CHAPTER 1. Introduction to the computational simulations of biomaterials. Historical evolution and projection.
CHAPTER 2. Main methods of modeling and simulation. Docking, Montecarlo and Molecular Dynamics.
CHAPTER 3. Force fields and resolution levels. Advantages and limitations. Multi-scale mappings.
CHAPTER 4. Algorithms and approximations. Consideration of short and long range forces, barostats, thermostats, periodic conditions.
CHAPTER 5. Analysis: deviations and fluctuations, density profiles, diffusion coefficients in 2 and 3 dimensions, autocorrelation functions, radial distribution functions, etc.
CHAPTER 6. Methods of calculation of Gibbs energies for different processes.
CHAPTER 7. Software and hardware: main computer tools and how to manage hardware resources. Computing engines, analysis packages and visualizers.
CHAPTER 8. Practical cases: self-association of small molecules, study of supramolecular aggregates, folding-deployment of macromolecules, micelles and membranes. |
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