Innovations in Biomolecular Modeling and Simulations

Volume 1 Beginnings;

Personal Perspective;

Fashioning NAMD, a History of Risk and Reward: Klaus Schulten Reminisces;

Towards Biomolecular Simulations with Explicit Inclusion of Polarizability: Development of a CHARMM Polarizable Force Field based on the Classical Drude Oscillator Model;

Integral Equation Theory of Biomolecules and Electrolytes;

Molecular Simulation in the Energy Biosciences;

Sampling and rates;

Dynamics Simulations with Trajectory Fragments;

Computing Reaction Rates in Biomolecular Systems using discrete macrostates;

Challenges in applying Monte Carlo sampling to biomolecular systems;

Coarse graining and multiscale models;

Coarse Grained Protein Models;

Generalized Multi-Level Coarse-Grained Molecular Simulation and Its Applucation to Myosin-V Movement;

Top-down Mesoscale Models and Free Energy Calculations of Multivalent Protein-Protein and Protein-Membrane Interactions in Nanocarrier Adhesion and Receptor Trafficking;

Studying Proteins and Peptides at Material Surfaces;

Multiscale Design: From Theory to Practice. Volume 2 Atomistic simulations of nucleic acids and nucleic acid complexes;

Modeling nucleic acid structure and flexibility: from atomic to mesoscopic scale;

Molecular dynamics and force field based methods for studying quadruplex nucleic acids;

Opposites attract: Shape and Electrostatic Complementarity in Protein/DNA Complexes;

Intrinsic motions of DNA polymerases underlie their remarkable specificity and selectivity and suggest a hybrid substrate binding mechanism;

Molecular Dynamics Structure Prediction of a Novel Protein/DNA Complex: Two HU Proteins with a DNA Four-way Junction;

Molecular Dynamics Simulations of RNA Molecules;

The Structure and Folding of Helical Junctions in RNA;

DNA folding, knotting, sliding and hopping;

Simulations of DNA Knots and Catenanes;

Monte Carlo Simulations of Nucleosome Chains to Idenitfy Factors that control DNA Compaction and Access;

Sliding Dynamics Along DNA: a Molecular Perspective;

Drug design;

Structure-based design technology: CONTOUR and its aplication to drug discovery;

Molecular simulation in computer-aided drug design: algorithms and applications;

Computer-aided drug discovery: two antiviral drugs for HIV AIDS