Excitation and Electron Transfer

Phys 301: Computational Biological Physics – Winter 2004


Phys 4500: Computational Biological Physics – Winter 2005




University of Illinois at Urbana Champaign
Beckman Institute for Advanced Science and Technology
Theoretical and Computational Biophysics Group







Excitation and Electron Transfer





Chalermpol Kanchanawarin Melih SenerCONTENTS 2
Contents
1 Tutorial on Excitation Transfer 4
1.1 File Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2 Architecture of Light Harvesting Complex II (LH II) . . . . . . . . . 4
1.2.1 Building block of LH II . . . . . . . . . . . . . . . . . . . . 5
1.2.2 Packing of two LH II structural units . . . . . . . . . . . . . 10
1.2.3 LH II ring . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.3 Excitation Transfer between two Bacteriochlorophyls in LH II . . . . 13
1.3.1 Orientation of BChl Transition Dipole Moments in LH II . . . 15
1.3.2 Calculation of Excitation transfer rate . . . . . . . . . . . . . 16
2 Tutorial on Electron Transfer 20
2.1 Starting your simulation . . . . . . . . . . . . . . . . . . . . . . . . 20
2.2 Interlude: Structure of cytochrome c . . . . . . . . . . . . . . . . . 212
2.3 a closer look at your configuration files . . . . . . . . . . . 22
2.4 Re running NAMD to read your previous trajectory . . . . . . . . . . 23
2.5 From the trajectory to the energy gap function . . . . . . . . . . . . . 24CONTENTS 3
Introduction
Life ...