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• W2492553142 abstract "Computational cell biology is a relatively new branch of computational sciences which sets computer simulation, as well as molecular biology, biochemistry and biophysics, at the center of its disciplines. This thesis first inspects this new field of science, putting emphases on its computational aspects, and identifies some distinct demands in design of simulation algorithms and software platforms. One important characteristic, amongst others, of computational cell biology is that it is highly heterogeneous in terms of modeling formalisms and computational methods. Different simulation techniques are used for different types of sub-systems in the cell, and these sub-systems are often represented by different timescales. We found that the scientific necessity to integrate these computational subcomponents to form higher order, multi-formalism, and composite models is becoming increasingly important. Secondly, this thesis proposes a novel computational framework based on a discreteevent scheduler, Hermite polynomial interpolation, and object-orientation that realizes efficient multi-algorithm and multi-timescale simulations without sacrifice of modularities of sub-models running on different simulation techniques. It is demonstrated that this framework can give a significant speed-up to a real biological simulation model of E. coli heat shock response by coupling Gillespie’s stochastic simulation algorithm and ODE solvers. It is also shown that this framework can boost a multi-timescale simulation of coupled harmonic oscillators. Lastly, this thesis describes design and implementation issues of E-Cell System Version 3, a newly developed software environment for modeling, simulation and analysis in computational cell biology, in which the new computational framework is implemented." @default.
• W2492553142 created "2016-08-23" @default.
• W2492553142 creator A5027217784 @default.
• W2492553142 date "2004-01-01" @default.
• W2492553142 modified "2023-09-27" @default.
• W2492553142 title "Multi-algorithm and multi-timescale cell biology simulation" @default.
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