Klenin K, Merlitz H, Langowski J
Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg.
Biophys J. 1998 Feb;74(2 Pt 1):780-8. doi: 10.1016/S0006-3495(98)74003-2.
For the interpretation of solution structural and dynamic data of linear and circular DNA molecules in the kb range, and for the prediction of the effect of local structural changes on the global conformation of such DNAs, we have developed an efficient and easy way to set up a program based on a second-order explicit Brownian dynamics algorithm. The DNA is modeled by a chain of rigid segments interacting through harmonic spring potentials for bending, torsion, and stretching. The electrostatics are handled using precalculated energy tables for the interactions between DNA segments as a function of relative orientation and distance. Hydrodynamic interactions are treated using the Rotne-Prager tensor. While maintaining acceptable precision, the simulation can be accelerated by recalculating this tensor only once in a certain number of steps.
为了解读kb范围内线性和环状DNA分子的溶液结构及动力学数据，以及预测局部结构变化对这类DNA整体构象的影响，我们开发了一种高效且简便的方法，用于基于二阶显式布朗动力学算法构建程序。DNA由一系列刚性片段组成的链来模拟，这些片段通过用于弯曲、扭转和拉伸的谐振子势相互作用。静电作用通过预先计算的DNA片段间相互作用能量表来处理，该能量表是相对取向和距离的函数。流体动力学相互作用使用Rotne-Prager张量来处理。在保持可接受精度的同时，通过在一定步数内仅重新计算一次该张量，可加速模拟。
