Molecular Dynamics Simulations of Polymers in Micro–environments

We provide an overview of ongoing work using large scale Molecular Dynamics (MD) simulations to study systems comprising macromolecules 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.