Theoretical Biology and Biophysics Group

https://doi.org/10.1101/143396 [HIGHLIGHTS]

Research Interests | Publications

Theoretical Biology & Biophysics | Stochastic Processes in Biology

R. Murugan (2025) Theory on the accurate estimation of Michaelis-Menten enzyme kinetic parameters from steady state and progress curve datasets. bioRxiv. PDF.

R. Murugan (2023) Theory on the power-law distribution of the Michaelis-Menten enzyme kinetic parameters. bioRxiv. PDF.

R. Murugan (2024) Theory on the rate equations of Michaelis-Menten type enzyme kinetics with competitive inhibition. PLOS ONE 19(7): e0302679. https://doi.org/10.1371/journal.pone.0302679 bioRxiv. https://www.biorxiv.org/content/10.1101/2022.11.28.518182v1

R. Murugan and G. Kreiman (2022) Multiple transcription autoregulatory loops can act as robust oscillators and decision-making motifs. Computational and Structural Biotechnology Journal. 20, 5115-5135. PDF.

R. Murugan (2022) Lattice Model on the Rate of DNA Hybridization. Phys. Rev. E. 105, 064410-26. bioarxiv. PDF https://www.biorxiv.org/content/10.1101/2021.12.22.473940v1

R. Murugan (2022) Approximate solutions to the response time problems of transcription autoregulatory gene networks. J. Math. Chem. 60, 586–604. https://link.springer.com/article/10.1007/s10910-021-01324-5.

R. Murugan (2021) A lattice model on the rate of in vivo site-specific DNA-protein interactions. Physical Biology. 18. 016005-17. https://iopscience.iop.org/article/10.1088/1478-3975/abbe9a

R. Murugan (2020) Theory of transcription bursting: Stochasticity in the transcription rates. J. Math. Chem. 58 (9) 2140-87.  https://doi.org/10.1007/s10910-020-01166-7. https://www.biorxiv.org/content/10.1101/2019.12.18.880435v1.

R. Murugan (2018). Theory On The Rate Equation Of Michaelis-Menten Type Single-Substrate Enzyme Catalyzed Reactions. J. Math. Chem, 56:508-556. bioRxiv.https://doi.org/10.1101/143396.

R. Murugan (2017) Theory on the mechanisms of combinatorial binding of transcription factors with DNA. https://arxiv.org/abs/1610.06311

G Niranjani, R Murugan (2016) Theory on the Mechanism of DNA Renaturation: Stochastic Nucleation and Zipping. PLoS ONE 11(4): e0153172.doi:10.1371/journal.pone.0153172

G Niranjani, R Murugan (2016) Generalized theory on the mechanism of site-specific DNA–protein interactions. Journal of Statistical Mechanics: Theory and Experiment. 2016(5): 053501-51. http://dx.doi.org/10.1088/1742-5468/2016/05/053501.

G Niranjani, R Murugan (2016) Theory on the mechanism of site-specific DNA–protein interactions in the presence of traps. Physical Biology. 13, 046003-17.

R Murugan (2014) Theory on the dynamics of oscillatory loops in the transcription factor networks. PLoS ONE. 9(8): e104328. doi:10.1371/journal.pone.0104328. http://arxiv.org/abs/1405.3881.

R Murugan and G Kreiman (2012) Theory on the coupled stochastic dynamics of transcription and splice-site recognition. PLoS Computational Biology 8(11): e1002747. doi:10.1371/journal.pcbi.1002747.

R Murugan (2012) Theory on the dynamics of feedforward loops in the transcription factor networks. PLoS ONE. a7(7): e41027. doi:10.1371/journal.pone.0041027.

R Murugan (2011) Theory on thermodynamic coupling of site-specific DNA-protein interactions with fluctuations in DNA-binding domains. J. Phys. A: Math. & Theor. 44, 505002-12.

 R Murugan and G Kreiman (2011) On the minimization of fluctuations in the response-times of gene-regulatory networks. Biophys. J. 101, 1297-1306.

R Murugan (2011) Theory on the dynamic memory in the transcription-factor-mediated transcription activation. Phys. Rev. E. 83, 041926–35.

R Murugan (2010) Theory of site-specific interactions of the combinatorial transcription factors with DNA. J. Phys. A: Math. & Theor. 43, 195003–23.

R Murugan (2010) Theory on the mechanism of distal-action of transcription factors: Looping of DNA versus tracking along DNA. J. Phys. A: Math. & Theor. 43, 415002–17.

R Murugan (2010) Theory of site-specific DNA-protein interactions in the presence of conformational fluctuations of DNA binding domains. Biophys. J. 99, 353–359.

R Murugan (2009) Directional dependent dynamics of protein molecules on DNA. Phys. Rev. E. 79, 041913–20.

R Murugan (2009) Packaging effects on site-specific DNA-protein interactions. Phys. Rev. E. 79, 061920–29.

R Murugan (2008) Multiple stochastic point processes in gene expression. J. Stat. Phys. 131, 153–165.

R Murugan (2007) Action at distance along the DNA: a random jump model on enhancer action. J. Theor. Biol. 248, 696–705. 14.

R Murugan (2007) Generalized theory of site-specific DNA protein interactions. Phys. Rev. E. 76, 011901–9.

R Murugan (2006) Critical jump sizes in DNA protein interactions. Biophys. Chem. 120, 143–147.

R Murugan (2006) Mean first passage time calculation for random walk with random step size. J. Phys. A: Math & Theor. 39, 1575–1580.

R Murugan and S Mazumdar (2006) Effect of alcohols on binding of camphor to cytochrome P450cam: spectroscopic and stopped flow transient kinetic studies. Arch. Biochem. Biophys. 455, 154-162.

R Murugan (2006) Stochastic transcription initiation: Time dependent transcription rates. Biophys. Chem. 121, 51–56.

R Murugan (2006) Mean first passage time calculation for one dimensional random walk with random absorbing boundary. J. Phys. A: Math & Theor. 39, L199–L255.

R Murugan (2006) Effect of external fluctuations on the affinity-specificity negative correlation in DNA probe interactions. Phys. Rev. E. 73, 051915–23.

R Murugan (2005) On the origin of affinity-specificity negative correlation in DNA- probe interactions. Biophys. Chem. 116, 105–9.

R Murugan and S Mazumdar (2005) Structure of the heme centre and its redox properties in the C357M mutant of cytochrome P450cam. Chem.Biochem. 6, 1204-11.

S Prasad, R Murugan and S Mitra (2005) An artificial electron donor supported catalytic cycle of Pseudomonas putida cytochrome P450cam. Biophys. Biochem. Res. Commun. 335, 590-6.

R Murugan (2004) DNA-protein interactions under random jump conditions. Phys. Rev. E. 69, 011911-17.

R Murugan and S Mazumdar (2004) A simple formalism on the dynamics of proteins on potential energy landscapes. Protein Science. 13, 487-493.

R Murugan and S Mazumdar (2004) Role of substrate on the conformational stability of the heme active site of cytochrome P450cam: Effect of temperature and low concentrations of denaturants. J. Biol. Inorg. Chem. 9, 477-788.

R Murugan (2003) Competitive model on denaturant-mediated protein unfolding. Biophys. J. 84, 770–774.

R Murugan (2003) A theory on the origin of cooperativity in DNA renaturation kinetics. Biophys. Chem. 106, 173–178.

R Murugan (2003) A stochastic model on DNA renaturation kinetics. Biophys. Chem. 104, 535–541.

R Murugan (2002) Solution to Michaleis-Menten enzyme kinetic equation via undetermined gauge functions: Resolving the non-linearity of Lineweaver-Burk plot. J. Chem. Phys. 117, 4178–84.

R Murugan (2002) Revised theory on DNA renaturation kinetics and its experimental verification. Biophys. Biochem. Res. Commun. 293, 870–873.

R Murugan (2002) Sample size autocorrelation of kinetic data: Resolving reaction path heterogeneity. J. Chem. Phys. 117, 6372–78.

Contact Details

R. Murugan, Ph.D (rmurugan @ iitm.ac.in / gmail.com)

Department of Biotechnology | Indian Institute of Technology Madras | Chennai | 600036 | Tamil Nadu | India | Ph. +91 44 2257 4116.