Biomolecular Computing System Design: Architecture, Synthesis, and Simulation
Date Issued
2015
Date
2015
Author(s)
Chiang, Katherine H.
Abstract
The advancements in systems and synthetic biology have been broadening the range of realizable systems with increasing complexity both in vitro and in vivo. Systems for digital logic operations, signal processing, analog computation, program flow control, as well as those composed of different functions — for example an on-site diagnostic system based on multiple biomarker measurements and signal processing – have been realized successfully. However, the efforts to date tend to tackle each design problem separately, relying on ad hoc strategies rather than providing more general solutions based on a unified and extensible architecture, resulting in long development cycle and rigid systems that require redesign even for small specification changes. Inspired by well-tested techniques adopted in electronics design automation (EDA), this work aims to remedy current design methodology by establishing a standardized, complete flow for realizing biomolecular systems. Given a behavior specification, the flow streamlines all the steps from modeling, synthesis, simulation, to final technology mapping onto implementing chassis. The resulted biomolecular systems of our design flow are all built on top of an FPGA-like reconfigurable architecture with recurring modules. Each module is designed the function of each module depends on the concentrations of assigned auxiliary species acting as the “tuning knobs.” Reconfigurability not only simplifies redesign for altered specification or post-simulation correction, but also makes post-manufacture fine-tuning — even after system deployment — possible. This flexibility is especially important in synthetic biology due to the unavoidable variations in both the deployed biological environment and the biomolecular reactions forming the designed system. In fact, by combining the system’s reconfigurability and neural network’s self-adaptiveness through learning, we further demonstrate the high compatibility of neuromorphic computation to our proposed architecture — the first work to consciously embed neuromorphic computing capability into molecular computing paradigm. With each module implementing a neuron of selected model (ex. spike-based, threshold-gate-like, etc.), accompanied by an appropriate choice of reconfigurable properties (ex. threshold value, synaptic weight, etc.), simulation results verified that the systems built from our proposed flow can indeed perform desired neuromorphic functions.
Subjects
molecular computing
reconfigurable computing
synthetic biology
hybrid simulation
neuromorphic engineering
Type
thesis
File(s)![Thumbnail Image]()
Loading...
Name
ntu-104-D01943033-1.pdf
Size
23.32 KB
Format
Adobe PDF
Checksum
(MD5):3006150400228114c62b06a25702479e