Title:
Student:
Date:
Supervisor/s:
Brownian dynamics simulation of enzymatic reactions. Study of the effect
of the macromolecular crowding.
Helena Muñoz Galan
June 2015
Dr. Eudald Vilaseca Font
Departament of Physical Chemistry
Enzymatic reactions following the Michaelis-Menten mechanism will be studied using a new
software called ReaDDy Brownian Dynamic Simulations Package. The effects of the
macromolecular crowding, which is characteristic of the cellular environments, on the kinetic
process have been studied by analyzing the diffusion and reactivity depending on the excluded
volume and the relative size between interactive and non-interactive particles. It has been done
by analyzing several cases, ones varying the concentration of crowder and keeping constant the
size of this one, and some others keeping constant the concentration and varying the size of the
crowder. By doing so, it has been studied the excluded volume and the relative size effect
respectively. A general trend has been observed from the concentration along the reaction time
and the diffusion constant.