Cell Systems and Mechanobiology Lab
About
We create physiologically realistic computational models of cells and organs to advance healthcare. Our "digital-twin" models and physiology-informed algorithms advance basic understanding of how biological systems work and inform decision making in clinical and pharmaceutical applications.
Biology has provided an enormous body of descriptive data in its bid to understand the organism. But these descriptions do not explain the dynamic organisational capacity of cell-based life.
At the Faculty of Engineering and Information Technology, the Cell Systems and Mechanobiology Lab is applying engineering sciences to create new ways to integrate and analyse biological data. We bring advanced imaging technology, biomechanics, systems biology, mechanobiology, mathematical modelling and artificial intelligence together within a vibrant, intellectually stimulating, multi-disciplinary team to solve fundamental mysteries of how biology works. We apply our algorithms and technologies to solve disease treatment, diagnosis and drug discovery applications.
Our goal is the development of dynamic simulations that explain changes to cellular systems, with models providing a new platform to test and develop new disease interventions.
Research
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Imaging cellular biology
Imaging is central to the group’s quest to develop predictive models of dynamic cellular processes.
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Modelling cellular dynamics
Expertise in physics and mathematics is being applied to biological systems to transform descriptive data and derive explanatory principles.
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Biomedical applications
A better understanding of cellular dynamics stands to impact on medical research.
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Biophysics and new technology platforms
Learning to define the dynamic processes that underlie cellular biology presents new avenues for technology development.
2022
Journal articles
Blanch, AJ.; Nunez-iglesias, J.; Namvar, A.; Menant, S.; Looker, O.; Rajagopal, V.; Tham, W-H.; Tilley, L.; Dixon, MWA. (2022) “Multimodal imaging reveals membrane skeleton reorganisation during reticulocyte maturation and differences in dimple and rim regions of mature erythrocytes” JOURNAL OF STRUCTURAL BIOLOGY-X ELSEVIER. pp: -. DOI: 10.1016/j.yjsbx.2021.100056
Hickey, T.; Devaux, J.; Rajagopal, V.; Power, A.; Crossman, D. (2022) “Paradoxes of Hymenoptera flight muscles, extreme machines.” Biophysical Reviews Springer Science and Business Media LLC. pp: 403-412. DOI: 10.1007/s12551-022-00937-7
Rajagopal, V.; Arumugam, S.; Hunter, PJ.; Khadangi, A.; Chung, J.; Pan, M. (2022) “The Cell Physiome: What Do We Need in a Computational Physiology Framework for Predicting Single-Cell Biology?” Annual Review of Biomedical Data Science Annual Reviews. pp: 341-366. DOI: 10.1146/annurev-biodatasci-072018-021246
Yu, Q.; Holmes, WR.; Thiery, JP.; Luwor, RB.; Rajagopal, V. (2022) “Cortical tension initiates the positive feedback loop between cadherin and F-actin” Biophysical Journal CELL PRESS. pp: 596-606. DOI: 10.1016/j.bpj.2022.01.006
Yu, Q.; Kim, T.; Rajagopal, V. (2022) “Role of actin filaments and cis binding in cadherin clustering and patterning.” Faeder, JR. (Ed.) PLOS Computational Biology Public Library of Science (PLoS). pp: e1010257-. DOI: 10.1371/journal.pcbi.1010257
2021
Journal articles
De Oliveira, DC.; Espino, DM.; Deorsola, L.; Mynard, JP.; Rajagopal, V.; Buchan, K.; Dawson, D.; Shepherd, DET. (2021) “A toolbox for generating scalable mitral valve morphometric models” Computers in Biology and Medicine PERGAMON-ELSEVIER SCIENCE LTD. pp: -. DOI: 10.1016/j.compbiomed.2021.104628
Gomez, J.; Areeb, Z.; Stuart, SF.; Nguyen, HPT.; Paradiso, L.; Zulkifli, A.; Madan, S.; Rajagopal, V.; Montgomery, MK.; Gan, HK.; Scott, AM.; Jones, J.; Kaye, AH.; Morokoff, AP.; Luwor, RB. (2021) “EGFRvIII Promotes Cell Survival during Endoplasmic Reticulum Stress through a Reticulocalbin 1-Dependent Mechanism” Cancers MDPI. pp: -. DOI: 10.3390/cancers13061198
Khadangi, A.; Boudier, T.; Rajagopal, V. (2021) “EM-stellar: benchmarking deep learning for electron microscopy image segmentation” Valencia, A. (Ed.) Bioinformatics OXFORD UNIV PRESS. pp: 97-106. DOI: 10.1093/bioinformatics/btaa1094
Kolesnik, K.; Bryan, D.; Harley, W.; Segeritz, P.; Guest, M.; Rajagopal, V.; Collins, DJ. (2021) “Respiration mask waveguide optimisation for maximised speech intelligibility” The Journal of the Acoustical Society of America ACOUSTICAL SOC AMER AMER INST PHYSICS. pp: 2030-2039. DOI: 10.1121/10.0006235
Kolesnik, K.; Hashemzadeh, P.; Peng, D.; Stamp, MEM.; Tong, W.; Rajagopal, V.; Miansari, M.; Collins, DJ. (2021) “Periodic Rayleigh streaming vortices and Eckart flow arising from traveling-wave-based diffractive acoustic fields” Physical Review E AMER PHYSICAL SOC. pp: -. DOI: 10.1103/PhysRevE.104.045104
Kolesnik, K.; Xu, M.; Lee, PVS.; Rajagopal, V.; Collins, DJ. (2021) “Unconventional acoustic approaches for localized and designed micromanipulation” Lab on a Chip ROYAL SOC CHEMISTRY. pp: 2837-2856. DOI: 10.1039/d1lc00378j
Conference Papers
Khadangi, A.; Boudier, T.; Rajagopal, V. (2021) “EM-net: Deep learning for electron microscopy image segmentation” 25th International Conference on Pattern Recognition (ICPR) IEEE COMPUTER SOC. pp: 31-38. DOI: 10.1109/ICPR48806.2021.9413098
Lam, L.; Cochrane, T.; Davey, C.; John, S.; Shaktivesh, S.; Ganesan, S.; Rajagopal, V. (2021) “Prototyping a transdisciplinary bioengineering curriculum development project” ASCILITE 2021: 38th International Conference on Innovation, Practice and Research in the Use of Educational Technologies in Tertiary Education Armidale, Australia. ASCILITE.
Lam, L.; Cochrane, T.; Davey, C.; John, S.; Shaktivesh, S.; Ganesan, S.; Rajagopal, V. (2021) “Improving student outcomes through trans-disciplinary curriculum design in biomedical engineering” Male, S.; Guzzomi, A. (Ed.) Research in Engineering Education Symposium and Australasian Association for Engineering Education Conference 2021 EZONE The University of Western Australia, Perth, WA. Australasian Association for Engineering Education.
Lam, L.; Cochrane, T.; Rajagopal, V.; Davey, K.; John, S. (2021) “Enhancing student learning through trans-disciplinary project-based assessment in bioengineering” SoTEL2021 Auckland University of Technology (AUT) Library. pp: 4-5. DOI: 10.24135/pjtel.v3i1.80
Other
Yu, Q.; Kim, T.; Rajagopal, V. (2021) “A Computational Study of the Dynamics of Cadherin-Catenin Complex Regulated by Actin Cytoskeleton” Cell Press. pp: 130A-130A. DOI: 10.1016/j.bpj.2020.11.992
2020
Journal articles
Hunt, H.; Tilūnaitė, A.; Bass, G.; Soeller, C.; Roderick, HL.; Rajagopal, V.; Crampin, EJ. (2020) “Ca2+ Release via IP3 Receptors Shapes the Cardiac Ca2+ Transient for Hypertrophic Signaling.” Biophysical Journal Biophysical Society. pp: 1178-1192. DOI: 10.1016/j.bpj.2020.08.001
Namvar, A.; Blanch, AJ.; Dixon, MW.; Carmo, OMS.; Liu, B.; Tiash, S.; Looker, O.; Andrew, D.; Chan, L-J.; Tham, W-H.; Lee, PVS.; Rajagopal, V.; Tilley, L. (2020) “Surface area-to-volume ratio, not cellular viscoelasticity, is the major determinant of red blood cell traversal through small channels” Cellular Microbiology WILEY. pp: -. DOI: 10.1111/cmi.13270
Wang, ZJ.; Wang, VY.; Gamage, TPB.; Rajagopal, V.; Cao, JJ.; Nielsen, PMF.; Bradley, CP.; Young, AA.; Nash, MP. (2020) “Efficient estimation of load-free left ventricular geometry and passive myocardial properties using principal component analysis” International Journal for Numerical Methods in Biomedical Engineering Wiley. pp: -. DOI: 10.1002/cnm.3313
Zmurchok, C.; Collette, J.; Rajagopal, V.; Holmes, WR. (2020) “Membrane Tension Can Enhance Adaptation to Maintain Polarity of Migrating Cells” Biophysical Journal CELL PRESS. pp: 1617-1629. DOI: 10.1016/j.bpj.2020.08.035
2019
Journal articles
Ghosh, S.; Hanssen, E.; Crampin, EJ.; Rajagopal, V. (2019) “How Does the Internal Structure of Cardiac Muscle Cells Regulate Cellular Metabolism?” Microscopy and Microanalysis Cambridge University Press (CUP). pp: 240-241. DOI: 10.1017/s1431927619001934
Khadangi, A.; Hanssen, E.; Rajagopal, V. (2019) “Automated segmentation of cardiomyocyte Z-disks from high-throughput scanning electron microscopy data.” BMC Medical Informatics and Decision Making BioMed Central. pp: -. DOI: 10.1186/s12911-019-0962-1
Ladd, D.; Tilunaite, A.; Roderick, HL.; Soeller, C.; Crampin, EJ.; Rajagopal, V. (2019) “Assessing Cardiomyocyte Excitation-Contraction Coupling Site Detection From Live Cell Imaging Using a Structurally-Realistic Computational Model of Calcium Release” Frontiers in Physiology Lausanne, Switzerland. Frontiers Media. pp: -. DOI: 10.3389/fphys.2019.01263
Liu, B.; Blanch, AJ.; Namvar, A.; Carmo, O.; Tiash, S.; Andrew, D.; Hanssen, E.; Rajagopal, V.; Dixon, MWA.; Tilley, L. (2019) “Multimodal analysis of Plasmodium knowlesi-infected erythrocytes reveals large invaginations, swelling of the host cell, and rheological defects” Cellular Microbiology WILEY. pp: -. DOI: 10.1111/cmi.13005
Wo, N.; Rajagopal, V.; Cheung, MMH.; Smolich, JJ.; Mynard, JP. (2019) “Assessment of single beat end-systolic elastance methods for quantifying ventricular contractility” Heart and Vessels Tokyo, Japan. Springer Verlag. pp: 716-723. DOI: 10.1007/s00380-018-1303-5
Other
Collette, J.; Holmes, W.; Rajagopal, V. (2019) “The Feedback between Cellular Mechanics and Chemical Signalling during Cytoskeletal Remodelling” CELL PRESS. pp: 414A-414A. DOI: 10.1016/j.bpj.2018.11.2233
Ladd, D.; Tilunaite, A.; Roderick, HL.; Soeller, C.; Crampin, E.; Rajagopal, V. (2019) “Detecting RyR Clusters with CaCLEAN: Validation and Influence of Spatial Heterogeneity” CELL PRESS. pp: 42A-43A. DOI: 10.1016/j.bpj.2018.11.273
2018
Journal articles
Ghosh, S.; Tran, K.; Delbridge, LMD.; Hickey, AJR.; Hanssen, E.; Crampin, EJ.; Rajagopal, V. (2018) “Insights on the impact of mitochondrial organisation on bioenergetics in high-resolution computational models of cardiac cell architecture” Mcculloch, AD. (Ed.) PLoS Computational Biology PUBLIC LIBRARY SCIENCE. pp: -. DOI: 10.1371/journal.pcbi.1006640
Hussain, A.; Ghosh, S.; Kalkhoran, SB.; Hausenloy, DJ.; Hanssen, E.; Rajagopal, V. (2018) “An automated workflow for segmenting single adult cardiac cells from large-volume serial block-face scanning electron microscopy data” Journal of Structural Biology ACADEMIC PRESS INC ELSEVIER SCIENCE. pp: 275-285. DOI: 10.1016/j.jsb.2018.02.005
Rajagopal, V.; Bass, G.; Ghosh, S.; Hunt, H.; Walkers, C.; Hanssen, E.; Crampin, E.; Soeller, C. (2018) “Creating a Structurally Realistic Finite Element Geometric Model of a Cardiomyocyte to Study the Role of Cellular Architecture in Cardiomyocyte Systems Biology” Journal of Visualized Experiments JOURNAL OF VISUALIZED EXPERIMENTS. pp: -. DOI: 10.3791/56817
Rajagopal, V.; Holmes, WR.; Lee, PVS. (2018) “Computational modeling of single-cell mechanics and cytoskeletal mechanobiology” Wiley Interdisciplinary Reviews: Systems Biology and Medicine WILEY. pp: -. DOI: 10.1002/wsbm.1407
Conference Papers
Hanssen, E.; Rajagopal, V.; Khadankishandi, A. (2018) “Automated framework to reconstruct 3D model of cardiac Z-disk: an image processing approach” Zheng, H.; Callejas, Z.; Griol, D.; Wang, H.; Hu, X.; Schmidt, H.; Baumbach, J.; Dickerson, J.; Zhang, L. (Ed.) 2018 IEEE International Conference on Bioinformatics and Biomedicine IEEE. pp: 877-884. DOI: 10.1109/BIBM.2018.8621515
Other
Hunt, H.; Bass, G.; Roderick, L.; Soeller, C.; Rajagopal, V.; Crampin, E. (2018) “Mixed Signals: Interaction between RyR and IP3R Mediated Calcium Release Shapes the Calcium Transient for Hypertrophic Signalling in Cardiomyocytes” Cell Press. pp: 212A-213A. DOI: 10.1016/j.bpj.2017.11.1189
2017
Journal articles
Jarosz, J.; Ghosh, S.; Delbridge, LMD.; Petzer, A.; Hickey, AJR.; Crampin, EJ.; Hanssen, E.; Rajagopal, V. (2017) “Changes in mitochondrial morphology and organization can enhance energy supply from mitochondrial oxidative phosphorylation in diabetic cardiomyopathy” American Journal of Physiology - Cell Physiology AMER PHYSIOLOGICAL SOC. pp: C190-C197. DOI: 10.1152/ajpcell.00298.2016
Lelliott, PM.; Huang, HM.; Dixon, MW.; Namvar, A.; Blanch, AJ.; Rajagopal, V.; Tilley, L.; Coban, C.; Mcmorran, BJ.; Foote, SJ.; Burgio, G. (2017) “Erythrocyte beta spectrin can be genetically targeted to protect mice from malaria” Blood Advances ELSEVIER. pp: 2624-2636. DOI: 10.1182/bloodadvances.2017009274
Conference Papers
Ghosh, S.; Crampin, EJ.; Hanssen, E.; Rajagopal, V. (2017) “A Computational Study of the Role of Mitochondrial Organization on Cardiac Bioenergetics” 39th Annual International Conference of the IEEE-Engineering-in-Medicine-and-Biology-Society (EMBC) IEEE. pp: 2696-2699. DOI: 10.1109/EMBC.2017.8037413
Hussain, A.; Hanssen, E.; Rajagopal, V. (2017) “A Semi-Automated Workflow for Segmenting Contents of Single Cardiac Cells from Serial-Block-Face Scanning Electron Microscopy Data” Cambridge University Press (CUP). pp: 240-241. DOI: 10.1017/s143192761700188x
Wang, ZJ.; Wang, VY.; Babarenda Gamage, TP.; Rajagopal, V.; Cao, JJ.; Nielsen, PMF.; Bradley, CP.; Young, AA.; Nash, MP. (2017) “Principal Component Analysis used to Derive Patient-Specific Load-Free Geometry and Estimate Myocardial Stiffness in the Heart” Computational and Mathematical Biomedical Engineering Zeta Computational Resources Ltd.
2015
Journal articles
Rajagopal, V.; Bass, G.; Walker, CG.; Crossman, DJ.; Petzer, A.; Hickey, A.; Siekmann, I.; Hoshijima, M.; Ellisman, MH.; Crampin, EJ.; Soeller, C. (2015) “Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca2+ Release Patterns in Cardiomyocytes” Beard, DA. (Ed.) PLoS Computational Biology PUBLIC LIBRARY SCIENCE. pp: -. DOI: 10.1371/journal.pcbi.1004417
2014
Journal articles
Hou, Y.; Crossman, DJ.; Rajagopal, V.; Baddeley, D.; Jayasinghe, I.; Soeller, C. (2014) “Super-resolution fluorescence imaging to study cardiac biophysics: alpha-actinin distribution and Z-disk topologies in optically thick cardiac tissue slices” Progress in Biophysics and Molecular Biology PERGAMON-ELSEVIER SCIENCE LTD. pp: 328-339. DOI: 10.1016/j.pbiomolbio.2014.07.003
People
Team members
Jared Collette, PhD student: Cancer cell motility and mechanobiology
Nathan Isles, PhD student: Cardiac cell mechanobiology
Afshin Khadangi, PhD student: Machine learning
Joshua Chung, PhD student: Calcium signalling in heart growth
Giovanni Guglielmi, PhD student: Cardiac growth and ageing- Joshua Forrest, PhD student: Bond graph modelling
Aidan Quinn, PhD student: Deep learning image segmentation- Dr. Michael Pan, Early Career Research Fellow: Bond graph modelling
Alumni
- Qilin Yu, was PhD student: Cancer cell motility and mechanobiology, now neoX Biotech
Arman Namvar, was PhD student: Red blood cell mechanics and malaria, now St Vincent Hospital
David Ladd, was PostDoc: Modelling cellular dynamics, now oNko-Innate Pty Ltd- Agne Tilunaite, was PostDoc: Cell Signalling, now InterAx Biotech
Hilary Hunt, was PhD student: Cell signalling, now University of Oxford
Shouryadipta Ghosh, was PhD: Diabetic cardiomyopathy, now CSIRO- Maciej Kubicki, PostDoc: Breast density and breast cancer risk
- Jan Jarosz, Diabetic cardiomyopathy
Contact us
- Address
- Building 261, 203 Bouverie Street
Department of Biomedical Engineering
The University of Melbourne
VIC 3010 Australia - vijay.rajagopal@unimelb.edu.au
- Phone
- +61 3 8344 1281
- Group: @cellsmb