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Dr. Srividhya Jeyaraman

IMA Post Doctoral Fellow 2008-2010

Institute for Mathematics and its Applications
114 Lind Hall
207 Church Street SE
Minneapolis, MN 55455
USA
Phone +1-(612)-626-1062
Email ​​​​​

My Vision

The ultimate aim of chemistry and biology is to understand biological systems sufficiently to enable accurate, quantitative predictions about the behaviors of the system. This includes predictions of the effects of modifications of the systems. To achieve a precise understanding about the system it is inevitable to simulate the behavior using a computer model and compare it with experiments. Interdisciplinary research alone can provide insights in the pursuit of this common goal. My career goal is to head an interdisciplinary mathematical biology/chemistry group and solve complex problems in chemistry and biology using computational and modeling approaches. I did my Ph.D. under the supervision of Prof. M. S. Gopinathan , Indian Institute of Technology Madras (IITM), India. I did my first post doctoral work with Dr. Santiago Schnell (University of Michigan Medical School) at Indiana University School of Informatics. I am currently a post doctoral fellow at the IMA for the year 2008-2009. I am a chemist, now conducting reserach in solving physico-chemical problems using modelling approaches.

Education

Master's in Chemistry from Dept of Chemistry , Indian Institute of Technology Madras , Chennai, India.

Ph.D. in Mathematical modeling of chemical and biological dynamical systems also from the Indian Institute of Technology Madras (IITM) with Prof. M. S. Gopinathan (IIITMK)

Positions

1. Research Fellow of Council of Scientific and Industrial Research (CSIR - India) from 2000-2005

2. Post Doctoral research associate in Indiana University School of Informatics with Dr. Santiago Schnell. (2005-2008)

3. Post Doctoral Fellow at Institue for Mathematics and its Applications (IMA) (2008-2009)

Research Interests

1. Modeling Biochemical Signal Transduction using dynamical systems approach

2. Method for inferring kinetics and network architecture (MIKANA)

3. Probing the mechanism of Oil/water interface

4. Mechanism of Protein digestion

CV

Find my CV here.

Collaborators

• Dr. Yongfeng Li (IMA)
• Dr. Joe Pomerening Dept. of Biology, Indiana University Bloomington
• Dr. Santiago Schnell, University of Michigan Medical School
• Dr. Marcio D. A. Maurao , School of Informatics, Indiana University Bloomington.

  Publications

  Journals

  1. Modeling experimental oscillations in liquid membranes using delay equations, J. Srividhya and M. S. Gopinathan, J. Phys. Chem. B, 2003, 107, pp 1438-1443. (pdf)

  2. Concentration of CO2 over Melting Ice Oscillates, S. Usharani, J. Srividhya, M. S. Gopinathan and T. Pradeep, Phys. Rev. Lett., 2004, 93(4), Article No: 048304, pp 1-4. (pdf)

  3. A simple time delay model for eukaryotic cell cycle, J. Srividhya and M. S. Gopinathan, J. theor. Biol., 2006, 214(3), pp 617-627. (pdf)

  4. Why substrate disappearance in enzyme digestion follows apparent first-order kinetics, J. Srividhya and Santiago Schnell, Comp. Biol. Chem., 2006, 30, pp 209-214. (pdf)

  5. Reconstructing biochemical pathways from time series data. J. Srividhya, Santiago Schnell, Edmund J Crampin and Patrick E McSharry, 2007, Proteomics, 7, 828 - 838. (invited paper) . (pdf)

  6. Effect of time delay in a model of phosphorylation-dephosphorylation network. J. Srividhya, M. S. Gopinathan and Santiago Schnell, Biophysical chemistry, 2007, 125, pp 286-297. (pdf)

  7. Enzyme catalyzed reactions: from experiments to mechanism reconstruction. J. Srividhya, Marcio D. A. Maurao, Edmund J. Crampin, Santiago Schnell, Comp. Biol.(accepted)

  8. A length induced positive feedback in open signal transduction cascades is revealed. J. Srividhya, Yongfeng Li and Joe Pomerening, PLoS Comp. Biol. (under revision)

  9. Goldbeter-Koshland model for open signaling cascades: A mathematical study. Yongfeng Li and J. Srividhya, J. Math. Biol. (submitted)

  10. Marcio D. A. Maurao and J. Srividhya, Reverse engineering in biology: Past, present and future.(To be submitted)

Software

1. A preliminary version of MIKANA is here. We are working on building a more concise version for general use. You can also find an other software for enzyme kinetics parameter estimation developed by (our) Dr. Schnell's group.
MIKANA
2. You can find a simulable version of my cell cycle model here.
Cell cycle model simulation

News

1. Our JTB paper was one of the 25 top downloaded article. Check it here!
2. Our Proteomics article was selected as in the Issue article and Dr. Schnell was interviewed. You can download the podcast titled "March, 2007" here!

Other Interests