Add Lloyd bibtex entry + software page update

Author: jbisits

_bibliography/papers.bib

@@ -10,11 +10,17 @@ @unpublished{Bisits2025b
    year = {In prep.},
    keywords = {paper},
 }
-@unpublished{Lloyd,
-   author = {Simon Lloyd and Josef I. Bisits and Gordana Popovic and Paul Osmond and David J. Roser and Stuart J. Khan},
-   title = { Swimming in urban estuaries: understanding stormwater contamination events and recovery from historical data},
-   year = {Submitted to: Water Research},
-   keywords = {paper},
+@article{Lloyd,
+   title = {Swimming in urban estuaries: understanding stormwater contamination events and recovery from historical data},
+   journal = {Water Research},
+   pages = {125686},
+   year = {2026},
+   issn = {0043-1354},
+   doi = {https://doi.org/10.1016/j.watres.2026.125686},
+   url = {https://www.sciencedirect.com/science/article/pii/S0043135426003684},
+   author = {Simon D. Lloyd and Josef I. Bisits and Gordana Popovic and Paul Osmond and David Roser and Stuart J. Khan},
+   keywords = {Urban bathing, stormwater, enterococci, estuary, salinity, recreational water quality},
+   abstract = {Cities globally are responding to public demand for water-based recreation by transforming urban rivers and estuaries into swimming destinations. Historical water quality compliance records may help diagnose contamination and recovery dynamics and serve as a valuable reference point for assessing the suitability of proposed urban swimming sites. This study analysed historical bathing water compliance data and concurrent hydrometeorological records to characterise long and short-term contamination and recovery patterns at current and proposed bathing sites in Sydney’s Parramatta River estuary. Generalised Linear Mixed Modelling (GLMM) was used to estimate site-specific recovery parameters and explore environmental drivers of variability in the faecal indicator bacteria (FIB) enterococci. Recovery times to health-relevant thresholds ranged from 3 to 125 hours, with background levels reached between 10 to 142 hours depending on initial contamination. Marine-dominated bathing sites were temporarily diluted to near-freshwater conditions following rainfall, as indicated by reductions of up to 97% in baseline salinity. A 10 mm rainfall threshold was identified as a practical trigger for event-based sampling. Salinity and solar exposure were the most influential environmental factors affecting recovery rates. This study demonstrates how routine, compliance datasets can be repurposed to derive short-term, site-specific recovery metrics, quantify stormwater intrusion using a practical salinity proxy (RSR%), and establish actionable rainfall triggers for event-based monitoring, providing an evidence-based blueprint to inform risk management for emerging urban bathing sites when high-frequency data are unavailable.}
 }
 @article{Bisits2025,
    abstract = {At constant pressure, a mixture of water parcels with equal density but differing salinity and temperature will be denser than the parent water parcels. This is known as cabbeling and is a consequence of the nonlinear equation of state for seawater density. With a source of turbulent vertical mixing, cabbeling has the potential to trigger and drive convection in gravitationally stable water columns and there is observational evidence that this process shapes the thermohaline structure of high-latitude oceans. However, the evolution and maintenance of turbulent mixing due to cabbeling has not been fully explored. Here, we use turbulence-resolving direct numerical simulations to investigate cabbeling’s impact on vertical mixing and pathways of energy in closed systems. We find that cabbeling can sustain convection in an initially gravitationally stable two-layer configuration where relatively cold/fresh water sits atop warm/salty water. We show the mixture of the cold/fresh and warm/salty water is constrained by a density maximum and that cabbeling enhances mixing rates by four orders of magnitude. Cabbeling’s effect is amplified as the static stability limit is approached, leading to convection being sustained for longer. We find that available potential energy, which is classically thought to only decrease with mixing, can increase with mixing due to cabbeling’s densification of the mixed water. Our direct numerical simulations support the notion that cabbeling could be a source of enhanced ocean mixing and that conventional definitions of energetic pathways may need to be reconsidered to take into account densification under mixing.},

_pages/software.md

@@ -5,11 +5,16 @@ header:
     overlay_color: "#333"
 ---
 
-I use the [Julia programming language](https://julialang.org/) as it is excellent for scientific computing, open source and has a great community.
+Throughout my research, I work with many different models of fluid flow ranging from turbulence resolving, process based models that require extremely fine resolution, all the to way global ocean-sea-ice models, that simulate the large scale circulation patterns of the ocean.
+Some of these models can be run on laptops, but many need be run on High Performance Computing systems such as [Gadi](https://nci.org.au/news-events/events/introduction-gadi) which is operated and maintained by the [National Computational Infrastructure](https://nci.org.au/) in Canberra.
+This domain of my research drives keen interest, most of the time obsession would be more accurate, and enthusiasm for open source software development and usage in science (and anywhere else it can help in life!).
+
+By choice, I use the [Julia programming language](https://julialang.org/) as it is excellent for scientific computing, open source and has a great community.
 I am the owner and maintainer of the packages: [StaircaseShenanigans.jl](https://github.com/jbisits/StaircaseShenanigans.jl), [TwoLayerDirectNumericalShenanigans.jl](https://github.com/jbisits/TwoLayerDirectNumericalShenanigans.jl), [RasterHistograms.jl](https://github.com/jbisits/RasterHistograms.jl) and [OceanRasterConversions.jl](https://jbisits.github.io/OceanRasterConversions.jl/dev/).
 I am currently involved in the development of [PassiveTracerFlows.jl](https://fourierflows.github.io/PassiveTracerFlowsDocumentation/stable/) and have contributed to several other packages including [FourierFlows.jl](https://github.com/FourierFlows/FourierFlows.jl), [GeophysicalFlows.jl](https://github.com/FourierFlows/GeophysicalFlows.jl) and [Oceananigans.jl](https://github.com/CliMA/Oceananigans.jl).
 
-I am also fluent with [R](https://www.r-project.org/), [python](https://www.python.org/), [MATLAB/Octave](https://octave.org/), [$\LaTeX$](https://www.latex-project.org/) and [git](https://git-scm.com/).
+I am also fluent with [R](https://www.r-project.org/), [python](https://www.python.org/), [MATLAB/Octave](https://octave.org/), [Fortran](https://fortran-lang.org/), [$\LaTeX$](https://www.latex-project.org/) and [git](https://git-scm.com/).
 
-I also experiment with writing themes for editors.
-I particularly like the [penumbra colour scheme](https://github.com/nealmckee/penumbra) which I have ported to [obsidian](https://github.com/jbisits/penumbra-obsidian-theme) and [zed](https://github.com/jbisits/penumbra-zed).
+Looking at screens full of code all day made me realise how important colour schemes for editors are.
+This encouraged me to explore the wide world of colour schemes!
+I particularly like the [penumbra colour scheme](https://github.com/nealmckee/penumbra) which I have ported to [obsidian](https://github.com/jbisits/penumbra-obsidian-theme) and [zed](https://github.com/jbisits/penumbra-zed) and I also have a version for [neovim](https://github.com/jbisits/penumbra.nvim) which I am currently working on.