EA, Scanes, P, Suthers, IM, Swadling, KM, Talbot, S, Thompson, P, Thomson, PG, Uribe-Palomino, J, Van Ruth, P, Waite, AM, Wright, S, and Richardson, AJ

Abstract

© The Author(s) 2018. Chlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal (https://portal.aodn.org.au/). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish.

Published
2018

17. Second-harmonic generation optical activity of a polypeptide α-helix at the air/water interface.

Author

Mitchell, S. A., McAloney, R. A., Moffatt, D., Mora-Diez, N., and Zgierski, M. Z.

Subjects
SECOND harmonic generation, QUANTITATIVE research, NONLINEAR optics, ION exchange (Chemistry), EXCHANGE reactions, PERTURBATION theory, CHARGE transfer
Abstract

Quantitative measurements of second-harmonic generation optical activity (SHG-OA) have been performed for α-helical polypeptides poly-(γ-benzyl-L-glutamate) and poly-(γ-ethyl-L-glutamate) adsorbed at the air/water interface, with the fundamental frequency hω=2.96 eV (λ=417 nm). The chiral component of the nonlinear susceptibility χXYZ(2) is small for both polymers, being comparable in magnitude with the susceptibility χXXZ(2) of the clean air/water interface. The microscopic origin of the nonlinear response has been investigated by using semiempirical ZINDO/S calculations in conjunction with standard time-dependent perturbation theory to evaluate the molecular hyperpolarizability tensor of a model α-helix composed of glycine residues. Calculated nonlinear susceptibilities (per monomer unit) are in good agreement with experimental measurements for both the chiral and achiral response. The computational results indicate that charge transfer transitions of the α-helix have a large influence on the achiral components of the hyperpolarizability tensor, and produce characteristic features in the response under suitable experimental conditions. The dominant origin of SHG-OA for the model α-helix is a structural effect due to the tilt of the plane of each amide group of the helix relative to the helical axis. SHG-OA is associated with the orientational distribution of isolated, achiral chromophores, and is present in the absence of electronic coupling between the amide subunits of the polypeptide α-helix. [ABSTRACT FROM AUTHOR]

Published
2005
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20. Hydrostatic pressure effects on TO–LO splitting and softening of infrared active phonons in α-quartz.

Author

Wong, P. T. T., Baudais, F. L., and Moffatt, D. J.

Subjects
INFRARED spectra, RAMAN effect, PHONONS
Abstract

Infrared spectra of crystalline α-quartz have been measured as a function of pressure up to 50.3 kbar. Pressure induced large frequency shifts, increase in TO–LO splittings and ‘‘softening’’ in various phonon bands have been observed. The pressure dependences of the mode Grüneisen parameters for selected phonons have been calculated. The results are discussed in terms of the pressure induced changes in crystal structure and Szigeti effective charge. [ABSTRACT FROM AUTHOR]

Published
1986
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23. Quantum random bit generation by stimulated Raman scattering

Author

Bustard, P.J., Moffatt, D., Lausten, R., Wu, G., Walmsley, I.A., and Sussman, B.J.

Subjects
Random number generators, Lasers, Vacuum fluctuations, Zero-point, Random number generation, Stimulated Raman scattering
Abstract

We introduce a quantum random number generator based on the phase measurement of Stokes light generated by amplification of zero-point vacuum fluctuations using stimulated Raman scattering in bulk diamond. © 2012 OSA., 2012 Conference on Lasers and Electro-Optics, CLEO 2012, 6 May 2012 through 11 May 2012, San Jose, CA

Published
2012

31. An automated biochemical assay for haptoglobin: prevention of interference from albumin

Author

Eckersall, P.D., Duthie, S., Safi, S., Moffatt, D., Horadagoda, N.U., Doyle, Sean, Parton, R., Bennett, D., Fitzpatrick, J.L., Eckersall, P.D., Duthie, S., Safi, S., Moffatt, D., Horadagoda, N.U., Doyle, Sean, Parton, R., Bennett, D., and Fitzpatrick, J.L.

Abstract

Measurement of the acute phase serum protein, haptoglobin (Hp), is performed by biochemical methods based on haemoglobin binding, in many veterinary diagnostic laboratories. During attempts to develop a robust biochemical assay for serum Hp it was discovered that serum albumin interfered with the assay system increasing results by as much as 0.28 mg/ml, which could affect interpretation of results especially in species with low normal Hp concentrations. A reagent cocktail (SB-7) was devised which inhibited the interfering effect of albumin. An automated assay for Hp utilising SB-7 was developed for production as a biochemical assay kit and was evaluated for use in veterinary diagnosis. The intra-assay coefficients of variation were of 0.9%, 0.9% and 1.3% for Hp concentrations of 2.0, 1.0 and 0.23 mg/ml, respectively and interassay coefficients of variation of 1.7% and 4.5% for Hp of 2.08 mg/ml and 0.24 mg/ml, respectively. The lower limit of detection of was 0.02 mg/ml, linearity extended to 8 mg/ml and recovery was 101±7% (mean ±SD). The assay had correlation coefficients (R2) of 0.96 and 0.90 when compared with immunodiffusion assays of canine Hp and bovine Hp, respectively. Lipaemia and bilirubinaemia caused no interference. Haemolysis did not affect measurement of low levels of Hp, but at serum Hp concentrations of 0.4 and 1.8 mg/ml the apparent Hp concentration was decreased. Elevated concentrations of Hp were measured in cattle with mastitis, dogs with polyarthritis and rats experimentally infected withBordetella pertussis. The automated assay is precise and has negligible interference from albumin.

Published
1999

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