Simulation of polymer translocation through small channels: A Molecular Dynamics study and a new Monte Carlo approach Michel Gauthier University of Ottawa With the recent completion of the Human Genome Project and the announcement of the $1000 Genome Race in 2003, the interest for developing faster and cheaper sequencing technologies is continually growing. Nanopore sequencing offers one of the most promising new ideas. This method consists in reading DNA as it passes through a small aperture perforated through a membrane; a technique similar to decoding a magnetic tape in a tape player. The process of linearly moving a flexible chain from one side of a small channel to the other is called polymer translocation. However, the physics behind this process is still not well understood. This talk is an overview of my PhD thesis that I submitted in September 2007 under the supervision of Dr. Gary W. Slater. I will present two simulation approaches that we used to investigate the translocation problem. In the first project, we used Molecular Dynamics simulations with explicit solvent particles to generate unbiased translocation events in order to characterize the screening of the hydrodynamic interactions by the membrane and to test the hypothesis that polymer translocation is a quasi-equilibrium process. The latter question is quite fundamental since this assumption is at the origin of most theoretical approaches. Our most surprising result is that 50% of the translocation process takes place in the last 12% of the translocation time, which means that there is a large acceleration at the late stage of the process. The goal of our second project was to clarify the nature of the transition between the two translocation regimes dominated by the pore-polymer friction and the hydrodynamic drag of the subchains outside the channel, respectively. However, such an investigation requires the ability to simulate translocation events with a very wide range of polymer lengths. We thus propose a new Monte Carlo method based on a one-dimensional random-walk representation of the translocation problem that can easily be used to study chain lengths as large as 10^7 monomers. This model works in conjunction with an exact calculation technique to compute the key results of the translocation events such as the probability to occur and the average time duration. It is used to validate previous and make new theoretical predictions about translocation dynamics as the polymer and channel lengths are varied. It is also applied to the study of chain heterogeneity effects.