Simulating the Recoil of DNA at Micro-Nanofluidic Interfaces Using Stochastic Rotation Dynamics
Date Issued
2013
Date
2013
Author(s)
Huang, Po-Han
Abstract
We use stochastic rotation dynamics (SRD) and molecular hybrid method to simulate the the recoiling process of DNA at two micro-nanofluidic interfaces bridged by a nanoslit, and make comparison with the recent experiment.
SRD uses coarse-grained fluid particles to describe the behavior of solvent, and therefore it is suitable for simulating solvent behavior at mesoscale. On the other hand, DNA is depicted by the bead-spring model and the Fraenkel spring model in unconfined and confined environment, respectively. The interaction between SRD particles and DNA is modeled by MD simulations. Thus, the system involving both fluid and DNA can be described by the SRD-MD hybrid method.
In this thesis, we first simulate the relation between the radius of gyration, the diffusivity and the relaxation time of DNA versus its contour length in unconfined system, and compare the results with literature to verify our code.
We then follow the DNA tug-of-war experiments of Yeh et al. to simulate DNA recoiling process at a nano-micro interface. We study the stretch-recoiling behavior of DNA under different slit lengths and heights, and discuss the relation of DNA projected length as a function of time. We also show that the Fraenkel spring model can depict the behavior of polymer well under confinement.
Subjects
隨機旋轉動力學法
SRD-MD 混合模擬法
介觀尺度
侷限環境
拉伸回縮
Type
thesis
File(s)![Thumbnail Image]()
Loading...
Name
ntu-102-R00524013-1.pdf
Size
23.54 KB
Format
Adobe PDF
Checksum
(MD5):e877f21429cc585e50962f29b8338a01