Dissipative Particle Dynamics Simulation Of The Coil-Globule Transition And Flow-Induced Polymer Translocation

The equilibrium properties and dynamics behaviors of polymers in dilute solution undergo various responses to different external changes. In recent decades of years, the extensive investigation in this area is primarily motivated by the intense current interest in the biophysics problems, e.g. protein folding; transport of protein or single-strand DNA through membrane channels. Besides, understanding the fundamental process of these phenomenons has a broad range of potential applications in Biological Engineering, Chemical Engineering and so on. For example, it helps diagnosing some diseases which are caused by mis-folding of related proteins; or it helps rapid DNA sequencing induced by an electric field. In this article, we use Dissipative Particle Dynamics method to investigate "coil-globule" transition and flow induced polymer translocation through microchannels.First, we investigate the dynamics behavior of "coil-globule" transition. Single polymer in solution collapses when solvent is quenched from good to poor. Researchers gradually noticed that hydrodynamics interaction and solvent-induced many-body effect play important roles in the collapse pathway and total duration. Dissipative Particle Dynamics is a mesoscopic coarse-grained simulation method in which the two effects are preserved naturally by incorporating explicit solvent particles in the model. Our simulation suggests a five-stage collapse pathway: localized clusters formation, cluster coarsening in situ, coarsening involving global backbone conformation change, rounding of a spheroid into a crumpled globule, and compaction of the globule. For all the quench depths and chain lengths used in our study, collapse proceeds along "pearl-necklace" pathway without the chain getting trapped in a metastable "sausage" configuration, as reported in some earlier studies. We obtain the time scales for each of the first four stages, as well as its scaling with the quench depthsξand chain lengths N. The total collapse time scales asτc～ξ-0.46N0.98, with the quench depthξand degree of polymerization N. Next, the dynamics of flow-induced translocation of polymers through a microchannel is investigated by dissipative particle dynamics approach. The simulations show that there are three stages in the translocation process of linear polymer chain:(1) the polymer chain initially drifts along the flow direction; (2) the polymer chain approaches the entrance of the narrow channel by undergoing a continuous conformational deformation to match the pore size of the narrow channel; (3) the polymer chain rapidly travels through the narrow channel to fulfill complete translocation. Our simulation confirmed that the threshold velocity flux of translocation is independent of chain lengths and the radius of microchannel. The results also show that the process from total retention to forced penetration is a smooth transition. Besides, we find that the average translocation time steadily increases with increase of the polymer lengths while decreases with the increase of fluid flux. Our results demonstrate that chain rigidity exerts a considerable influence on the dynamics of polymer translocations. The findings in this work may help facilitate understanding of the dynamic behaviors of fluid-driven polymer and/or DNA molecules during translocation processes.