The fundamental operating principles behind a vast majority of analytical tools in chemistry and molecular biology are rooted in elec- trokinetic phenomena. In particular, the separation of such important molecular entities as DNA and proteins rely on electrophoresis, i.e., the migration of molecules in an aqueous medium under the action of elec- tric forces. The imminent reality of large scale integration in the analyti- cal sciences (the so-called lab-on-a-chip) is challenging some conven- tional views which were derived from electrokinetic theories adapted to macroscopic systems (especially low surface-to-volume ratio ones). The theoretical exploration of electrokinetics in nanoscopic channels is important, because their advent promises more than the mere scaling down of existing technologies. Indeed, we can presumably exploit new physical effects that manifest themselves at the nanoscale and thus develop new separation methods that have no equivalent in their mac- roscopic analogue. Herein we describe how to use united-atom Mo- lecular Dynamics (MD) simulations to explore the physics of electro- phoretic and electroosmotic migration in a cylindrical, nanofluidic capil- lary.
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