Computational Modeling of Biological Systems

Part I. Molecular Modeling

Chapter 1. Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling

Chapter 2. The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules

Chapter 3. Discrete Molecular Dynamics Simulation of Biomolecules

Chapter 4. Small Molecule Docking from Theoretical Structural Models

Chapter 5. Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism

Chapter 6. Quantum Mechanical Insights into Biological Processes at the Electronic Level

Part II. Modeling Macromolecular Assemblies

Chapter 7. Multiscale Modeling of Virus Structure, Assembly and Dynamics

Chapter 8. Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model

Chapter 9. The Structure of Intrinsically Disordered Peptides Implicated in Amyloid Diseases: Insights from Fully Atomistic Simulations

Part III. Modeling Cells and Cellular Pathways

Chapter 10. Computer Simulations of Mechano-Chemical Networks: Choreographing Actin Dynamics in Cell Motility

Chapter 11. Computational and Modeling Strategies for Cell Motility

Chapter 12. Theoretical Analysis of Molecular Transport Across Membrane Channels and Nanopores

Part IV. Modeling Evolution

Chapter 13. Modeling Protein Evolution

Chapter 14. Modeling Structural and Genomic Constraints in the Evolution of Proteins

Chapter 15. Modeling Proteins at the Interface of Structure, Evolution, and Population Genetics

Dr. Nikolay Dokholyan joined the Department of Biochemistry and Biophysics in the University of North Carolina at Chapel Hill, School of Medicine as an Assistant Professor. In 2008, Dr. Dokholyan was promoted as Associate Professor. Dr. Dokholyan is currently the Director of the Center for Computational and Systems Biology and the Graduate Director of the Program in Molecular and Cellular Biophysics at UNC.