ICP Kolloquium: Dr. Pablo M. Blanco

Simulating reversible chemical reactions in macromolecular systems: a Monte Carlo approach

When reversible chemical reactions are present in macromolecular systems, they can significantly impact the physical properties of these systems. For example, weak polyelectrolytes and biomacromolecules can modulate their charge in response to their microenvironment through the acid/base equilibrium, a phenomenon known as charge regulation. To simulate these kinds of systems, the configuration space and the reaction degrees of freedom need to be simultaneously sampled because they are coupled. Nowadays, Monte Carlo (MC) simulations and coarse-grained models have become a popular approach to study these systems because they permit efficient sampling of the equilibrium properties of these systems. In this lecture, we will showcase different examples where MC simulations have explained how reversible chemical reactions affect the properties of macromolecular systems, in some occasions in a non-intuitive fashion. Furthermore, we will present the Python-based Molecule Builder for ESPResSo (pyMBE), an open-source software with tools to aid the setup of these MC simulations for custom coarse-grained models and pre-defined models of peptides and globular proteins in the Extensible Simulation Package for Research on Soft Matter (ESPResSo).