NCX_Mj通道是一種鈉-鈣交換機制，可以快速的將生物細胞內的鈣離子與外部環境交換。本篇論文利用VMD觀察NCX_Mj通道，並利用Matlab建構NCX_Mj通道。

NCX Mj channel is a sodium-calcium exchanger, it can exchange calcium ions with the external environment of biological cells quickly. This thesis using VMD observes NCX_Mj channel and using Matlab construct NCX_Mj channel.

1. 緒論 1
2. PDB介紹 1
3.NCX_Mj介紹 2
4.VMD介紹 3
4.1 讀取資料 4
4.2 VMD Main 4
4.3 Graphical Representations 4
4.4 Color Controls 5
4.5 原子移動 5
4.6 計算原子距離、角度 6
4.7 Tk Console 6
4.8 存取資料 7
5. NCX_Mj通道之建構 7
5.1 VMD部分 7
5.1.1 尋找NCX_Mj外通道出口位置 7
5.1.2 NCX_Mj通道切層觀察 11
5.1.3 Ca2+外通道切層 12
5.1.4 Na+外通道切層 14
5.2 MATLAB部分 16
5.2.1 3V5U.pdb檔原子資料匯入excel 16
5.2.2 Matlab繪製通道流程圖 19
5.2.3 Ca2+外通道繪製 21
5.2.4 Na+外通道繪製 24
5.2.5 繪製通道 26
6. 主要結果 29
附錄 30
程式碼1：繪製Ca2+外通道程式碼 30
程式碼2：繪製Na+外通道程式碼 33
程式碼3：繪製NCX_Mj通道程式碼 36
參考文獻 39

1.W.-J. Yong, A computational study of ion conductance in the KCSA K+ channel using a Nernst-Planck model with explicit resident ions. J. Chem. Phys. 2009.131(21);215101.
2.RCSB PDB,http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/index.html
3.Wikipedia,http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/index.html
4.H.-J. Hsieh, Potential profiles inside the X-shape channel of NCX_Mj. National Hsinchu University of Education. 2014.
5.VMD,http://www.ks.uiuc.edu/Research/vmd/
6.Wikipedia,http://en.wikipedia.org/wiki/Visual_Molecular_Dynamics
7.Liao, J. et al., Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger. Science Signaling. 2012. 335(6069):686-690.
8.Colgate Mineralogy,http://classes.colgate.edu/rapril/geol201/summaries/radius.htm