Satya Arjunan: Difference between revisions

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==Background==
==Background==
I am a PhD candidate supported by the Japanese Government (Monbukagakusho) scholarship at the [http://www.iab.keio.ac.jp/ Institute for Advanced Biosciences], Keio University. 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.
I completed my PhD in Systems Biology at the [http://www.iab.keio.ac.jp/ Institute for Advanced Biosciences], Keio University in 2009. My thesis can be found [http://openwetware.org/images/b/bc/2009.arjunan.keio.pdf here]. I developed a multicompartmental spatiotemporal stochastic simulation method, called [http://spatiocyte.org Spatiocyte], with applications in bacterial division site placement control. I am also a member of the [http://www.e-cell.org/ 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 work on multicompartmental spatiotemporal stochastic simulation algorithm with applications in molecular systems biology. My advisor is [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=masaru%20tomita Masaru Tomita]. I am also a member of the [http://www.e-cell.org/ E-Cell Project].
Currently I am a postdoc at the RIKEN Quantitative Biology Center in Osaka, Japan.
 
 
==Tech==
[http://openpolity.org/ OpenPolity.Org]: Aggregating ideas from everyday Malaysians.


==Journal Publications==
==Journal Publications==
*Arjunan, S. N. V. and Tomita, M. (2009). [http://precedings.nature.com/documents/3845/version/1 A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation]. Systems and Synthetic Biology. In press.
My Google Scholar page can be found [http://scholar.google.com/citations?user=FGHQqjkAAAAJ&hl=en here].
*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.
* Abdullah, A., Deris, S., Anwar, S. and '''Arjunan, S. N. V.''' (2013). [http://dx.plos.org/10.1371/journal.pone.0056310 An evolutionary Firefly Algorithm for the estimation of nonlinear biological model parameters]. PLoS ONE 8(3): e56310.
*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.
*'''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].
*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.
*'''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]
*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]
*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==
*Selvarajoo, K., Arjunan, S. N. V. and Tomita, M. In silico models for metabolic 'systems' engineering. In Handbook for Metabolic Pathway Engineering, Smolke, C. D., Palsson, B. and Lee, S. Y. (editors). CRC Press, San Diego. In press.
*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]
*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.
*'''Arjunan, S. N. V.''' (2013). [http://www.ncbi.nlm.nih.gov/books/NBK84261/ 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. [http://openwetware.org/images/0/05/2012.arjunan.chapter.landes.bioscience.pdf pdf]
 
*'''Arjunan, S. N. V.''', Dhar, P. K. and Tomita, M. (editors). (2013). [http://www.landesbioscience.com/books/iu/id/953/?nocache=2071954650 E-Cell System: Basic Concepts and Applications]. Landes Bioscience and Springer Science+Business Media.
==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==
==Contact==
Satya Nanda Vel Arjunan <br>
Satya Nanda Vel Arjunan <br>
satya.arjunan@[].com [gmail] <br>
satya.arjunan@[].com [gmail] <br>
+81-235-29-0800 (phone) <br>
Laboratory for Biochemical Simulation <br>
+81-235-29-0809 (fax) <br>
RIKEN Quantitative Biology Center <br>
Institute for Advanced Biosciences <br>
OLABB, Osaka University <br>
Keio University <br>
6-2-3, Furuedai, Suita <br>
14-1, Baba-cho, Tsuruoka <br>
Osaka 565-0874, JAPAN <br>
Yamagata, 997-0035 Japan <br>
Phone: +81-6-6155-0111 <br>
http://www.qbic.riken.jp/english/index.html


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Revision as of 16:10, 29 April 2013


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 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.

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


Journal Publications

My Google Scholar page can be found here.

Books and Book Chapters

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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