Computational simulations of whole cells : strategies for framework design and model parameterization
Abstract/Contents
- Abstract
- The complexity of living systems, and the mounting wealth of biological data, poses a challenge: can we unify our comprehension of a living system into one coherent representation - and if so, what would we learn? Herein I present strategies for the design of a framework that can integrate diverse mathematical submodels of cellular physiology into one hybrid computational simulation of a whole cell, extending and revising prior work in this space. This framework is realized in the form of a whole-cell model of E. coli that can dynamically reproduce several molecular, cellular, and population-level behaviors across multiple environments and cell cycles. I also present strategies for integrative parameter estimation in the context of whole-cell-like submodels, an emergent need consequent of limited or inconsistent biological data. This work identifies model formulation and parameterization techniques that facilitate exploration of the space of biological dynamics; it also identifies specific inconsistencies in the underlying data as well as systems-level hypotheses about metabolic control and dynamics. Altogether, this research comprises several conceptual and technical advancements towards the end of functionally complete single-cell simulations.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2018; ©2018 |
| Publication date | 2018; 2018 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Mason, John Christopher |
|---|---|
| Degree supervisor | Covert, Markus |
| Thesis advisor | Covert, Markus |
| Thesis advisor | Altman, Russ |
| Thesis advisor | Huang, Kerwyn Casey, 1979- |
| Degree committee member | Altman, Russ |
| Degree committee member | Huang, Kerwyn Casey, 1979- |
| Associated with | Stanford University, Department of Bioengineering. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | John Mason. |
|---|---|
| Note | Submitted to the Department of Bioengineering. |
| Thesis | Thesis Ph.D. Stanford University 2018. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2018 by John Christopher Mason
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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