Monte Carlo Study on Spontaneous Recoil of Confined DNA Chain

在外加电场作用下,长链DNA分子的一部分链段进入构象熵较小的受限区域,其余部分仍滞留在高熵区. 电场撤除后,位于受限区域的DNA链段将自发回弹到高熵区域. 采用键涨落算法对这一动力学过程进行了模拟研究. 链段的回弹速度逐渐增大,这与实验结果是一致的. 模拟结果揭显示,增加受限区域的障碍物的尺寸或缩小间距都会导致DNA链段回弹速度的增加. 进一步的分析表明链单元在受限区域内的有效熵正比于其在受限区所能到达部分占总受限区域面积的比例.     

正丙醇、正丁醇和正辛醇中Debye弛豫动力学的测量与分析

单羟基醇具有其他液体通常所不具备的Debye弛豫过程,随着研究工作的开展,一些与之相关的新现象和新问题也逐渐被发现,深化了对物质结构和动力学的认知.为了进一步研究Debye弛豫过程的动力学及其受分子构成影响的情况,本文通过介电谱方法对3种无支链无侧基伯醇中的Debye弛豫进行测量与分析,揭示了该过程的一些变化规律.在正丙醇、正丁醇和正辛醇这3种伯醇中Debye过程的特征温度、VogelFulcher-Tammann (VFT)温度的倒数和强度参量以及弛豫单元在高温极限下的激活能和固有振动频率的对数几乎都随分子内碳原子数的增加而线性增加.但是VFT温度变化不大,具有一致性,表明这3种单羟基醇中Debye过程的弛豫单元应该相同,进一步验证了Debye弛豫来源于氢键分子链中羟基的观点.将样品的沸点和熔点等信息与上述激活能的变化进行对比,表明氢键作用与分子之间的整体相互作用具有正相关性.另外,将强度参量的变化情况与相关理论进行结合,给出了研究液体脆性的一个可能视角;三者弛豫过程与乙醇结果的对比,显示出Debye弛豫与α弛豫的分离程度会受到分子链长的影响,也为Debye弛豫的研究提供了切入点.这...     

DNA分子链电子结构特性研究

在单电子紧束缚近似下，建立了一维无序二元DNA分子链模型，计算了链长为2×10⁴个碱基对的DNA分子链的电子态密度、局域化特性，并探讨了碱基对的不同组分、格点能量无序度对电子局域态的影响.结果表明：由于DNA分子链中格点能量无序及碱基对的不同组分的存在，其电子波函数呈现出局域化的特性，而局域长度作为衡量电子局域化程度的一个尺度，受碱基对的组分及格点能量无序度的影响. 关键词： DNA分子链 电子结构 电子局域态 局域长度     

一维导电聚合物中激发态的链间弛豫

本文系统地研究了顺式高强聚乙炔的Raman和发光光谱,根据其Raman和发光光谱随激发能量的变化规律,以及分子链之间距离的改变对这种变化规律的影响,证明了聚乙炔中存在着激发态的链间弛豫,井且,这种弛豫过程随着分子链之间距离的减小而被加快.     

一维导电聚合物中激发态的链间弛豫

本文系统地研究了顺式高强聚乙炔的Raman和发光光谱,根据其Raman和发光光谱随激发能量的变化规律,以及分子链之间距离的改变对这种变化规律的影响,证明了聚乙炔中存在着激发态的链间弛豫,井且,这种弛豫过程随着分子链之间距离的减小而被加快.     

激子旋转弛豫对低掺杂卟啉侧链聚合物荧光衰变过程的影响

利用激子旋转扩散理论研究了一类低掺杂卟啉侧链聚合物中卟啉侧链基团的旋转对其发光动力学过程的影响.研究表明,卟啉侧链基团的旋转行为是导致激发态无辐射能量弛豫的重要途径.基团旋转越容易,能量弛豫速度越快,这可导致一个快速的荧光衰变动力学过程.在卟啉低掺杂浓度和聚合物分子链间距离较大的情况下,卟啉侧链基团的旋转成为影响荧光寿命和发光效率的主要因素.对实验测得的两种样品的荧光弛豫过程进行了拟合,理论结果与实验结果符合较好. 关键词： 激子旋转弛豫 瞬态荧光 卟啉侧链聚合物     

DNA分子链的电子局域性质及电导的研究

将一维随机二元固体模型应用于DNA分子链，利用传输矩阵方法来研究系统电子态的局域性质并进而讨论系统的导电性质.对一个链长为50000个碱基对的DNA序列，数值分析了局域长度和电导随碱基对的摩尔百分数、本征能量和无序度的变化关系.结果表明，系统的局域长度和电导强烈地依赖于能量，在能带中心部分局域长度大于边沿部分.无序度也在一定程度上影响着局域长度，双方成反向变化的关系.对有限长度的DNA分子链，局域长度体现出明显的对碱基对摩尔百分数的依赖关系，对正常成分比例的随机DNA序列，在所有能量范围内系统的态都是局域的，系统的电导很小，系统呈现绝缘体行为.仅当一种碱基对在序列中所占比例很小时，系统中可以发现与特定分立能量值相对应的“扩展态”存在，处在这些态下的系统有较大的电导，但这些扩展态是不稳定的，在热力学极限之下会消失. 关键词： DNA分子链 电子局域 局域长度 电导     

DNA在熵受限管道中穿越过程的计算机模拟

利用Metropolis Monte-Carlo动力学方法结合键长涨落算法，模拟了单链DNA分子在电场作用下穿越熵受限管道的动力学过程.结果表明，DNA分子穿越管道时将经历无规迁移、受限迁移及快速迁移等几个显著不同的阶段.平均迁移率随外场增加而增大并最终达到饱和值μ0，受限时间的对数与所加场强的倒数之间基本满足线性关系.模拟结果不仅与文献所给的实验结果基本一致，而且还可以提供实验不能直接观察到的DNA分子较为详细的穿越过程.     

DNA分子力学性质的测量

利用单分子实验技术测量了DNA分子的力学性质.通过生化手段将单根DNA分子连在顺磁小球与玻璃侧壁之间,利用磁铁对顺磁球施加力进而拉伸DNA.图像分析得到小球运动的轨迹以及DNA的长度,利用均分定理可以求得施加的外力.测量发现在外力作用下DNA分子的力学反应与高分子物理学的蠕虫状链模型符合良好.     

分子串模型中空间弛豫模式的弛豫动力学的蒙特卡罗模拟

基于玻璃化转变的分子串模型的分子串弛豫方程,提出了更为精确的模拟分子串中所有空间弛豫模式(SRM)的蒙特卡罗模拟方案. 模拟得出各个SRM的弛豫时间随温度和分子串长度的变化结果与分子串模型中分子串弛豫方程的预言完全一致,即理论预期和模拟结果相互印证. 应当指出,分子串能否作为液态中集体单元的必要条件是在考虑到分子串之间的不均匀随机相互作用后,分子串的所有SRM的定性特征是不能改变的,这就需要对不同分子串的SRM之间的耦合进行研究. 但是迄今为止,仍未发现相关的严格解,仅有近似的自洽弛豫平均场方法. 由此可知,所提出的模拟方案为研究不同分子串的SRM之间的耦合(包括上述自洽场的可行性)提供了必要的基础. 关键词： 玻璃化转变 弛豫动力学 蒙特卡罗模拟 分子串     

方阱链流体在固液界面分布的密度泛函理论研究

应用Yethiraj的加权密度近似泛函理论研究平板狭缝中方阱链流体的密度分布，系统的Helm holtz自由能泛函分为理想气体的贡献利剩余贡献两部分，其中剩余贡献部分分别采用刘洪 来等人建立的基于空穴相关函数的方阱链流体状态方程和Gil-Villegas等人提出的统计缔合 流体理论状态方程(SAFT-VR)结合简单加权密度近似计算.考察了不同链长、温度、系统密度 和壁面吸引强度下平板狭缝中方阱链流体的密度分布，并与Monte Carlo(MC)模拟结果进行 了比较.结果表明采用不同的状态方程对密度分布的计算有明显的影响，对于受限于硬壁狭 缝中的方阱链流体，温度和密度比较高时，两种状态方程计算的结果均与MC模拟符合得比较 好，在低温和低密度下效果变差，SAFT-VR方程的计算结果更接近于MC模拟结果.对于受限于 方阱壁狭缝中的方阱链流体，由于系统密度分布的非均匀性加强，采用两种状态方程计算的 结果均与MC模拟结果有一定偏差，寻找更合适的权重函数是进一步改进的关键. 关键词： 密度泛函理论 非均匀流体 密度分布 固液界面 方阱链     

Dynamics of polymer chains in confined space. A computer simulation study

We studied the properties of simple models of star-branched polymer chains confined in a slit. The chains were constructed of united atoms (segments) and were restricted to vertices of a simple cubic lattice. We modeled good solvent conditions and thus the chains interacted with the excluded volume only. The macromolecules were put between two parallel and impenetrable surfaces and the surfaces were attractive for polymer segments. The properties of the model chains were determined by means of Monte Carlo simulations with a sampling algorithm based on chain's local changes of conformation. The differences and similarities in the structure for different adsorption regimes and the size of the slit were shown and discussed. The dependence of the short- and long-time scale dynamic behavior of chains on these factors was determined.     

Absence of simulation evidence for critical depletion in slit pores

Recent Monte Carlo simulation studies of a Lennard-Jones fluid confined to a mesoscopic slit pore have reported evidence of "critical depletion" in the pore local number density near the liquid-vapor critical point. In this Brief Report we demonstrate that the observed depletion effect is in fact a simulation artifact arising from small systematic errors associated with the use of long range corrections for the potential truncation. Owing to the large near-critical compressibility, these errors lead to significant changes in the pore local number density. We suggest ways of avoiding similar problems in future studies of confined fluids.     

Intersubband relaxation of hot carriers in quantum well systems

We use an ensemble Monte Carlo simulation of coupled electrons, holes and nonequilibrium polar optical phonons in multiple quantum well systems to model the intersubband relaxation of hot carriers measured in ultra-fast optical experiments. We have investigated the effect of various models of confined photon modes on the energy relaxation and intersubband transition rate in single quantum well and coupled well systems. In particular, the symmetry of the atomic displacement with respect to the quantum well has a marked effect on the relative intersubband versus intrasubband scattering rates, depending on whether one considers electrostatic boundary conditions(slab modes) or mechanical boundary conditions(guided modes). In single quantum wells systems, the overall intersubband relaxation time is not found to be strongly dependent on the confined mode model used due to competing effects of hot phonons and the relative intrasubband scattering rates. For coupled well systems, the relaxation rate is much more dependent on the exact nature of the phonon amplitude. Large effects are found associated with localized AlAs interface modes which dominate the intersubband relaxation time.     

The mica slit-pore as a tool to control the orientation and distortion of simple liquid monolayers

Grand canonical ensemble Monte Carlo computer simulations have been used to study mono-layer octamethylcyclotetrasiloxane (OMCTS) and cyclohexane films confined between mica-like surfaces to determine the effect of the mica surfaces on the orientation and distortion of the films at different surface alignments. The film molecules are packed as a highly ordered lattice. The orientation of the lattice is fixed relative to the mica surfaces and depends on the size of the film molecule. Registry shifts distort the film lattice by effectively stretching it along a particular direction that depends on the size of the film molecule. For a particular registry, OMCTS and cyclohexane monolayers are stretched in perpendicular directions. Coupling between the monolayers and the mica surfaces generates a nonzero shear stress when the surfaces are out of alignment, but the film does not become disordered or melt. It is possible that precisely controlled solid surfaces could be used to create packed arrays of film molecules with desired orientation and degree of distortion that may be useful in nanotechnological applications.     

Evaluation of bridge function for hard sphere fluid confined in a narrow slit-pore via TMMC Mayer-sampling

The bridge function required to yield a singlet integral equation (IE) up to the second order in density expansion for the hard sphere fluid confined in a slit-pore is evaluated. The slit-fluid bridge function can be divided into wall-particle bridge diagrams with h _b-bond, which were evaluated by recently proposed Transition Matrix Monte Carlo (TMMC) Mayer-sampling method. The bulk-fluid total correlation function h _b(r) used in cluster integrals is determined by solution of the bulk-fluid Ornstein–Zernike (OZ) equation with a hypernetted chain closure (HNC). The calculation is performed for the reduced density of bulk fluid in equilibrium with the fluid in slit-pores from 0.3 to 0.7 with narrow slit width of 3.0σ and 4.0σ. The quantity of the slit-fluid bridge function is assessed by comparison of the density profile obtained from the singlet IE theory and the grand canonical Monte Carlo (GCMC) simulation. Good agreement between the proposed approach and the GCMC data is observed. The reduced normal pressure is also calculated, and agrees well with the simulation data at low to medium densities but becomes a little larger at high density. It is expected that the result can be improved by adding higher order bridge coefficients. The direct evaluation of the slit-fluid bridge function seems to be practical since a great improvement of the quality of the singlet IE theory has been achieved for predicting the structural and thermodynamic properties of fluids confined in narrow slit pores.     

单分子荧光过程的Monte-Carlo模拟

从单分子发光过程中电子在激发态上的停留时间t服从P(t)=γe^-γt分布出发,对单分子荧光过程进行M-C(Monte-Carlo)随机试验,得到了单分子的激发态相邻两次发光的时间间隔的统计结果以及单分子荧光强度的自相关函数,并对其进行了详细地讨论,这些结果与目前文献报道的实验结果相一致.     

Grand Canonical Ensemble Monte Carlo Simulation of Depletion Interactions in Colloidal Suspensions

Depletion interactions in colloidal suspensions confined between two parallel plates are investigated by using acceptance ratio method with grand canonical ensemble Monte Carlo simulation. The numerical results show that both the depletion potential and depletion force are affected by the confinement from the two parallel plates. Furthermore, it is found that in the grand canonical ensemble Monte Carlo simulation, the depletion interactions are strongly affected by the generalized chemical potential.     

玻璃化转变的分子串模型中分子串弛豫模式的计算机模拟

基于玻璃化转变的分子串模型的哈密顿量(Hamiltonian),提出了模拟分子串第一和第二弛豫模式的蒙特卡罗(Monte Carlo)模拟方案.模拟得出的第一和第二弛豫模式的弛豫时间,与分子串模型中分子串弛豫方程所预言的结果完全一致,即理论预期和模拟结果相互印证.这不仅说明了分子串模型的分子串弛豫方程、至少是第一和第二弛豫模式的理论预言的正确性,同时也表明了本文所提出的模拟方法的有效性,并进一步明晰了分子串中分子的随机涨落和跃迁运动的图像,也为三态甚至是多态的分子串弛豫动力学研究,以及对进一步模拟分子串之 关键词： 弛豫动力学 蒙特卡罗模拟 分子串