以隨機旋轉動力學法模擬於微奈米界面DNA之鬆弛行為

Abstract

我們使用隨機旋轉動力學法(stochastic rotation dynamics，SRD)混和分子模擬法(molecular dynamics)來模擬DNA侷限在微奈米界面之鬆弛行為，並將結果與近年的實驗相驗證。 SRD模擬法藉由粗化(coarse-grain)流體粒子，以降低模擬所需時間，並仍可在介觀尺度下精確地模擬純流體的行為。DNA則以bead-spring model或Fraenkel spring model描述其在非侷限環境或侷限環境下之行為。結合兩者即可模擬DNA與流體之間的關係。 我們首先模擬在非侷限環境下單一DNA的環動半徑、擴散係數、鬆弛時間與高分子鏈長的關係，再與文獻比較以驗證我們的程式。接著，我們參考最近的實驗文獻，設計一微奈米界面之通道，將DNA置入奈米侷限夾縫中，使其橫跨兩微米區域，觀察當DNA之一端進入奈米通道後經由拉伸回縮(entropic recoil)與縮回(retraction)後至完全離開而恢復其纏繞型態之鬆弛過程。觀察並探討在不同通道高度長度下，拉伸回縮時DNA之長度與時間之關係式。本研究亦探討了在侷限環境下以Fraenkel spring 描述高分子之正確性。

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.