Computational models have become an essential tool in engineering and science. Modeling and simulation platforms are being used to describe complex systems where the user builds a model by describing autonomous agents with different attributes that can interact with each other and dynamically influence overall system development. There are many formalisms for modeling but not as many standard programming languages for modeling and simulation platforms. Programming language formalisms are particularly attractive because of their ability to accommodate new objects and new behavioral attributes, as the complex system becomes better understood.
This work focuses on programming languages and their applications to computational biology and systems modeling. The theoretical contributions towards this aim are three novel programming languages: BioScape, BioScapeL and Parallel BioScape. The first, BioScape, is a high-level modeling language for the stochastic simulation of biological and biomaterials processes in a reactive environment in 3D space. The novel aspects of BioScape include high-level syntactic primitives to declare the scope in space where species can have movement, diffusion rate, shape, and reaction distance, and an operational semantics that deals with the specifics of 3D locations, verifying reaction distance, and featuring random movement. We define a translation from the non-stochastic fragment of BioScape to a low-level π-calculus with 3D primitives (3π) and prove its soundness with respect to the operational semantics. The second, BioScapeL, is an extension of BioScape with three novel features: programmable entity's location, random translation and scaling. The motivation for the extension comes from the need to accommodate phenomena like diffusion, collision, and confinement within part of the semantics of the calculus, instead of being a burden to the programmer. The third, Parallel BioScape, is an extension of BioScape with fully parallel semantics that may take advantage of the new multi-core and GPU architectures.
Towards the experimental and application contributions, we build computational models to study pH-triggered antibacterial coatings, bifunctional surfaces, intracellular viral traffic, JAK-STAT signal transduction pathway and effects of counterfeit components in the performance of a complex multi-component system.
|Commitee:||Duggan, Dominic, Giannini, Paola, Leopold, Philip|
|School:||Stevens Institute of Technology|
|School Location:||United States -- New Jersey|
|Source:||DAI-B 78/07(E), Dissertation Abstracts International|
|Keywords:||Computational biology, Computational modeling, Programming languages, Simulations, Systems and design, Visualization|
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