Simulation of cell signalling communications using event-driven algorithms

Abstract

In this paper we present two implementations of event-driven algorithms for simulating molecular dynamics using the Omnet++ Simulation Framework and its Future Event Set (FES) implementation. The first one uses a cell-linked list algorithm. The second one extends the cell-linked list algorithm incorporating a Verlet neighbor list algorithm. We also present results and compare both algorithms over a set of different scenarios. Finally, we discuss the advantages of using the Omnet++ Simulation Framework and the implemented algorithm for simulating cell-signaling communications.