平行板纳米通道中生物分子迁移的分子模拟-JournalofNortheastern.PDF

第32 卷第7期 东 北 大 学 学 报 ( 自 然 科 学 版 ) Vol32, No. 7 2 0 1 1 年 7 月 Journal of Northeastern U ni ersity( Natural Science) Jul. 2 0 1 1 1 2 1 1 刘 坤 , 张晓玲 , 肖松文 , 巴德纯 ( 1. , 110819; 2. , 100076) : GROMACS , , 31nm , 3 : , , 2 500 kg/ m , ; , ; , : ; ; ; ; : T B 115 : A : 1005-3026( 2011) 07- 10 12-04 Molecular Simulation of Flow Characteristics of the Biomolecules and Ions in Paralle-l Plate Nanofluidic Channels 1 2 1 1 LIU Kun , ZHANG Xiao-ling , XIA OSong-wen , BA De-chun ( 1. School of Mechanical Engineering Automat ion, Northeastern Uni ersity, Shenyang 110819, China; 2. Capital Aerospace Machinery Company, Beijing 100076, China. Corresponding author : LIU Kun, E-mail: kliu @ mail. neu. edu. cn) Abstract: M olecular simulations w ere performed to simulate the transport process of biomolecules in paralle-l plate nanofluidic channels based on GROMACS program package. Models were built w ith a series of simplifications and assumptions and simulated the process in the 3. 1 nm high channel. Then the simulation results w ere discussed, such as the RM SD ( root mean square de iations) , density distribution of w ater molecules, and concentration distribution of the ions. T he follow ing conclusions w ere draw n: near the channel w all, w ater molecules delaminate and 3 form compact layers w ith a density high up to 2 500 kg/ m while the distribution is smooth in the middle area. The protein molecules pass through the channel along the electric field direction accompanying w ith rotations and transl