Polynomial Evaluation through Biochemical Reactions in Equilibrium
Date Issued
2014
Date
2014
Author(s)
Huang, Ruei-Yang
Abstract
Computation with biochemical elements is one of the major goals of synthetic biology. Engineering biochemical reactions has the potential to implement computations.
We discuss about synthetic approaches to biochemical arithmetic operation. In particular, computation of polynomial is fundamental and important because
we can approximate many non-linear functions with polynomials. In this thesis, we provide two bottom-up design strategies for polynomial evaluation. One is the
integer valued polynomial evaluation, where polynomials are computed by single multiplication module using a time multiplexing strategy. In the infrastructure, reactions
are regarded as atomic instruction marked with definite start time and finish time. The other is real valued polynomial evaluation, where the value is determined
by precise control of molecular concentrations at their biochemical equilibrium. To produce output, reactions are used as configurable controller for species generation and degradation. For both methods, we run deterministic computer simulation and verify their output correctness through case studies. Our biochemical polynomials
are applied to model pattern formations and provide a possible mechanism of reaction-diffusion system. In the future, we hope to impose more biological factors
to our model and realize it in living cells.
Subjects
生化平衡
多項式
合成生物學
生化模型模擬
人工生化反應
Type
thesis
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