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Limits and tradeoffs in the control ...

Chandra, Fiona.

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Limits and tradeoffs in the control of autocatalytic systems.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Limits and tradeoffs in the control of autocatalytic systems./
Author:	Chandra, Fiona.
Description:	93 p.
Notes:	Source: Dissertation Abstracts International, Volume: 75-02(E), Section: B.
Contained By:	Dissertation Abstracts International75-02B(E).
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3598803
ISBN:	9781303476334

Limits and tradeoffs in the control of autocatalytic systems.
Chandra, Fiona.

Limits and tradeoffs in the control of autocatalytic systems. - 93 p.

Source: Dissertation Abstracts International, Volume: 75-02(E), Section: B.

Thesis (Ph.D.)--California Institute of Technology, 2013.

Despite the complexity of biological networks, we find that certain common architectures govern network structures. These architectures impose fundamental constraints on system performance and create tradeoffs that the system must balance in the face of uncertainty in the environment. This means that while a system may be optimized for a specific function through evolution, the optimal achievable state must follow these constraints. One such constraining architecture is autocatalysis, as seen in many biological networks including glycolysis and ribosomal protein synthesis. Using a minimal model, we show that ATP autocatalysis in glycolysis imposes stability and performance constraints and that the experimentally well-studied glycolytic oscillations are in fact a consequence of a tradeoff between error minimization and stability. We also show that additional complexity in the network results in increased robustness. Ribosome synthesis is also autocatalytic where ribosomes must be used to make more ribosomal proteins. When ribosomes have higher protein content, the autocatalysis is increased. We show that this autocatalysis destabilizes the system, slows down response, and also constrains the system's performance. On a larger scale, transcriptional regulation of whole organisms also follows architectural constraints and this can be seen in the differences between bacterial and yeast transcription networks. We show that the degree distributions of bacterial transcription network follow a power law distribution while the yeast network follows an exponential distribution. We then explored the evolutionary models that have previously been proposed and show that neither the preferential linking model nor the duplication-divergence model of network evolution generates the power-law, hierarchical structure found in bacteria. However, in real biological systems, the generation of new nodes occurs through both duplication and horizontal gene transfers, and we show that a biologically reasonable combination of the two mechanisms generates the desired network.

ISBN: 9781303476334Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Limits and tradeoffs in the control of autocatalytic systems.
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100 1 $a Chandra, Fiona. $3 2101710
245 1 0 $a Limits and tradeoffs in the control of autocatalytic systems.
300 $a 93 p.
500 $a Source: Dissertation Abstracts International, Volume: 75-02(E), Section: B.
500 $a Adviser: John C. Doyle.
502 $a Thesis (Ph.D.)--California Institute of Technology, 2013.
520 $a Despite the complexity of biological networks, we find that certain common architectures govern network structures. These architectures impose fundamental constraints on system performance and create tradeoffs that the system must balance in the face of uncertainty in the environment. This means that while a system may be optimized for a specific function through evolution, the optimal achievable state must follow these constraints. One such constraining architecture is autocatalysis, as seen in many biological networks including glycolysis and ribosomal protein synthesis. Using a minimal model, we show that ATP autocatalysis in glycolysis imposes stability and performance constraints and that the experimentally well-studied glycolytic oscillations are in fact a consequence of a tradeoff between error minimization and stability. We also show that additional complexity in the network results in increased robustness. Ribosome synthesis is also autocatalytic where ribosomes must be used to make more ribosomal proteins. When ribosomes have higher protein content, the autocatalysis is increased. We show that this autocatalysis destabilizes the system, slows down response, and also constrains the system's performance. On a larger scale, transcriptional regulation of whole organisms also follows architectural constraints and this can be seen in the differences between bacterial and yeast transcription networks. We show that the degree distributions of bacterial transcription network follow a power law distribution while the yeast network follows an exponential distribution. We then explored the evolutionary models that have previously been proposed and show that neither the preferential linking model nor the duplication-divergence model of network evolution generates the power-law, hierarchical structure found in bacteria. However, in real biological systems, the generation of new nodes occurs through both duplication and horizontal gene transfers, and we show that a biologically reasonable combination of the two mechanisms generates the desired network.
590 $a School code: 0037.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Biology, Systematic. $3 1676856
690 $a 0715
690 $a 0423
710 2 $a California Institute of Technology. $b Bioengineering. $3 2101711
773 0 $t Dissertation Abstracts International $g 75-02B(E).
790 $a 0037
791 $a Ph.D.
792 $a 2013
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3598803