DocumentCode :
2880117
Title :
Stochastic simulation of biological cellular processes using VHDL-AMS
Author :
Peterson, Gregory D. ; Lancaster, Joseph M.
Author_Institution :
Electr. & Comput. Eng., Tennessee Univ., USA
fYear :
2002
fDate :
6-8 Oct. 2002
Firstpage :
118
Lastpage :
122
Abstract :
Accurate, predictive models of biological cellular processes are a key component of the quest to transform the engineering of genetic controls within organisms. Biological systems include a dizzying variety of interacting biochemical pathways, each consisting of numerous reactions and chemical species. Moreover, such classical assumptions of differential equations models as equilibrium (including well-stirred species) and a large number of reactants do not hold for mesoscalar, intra-cellular modeling. In fact, these systems require the seamless, accurate modeling of interacting discrete and continuous behaviors. Previous research has demonstrated the potential of using portions of biochemical pathways as switches to control behavior, with emergent behaviors such as logic gates created. Accurate, efficient models require the ability to mix discrete and continuous descriptions while providing for the high-fidelity interaction between these domains. Although a number of previous researchers have discussed the use of analog and mixed signal hardware description languages (AMS HDLs) such as VHDL-AMS and Verilog-AMS for representing the behavior of MEMS, microfluidic, optical, and thermal systems, similar benefits can result from the use of AMS HDLs for biological systems modeling. We present preliminary research into the VHDL-AMS representation of biological systems at different levels of abstraction and the capability to support multi-resolution modeling. We discuss the role of this research within the context of the DARPA BioSPICE research program, our modeling and simulation approach, and future plans.
Keywords :
biology computing; genetics; hardware description languages; mixed analogue-digital integrated circuits; stochastic processes; DARPA BioSPICE research program; MEMS; VHDL-AMS; Verilog-AMS; analog signal; biochemical pathways; biological cellular processes; biological systems; chemical species; continuous behaviors; differential equations models; genetic controls; hardware description languages; high-fidelity domain interaction; interacting discrete behaviors; logic gates; microfluidic systems; mixed signal; multiresolution modeling; optical systems; stochastic simulation; thermal systems; Biological control systems; Biological system modeling; Biological systems; Chemicals; Context modeling; Genetic engineering; Hardware design languages; Organisms; Predictive models; Stochastic processes;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Behavioral Modeling and Simulation, 2002. BMAS 2002. Proceedings of the 2002 IEEE International Workshop on
Print_ISBN :
0-7803-7634-X
Type :
conf
DOI :
10.1109/BMAS.2002.1291069
Filename :
1291069
Link To Document :
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