Bridging molecular and systems scales in membrane biology

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biophysics & Quant Biology

Grantor

University of Illinois Urbana-Champaign

Year dc:date

2025

Author dc:creator

• Chan, Aaron

Contributors dc:contributor

• Tajkhorshid, Emad
• Luthey-Schulten, Zaida
• Gruebele, Martin
• Pogorelov, Taras

• computational biology
• membrane biology
• molecular simulation

Statement dc:rights

• Copyright 2025 Aaron Chan

Language dc:language

en

Handle dc:identifier

https://hdl.handle.net/2142/132723

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/132723