完全非均匀DNA链中的非线性分子激发

DNA分子链中的微扰孤子激发

Perturbed soliton excitations in DNA molecular chain

在动态平面-碱基旋转体模型下，考虑碱基在垂直于螺旋轴的平面内的角旋转，研究了周期性非均匀DNA双螺旋链的非线性动力学。动力学是由扰动sine-Gordon方程。利用多尺度孤子微扰理论得到了微扰孤子解。微扰扭结-反扭结孤子代表了DNA中具有涨落的开态构型的形成。

扭转孤子在实DNA链中的传输

Propagation of twist solitons in real DNA chains

我们报告的数值研究孤子在一个真正的DNA链（人类腺病毒2）中的传播，使用一个现实的DNA扭转动力学模型，这充分考虑到在真正的链的不均匀性。我们发现，扭转孤子传播相当长的距离（2 - 10倍的直径）之前停止由于声子发射。我们的结果表明，扭曲孤子可能存在于真正的DNA链，并在更一般的水平上，孤子的传播可以发生在高度不均匀的介质。

Nonlinear dynamics of DNA systems with inhomogeneity effects

We investigate the nonlinear dynamics of the Peyrard-Bishop DNA model taking into account site dependent inhomogeneities. By means of the multiple-scale expansion in the semi-discrete approximation, the dynamics is governed by the perturbed nonlinear Schrodinger equation. We carry out a multiple-scale soliton perturbation analysis to find the effects of the variety of nonlinear inhomogeneities on the breatherlike soliton solution. During the crossing of the inhomogeneities, the coherent structure of the soliton is found stable. The global shape of the inhomogeneous molecule is merged with the …

螺旋DNA中的类孤子碱基对开口：与helimagnet和胆甾类的类比

Soliton-like base pair opening in a helicoidal DNA: An analogy with helimagnet and cholesterics

我们提出了一个DNA动力学模型，通过扭曲变形引入螺旋结构，类似于helimagnet和胆甾相液晶系统的结构。在这种情况下的动力学被发现是由完全可积的sine-Gordon方程，其中承认扭结-反扭结孤子与增加的宽度表示宽碱基对开放配置的DNA。结果表明，螺旋度引入了长度尺度的变化，从而提供了一个更好的表示在DNA中的碱基对开放。

粘性介质中蛋白质分子诱导的DNA双螺旋结构的碱基对开放和气泡输运

Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium

研究了在粘性介质中，在生理温度下，蛋白质-DNA分子系统的非线性动力学，将DNA看作是一组耦合的线性链，蛋白质以线性链的形式沿着DNA滑动.上述分子系统的非线性动力学一般由扰动的非线性薛定谔方程控制。在非粘性极限下，方程化为完全可积的非线性薛定谔方程，该方程存在N个孤子解。DNA碱基的孤立子激发使DNA碱基对局部打开，并以气泡的形式沿DNA链传播。这可能代表在转录过程中当RNA聚合酶结合到DNA双螺旋链中的启动子位点时产生的气泡。通过将周围环境的粘性效应视为弱扰动，利用微扰理论求解了扰动的NLS方程，结果表明，溶剂在周围环境中的粘性对孤子的振幅有阻尼作用。

Flat-floor bubbles, dark solitons, and vortices stabilized by inhomogeneous nonlinear media

We consider one- and two-dimensional (1D and 2D) optical or matter-wave media with a maximum of the local self-repulsion strength at the center, and a minimum at periphery. If the central area is broad enough, it supports ground states in the form of flat-floor \textquotedblleft bubbles", and topological excitations, in the form of dark solitons in 1D and vortices with winding number $m$ in 2D. Unlike bright solitons, delocalized bubbles and dark modes were not previously considered in this setting. The ground and excited states are accurately approximated by the Thomas-Fermi expressions. The …