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.