Methods in Theoretical Systems Biology: Case Studies in Arabidopsis thaliana and Daphnia magna

Pal, Tushar (2025) Methods in Theoretical Systems Biology: Case Studies in Arabidopsis thaliana and Daphnia magna. Masters thesis, Indian Institute of Science Education and Research Kolkata.

Text (MS Dissertation pof Tushar Pal (20MS106)) 20MS106_Thesis_file.pdf - Submitted Version Restricted to Repository staff only Download (2MB)

Abstract

Mathematical modeling plays an important role in understanding the complex dynamics of biological systems. This thesis addresses two different approaches to modeling in systems biology: mechanistic modeling with ordinary differential equations (ODEs) and data-driven modeling via sparse regression techniques. In the first part, an ODE-based model is developed to simulate light-dependent growth in Arabidopsis thaliana, focusing on the regulatory interactions that control hypocotyl elongation and cotyledon growth under varying photoperiods. The model investigates the nature of interactions in a protein network centered around PHYTOCHROME INTERACTING FACTORs (PIFs) and identifies the role of ANGUSTIFOLIA as a key regulator of cotyledon development. In the second part, a data-driven sparse regression algorithm is used to infer stochastic equations governing the motion of Daphnia magna from simulated trajectory data.

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