Using extended harmonic oscillators to identify and understand circadian rhythms
Authors
De los Santos, Hannah
ORCID
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Other Contributors
Bennett, Kristin P.
Hurley, Jennifer M.
Magdon-Ismail, Malik
Zaki, Mohammed J., 1971-
Hurley, Jennifer M.
Magdon-Ismail, Malik
Zaki, Mohammed J., 1971-
Issue Date
2020-05
Keywords
Computer science
Degree
PhD
Terms of Use
This electronic version is a licensed copy owned by Rensselaer Polytechnic Institute, Troy, NY. Copyright of original work retained by author.
Full Citation
Abstract
The first model in the PAICE Suite, ECHO (Extended Circadian Harmonic Oscillator), uses an optimization approach that fits the solution to the differential equation corresponding to an underlying negative feedback loop with external influences to omics scale data, thus extending the simple harmonic equation to identify and classify the degree of amplitude change. To do this, we have also developed novel starting point heuristics and weighting schemes for nonlinear least squares that find more accurate parameter values than other prevalent methods. We also extend rhythm identification outside of circadian periods through the specification of unconstrained problems, which allow for shorter and longer periods. Using biological datasets in various organisms, we find that rhythms of different Amplitude Change (AC) categories, including damping and forcing, reveal functional biological differences.
Description
May 2020
School of Science
School of Science
Department
Dept. of Computer Science
Publisher
Rensselaer Polytechnic Institute, Troy, NY
Relationships
Rensselaer Theses and Dissertations Online Collection
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