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.