Department of Chemical Engineering and Material Science, University of Minnesota-Twin Cities , 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA.
Biomicrofluidics. 2015 Apr 7;9(2):024112. doi: 10.1063/1.4917269. eCollection 2015 Mar.
We use Brownian dynamics with hydrodynamic interactions to calculate both the Kirkwood (short-time) diffusivity and the long-time diffusivity of DNA chains from free solution down to channel confinement in the de Gennes regime. The Kirkwood diffusivity in confinement is always higher than the diffusivity obtained from the mean-squared displacement of the center-of-mass, as is the case in free solution. Moreover, the divergence of the local diffusion tensor, which is non-zero in confinement, makes a negligible contribution to the latter diffusivity in confinement. The maximum error in the Kirkwood approximation in our simulations is about 2% for experimentally relevant simulation times. The error decreases with increasing confinement, consistent with arguments from blob theory and the molecular-weight dependence of the error in free solution. In light of the typical experimental errors in measuring the properties of channel-confined DNA, our results suggest that the Kirkwood approximation is sufficiently accurate to model experimental data.
我们使用布朗动力学与流体力学相互作用来计算 DNA 链的 Kirkwood（短时间）扩散系数和长时间扩散系数，范围从自由溶液到德热内（de Gennes） regime 的通道限制。限制内的 Kirkwood 扩散系数总是高于从质心均方位移获得的扩散系数，就像在自由溶液中的情况一样。此外，在限制内不为零的局部扩散张量的发散对限制内的后者扩散系数的贡献可以忽略不计。在我们的模拟中，Kirkwood 近似的最大误差约为 2%，对于实验相关的模拟时间。随着限制的增加，误差减小，这与 blob 理论和自由溶液中误差的分子量依赖性一致。考虑到测量通道限制 DNA 特性的典型实验误差，我们的结果表明，Kirkwood 近似足以准确地模拟实验数据。
