Satya Arjunan

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==Journal Publications==
==Journal Publications==
My Google Scholar Citations page can be found [http://scholar.google.com/citations?user=FGHQqjkAAAAJ&hl=en here].
My Google Scholar Citations page can be found [http://scholar.google.com/citations?user=FGHQqjkAAAAJ&hl=en here].
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*Arjunan, S. N. V. and Tomita, M. (2010). [http://www.springerlink.com/content/438375471t332vx6 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 [http://www.springerlink.com/content/438375471t332vx6/fulltext.pdf Published online].
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*Arjunan, S. N. V. and Tomita, M. (2010). [http://www.springerlink.com/content/438375471t332vx6 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 [http://www.springerlink.com/content/438375471t332vx6/fulltext.pdf pdf].
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*Arjunan, S. N. V. and Tomita, M. (2009). [http://precedings.nature.com/documents/3526/version/1 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.
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*Arjunan, S. N. V. and Tomita, M. (2009). [http://precedings.nature.com/documents/3526/version/1 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. [http://precedings.nature.com/documents/3526/version/1/files/npre20093526-1.pdf pdf]
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*Yeo, Z. X., Wong, S. T., Arjunan, S. N. V., Piras, V., Tomita, M., Selvarajoo, K., Giuliani, A. and Tsuchiya, M. (2007). [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000776 Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions]. PLoS ONE 2(8): e776.
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*Yeo, Z. X., Wong, S. T., Arjunan, S. N. V., Piras, V., Tomita, M., Selvarajoo, K., Giuliani, A. and Tsuchiya, M. (2007). [http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000776 Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions]. PLoS ONE 2(8): e776. [http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=3EA7966B9EA32BC46DFCD562DE1DCDB0?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0000776&representation=PDF pdf]
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*Takahashi, K., Arjunan, S. N. V. and Tomita, M. (2005). [http://www.e-cell.org/ecell/papers/takahashi2005.pdf Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico]. FEBS Letters 579(8): 1783-1788.
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*Takahashi, K., Arjunan, S. N. V. and Tomita, M. (2005). [http://www.sciencedirect.com/science/article/pii/S0014579305001857 Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico]. FEBS Letters 579(8): 1783-1788. [http://www.e-cell.org/ecell/papers/takahashi2005.pdf pdf]
==Books and Book Chapters==
==Books and Book Chapters==
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*Selvarajoo, K., Arjunan, S. N. V. and Tomita, M. (2009). [http://books.google.com/books?id=zCqHswQYAfgC&lpg=PT6&pg=PT363#v=onepage&q=&f=false 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).
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*Selvarajoo, K., Arjunan, S. N. V. and Tomita, M. (2010). [http://books.google.com/books?id=zCqHswQYAfgC&lpg=PT6&pg=PT363#v=onepage&q=&f=false 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). [http://openwetware.org/images/b/b4/2010.selvarajoo.chapter.crc.press.pdf pdf]
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*Arjunan, S. N. V., Dhar, P. K. and Tomita, M. (editors). E-Cell System: Basic Concepts and Applications. Landes Bioscience (Georgetown, Texas) and Springer Science+Business Media (New York, N. Y.). In press.
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*Arjunan, S. N. V. (2012). [http://www.landesbioscience.com/curie/chapter/5351/ 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 (Georgetown, Texas) and Springer Science+Business Media. [http://openwetware.org/images/b/b4/2010.selvarajoo.chapter.crc.press.pdf pdf]
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*Arjunan, S. N. V., Dhar, P. K. and Tomita, M. (editors). [http://www.landesbioscience.com/books/iu/id/953/?nocache=2071954650 E-Cell System: Basic Concepts and Applications]. Landes Bioscience (Georgetown, Texas) and Springer Science+Business Media. [http://openwetware.org/images/0/05/2012.arjunan.chapter.landes.bioscience.pdf pdf]
==Conferences==
==Conferences==

Revision as of 20:06, 2 February 2012

Image:satya.arjunan.png


Contents

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 multicompartmental spatiotemporal stochastic simulation algorithm, 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.

Currently I am a postdoc at the RIKEN Quantitative Biology Center in Osaka, Japan.


Journal Publications

My Google Scholar Citations page can be found here.

Books and Book Chapters

Conferences

  • Arjunan, S. N. V. and Tomita, M. A 3D pole-to-pole oscillation model of MinD spiral formation on growing Escherichia coli membrane. Seventh International Conference on Systems Biology (ICSB 2006), Yokohama, Japan.
  • Arjunan, S. N. V., Kratz, A. and Tomita, M. 3D Monte Carlo stochastic simulation of bacterial division site placement on a graphics processing unit is significantly faster than conventional CPU implementation. Seventh International Conference on Systems Biology (ICSB 2006), Yokohama, Japan.
  • Arjunan, S. N. V., Yeo, Z. X., Tomita, M. and Tsuchiya, M. Cellogica: A tool to analyze and control the dynamics of cis-regulatory systems. Seventh International Conference on Systems Biology (ICSB 2006), Yokohama, Japan.
  • Arjunan, S. N. V. and Selvarajoo, K. Factoring glucokinase sequestration in silico affects glycolytic network kinetics. Seventh International Conference on Systems Biology (ICSB 2006), Yokohama, Japan.
  • Arjunan, S. N. V., Takahashi, K. and Tomita, M. (Nov 2003). Shared-Memory Multiprocessing of Gillespie's Stochastic Simulation Algorithm on E-Cell 3. Fourth International Conference on Systems Biology (ICSB 2003), St. Louis, USA.
  • Takahashi, K., Sakurada, T., Kaizu, K., Kitayama, T., Arjunan, S. N. V., Ishida, T., Bereczki, G., Ito, D., Sugimoto, M., Komori, T., Seiji, O. and Tomita, M. (2003). E-Cell System Version 3: A Software Platform for Integrative Computational Biology. In Genome Informatics 2003, M. Gribskov, M. Kanehisa, S. Miyano, and T. Takagi (editors). Universal Academy Press, Tokyo. Pages: 294-295

Talks

  • Arjunan, S. N. V. (March 2005). Mesoscale Simulation Approaches in Systems Biology: Recent Advances and Future Directions. Workshop on Particle Methods and Mesoscale Simulation of Liquids, Warrington, U. K.

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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