We investigate conformations and dynamics of a polymer considering its monomers to be active Brownian particles. This active polymer shows very intriguing physical behavior which is absent in an active Rouse chain. The chain initially shrinks with active force, which starts swelling on further increase in force. The shrinkage followed by swelling is attributed purely to excluded-volume interactions among the monomers. In the swelling regime, chain shows a cross-over from the self-avoiding behavior to Rouse-behavior with scaling exponent $ν_a \simeq 1/2$ for end-to-end distance. The non-monotonicity in the structure is analysed through various physical quantities specifically, radial distribution function of monomers, scattering time, as well as various energy calculations. The chain relaxes faster than the Rouse chain in the intermediate force regime, with a cross-over in variation of relaxation time at large active force as given by a power-law $τ_r \sim Pe^{-4/3}$ (P e is Péclet number).
Conformations of a single semiflexible polymer chain dissolved in a low molecular weight liquid crystalline solvents (nematogens) are examined by using a mean field theory. We takes into account a stiffness and partial orientational ordering of the polymer. As a result of an anisotropic coupling between the polymer and nematogen, we predict a discontinuous (or continuous) phase transition from a condensed-rodlike conformation to a swollen-one of the polymer chain, depending on the stiffness of the polymer. We also discuss the effects of the nematic interaction between polymer segments.
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…
A mode-coupling theory for dense polymeric systems is developed which unifyingly incorporates the segmental cage effect relevant for structural slowing down and polymer chain conformational degrees of freedom. An ideal glass transition of polymer melts is predicted which becomes molecular-weight independent for large molecules. The theory provides a microscopic justification for the use of the Rouse theory in polymer melts, and the results for Rouse-mode correlators and mean-squared displacements are in good agreement with computer simulation results.
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 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 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 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 report on quantitative comparisons between simulation results of a bead-spring model and mode-coupling theory calculations for the structural and conformational dynamics of a supercooled, unentangled polymer melt. We find semiquantitative agreement between simulation and theory, except for processes that occur on intermediate length scales between the compressibility plateau and the amorphous halo of the static structure factor. Our results suggest that the onset of slow relaxation in a glass-forming melt can be described in terms of monomer-caging supplemented by chain connectivity. Furthe…
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…
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…
By means of sophisticated Monte Carlo methods, we investigate the conformational phase diagram of a simple model for flexible polymers with explicit thickness. The thickness constraint, which is introduced geometrically via the global radius of curvature of a polymer conformation, accounts for the excluded volume of the polymer and induces cooperative effects supporting the formation of secondary structures. In our detailed analysis of the temperature and thickness dependence of the conformational behavior for classes of short tubelike polymers, we find that known secondary-structure segments …
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 study ground states of a hybrid system consisting of a polymer and an attractive nanowire by means of computer simulations. Depending on structural and energetic properties of the substrate, we find different adsorbed polymer conformations, amongst which are spherical droplets attached to the wire and monolayer tubes surrounding it. We construct the complete conformational phase diagram and analyze in more detail particularly interesting polymer-tube conformations.
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）
The present communication reports the first direct measurement of the conformation of a polymer corona grafted around silica nano-particles dispersed inside a nanocomposite, a matrix of the same polymer. This measurement constitutes an experimental breakthrough based on a refined combination of chemical synthesis, which permits to match the contribution of the neutron silica signal inside the composite, and the use of complementary scattering methods SANS and SAXS to extract the grafted polymer layer form factor from the inter-particles silica structure factor. The modelization of the signal o…
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…
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…
In this paper, we analyze the effect of geometrical constraint on the conformational properties of an infinitely long linear semiflexible polymer chain confined in-between two constraints under good solvent condition in two dimensions. The constraints are two impenetrable stair shaped surface and for two dimensional space, the surface is a one dimensional line. The semiflexibility of the chain is accounted by introducing a Boltzmann weight of bending energy required to produce each turn in the chain and good solvent condition was accounted by using self avoiding walk model of the chain. We hav…
One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, $\langle τ\rangle/N_K$ is longer than the relaxation time $τ_0$ of the polymer. Towards an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collisi…
Chemically-responsive polymers are macromolecules that respond to local variations of the chemical composition of the solution by changing their conformation, with notable examples including polyelectrolytes, proteins and DNA. The polymer conformation changes can occur in response to changes to the pH, the ionic strength or to the concentration of a generic solute that interacts with the polymer. These chemical stimuli can lead to drastic variations of the polymer flexibility and even trigger a transition from a coil to a globule polymer conformation. In many situations the spatial distributio…
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 conformational behavior of polarizable polymer chain under an external homogeneous electric field within the Flory type self-consistent field theory. We consider the influence of electric field on the polymer coil as well as on the polymer globule. We show that when the polymer chain conformation is a coil, application of external electric field leads to its additional swelling. However, when the polymer conformation is a globule, a sufficiently strong field can induce a globule-coil transition. We show that such $"$field-induced$"$ globule-coil transition at the sufficiently smal…
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…
Small angle X-ray scattering (SAXS) in poly[2-methoxy-5-(2-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) solution has shown the important role of pi-electron conjugation in controlling the chain conformation and assembly. By increasing the extent of conjugation from 30 to 100 %, the persistence length (l_p) increases from 20 to 66 Angstrom. Moreover, a pronounced second peak in the pair distribution function has been observed in fully conjugated chain, at larger length scales. This feature indicates that the chain segments tend to self-assemble as the conjugation along the chain increases.…
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…
We map the conformation space of a simple lattice polymer chain to a network, where (i) the vertices of the network have a one-to-one correspondence to the conformations of the chain, and (ii) a link between two vertices indicates the possibility of switching from one conformation to the other by a single Monte Carlo move of the chain. We find that the geometric properties of this network are similar to those of small-world networks, namely, the diameter of conformation space increases, for large networks, as the logarithm of the number of conformations, while locally the network appears to ha…
In the present work, we study the equilibrium conformations of linear polyelectrolytes tethered onto a spherical, oppositely charged core in equilibrium with an ionic reservoir of fixed concentration. Particular focus is placed on the situation of stretched chains, where the monomer concentration is known to display an inverse square-law decay far away from the spherical surface, which is then further extrapolated all the way down to the grafting core. While the equilibrium distributions of mobile ions are computed in the framework of a classical Density Functional Theory (cDFT) that incorpora…
We study the conformational behavior of a polymer adsorbed at an attractive nanostring and construct the complete structural phase diagram in dependence of the binding strength and effective thickness of the string. For this purpose, Monte Carlo optimization techniques are employed to identify lowest-energy structures for a coarse-grained hybrid polymer-wire model. Among the representative conformations in the different phases are, for example, compact droplets attached to the string and also nanotube-like monolayer films wrapping the string in a very ordered way. We here systematically analyz…
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.
The behavior of a strongly charged polymer adsorbed on an oppositely charged surface of low-dielectric constant is formulated by the functional integral method. By separating the translational, conformational, and fluctuational degrees of freedom, the scaling behaviors for both the height of the polymer and the thickness of the diffusion layer are determined. Unlike the results predicted by scaling theory, we identified the continuous crossover from the weak compression to the compression regime. All teh analytical results are found to be consistent with Monte-Carlo simulations. Finally, an al…
One measure of geometrical complexity of a spatial curve is the number of crossings in a planar projection of the curve. For $N$-noded ring polymers with a fixed knot type, we evaluate numerically the average of the crossing number over some directions. We find that the average crossing number under the topological constraint are less than that of no topological constraint for large $N$. The decrease of the geometrical complexity is significant when the thickness of polymers is small. The simulation with or without a topological constraint also shows that the average crossing number and the av…
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses -- one yielding an energy penalty for local bends (energetic stiffness) and the other two forbidding certain classes of chain conformations (entropic stiffness). Using detailed Wang-Landau microcanonical Monte Carlo simulations, we study the interplay between the nature of the stiffness and the ground state conformation of a self-attracting chain. We find a wide range of ground state conformations…
The coil-stretch transition in extensional flows of viscoelastic dilute polymer solutions is known to be associated with a strong hysteresis in molecular conformations and rheo-optical properties. At infinite dilution, hysteresis is caused by the large difference in frictional drag coefficient between undeformed isotropic polymer coils and highly stretched conformations. At the low extension rates in the hysteresis regime, stretched molecules pervade larger volumes than equilibrium coils since the flow is too weak to suppress transverse fluctuations. The onset of intermolecular overlap occurs …
We study the mechanical and conformational properties of networks of helical polymers with a combination of Monte Carlo simulations based on the Wang-Landau algorithm and the Three-chain Model. We find that the stress-strain behavior of these networks has novel features not observed in typical networks made of synthetic polymers. In particular, we find that as these networks are stretched they first strengthen, then soften and finally strengthen again. This non-monotonic behavior of the stress correlates with the one of the helical content and is rationalized by the elongation-induced formatio…
Two types of average structures of a single knotted ring polymer are studied by Brownian dynamics simulations. For a ring polymer with N segments, its structure is represented by a 3N -dimensional conformation vector consisting of the Cartesian coordinates of the segment positions relative to the center of mass of the ring polymer. The average structure is given by the average conformation vector, which is self-consistently defined as the average of the conformation vectors obtained from a simulation each of which is rotated to minimize its distance from the average conformation vector. From e…
The interplay between concentration, flow, hydrodynamic interactions (HI), and topological interactions governing semidilute polymer dynamics in strong flows are challenging to characterize. Brownian dynamics (BD) simulations are particularly valuable as a way to direct visualize how molecular interactions arise in these systems; however, BD simulations are often computationally limited by the need to calculate the correlated Brownian noise via decomposition of the diffusion tensor. Previously we have introduced an iterative conformational averaging (CA) method for BD simulations which bypasse…
In this paper we derive the general equilibrium equations of a polymer chain with a noncircular cross section by the variation of the free energy functional. From the equilibrium equation of the elastic ribbon we derive analytically the equilibrium conformations both of the helical ribbons and the twisted ribbons. We find that the pitch angle of the helical ribbons depends on the ratio of the torsional rigidity to the bending one. For the twisted ribbons, the rotation rate depends on the spontaneous torsion, which is determined by the elastic properties of the polymers. Our results for helical…
