We probe the mechanisms at work in the build-up of thermoreversible gel networks, with the help of hybrid gelatin gels containing a controlled density of irreversible, covalent crosslinks (CL), which we quench below the physical gelation temperature. The detailed analysis of the dependence on covalent crosslink density of both the shear modulus and optical activity evolutions with time after quench enables us to identify two stages of the physical gelation process, separated by a temperature dependent crossover modulus: (i) an early nucleation regime during which rearrangements of the triple-helix CL play a negligible role, (ii) a late, logarithmic aging one, which is preserved, though slowed down, in the presence of irreversible CL. We show that aging is fully controlled by rearrangements and discuss the implication of our results in terms of the switch from an early, local dynamics to a late, cooperative long-range one.
We performed Langevin dynamics simulations of amphiphilic polymers that contain strongly associating stickers connected by long soluble chain segments. We explored the aging of a thermoreversible gel which is crosslinked by aggregates (clusters) of the stickers and observed a dramatic increase of their lifetime with aging. We find that the observed aging is the result of structural reorganization of the network: the number of crosslinks decreases with time as small clusters disintegrate and their stickers are reabsorbed by large clusters that grow and become more stable by forming additional i…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in separating the effects of thermodynamics and chemical kinetics on the dynamics and mechanics of these systems, and is extensible to arbitrarily nonequilibrium situations and nonlinear mechanical properties. We examine the model's quiescent (and heterogeneous) dynamics, nonequilibrium chemical dynamics, and mechanical properties. Many of our results may be understood …
We address the problem of inverse polymer swelling. This phenomenon, in which a collapsed polymer chain swells upon decreasing temperature, can be observed experimentally in so-called thermoreversible homopolymers in aqueous solution, and is believed to be related to the role of hydrophobicity in protein folding. We consider a lattice-fluid model of water, defined on a body-centered cubic lattice, which has been previously shown to account for most thermodynamic anomalies of water and of hydrophobic solvation for monomeric solutes. We represent the polymer as a self-avoiding walk on the same l…
Through a combination of rheological characterization and temperature-variable imaging methods, a novel gelation pathway in dilute solutions of a semiconducting polymer to achieve interconnected, crystalline networks with hierarchical porosity is reported. Upon rapid cooling, solutions of regioregular poly(3-hexylthiophene) (RR-P3HT) in ortho-dichlorobenzene formed thermoreversible gels. Temperature-variable confocal microscopy revealed cooling-induced structural rearrangement to progress through viscoelastic phase separation. The phase separation process arrested prematurely during the format…
Using Langevin dynamics simulations in three dimensions (3D), we investigate the dynamics of polymer translocation into the regions between two parallel plane walls with separation $R$ under a driving force $F$, respectively. Compared with an unconfined environment, the translocation dynamics is greatly changed due to the crowding effect of the partially translocated monomers. Translocation time $τ$ initially decreases rapidly with increasing $R$ and then saturates for larger $R$, and the confined environment leads to a nonuniversal dependence of $τ$ on $F$.
Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules in box-like cavities with strong confinement in one direction and with square and elliptical cross sections in the lateral plane. Motivated by these experiments, we employ Monte Carlo and Brownian dynamics simulations to study the physical behaviour of two polymers confined to small cavities with shapes comparable to those used in the experiments. We quantif…
The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes to the late time diffusive regime, highly coarse grained models with purely repulsive interactions between monomers are widely used since they are computationally the most efficient. Here using large scale molecular dynamics simulations the effect of including the attractive interaction between monomers on the dynamics of entangled polymers melts is explored…
In a previous article [E.M. Blokhuis, K.I. Skau, and J.B. Avalos, J. Chem. Phys. 119, 3483 (2003)], a self-consistent field formalism was derived for weakly adsorbing polymers, valid for any chain length. It was shown that the presence of a solid wall induces an ordering of the polymers on the scale of the radius of gyration far away from the surface (the distal region). These oscillations in the polymer concentration profile were first noted in work by Semenov et al., and later observed in numerical solutions of the Scheutjens and Fleer self-consistent field model. In the present paper, we co…
Ultrathin polymer films that are produced e.g. by spin-coating are believed to be stressed since polymers are 'frozen in' into out-of-equilibrium configurations during this process. In the framework of a viscoelastic thin film model, we study the effects of lateral residual stresses on the dewetting dynamics of the film. The temporal evolution of the height profiles and the velocity profiles inside the film as well as the dissipation mechanisms are investigated in detail. Both the shape of the profiles and the importance of frictional dissipation vs. viscous dissipation inside the film are fou…
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance between the centers of mass of the polymers, lambda, and examine the effects on the free energy functions of varying the channel diameter D and length L, as well as the polymer length N and bending rigidity, kappa. For infinitely long cylinders, F is a maximum at lambda=0, and decreases with lambda until the polymers are no longer in contact. For flexible cha…
We present an analysis of a partially directed walk model of a polymer which at one end is tethered to a sticky surface and at the other end is subjected to a pulling force at fixed angle away from the point of tethering. Using the kernel method, we derive the full generating function for this model in two and three dimensions and obtain the respective phase diagrams. We observe adsorbed and desorbed phases with a thermodynamic phase transition in between. In the absence of a pulling force this model has a second-order thermal desorption transition which merely gets shifted by the presence of …
Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides employed in experiments [W.A. Petka et al., Science 281, 389 (1998)], the endblocks of the polymer chains are modeled as hydrophobic rods representing the alpha-helical part of the polypeptides whereas the central B-block is hydrophilic and semi-flexible. We have determined structural properties, such as the hydrophobic cluster-size distribution function, the g…
The dynamic and static properties of a supercooled (non-entangled) polymer melt are investigated via molecular dynamics (MD) simulations. The system is confined between two completely smooth and purely repulsive walls. The wall-to-wall separation (film thickness), $D$, is varied from about 3 to about 14 times the bulk radius of gyration. Despite the geometric confinement, the supercooled films exhibit many qualitative features which were also observed in the bulk and could be analyzed in terms of mode-coupling theory (MCT). Examples are the two-step relaxation of the incoherent intermediate sc…
A co-polycondensation reaction is discussed analytically and by Monte-Carlo simulations where two reactive units compete for reactions with an alternating third reactive unit, whereby irreversible reactions replace bonds which are able to undergo exchange reactions. The resulting number average molar mass, $M_{\text{n}}$, exhibits only one distinct peak at the stoichiometric condition of both competitors with the alternating partner. The weight average molar mass, $M_{\text{w}}$, reaches an additional second peak at the stoichiometric condition between the dominating competitor and the alterna…
Recent experiments have imposed controlled swelling patterns on thin polymer films, which subsequently buckle into three-dimensional shapes. We develop a solution to the design problem suggested by such systems, namely, if and how one can generate particular three-dimensional shapes from thin elastic sheets by mere imposition of a two-dimensional pattern of locally isotropic growth. Not every shape is possible. Several types of obstruction can arise, some of which depend on the sheet thickness. We provide some examples using the axisymmetric form of the problem, which is analytically tractable…
We have studied the pearling instability induced on hollow tubular lipid vesicles by hydrophilic polymers with hydrophobic side groups along the backbone. The results show that the polymer concentration is coupled to local membrane curvature. The relaxation of a pearled tube is characterized by two different well-separated time scales, indicating two physical mechanisms. We present a model, which explains the observed phenomena and predicts polymer segregation according to local membrane curvature at late stages.
We introduce a kinetic model of coarsening of transient polymer networks during the intermediate stages of phase separation in polymer systems. The model explicitly takes into account the effect of the connectivity of polymer chains. We show that during the intermediate stages the size of the droplet grows according to an unusual coarsening law $R \sim t^{1/(d + 3)}$. When the network structure breaks up, the coarsening law may cross over to $R \sim \ln t^{-1}$, until only at very late stages the Lifshitz-Slyozov coarsening law $R \sim t^{1/3}$ is recovered.
Large scale Monte Carlo simulations of dense layers of grafted polymer chains in good solvent conditions are used to explore the relaxation of a polymer brush. Monomer displacements are analyzed for the directions parallel and perpendicular to the grafting plane. Auto-correlation functions of individual segments or chain sections are monitored as function of time. We demonstrate that the terminal relaxation time $τ$ of grafted layers well in the brush regime grows exponentially with degree of polymerization $N$ of the chains, $τ\propto N^{3}\exp(N/N_{e})$, with $N_{e}$ the entanglement degree …
We study the activated motion of adsorbed polymers which are driven over a structured substrate by a localized point force.Our theory applies to experiments with single polymers using, for example, tips of scanning force microscopes to drag the polymer.We consider both flexible and semiflexible polymers,and the lateral surface structure is represented by double-well or periodic potentials. The dynamics is governed by kink-like excitations for which we calculate shapes, energies, and critical point forces. Thermally activated motion proceeds by the nucleation of a kink-antikink pair at the poin…
We solve the dynamic equations of motion for a growing semi-flexible polymer, or fiber, approaching a fluctuating membrane at an angle. At late times we find three different regimes: fiber {\em stalling}, when fiber growth stops due to membrane resistence, {\em run-away}, in which the polymer bends away from the membrane, and another regime in which the membrane response is nonlinear and tubular membrane {\em spicules} are formed. We discuss which regions of the resulting `phase diagram' are explored by (i) single and bundled actin fibers in living cells, (ii) sickle hemoglobin fibers in red b…
An extended Molecular-Dynamics study of the short-time "glassy" elasticity exhibited by a polymer melt of linear fully-flexible chains above the glass transition is presented. The focus is on the infinite-frequency shear modulus $G_\infty$ manifested in the picosecond time scale and the relaxed plateau $G_p$ reached at later times and terminated by the structural relaxation. The local stiffness of the interactions with the first neighbours of each monomer exhibits marked distribution with average value given by $G_\infty$. In particular, the neighbourhood of the end monomers of each chain are …
The polymerization dynamics of double-stranded polymers, such as actin filaments, is investigated theoretically using simple chemical kinetic models that explicitly take into account some microscopic details of the polymer structure and the lateral interactions between the protofilaments. By considering all possible molecular configurations, the exact analytical expressions for the growth velocity and dispersion for two-stranded polymers are obtained in the case of the growing at only one end, and for the growth from both polymer ends. Exact theoretical calculations are compared with the predi…
The dynamic structure factor of semiflexible polymers in solution is derived from the wormlike chain model. Special attention is paid to the rigid constraint of an inextensible contour and to the hydrodynamic interactions. For the cases of dilute and semidilute solutions exact expressions for the initial slope are obtained. When the hydrodynamic interaction is treated on the level of a renormalized friction coefficient, the decay of the structure factor due to the structural relaxation obeys a stretched exponential law in agreement with experiments on actin. We show how the characteristic para…
In earlier work we provided the first evidence that the collapse, or coil-globule, transition of an isolated polymer in solution can be seen in a four-dimensional model. Here we investigate, via Monte Carlo simulations, the canonical lattice model of polymer collapse, namely interacting self-avoiding walks, to show that it not only has a distinct collapse transition at finite temperature but that for any finite polymer length this collapse has many characteristics of a rounded first-order phase transition. However, we also show that there exists a `$θ$-point' where the polymer behaves in a sim…
We present Monte Carlo simulations of colloidal particles pulled into grafted polymer layers by external fields. The insertion free energy of a single colloid into the polymer layer is qualitatively different for surfaces with an ordered and a disordered distribution of grafting points. Moreover, the tendency of colloidal particles to traverse the grafting layer is strongly size dependent. In dense colloidal suspensions, under the influence of sufficiently strong external force, a collective instability allows the colloids to penetrate and form internally ordered, columnar structures spanning …
Using molecular dynamics simulation of a polymer glass model we investigate free-standing polymer films focusing on the in-plane shear modulus $μ$ and the corresponding shear-stress relaxation modulus $G(t)$ as functions of temperature $T$, film thickness $H$ (tuned by means of the lateral box size $L$) and sampling time $Δt$. Various observables are seen to vary linearly with $1/H$ demonstrating thus the (to leading order) linear superposition of bulk and surface properties. In agreement with recent studies on three-dimensional polymer glass-formers, $μ$ and $G(t)$ are found to decrease conti…
The cytoskeleton of eukaryotic cells provides mechanical support and governs intracellular transport. These functions rely on the complex mechanical properties of networks of semiflexible protein filaments. Recent theoretical interest has focused on mesoscopic properties of such networks and especially on the effect of local, non-affine bending deformations on mechanics. Here, we study the impact of local network deformations on the scale-dependent mobility of probe particles in entangled networks of semiflexible actin filaments by high-bandwidth microrheology. We find that micron-sized partic…
Thermo-mechanical properties of polymer networks depend on functionality of the monomer precursors -- an association that is frequently exploited in materials science. We use molecular simulations to generate spatial networks from chemically different monomers with identical functionality and show that such networks have several universal graph-theoretical properties as well as near universal Young's modulus. The vitrification temperature is shown to be universal only up to a certain density of the network, as measured by the bond conversion. The latter observation is explained by the fact tha…
Shear flow is known to induce huge density fluctuations in otherwise clear and uniform polymer solutions. This effect is rooted in the elasticity of the entangled polymer network, and can span distances over a thousand chains wide. It has been observed in many scattering experiments, and later explained by mathematical theories. Here we inspect this phenomenon from a direct particle simulation viewpoint. The main novelty is a velocity dependent friction force, coupling the entire system and solved efficiently with sparse matrix algebra. Our minimalist model runs on a desktop PC and the results…
We investigate the dynamics of spreading in a regime where the shape of the drop is close to a spherical cap. The latter simplification is applicable in the late (viscous) stage of spreading for highly viscous drops with a diameter below the capillary length. Moreover, it applies to the spreading of a drop on a swellable polymer brush, where the complex interaction with the substrate leads to a very slow spreading dynamics. The spherical cap geometry allows to derive a closed ordinary differential equation (ODE) for the spreading if the capillary number is a function of the contact angle as it…
Finite-size scaling arguments naturally lead us to introduce a coordinate-dependent diffusion coefficient in a Fokker-Planck description of the late stage dynamics of unbiased polymer translocation through a membrane pore. The solution for the probability density function of the chemical coordinate matches the initial-stage subdiffusive regime and takes into account the equilibrium entropic drive. Precise scaling relations connect the subdiffusion exponent to the divergence with the polymer length of the translocation time, and also to the singularity of the probability density function at the…
We study theoretically the dynamics of living polymers which can add and subtract monomer units at their live chain ends. The classic example is ionic living polymerization. In equilibrium, a delicate balance is maintained in which each initiated chain has a very small negative average growth rate (``velocity'') just sufficient to negate the effect of growth rate fluctuations. This leads to an exponential molecular weight distribution (MWD) with mean Nbar. After a small perturbation of relative amplitude epsilon, e.g. a small temperature jump, this balance is destroyed: the velocity acquires a…
We study the phase behavior of a symmetric binary polymer blend which is confined into a thin film. The film surfaces interact with the monomers via short range potentials. We calculate the phase behavior within the self-consistent field theory of Gaussian chains. Over a wide range of parameters we find strong first order wetting transitions for the semi-infinite system, and the interplay between the wetting/prewetting behavior and the phase diagram in confined geometry is investigated. Antisymmetric boundaries, where one surface attracts the A component with the same strength than the opposit…
Speed of sound waves in gases and liquids is governed by medium compressibility. There exists another type of non-dispersive waves which speed depends on stress instead of medium elasticity. A well-known example is the Alfven wave propagating, with a speed determined by a magnetic tension, in plasma permeated by a magnetic field. Later, an elastic analog of the Alfven waves has been predicted in a flow of dilute polymer solution, where elastic stress engendered by polymer stretching determines the elastic wave speed. Here, we present quantitative evidence of elastic Alfven waves observed in el…
We study irreversible polymer adsorption from dilute solutions theoretically. Universal features of the resultant non-equilibrium layers are predicted. Two cases are considered, distinguished by the value of the local monomer-surface sticking rate Q: chemisorption (very small Q) and physisorption (large Q). Early stages of layer formation entail single chain adsorption. While single chain physisorption times tau_ads are typically microsecs, for chemisorbing chains of N units we find experimentally accessible times tau_ads = Q^{-1} N^{3/5}, ranging from secs to hrs. We establish 3 chemisorption…
We present dynamic light scattering (DLS) measurements of soft polymethyl-methacrylate (PMMA) and polyacrylamide(PA) polymer gels prepared with trapped bodies (latex spheres or maghemite nanoparticles). We show that the anomalous diffusivity of the trapped particles can be analyzed in terms of a fractal Gaussian network gel model for the entire time range probed by DLS technique. This model is a generalization of the Rouse model for linear chains extended for structures with power law network connectivity scaling, which includes both percolating and uniform bulk gel limits. For a dilute disper…
Recent experiments have shown that trivalent ion, spermidine$^{3+}$, can provoke lateral microphase segregation in DNA brushes. Using molecular simulations and simple theoretical arguments, we explore the effects of trivalent counterions on polyelectrolyte brushes. At a proper range of grafting density, polymer size, and ion concentration, the brush polymers collapse heterogeneously into octopus-like surface micelles. Remarkably, the heterogeneity in brush morphology is maximized and the relaxation dynamics of chain and condensed ion are the slowest at the 1:3 stoichiometric concentration of t…
