Dissipative particle dynamics for advanced coarse-grained molecular dynamics simulation

Abstract

Recently advances in biological science have been dependent in corresponding advances in the field of DNA and protein separation. It therefore also requires the progress of the related electro-mechanical devices, in terms accuracy and speed of analysis. Most of these devices are composed of micro- and/or nano- channels which involve flow of complex phenomena. Our focus is on these micro/nano channel devices, consisting of many entropic traps, which were designed and fabricated for the separation of long DNA molecules. The channel comprises narrow constriction and wider regions that cause sizedependent trapping of DNA at the onset of a constriction. This process creates electrophoretic mobility differences, thus enabling efficient separation without gel matrix or pulsed electric fields [1-3]. Simulation and in particular numerical simulation is an efficient way to investigate the complex flow in the related electro-mechanical devices. Investigations for different simulation methods were carried out and we came into conclusion that the Dissipative Particle Dynamics method, which groups a number of atoms/molecules into particles, is most suitable for the above-mentioned applications.