半柔性鏈在侷限且具吸引力環境下動力學與靜力學研究

Static and dynamic properties of confined semi-flexible chain in attractive environments

簡瑋(Wei Chien)

指導教授 ： 陳彥龍

共同指導教授 ： 張嘉升(Chia-Seng Chang)

國立臺灣大學/理學院/物理研究所/博士(2018年)

https://doi.org/10.6342/NTU201800710

摘要

本論文聚焦於了解單一半柔性鏈在複雜且有特殊交互作用的環境下的動力學與靜力學性質。近年來，因具備定序與診斷的應用潛力，DNA在微流通道中的動力學很受關注。這些微流通道的幾何尺度小至20奈米、大至幾個微米。這樣的尺度跨越了DNA分子的迴轉半徑(the radius of gyration)與鏈的持續長度(persistent length)。許多實驗觀察到非預期的現象，例如DNA與同帶負電介面的相吸行為以及非典型的擴散行為。這些現象引起了我們的興趣。
我們使用介觀模型，系統性地利用電腦模擬計算去研究高分子在不同環境下的型態與動力學變化。這些環境參數包括表面的性質、環境的侷限性、高分子的鋼度等等。
主要結果分為兩個部分:
其一，我們量化界面的吸附性質。我們討論鏈長、鋼度、吸引力幾何尺度、吸引力強度對吸附的影響。並著重於討論空間侷限性和鏈的自我迴避性(self-avoidance)。這些都是在實際應用下可用來調變吸附的參數。結果顯示理想彈性高分子的臨界吸附強度只微弱地受環境侷限度影響。而有自我迴避性的彈性高分子，環境侷限度顯著地增加臨界吸附強度。
其二，我們研究DNA在具吸引力界面的微米柱陣列中的擴散行為。DNA的擴散行為與界面的吸附性質密切相關。我們可以觀察到在特定情況下，隨著柱陣列密度增加，擴散變得更快，和先前的實驗觀測吻合。我們更藉由微觀的圖像看到了這個由高分子型態波動所調製的傳輸行為。我們也初步的分析一個最簡單的模型應該具備的機制。
我們希望我們的工作能對提供設計微流通道晶片設計一個易理解的設計指標。此外，這個簡單系統也能幫助理解生物膜環境中複雜的輸送行為。

關鍵字

半柔性鏈 ； 高分子吸附 ； 非典型擴散 ； 侷限高分子 ； 微流控

並列摘要

This thesis focuses on understanding the static and dynamic properties of a single semi-flexible chain in complex, interactive environments. In recent years, lots of studies have investigated DNA molecules in microfluidics for the purpose of diagnostics and sequencing. These microfluidic devices scale down from a few micrometers to as small as 20 nanometers and approach to critical length scales of DNA molecules such as the radius of gyration and the persistence length. Experimental studies have reported unexpected phenomena such as like-charge attraction between DNA and the surface, abnormal diffusive behavior and drive our attention to those systems.
We aim to reconstruct the complex dynamics observed in experiments via mesoscopic computer simulations and systematically investigate the impacts on the conformation and transport of macromolecular in varied environmental conditions. Critical factors including surface properties, confinement, and polymer rigidity etc. are studied.
The results can be divided into two parts:
In the first part, we aim to quantify the surface adsorption properties. Parametric studies on factors including the chain length, the bending rigidity and the range of the attractive interaction are revisited and we put further interests on the effects of the confinement and the self-avoidance effects which are important factors controlled in advanced applications. It turns out that the critical point of adsorption for ideal flexible polymers depends weakly on confinement. However, the critical point of adsorption has significant increase for self-avoiding flexible polymers under strong confinement.
In the second part, we study the diffusive behavior of DNA in attractive micro-post arrays. The diffusive behavior in this environment is strongly dependent on the surface adsorption property, and we observe a regime where the polymer diffusivity increases as the post density increases which explains the phenomenon observed in previous experiments. We also identify the cross-post translation mechanism mediated by polymer conformation fluctuations and investigate how diffusion in this environment influenced by the adsorption strength and the chain length.
We hope our studies can provide a comprehensive guide for designing microfluidics devices with biotechnical applications and as a simple model system for studying complex transport phenomenon in crowded environments like the biomembrane.

並列關鍵字

Semi-flexible chain ； polymer adsorption ； abnormal diffusion ； confined polymer ； microfluidics

參考文獻

REFERENCE:

[1] C.-H. Hung, Tube-Like Motion of ds-DNA in Post Arrays Confined in Nanoslit, National Taiwan University Master Thesis, DOI (2009).

[2] P.-K. Lin, Statics and Dynamics of Single DNA Confined in Nanoslits, National Taiwan University Doctoral Dissertation DOI (2008).

[3] F.T. Chien, P.K. Lin, W. Chien, C.H. Hung, M.H. Yu, C.F. Chou, Y.L. Chen, Crowding-facilitated macromolecular transport in attractive micropost arrays, Sci Rep, 7 (2017) 1340.

[4] P.-k. Lin, C.-C. Hsieh, Y.-L. Chen, C.-F. Chou, Effects of Topology and Ionic Strength on Double-Stranded DNA Confined in Nanoslits, Macromolecules, 45 (2012) 2920-2927.