摘要翻译：
我们报告了DNA单链的模型计算，描述了发夹形成和熔融的平衡动力学和动力学。建模是在单基地的水平。用简单的聚合物模型描述钢绞线的刚度；本文报道了使用自由旋转链和离散Kratky-Porod模型进行的替代计算。茎的形成是根据Peyrard-Bishop-Dauxois哈密顿模型。开闭动力学用有效自由能景观中的扩散控制运动来描述。熔融曲线、熔融温度对环长度的依赖关系以及动力学时间尺度与荧光DNA信标形成poly(T)环的实验数据是半定量一致的。在形成聚(A)环的发夹中，丝股刚度的变化不足以解释闭合活化焓大和环长依赖性强的原因。对DNA或RNA单链建模的含义进行了讨论。
---
英文标题：
《Modeling DNA beacons at the mesoscopic scale》
---
作者：
Jalal Errami, Michel Peyrard and Nikos Theodorakopoulos
---
最新提交年份：
2007
---
分类信息：

一级分类：Physics        物理学
二级分类：Soft Condensed Matter        软凝聚态物质
分类描述：Membranes, polymers, liquid crystals, glasses, colloids, granular matter
膜，聚合物，液晶，玻璃，胶体，颗粒物质
--
一级分类：Physics        物理学
二级分类：Statistical Mechanics        统计力学
分类描述：Phase transitions, thermodynamics, field theory, non-equilibrium phenomena, renormalization group and scaling, integrable models, turbulence
相变，热力学，场论，非平衡现象，重整化群和标度，可积模型，湍流
--
一级分类：Physics        物理学
二级分类：Biological Physics        生物物理学
分类描述：Molecular biophysics, cellular biophysics, neurological biophysics, membrane biophysics, single-molecule biophysics, ecological biophysics, quantum phenomena in biological systems (quantum biophysics), theoretical biophysics, molecular dynamics/modeling and simulation, game theory, biomechanics, bioinformatics, microorganisms, virology, evolution, biophysical methods.
分子生物物理、细胞生物物理、神经生物物理、膜生物物理、单分子生物物理、生态生物物理、生物系统中的量子现象（量子生物物理）、理论生物物理、分子动力学/建模与模拟、博弈论、生物力学、生物信息学、微生物、病毒学、进化论、生物物理方法。
--

---
英文摘要：
  We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are discussed.
---
PDF链接：
https://arxiv.org/pdf/706.2458