以隨機旋轉動力學法模擬侷限於二維狹縫中DNA之行為

Abstract

我們使用隨機旋轉動力學法（stochastic rotation dynamics，SRD模擬法）配合分子模擬法(molecular dynamics) 模擬DNA在狹縫型侷限通道間的行為，計算DNA於平衡狀態下的靜態與動態性質，並將結果與近年相關的實驗結果相驗證。 SRD模擬法屬於介觀尺度的模擬，經由粗化（coarse-grained）過程可大幅降低系統所需計算的流體粒子數，但仍能精確地模擬單純流體的行為。DNA則以bead-spring model描述，整體系統則以SRD-MD hybrid method模擬DNA分子在流體中的行為。 我們首先以SRD模擬非穩態的Poiseuille flow和Couette flow，再將模擬結果與Navier-Stokes equation之解析解比較，確定SRD模擬之正確性。接著我們再模擬單一DNA在平衡狀態下的鬆弛與擴散情形，驗證理想鏈與真實鏈之DNA本身的環動半徑、鬆弛時間與擴散係數和高分子鏈長的關係符合理論與文獻值。 由於SRD模擬法可簡易地加入或移除DNA分子間的流體動力作用（hydrodynamic interaction），因此我們選取適當長度的DNA置入不受侷限與受侷限的通道中，發現即使在DNA受侷限時，流體動力作用依舊對DNA的行為有不可忽略的影響性。 最後，我們模擬DNA在侷限於平板型狹縫中的行為，其靜態與動態性質和DNA鏈長與侷限強度間的關係與最近發表的實驗結果十分接近，藉此與blob theory比較，確認DNA的虛擬圓球（blob）在侷限通道中受到不完全的流體動力作用影響，虛擬圓球內應為部分排液（partial draining），而非不排液（nondraining）的現象。

We simulate the behavior of DNA in slit-like confinement using stochastic rotation dynamics(SRD) and molecular dynamics hybrid method. We examine the static and dynamic properties of DNA at equilibrium, and make comparison with the recent experimental observation. SRD is a particle-based mesoscale simulation method which coarse-grains small fluid molecules to large fluid parcels, but it still can simulate the large length scale and long-time scale behavior of pure solvents precisely. The behavior of DNA is simulated using bead-spring model with molecular dynamics. The complex fluid system consists of simple fluid and DNA is then described by the SRD-MD hybrid method. We first verify the ability of SRD to simulate the behavior of simple fluids. The results of SRD for unsteady Poiseuille flow and Couette flow agree perfectly with the theoretical prediction given by the exact solution of the Navier-Stokes equation. Next, we simulate the relaxation and diffusion of single DNA molecule at equilibrium. The scaling between radius of gyration, relaxation time and diffusivity versus DNA length is also in agreement with the theoretical prediction and experimental data. One important feature of SRD is that it can easily “turn” on or off the hydrodynamic interaction between DNA molecules. Using this feature, we discover that the hydrodynamic interaction has significant effects on DNA dynamics, even when DNA is highly confined. This is different from the common anticipation based on polymer physics. Finally, we simulate the behavior of DNA confined in slit-like geometry. The scaling of static and dynamic properties with DNA length and slit height agrees with recently experiment results. We compare the results with blob theory and confirm the blobs in confinement are partial draining, not nondraining.