具有缺陷的DNA中碱基对呼吸的自组织临界性
Self-organised criticality in base-pair breathing in DNA with a defect
摘要：
我们分析了一个12个碱基对的DNA序列中的碱基对呼吸，其中心有一个有缺陷的碱基。我们使用全原子分子动力学（MD）模拟和随机微分方程系统（SDD）。在这两种情况下，傅立叶分析的轨迹揭示了自组织的关键行为的呼吸的碱基对。基间距离的傅里叶变换（FT）显示出幂律行为，梯度接近-1。尺度不变的行为，我们已经发现的碱基对呼吸对应于大规模DNA开放（或“融化”）的成核阶段，这个过程是一个（二阶）相变的观点提供了证据。虽然在我们的随机力的系统中引入了白噪声，FT的位移表现出粉红色的噪声，在AMBER/MD模拟的位移。
英文摘要：
We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FT) of the interbase distances show power-law behaviour with gradients close to -1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or 'melting') and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.
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