| 致谢 | 第5-8页 |
| 摘要 | 第8-10页 |
| ABSTRACT | 第10-11页 |
| LIST OF ABBREVIATIONS | 第12-14页 |
| 1 INTRODUCTION | 第14-22页 |
| 1.1 RNA Interference in Plants | 第14-15页 |
| 1.2 Interaction between Viruses and Their Host Plants | 第15-16页 |
| 1.3 Molecular Modeling Methods | 第16-18页 |
| 1.3.1 Quantum Mechanics(QM) | 第16-17页 |
| 1.3.2 Molecular Mechanics(MM) | 第17页 |
| 1.3.3 Classical Force Field | 第17-18页 |
| 1.4 Computational Simulation | 第18-22页 |
| 1.4.1 Ab initio Molecula r Dynamics Simulation | 第19-20页 |
| 1.4.2 Molecular Dynamics Simulation | 第20页 |
| 1.4.3 Monte Carlo Simulations | 第20-22页 |
| 2 RECOGNITION MECHANISM OF SI-RNA BY VIRAL P19 SUPPRESSOR OF RNASILENCING | 第22-42页 |
| 2.1 Introduction | 第22-25页 |
| 2.2 Systems and Methods | 第25-28页 |
| 2.3 Results and Discussions | 第28-39页 |
| 2.3.1 Normal MD Not Sufficient to Show the Difference within the Simulation Length | 第28-32页 |
| 2.3.2 p19 Mutants Showing Stronger Tendency to Be Decompounded in SMD | 第32-33页 |
| 2.3.3 Loss of Stacking Interactions Responsible for Less Stable Mutant Structures | 第33-37页 |
| 2.3.4 Free Energy Perturbation(FEP) Revealing Lower Binding Affinity for p19 Mutants | 第37-39页 |
| 2.4 Conclusion | 第39-42页 |
| 3 MOLECULAR DYNAMICS SIMULATIONS OF AGO SILENCING COMPLEXES REVEALLARGE DOMAIN MOTIONS IN AGO PROTEIN DURING THE GUIDE-TARGETRECOGNITION | 第42-71页 |
| 3.1 Introduction | 第42-44页 |
| 3.2 Systems and Methods | 第44-46页 |
| 3.3 Results and Discussion | 第46-67页 |
| 3.3.1 Increasing Mutations in Seed Region Distortion the A-Form Helix Formation | 第46-47页 |
| 3.3.2 Mismatches in Seed Region Induced THE Motion of PAZ domain | 第47-53页 |
| 3.3.3 Novel Cleavage Mechanism Indicated By the Indi rectly Interaction Between Seed Region and Ago Domains | 第53-58页 |
| 3.3.4 Similar results found in Ago-RNA-mRNA complexes | 第58-59页 |
| 3.3.5 Stable Structures Found for Ago Complexes with Longer Guide-Target Nucleic-Acid Duplex | 第59-67页 |
| 3.4 Conclusion | 第67-71页 |
| 4 USING A MUTUAL INFORMATION BASED SITE TRANSITION NETWORK TO MAP THEGENETIC EVOLUTION OF INFLUENZA A/H3N2 VIRUS | 第71-91页 |
| 4.1 Introductions | 第71-73页 |
| 4.2 Methods and Materials | 第73-75页 |
| 4.2.1 Network Inference Algorithm:MI | 第73-74页 |
| 4.2.2 Data Collection and Preparation | 第74页 |
| 4.2.3 Predicting Future Site Mutations | 第74-75页 |
| 4.3 Results and Discussion | 第75-89页 |
| 4.3.1 Site Transition Network for Influenza A/H3N2 HA1 | 第75-81页 |
| 4.3.2 Cluster Analysis Revealing Co-Evolving Sites Responsible for Antigenic Drift | 第81-85页 |
| 4.3.3 Strong Selection Pressures on Certain Sites | 第85-87页 |
| 4.3.4 Network guided prediction of the A/H3N2 Evolution | 第87-89页 |
| 4.4 Conclusion | 第89-91页 |
| CONCLUSION | 第91-95页 |
| REFERENCE | 第95-104页 |
| 个人简介 | 第104-105页 |
| PUBLICATIONS | 第105页 |
