Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/136518
Title: ANALYSIS OF BIOPATHWAY MODELS USING PARALLEL ARCHITECTURES
Authors: RAMANATHAN RAJENDIRAN
Keywords: systems biology, ordinary differential equations, hybrid systems, statistical model checking, simulation, graphics processing units
Issue Date: 31-Mar-2017
Source: RAMANATHAN RAJENDIRAN (2017-03-31). ANALYSIS OF BIOPATHWAY MODELS USING PARALLEL ARCHITECTURES. ScholarBank@NUS Repository.
Abstract: We study models of bio-pathways that arise in systems biology. Often a bio-pathway can be viewed as a network of bio-chemical reactions. One can then model the network as a dynamical system. In this thesis, we explore two classes of such models, namely, a single system of ordinary differential equations and hybrid dynamical systems. Hybrid systems are multi-mode dynamical systems which evolve over continuous time. The dynamics in each mode is governed by a mode-specific system of differential equations and at discrete instances there can be instantaneous jumps between modes depending typically on the current continuous state. Both these models ---especially when used in systems biology context--- are difficult to analyze and the analysis methods one develops are usually computationally intensive and hence difficult to scale. With this as motivation, we broadly explore the twin themes of (i) Probabilistic approximations of ODEs systems and hybrid systems accompanied by a probabilistic verification technique known as statistical model checking, (ii) GPU based implementations of the SMC procedures and the related analysis techniques. We have applied our methods to a number of realistic models. The results indicate that our approximation schemes scale well and can be applied in a number of different settings.
URI: http://scholarbank.nus.edu.sg/handle/10635/136518
Appears in Collections:Ph.D Theses (Open)

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