Monte Carlo methods are used in various fields of computational biology, for example for Bayesian inference in phylogeny, or for studying biological systems such as genomes, proteins, or membranes. The systems can be studied in the coarse-grained or ab initio frameworks depending on the desired accuracy. Computer simulations allow monitoring of the local environment of a particular molecule to see if some chemical reaction is happening for instance. In cases where it is not feasible to conduct a physical experiment, thought experiments can be conducted (for instance: breaking bonds, introducing impurities at specific sites, changing the local/global structure, or introducing external fields).