Stretching of semiflexible polymers with elastic bonds

A semiflexible harmonic chain model with extensible bonds is introduced and applied to the stretching of semiflexible polymers or filaments. The semiflexible harmonic chain model allows to study effects from bending rigidity, bond extension, discrete chain structure, and finite length of a semiflexible polymer in a unified manner. The interplay between bond extension and external force can be described by an effective inextensible chain with increased stretching force, which leads to apparently reduced persistence lengths in force-extension relations. We obtain force-extension relations for strong- and weak-stretching regimes which include the effects of extensible bonds, discrete chain structure, and finite polymer length. We discuss the associated characteristic force scales and calculate the crossover behaviour of the force-extension curves. Strong stretching is governed by the discrete chain structure and the bond extensibility. The linear response for weak stretching depends on the relative size of the contour length and the persistence length which affects the behaviour of very rigid filaments such as F-actin. The results for the force-extension relations are corroborated by transfer matrix and variational calculations.PACS: 87.15.-v Biomolecules: structure and physical properties - 87.15.Aa Theory and modeling; computer simulation - 87.15.La Mechanical properties     

AFM‐Based Single Molecule Force Spectroscopy of Polymer Chains: Theoretical Models and Applications

Abstract

In recent years, remarkable advances in research of the mechanical and structural properties of single polymer chains have been achieved thanks to atomic force microscope (AFM)‐based single molecule force spectroscopy (SMFS). This technique offers great possibilities to investigate the mechanical properties of a single polymer chain by static/dynamic force‐extension measurements at the mesoscale level. Data are analyzed with the help of appropriate theoretical models, such as statistical mechanics models for freely jointed chains (FJC) or worm‐like chains (WLC), which can well describe the moderate entropy‐controlled stretch of most polymers, and with semiclassical models, which are being modified using quantum mechanics principles to account for entropic and enthalpic contributions to stretching in the high‐force Hookean regime. In this article we review the theoretical models of single chain stretching, the latest progress in force‐extension measurements by static and dynamic AFM modes for polymer chains dispersed in different solvents and subjected to a force that may induce their conformational transformations, as well as relevant applications.     

A steered molecular dynamics study on the elastic behaviour of knotted polymer chains

In this paper the influence of a knot on the structure of a polymethylene （PM） strand in the tensile process is investigated by using the steered molecular dynamics （SMD） method. The gradual increasing of end-to-end distance, R, results in a tighter knot and a more stretched contour. That the break in a knotted rope almost invariably occurs at a point just outside the ＇entrance＇ to the knot, which has been shown in a good many experiments, is further theoretically verified in this paper through the calculation of some structural and thermodynamic parameters. Moreover, it is found that the analyses on bond length, torsion angle and strain energy can facilitate to the study of the localization and the size of a knot in the tensile process. The symmetries of torsion angles, bond lengths and bond angles in the knot result in the whole symmetry of the knot in microstructure, thereby adapting itself to the strain applied. Additionally, the statistical property of the force-dependent average knot size illuminates in detail the change in size of a knot with force f, and therefore the minimum size of the knot in the restriction of the potentials considered in this work for a PM chain is deduced. At the same time, the difference in response to uniaxial strain, between a knotted PM strand and an unknotted one is also investigated. The force-extension profile is easily obtained from the simulation. As expected, for a given f, the knotted chain has an R significantly smaller than that of an unknotted polymer. However, the scaled difference becomes less pronounced for larger values of N, and the results for longer chains approach those of the unknotted chains.     

Static and dynamic properties of polymer brush with topological ring structures: Molecular dynamic simulation

By defining a topological constraint value(rn),the static and dynamic properties of a polymer brush composed of moderate or short chains with different topological ring structures are studied using molecular dynamics simulation,and a comparison with those of linear polymer brush is also made.For the center-of-mass height of the ring polymer brush scaled by chain length h~N~v,there is no significant difference of exponent from that of a linear brush in the small topological constraint regime.However,as the topological constraint becomes stronger,one obtains a smaller exponent.It is found that there exists a master scaling power law of the total stretching energy scaled by chain length N for moderate chain length regime,F_(ene)~Np~v,for ring polymer brushes,but with a larger exponent v than 5/6,indicating an influence of topological constraint to the dynamic properties of the system.A topological invariant of free energy scaled by(c)~(5/4) is found.     

Stretching DNA: Role of electrostatic interactions

The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent variational approach. For small values of the external force f, we find the extension scales as where is the Debye screening length. In the limit of large force the electrostatic effects can be accounted for within the semiflexible chain model of DNA by assuming that only small excursions from rod-like conformations are possible. In this regime the extension approaches the contour length as where f is the magnitude of the external force. The theory is used to analyze experiments that have measured the extension of double-stranded DNA subject to tension at various salt concentrations. The theory reproduces nearly quantitatively the elastic response of DNA at small and large values of f and for all concentration of the monovalent counterions. The limitations of the theory are also pointed out. Received 13 October 1998 and Received in final form 9 June 1999     

抛物碟式太阳能聚光器的聚光特性分析与设计

点聚焦碟式太阳能聚光反射器,应用光线追迹法模拟分析了存在太阳张角时,相同开口采光面积、不同形状的聚光器分别在相同焦距、相同边缘角情况下的聚光特性。考虑到太阳形状、开口采光面形状、抛物面焦距、抛物面边缘角及接收器的遮挡作用等几何因素,并结合旋转抛物面聚光器的光学特性,建立了模拟仿真的几何模型。采用光线追迹法直观地模拟了聚光接收面上的平均能流分布特性。为对聚光器的聚光特性进行定量评价,采用了面积效率因子的概念。模拟结果表明,采光面积相同时,等焦距的4种不同开口形状的聚光器具有相近的聚光能流比;等边缘角时,除圆形聚光器外的3种聚光器有较大光能损失。设计了多碟共焦聚光器,用低聚光比聚光器组合达到高倍聚光效果,并分析了聚光特性,为碟式太阳能聚光反射系统的设计和优化提供了参考。     

静态堆积颗粒中的力链分布

颗粒物质是由众多离散颗粒组成的软凝聚态物质,涉及多个物理层次结构和机制,是多尺度问题. 首先阐述了颗粒物质多尺度力学的研究框架,指出颗粒间接触力链构成的细观尺度是核心,颗粒物质显示出的独特静态堆积特性和动态流变特性都与细观尺度力链的复杂演变规律直接相关. 围绕着定量描述力链特征这一目标,采用严格的球形颗粒Hertz法向接触理论和Mindlin-Deresiewicz切向接触理论,对重力作用下12000个球心共面的二维等径颗粒静态堆积进行了离散动力学模拟,对力链分布特征、接触力规律等做了量化分析,考察了颗粒 关键词： 颗粒物质 力链 离散模型 多尺度力学     

Deformation of a tethered polymer in uniform flow

Static properties of a single polymer fixed at one end and subjected to a uniform flow field are investigated for several polymer models: the Gaussian chain, the freely jointed chain, and the FENE (Finitely Extensible Nonlinear Elastic) chain. By taking into account first the excluded-volume interaction and subsequently also the hydrodynamic interaction, the polymer models are gradually completed and the relevance of each effect for the polymer deformation can be identified. Results from computer simulations of these bead spring chains are compared with analytical calculations using either the conformational distribution function or blob models. To this end, in contrast to the blob model with non-draining blobs introduced for a tethered polymer by Brochard-Wyart, we here develop also a model with free-draining blobs. It turns out that a limited extensibility of the polymer – described by nonlinear spring forces in the model – leads to a flow velocity dependence of the end-to-end distance, segment density, etc. which agrees with the power law predictions of the blob model only for very long chains and in a narrow range of flow velocities. This result is important for comparison with recent experiments on DNA molecules which turn out to be still rather short in this respect. The relative importance of finite extensibility, the excluded-volume effect, and hydrodynamic interactions for polymers in flow is not fully understood at present. The simulation of reasonably long chains becomes possible even when fluctuating hydrodynamic interactions are taken into account without employing averaging procedures by introducing efficient numerical approximation schemes. At medium velocity of the uniform flow the polymer is partially uncoiled and simulations show that the effects of excluded-volume and hydrodynamic interactions are position-dependent. Both are stronger near the free end than near the tethered end of the polymer. A crossover from a nearly non-draining polymer at small flow velocities to a free-draining almost uncoiled chain at large velocities is found in the simulations. Accordingly, models assuming the polymer to be composed of either free- or non-draining subunits, like the two blob models, cannot correctly describe the extension and shape of a tethered polymer in flow, and simple power laws for the polymer extension, etc. cannot be expected. Received 21 June 1999     

Effect of Interaction upon Translocation of Confined Polymer Chain Through Nanopore

运用二维的键长涨落模型和蒙特卡洛方法研究高分子链从一个受限空间到自由空间穿孔过程中,链单体与纳米孔之间的相互作用.结果表明,在不同的链长和纳米孔交互作用下,高分子链成功穿越自由能能垒取决于链长和纳米孔长度,并且由于交互作用降低了自由能能垒,导致高分子链在纳米管的平均捕获时间缩短.     

A novel quasi-exactly solvable spin chain with nearest-neighbors interactions

In this paper we study a novel spin chain with nearest-neighbors interactions depending on the sites coordinates, which in some sense is intermediate between the Heisenberg chain and the spin chains of Haldane–Shastry type. We show that when the number of spins is sufficiently large both the density of sites and the strength of the interaction between consecutive spins follow the Gaussian law. We develop an extension of the standard freezing trick argument that enables us to exactly compute a certain number of eigenvalues and their corresponding eigenfunctions. The eigenvalues thus computed are all integers, and in fact our numerical studies evidence that these are the only integer eigenvalues of the chain under consideration. This fact suggests that this chain can be regarded as a finite-dimensional analog of the class of quasi-exactly solvable Schrödinger operators, which has been extensively studied in the last two decades. We have applied the method of moments to study some statistical properties of the chain's spectrum, showing in particular that the density of eigenvalues follows a Wigner-like law. Finally, we emphasize that, unlike the original freezing trick, the extension thereof developed in this paper can be applied to spin chains whose associated dynamical spin model is only quasi-exactly solvable.     

Fluctuations in granular media

Dense slowly evolving or static granular materials exhibit strong force fluctuations even though the spatial disorder of the grains is relatively weak. Typically, forces are carried preferentially along a network of "force chains." These consist of linearly aligned grains with larger-than-average force. A growing body of work has explored the nature of these fluctuations. We first briefly review recent work concerning stress fluctuations. We then focus on a series of experiments in both two- and three-dimension [(2D) and (3D)] to characterize force fluctuations in slowly sheared systems. Both sets of experiments show strong temporal fluctuations in the local stress/force; the length scales of these fluctuations extend up to 10(2) grains. In 2D, we use photoelastic disks that permit visualization of the internal force structure. From this we can make comparisons to recent models and calculations that predict the distributions of forces. Typically, these models indicate that the distributions should fall off exponentially at large force. We find in the experiments that the force distributions change systematically as we change the mean packing fraction, gamma. For gamma's typical of dense packings of nondeformable grains, we see distributions that are consistent with an exponential decrease at large forces. For both lower and higher gamma, the observed force distributions appear to differ from this prediction, with a more Gaussian distribution at larger gamma and perhaps a power law at lower gamma. For high gamma, the distributions differ from this prediction because the grains begin to deform, allowing more grains to carry the applied force, and causing the distributions to have a local maximum at nonzero force. It is less clear why the distributions differ from the models at lower gamma. An exploration in gamma has led to the discovery of an interesting continuous or "critical" transition (the strengthening/softening transition) in which the mean stress is the order parameter, and the mean packing fraction, gamma, must be adjusted to a value gamma(c) to reach the "critical point." We also follow the motion of individual disks and obtain detailed statistical information on the kinematics, including velocities and particle rotations or spin. Distributions for the azimuthal velocity, V(theta), and spin, S, of the particles are nearly rate invariant, which is consistent with conventional wisdom. Near gamma(c), the grain motion becomes intermittent causing the mean velocity of grains to slow down. Also, the length of stress chains grows as gamma-->gamma(c). The 3D experiments show statistical rate invariance for the stress in the sense that when the power spectra and spectral frequencies of the stress time series are appropriately scaled by the shear rate, Omega, all spectra collapse onto a single curve for given particle and sample sizes. The frequency dependence of the spectra can be characterized by two different power laws, P proportional, variant omega(-alpha), in the high and low frequency regimes: alpha approximately 2 at high omega; alpha<2 at low omega. The force distributions computed from the 3D stress time series are at least qualitatively consistent with exponential fall-off at large stresses. (c) 1999 American Institute of Physics.     

Direct atomic structure by holographic diffuse LEED

A multiple-energy phase-summing method is applied to diffuse low-energy electron diffraction intensity spectra to obtain three-dimensional images of surface atoms. In this demonstration, calculated DLEED intensity spectra from a multiple scattering method are directly inverted to produce high-fidelity 3D images of near-neighbor atoms measured from an adatom. No prior knowledge of adsorption site, bond length, bond angle, or type of atom is needed. The images are essentially free from artifacts and have a spatial resolution of ~ 1 Å when viewed along any cut-plane. These results demonstrate that holographic DLEED has the potential of being an accurate and direct structural tool for low-density disordered adsorption systems.     

A simple model of structural disorder in III–V quaternary alloys

A model is proposed describing the bond length and bond-bending angle distributions in quaternary A³B⁵ alloys with ZB structure in quasi-continuum approximation. The model allows to consider reasonably large crystal lattice clusters employing minimum computing resources. Analytical expressions are derived for the radial distribution functions. The developed approach is applied to the analysis of available experimental data on structural disorder in III–V alloys. Employing the valence force field Keating model the deformation energy for several alloys is evaluated.     

An extended chain Ising model and its Glauber dynamics

It was first proposed that an extended chain Ising (ECI) model contains the Ising chain model, single spin double-well potentials and a pure phonon heat bath of a specific energy exchange with the spins. The extension method is easy to apply to high dimensional cases. Then the single spin-flip probability (rate) of the ECI model is deduced based on the Boltzmann principle and general statistical principles of independent events and the model is simplified to an extended chain Glauber-Ising (ECGI) model. Moreover, the relaxation dynamics of the ECGI model were simulated by the Monte Carlo method and a comparison with the predictions of the special chain Glauber-Ising (SCGI) model was presented. It was found that the results of the two models are consistent with each other when the Ising chain length is large enough and temperature is relative low, which is the most valuable case of the model applications. These show that the ECI model will provide a firm physical base for the widely used single spin-flip rate proposed by Glauber and a possible route to obtain the single spin-flip rate of other form and even the multi-spin-flip rate.     

Geometrical structures,vibrational frequencies,force constants and dissociation energies of isotopic water molecules （H2O,HDO, D2O,HTO, DTO,and T2O） under dipole electric field

The dissociation limits of isotopic water molecules are derived for the ground state. The equilibrium geometries, the vibrational frequencies, the force constants and the dissociation energies for the ground states of all isotopic water molecules under the dipole electric fields from -0.05 a.u. to 0.05 a.u. are calculated using B3P86/6-311++G(3df,3pf). The results show that when the dipole electric fields change from -0.05 a.u. to 0.05 a.u., the bond length of H-O increases whereas the bond angle of H-O-H decreases because of the charge transfer induced by the applied dipole electric field. The vibrational frequencies and the force constants of isotopic water molecules change under the influence of the strong external torque. The dissociation energies increase when the dipole electric fields change from -0.05 a.u. to 0.05 a.u. and the increased dissociation energies are in the order of H2O, HDO, HTO, D2O, DTO, and T2O under the same external electric fields.     

Curved polymer and polyelectrolyte brushes beyond the Daoud-Cotton model

We revise the classical Daoud-Cotton (DC) model to describe conformations of polymer and polyelectrolyte chains end-grafted to convex spherical and cylindrical surfaces. In the framework of the DC model, local stretching of chains in the brush does not depend on the degree of polymerization of grafted chains, and the polymer density profile follows a single-exponent power law. This model, however, does not correspond to a minimum in free energy of the curved brush. The nonlocal (NL) approximation exploited in the present paper implies the minimization of the overall free energy of the brush and predicts that the polymer density profile does not follow a single-exponent power law. In the limit of large surface curvature the NL approximation provides the same scaling laws for brush thickness and free energy as the local DC model. Numerical prefactors are however different. Extra extension of chains in the brush interior region leads to larger equilibrium brush thickness and lower free energy per chain. A significant difference between outcomes of the two models is found for brushes formed by ionic polymers, particularly for weakly dissociating (p H-sensitive) polyelectrolytes at low solution salinity.     

Molecular Dynamics Simulation of Effects of Stretching and Compressing on Thermal Conductivity of Aligned Silicon Oxygen Chains

The effects of stretching and compressing on the thermal conductivity(TC) of silicon oxygen chain are studied by means of non-equilibrium molecular dynamics simulation. It is found that stretching can improve TC, and compressing may reduce the TC and can also increase the TC. This mechanism is explained based on the variation of phonon group velocity and the specific heat per volume with stretching and compressing. The distributions of bond angle and bond length under different normalized chain lengths are given. It is found that the bond length and bond angle in the skeleton chain would deviate from their original position. In addition, the phonon density of states(PDOSs) of silicon and oxygen atoms in the chains under different normalized chain lengths are analyzed. The overall trend is that the TC increases and the peaks of PDOSs move towards higher frequency with increasing stretch strain.     

Extension of chains composed of freely joined elastic segments

A relatively simple formula for the mean distance between the ends of a model chain composed of elastic freely joined segments as a function of an extending force applied to its ends was derived. It was assumed that the stiffness coefficient, which characterizes the ability of the segment to extend and contract, is rather high. In the limit of infinite stiffness the relationship obtained transforms into the Langevin function. The formula predicts the existence of two Hook regions in the force-relative extension dependence. The first of them is characterized by small extensions, whereas the second one, by extensions exceeding the equilibrium contour length. The existence of the latter is confirmed by recent experiments. The magnitude of fluctuations of the relative extension was estimated. The obtained relationships for the relative extension and its scatter are in close agreement with the results of computer simulations performed using collisional molecular dynamics for chains composed of 25, 50, 100, and 200 segments.     

Determination of interfacial parameters in fiber-polymer systems from pull-out test data using a bilinear bond law

We propose a new model for characterization of strength properties of fiber-polymer interfaces by means of a single fiber pull-out test. Our model is based on shear-lag analysis using a bilinear bond law (stress–slip relationship) which, in turn, is a simplified representation of the true stress behavior as a function of strain for cold-drawing polymers. According to this law, the fiber-polymer interface is subjected to the following successive processes: (1) linear loading within the elastic region; (2) yielding and subsequent bond strengthening with increasing strain; (3) local debonding and interfacial crack propagation along the interface; (4) post-debonding friction. Both crack propagation and extension of the yielded zone can be stable and unstable, depending on the values of interfacial parameters and the load applied to the free fiber end. The procedure of construction of theoretical force–displacement curves for a pull-out test is described in detail. Theoretical curves exhibit such features as multiple kinks and non-linear regions, whose positions and shape are related to interfacial parameters. By fitting experimental curves with theoretical ones, these parameters can be determined for each separate pull-out specimen. Practical examples are provided for basalt fiber–polypropylene and glass fiber–polypropylene specimens.     

Intriguing heat conduction of a chain with transverse motions

We study heat conduction in a one-dimensional chain of particles with longitudinal as well as transverse motions. The particles are connected by two-dimensional harmonic springs together with bending angle interactions. Using equilibrium and nonequilibrium molecular dynamics, three types of thermal conducting behaviors are found: a logarithmic divergence with system sizes for large transverse coupling, 1/3 power law at intermediate coupling, and 2/5 power law at low temperatures and weak coupling. The results are consistent with a simple mode-coupling analysis of the same model. We suggest that the 1/3 power-law divergence should be a generic feature for models with transverse motions.