Weak violation of universality for polyelectrolyte chains: Variational theory and simulations

A variational approach is considered to calculate the free energy and the conformational properties of a polyelectrolyte chain in d dimensions. We consider in detail the case of pure Coulombic interactions between the monomers, when screening is not present, in order to compute the end-to-end distance and the asymptotic properties of the chain as a function of the polymer chain length N. We find R≃N ^ν(log N)^γ, where ν = and λ is the exponent which characterizes the long-range interaction U∝ 1/r ^λ. The exponent γ is shown to be non-universal, depending on the strength of the Coulomb interaction. We check our findings by a direct numerical minimization of the variational energy for chains of increasing size 2⁴ < N < 2¹⁵. The electrostatic blob picture, expected for small enough values of the interaction strength, is quantitatively described by the variational approach. We perform a Monte Carlo simulation for chains of length 2⁴ < N < 2¹⁰. The non-universal behavior of the exponent γ previously derived within the variational method is also confirmed by the simulation results. Non-universal behavior is found for a polyelectrolyte chain in d = 3 dimension. Particular attention is devoted to the homopolymer chain problem, when short-range contact interactions are present. Received 8 August 2000 and Received in final form 19 December 2000     

Force-extension behavior of folding polymers

The elastic response of flexible polymers made of elements which can be either folded or unfolded, having different lengths in these two states, is discussed. These situations are common for biopolymers as a result of folding interactions intrinsic to the monomers, or as a result of binding of other smaller molecules along the polymer length. Using simple flexible-chain models, we show that even when the energy ε associated with maintaining the folded state is comparable to k _B T, the elastic response of such a chain can mimic usual polymer linear elasticity, but with a force scale enhanced above that expected from the flexibility of the chain backbone. We discuss recent experiments on single-stranded DNA, chromatin fiber and double-stranded DNA with proteins weakly absorbed along its length which show this effect. Effects of polymer semiflexiblity and torsional stiffness relevant to experiments on proteins binding to dsDNA are analyzed. We finally discuss the competition between electrostatic self-repulsion and folding interactions responsible for the complex elastic response of single-stranded DNA. Received 7 August 2002 and Received in final form 7 March 2003 / Published online: 15 April 2003 RID="a" ID="a"e-mail: jmarko@uic.edu     

Off equilibrium dynamics in disordered quantum spin chain

We study the non-equilibrium time evolution of the average transverse magnetisation and end-to-end correlation functions of the random Ising quantum chain. Starting with fully magnetised states, either in the x or z direction, we compute numerically the average quantities. They show similar behaviour to the homogeneous chain, that is an algebraic decay in time toward a stationary state. During the time evolution, the spatial correlations, measured from one end to the other of the chain, are building up and finally at long time they reach a size-dependent constant depending on the distance from criticality. Analytical arguments are given which support the numerical results. Received 11 July 2002 / Received in final form 9 September 2002 Published online 29 October 2002     

Universal properties of shortest paths in isotropically correlated random potentials

We consider the optimal paths in a d-dimensional lattice, where the bonds have isotropically correlated random weights. These paths can be interpreted as the ground state configuration of a simplified polymer model in a random potential. We study how the universal scaling exponents, the roughness and the energy fluctuation exponent, depend on the strength of the disorder correlations. Our numerical results using Dijkstra's algorithm to determine the optimal path in directed as well as undirected lattices indicate that the correlations become relevant if they decay with distance slower than 1/r in d = 2 and 3. We show that the exponent relation 2ν - ω = 1 holds at least in d = 2 even in case of correlations. Both in two and three dimensions, overhangs turn out to be irrelevant even in the presence of strong disorder correlations. Received 20 December 2002 / Received in final form 10 April 2003 Published online 20 June 2003 RID="a" ID="a"e-mail: schorr@lusi.uni-sb.de     

Partitioning of a heterotelechelic polystyrene to separate interfaces of thin films

Heterotelechelic deuteropolystyrenes have been synthesised with a tertiary amine functionality at one end and a fluorocarbon group at the other end of the polymer chain. A layer of this polymer, circa 120 ? thick, has been attached to the surface of a silicon substrate and subsequently covered with a much thicker layer of hydrogenous polystyrene. The combination has then been annealed at 413 K under vacuum for defined times and the subsequent distribution of the deutero heterotelechelic polymer determined using nuclear reaction analysis and neutron reflectometry. The influences of annealing time, molecular weight and thickness of the hydrogenous polymer have been examined. Nuclear reaction analysis showed that an excess of the heterotelechelic polymer formed at both interfaces with a larger excess remaining at the substrate-polymer interface. When the molecular weight of the hydrogenous polymer is lower than that of the deuteropolymer, the deutero layer is initially swollen by the hydrogenous polymer but the thickness then decreases as deutero polymer becomes detached from the silicon substrate and an additional excess layer is eventually formed at the vacuum-polymer surface. When the molecular weight of the hydrogenous polymer is higher, there is an initial shrinkage of the deuteropolymer layer, but the original thickness (∼ radius of gyration of the deuteropolymer) is regained on prolonged annealing. There is no evidence for bridging between the two interfaces by the heterotelechelic polymer. After five days annealing the volume fraction distribution of the deuteropolymer at the silicon substrate was well described by a self-consistent field model where the only adjustable parameter was the sticking energy of the tertiary amine group to the silicon substrate for which a value of 8k _B T was obtained. Comparison of the dependence of the equilibrium layer thickness of the deuteropolymer on the equilibrium grafting density at the silicon surface with the predictions of scaling theory for brush-like polymer layers suggested that the grafted molecules were in the ideal, unperturbed brush region. Received 12 October 2000 and Received in final form 27 March 2001     

Mobility in thin polymer films ranging from local segmental motion, Rouse modes to whole chain motion: A coupling model consideration

Large increases of mobility of local segmental relaxation observed in polymer films as the film thickness is decreased, as evidenced by decreases of the glass temperature, are not found for relaxation mechanisms that have longer length scales including the Rouse relaxation modes and the diffusion of entire polymer chains. We show that the coupling model predictions, when extended to consider polymer thin films, are consistent with a large increase of the mobility of the local segmental motions and the lack of such a change for the Rouse modes and the diffusion of entire polymer chains. There are two effects that can reduce the coupling parameter of the local segmental relaxation in thin films. One is the chain orientation that is induced parallel to the surface when the film thickness h becomes smaller than the end-to-end distance of the chains and the other is a finite-size effect when h is no longer large compared to the cooperative length scale. Extremely thin ( ≈ 1.5 nm) films obtained by intercalating a polymer into layered silicates have thickness significantly less than the cooperative length scale near the bulk polymer glass transition temperature. As a result, the coupling parameter of the local segmental relaxation in such thin films is reduced almost to zero. With this plausible assumption, we show the coupling model can explain quantitatively the large decrease of the local segmental relaxation time found experimentally. Received 1 August 2001 and Received in final form 1 December 2001     

The secondary structure of RNA under tension

We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second-order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a macroscopic end-to-end distance at high forces. At low temperatures, the sequence inhomogeneities modify the critical behaviour. We provide numerical evidence for the universality of the critical exponents which, by extrapolation of the scaling laws to zero force, contain useful information on the ground-state (f = 0) properties. This provides a good method for quantitative studies of scaling exponents characterizing the collapsed globule. In order to get rid of the blurring effect of thermal fluctuations, we restrict ourselves to the ground state at fixed external force. We analyze the statistics of rearrangements, in particular below the critical force, and point out its implications for force-extension experiments on single molecules. Received 18 June 2002 and Received in final form 23 September 2002 RID="a" ID="a"e-mail: muller@ipno.in2p3.fr     

Energy landscapes, lowest gaps, and susceptibility of elastic manifolds at zero temperature

We study the effect of an external field on (1 + 1) and (2 + 1) dimensional elastic manifolds, at zero temperature and with random bond disorder. Due to the glassy energy landscape the configuration of a manifold changes often in abrupt, “first order”-type of large jumps when the field is applied. First the scaling behavior of the energy gap between the global energy minimum and the next lowest minimum of the manifold is considered, by employing exact ground state calculations and an extreme statistics argument. The scaling has a logarithmic prefactor originating from the number of the minima in the landscape, and reads ΔE ₁∼L ^θ[ln(L _z L ^{- ζ})]^-1/2, where ζ is the roughness exponent and θ is the energy fluctuation exponent of the manifold, L is the linear size of the manifold, and L_z is the system height. The gap scaling is extended to the case of a finite external field and yields for the susceptibility of the manifolds ∼L ^{2D + 1 - θ}[(1 - ζ)ln(L)]^1/2. We also present a mean field argument for the finite size scaling of the first jump field, h ₁∼L ^{d - θ}. The implications to wetting in random systems, to finite-temperature behavior and the relation to Kardar-Parisi-Zhang non-equilibrium surface growth are discussed. Received December 2000 and Received in final form April 2001     

Elastic rod model of a supercoiled DNA molecule

We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod-like chain, involving two elastic constants, the bending and the twist rigidities. Writing this model in terms of Euler angles, we show that the corresponding Hamiltonian is singular and needs a small distance cut-off, which is a natural length scale giving the limit of validity of the model, of the order of the double-helix pitch. The rod-like chain in the presence of the cut-off is able to reproduce quantitatively the experimentally observed effects of supercoiling on the elongation-force characteristics, in the small supercoiling regime. An exact solution of the model, using both transfer matrix techniques and its mapping to a quantum mechanics problem, allows to extract, from the experimental data, the value of the twist rigidity. We also analyse the variation of the torque and the writhe-to-twist ratio versus supercoiling, showing analytically the existence of a rather sharp crossover regime which can be related to the excitation of plectoneme-like structures. Finally we study the extension fluctuations of a stretched and supercoiled DNA molecule, both at fixed torque and at fixed supercoiling angle, and we compare the theoretical predictions to some preliminary experimental data. Received 1 April 1999 and Received in final form 4 January 2000     

Delocalization in disordered chains with random symmetrical impurities

We study in this paper, with the context of a tight-binding on-side model, the electronic properties of one-dimensional random lattices with correlated impurities. We show that, when symmetrical impurities are inserted in a host chain of site energy and a constant hopping interaction V, diffusion will occur even when is random. We provide analytic expressions for the transmittance and confirm the theoretical results by a great deal of numerical calculations. When = V, we find that the mean-square displacement (MSD) follows the law m ² ∝t ^β with β = 2.0 for = constant and β = 1.0 for = = random, respectively. Received 15 January 2001 and Received in final form 30 April 2001     

Fibril stability in solutions of twisted -sheet peptides: a new kind of micellization in chiral systems

The problem of fibril (fibre) formation in chiral systems is explored theoretically being supported by experiments on synthetic de novo 11-mer peptide forming self-assembled -sheet tapes. Experimental data unambiguously indicate that the tapes form fibrils of nearly monodisperse thickness ca . 8-10 nm. Fibril formation and stabilisation are attributed to inter-tape face-to-face attraction and their intrinsic twist, correspondingly. The proposed theory is capable of predicting the fibril aggregation number and its equilibrium twist in terms of molecular parameters of the primary tapes. The suggested novel mechanism of twist stabilisation of finite aggregates (fibrils) is different to the well-known stabilisation of micelles in amphiphilic systems, and it is likely to explain the formation and stability of fibrils in a wide variety of systems including proteinaceous amyloid fibres, sickle-cell hemoglobin fibres responsible for HbS anemia, corkscrew threads found in chromonics in the presence of chiral additives and native cellulose microfibrillar crystallites. The theory also makes it possible to extract the basic molecular parameters of primary tapes (inter-tape attraction energy, helical twist step, elastic moduli) from the experimental data. Received 7 May 1999 and Received in final form 15 February 2000     

Glassy effects in the swelling/collapse dynamics of homogeneous polymers

We investigate, using numerical simulations and analytical arguments, a simple one-dimensional model for the swelling or the collapse of a closed polymer chain of size N, representing the dynamical evolution of a polymer in a Θ-solvent that is rapidly changed into a good solvent (swelling) or a bad solvent (collapse). In the case of swelling, the density profile for intermediate times is parabolic and expands in space as t ^1/3, as predicted by a Flory-like continuum theory. The dynamics slows down after a time ∝N ² when the chain becomes stretched, and the polymer gets stuck in metastable “zig-zag” configurations, from which it escapes through thermal activation. The size of the polymer in the final stages is found to grow as . In the case of collapse, the chain very quickly (after a time of order unity) breaks up into clusters of monomers (“pearls”). The evolution of the chain then proceeds through a slow growth of the size of these metastable clusters, again evolving as the logarithm of time. We enumerate the total number of metastable states as a function of the extension of the chain, and deduce from this computation that the radius of the chain should decrease as 1/ln(ln t). We compute the total number of metastable states with a given value of the energy, and find that the complexity is non-zero for arbitrary low energies. We also obtain the distribution of cluster sizes, that we compare to simple “cut-in-two” coalescence models. Finally, we determine the aging properties of the dynamical structure. The subaging behaviour that we find is attributed to the tail of the distribution at small cluster sizes, corresponding to anomalously “fast” clusters (as compared to the average). We argue that this mechanism for subaging might hold in other slowly coarsening systems. Received 23 October 2000     

Failure time and critical behaviour of fracture precursors in heterogeneous materials

The acoustic emission of fracture precursors, and the failure time of samples of heterogeneous materials (wood, fiberglass) are studied as a function of the load features and geometry. It is shown that in these materials the failure time is predicted with a good accuracy by a model of microcrack nucleation proposed by Pomeau. We find that the time interval δt between events (precursors) and the energy ɛ are power law distributed and that the exponents of these power laws depend on the load history and on the material. In contrast, the cumulated acoustic energy E presents a critical divergency near the breaking time τ which is E∼ . The positive exponent γ is independent, within error bars, on all the experimental parameters. Received 31 July 2001 and Received in final form 17 December 2001     

Evidence for a proton halo in 27P through measurements of reaction cross-sections at intermediate energies

Measurements of reaction cross-sections ( σ_R's) for some proton-rich nuclei ( N = 11–15 isotones) on carbon target at intermediate energies have been performed on RIBLL of HIRFL. A larger enhancement of the σ_R for ²⁷P has been observed than for its neighboring nuclei. A large difference between the proton and neutron density distributions (proton halo) is necessary to explain the enhanced cross-section for ²⁷P within the framework of the Glauber model. Density distributions with HO-type core plus Yukawa-square tail and rms radii for ²⁷P have been deduced from the measured σ_R data for the first time, which conform the long tail in its densities as predicted by RMF calculations. Received: 23 May 2001 / Accepted: 7 November 2001     

Phase equilibria in random multiblock copolymers

A mean-field theory for domain structures in random multiblock copolymer melts is developed. We focus on the finite molecular weight effects resulting in a competition between macroscopic phase separation and microdomain formation in the system. We identify an essential parameter N ε controlling the phase behavior of the system, where N is the number of blocks per chain and ε is the composition asymmetry parameter (= the difference between the mean copolymer composition and its critical value). The phase diagram involving N ε and the reduced temperature as variables is obtained. The regions of coexistence of two or more phases are identified. We show that a superstructure formation on cooling is always pre-empted by a macroscopic phase separation of the macroscopically homogeneous (disordered) system yielding two homogeneous phases: H ₀↦H ₁ + H ₂. The third (lamellar) phase separates on further cooling. Then hexagonal and body-centred-cubic phases take over if N ε 1. As the Flory interaction parameter χ increases further, the standard transitions BCC↦HEX↦LAM take place. Received 13 July 2001     

Non-homogeneous random walks, generalised master equations, fractional Fokker-Planck equations, and the generalised Kramers-Moyal expansion

A generalised random walk scheme for random walks in an arbitrary external potential field is investigated. From this concept which accounts for the symmetry breaking of homogeneity through the external field, a generalised master equation is constructed. For long-tailed transfer distance or waiting time distributions we show that this generalised master equation is the genesis of apparently different fractional Fokker-Planck equations discussed in literature. On this basis, we introduce a generalisation of the Kramers-Moyal expansion for broad jump length distributions that combines multiples of both ordinary and fractional spatial derivatives. However, it is shown that the nature of the drift term is not changed through the existence of anomalous transport statistics, and thus to first order, an external potential Φ(x) feeds back on the probability density function W through the classical term ∝/ x (x)W(x, t), i.e., even for Lévy flights, there exists a linear infinitesimal generator that accounts for the response to an external field. Received 30 June 2000 and Received in final form 12 November 2000     

Dynamical properties of the slithering-snake algorithm: A numerical test of the activated-reptation hypothesis

Correlations in the motion of reptating polymers in a melt are investigated by means of Monte Carlo simulations of the three-dimensional slithering-snake version of the bond-fluctuation model. Surprisingly, the slithering-snake dynamics becomes inconsistent with classical reptation predictions at high chain overlap (created either by chain length N or by the volume fraction φ of occupied lattice sites), where the relaxation times increase much faster than expected. This is due to the anomalous curvilinear diffusion in a finite time window whose upper bound (N) is set by the density of chain ends φ/N. Density fluctuations created by passing chain ends allow a reference polymer to break out of the local cage of immobile obstacles created by neighboring chains. The dynamics of dense solutions of “snakes” at t ≪ is identical to that of a benchmark system where all chains but one are frozen. We demonstrate that the subdiffusive dynamical regime is caused by the slow creeping of a chain out of its correlation hole. Our results are in good qualitative agreement with the activated-reptation scheme proposed recently by Semenov and Rubinstein (Eur. Phys. J. B, 1 (1998) 87). Additionally, we briefly comment on the relevance of local relaxation pathways within a slithering-snake scheme. Our preliminary results suggest that a judicious choice of the ratio of local to slithering-snake moves is crucial to equilibrate a melt of long chains efficiently. Received: 18 December 2002 / Accepted: 3 April 2003 / Published online: 12 May 2003 RID="a" ID="a"e-mail: jwittmer@dpm.univ-lyon1.fr RID="b" ID="b"Current address: University of Illinois at Urbana-Champaign.     

Quark-hadron duality in electron-pion scattering

We explore the relationship between exclusive and inclusive electromagnetic scattering from the pion, focusing on the transition region at intermediate Q². Combining Drell-Yan data on the leading twist quark distribution in the pion with a model for the resonance region at large x, we calculate QCD moments of the pion structure function over a range of Q², and quantify the role of higher twist corrections. Using a parameterization of the pion elastic form factor and phenomenological models for the π↦ρ transition form factor, we further test the extent to which local duality may be valid for the pion. Received: 10 February 2003 / Accepted: 12 March 2003 / Published online: 27 May 2003     

Drift of a polymer chain in a porous medium --A Monte Carlo study

We investigate the drift of an end-labeled telehelic polymer chain in a frozen disordered medium under the action of a constant force applied to the one end of the macromolecule by means of an off-lattice bead spring Monte Carlo model. The length of the polymers N is varied in the range 8 < N < 128, and the obstacle concentration in the medium C is varied from zero up to the percolation threshold C≈ 0.75. For field intensities below a C-dependent critical field strength B _c, where jamming effects become dominant, we find that the conformational properties of the drifting chains can be interpreted as described by a scaling theory based on Pincus blobs. The variation of drag velocity with C in this interval of field intensities is qualitatively described by the law of Mackie-Meares. The threshold field intensity B _c itself is found to decrease linearly with C. Received 20 August 2001 and Received in final form 19 November 2001     

Polymers with self-avoiding interaction in random medium: a localization-delocalization transition

In this paper we investigate the problem of a long self-avoiding polymer chain immersed in a random medium. We find that in the limit of a very long chain and when the self-avoiding interaction is weak, the conformation of the chain consists of many “blobs” with connecting segments. The blobs are sections of the molecule curled up in regions of low potential in the case of a Gaussian distributed random potential or in regions of relatively low density of obstacles in the case of randomly distributed hard obstacles. We find that as the strength of the self-avoiding interaction is increased the chain undergoes a delocalization transition in the sense that the appropriate free energy per monomer is no longer negative. The chain is then no longer bound to a particular location in the medium but can easily wander around under the influence of a small perturbation. For a localized chain we estimate quantitatively the expected number of monomers in the “blobs” and in the connecting segments. Received 13 November 2002 Published online 14 March 2003