Part I Molecular Modeling.- Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling.- The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules.- Discrete Molecular Dynamics Simulation of Biomolecules.- Small Molecule Docking from Theoretical Structural Models.- Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism.- Quantum Mechanical Insights into Biological Processes at the Electronic Level.- Part II Modeling Macromolecular Assemblies.- Multiscale Modeling of Virus Structure, Assembly and Dynamics.- Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model.- The Structure of Intrinsically Disordered Peptides Implicated in Amyloid Diseases: Insights from Fully Atomistic Simulations.- Part III Modeling Cells and Cellular Pathways.- Computer Simulations of Mechano-Chemical Networks: Choreographing Actin Dynamics in Cell Motility.- Computational and Modeling Strategies for Cell Motility.- Theoretical Analysis of Molecular Transport Across Membrane Channels and Nanopores.- Part IV Modeling Evolution.- Modeling Protein Evolution.- Modeling Structural and Genomic Constraints in the Evolution of Proteins.- Modeling Proteins at the Interface of Structure, Evolution, and Population Genetics.