Welcome

Welcome to the Systems Biology Laboratory at the University of Melbourne, Australia.

At the Systems Biology Lab we build and analyse dynamical mathematical models of biological processes, pathways and networks, and we apply these models in medicine and biotechnology including heart disease, cancer, nanomedicine, and synthetic biology.

We are based in the School of Mathematics and Statistics and in the Department of Biomedical Engineering at the University of Melbourne.

We are part of the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology.

For more information contact Lab Director Professor Edmund Crampin
edmund.crampin@unimelb.edu.au

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Victoria Fellowship awarded to Stuart Johnston

Many congratulations to Stuart Johnston who has been awarded a 2019 Victoria Fellowship!

https://www.veski.org.au/2019_Victoria_Fellows#stuart

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ARC DECRA awarded to Dr Stuart Johnston

Huge congratulations to Stuart, who has been awarded a DECRA fellowship from the ARC for his project entitled “From cells to whales: A mathematical framework to understand navigation”.

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New Preprint: Isolating the sources of heterogeneity in nanoparticle-cell interactions

Experiments show that interactions between nanoparticles and cells are heterogeneous – there is a distribution of nanoparticle-cell uptake even when the nanoparticles being delivered are nominally identical. This is important because delivering the appropriate dose of a nanomedicine, in part, determines its efficacy.

Significantly, this heterogeneity changes over time following exposure of nanoparticles to cells. Our new paper uses a combination of modelling and experimental work to figure out why heterogeneity in nanoparticle-cell interactions appears to change over time, and to determine what are the potential sources of heterogeneity underlying this phenomenon.

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Our study, led by Dr Stuart Johnston, shows that the key mechanisms driving early-time interactions and late-time interactions are different, and this transition between mechanisms makes it appear that heterogeneity changes over time. Read more about it here:

S.T. Johnston, M. Faria, E.J. Crampin
Isolating the sources of heterogeneity in nanoparticle-cell interactions
bioRXiv:10.1101/817569

This work was in part funded by the Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology (CE140100036).

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Assessing detection of calcium release sites from live cell imaging data

Our latest paper reports on computational modelling to simulate calcium release within realistic cardiomyocyte cell geometries to determine how cellular architecture can affect what you see under the microscope.

Read more in our paper:

D. Ladd, A. Tilunaite, H.L. Roderick, C. Soeller, E.J. Crampin, V. Rajagopal (2019)
Assessing cardiomyocyte excitation-contraction coupling site detection from live cell imaging using a structurally-realistic computational model of calcium release
Frontiers in Physiology 10:1263

For example, the image below indicates how the density of calcium release sites (ryanodine receptors, RyRs) within the cell will affect what you see in your confocal image.

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Algorithms that detect “hot-spots” of calcium in these images as RyR sources will be affected by the density of RyRs that are present within the confocal plane, as well as ‘out of plane’ RyRs that are at a distance from the imaging plane.

This work was undertaken by David Ladd, and was lead by Vijay Rajagopal, and is the outcome of a great collaboration between Christian Soeller (@SoellerLab), Llew Roderick (@roderick_cardio) and the Crampin and Rajagopal (@cellsmb) groups.

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Two new papers on bio-nano interactions

Announcing two new papers, recently published, arising from our collaborations with the Caruso and Kent groups at UniMelb in the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology (CBNS)!

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M. Faria, K.F. Noi, Q. Dai, M. Björnmalm, S.T. Johnston, K. Kempe, F. Caruso, E.J. Crampin (2019)
Revisiting cell–particle association in vitro: A quantitative method to compare particle performance
Journal of Controlled Release 307, 355–367

A.C.G. Weiss, H.G. Kelly, M. Faria, Q.A. Besford, A.K. Wheatley, C.-S. Ang, E.J. Crampin, F. Caruso, S.J. Kent (2019)
Link between Low-Fouling and Stealth ‒ A Whole Blood Biomolecular Corona and Cellular Association Analysis on Nanoengineered Particles
ACS Nano 13 (5), 4980–4991

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Want to do a PhD in Computational Cell / Systems / Synthetic Biology?

Join Prof Michael Stumpf, Prof Karin Verspoor, Dr Heejung Shim and me at the University of Melbourne and learn how to model whole cells as part of a multidisciplinary & supportive research team!
Contact me at edmund.crampin@unimelb.edu.au to find out more.
stumpf positions
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Pair correlation functions for environments with obstacles – new paper published in Physical Review E

Pair correlation is used widely across biology, ecology and physics, as well as in other areas, to obtain estimates of spatial structure. Environments with obstacles or voids that inhibit and alter the motion of individuals within that environment can give rise to spurious spatial correlations. We present a corrected pair correlation function for lattice-based domains that accounts for obstacles contained within the domain, and show that this ‘obstacle pair correlation function’ is necessary for isolating the correlation associated with the behavior of individuals, rather than the structure of the environment.

Congratulations to Stuart on this paper!

S.T. Johnston, E.J. Crampin (2019)
Corrected pair correlation functions for environments with obstacles
Physical Review E 99, 032124

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