Molecular Dynamics Simulations of Polymers in Micro–environments M. Kenward, F. Tessier, Y. Tatek, Y. Gratton, S. Guillouzic, and G. W. Slater a a Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, ON, K1N 6N5, gslater@science.uottawa.ca We provide an overview of ongoing work using large scale Molecular Dynamics (MD) simulations to study systems comprising macro- molecules and explicit fluid in various contexts relevant to emerging bioanalytical microdevices and single molecule manipulation techniques. In particular, we discuss the application of MD simulations to polymer translocation through a nanopore, electroosmotic flow control in small capillaries, polymer stretching, and polymer collisions with obstacles. We also present more fundamental applications of MD to the study of molecular-scale friction coefficients and planar perturbations in a fluid. The simultaneous increase in available computational resources and decrease in relevant system dimensions offers unprecedented opportunities to perform realistic simulations to refine our knowledge of these issues and guide future developments in this field. Nous pr´ esentons un panorama de nos travaux bas´ es sur la dynamique mol´ eculaire (DM) ` a grande ´ echelle appliqu´ ee ` a des syst` emes comportant des macromol´ ecules et des fluides dans divers contextes reli´ es aux dispositifs bioanalytiques en ´ emergence ou aux techniques de manipulation de mol´ ecules individuelles. En particulier, nous discutons de l’application de la DM au d´ eplacement d’un polym` ere ` a travers un nanopore, au contrˆ ole d’´ ecoulement ´ electro-osmotique dans les capillaires, ` a l’´ etirement des polym` eres et aux collisions des polym` eres avec des obstacles. Nous pr´ esentons aussi des applications plus fondamentales de la DM ` a l’´ etude des coefficients de frottement ` a l’´ echelle mol´ eculaire et aux perturbations planaires dans un fluide. L’augmentation de la puissance de calcul, combin´ ee ` a la diminution de la taille des syst` emes d’int´ erˆ et, nous permet d’effectuer des simulations r´ ealistes et ainsi de raffiner notre compr´ ehension du domaine et de guider les d´ eveloppements futurs. 1 Introduction With the development of micro- and even nanofluidic de- vices, more robust modeling is required in order to under- stand observed behaviour in these systems. Many of the physical mechanisms involved have no macroscopic ana- logue and are ill understood. For example, there is a major effort to design and utilize microelectromechanical systems (MEMS) in a variety of situations ranging from diagnos- tic tools to smart materials, and in order to effectively do so we need to understand the dynamics of the components which constitute these devices. Of particular interest to our group are systems which incorporate polymeric materials, at either the micro- or nanoscale. In this paper we combine computer simulations and theoretical methods to examine the behaviour of polymers and other macromolecules in a number of model systems. Large scale computer simulations which aim to explore mesoscale systems (with upwards of millions of parti- cles), have become an invaluable research tool. Simula- tion methodologies including Monte Carlo [1,2], contin- uum models such as Navier-Stokes [3], coarse grained and atomistic Molecular Dynamics [4,5] and Brownian Dy- namics are the most prevalent form of simulation for these types of systems. The simulation method used depends on a balance between the: 1. Required level of detail (e.g., length scales). 2. Time scales associated with observed behaviour. 3. Available computational resources. 4. Effort required for a timely implementation. Figure 1 illustrates the level of detail and computational time of each method. For the particular systems we are ex- amining, coarse grained Molecular Dynamics provides the most useful length and time scales, along with the preser- vation of hydrodynamics and the molecular properties of the system. Figure 1. Schematic illustration of several methods of simulation in terms of their relative computational time and level of detail. 1.1 Molecular Dynamics: A brief overview Since the aim of this paper is to illustrate the applica- tion of MD simulations to a variety of systems and not to provide a detailed description of Molecular Dynamics, we only give a brief overview and list appropriate references for the interested reader. In short, from the perspective of