Type
Text
Type
Dissertation
Advisor
Fernandez-Serra, Marivi | Dill, Ken A | Metcalf, Harold J | Balazsi, Gabor.
Date
2016-12-01
Keywords
bibliometrics, Entropy, non-equilibrium thermodynamics, Protein stability | Physics
Department
Department of Physics
Language
en_US
Source
This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree.
Identifier
http://hdl.handle.net/11401/76642
Publisher
The Graduate School, Stony Brook University: Stony Brook, NY.
Format
application/pdf
Abstract
This dissertation will cover three distinct topics of protein stability, non-equilibrium thermodynamics and scientometrics. In senescent organisms aging is correlated with oxidative damage of proteins. The damage done to proteins destabilizes them inhibiting their function. The implications of a simplified model based on side-chain modification of charged residues using Debye-H\"{u}ckel theory will be presented. Short length and highly charged proteins are susceptible to destabilization from oxidative damage. Among these proteins already studied in aging several proteins fit this description of being short and highly charged. There is a noticeable enrichment of short-highly-charged proteins in categories of proteins known to be important in aging. Maximum Caliber (MaxCal) is a potential theory of non-equilibrium statistical mechanics. It will be shown how MaxCal is used to derive the Onsager reciprocal relations, Green-Kubo relations and Prigogine’s Principle and extend these relations beyond the near-equilibrium regime. The last topic is the citation and publication trends of papers and authors, respectively. A discussion of how pure-birth processes can be applied to understanding citation trends and how birth-processes can be used in classifying papers into different categories of performance. | This dissertation will cover three distinct topics of protein stability, non-equilibrium thermodynamics and scientometrics. In senescent organisms aging is correlated with oxidative damage of proteins. The damage done to proteins destabilizes them inhibiting their function. The implications of a simplified model based on side-chain modification of charged residues using Debye-H\"{u}ckel theory will be presented. Short length and highly charged proteins are susceptible to destabilization from oxidative damage. Among these proteins already studied in aging several proteins fit this description of being short and highly charged. There is a noticeable enrichment of short-highly-charged proteins in categories of proteins known to be important in aging. Maximum Caliber (MaxCal) is a potential theory of non-equilibrium statistical mechanics. It will be shown how MaxCal is used to derive the Onsager reciprocal relations, Green-Kubo relations and Prigogine’s Principle and extend these relations beyond the near-equilibrium regime. The last topic is the citation and publication trends of papers and authors, respectively. A discussion of how pure-birth processes can be applied to understanding citation trends and how birth-processes can be used in classifying papers into different categories of performance. | 90 pages
Recommended Citation
Hazoglou, Michael John, "Topics in Statistical Physics: Protein Stability, Non-Equilibrium Thermodynamics, and" (2016). Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions). 2530.
https://commons.library.stonybrook.edu/stony-brook-theses-and-dissertations-collection/2530