Completed notes of the course

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Molecular Modeling of materials L A T E X notes 2021 Prof. Guido Raos Giuseppe Lauricella 1 Introduction Computer simulations can be a valid alternative to experiments, in the study and develop- ment of new materials. The Moore's law highlights that there is a limit fo the clock's speed, due to quantum mechanics and energy e ciency. The only to go beyond this limit in computer simulations is by putting together more pro- cessors, in the so called parallel computing . Nowadays it is possible to simulate millions of atoms and this is particularly appealing in biology. 64 million atoms are included in the HIV-1 capside model, shown in gure 1. Figure 1: A model of HIV virus, combining experiments and molecular modeling (Schulten et al. , Nature 2013.) The data coming from simulations can be clustered to get similarities within the evolution of protein's folding, and so on. In 2020, a paper has been published, related to a virus simulation of 121 ns (which is a lot), containing ∼160 million atoms. The applications are dierent. In biology the folding of proteins can be investigated, together with protein-protein and protein-DNA interactions, enzymatic catalysis. In general, quan- tum mechanics (QM) is required: there is no totally reliable ways to deal with it without considering the electronic structure of atoms. Depending on the problem, the electronic structure may be relevant or not. In a st level, the forces and energies are calculated based on the electronic structure . Then, we move to empirical force elds and molecular dynamics, with coarse grained simulations. The behaviour of the model can be explored with energy minimization techniques, MD, Monte Carlo applied to MD and many more. 1 NOTE that the former are models , the latter are methods . Moving on the time and…