Integral equation theory for athermal solutions of linear polymers

An integral equation model is developed for athermal solutions of flexible linear polymers with particular reference to good solvent conditions. Results from scaling theory are used in formulating form factors for describing the single chain structure, and the impact of solvent quality on the chain fractal dimension is accounted for. Calculations are performed within the stringlike implementation of the polymer reference interaction site model with blobs (as opposed to complete chains) treated as the constituent structural units for semidilute solutions. Results are presented for the second virial coefficient between polymer coils and the osmotic compressibility as functions of the chain length and polymer volume fraction, respectively. Findings from this model agree with results from scaling theory and experimental measurements, as well as with an earlier investigation in which self-avoiding chains were described using Gaussian form factors with a chain length and concentration-dependent effective statistical segment length. The volume fractions at the threshold for connectedness percolation are evaluated within a coarse-grained closure relation for the connectedness Ornstein-Zernike equation. Results from these calculations are consistent with the usual interpretation of the semidilute crossover concentration for model solutions of both ideal and swollen polymer coils.     

Computer simulation of bottle-brush polymers with flexible backbone: good solvent versus theta solvent conditions

By molecular dynamics simulation of a coarse-grained bead-spring-type model for a cylindrical molecular brush with a backbone chain of N(b) effective monomers to which with grafting density σ side chains with N effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range 5 ≤ N ≤ 40, backbone chain lengths are in the range 50 ≤ N(b) ≤ 200, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, N(b) ≤ 1027, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of the side chains and the backbone chain and discuss their N-dependence in terms of power laws and the associated effective exponents. We show that even at the theta point the side chains are considerably stretched, their linear dimension depending on the solvent quality only weakly. Effective persistence lengths are extracted both from the orientational correlations and from the backbone end-to-end distance; it is shown that different measures of the persistence length (which would all agree for Gaussian chains) are not mutually consistent with each other and depend distinctly both on N(b) and the solvent quality. A brief discussion of pertinent experiments is given.     

Modeling diffusional transport in the interphase cell nucleus

In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: Randomly distributed, noninterconnected obstacles, a random walk chain model, and a self-avoiding random walk chain model with persistence length. By comparing a discrete and a continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter particle diffusion. The influence of the three dimensional geometry of the fiber network on the particle diffusion is investigated in detail while varying the occupation volume, chain length, persistence length, and walker size. It is shown that adjacency of the monomers, the excluded volume effect incorporated in the self-avoiding random walk model, and, to a lesser extent, the persistence length affect particle diffusion. It is demonstrated how the introduction of the effective chain occupancy, which is a convolution of the geometric chain volume with the walker size, eliminates the conformational effects of the network on the diffusion, i.e., when plotting the diffusion coefficient as a function of the effective chain volume, the data fall onto a master curve.     

The role of chromatin conformations in diffusional transport of chromatin-binding proteins: Cartesian lattice simulations

In this paper, a lattice model for the diffusional transport of chromatin-binding particles in the interphase cell nucleus is proposed. Sliding effects are studied in dense networks of chromatin fibers created by three different methods: Randomly distributed, noninterconnected obstacles, a random walk chain model with an attractive step potential, and a self-avoiding random walk chain model with a hard repulsive core and attractive surroundings. By comparing a discrete and continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter the diffusion of chromatin-binding particles. The influence of conformational properties of the fiber network on the particle sliding is investigated in detail while varying occupation volume, sliding probability, chain length, and persistence length. It is observed that adjacency of the monomers, the excluded volume effect incorporated in the self-avoiding random walk model, and the persistence length affect the chromatin-binding particle diffusion. It is demonstrated that sliding particles sense local chain structures. When plotting the diffusion coefficient as a function of the accessible volume for diffusing particles, the data fall onto master curves depending on the persistence length. However, once intersegment transfer is involved, chromatin-binding proteins no longer perceive local chain structures.     

Chains are more flexible under tension

The mechanical response of networks, gels, and brush layers is a manifestation of the elastic properties of the individual macromolecules. Furthermore, the elastic response of macromolecules to an applied force is the foundation of the single-molecule force spectroscopy techniques. The two main classes of models describing chain elasticity include the worm-like and freely-jointed chain models. The selection between these two classes of models is based on the assumptions about chain flexibility. In many experimental situations the choice is not clear and a model describing the crossover between these two limiting classes is therefore in high demand. We are proposing a unified chain deformation model which describes the force-deformation curve in terms of the chain bending constant K and bond length b. This model demonstrates that the worm-like and freely-jointed chain models correspond to two different regimes of polymer deformation and the crossover between these two regimes depends on the chain bending rigidity and the magnitude of the applied force. Polymer chains with bending constant K>1 behave as a worm-like chain under tension in the interval of the applied forces f ≤ Kk(B)T/b and as a freely-jointed chain for f ≥ Kk(B)T/b (k(B) is the Boltzmann constant and T is the absolute temperature). The proposed crossover expression for chain deformation is in excellent agreement with the results of the molecular dynamics simulations of chain deformation and single-molecule deformation experiments of biological and synthetic macromolecules.     

高分子链形状与尺寸关联的Monte Carlo模拟

运用MonteCarlo方法对线型高分子链格点模型的构型进行了模拟,研究了构型的尺寸(采用平方末端距R²,平方回转半径S²来表征)和形状(由非球形因子A表征)之间的关联.对任何长度的高分子链,其关联系数CA,R²和CA,S²均为正值,表明高分子链的形状与尺寸之间存在正关联,即尺寸小的构型其非球形因子A一般也小,反之尺寸大的构型其非球形因子A一般也大.关联系数CA,R²和CA,S²均随链长的增大而减小,近似地与链长的倒数(n^-1)成正比.研究还表明,关联系数的极限值(链长n很大时)与格点的类型无关,与链样本产生的方式也无关,但与链是否考虑排斥体积有关,考虑了排斥体积后,关联系数增大.     

Continuum formulation of the Scheutjens-Fleer lattice statistical theory for homopolymer adsorption from solution

Homopolymer adsorption from a dilute solution on an interacting (attractive) surface under static equilibrium conditions is studied in the framework of a Hamiltonian model. The model makes use of the density of chain ends n(1,e) and utilizes the concept of the propagator G describing conformational probabilities to locally define the polymer segment density or volume fraction phi; both n(1,e) and phi enter into the expression for the system free energy. The propagator G obeys the Edwards diffusion equation for walks in a self-consistent potential field. The equilibrium distribution of chain ends and, consequently, of chain conformational probabilities is found by minimizing the system free energy. This results in a set of model equations that constitute the exact continuum-space analog of the Scheutjens-Fleer (SF) lattice statistical theory for the adsorption of interacting chains. Since for distances too close to the surface the continuum formulation breaks down, the continuum model is here employed to describe the probability of chain configurations only for distances z greater than 2l, where l denotes the segment length, from the surface; instead, for distances z < or = 2l, the SF lattice model is utilized. Through this novel formulation, the lattice solution at z = 2l provides the boundary condition for the continuum model. The resulting hybrid (lattice for distances z < or = 2l, continuum for distances z > 2l) model is solved numerically through an efficient implementation of the pseudospectral collocation method. Representative results obtained with the new model and a direct application of the SF lattice model are extensively compared with each other and, in all cases studied, are found to be practically identical.     

Characterization of the chain stiffness for a mesogen-jacketed liquid crystal polymer: Poly{2,5-BIS [(4-Methoxybenzoyl)Oxy] Styrene}

Narrow-distribution fractions of poly{2,5-bis[(4-methoxybenzoyl)oxy] styrene} ranging in weight-average molecular weight Mw from 1.1 × 10⁵ to 1.96 × 10⁶ were studied by static light scattering and viscometry in THF at 25 ^° C. From Mw and the intrinsic viscosity [ η ] Mark-Houwink-Sakurada equation was formulated with K=7.54×10⁻⁴ and ≈=0.82. The relation between [ η ] and Mw was analyzed according to Bohdanecky for the Kratky-Porod wormlike chain, the ranges of the mass per unit length M_L and the persistence length q were estimated as 35 nm⁻¹ M<_L42 nm<₋₁ and 11.5 nm <13.5 nm, respectively. The values of ≈ and q indicate that the polymer, though a liquid crystal polymer of the side-chain type, has wormlike chain in dilute solution as most main chain liquid crystal polymers.     

Adsorption Transition of a Polymer Chain at a Weakly Attractive Surface: Monte Carlo Simulation of Off‐Lattice Models

A bead‐spring model of a polymer chain with one end attached to a wall is studied by Monte Carlo simulations for chain lengths 16 ≤ N ≤ 256. Two types of adsorption potentials, 9‐3 and 10‐4 Lennard‐Jones (LJ) potentials, between the effective monomers and the wall are assumed. For both cases the adsorption transition where the chain changes its asymptotic statistical properties from a three‐dimensional to a two‐dimensional configuration is located using a scaling analysis. It is shown that the crossover exponent φ = 0.50 ± 0.02 is the same for both LJ potentials. This value is compatible with recent theoretical predictions and simulation results for lattice models with short‐range wall potentials. The results of our study support the expectation that the exponents describing the adsorption transition are universal, i.e., they are not influenced by the precise form and the long‐range character of the adsorption potentials used. The technical aspects of the simulations (which use configurational bias methods as well as histogram re‐weighting) are also carefully discussed.

Snapshot pictures of a bead‐spring model of a polymer chain with N = 256 beads with one end anchored on the surface: (a)“mushroom configuration”, (b) ε_a ≈ ε_w at the adsorption transition, and (c)“pancake configuration” of a strongly adsorbed chain.     

Equilibrium and dynamical properties of gaussian stiff chain molecules

We present a novel analytically tractable model for stiff chain molecules. The equilibrium distribution function of the chain is derived using the maximum-entropy principle. For that purpose, we first formulate a discrete chain model, where the connections of the points and the restriction on bending are taken into account via constraints. We then perform the limit to a continuous chain and show that the mean-square end-to-end distance and the radius of gyration of the continuous chain are identical with the same quantities of the Kratky-Porod wormlike chain. The dynamics of our chain is investigated in dilute solution without hydrodynamic interactions. The linear dynamical equation is solved by a normal mode analysis. We discuss the dependence of the relaxation times on the single parameter of the model, the persistence length. For small persistence lengths we obtain the well known relaxation times of the Rouse model. In the stiff-chain limit, we find the pure bending relaxation times and, in addition, the rotational relaxation time.     

Perturbation Theory of Polymer Chains Revisited, 2—Intermolecular Excluded Volume of Random and Self‐Avoiding Walks

The intermolecular compatibility of 10⁷–10⁸ independent pair configurations of linear chains (chain length 64 ≤ N ≤ 8192) with and without intramolecular interaction on various lattices is checked and the intermolecular excluded volume u evaluated. From the (average) number of possible i‐tuples of overlaps in the pair configurations the parameters C_k of the perturbation theory are calculated. Differences between the various lattice types at finite N vanish completely for N → ∞. While the theoretical values of C₁ and C₂ were recovered within very narrow limits for chains without intramolecular interaction, markedly higher figures apply to self‐avoiding walks. The excluded volume u itself and higher C_k parameters are called upon to test several classical and renormalized perturbation theories.

     

Monte Carlo calculations on polypeptide chains. VIII. Distribution functions for the end-to-end distance and radius of gyration for hard-sphere models of randomly coiling poly(glycine) and poly(L-alanine).

A Monte Carlo study of the distribution functions for the end-to-end distance and radius of gyration for hard-sphere models of poly(glycine) and poly(L-alanine) random coils has been conducted in the chain-length range n = 3 to 100 monomer units for both unperturbed chains and chains perturbed by long-range interactions (excluded volume effects). The distribution functions for the radius of gyration in all cases have been very precisely calculated, those for the perturbed end-to-end distance less precisely, and those for the unperturbed end-to-end distance least precisely. Empirical distribution functions of the form W(p) = ap-b exp(-cp-d) for the reduced end-to-end distance p = r/"r-2"-one-half and a similar form for the reduced radius of gyration could be least-squares fit to the Monte Carlo data. The expansion factors alpha-r and alpha-s were calculated vs. chain length and were used to test various versions of the two-parameter theory of the excluded volume effect. To be consistent with the chain-length dependence of alpha-r and alpha-s as determined by the Monte Carlo calculations, each of these theories required two different binary cluster integrals, a beta-r based on alpha-r and a beta-s based on alpha-s, both of which were strongly chain-length dependent. Both of these results suggest that the two-parameter theory is not applicable to the models used in this study. It was also found that, except for very short chain lengths, plots of ln alphs-r vs. ln n were linear, and thus that alpha-r could be estimated for long chain lengths. Comparison of these estimates with the experimental data on four polypeptide chains in one-earth solvents that the hard-sphere models used in this study yield expansion factors that do not seriously overestimate the magnitude of the excluded volume effect.     

二维HP格点模型中的紧密高分子链构象及其热力学性质的研究

采用二维HP模型用精确计数法和MonteCarlo方法研究了链长为N(≤ 2 2 )的紧密高分子链的构象和热力学性质 .发现不同HP序列的紧密高分子链的平均自由能和平均配分函数与链长N存在关系 :〈F〉=aN+b ,　ln〈Z〉=a′N +b′ .同时发现对于可折叠成基态且简并度为 1的紧密高分子链 ,其平均自由能和平均配分函数与链长N也存在相似的关系 .在HP模型中对于链长为N的紧密高分子链 ,存在着 2 N + 1 个不同的HP序列 .我们发现可以折叠成基态且简并度为 1的蛋白质分子的HP序列数目NS 为NS =a× 2 N+ 1 　 (a =0 0 2 5 ) ,对应的HP序列中 ,疏水基团 (H)数目的含量为 4 0 %～ 6 0 %的序列出现的几率最大 .同时在这些紧密高分子链中有些具有相同的结构 ,发现结构的‘简并度’为 3 3～ 4 0 (10≤N≤ 16 ) .在紧密高分子链折叠过程中 ,折叠的初期能量下降比较快 ,折叠的中期能量下降比较缓慢 ,折叠的后期能量下降也是比较快     

拉力诱导下的紧密高分子链相变行为

采用相互作用自回避行走(interacting self-avoiding walks,ISAWS)模型研究了一端固定的紧密高分子链在拉伸过程中的低温相变行为,观察到在拉伸过程中当温度T<0.1时平均拉力会出现一个震荡,随着温度的升高这种震荡现象又渐渐消失,这是由于紧密高分子链在低温时类似于β折叠的"冻结构象"被拉开而引起的.比较吸附条件下和无吸附作用下平均拉力、自由能以及相变行为的差别,发现在吸附条件下在拉伸的初始阶段为了克服表面吸附的相互作用,拉力会出现一个峰.吸附作用也使得外界作用到高分子链上的实际有效拉力减小,造成崩塌相态(collapsed phase)区域面积减少.另外发现在吸附条件下平均拉力还受温度变化的影响.在拉伸的初期由于单体间存在体积排除效应,平均拉力是随着温度的升高而降低,随着拉伸的深入当末端距到达一定长度时平均拉力是随着温度的升高而增加.并同Kumar等人在不考虑吸附作用下拉伸紧密高分子链得到的结果进行了比较.这些研究对于进一步研究外力诱导下吸附紧密高分子的相变有一定的参考价值.     

Spherical polymer brushes under good solvent conditions: molecular dynamics results compared to density functional theory

A coarse grained model for flexible polymers end-grafted to repulsive spherical nanoparticles is studied for various chain lengths and grafting densities under good solvent conditions by molecular dynamics methods and density functional theory. With increasing chain length, the monomer density profile exhibits a crossover to the star polymer limit. The distribution of polymer ends and the linear dimensions of individual polymer chains are obtained, while the inhomogeneous stretching of the chains is characterized by the local persistence lengths. The results on the structure factor of both single chain and full spherical brush as well as the range of applicability of the different theoretical tools are presented. Finally, a brief discussion of the experiment is given.     

Force-length relations in deformed coils above and below the theta state. Possible bimodality in the chain distribution function

Stretching of flexible macromolecules by an external force, acting on the chain ends, in solvents of variable quality was simulated by the Monte Carlo method on a tetrahedral lattice. The forcelength relations and the stress-induced changes in the population of the gauche conformers were calculated for coils in theta and athermal solvents. In poor solvents, the stretching of a collapsed coil involves a rather abrupt upturn of the force-length curve explained as a transition of a globular coil into an extended coil. In conformity with this interpretation, a bimodal shape of the chain vector distribution function P(R) was found in the intermediate range of deformation of collapsed coils. The significance of the results to the stress-strain behavior of networks with pronounced interaction (such as collapsed gels) are discussed.     

End-monomer Dynamics in Semiflexible Polymers

Spurred by an experimental controversy in the literature, we investigate the end-monomer dynamics of semiflexible polymers through Brownian hydrodynamic simulations and dynamic mean-field theory. Precise experimental observations over the last few years of end-monomer dynamics in the diffusion of double-stranded DNA have given conflicting results: one study indicated an unexpected Rouse-like scaling of the mean squared displacement (MSD) ?r(2)(t)? ~ t(1/2) at intermediate times, corresponding to fluctuations at length scales larger than the persistence length but smaller than the coil size; another study claimed the more conventional Zimm scaling ?r(2)(t)? ~ t(2/3) in the same time range. Using hydrodynamic simulations, analytical and scaling theories, we find a novel intermediate dynamical regime where the effective local exponent of the end-monomer MSD, α(t) = d log?r(2)(t)?/d log t, drops below the Zimm value of 2/3 for sufficiently long chains. The deviation from the Zimm prediction increases with chain length, though it does not reach the Rouse limit of 1/2. The qualitative features of this intermediate regime, found in simulations and in an improved mean-field theory for semiflexible polymers, in particular the variation of α(t) with chain and persistence lengths, can be reproduced through a heuristic scaling argument. Anomalously low values of the effective exponent α are explained by hydrodynamic effects related to the slow crossover from dynamics on length scales smaller than the persistence length to dynamics on larger length scales.     

Universal consequences of the presence of excluded volume interactions in dilute polymer solutions undergoing shear flow

The role of solvent quality in determining the universal material properties of dilute polymer solutions undergoing steady simple shear flow is examined. A bead-spring chain representation of the polymer molecule is used, and the influence of solvent molecules on polymer conformations is modelled by a narrow Gaussian excluded volume potential that acts pairwise between the beads of the chain. Brownian dynamics simulations data, acquired for chains of finite length, and extrapolated to the limit of infinite chain length, are shown to be model independent. This feature of the narrow Gaussian potential, which leads to results identical to a delta-function repulsive potential, enables the prediction of both universal crossover scaling functions and asymptotic behavior in the excluded volume limit. Universal viscometric functions, obtained by this procedure, are found to exhibit increased shear thinning with increasing solvent quality. In the excluded volume limit, they are found to obey power law scaling with the characteristic shear rate beta, in close agreement with previously obtained renormalization group results. The presence of excluded volume interactions is also shown to lead to a weakening of the alignment of the polymer chain with the flow direction.     

Scale-free center-of-mass displacement correlations in polymer melts without topological constraints and momentum conservation: a bond-fluctuation model study

By Monte Carlo simulations of a variant of the bond-fluctuation model without topological constraints, we examine the center-of-mass (COM) dynamics of polymer melts in d = 3 dimensions. Our analysis focuses on the COM displacement correlation function C(N)(t)≈?(t) (2)h(N)(t)/2, measuring the curvature of the COM mean-square displacement h(N)(t). We demonstrate that C(N)(t) ≈ -(R(N)∕T(N))(2)(ρ?/ρ)?f(x = t/T(N)) with N being the chain length (16 ≤ N ≤ 8192), R(N) ～ N(1/2) is the typical chain size, T(N) ～ N(2) is the longest chain relaxation time, ρ is the monomer density, ρ(*)≈N/R(N) (d) is the self-density, and f(x) is a universal function decaying asymptotically as f(x) ～ x(-ω) with ω = (d + 2) × α, where α = 1/4 for x ? 1 and α = 1/2 for x ? 1. We argue that the algebraic decay NC(N)(t) ～ -t(-5/4) for t ? T(N) results from an interplay of chain connectivity and melt incompressibility giving rise to the correlated motion of chains and subchains.