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Microbes drive largescale processes in human health, industrial applications, and the environment, and have traditionally been sampled and studied at these larger scales. However, the collective behaviour of microbes emerges from their microscopic behaviour and finescale interactions with one another and their environment. Our research group uses mathematical modelling and quantitative videomicroscopy to study a range of dynamic processes in biology – crucially at the scale of individual cells – with specific applications in bacterial motility, symbioses, nutrient cycling and flows around coral reefs.
A full list of publications can also be found on Google Scholar.
Machine learning driven image segmentation and shape clustering of algal microscopic images obtained from various water types
F. Nelli, Z. Ge, L. Blackall, N. Taheriashtiani, R. Henry, D.R. Brumley, M. Grace, A. Jex, M. Burch, T.F. Lin, C. Bertelkamp, A. Willis, L. Gao, J. Schmidt, N.D. Crosbie, A. Zamyadi
bioRxiv (2024)
Unique photosynthetic strategies employed by closely related Breviolum minutum strains under rapid shortterm cumulative heat stress
P. Deore, S.J.T.M. Ching, M.R. Nitschke, D. Rudd, D.R. Brumley, E. Hinde, L.L. Blackall, M.J.H. van Oppen
Journal of Experimental Botany erae170 (2024)
The propulsion direction of nanoparticles trapped in an acoustic field
P. Li, A.R. Nunn, D.R. Brumley, J.E. Sader, J.F. Collis
Journal of Fluid Mechanics 984, R1 (2024) [pdf]
Cutting through host autofluorescence: fluorescence lifetime imaging microscopy for visualising intracellular bacteria in Symbiodiniaceae
P. Deore, S.J. Tsang Min Ching, D.R. Brumley, M.J.H. van Oppen, E. Hinde, L.L. Blackall
bioRxiv (2024)
Swimming towards each other: The role of chemotaxis in bacterial interactions
J.R. Seymour*, D.R. Brumley*, R. Stocker, J.B. Raina*
Trends in Microbiology (2024)
Point torque representations of ciliary flows
S.A. Selvan, P.W. Duck, D. PihlerPuzović, D.R. Brumley
Physical Review Fluids 8, 123103 (2023)
Structure of the streaming flow generated by a sphere in a fluid undergoing rectilinear oscillation
P. Li, J.F. Collis, D.R. Brumley, L. Schneiders, J.E. Sader
Journal of Fluid Mechanics 974, A37 (2023)
Frontiers of Mathematical Biology: A workshop honouring Professor Edmund Crampin
R. Araujo, D.R. Brumley, J. Cursons, K. Day, M. Faria, J. Flegg, D. Germano, H. Hunt, P. Hunter, A. Jenner, S. Johnston, J.M. McCaw, P. Maini, C. Miller, W. Muskovic, J. Osborne, M. Pan, N. Shahidi, I. Siekmann, M. Stumpf, A. Zanca
Mathematical Biosciences 359 (2023)
Chemotaxis increases metabolic exchanges between marine picophytoplankton and heterotrophic bacteria
J.B. Raina*, M. Giardina*, D.R. Brumley*, P.L. Clode, M. Pernice, P. Guagliardo, J. Bougoure, H. Mendis, S. Smriga, E. Sonnenschein, M.S. Ullrich, R. Stocker, J.R. Seymour
Nature Microbiology 8, 510521 (2023)
Simultaneous visualization of flow fields and oxygen concentrations to unravel transport and metabolic processes in biological systems
S. Ahmerkamp, F. M. Jalaluddin, Y. Cui, D. R. Brumley, C. O. Pacherres, J. Berg, R. Stocker, M. MM Kuypers, K. Koren, L. Behrendt
Cell Reports Methods 2, 100216 (2022)
Feedback loops between mathematics and microbiology
D. R. Brumley
Microbiology Australia 43, 3235 (2022)
Fluorescence lifetime imaging microscopy (FLIM): a nontraditional approach to study hostmicrobial symbioses
P. Deore, I. Wanigasuriya, Sarah Jane T. M. Ching, D. R. Brumley, M. J. H. van Oppen, L. L. Blackall, E. Hinde
Microbiology Australia 43, 2227 (2022)
Pairwise scattering and bound states of spherical microorganisms
C. Darveniza, T. Ishikawa, T. J. Pedley, D. R. Brumley
Physical Review Fluids 7, 013104 (2022)
Rheology of a concentrated suspension of spherical squirmers: monolayer in simple shear flow
T. Ishikawa, D. R. Brumley, T. J. Pedley
Journal of Fluid Mechanics 914, A26 (2021)
Cutting through the noise: bacterial chemotaxis in marine microenvironments
D. R. Brumley, F. Carrara, A. M. Hein, G. I. Hagstrom, S. A. Levin, R. Stocker
Frontiers in Marine Science 7 (2020) [pdf]
Generating Controlled, Dynamic Chemical Landscapes to Study Microbial Behavior
F. Carrara, D. R. Brumley, A. M. Hein, Y. Yawata, M. M. Salek, K. S. Lee, E. Sliwerska, S. A. Levin, R. Stocker
Journal of Visualized Experiments (155), e60589 (2020)
Bacteria push the limits of chemotactic precision to navigate dynamic chemical gradients
D. R. Brumley, F. Carrara, A. M. Hein, Y. Yawata, S. A. Levin, R. Stocker
Proceedings of the National Academy of Sciences 116 (22) 1079210797 (2019) [pdf]
Stability of arrays of bottomheavy spherical squirmers
D. R. Brumley and T. J. Pedley
Physical Review Fluids 4, 053102 (2019) [pdf]
Transitions in synchronization states of model cilia through basalconnection coupling
Y. Liu, R. Claydon, M. Polin, D. R. Brumley
Journal of the Royal Society Interface 15:20180450 (2018) [pdf]
Highavidity IgA protects the intestine by enchaining growing bacteria
K. Moor, M. Diard, M. E. Sellin, B. Felmy, S. Y. Wotzka, A. Toska, E. Bakkeren, M. Arnoldini, F. Bansept, A. Dal Co, T. Völler, A. Minola, B. FernandezRodriguez, G. Agatic, S. Barbieri, L. Piccoli, C. Casiraghi, D. Corti, A. Lanzavecchia, R. R. Regoes, C. Loverdo, R. Stocker, D. R. Brumley*, W.D. Hardt*, E. Slack*
Nature 544, 498502 (2017) [pdf]
Longrange interactions, wobbles, and phase defects in chains of model cilia
D. R. Brumley, N. Bruot, J. Kotar, R. E. Goldstein, P. Cicuta, M. Polin
Physical Review Fluids 1, 081201(R) (2016) [pdf]
Natural search algorithms as a bridge between organisms, evolution, and ecology
A. M. Hein, F. Carrara, D. R. Brumley, R. Stocker, S. A. Levin
Proceedings of the National Academy of Sciences 113(34), 9413–9420 (2016) [pdf]
Squirmers with swirl: a model for Volvox swimming
T. J. Pedley, D. R. Brumley, R. E. Goldstein
Journal of Fluid Mechanics 798, 165186 (2016) [pdf]
Physical Limits on Bacterial Navigation in Dynamic Environments
A. M. Hein, D. R. Brumley, F. Carrara, R. Stocker, S. A. Levin
Journal of the Royal Society Interface 13: 20150844 (2016) [pdf]
Flagella, flexibility and flow: physical processes in microbial ecology
D. R. Brumley, R. Rusconi, K. Son, R. Stocker
European Physical Journal Special Topics 224, 31193140 (2015) [pdf]
Live from under the lens: Exploring microbial motility with dynamic imaging and microfluidics
K. Son, D. R. Brumley, R. Stocker
Nature Reviews Microbiology 13, 761775 (2015) [pdf]
Metachronal Waves in the Flagellar Beating of Volvox and Their Hydrodynamic Origin
D. R. Brumley, M. Polin, T. J. Pedley, R. E. Goldstein
Journal of the Royal Society Interface 12: 20141358 (2015) [pdf]
Flagellar Synchronization Through Direct Hydrodynamic Interactions
D. R. Brumley, K. Y. Wan, M. Polin, R. E. Goldstein
eLife 3, e02750 (2014) [pdf]
Hydrodynamic Synchronization and Metachronal Waves on the Surface of the Colonial Alga Volvox carteri
D. R. Brumley, M. Polin, T. J. Pedley, R. E. Goldstein
Physical Review Letters 109, 268102 (2012) [pdf]
Oscillation of Cylinders of Rectangular CrossSection Immersed in Fluid
D. R. Brumley, M. Willcox, J. E. Sader.
Physics of Fluids 22, 052001 (2010) [pdf]

Paper in Journal of Experimental Botany
Congratulations to Dr. Pranali Deore for her latest publication, "Unique photosynthetic strategies employed by closely related Breviolum minutum strains under rapid shortterm cumulative heat stress". While variation in thermal tolerance between species is well documented, variation between conspecific strains is understudied. This paper, published in Journal of Experimental Botany, found that Breviolum minutum strains employ distinct photoprotective strategies, resulting in different …
Publications, News 
Honourable Mention for Xinyi Yang
Congratulations to Xinyi Yang, whose poster, “Microswimmers in vortical flows”, received an Honourable Mention at the 7th Microscale Ocean Biophysics Meeting on Heron Island this week. This meeting brought together more than 70 participants working across many disciplines, including marine biology, ecology, physical oceanography, soft and active matter, applied mathematics, and engineering.
News 
VicANZIAM prize for Tristan Bunnage
Congratulations to MSc student Tristan Bunnage (cosupervised with Dr. Edward Hinton), who won second prize ($125) at the oneday meeting of the Australian and New Zealand Industrial and Applied Mathematics Society (ANZIAM, Victorian Branch). Tristan's talk was entitled “Miscible viscous fingering under an oscillating background flow”.
News 
Paper in Journal of Fluid Mechanics (Rapids)
Congratulations to Peijing Li, for the second paper from her PhD, published today in Journal of Fluid Mechanics. This paper identifies the mechanism underlying reversal of propulsion direction of spherical particles trapped in an acoustic standing wave. This has implications for studying the flow field around particles of nonspherical geometries and for modelling suspensions of particles in acoustic fields.
Publications, News 
Best student paper prize for Antony Selvan
Congratulations to Antony Selvan, who won the Best Student Paper Prize at the 2024 Mathematical Biology Special Interest Group (MBSIG) workshop at the University of South Australia. Antony’s paper, entitled “Point torque representations of ciliary flows” developed new singularity methods for representing the flow fields generated by cilia and flagella. This prize is for an exceptional paper in the field …
News 
ANZIAM Honourable mention for Xinyi Yang
Congratulations to Xinyi Yang for receiving an Honourable Mention in the Thomas Cherry Prize at the 2024 Australian and New Zealand Industrial and Applied Mathematics (ANZIAM) conference. Xinyi’s talk was entitled “Escape motility of multicellular magnetotactic prokaryotes”.
News 
Fluorescence lifetime imaging microscopy paper
Our preprint posted on bioRxiv, led by Dr. Pranali Deore, uses fluorescence lifetime imaging microscopy (FLIM) and FISH to visualise intracellular bacteria in Symbiodiniaceae. Significant changes in the abundance of intracellular bacteria relative to autofluorescence in B. minutum cells were observed at initiation of light and dark conditions. We suggest that the onset of bacterial endosymbiosis is linked to the …
Publications, News 
Paper in Trends in Microbiology
Our latest work, published in collaboration with colleagues at University of Technology Sydney and ETH Zurich, examines the role of chemotaxis in bacterial interactions. The paper in Trends in Microbiology discusses how chemotactic sensing could represent an important, but largely overlooked, phenotype within bacterial interactions, and play a major role in shaping cooperative and competitive relationships. Artwork by Philippe Plateaux.
Publications, News 
Paper in Physical Review Fluids
Congratulations to Antony Selvan for the first paper from his PhD. This work, published in Physical Review Fluids, employs a point torque (or “rotlet”) model to capture the timeaveraged ciliary flow above a planar rigid wall.
Publications, News 
Paper in Journal of Fluid Mechanics
Congratulations to Peijing Li for the first paper from her PhD, published recently in Journal of Fluid Mechanics. This work explores the streaming flow generated by a sphere in a fluid undergoing rectilinear oscillation.
Publications, News
Staff
Postdoctoral Fellows

Vicky Waymouth
Dr Vicky Waymouth is a Postdoctoral Research Fellow working on an interdisciplinary ARC Discovery Project (cosupervised with Prof. Michelle Watt). Her work focuses on modelling microorganism interactions in the rhizosphere using fabricated ecosystems and microfluidic devices.
Postdocs 
Pranali Deore
Dr Pranali Deore is a Postdoctoral Research Fellow (Mary Lugton Fellowship) working in areas of marine microbial symbiosis. She uses expansion microscopy, fluorescence lifetime imaging microscopy and microfluidics to visualise the association between coral harbouring microalgae (Symbiodiniaceae) and bacteria.
Postdocs
Graduate Research Students

Howie Zhou
Howie Zhou is a Masters student at the School of Mathematics and Statistics. His research investigates ciliary flows generated by coral surfaces, in the presence of nonNewtonian fluids.
Students 
Olle Pontén
Olle is a PhD student (cosupervised with Prof. Madeleine van Oppen) at the University of Melbourne’s School of Mathematics and Statistics. His research topics include motility and chemotaxis of Symbiodiniaceae microalgae, in silico and in vitro studies using microfluidics, and modelling the effect of stressors on the coral holobiont.
Students 
Rebecca Rasmussen
Rebecca Rasmussen's research uses experiments and mathematical modelling to investigate the flow patterns produced by the motion of an aquatic insect, the water boatman, exploring what ecological advantages may be conferred by their specific methods of locomotion.
Students 
Xinyi Yang
Xinyi Yang is a PhD student in the School of Mathematics and Statistics at the University of Melbourne. Her research focuses on modelling the navigation of microswimmers under the influence of fluid flows, external fields, and confinement.
Students 
Matthew Walker
Matthew Walker is a PhD student working in nonNewtonian fluid dynamics (cosupervised by Dr. Edward Hinton and Dr. Jesse Collis). He is particularly interested in applying these flows to geophysical problems and investigating how rheological intricacies govern the movement of lava, mud and concrete.
Students 
Amelia Keynton
Amelia Keynton is a PhD student (cosupervised by Prof. Michelle Watt, Dr. Vicky Waymouth and Prof. Berit Ebert). Her research investigates the role of organelle trafficking and plant cell wall composition in rootmicrobe interactions using Arabidopsis thaliana.
Students 
Rodney Dharma
Rodney is a PhD student at the University of Melbourne's School of Mathematics and Statistics. His research centres around using analytical and numerical methods to model microbial motility, chemotaxis, symbiosis, and poroustype flows.
Students 
Sarah Brook
Students

Nitay Ben Shachar
Nitay is a PhD student at the School of Mathematics and Statistics. His research is on noncontinuum flows, exhibited by gases in microstructures and electrons in highmobility electronic devices.
Students 
Tristan Bunnage
Tristan is a Masters student (cosupervised with Dr. Edward Hinton) at the School of Mathematics and Statistics. He is using numerical methods to model diffusion in interfacial flows, paying particular attention to the SaffmanTaylor instability.
Students 
Peijing Li
Peijing is a PhD student who is cosupervised by Dr. Jesse Collis at the School of Mathematics and Statistics. Her research is on the behaviours of small solid particles in an acoustic field and the associated steady flows arising from the timeharmonic wave motions.
Students 
Rania Ismail
Students

Allison Mertin
Allison Mertin is PhD student (cosupervised with Prof. Linda Blackall and the Royal Botanic Gardens Sydney). Her research focusses on characterisation of the seed microbiome of Australian native plants; microbeplant and microbemicrobe interactions and chemotaxis.
Students 
Antony Selvan
Antony Selvan is a PhD student whose research focuses on mathematical modelling of ciliary flows around coral surfaces, examining the effects on mass transport and bacterial motility.
Students
Former Group Members
 Rebecca Rasmussen, MSc “Impulsive breaststroke swimming at low Reynolds number, with application to Corixidae”
 Shenru Duan, MSc “Noise Influences on Synchronization of Flagella Through Hydrodynamics and Basal Body Coupling”
 Xinyi Yang, MSc “Navigation of magnetotactic bacteria in complex environments”
 Rodney Dharma, MSc “Resolving Spatial Heterogeneity in Microbial Symbiosis”
 Asher Pennicuik, MSc “An Investigation of Active Particle Systems by a Combined Complex Networks and Dynamical Systems Approach”
 Timothy Cooper, MSc “Bacterial chemotaxis in multisource nutrient environments”
 Chris Darveniza, MSc “Bumping bacteria: a model for dense suspensions of selfpropelling microbes”
 Angus Butler, MSc “Ciliary flows of corals: An analytic representation”
 Khaya Mpehle, MSc “A fluid dynamic model for the coral’s ciliary flows”
Dr. Douglas R. Brumley
School of Mathematics and Statistics
The University of Melbourne
Victoria 3010
Australia
Email: d.brumley@unimelb.edu.au
Phone: (+61) 03 8344 6534
Twitter: @BrumleyLab