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 with the passive case for active force values below the transition. For the values above the transition range the scaling of these quantities switches to different values.
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 employ the recently introduced generalized microcanonical inflection point method for the statistical analysis of phase transitions in flexible and semiflexible polymers and study the impact of the bending stiffness upon the character and order of transitions between random-coil, globules, and pseudocrystalline conformations. The high-accuracy estimates of the microcanonical entropy and its derivatives required for this study were obtained by extensive replica-exchange Monte Carlo simulations. We observe that the transition behavior into the compact phases changes qualitatively with increas…
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）
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…
We study the behavior of a flexible polymer chain in the presence of a low-molecular weight solvent in the vicinity of a liquid-gas critical point within the framework of a self-consistent field theory. The total free energy of the dilute polymer solution is expressed as a function of the radius of gyration of the polymer and the average solvent number density within the gyration volume at the level of the mean-field approximation. Varying the strength of attraction between polymer and solvent we show that two qualitatively different regimes occur at the liquid-gas critical point. In case of w…
We show that the problem of describing the conformations of a semiflexible polymer confined to a channel can be mapped onto an exactly solvable model in the so-called extended de Gennes regime. This regime (where the polymer is neither weakly nor strongly confined) has recently been studied intensively experimentally and by means of computer simulations. The exact solution predicts precisely how the conformational fluctuations depend upon the channel width and upon the microscopic parameters characterising the physical properties of the polymer.
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 …
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…
Multiple loop formation in polymer macromolecules is an important feature of the chromatin organization and DNA compactification in the nuclei. We analyze the size and shape characteristics of complex polymer structures, containing in general $f_1$ loops (petals) and $f_2$ linear chains (branches). Within the frames of continuous model of Gaussian macromolecule, we apply the path integration method and obtain the estimates for gyration radius $R_g$ and asphericity $\hat{A}$ of typical conformation as functions of parameters $f_1$, $f_2$. In particular, our results qualitatively reveal the exte…
We consider the lattice model for an ideal-linear polymer chain to mimic the conformations of the semi-flexible homo-polymer chain. The polymer chain is assumed to confine in the fairly small area, such that the flexible chain conformations are easily polymerized in the nano-area. It has been described using analytical calculations that such a situation may lead to interesting and distinct theoretical findings of the thermodynamics of semi-flexible homo-polymeric macromolecules where the macromolecules are confined in the nano-length scale. We also discuss the characteristics of the persistent…
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…
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 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…
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 …
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…
We describe a microscope-based optical setup that allows us to perform space-and time-resolved measurements of the spectral reflectance of transparent substrates coated with ultrathin films. This technique is applied to investigate the behavior in water of thermosensitive polymer brushes made of poly(N-isopropylacrylamide) grafted on glass. We show that spectral reflectance measurements yield quantitative information about the conformation and axial structure of the brushes as a function of temperature. We study how molecular parameters (grafting density, chain length) affect the hydra-tion st…
Chain conformations in adsorbed layer during polymer capillary imbibition
South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology（华南先进软物质研究院， emergent soft matter 学院，华南理工大学）；Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology（广东省功能与智能杂化材料器件重点实验室，华南理工大学）；National-Certified Enterprise Technology Center, Kingfa Science and Technology Co., LTD.（国家认定企业技术中心，金发科技股份有限公司）
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…
