University of Illinois Urbana-Champaign

Bridging molecular and systems scales in membrane biology

Chan, Aaron

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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
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.
Graduation Semester
2025-12
Type of Resource
Thesis
Handle URL
https://hdl.handle.net/2142/132723
Copyright and License Information
Copyright 2025 Aaron Chan

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