Intramolecular long-range correlations in polymer melts: the segmental size distribution and its moments

Normal and abnormal glycogen structure - A review

Glycogen, a complex branched glucose polymer, is found in animals and bacteria, where it serves as an energy storage molecule. It has linear (1 → 4)-α glycosidic bonds between anhydroglucose monomer units, with branch points connected by (1 → 6)-α bonds. Individual glycogen molecules are referred to as β particles. In organs like the liver and heart, these β particles can bind into larger aggregate α particles, which exhibit a rosette-like morphology. The mechanisms and bonding underlying the aggregation process are not fully understood. For example, mammalian liver glycogen has been observed to be molecularly fragile under certain conditions, such as glycogen from diabetic livers fragmenting when exposed to dimethyl sulfoxide (DMSO), while glycogen from healthy livers is much less fragile; this indicates some difference, as yet unknown, in the bonding between β particles in healthy and diabetic glycogen. This fragility may have implications for blood sugar regulation, especially in pathological conditions such as diabetes.

On the Swelling of Polymer Network Strands

Large scale computer simulations are employed to analyze the conformations of network strands in polymer networks at preparation conditions (characterized by a polymer volume fraction of ϕ0) and when swollen to equilibrium (characterized by a polymer volume fraction ϕ < ϕ0). Network strands in end-linked model networks are weakly stretched and partially swollen at preparation conditions as compared to linear polymers in the same solvent at ϕ0. Equilibrium swelling causes non-ideal chain conformations characterized by an effective scaling exponent approaching 7/10 on intermediate length scales for increasing overlap of the chains. The chain size in a network consists of a fluctuating and a time average "elastic" contribution. The elastic contribution swells essentially affinely ∝(ϕ0/ϕ)2/3, whereas the swelling of the fluctuating part lies between the expected swelling of the entanglement constraints and the swelling of non-cross-linked chains in a comparable semi-dilute solution. The total swelling of chain size results from the changes of both fluctuating and non-fluctuating contributions.

Non-Rouse behavior of short ring polymers in melts by molecular dynamics simulations

Short ring polymers are expected to behave nearly Rouse-like due to the little effect of topological constraints of non-knot and non-concatenation. However, this notion is questioned because of several simulation and experiment findings in recent times, which requires a further more quantitative study. Therefore, we perform a deep investigation of statics and dynamics of flexible short ring polymers (N < 2Ne) in melts via molecular dynamics simulations by further taking linear analogues as well as all-crossing ring and linear polymers with switched off topological constraints for comparisons and demonstrate the noticeable deviations from the Rouse model in terms of local and global scales. Although the overall size is compact, the subchains are swollen, which is traced back to the deeper "segmental correlation hole" effect. The same scaling relationship of the non-Gaussian deviation of the static structure factor holds, but the deviation magnitude of rings is larger than that of linear analogues. By checking the non-Gaussian parameter and autocorrelation function of center-of-mass velocity, the physical origin of anomalous sub-diffusions of short rings is identified as unscreened viscoelastic hydrodynamic interactions and not correlation hole effects, like linear analogues.

Statistical field theory for nonlinear elasticity of polymer networks with excluded volume interactions

Polymer networks formed by cross linking flexible polymer chains are ubiquitous in many natural and synthetic soft-matter systems. Current micromechanics models generally do not account for excluded volume interactions except, for instance, through imposing a phenomenological incompressibility constraint at the continuum scale. This work aims to examine the role of excluded volume interactions on the mechanical response. The approach is based on the framework of the self-consistent statistical field theory of polymers, which provides an efficient mesoscale approach that enables the accounting of excluded volume effects without the expense of large-scale molecular modeling. A mesoscale representative volume element is populated with multiple interacting chains, and the macroscale nonlinear elastic deformation is imposed by mapping the end-to-end vectors of the chains by this deformation. In the absence of excluded volume interactions, it recovers the closed-form results of the classical theory of rubber elasticity. With excluded volume interactions, the model is solved numerically in three dimensions using a finite element method to obtain the energy, stresses, and linearized moduli under imposed macroscale deformation. Highlights of the numerical study include: (i) the linearized Poisson's ratio is very close to the incompressible limit without a phenomenological imposition of incompressibility; (ii) despite the harmonic Gaussian chain as a starting point, there is an emergent strain-softening and strain-stiffening response that is characteristic of real polymer networks, driven by the interplay between the entropy and the excluded volume interactions; and (iii) the emergence of a deformation-sensitive localization instability at large excluded volumes.

Multiscale equilibration of highly entangled isotropic model polymer melts

We present a computationally efficient multiscale method for preparing equilibrated, isotropic long-chain model polymer melts. As an application, we generate Kremer-Grest melts of 1000 chains with 200 entanglements and 25 000-2000 beads/chain, which cover the experimentally relevant bending rigidities up to and beyond the limit of the isotropic-nematic transition. In the first step, we employ Monte Carlo simulations of a lattice model to equilibrate the large-scale chain structure above the tube scale while ensuring a spatially homogeneous density distribution. We then use theoretical insight from a constrained mode tube model to introduce the bead degrees of freedom together with random walk conformational statistics all the way down to the Kuhn scale of the chains. This is followed by a sequence of simulations with carefully parameterized force-capped bead-spring models, which slowly introduce the local bead packing while reproducing the larger-scale chain statistics of the target Kremer-Grest system at all levels of force-capping. Finally, we can switch to the full Kremer-Grest model without perturbing the structure. The resulting chain statistics is in excellent agreement with literature results on all length scales accessible in brute-force simulations of shorter chains.

Distribution Cutoff for Clusters near the Gel Point

The mechanical and dynamic properties of developing networks near the gel point are susceptible to the distribution of clusters coexisting with percolating networks. The distribution of cluster numbers follows a broad power law, wrapped by a cutoff function that rapidly decays at a characteristic size. The form of the cutoff function has been speculated based on known results from lattice percolation and, in certain cases, solved. We obtained this cutoff function from simulated dynamic clusters of polymeric precursor chains using a hybrid Monte Carlo algorithm. The results obtained from three different precursor chain lengths are consistent with each other and are consistent with the expectation from lattice percolation.

Role of torsional potential in chain conformation, thermodynamics, and glass formation of simulated polybutadiene melts

For polymer chains, the torsional potential is an important intramolecular energy influencing chain flexibility and segmental dynamics. Through molecular dynamics simulations of an atomistic model for melts of cis-trans-1,4-polybutadiene (PBD), we explore the effect of the torsions on conformational properties (bond vector correlations and mean-square internal distances), fundamental thermodynamic quantities (density, compressibility, internal energy, and specific heat), and glass transition temperature T_g. This is achieved by systematically reducing the strength of the torsional potential, starting from the chemically realistic chain (CRC) model with the full potential toward the freely rotating chain (FRC) model without the torsional potential. For the equilibrium liquid, we find that the effect of the torsions on polymer conformations is very weak. Still weaker is the influence on the monomer density ρ and isothermal compressibility κ_T of the polymer liquid, both of which can be considered as independent of the torsional potential. We show that a van der Waals-like model proposed by Long and Lequeux [Eur. Phys. J. E 4, 371 (2001)] allows us to describe very well the temperature (T) dependence of ρ and κ_T. We also find that our data obey the linear relation between 1/k_BTρκ_T and 1/T (with the Boltzmann constant k_B) that has recently been predicted and verified on the experiment by Mirigian and Schweizer [J. Chem. Phys. 140, 194507 (2014)]. For the equilibrium liquid, simulations result in a specific heat, at constant pressure and at constant volume, which increases on cooling. This T dependence is opposite to the one found experimentally for many polymer liquids, including PBD. We suggest that this difference between simulation and experiment may be attributed to quantum effects due to hydrogen atoms and backbone vibrations, which, by construction, are not included in the classical united-atom model employed here. Finally, we also determine T_g from the density-temperature curve monitored in a finite-rate cooling process. While the influence of the torsional potential on ρ(T) is vanishingly small in the equilibrium liquid, the effect of the torsions on T_g is large. We find that T_g decreases by about 150 K when going from the CRC to the FRC model.

Facile equilibration of well-entangled semiflexible bead-spring polymer melts

The widely used double-bridging hybrid (DBH) method for equilibrating simulated entangled polymer melts [Auhl et al., J. Chem. Phys. 119, 12718-12728 (2003)] loses its effectiveness as chain stiffness increases into the semiflexible regime because the energy barriers associated with double-bridging Monte Carlo moves become prohibitively high. Here we overcome this issue by combining DBH with the use of core-softened pair potentials. This reduces the energy barriers substantially, allowing us to equilibrate melts with N ≃ 40N_e and chain stiffnesses all the way up to the isotropic-nematic transition using simulations of no more than 100 × 10⁶ time steps. For semiflexible chains, our method is several times faster than the standard DBH; we exploit this speedup to develop improved expressions for Kremer-Grest melts' chain-stiffness-dependent Kuhn length ℓ_K and entanglement length N_e.

The Physical Behavior of Interphase Chromosomes: Polymer Theory and Coarse-Grain Computer Simulations

Fluorescence in situ hybridization and chromosome conformation capture methods point to the same conclusion: that chromosomes appear to the external observer as compact structures with a highly nonrandom three-dimensional organization. In this work, we recapitulate the efforts made by us and other groups to rationalize this behavior in terms of the mathematical language and tools of polymer physics. After a brief introduction dedicated to some crucial experiments dissecting the structure of interphase chromosomes, we discuss at a nonspecialistic level some fundamental aspects of theoretical and numerical polymer physics. Then, we inglobe biological and polymer aspects into a polymer model for interphase chromosomes which moves from the observation that mutual topological constraints, such as those typically present between polymer chains in ordinary melts, induce slow chain dynamics and "constraint" chromosomes to resemble double-folded randomly branched polymer conformations. By explicitly turning these ideas into a multi-scale numerical algorithm which is described here in full details, we can design accurate model polymer conformations for interphase chromosomes and offer them for systematic comparison to experiments. The review is concluded by discussing the limitations of our approach and pointing to promising perspectives for future work.

Characterization of Monte Carlo Dynamic/Kinetic Properties of Local Structure in Bond Fluctuation Model of Polymer System

We report the results of the characterization of local Monte Carlo (MC) dynamics of an equilibrium bond fluctuation model polymer matrix (BFM), in time interval typical for MC simulations of non-linear optical phenomena in host-guest systems. The study contributes to the physical picture of the dynamical aspects of quasi-binary mosaic states characterized previously in the static regime. The polymer dynamics was studied at three temperatures (below, above and close to the glass transition), using time-dependent generalization of the static parameters which characterize local free volume and local mobility of the matrix. Those parameters play the central role in the kinetic MC model of host-guest systems. The analysis was done in terms of the probability distributions of instantaneous and time-averaged local parameters. The main result is the characterization of time scales characteristic of various local structural processes. Slowing down effects close to the glass transition are clearly marked. The approach yields an elegant geometric criterion for the glass transition temperature. A simplified quantitative physical picture of the dynamics of guest molecules dispersed in BFM matrix at low temperatures offers a starting point for stochastic modeling of host-guest systems.

Molecular Characterization of Polymer Networks

Polymer networks are complex systems consisting of molecular components. Whereas the properties of the individual components are typically well understood by most chemists, translating that chemical insight into polymer networks themselves is limited by the statistical and poorly defined nature of network structures. As a result, it is challenging, if not currently impossible, to extrapolate from the molecular behavior of components to the full range of performance and properties of the entire polymer network. Polymer networks therefore present an unrealized, important, and interdisciplinary opportunity to exert molecular-level, chemical control on material macroscopic properties. A barrier to sophisticated molecular approaches to polymer networks is that the techniques for characterizing the molecular structure of networks are often unfamiliar to many scientists. Here, we present a critical overview of the current characterization techniques available to understand the relation between the molecular properties and the resulting performance and behavior of polymer networks, in the absence of added fillers. We highlight the methods available to characterize the chemistry and molecular-level properties of individual polymer strands and junctions, the gelation process by which strands form networks, the structure of the resulting network, and the dynamics and mechanics of the final material. The purpose is not to serve as a detailed manual for conducting these measurements but rather to unify the underlying principles, point out remaining challenges, and provide a concise overview by which chemists can plan characterization strategies that suit their research objectives. Because polymer networks cannot often be sufficiently characterized with a single method, strategic combinations of multiple techniques are typically required for their molecular characterization.

Modeling of Nonlinear Optical Phenomena in Host-Guest Systems Using Bond Fluctuation Monte Carlo Model: A Review

We review the results of Monte Carlo studies of chosen nonlinear optical effects in host-guest systems, using methods based on the bond-fluctuation model (BFM) for a polymer matrix. In particular, we simulate the inscription of various types of diffraction gratings in degenerate two wave mixing (DTWM) experiments (surface relief gratings (SRG), gratings in polymers doped with azo-dye molecules and gratings in biopolymers), poling effects (electric field poling of dipolar molecules and all-optical poling) and photomechanical effect. All these processes are characterized in terms of parameters measured in experiments, such as diffraction efficiency, nonlinear susceptibilities, density profiles or loading parameters. Local free volume in the BFM matrix, characterized by probabilistic distributions and correlation functions, displays a complex mosaic-like structure of scale-free clusters, which are thought to be responsible for heterogeneous dynamics of nonlinear optical processes. The photoinduced dynamics of single azopolymer chains, studied in two and three dimensions, displays complex sub-diffusive, diffusive and super-diffusive dynamical regimes. A directly related mathematical model of SRG inscription, based on the continuous time random walk (CTRW) formalism, is formulated and studied. Theoretical part of the review is devoted to the justification of the a priori assumptions made in the BFM modeling of photoinduced motion of the azo-polymer chains.

Can Soft Models Describe Polymer Knots?

Similar to macroscopic ropes and cables, long polymers create knots. We address the fundamental question whether and under which conditions it is possible to describe these intriguing objects with crude models that capture only mesoscale polymer properties. We focus on melts of long polymers which we describe by a model typical for mesoscopic simulations. A worm-like chain model defines the polymer architecture. To describe nonbonded interactions, we deliberately choose a generic "soft" repulsive potential that leads to strongly overlapping monomers and coarse local liquid structure. The soft model is parametrized to accurately reproduce mesoscopic structure and conformations of reference polymer melts described by a microscopic model. The microscopically resolved samples retain all generic features affecting polymer topology and provide, therefore, reliable reference data on knots. We compare characteristic knotting properties in mesoscopic and microscopically resolved melts for different cases of chain stiffness. We conclude that mesoscopic models can reliably describe knots in those melts, where the length scale characterizing polymer stiffness is substantially larger than the size of monomer-monomer excluded volume. In this case, simplified local liquid structure influences knotting properties only marginally. In contrast, mesoscopic models perform poorly in melts with flexible chains. We qualitatively explain our findings through a free energy model of simple knots available in the literature.

Microstructural Capture of Living Ultrathin Polymer Brush Evolution via Kinetic Simulation Studies

Performing dynamic off-lattice multicanonical Monte Carlo simulations, we study the statics, dynamics, and scission-recombination kinetics of a self-assembled in situ-polymerized polydisperse living polymer brush (LPB), designed by surface-initiated living polymerization. The living brush is initially grown from a two-dimensional substrate by end-monomer polymerization-depolymerization reactions through seeding of initiator arrays on the grafting plane which come in contact with a solution of nonbonded monomers under good solvent conditions. The polydispersity is shown to significantly deviate from the Flory-Schulz type for low temperatures because of pronounced diffusion limitation effects on the rate of the equilibration reaction. The self-avoiding chains take up fairly compact structures of typical size R_g(N) ∼ N^ν in rigorously two-dimensional (d = 2) melt, with ν being the inverse fractal dimension (ν = 1/d). The Kratky description of the intramolecular structure factor F(q), in keeping with the concept of generalized Porod scattering from compact particles with fractal contour, discloses a robust nonmonotonic fashion with q^dF(q) ∼ (qR_g)^-3/4 in the intermediate-q regime. It is found that the kinetics of LPB growth, given by the variation of the mean chain length, follows a power law ⟨N(t)⟩ ∝ t^1/3 with elapsed time after the onset of polymerization, whereby the instantaneous molecular weight distribution (MWD) of the chains c(N) retains its functional form. The variation of ⟨N(t)⟩ during quenches of the LPB to different temperatures T can be described by a single master curve in units of dimensionless time t/τ_∞, where τ_∞ is the typical (final temperature T^∞-dependent) relaxation time which is found to scale as τ_∞ ∝ ⟨N(t = ∞)⟩⁵ with the ultimate average length of the chains. The equilibrium monomer density profile ϕ(z) of the LPB varies as ϕ(z) ∝ ϕ^-α with the concentration of segments ϕ in the system and the probability distribution c(N) of chain lengths N in the brush layer scales as c(N) ∝ N^-τ. The computed exponents α ≈ 0.64 and τ ≈ 1.70 are in good agreement with those predicted within the context of the Diffusion-Limited Aggregation theory, α = 2/3 and τ = 7/4.

Field theoretic approach for block polymer melts: SCFT and FTS

This perspective addresses the development of polymer field theory for predicting the equilibrium phase behavior of block polymer melts. The approach is tailored to the high-molecular-weight limit, where universality reduces all systems to the standard Gaussian chain model, an incompressible melt of elastic threads interacting by contact forces. Using mathematical identities, this particle-based version of the model is converted to an equivalent field-based version that depends on fields rather than particle coordinates. The statistical mechanics of the field-based model is typically solved using the saddle-point approximation of self-consistent field theory (SCFT), which equates to mean field theory, but it can also be evaluated using field theoretic simulations (FTS). While SCFT has matured into one of the most successful theories in soft condensed matter, FTS are still in its infancy. The two main obstacles of FTS are the high computational cost and the occurrence of an ultraviolet divergence, but fortunately there has been recent groundbreaking progress on both fronts. As such, FTS are now well poised to become the method of choice for predicting fluctuation corrections to mean field theory.

The Concentration Dependence of the Size and Symmetry of a Bottlebrush Polymer in a Good Solvent

Bottlebrush polymers consist of a linear backbone with densely grafted side chains which impact the rigidity of the molecule. The persistence length of the bottlebrush backbone in solution is influenced by both the intrinsic structure of the polymer and by the local environment, such as the solvent quality and concentration. Increasing the concentration reduces the overall size of the molecule due to the reduction in backbone stiffness. In this study we map out the size of a bottlebrush polymer as a function of concentration for a single backbone length. Small-angle neutron scattering (SANS) measurements are conducted on a polynorbornene-based bottlebrush with polystyrene side chains in a good solvent. The data are fit using a model which provides both the long and short axis radius of gyration (R g,2 and R g,1, respectively), providing a measure for how the conformation changes as a function of concentration. At low concentrations a highly anisotropic structure is observed (R g,2/R g,1 ≈ 4), becoming more isotropic at higher concentrations (R g,2/R g,1 ≈ 1.5). The concentration scaling for both R g,2 and the overall R g are evaluated and compared with predictions in the literature. Coarse-grained molecular dynamics simulations were also conducted to probe the impact of concentration on bottlebrush conformation showing qualitative agreement with the experimental results.

The Persistence Length of Semiflexible Polymers in Lattice Monte Carlo Simulations

While applying computer simulations to study semiflexible polymers, it is a primary task to determine the persistence length that characterizes the chain stiffness. One frequently asked question concerns the relationship between persistence length and the bending constant of applied bending potential. In this paper, theoretical persistence lengths of polymers with two different bending potentials were analyzed and examined by using lattice Monte Carlo simulations. We found that the persistence length was consistent with theoretical predictions only in bond fluctuation model with cosine squared angle potential. The reason for this is that the theoretical persistence length is calculated according to a continuous bond angle, which is discrete in lattice simulations. In lattice simulations, the theoretical persistence length is larger than that in continuous simulations.

Hierarchical modelling of polystyrene melts: from soft blobs to atomistic resolution

We demonstrate that hierarchical backmapping strategies incorporating generic blob-based models can equilibrate melts of high-molecular-weight polymers, described with chemically specific, atomistic models. The central idea is first to represent polymers by chains of large soft blobs (spheres) and efficiently equilibrate the melt on large scales. Then, the degrees of freedom of more detailed models are reinserted step by step. The procedure terminates when the atomistic description is reached. Reinsertions are feasible computationally because the fine-grained melt must be re-equilibrated only locally. We consider polystyrene (PS) which is sufficiently complex to serve method development because of stereo-chemistry and bulky side groups. Our backmapping strategy bridges mesoscopic and atomistic scales by incorporating a blob-based, a moderately coarse-grained (CG), and a united-atom model of PS. We demonstrate that the generic blob-based model can be parameterised to reproduce the mesoscale properties of a specific polymer - here PS. The moderately CG model captures stereo-chemistry. To perform backmapping we improve and adjust several fine-graining techniques. We prove equilibration of backmapped PS melts by comparing their structural and conformational properties with reference data from smaller systems, equilibrated with less efficient methods.

Mapping onto Ideal Chains Overestimates Self-Entanglements in Polymer Melts

We analyze the occurrence of knots, their spectrum, and sizes in polymer melts. Surprisingly, the number of knots in melt conformations is much lower than expected from a mapping to a random walk with the same Kuhn segment length. The effective random walk severely overrates the occurrence of knots and their complexity, particularly when compared to melts of flexible chains, indicating that nontrivial effects due to remnants of self-avoidance play a role for the chain lengths considered in this numerical study. For melt chains with higher persistence length, the effect is less pronounced. In addition, we find that chains in a melt have a knot structure very similar to dilute single chains close to the collapse transition. We finally show that typical equilibration procedures are well-suited to relax the topology in melts.

Exploring glycogen biosynthesis through Monte Carlo simulation

Glycogen, a complex branched polymer of glucose (average chain length ~10 monomer units), is the blood-sugar reservoir in humans and other animals. Certain aspects of its molecular structure relevant to its biological functions are currently unamenable to experimental exploration. Knowledge of these is needed to develop future models for quantitative data-fitting to obtain mechanistic understanding of the biosynthetic processes that give rise to glycogen structure. Monte Carlo simulations of the biosynthesis of this structure with realistic macromolecular parameters reveal how chain growth and stoppage (the latter assumed to be through both the action of glycogen branching enzyme and other degradative enzymes, and by hindrance) control structural features. The simulated chain-length, pair-distance and radial density distributions agree semi-quantitatively with the limited available data. The simulations indicate that a steady state in molecular structure and size is rapidly obtained, that molecular density reaches a maximum near the center of the particle (not at the periphery, as is the case with dendrimers), and that particle size is controlled by both enzyme activity and hindrance. This knowledge will aid in the understanding of diabetes (loss of blood-sugar control), which has been found to involve subtle differences in glycogen molecular structure.

Local Chain Segregation and Entanglements in a Confined Polymer Melt

The reptation mechanism, introduced by de Gennes and Edwards, where a polymer diffuses along a fluffy tube, defined by the constraints imposed by its surroundings, convincingly describes the relaxation of long polymers in concentrated solutions and melts. We propose that the scale for the tube diameter is set by local chain segregation, which we study analytically. We show that the concept of local segregation is especially operational for confined geometries, where segregation extends over mesoscopic domains, drastically reducing binary contacts, and provide an estimate of the entanglement length. Our predictions are quantitatively supported by extensive molecular dynamics simulations on systems consisting of long, entangled chains.

On the Pseudo Phase Diagram of Single Semi-Flexible Polymer Chains: A Flat-Histogram Monte Carlo Study

Local stiffness of polymer chains is instrumental in all structure formation processes of polymers, from crystallization of synthetic polymers to protein folding and DNA compactification. We present Stochastic Approximation Monte Carlo simulations-a type of flat-histogram Monte Carlo method-determining the density of states of a model class of single semi-flexible polymer chains, and, from this, their complete thermodynamic behavior. The chains possess a rich pseudo phase diagram as a function of stiffness and temperature, displaying non-trivial ground-state morphologies. This pseudo phase diagram also depends on chain length. Differences to existing pseudo phase diagrams of semi-flexible chains in the literature emphasize the fact that the mechanism of stiffness creation matters.

The formation and structure of Olympic gels

Different methods for creating Olympic gels are analyzed using computer simulations. First ideal reference samples are obtained from freely interpenetrating semi-dilute solutions and melts of cyclic polymers. The distribution of pairwise concatenations per cyclic molecule is given by a Poisson-distribution and can be used to describe the elastic structure of the gels. Several batches of linear chains decorated with different selectively binding groups at their ends are mixed in the "DNA Origami" technique and network formation is realized. While the formation of cyclic molecules follows mean field predictions below overlap of the precursor molecules, an enhanced ring formation above overlap is found that is not explained by mean field arguments. The "progressive construction" method allows to create Olympic gels with a single reaction step from a concentrated mixture of large compressed rings with a low weight fraction of short chains that are below overlap concentration. This method, however, is limited by the difficulty to obtain a sufficiently high degree of polymerization of the large rings.

Multiscale approach to equilibrating model polymer melts

We present an effective and simple multiscale method for equilibrating Kremer Grest model polymer melts of varying stiffness. In our approach, we progressively equilibrate the melt structure above the tube scale, inside the tube and finally at the monomeric scale. We make use of models designed to be computationally effective at each scale. Density fluctuations in the melt structure above the tube scale are minimized through a Monte Carlo simulated annealing of a lattice polymer model. Subsequently the melt structure below the tube scale is equilibrated via the Rouse dynamics of a force-capped Kremer-Grest model that allows chains to partially interpenetrate. Finally the Kremer-Grest force field is introduced to freeze the topological state and enforce correct monomer packing. We generate 15 melts of 500 chains of 10.000 beads for varying chain stiffness as well as a number of melts with 1.000 chains of 15.000 monomers. To validate the equilibration process we study the time evolution of bulk, collective, and single-chain observables at the monomeric, mesoscopic, and macroscopic length scales. Extension of the present method to longer, branched, or polydisperse chains, and/or larger system sizes is straightforward.

Semiflexible Chains at Surfaces: Worm-Like Chains and beyond

We give an extended review of recent numerical and analytical studies on semiflexible chains near surfaces undertaken at Institut Charles Sadron (sometimes in collaboration) with a focus on static properties. The statistical physics of thin confined layers, strict two-dimensional (2D) layers and adsorption layers (both at equilibrium with the dilute bath and from irreversible chemisorption) are discussed for the well-known worm-like-chain (WLC) model. There is mounting evidence that biofilaments (except stable d-DNA) are not fully described by the WLC model. A number of augmented models, like the (super) helical WLC model, the polymorphic model of microtubules (MT) and a model with (strongly) nonlinear flexural elasticity are presented, and some aspects of their surface behavior are analyzed. In many cases, we use approaches different from those in our previous work, give additional results and try to adopt a more general point of view with the hope to shed some light on this complex field.

Monte Carlo simulation of dense polymer melts using event chain algorithms

We propose an efficient Monte Carlo algorithm for the off-lattice simulation of dense hard sphere polymer melts using cluster moves, called event chains, which allow for a rejection-free treatment of the excluded volume. Event chains also allow for an efficient preparation of initial configurations in polymer melts. We parallelize the event chain Monte Carlo algorithm to further increase simulation speeds and suggest additional local topology-changing moves ("swap" moves) to accelerate equilibration. By comparison with other Monte Carlo and molecular dynamics simulations, we verify that the event chain algorithm reproduces the correct equilibrium behavior of polymer chains in the melt. By comparing intrapolymer diffusion time scales, we show that event chain Monte Carlo algorithms can achieve simulation speeds comparable to optimized molecular dynamics simulations. The event chain Monte Carlo algorithm exhibits Rouse dynamics on short time scales. In the absence of swap moves, we find reptation dynamics on intermediate time scales for long chains.

Monte Carlo simulations of lattice models for single polymer systems

Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length N~O(10(4)). Based on the standard simple cubic lattice model (SCLM) with fixed bond length and the bond fluctuation model (BFM) with bond lengths in a range between 2 and √10, we investigate the conformations of polymer chains described by self-avoiding walks on the simple cubic lattice, and by random walks and non-reversible random walks in the absence of excluded volume interactions. In addition to flexible chains, we also extend our study to semiflexible chains for different stiffness controlled by a bending potential. The persistence lengths of chains extracted from the orientational correlations are estimated for all cases. We show that chains based on the BFM are more flexible than those based on the SCLM for a fixed bending energy. The microscopic differences between these two lattice models are discussed and the theoretical predictions of scaling laws given in the literature are checked and verified. Our simulations clarify that a different mapping ratio between the coarse-grained models and the atomistically realistic description of polymers is required in a coarse-graining approach due to the different crossovers to the asymptotic behavior.

Conformations of a Long Polymer in a Melt of Shorter Chains: Generalizations of the Flory Theorem

Large-scale simulations of the swelling of a long N-mer in a melt of chemically identical P-mers are used to investigate a discrepancy between theory and experiments. Classical theory predicts an increase of probe chain size R ∼ P^-0.18 with decreasing degree of polymerization P of melt chains in the range of 1 < P < N^1/2. However, both experiment and simulation data are more consistent with an apparently slower swelling R ∼ P^-0.1 over a wider range of melt degrees of polymerization. This anomaly is explained by taking into account the recently discovered long-range bond correlations in polymer melts and corrections to excluded volume. We generalize the Flory theorem and demonstrate that it is in excellent agreement with experiments and simulations.