2004-11-012024-05-18https://scholars.lib.ntu.edu.tw/handle/123456789/710889摘要：我們致力於開發一套在理論上支持並有實用性的多尺度模擬計算.在這套方法中,把一&#32675;原子當成模型單元,稱為blob.我們不直接進行全原子分子模擬,轉而研究如何建構一個粗粒化模型,使得粗粒化blob 間勢能可由潛藏的原子間作用勢能組成.我們建議再繼續發展此粗粒化模型並且測試應用到從小的有機官能基分子到生物巨分子的可行性.對小分子我們可用先進的電子結構計算來產生高品質全始算勢能資料.對於巨分子,我們用良好測試的原子力場來取得分子間勢能,我們便能進行聚合物介面多尺度模擬.本計畫著重於兩個目前實驗上有興趣的主題. 一是星形塊狀異質PINIPAM-PEG 聚合物的展延或凝聚動力學.另一是有關使用生物晶片探測CRP 蛋白質的研究. 為了模擬PNIPAM 的官能基，建議使用amide/acrylamide 和異丙烷當成blob，而為了模擬PEG 的官能基，則採用dimethylether 當成blob。我們打算以雙體進行以MP2 / 6 - 31G 層級計算或更高層級 ( 如CCSD (T)方法)的全始算。對大分子,如CRP,使用全始算或半經驗式方法計算分子間的作用力是不切實際的.為此我<br> Abstract: In the past two years, we have devoted to developing a theoretically sound and practically useful multiscale simulation scheme. In this methodology groups of atoms are treated as model units, called blobs. Instead of performing full atomistic molecular simulations for a polymeric system, we were motivated to construct a coarse grained blob model where a coarse grained inter-blob potential can be built from the embedded interatomic potentials. We propose to further develop the coarse-grained rigid blob model and test its applicability to systems from small organic functional groups towards biomacromolecules. For small molecules we use advanced electronic structure theories, such as the density functional theory (DFT) and quantum chemistry methods, to generate high quality ab initio potential energy data. For macromolecules, we resort to well tested atomic force fields to obtain the intermolecular potentials. These data are then used to obtain the required parameters of the derived inter-blob potentials through nonlinear modeling. Using these potentials, we can perform mesoscale molecular simulations on polymeric systems. In this proposal we focus on two topics of recent experimental interests. One is the swelling/unswelling dynamics of star block PNIPAM-co-PEG polymers and the other is the detection of CRP’s using biosensors. To model the functional groups of a PNIPAM, we propose to consider amide/acrylamide, and iso-propane as our model units. To model the functional groups of a PEG, we propose to consider dimethylether as the model unit. We propose to perform ab initio calculations at the MP2/6-31G level or above (such as the CCSD(T) method using pvXZ type basis functions) for the dimers. For macromolecules such as CRP’s, ab initio calculations or semi-empirical methods are not feasible for obtaining intermolecular interactions. We propose to use atomic force fields (AMBER or CFF) to calculate the inter-CRP, inter-anti-CRP and CRP-anti-CRP potentials for several different configurations. We expect to obtain accurate ab initio intermolecular potential data for small molecules, which will be used to construct suitable coarse grained intermolecular interactions. For large molecules, we will use atomic force fields to obtain intermolecular potential data and then coarse grained interactions. We expect to perform several molecular dynamics simulations and geometry optimizations using the constructed potentials多尺度模擬粗粒化模型分子間作用勢能聚合物multiscale simulationcoarse grained modelintermolecular potentialpolymer