Satya Arjunan

Background

I completed my PhD in Systems Biology at the Institute for Advanced Biosciences, Keio University in 2009. My thesis can be found here. I developed a stochastic particle simulation method, called Spatiocyte, with applications in bacterial division site placement control. I am also a member of the E-Cell Project. In the past, I have worked on protein secondary structure prediction and distributed parallel computing. I completed my MSc in Computer Science and BEng in Electronics Engineering at Universiti Teknologi Malaysia.

At present, I am a Postdoctoral Fellow at the UNSW School of Medicine in Sydney and a Visiting Scientist at the RIKEN Center for Biosystems Dynamics Research in Osaka.

Journal Publications

My Google Scholar page can be found here.

• Watabe, M., Yoshimura, H., Arjunan, S. N. V., Kaizu, K. & Takahashi, K. (2020). Signaling activations through G-protein-coupled-receptor aggregations. Physical Review E 102: 032413
• Arjunan, S. N. V., Miyauchi, A., Iwamoto, K. & Takahashi, K. (2020). pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems. BMC Bioinformatics 21, 33.
• Watabe, M., Arjunan, S. N. V., Chew, W.-X., Kaizu, K. & Takahashi, K. (2019). Cooperativity transitions driven by higher-order oligomer formations in ligand-induced receptor dimerization. Physical Review E 100, 062407
• Watabe, M., Arjunan, S. N. V., Chew, W.-X., Kaizu, K. & Takahashi, K. (2019). Simulation of live-cell imaging system reveals hidden uncertainties in cooperative binding measurements. Physical Review E 100, 010402(R)
• Chew, W.-X., Kaizu, K., Watabe, M., Muniandy, S. V., Takahashi, K. and Arjunan, S. N. V. (2019). Surface reaction-diffusion kinetics on lattice at the microscopic scale. Physical Review E 99, 042411
• Chew, W.-X., Kaizu, K., Watabe, M., Muniandy, S. V., Takahashi, K. and Arjunan, S. N. V. (2018). Reaction-diffusion kinetics on lattice at the microscopic scale. Physical Review E 98: 032418.
• Arjunan, S. N. V. and Takahashi, K. (2017) Multi-algorithm particle simulations with Spatiocyte. Methods in Molecular Biology, 1611: 219-236.
• Watabe, M., Arjunan, S. N. V., Fukushima, S., Iwamoto, K., Kozuka, J., Matsuoka, S., Shindo, Y., Ueda, M. and Takahashi, K. (2015). A Computational Framework for Bioimaging Simulation. PLoS ONE 10(7): e0130089.
• Shimo, H., Arjunan, S. N. V., Machiyama, H., Nishino, T., Suematsu, M., Fujita, H., Tomita M. and Takahashi, K. (2015). Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. PLoS Computational Biology 2015, 11:e1004210.
• Abdullah, A., Deris, S., Anwar, S. and Arjunan, S. N. V. (2013). An evolutionary Firefly Algorithm for the estimation of nonlinear biological model parameters. PLoS ONE 8(3): e56310.
• Arjunan, S. N. V. and Tomita, M. (2010). A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. Systems and Synthetic Biology 4(1): 35-53 pdf.
• Arjunan, S. N. V. and Tomita, M. (2009). Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System. International Journal of Computer Science and Information Security. 3(1): 211–216. pdf
• Yeo, Z. X., Wong, S. T., Arjunan, S. N. V., Piras, V., Tomita, M., Selvarajoo, K., Giuliani, A. and Tsuchiya, M. (2007). Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions. PLoS ONE 2(8): e776. pdf
• Takahashi, K., Arjunan, S. N. V. and Tomita, M. (2005). Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico. FEBS Letters 579(8): 1783-1788. pdf,

Books and Book Chapters

• Selvarajoo, K., Arjunan, S. N. V. and Tomita, M. (2010). In silico models for metabolic 'systems' engineering. In: The Metabolic Pathway Engineering Handbook: Tools and Applications, Smolke, C. D., Palsson, B. and Lee, S. Y. (editors). CRC Press (Boca Raton, FL). pdf
• Arjunan, S. N. V. (2013). A guide to Modeling Reaction-Diffusion of Molecules with the E-Cell System. In: E-Cell System: Basic Concepts and Applications, Arjunan, S. N. V., Dhar, P. K. and Tomita, M. (editors). Landes Bioscience and Springer Science+Business Media. pdf
• Arjunan, S. N. V., Dhar, P. K. and Tomita, M. (editors). (2013). E-Cell System: Basic Concepts and Applications. Landes Bioscience and Springer Science+Business Media.

Contact

Satya Nanda Vel Arjunan
satya.arjunan@[].com [gmail]
Laboratory for Biochemical Simulation
RIKEN Quantitative Biology Center
OLABB, Osaka University
6-2-3, Furuedai, Suita
Osaka 565-0874, JAPAN
Phone: +81-6-6155-0111
http://www.qbic.riken.jp/english/index.html

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