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Publication

Simulation of the Flow of a Single Stranded Dna in a Channel Using Dissipative Particle Dynamics

Simon, Saumya Susan
Abstract
Separation of DNA has significant importance in understanding the genome of an organism for genetic engineering and DNA profiling for forensics. The purpose of the study was to simulate a system containing solvent and DNA particles through a pressure-driven two-dimensional microchannel using Dissipative Particle Dynamics. This computational fluid method is simulated in Matlab using the modified velocity-Verlet algorithm. The computational method DPD was modified and the simulated channel flow was compared to the theoretical flow between two-dimensional parallel plates. The boundary conditions include both solid `frozen' particle walls and periodic boundary conditions. The DNA particles are then inserted into the channel to understand their physical properties as they migrate through a pressure-driven channel. Their extension due to stretching and folding is studied to understand the relaxation time of the DNA strand in the channel for a set of varied conditions. no-slip boundary region was altered to enforce the wall boundary conditions and to prevent the wall penetration by DPD fluid particles. The modified DPD weighting functions resolve the low Schmidt number and low viscosity typical of DPD and increase particle interaction between DPD fluid particles. However, this modification cannot be performed when simulating DNA particles as worm-like chain models as they do not generate accurate physical properties of DNA particles. The extensions of the DNA strands are simulated under the influence of different external forces and the relaxation time was reported.
Date
2011-12-01
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