DENATURATION AND PROPAGATION OF THE LOCALIZED EXCITATION IN DNA

The thermal denaturation and propagation of the localized excitation in desoxyribonucleic acid (DNA) molecules are studied in the unified way under a new Hamiltonian proposed in this work and the large amplitude motion of the DNA molecules is investigated during the propagation of the localized excitation. We discussed the nonlinear effect on the formation of the localized excitation, and showed that our model not only can reproduce the experimental results of the DNA thermal denaturation, but also can describe the process of the nonlinear localized excitation of fluctuational opening in DNA molecules.     

Theoretical Study on Effects of Salt and Temperature on Denaturation Transition of Double-stranded DNA

We investigate the statistical mechanics properties of a nonlinear dynamics model of the denaturation of the DNA double-helix and study the effects of salt concentration and temperature on denaturation transition of DNA. The specific heat, entropy, and denaturation temperature of the system versus salt concentration are obtained. These results show that the denaturation of DNA not only depends on the temperature but also is influenced by the salt concentration in the solution of DNA, which are in agreement with experimental measurement.     

脱氧核糖核酸的核磁共振研究简介

从NMR谱峰归属,NMR约束及结构计算,NMR谱的主要特征,化学位移的环流效应,以及溶液动力学等几个方面简要地介绍了核磁共振在DNA结构和动力学研究中的应用. 指出了DNA的NMR研究中存在着的一些问题. 这些问题主要包括：分子力场中的二面角参数不符合非规整DNA结构中的许多二面角;用分子模拟软件重建DNA结构时没有很好的重现性;DNA的化学位移环流效应理论尚未成熟;“无模型(model-free)”模型在定量解释异核稳态NOE时不理想. 然而,NMR所提供的结构和动力学信息仍然是十分重要的并且极大地深化了人们对DNA的了解.     

Fluctuations in order–disorder transitions in the DNA–ligand complexes with various binding mechanisms

The melting of the DNA–ligand complex is considered theoretically for the ligands binding with the DNA by two mechanisms. The obtained results describe the experimentally observed behavior of such quantities as the denaturation degree and the correlation length depending on the concentration of ligands. It is shown that the heat and cold denaturations of the DNA–ligand complexes exhibit the same cooperativity, as the heat denaturation of the pure DNA. At the same time, the temperature range of the cold denaturation is essentially narrower than the interval for the heat denaturation of the pure DNA and the DNA–ligand complexes.     

Statistical mechanics of thermal denaturation of DNA oligomers

Double stranded DNA chain is known to have non-trivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian. The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at different parts of the chain.     

Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent c, for which we find the new value c = 4 nu-1/2 such that the transition is second order with c = 1.85 < 2 in d = 3. We show that a finite stretching force F destabilizes DNA, corresponding to a lower melting temperature T(F), in agreement with single-molecule DNA stretching experiments.     

DNA melting induced by alcohols: Role of the solvent properties

Summary The isothermal denaturation of calf thymus DNA, induced by the presence of some monohydric alcohols in the solution, was investigated. Measurements were performed at a temperature (67.2°C) at which the denaturation, in the absence of alcohols, is about 20% and melting profiles at varying temperatures were also recorded. Results show that with increasing alcohol concentration and alkyl group size DNA denaturation first reaches a maximum and then falls back. This behaviour, ascribed to ?unusual? water properties as inferred also from compressibility measurements, indicates that hydrophobic and electrostatic effects are connected in a complex way. Partially supported by Consiglio Nazionale delle Ricerche, Italy.     

New results on the melting thermodynamics of a circular DNA chain

We investigate the impact of supercoil period and nonzero supercoil formation energy on the thermal denaturation of a circular DNA. Our analysis is based on a recently proposed generalization of the Poland-Scheraga model that allows the DNA melting to be studied for plasmids with circular topology, where denaturation is accompanied by formation of supercoils. We find that the previously obtained first-order melting transition persists under the generalization discussed. The dependence of the size of the order-parameter jump at the transition point and the associated melting temperature are obtained analytically.     

Thermal denaturation of fluctuating DNA driven by bending entropy

A statistical model of homopolymer DNA, coupling internal base-pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the fraction of denaturation bubbles and their correlation length is deduced. The thermal denaturation transition emerges naturally when the chain fluctuations are integrated out and is driven by the difference in bending (entropy dominated) free energy between broken and unbroken segments. Conformational properties of DNA, such as persistence length and mean-square-radius, are also explicitly calculated, leading, e.g., to a coherent explanation for the experimentally observed thermal viscosity transition.     

C60中非线性激发的动力学研究

用电子－晶格耦合的紧束缚模型和求解实时牛顿动力学方程的方法研究了Ｃ₆₀受光激发后的动力学过程，得到了受光激发后Ｃ₆₀分子的能量，键结构和电子状态的动态演化，结果表明光激发Ｃ₆₀分子演化成环状双极化子激子。该计算结果与中性富勒烯材料的荧光实验所得出的结论一致。 关键词：     

Nonlinear lattice dynamics of Bose-Einstein condensates

The Fermi-Pasta-Ulam (FPU) model, which was proposed 50 years ago to examine thermalization in nonmetallic solids and develop "experimental" techniques for studying nonlinear problems, continues to yield a wealth of results in the theory and applications of nonlinear Hamiltonian systems with many degrees of freedom. Inspired by the studies of this seminal model, solitary-wave dynamics in lattice dynamical systems have proven vitally important in a diverse range of physical problems-including energy relaxation in solids, denaturation of the DNA double strand, self-trapping of light in arrays of optical waveguides, and Bose-Einstein condensates (BECs) in optical lattices. BECs, in particular, due to their widely ranging and easily manipulated dynamical apparatuses-with one to three spatial dimensions, positive-to-negative tuning of the nonlinearity, one to multiple components, and numerous experimentally accessible external trapping potentials-provide one of the most fertile grounds for the analysis of solitary waves and their interactions. In this paper, we review recent research on BECs in the presence of deep periodic potentials, which can be reduced to nonlinear chains in appropriate circumstances. These reductions, in turn, exhibit many of the remarkable nonlinear structures (including solitons, intrinsic localized modes, and vortices) that lie at the heart of the nonlinear science research seeded by the FPU paradigm.     

白蛋白酸致变性的动态激光散斑研究

利用动态激光散斑的方法研究了白蛋白的酸致变性过程。首先,利用动态散斑理论模拟生成了动态散斑序列图;然后,利用模拟和实验散斑图的时间序列散斑图及其灰度共生矩阵对白蛋白的酸致变性过程进行了分析;接着,又利用灰度共生矩阵的惯性矩和不同阶段的四幅散斑图的平均对比度图对该过程进行了更深入的研究。理论模拟和实验研究结果表明,在白蛋白酸致变性过程中,胶体溶液中的蛋白质微粒的运动由剧烈逐渐变得缓慢;同时,微粒数量减少而微粒尺寸增加。研究表明,动态激光散斑方法是一种实时、快速、有效的研究白蛋白变性过程的新手段。     

单晶硅纳米薄膜面向导热MD研究的探讨

本文分析了经典分子动力学(Molecular Dynamics)技术在模拟厚度在纳米量级的单晶硅薄膜平行于薄膜平面方向的热导率时出现的用难,指出精确计算薄膜表面附近处的原子运动状态对于单晶硅纳米薄膜面向热导率的分子动力学模拟具有重要意义,并在此基础上提出采用基于分子动力学和预处理共轭梯度法(Preconditioned conjugate Gradients)的Ab Initio方案模拟面向热导率。     

核黄素与鲱鱼精DNA相互作用的荧光光谱

荧光光谱法研究了核黄素(RF)与鲱鱼精DNA的相互作用.考查了离子强度、温度及磷酸盐对RF-DNA体系的影响.结果表明,DNA的存在使得RF的荧光光谱发生了规律性猝灭,其猝灭机制为静态猝灭;运用Stern-Volmer方程对实验数据进行了分析,得到了猝灭常数为2.82×103L·mol-1、结合位点数为1.17.核黄素...     

Torsion and entropy driven denaturation of DNA

A unified theory of the denaturation transition having torsion energy as the control parameter has been formulated here in the framework of the mapping of a DNA molecule onto a Heisenberg spin system. The torsion energy incorporates the torque, tension and temperature, the latter being associated with the twist angle. The denaturation transition can be mapped onto the quantum phase transition induced by a quench when the temperature effect is incorporated in the quench time and torsion takes the role of the external field. The denaturation transition occurs when the entanglement entropy of the spin system vanishes.     

光谱法研究普利沙星与小牛胸腺DNA的结合作用

利用紫外光谱,荧光光谱及流体动力学方法,研究了普利沙星与小牛胸腺DNA的作用机理。讨论了不同浓度普利沙星与DNA作用的紫外光谱,荧光光谱,磷酸盐效应以及离子强度对两者相互作用的影响,测量了DNA的热变性温度和粘度。从紫外光谱图上看出DNA发生了明显的减色效应, 说明普利沙星可能与DNA发生作用。普利沙星的荧光光谱发生了有规律的猝灭,最大发射峰发生红移, 猝灭常数为3.1×104 L·mol-1, 为静态猝灭,表明普利沙星与DNA结合生成了二元复合物。磷酸盐效应表明普利沙星与DNA的磷酸基团不发生静电作用。普利沙星引起了DNA的热变性温度略微升高(≤7℃)和DNA粘度略微下降, 表明普利沙星与DNA之间不存在插入作用, 只是在DNA的外部发生沟槽作用。     

高压沿面放电烟气脱硫技术动态实验研究

本文针对高压沿面放电活化气体的烟气脱硫技术,在静态实验研究的基础上进行了实验室冷态动态的实验研究。设计了便于反应和测量的动态实验装置。实验解释了电子束法脱硫技术中导致氨气泄漏的部分原因,验证了高压沿面放电脱硫技术可以在较低的运行电压下,达到提高脱硫效率,减少氨气泄漏的作用。     

盐对DNA相变影响的非线性特性研究

在Prohofsky，Peyrard-Bishop等提出的描述DNA双螺旋分子结构模型以及实验测量的基础上 , 给出了与盐(指NaCl)浓度有关的哈密顿模型, 得到了非线性动力学方程及扭结孤波解.并 由此求出了DNA变性相变所需要的Peierls相变力. 进一步讨论了盐浓度对相界面和相变力的 影响, 得到的结果与实验测量一致. 关键词： DNA 盐浓度 相界面 相变力     

Supercoiling and denaturation of DNA loops

We study the statistical mechanics of small DNA loops emphasizing the competition between elasticity, supercoiling, and denaturation. Motivated by recent experiments and atomistic molecular dynamics simulation, we propose a new coarse-grained phenomenological model of DNA. We extend the classical elastic rod models to include the possibility of denaturation and nonlinear twist elasticity. Using this coarse-grained model, we obtain a phase diagram in terms of fractional overtwist and loop size that can be used to rationalize a number of experimental results which have also been confirmed by atomistic simulations.     

Random Walks and Polymers in the Presence of Quenched Disorder

After a general introduction to the field, we describe some recent results concerning disorder effects on both ‘random walk models’, where the random walk is a dynamical process generated by local transition rules, and on ‘polymer models’, where each random walk trajectory representing the configuration of a polymer chain is associated to a global Boltzmann weight. For random walk models, we explain, on the specific examples of the Sinai model and of the trap model, how disorder induces anomalous diffusion, aging behaviours and Golosov localization, and how these properties can be understood via a strong disorder renormalization approach. For polymer models, we discuss the critical properties of various delocalization transitions involving random polymers. We first summarize some recent progresses in the general theory of random critical points: thermodynamic observables are not self-averaging at criticality whenever disorder is relevant, and this lack of self-averaging is directly related to the probability distribution of pseudo-critical temperatures T _c(i,L) over the ensemble of samples (i) of size L. We describe the results of this analysis for the bidimensional wetting and for the Poland–Scheraga model of DNA denaturation.Conference Proceedings “Mathematics and Physics”, I.H.E.S., France, November 2005