2026-09-21T13:31:16Z https://www.ideals.illinois.edu/oai-pmh

oai:www.ideals.illinois.edu:2142/132723 2026-03-24 col_2142_5131 col_2142_14828 com_2142_5130 com_2142_14827 com_2142_14793 com_2142_8903

application/pdf en text Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-12-01 The student, Aaron Chan, accepted the attached license on 2025-08-01 at 15:19. The student, Aaron Chan, submitted this Dissertation for approval on 2025-08-01 at 16:10. This Dissertation was approved for publication on 2025-08-12 at 09:48. DSpace SAF Submission Ingestion Package generated from Vireo submission #22745 on 2026-02-19 at 20:07:50 Bridging molecular and systems scales in membrane biology Chan, Aaron 2025-08-12 Tajkhorshid, Emad Tajkhorshid, Emad Luthey-Schulten, Zaida Gruebele, Martin Pogorelov, Taras computational biology membrane biology molecular simulation eng 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. 2025-12 Thesis https://hdl.handle.net/2142/132723 Copyright 2025 Aaron Chan School of Molecular & Cell Bio Biophysics & Quant Biology University of Illinois Urbana-Champaign Ph.D. Dissertation