生物介质中加速离子诱导shock waves的分子动力学研究
Molecular dynamics study of accelerated ion-induced shock waves in biological media
摘要：
我们提出了一个分子动力学研究的影响，碳和铁离子诱导冲击波的DNA双链体在液态水。我们使用MBN Explorer模拟包中实现的CHARMM力场来优化和平衡不同大小和形状的液体水箱中的DNA双链体。根据离子沉积的能量激发水分子的平移和振动自由度，并模拟了液态水中的后续冲击波。所产生的压力波进行了研究，并与分析流体动力学模型，作为一个基准，用于评估模拟箱的适用性进行了比较。DNA主链键中的能量沉积也被监测为生物损伤的估计，这超出了分析模型的可能性。
英文摘要：
We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which lies beyond the possibilities of the analytical model.
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