DNA超分子水凝胶的粗粒化建模与模拟

DNA超分子水凝胶在生物、医学领域具有广阔的应用前景,基于计算模拟技术研究其分子结构与其宏观性能关系具有重要意义.归因于其复杂的结构和较大的相关时间空间尺度,目前针对DNA水凝胶的分子建模与模拟研究比较缺乏.本文建立了一种DNA水凝胶的粗粒化模型,采用分子动力学模拟的方法针对一种模块化纯DNA水凝胶进行了研究.模拟结果表明其凝胶态介观结构为多孔海绵状,其交联度与水凝胶的浓度成正相关,并得出了其转变温度的范围等.模拟结果与相关实验定性或半定量符合,表明该模型可能用于该模块化DNA水凝胶等类似系统的结构功能关系研究.     

Active thermophoresis and diffusiophoresis

Thermophoresis and diffusiophoresis respectively refer to the directed drift of suspended particles in solutions with external thermal and chemical gradients, which have been widely used in the manipulation of mesoscopic particles. We here study a phoretic-like motion of a passive colloidal particle immersed in inhomogeneous active baths, where the thermal and chemical gradients are replaced separately by activity and concentration gradients of the active particles. By performing simulations, we show that the passive colloidal particle experiences phoretic-like forces that originate from its interactions with the inhomogeneous active fluid, and thus drifts along the gradient field, leading to an accumulation. The results are similar to the traditional phoretic effects occurring in passive colloidal suspensions, implying that the concepts of thermophoresis and diffusiophoresis could be generalized into active baths.     

统计物理和复杂系统专题编者按

从20世纪中叶至今,复杂系统研究迅速发展,成为了引人注目并具有广泛应用的新领域.复杂系统要么具有结构的复杂性,要么具有演化的复杂性,在多数情况下二者兼具.不同于传统物理学通常处理的规则介质,许多复杂系统具有复杂结构,近年来受到极大关注的复杂网络结构就是其中最典型的代表.同时复杂系统也可表现为演化行为的多样性和复杂性.即便系统结构并不复杂,系统中的非线性相互作用可能产生复杂的演化行为,包括:形形色色的不稳定性;丰富的斑图动力学;各种各样的自组织、涌现及进化行为等等.物理学从一开始就深深进入了复杂系统研究领域,其中统计物理无疑是研究和理解复杂系统最主要的工具.     

Molecular dynamics simulations on the dynamics of two-dimensional rounded squares

The collective motion of rounded squares with different corner-roundness ζ is studied by molecular dynamics(MD)simulation in this work. Three types of translational collective motion pattern are observed, including gliding, hopping and a mixture of gliding and hopping. Quantitatively, the dynamics of each observed ordered phase is characterized by both mean square displacement and van Hove functions for both translation and rotation. The effect of corner-roundness on the dynamics is further studied by comparing the dynamics of the rhombic crystal phases formed by different corner-rounded particles at a same surface fraction. The results show that as ζ increases from 0.286 to 0.667, the translational collective motion of particles changes from a gliding-dominant pattern to a hopping-dominant pattern, whereas the rotational motion pattern is hopping-like and does not change in its type, but the rotational hopping becomes much more frequent as ζincreases(i.e., as particles become more rounded). A simple geometrical model is proposed to explain the trend of gliding motion observed in MD simulations.     

A minimal model for the auxetic response of liquid crystal elastomers

We develop a minimal phenomenological model to describe the auxetic response recently observed in liquid crystal elastomers, and further determine by theoretical calculation the critical condition required for the auxetic response to occur.     

Nonvanishing optimal noise in cellular automaton model of self-propelled particles

A minimal cellular automaton model is introduced to describe the collective motion of self-propelled particles on two-dimensional square lattice. The model features discretization of directional and positional spaces and single-particle occupation on one lattice site. Contrary to the Vicsek model and its variants, our model exhibits the nonvanishing optimal noise. When the particle density increases, the collective motion is promoted with optimal noise strength and reduced with noise strength out of optimal region. In addition, when the square lattice undergoes edge percolation process, no abrupt change of alignment behaviors is observed at the critical point of percolation.     

New insight into the mechanism of DNA polymerase I revealed by single-molecule FRET studies of Klenow fragment

We use single-molecule FRET and newly-developed D-loop techniques to investigate strand displacement activity of Klenow fragment (exo-) of DNA polymerase I in DNA sequences rich in guanine and cytosine (GC) bases. We find that there exist in the FRET traces numerous ascending jumps, which are induced by the backsliding of Klenow fragment on DNA chains. Our measurements show that the probability of backsliding is closely related to the GC-richness and dNTP concentration: increasing the GC-richness leads to an increase in the backsliding probability, and increasing the dNTP concentration however leads to a decrease in the backsliding probability. These results provide a new insight into the mechanism of DNA polymerase I.     

Solid-to-molecular-orientational-hexatic melting induced by local environment determined defect proliferations

Two-dimensional (2D) melting is a fundamental research topic in condensed matter physics, which can also provide guidance on fabricating new functional materials. Nevertheless, our understanding of 2D melting is still far from being complete due to existence of possible complicate transition mechanisms and absence of effective analysis methods. Here, using Monte Carlo simulations, we investigate 2D melting of 60° rhombs which melt from two different surface-fully-coverable crystals, a complex hexagonal crystal (cHX) whose primitive cell contains three rhombs, and a simple rhombic crystal (RB) whose primitive cell contains one rhomb. The melting of both crystals shows a sequence of solid, hexatic in molecular orientation (H^mo), and isotropic phases which obey the Berezinskii-Kosterlitz-Thouless-Halperin-Nelson-Young (BKTHNY) theory. However, local polymorphic configuration (LPC) based analysis reveals different melting mechanisms: the cHX-H^mo transition is driven by the proliferation of point-like defects during which defect-associated LPCs are generated sequentially, whereas the RB-H^mo transition is driven by line defects where defect-associated LPCs are generated simultaneously. These differences result in the observed different solid-H^mo transition points which are φ_A=0.812 for the cHX-H^mo and φ_A=0.828 for the RB-H^mo. Our work will shed light on the initial-crystal-dependence of 2D melting behavior.