Conformation-dependent design of polymer sequences can be considered as a tool to control macromolecular self-assembly. We consider the monomer unit sequences created via the modification of polymers in a homogeneous melt in accordance with the spatial positions of the monomer units. The geometrical patterns of lamellae, hexagonally packed cylinders, and balls arranged in a body-centered cubic lattice are considered as typical microphase-separated morphologies of block copolymers. Random trajectories of polymer chains are described by the diffusion-type equations and, in parallel, simulated in the computer modeling. The probability distributions of block length $k$, which are analogous to the first-passage probabilities, are calculated analytically and determined from the computer simulations. In any domain, the probability distribution can be described by the asymptote $~k^{-3/2}$ at moderate values of $k$ if the spatial size of the block is less than the smallest characteristic size of the domain. For large blocks, the exponential asymptote $exp(-const \, k a^2/d_{as}^2)$ is valid, $d_{as}$ being the asymptotic domain length (a is the monomer unit size). The number average block lengths and their dispersities change linearly with the block length for lamellae, cylinders, and balls, when the domain is characterized by a single characteristic size. If the domain is described by more than one size, the number average block length can grow nonlinearly with the domain sizes and the length das can depend on all of them.
We study conformations and dynamics of active star polymers. The analysis shows that active star polymers stretching behaviour is quite different from that of active linear chains. The visual inspection of conformations and bond-bond correlations reveal a better coordination for the alignment and coordination of bonds for the star polymers than for the linear counterparts. The architecture substantially affects the chain extension transition at high values of active force. The scaling laws for the shape factor and the arm asphericity ratio established for the passive star polymers coincide wit…
We have generalized the Edwards' method of collective description of dense polymer systems in terms of effective potentials to polymer blends in the presence of a surface. With this method we have studied conformationally asymmetric athermic polymer blends in the presence of a hard wall to the first order in effective potentials. For polymers with the same gyration radius $R_g$ but different statistical segment lengths $l_{A}$ and $l_{B}$ the excess concentration of stiffer polymers at the surface is derived as $% δρ_{A}(z=0)\sim (l_{B}^{-2}-l_{A}^{-2}){\ln (}R_{g}^{2}/l_{c}^{2}{)%}$, where $l…
We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. By performing simulations of single chains in a shear flow, we identify which of these phenomena are of collective nature and arise through interchain interactions and which are already present in dilute systems. Building upon these microscopic simulations we identify by m…
Extensive coarse grained molecular dynamics simulations are performed to investigate the conformational phase diagram of a neutral polymer in the presence of attractive crowders. We show that, for low crowded densities, the polymer predominantly shows three phases as a function of both intra polymer and polymer-crowder interactions: (1) weak intra polymer and weak polymer-crowder attractive interactions induce extended or coil polymer conformations (phase E) (2) strong intra polymer and relatively weak polymer-crowder attractive interactions induce collapsed or globular conformations (phase CI…
We present a detailed account of a recently proposed phenomenological theory for noncatenated ring polymer melts (Phys. Rev. Lett. 106, 167802 (2011)). A basic assumption lies in the implementation of the noncatenation constraint via the effective excluded-volume effect, from which a geometrical picture of melts emerges. The result captures many of the salient features observed so far, including (i) the overall spacial size of rings, (ii) the coordinate number, i.e., the number of rings surrounding a given ring, (iii) the topological length scale as a function of the molecular weight and (iv) …
The size of rings (also called cyclic polymers) in bidisperse blends of chemically identical rings is analyzed by computer simulations. Data of entangled ring blends and blends of interpenetrating rings are compared and it is shown that the compression of entangled rings can be explained by the changes in the penetrable fraction of the minimal surface bounded by the ring. Corrections for small rings can be approximated by a concatenation probability $1-P_{OO}$ that a ring entraps at least one other ring. Both results are in line with a previous work [1] to explain the compression of entangled …
Over the past two decades polymer nanocomposites have received tremendous interest from industry and academia due to their advanced properties comparative to polymer blends. Many computational studies have revealed that the macroscopic properties of polymer nanocomposites depend strongly on the microscopic polymer structure and conformations. In this article we review simulation studies of the fundamental problem of polymer structure and dimensions in nanocomposites containing bare spherical or rod nanoparticles. Experimentally, there is controversy over whether the addition of nanoparticles i…
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded polymers, we model polymers as penetrable ellipsoids, whose shape fluctuations are governed by the statistics of self-avoiding walks, appropriate for a polymer in a good solvent. Within this coarse-grained model, we perform Monte Carlo simulations of mixtures of polymers and hard-nanosphere crowders, including trial changes in polymer size and shape. Penetration of…
How Spatially Modulated Activity Reshapes Active Polymer Conformations
Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IET-2), Forschungszentrum Jülich（亥姆霍兹埃尔朗根-纽伦堡可再生能源研究所（IET-2），于利希研究中心）；Department of Physics and Astronomy, University of Padova（帕多瓦大学物理与天文学系）；INFN, Sezione di Padova（意大利国家核物理研究所，帕多瓦分部）
Nonlinear extensional flows are common in polymer processing but remain challenging theoretically because dramatic stretching of chains deforms the entanglement network far from equilibrium. Here, we present coarse-grained simulations of extensional flows in entangled polymer melts for Rouse-Weissenberg numbers $Wi_R=0.06$-$52$ and Hencky strains $ε\geq6$. Simulations reproduce experimental trends in extensional viscosity with time, rate and molecular weight. Studies of molecular structure reveal an elongation and thinning of the confining tube with increasing $Wi_R$. The rising stress is quan…
We study the dynamics and conformation of polymers composed by active monomers. By means of Brownian dynamics simulations we show that when the direction of the self-propulsion of each monomer is aligned with the backbone, the polymer undergoes a coil-to-globule-like transition, highlighted by a marked change of the scaling exponent of the gyration radius. Concurrently, the diffusion coefficient of the center of mass of the polymer becomes essentially independent of the polymer size for sufficiently long polymers or large magnitudes of the self-propulsion. These effects are reduced when the se…
We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding agents, studying polymer shapes and conformations as a function of the confining potential, solvent quality and the density of crowders. The conformations of the polymer under good solvent conditions are largely independent of crowder density, even when the polymer is strongly confined. However, for poor solvents and attractive walls, the polymer shows a transition between an adsorbed extended state to a globular conformation on the surface as a function of crowder parti…
Based on non-equilibrium molecular dynamics simulations of entangled polymer melts, a recent Letter [Phys. Rev. Lett. $\textbf{121}$, 047801 (2018), arXiv:1806.09509] claims that the rising extensional stress is quantitatively consistent with the decreasing entropy of chains at the equilibrium entanglement length. We point out that exactly the opposite is true: the intrachain entropic stress arising from individual entanglement strands generally does not agree with the total "macroscopic" stress. The conclusion of the Letter is based on an incomplete and questionable analysis of a limited rang…
We study the dynamics and conformations of a single active semiflexible polymer whose monomers experience a propulsion force perpendicular to the local tangent, with the end beads being different from the inner beads ("end-tailored"). Using Langevin simulations, we demonstrate that, apart from sideways motion, the relative propulsion strength between the end beads and the polymer backbone significantly changes the conformational properties of the polymers as a function of bending stiffness, end-tailoring and propulsion force. Expectedly, for slower ends the polymer curves away from the moving …
The flow behavior of a semiflexible polymer in microchannels is studied using Multiparticle Collision Dynamics (MPC), a particle-based hydrodynamic simulation technique. Conformations, distributions, and radial cross-streamline migration are investigated for various bending rigidities, with persistence lengths Lp in the range 0.5 < Lp/Lr < 30. The flow behavior is governed by the competition between a hydrodynamic lift force and steric wall-repulsion, which lead to migration away from the wall, and a locally varying flow-induced orientation, which drives polymer away from the channel center an…
We investigate the phase transition properties of the polymer-Potts model, a chain composed of monomers with magnetic degrees of freedom, with the motivation to study the conformation and mark switching dynamics of chromatin. By the mean-field approximation, we find that the phase transition between the swollen-disordered state and the compact-ordered state is discrete; it is first-order as in the long-range Potts model, but with a significantly larger jump in magnetization (i.e., mark coherence) upon the ordering transition. The results imply how small changes in epigenetic writer concentrati…
The modeling of conformations and dynamics of (bio)polymers is of primary importance for understanding physicochemical properties of soft matter. Although short-range interactions such as covalent and hydrogen bonding control the local arrangement of polymers, non-covalent interactions play a dominant role in determining the global conformations. Here we focus on how the inclusion of many-body effects in van der Waals dispersion affects the outcome of geometry optimizations and molecular dynamics simulations of model polymers. We find that delocalized force contributions are key to explore the…
To predict flow behavior of entangled polymer melt, we have developed multiscale simulation composed of Lagrangian fluid particle simulation and coarse-grained polymer dynamics simulation. We have introduced a particle deformation in the Lagrangian fluid particle simulation to describe elongation flow at a local point. The particle deformation is obtained to be consistent with the local polymer deformation.
The tube model is a central concept in polymer physics, and allows to reduce the complex many-filament problem of an entangled polymer solution to a single filament description. We investigate the probability distribution function of conformations of confinement tubes and single encaged filaments in entangled semiflexible polymer solution. Computer simulations are developed that mimic the actual dynamics of confined polymers in disordered systems with topological constraints on time scales above local equilibration but well below large scale rearrangement of the network. We observe the statist…
We investigate theoretically the physics of diffusion-limited intramolecular polymer reactions. The present work completes and goes beyond a previous study [Nat. Chem. 4, 268 (2012)] that showed that the distribution of the polymer conformations at the very instant of reaction plays a key role in the cyclization kinetics, and takes explicitly into account the non-Markovian nature of the reactant motion. Here, we present in detail this non-Markovian theory, and compare it explicitly with existing Markovian theories and with numerical stochastic simulations. A large focus is made on the descript…
We report dynamic Monte Carlo simulation on conformational transition of H-shaped branched polymers by varying main chain (backbone) and side chain (branch) length. H-shaped polymers in comparison with equivalent linear polymers exhibit a depression of theta temperature accompanying with smaller chain dimensions. We observed that the effect of branches on backbone dimension is more pronounced than the reverse, and is attributed to the conformational heterogeneity prevails within the molecule. With increase in branch length, backbone is slightly stretched out in coil and globule state. However,…
We investigate theoretically a diffusion-limited reaction between a reactant attached to a Rouse polymer and an external fixed reactive site in confinement. The present work completes and goes beyond a previous study [T. Guérin, O. Bénichou and R. Voituriez, Nat. Chem., 4, 268 (2012)] that showed that the distribution of the polymer conformations at the very instant of reaction plays a key role in the reaction kinetics, and that its determination enables the inclusion of non-Markovian effects in the theory. Here, we describe in detail this non-Markovian theory and we compare it with numerical …
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and exten…
Based on classical nucleation theory, we propose a couple of theoretical models for the nucleation of polymer crystallization, i.e. one for a single chain system (Model S) and the other for a multi-chain system (Model M). In these models, we assume that the nucleus is composed of tails, loops and a cylindrical ordered region, and we evaluate the conformation entropy explicitly by introducing a transfer matrix. Using these two models, we evaluate the occurrence probability of critical nucleus as a function of the polymer chain stiffness. We found that the critical nucleus in Model M is easier t…
Universal scaling of conformations of tangentially driven ring polymers
Istituto Applicazioni Calcolo, Consiglio Nazionale delle Ricerche (CNR)（计算应用研究所，意大利国家研究委员会）；Institute for Advanced Simulation, Forschungszentrum Jülich（先进模拟研究所，于利希研究中心）
We investigate the wrapping conformations of a strongly adsorbed polymer chain on an oppositely charged nano-sphere by employing a reduced (dimensionless) representation of a primitive chain-sphere model. This enables us to determine the global phase behavior of the chain conformation in a wide range of values for the system parameters including the chain contour length, its linear charge density and persistence length as well as the nano-sphere charge and radius, and also the salt concentration in the bathing solution. The phase behavior of a charged chain-sphere complex can be described in t…
We have used neutron scattering to investigate the influence of concentration on the conformation of a star polymer. By varying the contrast between the solvent and isotopically labeled stars, we obtain the distributions of polymer and solvent within a star polymer from analysis of scattering data. A correlation between the local desolvation and the inward folding of star branches is discovered. From the perspective of thermodynamics, we find an analogy between the mechanism of polymer localization driven by solvent depletion and that of the hydrophobic collapse of polymers in solutions.
We study conformational properties of diluted dumbbell polymers which consist of two rings that are attached to both ends of a linear spacer segment by using analytical methods of field theory and bead-spring coarse-grained molecular dynamics simulations. We investigate the influence of the relative length of the spacer segment to the length of side rings on the shape and the relative size of dumbbells as compared to linear polymers of equal mass. We find that dumbbells with short spacers are much more compact than linear polymers. Oppositely, we observe that the influence of side rings on the…
We study equilibrium statistics of single semi-flexible polymer chain in the presence of defects. The defects are lying along a line in the two and three dimensions and the monomers are interacting with the onsite potential of the defects. A fully directed self-avoiding walk model is used in two and three dimensions to describe thermo-dynamical behaviour of the chain in the presence of m defects. We have found that the number of conformations of the semiflexible polymer chain may be controlled by means of introduction of such defects so that a particular fraction of the chain conformations may…
Polymer melts undergoing large deformation by uniaxial elongation are studied by molecular dynamics simulations of bead-spring chains in melts. Applying a primitive path analysis to strongly deformed polymer melts, the role of topological constrains in highly entangled polymer melts is investigated and quantified. We show that the over-all, large scale conformations of the primitive paths (PPs) of stretched chains follow affine deformation while the number and the distribution of entanglement points along the PPs do not. Right after deformation, PPs of chains retract in both directions paralle…
Equilibration of polymer melts containing highly entangled long polymer chains in confinement or with free surfaces is a challenge for computer simulations. We approach this problem by first studying polymer melts based on the soft-sphere coarse-grained model confined between two walls with periodic boundary conditions in two directions parallel to the walls. Then we apply backmapping to reinsert the microscopic details of the underlying bead-spring model. Tuning the strength of the wall potential, the monomer density of confined polymer melts in equilibrium is kept at the bulk density even ne…
The generalized entropy theory (GET) offers many insights into how molecular parameters influence polymer glass-formation. Given the fact that chain rigidity often plays a critical role in understanding the glass-formation of polymer materials, the GET was originally developed based on models of semiflexible chains. Consequently, all previous calculations within the GET considered polymers with some degree of chain rigidity. Motivated by unexpected results from computer simulations of fully flexible polymer melts concerning the dependence of thermodynamic and dynamic properties on the cohesive…
We analyze the universal size characteristics of flexible ring polymers in solutions in presence of structural obstacles (impurities) in d dimensions. One encounters such situations when considering polymers in gels, colloidal solutions, intra- and extracellular environments. A special case of extended impurities correlated on large distances r according to a power law \sim r^{-a} is considered. Applying the direct polymer renormalization scheme, we evaluate the estimates for averaged gyration radius $\langle R_{g\,{\rm ring}} \rangle$ and spanning radius $\langle R_{1/2\,{\rm ring}} \rangle$ …
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as flexible hard-sphere chains, and the box has a square cross-section of side length $L$ and a height that is small enough to compress the polymers in that dimension. For sufficiently large $L$, the system behaviour approaches that of an isolated polymer in a slit. However, the combined effects of crowding and confinement on the polymer organization, conformat…
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the poly…
The calculation of discrete or continuous relaxation time spectra from rheometric measurables of polydisperse polymers is an ill-posed problem. In this paper, a curve fitting method for solving this problem is presented and compared to selected models from the literature. It is shown that the new method is capable of correctly predicting the molecular mass distributions of linear polydisperse polymer melts as well as their relaxation time spectra.
