The Effects of Nonlinearities on Information Transfer in Biological Signaling Networks
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Case Western Reserve University School of Graduate Studies / OhioLINK
2021
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| Online Access: | http://rave.ohiolink.edu/etdc/view?acc_num=case1600164205492173 |
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ndltd-OhioLink-oai-etd.ohiolink.edu-case16001642054921732021-08-03T07:16:22Z The Effects of Nonlinearities on Information Transfer in Biological Signaling Networks Weisenberger, Casey M. Biophysics Cells require accurate, real-time data about their environment to function, which they receive through complicated cascades of signaling networks. Due to the stochastic nature of the underlying chemical reactions, this inevitably introduces noise. Noise is typically considered an impediment for information processing. In this thesis, we will investigate how effectively noise can be reduced, how noise reduction can be affected by modifications like feedback from downstream to upstream components, and how noise is propagated between multiple levels of a cascade. We will investigate the noise filter optimization problem, the Wiener-Kolmogorov solution, and how to translate it to a biological context. The first application is to the simplest signaling circuit: a two-species push-pull loop. We will then examine whether this tuning can be implemented in a biological setting, by relating the two-species example to the parameters of a kinase-phosphatase enzyme reaction network. Next, we show how Wiener-Kolmogorov theory can be applied to two specific more complex signaling networks: a cascade consisting of a series of push-pull loops and a two-species network with negative feedback from output to input. At first, we will look at the linear cases and we will finally introduce nonlinearities to investigate whether this can reduce noise beyond the Wiener-Kolmogorov bounds. We find that we are able to beat the Wiener-Kolmogorov bound in a negative feedback network with a nonlinear perturbation to the linear feedback function. Similarly, we can beat the bound for a cascade with nonlinear production functions. In both cases, the violation is small, so while nonlinearity can provide a benefit, the reward is surprisingly small in the cases we have considered. Lastly, we provide an outlook for future studies in this area, considering steps that could be taken to figure out how to begin modeling more complicated chemical reaction networks that are biologically realistic. 2021-01-26 English text Case Western Reserve University School of Graduate Studies / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=case1600164205492173 http://rave.ohiolink.edu/etdc/view?acc_num=case1600164205492173 unrestricted This thesis or dissertation is protected by copyright: some rights reserved. It is licensed for use under a Creative Commons license. Specific terms and permissions are available from this document's record in the OhioLINK ETD Center. |
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NDLTD |
| language |
English |
| sources |
NDLTD |
| topic |
Biophysics |
| spellingShingle |
Biophysics Weisenberger, Casey M. The Effects of Nonlinearities on Information Transfer in Biological Signaling Networks |
| author |
Weisenberger, Casey M. |
| author_facet |
Weisenberger, Casey M. |
| author_sort |
Weisenberger, Casey M. |
| title |
The Effects of Nonlinearities on Information Transfer in Biological Signaling Networks |
| title_short |
The Effects of Nonlinearities on Information Transfer in Biological Signaling Networks |
| title_full |
The Effects of Nonlinearities on Information Transfer in Biological Signaling Networks |
| title_fullStr |
The Effects of Nonlinearities on Information Transfer in Biological Signaling Networks |
| title_full_unstemmed |
The Effects of Nonlinearities on Information Transfer in Biological Signaling Networks |
| title_sort |
effects of nonlinearities on information transfer in biological signaling networks |
| publisher |
Case Western Reserve University School of Graduate Studies / OhioLINK |
| publishDate |
2021 |
| url |
http://rave.ohiolink.edu/etdc/view?acc_num=case1600164205492173 |
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AT weisenbergercaseym theeffectsofnonlinearitiesoninformationtransferinbiologicalsignalingnetworks AT weisenbergercaseym effectsofnonlinearitiesoninformationtransferinbiologicalsignalingnetworks |
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