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Microbes drive large-scale 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 fine-scale interactions with one another and their environment. Our research group uses mathematical modelling and quantitative video-microscopy 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.
Escape motility of multicellular magnetotactic prokaryotes
X. Yang, M. Prakash, D.R. Brumley
Journal of the Royal Society Interface 21:20240310 (2024) [pdf]
Slower swimming promotes chemotactic encounters between bacteria and small phytoplankton
R. Foffi, D.R. Brumley, F. Peaudecerf, R. Stocker, J. Słomka
arXiv preprint 2410.03641 (2024)
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
Computational and Structural Biotechnology Reports 1, 100014 (2024) [bioRxiv] [pdf]
Unique photosynthetic strategies employed by closely related Breviolum minutum strains under rapid short-term 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 75(13) 4005–4023 (2024) [pdf]
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 32, 640-649 (2024)
Point torque representations of ciliary flows
S.A. Selvan, P.W. Duck, D. Pihler-Puzović, 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, 510-521 (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, 32-35 (2022)
Fluorescence lifetime imaging microscopy (FLIM): a non-traditional approach to study host-microbial 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, 22-27 (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) 10792-10797 (2019) [pdf]
Stability of arrays of bottom-heavy spherical squirmers
D. R. Brumley and T. J. Pedley
Physical Review Fluids 4, 053102 (2019) [pdf]
Transitions in synchronization states of model cilia through basal-connection coupling
Y. Liu, R. Claydon, M. Polin, D. R. Brumley
Journal of the Royal Society Interface 15:20180450 (2018) [pdf]
High-avidity 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. Fernandez-Rodriguez, 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, 498-502 (2017) [pdf]
Long-range 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, 165-186 (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, 3119-3140 (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, 761-775 (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 Cross-Section Immersed in Fluid
D. R. Brumley, M. Willcox, J. E. Sader.
Physics of Fluids 22, 052001 (2010) [pdf]
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Research Grant from Gordon and Betty Moore Foundation
We are excited to receive a Research Grant from the Gordon and Betty Moore Foundation, as part of the Symbiosis Model Systems Initiative. The project, "New Tools for Advancing Model Systems in Aquatic Symbiosis", is led by Douglas Brumley and in collaboration with Professor Linda Blackall.
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Magnetotaxis paper in Royal Society Interface
Congratulations to Xinyi Yang, for the first paper from her PhD, "Escape motility of multicellular magnetotactic prokaryotes", published today in Journal of the Royal Society Interface. Together with Prof. Manu Prakash at Stanford University, we examined how multicellular bacteria are capable of simultaneously responding to magnetic fields and oxygen gradients.
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Chemotaxis paper preprint
Congratulations to Riccardo Foffi and Jonasz Słomka from ETH Zürich for leading this work, "Slower swimming promotes chemotactic encounters between bacteria and small phytoplankton". A preprint is now available on arXiv here: https://arxiv.org/abs/2410.03641. Chemotaxis enables marine bacteria to increase encounters with phytoplankton cells by reducing their search times, provided that bacteria detect noisy chemical gradients around phytoplankton. To date, it has …
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Machine Learning Paper in Computational and Structural Biotechnology Reports
Congratulations to Filippo and Arash for leading this work, ``Machine learning driven image segmentation and shape clustering of algal microscopic images obtained from various water types''. Accurate identification and quantification of algae and cyanobacteria are vital for ecological research, water quality monitoring, and public health safety. However, traditional methods of manually counting and morphologically identifying these microorganisms are time-consuming and prone …
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Peijing Li – PhD completion
Congratulations to Peijing Li for completing the PhD degree! Co-supervised with Jesse Collis and John Sader, Peijing's thesis examined the streaming forces acting on small solid particles in viscous fluids. Thesis Title: The steady streaming flows generated by spherical particles suspended in acoustic waves. Summary: This doctoral project primarily aims to investigate the association between radiation and streaming forces acting on small …
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Editorial Board of PLOS Computational Biology
Douglas Brumley is excited to join the Editorial Board for PLOS Computational Biology, a journal dedicated to investigating living systems at all scales, through the application of computational methods.
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Associate Editor at Bulletin of Mathematical Biology
Douglas Brumley is excited to join as an Associate Editor of the Bulletin of Mathematical Biology, a journal devoted to research at the junction of computational, theoretical, and experimental biology.
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Model citizens: how mathematicians are helping the planet
On Monday 12 August, Dr Douglas Brumley, Professor Jennifer Flegg, and Associate Professor Guoqi Qian joined in a lively panel, hosted by science communicator Graham Phillips, to discuss how they dedicate their working days to helping people and our planet using the power of numbers, big data and new mathematical models. A short summary of the event is shown below: …
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Tristan Bunnage MSc completion
Congratulations to Tristan Bunnage for completing the Master of Science (Mathematics and Statistics). Tristan's research project, co-supervised with Dr. Edward Hinton, examined "Miscible Viscous Fingering Subject to an Oscillating Injection".
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Vicky Waymouth receives Women In Science of the Environment (WISE) Fellowship
Congratulations to Vicky Waymouth for being awarded $6000 through the Women in Science of the environment (WISE) Fellowship. Vicky (co-supervised with Professor Michelle Watt) will use the awarded funds to attend the 12th International Conference on Mycorrhizae (ICOM12) in Manchester this year.
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Cover image of Trends in Microbiology
We are excited to see that our paper, "Swimming towards each other: the role of chemotaxis in bacterial interactions", has been featured on the cover of this month's issue of Trends in Microbiology. Our work, published in collaboration with colleagues at University of Technology Sydney and ETZ Zurich, highlights how chemotactic sensing could represent an important, but largely overlooked, phenotype within …
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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 short-term 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 …
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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.
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VicANZIAM prize for Tristan Bunnage
Congratulations to MSc student Tristan Bunnage (co-supervised with Dr. Edward Hinton), who won second prize ($125) at the one-day 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”.
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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 non-spherical geometries and for modelling suspensions of particles in acoustic fields.
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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 …
Staff
Postdoctoral Fellows
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Vicky Waymouth
Dr Vicky Waymouth is a Postdoctoral Research Fellow working on an interdisciplinary ARC Discovery Project (co-supervised with Prof. Michelle Watt). Her work focuses on modelling microorganism interactions in the rhizosphere using fabricated ecosystems and microfluidic devices.
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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.
Graduate Research Students
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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 non-Newtonian fluids.
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Olle Pontén
Olle is a PhD student (co-supervised 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.
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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.
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Matthew Walker
Matthew Walker is a PhD student working in non-Newtonian fluid dynamics (co-supervised 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.
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Amelia Keynton
Amelia Keynton is a PhD student (co-supervised 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 root-microbe interactions using Arabidopsis thaliana.
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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 porous-type flows.
- Sarah Brook
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Nitay Ben Shachar
Nitay is a PhD student at the School of Mathematics and Statistics. His research is on non-continuum flows, exhibited by gases in microstructures and electrons in high-mobility electronic devices.
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Peijing Li
Peijing is a PhD student who is co-supervised 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 time-harmonic wave motions.
- Rania Ismail
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Allison Mertin
Allison Mertin is PhD student (co-supervised with Prof. Linda Blackall and the Royal Botanic Gardens Sydney). Her research focusses on characterisation of the seed microbiome of Australian native plants; microbe-plant and microbe-microbe interactions and chemotaxis.
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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.
Former Group Members
- Tristan Bunnage, MSc “Miscible Viscous Fingering Subject to an Oscillating Injection”
- 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 multi-source nutrient environments”
- Chris Darveniza, MSc “Bumping bacteria: a model for dense suspensions of self-propelling 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