Electrophoresis of a Charged Polymer in a Microfabricated Channel

There are two topics studied in this work on the basis of Monte Carlo (MC) and Brownian Dynamics (BD) simulation separately. Firstly, the DNA electrophoresis in dilute polymer solutions is investigated by MC and BD methods. We all know when the DNA goes through the dilute polymer solution; it will be entangled by the polymer dispersed in the solution. When the volume fraction of polymers is 0.2, the DNA’s mobility of electrophoresis is increased by shorter length of polymers in the solution. In the result of the simulation, we can’t be sure the exactly separation of different length of DNA, because of the uncertainty of the data. In the 0.02 of volume fraction, we found the mobility of different length of DNA is almost unvaried. As the result of the Monte Carlo method is too time-consuming in the situation of too many beads, we switched to the Brownian Dynamics and it will also provide the real solution effect. When the volume fraction of polymers is 0.2 in BD method, the mobility of DNA will be decreased by the longer length of polymers, which have larger contact aria with DNA, in solution. Totally speaking, we can’t be sure whether the different length of DNA could be separated in dilute polymer solution or not, when not considering the hydrodynamic effect.
In the second part of this work, the Electrophoresis of a charged polymer (DNA) in a microfabricated channel is investigated by BD method. The results showed when the electric field is 0.7, we can’t separate the different length of DNA in most of the situations. In order to improve the result, we suggest that: (1) to increase the entopic trapping (height of channel); (2) to increase the length of the thin region. When 0.2 of electric field is used, the results of separating the different length of DNA are better. As the ratio of thick and thin region is one, longer the total length of thick and thin region, higher the mobility of DNA. In another way, the effect of the thick region is very obvious that longer the length of the thick region, higher the mobility of DNA in same length.