Computational nanoscience of flow and mass transport through biological membranes

Abstract

The study presented in this document is the result of three years of research into the complex world of Molecular Dynamics applied to biological cell membranes. The simulation of biological tissues involves not only an excellent knowledge of the numerical calculus and its related tools, but a profound comprehension of the biological and medical literature associated with the phenomenon. By the other hand, the use of high performance facilities is essential for the computation of the Molecular Dynamics models in order to obtain results in acceptable times, so the latest technological advances have played a decisive and important part in this eld of research. The presented obtained results about shock wave interaction with biological membranes, as well as the air ow through the alveolar surface, are part of a new line of research usually known as "virtual experimental". This name comes from the fact that any physical or chemical situation can be re-created into a computer system to calculate its propagation in time. The results of the interaction of shock waves with biological cell membranes have been particularly satisfactory and they have opened a new line of investigation into cancer research. A numerical proportional relation between the shock wave impulse and the value of lateral di usion (from 9.80 to 12.84 10 .7

cm2 s ), as well as the simulation of the transient provoked by the wave into a NPT ensemble are a successful achievement. Other computations of this type of interaction have been simulated into an NVE ensemble as well, however the obtained results for the lateral di usion, in the order of 10 .7

cm2 s , showed no trend regarding the shock wave and the transient e ect could not be simulated. On the other hand, the recreation of the air ow through the alveolar surface is an initial step into the solution of all the controversy surrounding this extremely complex system known as alveolar surface network. An alveolar membrane of around 7 nm has been successfully simulated in agreement with Scarpelli's experiments. This lipid-protein membrane model simulated can serve as a virtual experiment in order to solve the controversy about the alveolar surface. It points to the possibility of air ow through a stable two-layered DPPC phospholipid structure either from a numerical or physical and biological point of view and the existence of an alveolar membrane at the end of the bronchial tubes.