Bridging molecular and systems scales in membrane biology
Chan, Aaron
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Permalink
https://hdl.handle.net/2142/132723
Description
Title
Bridging molecular and systems scales in membrane biology
Author(s)
Chan, Aaron
Issue Date
2025-08-12
Director of Research (if dissertation) or Advisor (if thesis)
Tajkhorshid, Emad
Doctoral Committee Chair(s)
Tajkhorshid, Emad
Committee Member(s)
Luthey-Schulten, Zaida
Gruebele, Martin
Pogorelov, Taras
Department of Study
School of Molecular & Cell Bio
Discipline
Biophysics & Quant Biology
Degree Granting Institution
University of Illinois Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
computational biology
membrane biology
molecular simulation
Language
eng
Abstract
Membrane proteins serve a variety of roles which include mediating transport, serving as a trigger for cellular response, and catalyzing bioenergetic reactions.
This body of work uses computational methods to study different aspects of membrane biology.
The first two studies presented in my thesis use approaches based in molecular simulation, to study the influence of protein-lipid (Chapter 3) and protein-protein interactions (Chapter 4) on molecular diffusion in photosynthetic processes.
The next two studies are focused on using non-equilibrium MD methods such as steered molecular dynamics (SMD), coupled with umbrella sampling (US), and Alchemical Free-Energy Perturbation (Alchemical FEP) to study how the structural changes associated with point mutations affect mechanical aspects of conformational change in channels, such as hERG (Chapter 5), and the ability of growth factors to bind and activate growth factor receptors, such as VEGFR-2 (Chapter 6).
The last chapter showcases the application of different computational methods, which integrates molecular simulation and metabolic modeling in the development of a whole-cell model for the photosynthetic bacteria \textit{Procholorococcus marinus} MED4.
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