Recently it has been shown that a two-dimensional model of self-attracting polymers based on attracting segments displays two phase transitions, a theta-like collapse between swollen polymers and a globular state and another between the globular state and a polymer crystal. On the other hand, the canonical model based on attracting monomers on lattice sites displays only one: the standard tricritical theta collapse transition. Here we show that by considering both models with the addition of stiffness the two models display the same generic phase diagram. In fact we claim that any two-dimensional model of a self-attracting single polymer in solution based upon a fully volume-excluded backbone with isotropic short range attraction should show this same phase structure. We point to the model of hydrogen bonded polymers to demonstrate this observation. In three dimensions we note that more than one crystalline phase may occur.
We investigate interfacial properties between two highly incompatible polymers of different stiffness. The extensive Monte Carlo simulations of the binary polymer melt yield detailed interfacial profiles and the interfacial tension via an analysis of capillary fluctuations. We extract an effective Flory-Huggins parameter from the simulations, which is used in self-consistent field calculations. These take due account of the chain architecture via a partial enumeration of the single chain partition function, using chain conformations obtained by Monte Carlo simulations of the pure phases. The a…
We study the aggregation transition of a finite theta-polymer system in dependence on the bending stiffness $κ$ with the help of parallel multicanonical simulations. In order to distinguish amorphous aggregates from polymer bundles we introduce an order parameter, measuring the correlation of the end-to-end vectors. With the help of this order parameter, we construct generic $T$-$κ$ phase diagrams for systems with $2$ and $8$ polymers and discuss the occurring phases from amorphous aggregates to bundle structures. For an intermediate stiffness range we find multiple aggregated phases which cha…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on folding. Hydrophobic polymers display parabolic, protein-like, temperature-dependent free energy of unfolding. Folded states of small attractive polymers are marginally stable at 300 K, and can be unfolded by heating or cooling. Increasing the lengthscale or decreasing the polymer-water attractions stabilizes folded states significantly, the former dominated…
Molecular dynamics simulation of a generic polymer model is applied to study melts of polymers with different types of intrinsic stiffness. Important static observables of the single chain such as gyration radius or persistence length are determined. Additionally we investigate the overall static melt structure including pair correlation function, structure function and orientational correlation function.
The lattice cluster theory (LCT) for semiflexible linear telechelic melts, developed in paper I, is applied to examine the influence of chain stiffness on the average degree of self-assembly and the basic thermodynamic properties of linear telechelic polymer melts. Our calculations imply that chain stiffness promotes self-assembly of linear telechelic polymer melts that assemble on cooling when either polymer volume fraction $ϕ$ or temperature $T$ is high, but opposes self-assembly when both $ϕ$ and $T$ are sufficiently low. This allows us to identify a boundary line in the $ϕ$-$T$ plane that …
Using extensive molecular dynamics simulations, we investigate the slowing down of dynamics in a 3D system of ring polymers by varying the ambient pressure and the stiffness of the rings. Our study demonstrates that the stiffness of the rings determines the dynamics of the ring polymers, leading to glassiness at lower pressures for stiffer rings. The threading of the ring polymers, a unique feature that emerges only due to the topological nature of such polymers in three dimensions, is shown to be the determinant feature of dynamical slowing down, albeit only in a certain stiffness range. Our …
The Kremer-Grest (KG) model is a standard for studying generic polymer properties. Here we have equilibrated KG melts up to and beyond $200$ entanglements per chain for varying chain stiffness. We present methods for estimating the Kuhn length corrected for incompressibility effects, for estimating the entanglement length corrected for chain stiffness, for estimating bead frictions and Kuhn times taking into account entanglement effects. These are the key parameters for enabling quantitative, accurate, and parameter free comparisons between theory, experiment and simulations of KG polymer mode…
The efficiency of nanopore-based polymer sensing devices depends on the fast capture of anionic polyelectrolytes by negatively charged pores. This requires the cancellation of the electrostatic barrier associated with repulsive polymer-pore interactions. We develop a correlation-corrected theory to show that the barrier experienced by the polymer can be efficiently overcome by the addition of multivalent cations into the electrolyte solution. Cation adsorption into the pore enhances the screening ability of the pore medium with respect to the bulk reservoir which translates into an attractive …
We use molecular simulations to study jamming of a crumpled bead-spring model polymer in a finite container and compare to jamming of repulsive spheres. After proper constraint counting, the onset of rigidity is seen to occur isostatically as in the case of repulsive spheres. Despite this commonality, the presence of the curved container wall and polymer backbone bonds introduce new mechanical properties. Notably, these include additional bands in the vibrational density of states that reflect the material structure as well as oscillations in local contact number and density near the wall but …
We investigate the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. An attractive interaction can greatly improve translocation probability. At the same time, it also increases translocation time slowly for weak attraction while exponential dependence is observed for strong attraction. For fixed driving force and chain length the histogram of translocation time has a transition from Gaussian distribution to long-tailed distribution with increasing attraction. Under a weak driving force and a strong attractive force, both the translocatio…
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…
We study the effect of physical confinement on the capillary infiltration of polymers into cylindrical nanopores using molecular dynamics simulations. In particular, we probe whether the critical contact angle above which capillary rise infiltration ceases to occur changes for long chain polymers, possibly due to loss of conformation entropy induced by chain confinement. Surprisingly, the critical contact angle does not strongly depend on the length of polymer chains and stays constant for large N. A free energy model is developed to show that the critical angle for infiltration depends strong…
Performing light scattering experiments we show that introducing short-ranged attraction to a colloidal suspension of nearly hard spheres by addition of free polymer produces new glass transition phenomena. We observe a dramatic acceleration of the density fluctuations amounting to the melting of a colloidal glass. Increasing the strength of the attractions the system freezes into another nonergodic state sharing some qualitative features with gel states occurring at lower colloid packing fractions. This reentrant glass transition is in qualitative agreement with recent theoretical predictions…
We constrast the dynamics in model unentangled polymer melts of chains of three different stiffnesses: flexible, intermediate, and rodlike. Flexible and rodlike chains, which readily solidify into close-packed crystals (respectively with randomly oriented and nematically aligned chains), display simple melt dynamics with Arrhenius temperature dependence and a discontinuous change upon solidification. Intermediate-stiffness chains, however, are fragile glass-formers displaying Vogel-Fulcher dynamical arrest, despite the fact that they also possess a nematic-close-packed crystalline ground state…
Wetting and drying phenomena are studied for flexible and semiflexible polymer solutions via coarse-grained molecular dynamics simulations and density functional theory calculations. The study is based on the use of Young's equation for the contact angle, determining all relevant surface tensions from the anisotropy of the pressure tensor. The solvent quality (or effective temperature, equivalently) is varied systematically, while all other interactions remain unaltered. For flexible polymers, the wetting transition temperature $T_{\rm w}$ increases monotonically with chain length $N$, while t…
When the local intrinsic stiffness of a polymer chain varies over a wide range, one can observe both a crossover from rigid-rod-like behavior to (almost) Gaussian random coils and a further crossover towards self-avoiding walks in good solvents. Using the pruned-enriched Rosenbluth method (PERM) to study self-avoiding walks of up to $N_b=50000$ steps and variable flexibility, the applicability of the Kratky-Porod model is tested. Evidence for non-exponential decay of the bond-orientational correlations $<\cos θ(s) >$ for large distances $s$ along the chain contour is presented, irrespective of…
We investigate the mechanical properties of amorphous polymers by means of coarse-grained simulations and nonaffine lattice dynamics theory. A small increase of polymer chain bending stiffness leads first to softening of the material, while hardening happens only upon further strengthening of the backbones. This nonmonotonic variation of the storage modulus $G'$ with bending stiffness is caused by a competition between additional resistance to deformation offered by stiffer backbones and decreased density of the material due to a necessary decrease in monomer-monomer coordination. This counter…
We study the influence of chain stiffness on droplet flow in a nano-channel, coated with semiflexible hydrophobic polymers by means of non-equilibrium molecular-dynamics simulations. The studied system is then a moving droplet in the slit channel, coexisting with its vapor and subjected to periodic boundary conditions in the flow direction. The polymer chains, grafted by the terminal bead to the confining walls, are described by a coarse-grained model that accounts for chain connectivity, excluded volume interactions and local chain stiffness. The rheological, frictional and dynamical properti…
Recently it has been shown that a two-dimensional model of self-attracting polymers based on attracting segments with the addition of stiffness displays three phases: a swollen phase, a globular, liquid-like phase, and an anisotropic crystal-like phase. Here, we consider the attracting segment model in three dimensions with the addition of stiffness. While we again identify a swollen and two distinct collapsed phases, we find that both collapsed phases are anisotropic, so that there is no phase in which the polymer resembles a disordered liquid drop. Moreover all the phase transitions are firs…
Polymeric single-chain nanoparticles (SCNPs) are soft nano-objects synthesized by purely intramolecular cross-linking of single polymer chains. By means of computer simulations, we investigate the conformational properties of SCNPs as a function of the bending stiffness of their linear polymer precursors. We investigate a broad range of characteristic ratios from the fully flexible case to those typical of bulky synthetic polymers. Increasing stiffness hinders bonding of groups separated by short contour distances and increases looping over longer distances, leading to more compact nanoparticl…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase diagram for the complete range of semi-flexible polymers, from flexible to stiff. Although a simple model, we observe a rich variety of conformational phases, reminiscent of conformations observed for synthetic polymers or biopolymers. Changing the internal bending stiffness, the model exhibits different pseudo phases like bent, hairpin or toroidal. In partic…
The lattice cluster theory (LCT) for strongly interacting, self-assembling telechelic polymers provides a theoretical tool that enables establishing the connections between important microscopic molecular details of self-assembling polymers and their bulk thermodynamics. The original LCT for self-assembly of telechelic polymers considers a model of fully flexible linear chains [J. Dudowicz and K. F. Freed, J. Chem. Phys. \textbf{136}, 064902 (2012)], while our recent work introduces a significant improvement to the LCT by including a description of chain semiflexibility for the bonds within ea…
Electroconvection in rechargeable batteries enhances the growth of dendrites at the electrode surface. The addition of low molecular weight polymers to the electrolyte in batteries results in the formation of a thin layer of higher polymer concentration near the electrode. This is due to van der Waals forces of attraction between the metal electrode and the polymers dissolved in the electrolyte. The van der Waals forces act as a restoring body force on the electrolyte and oppose the growth of perturbations. Using linear stability analysis, we show that this force opposes electroconvective flow…
We analyse the nature of the confinement of an infinitely long (and finite) linear semiflexible homo-polymer chain confined in between two geometrical constraints (A&B) under good solvent condition in two dimensions. The constraints are stair shaped impenetrable lines. A lattice model of fully directed self avoiding walk is used to list information of walks of the confined chain and the exact enumeration technique is used for the canonical ensemble of conformations of the confined chain to discuss equilibrium statistics of the chain. We obtain the probability of polymerization of the confined …
We employ computer simulations and thermodynamic integration to analyse the effects of bending rigidity and slit confinement on the free energy cost of tying knots, $ΔF_{\rm knotting}$, on polymer chains under tension. A tension-dependent, non-zero optimal stiffness $κ_{\rm min}$ exists, for which $ΔF_{\rm knotting}$ is minimal. For a polymer chain with several stiffness domains, each containing a large amount of monomers, the domain with stiffness $κ_{\rm min}$ will be preferred by the knot. A {\it local} analysis of the bending in the interior of the knot reveals that local stretching of cha…
We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test charge theory to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loop level electrostatic correlation effects such as the ionic cloud deformation around the strongly charged DNA molecule as well as image-charge forces induced by the low DNA permittivity. Our model can reproduce and explain various characteristics of the experimental phase diagrams for polymer solutions. First, the addition of polyvalent cations to the el…
Hydrogels have a distinct combination of mechanical and water-transport behaviors. As hydrogels stiffen, they become less permeable. Here, we combine semi-dilute polymer theory with the Kozeny-Carman equation to develop a simple scaling law describing the relationship between hydraulic permeability and mechanical stiffness. We find that these properties are dictated by the polymer strand spacing, explained via analogy of a bowl of noodle soup. We find a remarkably close agreement between our scaling law and experimental results across four different polymer families with varied crosslinkings.
We study the static properties of a semiflexible polymer exposed to a quenched random environment by means of computer simulations. The polymer is modeled as two-dimensional Heisenberg chain. For the random environment we consider hard disks arranged on a square lattice. We apply an off-lattice growth algorithm as well as the multicanonical Monte Carlo method to investigate the influence of both disorder occupation probability and polymer stiffness on the equilibrium properties of the polymer. We show that the additional length scale induced by the stiffness of the polymer extends the well-kno…
We map out the solid-state morphologies formed by model soft-pearl-necklace polymers as a function of bending stiffness $k_b$ spanning the range from fully flexible to rodlike chains. The ratio of Kuhn length to bead diameter ($l_K/r_0$) increases monotonically with increasing $k_b$ and yields a one-parameter model that relates chain shape to bulk morphology and yields insights into the packing of anisotropic particles. In the flexible limit, monomers occupy the sites of close-packed crystallites while chains retain random-walk-like order. In the rodlike limit, nematic chain ordering typical o…
We study analytically a model of a two dimensional, partially directed, flexible or semiflexible polymer, attached to an attractive wall which is perpendicular to the preferred direction. In addition, the polymer is stretched by an externally applied force. We find that the wall has a dramatic effect on the polymer. For wall attraction smaller than the non-sequential nearest neighbor attraction, the fraction of monomers at the wall is zero and the model is the same as that of a polymer without a wall. However, for greater than, the fraction of monomers at the wall undergoes a first order trans…
An extended Molecular-Dynamics study of the short-time "glassy" elasticity exhibited by a polymer melt of linear fully-flexible chains above the glass transition is presented. The focus is on the infinite-frequency shear modulus $G_\infty$ manifested in the picosecond time scale and the relaxed plateau $G_p$ reached at later times and terminated by the structural relaxation. The local stiffness of the interactions with the first neighbours of each monomer exhibits marked distribution with average value given by $G_\infty$. In particular, the neighbourhood of the end monomers of each chain are …
We investigate the addition of stiffness to the lattice model of hydrogen-bonded polymers in two and three dimensions. We find that, in contrast to polymers that interact via a homogeneous short-range interaction, the collapse transition is unchanged by any amount of stiffness: this supports the physical argument that hydrogen bonding already introduces an effective stiffness. Contrary to possible physical arguments, favouring bends in the polymer does not return the model's behaviour to that comparable to the semi-flexible homogeneous interaction model, where the canonical $θ$-point occurs fo…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are coupled via harmonic springs, the non-neighboring monomers interact via a hard core and a short-ranged attractive potential. For a sufficiently small interaction range λ, the system undergoes a first-order freezing transition from an expanded, disordered phase to a compact crystalline state. Using a new shooting move tailored to polymers combined with a committ…
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.
The reptation concept in polymer dynamics is studied for model chains with added stiffness. The main idea of a chain diffusing inside a tube can be transferred from fully flexible chains. However, the picture, which renormalizes the chain of locally stiff Kuhn segments onto a flexible chain of fewer segments fails. The entanglement length shrinks with increasing persistence length. If entanglement length and persistence length come to the same order of magnitude the picture of a tight tube is better suited, in which chain segments can move only along the contour, any transverse motion being mu…
A self-interacting polymer with one end attached to a sticky surface has been studied by means of a flat-histogram stochastic growth algorithm known as FlatPERM. We examined the four-dimensional parameter space of the number of monomers up to 91, self-attraction, surface attraction and force applied to an end of the polymer. Using this powerful algorithm the \emph{complete} parameter space of interactions and force has been considered. Recently it has been conjectured that a hierarchy of states appears at low temperature/poor solvent conditions where a polymer exists in a finite number of laye…
We revisit a model of semiflexible Gaussian chains proposed by Winkler \textit{et al}, solve the dynamics of the discrete description of the model and derive exact algebraic expressions for some of the most relevant dynamical observables, such as the mean-square displacement of individual monomers, the dynamic structure factor, the end-to-end vector relaxation and the shear stress relaxation modulus. The mathematical expressions are verified by comparing them with results from Brownian dynamics simulations, reporting an excellent agreement. Then, we generalize the model to linear polymer chain…
Twist stiffness and an asymmetric bending stiffness of a polymer or a polymer bundle is captured by the elastic ribbon model. We investigate the effects a ring geometry induces to a thermally fluctuating ribbon, finding bend-bend coupling in addition to twist-bend coupling. Furthermore, due to the geometric constraint the polymer's effective bending stiffness increases. A new parameter for experimental investigations of polymer bundles is proposed: the mean square diameter of a ribbonlike ring, which is determined analytically in the semiflexible limit. Monte Carlo simulations are performed wh…
Stretching response of polymer chains under external force is crucial in understanding polymer dynamics under equilibrium and non-equilibrium conditions. Here we measure the elastic response of poly(ethylene glycol) using a lock-in based amplitude modulation-AFM with sub-angstrom amplitude in both low and high frequency regime. Appropriate analysis that takes into account the cantilever geometry and hydrodynamic loading effects of oscillating cantilever in liquid, relates X signal of lock-in amplifier linearly to stiffness.Stiffness data extracted from X signal was compared with stiffness from…
The generalized entropy theory is applied to assess the joint influence of the microscopic cohesive energy and chain stiffness on glass formation in polymer melts using a minimal model containing a single bending energy and a single (monomer averaged) nearest neighbor van der Waals energy. The analysis focuses on the combined impact of the microscopic cohesive energy and chain stiffness on the magnitudes of the isobaric fragility parameter $m_P$ and the glass transition temperature $T_g$. The computations imply that polymers with rigid structures and weak nearest neighbor interactions are the …
Based on our previous paper [cond-mat/0507477], we establish a general model for the whip-toroid transitions of a semiflexible homopolymer chain using the path integral method and the O(3) nonlinear sigma model on a line segment with the local inextensibility constraint. We exactly solve the energy levels of classical solutions, and show that some of its classical configurations exhibit toroidal forms, and the system has phase transitions from a whip to toroidal states with a conformation parameter $c=\frac{W}{2 l} (\frac{L}{2π})^2$. We also discuss the stability of the toroid states and propo…
Using video-microscopy imaging we demonstrate the existence of a short-ranged equilibrium attraction between heavy silica colloids diffusing on soft surfaces of cross-linked polymer gels. The inter-colloid potential can be tuned by changing the gel stiffness or by coating the colloids with a polymer layer. On sufficiently soft substrates, the interaction induced by the polymer matrix leads to large-scale colloidal aggregation. We correlate the in-plane interaction with a colloid-surface attraction.
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to an applied torque through the relation Lk = Tw + Wr. We explore this coupling and find agreement between the predictions of our model and recent experimental results on single lambda-DNA molecules. This analysis affords an experimental determination of the microscopic twist stiffness (averaged over a helix repeat). Quantitative agreement between theory and …
We make use of the previously developed formalism for a monomer ensemble and include angular dependence of the segments of the polymer chains thus described. In particular we show how to deal with stiffness when the polymer chain is confined to certain regions. We investigate the stiffness from the perspectives of a differential equation, integral equations, or recursive relations for both continuum and lattice models. Exact analytical solutions are presented for two cases, whereas numerical results are shown for a third case.
The nature of the globule-coil transition of surface-confined polymers has been an issue of debate. Here this 2D collapse transition is studied through a partially directed lattice model. In the general case of polymers with positive bending stiffness ($Δ>0$), the collapse transition is {\em first-order}; it becomes {\em second-order} only in the limiting case of zero bending stiffness ($Δ\equiv 0$). These analytical results are confirmed by Monte Carlo simulations. We also suggest some possible future experiments.
