A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate these transitions we have performed Monte Carlo simulations of a bond-fluctuation model with Wang-Landau and umbrella sampling algorithms in a two-dimensional state space. The simulations' density of states results have been evaluated for interaction parameters spanning the range from good to poor solvent conditions and from repulsive to strongly attractive surfaces. In this work, we describe the simulation method and present results for the overall phase behavior and for some of the transitions. For adsorption in good solvent, we compare with Metropolis Monte Carlo data for the same model and find good agreement between the results. For the collapse transition, which occurs when the solvent quality changes from good to poor, we consider two situations corresponding to three-dimensional (hard surface) and two-dimensional (very attractive surface) chain conformations, respectively. For the hard surface, we compare tethered chains with free chains and find very similar behavior for both types of chains. For the very attractive surface, we find the two-dimensional chain collapse to be a two-step transition with the same sequence of transitions that is observed for three-dimensional chains: a coil-globule transition that changes the overall chain size is followed by a local rearrangement of chain segments.
Computer simulations are used to characterize the entropic force of one or more polymers tethered to the tip of a hard conical object that interact with a nearby hard flat surface. Pruned-enriched-Rosenbluth-method (PERM) Monte Carlo simulations are used to calculate the variation of the conformational free energy, $F$, of a hard-sphere polymer with respect to cone-tip-to-surface distance, $h$, from which the variation of the entropic force, $f\equiv |dF/dh|$, with $h$ is determined. We consider the following cases: (1) a single freely-jointed tethered chain, (2) a single semiflexible tethered…
We report molecular dynamics simulations of a system of repulsive, polymer-tethered colloidal particles. We use an explicit polymer model to explore how the length and the behavior of the polymer (ideal or self-avoiding) affect the ability of the particles to organize into ordered structures when the system is compressed to moderate volume fractions. We find a variety of different phases whose origin can be explained in terms of the configurational entropy of polymers and colloids. Finally, we discuss and compare our results to those obtained for similar systems using simplified coarse-grained…
Recent advances in single macromolecule experiments have sparked interest in the ensemble dependence of force-extension relations. The thermodynamic limit may not be attainable for such systems, that leads to inequivalence of the fixed-force and the fixed-extension ensemble. We consider an ideal Gaussian chain described by the Edwards Hamiltonian with one end tethered to a rigid planar substrate. We analytically calculate the force-extension relation in the two ensembles and we show their inequivalence which is caused by the confinement of the polymer to half space. The inequivalence is quite …
The properties of a semiflexible polymer with fixed ends exposed to oscillatory shear flow are investigated by simulations. The two-dimensionally confined polymer is modeled as a linear bead-spring chain, and the interaction with the fluid is described by the Brownian multiparticle collision dynamics approach. For small shear rates, the tethering of the ends leads to a more-or-less linear oscillatory response. However, at high shear rates, we found a strongly nonlinear reaction, with a polymer (partially) wrapped around the fixation points. This leads to an overall shrinkage of the polymer. Dy…
Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective phases of end-grafted polymers in a nanopore and to study their relative stability as a function of intermolecular interactions. Over a range of system parameters that is relevant for nuclear pore complexes, we observe two distinct phases: one with the bulk of the polymers condensed at the wall of the pore, and the other with the polymers condensed along it…
Shape transformations of hairy nanoparticles under confinement are studied using molecular dynamic simulations. We discuss the behavior of these particles in slits with inert or attractive walls. We assume that only chain-wall interactions are attractive. The impact of the strength of interactions with the walls and the width of the slits on the particle configuration is shown. In the case of attractive surfaces, we found new structures in which the chains are connected with both walls and form bridges between them: pillars, symmetrical and asymmetrical spools, and hourglasses. In wide pores w…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three regions: a classical MD region, a continuum domain where the dynamical equations are solved by standard CFD methods, and an overlap domain where transport information from the other two domains is exchanged. The exchange of information in the overlap region ensures that momentum, energy and mass are conserved. The validity of the hybrid code is demonstrated by stu…
We study self-assembly of a binary mixture of components A and B confined in a slit-like pore with the walls modified by the stripes of tethered brushes made of beads of a sort A. The emphasis is on solvent mediated transitions between morphologies when the composition of the mixture varies. For certain limiting cases of the pore geometry we found that an effective reduction of the dimensionality may lead to a quasi one- and two-dimensional demixing. The change of the environment for the chains upon changing the composition of the mixture from polymer melt to a good solvent conditions provides…
The crazing behavior of polymer nanocomposites formed by blending polymer grafted nanoparticles with an entangled polymer melt is studied by molecular dynamics simulations. We focus on the three key differences in the crazing behavior of a composite relative to the pure homopolymer matrix, namely, a lower yield stress, a smaller extension ratio and a grafted chain length dependent failure stress. The yield behavior is found to be mostly controlled by the local nanoparticle-grafted polymer interfacial energy, with the grafted polymer-polymer matrix interfacial structure being of little to no re…
We present an analysis of a partially directed walk model of a polymer which at one end is tethered to a sticky surface and at the other end is subjected to a pulling force at fixed angle away from the point of tethering. Using the kernel method, we derive the full generating function for this model in two and three dimensions and obtain the respective phase diagrams. We observe adsorbed and desorbed phases with a thermodynamic phase transition in between. In the absence of a pulling force this model has a second-order thermal desorption transition which merely gets shifted by the presence of …
The recently proposed fluctuation relation in unfolding forces [Phys. Rev. E ${\bf 84}$, $060101$(R) $(2011)$] is re-examined taking into account the explicit time dependence of the force distribution. The stretching of a tethered Rouse polymer is exactly solved and the ratio of the probabilities of positive to negative forces is shown to be an exponential in force. Extensive steered molecular dynamics simulations of unfolding of deca alanine peptide confirm the form of fluctuation relation proposed earlier, but with explicit correct time dependence of unfolding forces taken into account. From…
We present results of Brownian dynamics simulations of tethered nanospheres and tethered nanorods. Immiscibility between tether and nanoparticle facilitates microphase separation into the bicontinuous, double gyroid structure (first reported by Iacovella et al. [Phys. Rev. E 75 (2007)] and Horsch et al. [J. Chem. Phys. 125 (2006)] respectively). We demonstrate the ability of these nanoparticles to adopt distinct, minimal energy local packings, in which nanospheres form icosahedral-like clusters and nanorods form splayed hexagonal bundles. These local structures reduce packing frustration withi…
We present results of molecular simulations that predict the phases formed by the self-assembly of model nanospheres functionalized with a single polymer "tether", including double gyroid, perforated lamella and crystalline bilayer phases. We show that microphase separation of the immiscible tethers and nanospheres causes confinement of the nanoparticles, which promotes local icosahedral packing that stabilizes the gyroid and perforated lamella phases. We present a new metric for determining the local arrangement of particles based on spherical harmonic "fingerprints", which we use to quantify…
A simple application of classical density functional theory is derived and applied to a system of polymers grafted to a plane. The system is assumed to have symmetry in directions parallel to the grafting plane hence it being a '1-dimensional' problem. A quick introduction to using propagators in the theory of chains in the presence of external fields and a numerical algorithm for solving the modified diffusion (or Fokker-Planck) equation are presented. Density profiles are found for hard-sphere chains which agree with results in the literature (see Murat,.., Milner,.., Muhukumar and others) a…
The thermal fluctuation spectrum of a fluid membrane coupled harmonically to a solid support by an array of tethers is calculated. For strong tethers, this spectrum exhibits non-monotonic, anisotropic behavior with a relative maximum at a wavelength about twice the tether distance. The root mean square displacement is evaluated to estimate typical membrane displacements. Possible applications cover pillar-supported or polymer-tethered membranes.
An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent quality and surface attraction are reflected in equilibrium force-extension curves that can be measured in experiments. To investigate these effects theoretically, we study tethered chains under tension with Wang-Landau simulations of a bond-fluctuation lattice model. Applying our model to pulling experiments on biological molecules we obtain a good description…
Tethered particle motion (TPM) --- the motion of a micro- or nanoparticle tethered to a substrate by a macromolecule --- is a system that has proven extremely useful for its ability to reveal physical features of the tether, because the thermal motion of the bound particle reports sensitively on parameters like the length, the rigidity, or the folding state of its tether. In this paper, we discuss a novel application of TPM, surveying its utility in probing the kinetics of single secondary bonds: bonds that form and break between the tethered particle and a substrate due, for instance, to rece…
In this paper we study a system of entangled chains that bear reversible cross-links in a melt state. The cross-links are tethered uniformly on the backbone of each chain. A slip-link type model for the system is presented and solved for the relaxation modulus. The effects of entanglements and reversible cross-linkers are modelled as discrete form of constraints that influence the motion of the primitive path. In contrast to a non-associating entangled system the model calculations demonstrate that the elastic modulus has a much higher first plateau and a delayed terminal relaxation. These eff…
Charged polymer brushes are layers of surface-tethered chains. Experimental systems are frequently strongly charged. Here we calculate phase diagrams for such brushes in terms of salt concentration n_s, grafting density and polymer backbone charge density. Electrostatic stiffening and counterion condensation effects arise which are absent from weakly charged brushes. In various phases chains are locally or globally fully stretched and brush height H has unique scaling forms; at higher salt concentrations we find H ~ n_s^(-1/3), in good agreement with experiment.
Bottle brushes are polymeric macromolecules made of a linear polymeric backbone grafted with side chains. The choice of the grafting density σg, the length ns the grafted side chains and their chemical nature fully determines the properties of each macromolecule, such as its elasticity and its folding behaviour. Typically, experimental bottle brushes are systems made of tens of thousands of monomeric units, rendering a computational approach extremely expensive, especially in the case of bottle brush solutions. A proper coarse graining description of these macromolecules thus appears essential…
We study the conformational properties of complex Gaussian polymers containing $f_c$ linear branches and $f_r$ closed loops, periodically tethered at $n$ branching points to either a linear polymer backbone (generalized bottlebrush structures) or closed polymer ring (decorated ring structure). Applying the path integration method, based on Edwards continuous chain model, we obtain in particular the exact values for the size ratios comparing the gyration radii of considered complex structures and linear chains of the same total molecular weight, as functions of $n$, $f_c$ and $f_r$. Compactific…
In the gelation theory it has been implicitly assumed that (I) a cyclic bond is a finite bond that returns to itself; (II) cyclic bonds distribute at random in network structures. In this paper these two assumptions are reexamined from a new point of view. The physical soundness of the assumptions is assessed through comparison with experimental observations.
We perform thorough molecular-dynamics simulations to compare elasticity and yielding of atomic crystals and model semicrystalline polymers, the latter characterized by very similar positional ordering with respect to atomic crystals and considerable bond disorder. We find that the elastic modulus, the shear yield strength and the critical yield strain of semicrystalline polymers are higher than (modulus and yield strength), or comparable to (critical strain), the corresponding ones of atomic crystals. The findings suggest that the bond disorder suppresses dislocation-mediated plasticity in po…
Bead spring models for polymers in solution are nonlinear if either the finite extensibility of the polymer, excluded volume effects or hydrodynamic interactions between polymer segments are taken into account. For such models we use a powerful method for the determination of the complete relaxation spectrum of fluctuations at {\it steady state}. In general, the spectrum and modes differ significantly from those of the linear Rouse model. For a tethered polymer in uniform flow the differences are mainly caused by an inhomogeneous distribution of tension along the chain and are most pronounced …
The isothermal, isobaric spontaneous crystallization of a supercooled polymer melt is investigated by MD simulation of an ensemble of fully-flexible linear chains. Frustration is introduced via two incommensurate length scales set by the bond length and the position of the minimum of the non-bonding potential. Marked polymorphism with considerable bond disorder, distortions of both the local packing and the global monomer arrangements is observed. The analyses in terms of: i) orientational order parameters characterizing the global and the local order and ii) the angular distribution of the ne…
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…
Sacrificial bonds and hidden length (SBHL) in structural molecules provide a mechanism for energy dissipation at the nanoscale. It is hypothesized that their presence leads to greater fracture toughness than what is observed in materials without such features. Here, we investigate this hypothesis using a simplified model of a mineralized collagen fibril sliding on a polymeric interface with SBHL systems. A 1D coarse-grained nonlinear spring-mass system is used to model the fibril. Rate-and-displacement constitutive equations are used to describe the mechanical properties of the polymeric syste…
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…
We consider a simple lattice model of a topological phase transition in open polymers. To be precise, we study a model of self-avoiding walks on the simple cubic lattice tethered to a surface and weighted by an appropriately defined writhe. We also consider the effect of pulling the untethered end of the polymer from the surface. Regardless of the force we find a first-order phase transition which we argue is a consequence of increased knotting in the lattice polymer, rather than due to other effects such as the formation of plectonemes.
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $σ$ are varied over a wide range and the crossover from ``mushroom'' to ``brush'' behavior is studied for three pore diameters. The monomer density profile and the distribution of the free chain ends are computed and compared to the corresponding model of polymer brushes at flat substrates. It is found that there exists a regime of $N$ and $σ$ for large enough pore diameter where the brush…
While the $Θ$-collapse of single long polymers in bad solvents is usually a continuous (tri-critical) phase transition, there are exceptions where it is preempted by a discontinuous crystallization (liquid $\leftrightarrow$ solid) transition. For a version of the bond-fluctuation model (a model where monomers are represented as $2\times 2\times 2$ cubes, and bonds can have lengths between 2 and $\sqrt{10}$) it was recently shown by F. Rampf {\it et al.} that there exist distinct collapse and crystallization transitions for long but {\it finite} chains. But as the chain length goes to infinity,…
The scaling of the bond-bond correlation function $C(s)$ along linear polymer chains is investigated with respect to the curvilinear distance, $s$, along the flexible chain and the monomer density, $ρ$, via Monte Carlo and molecular dynamics simulations. % Surprisingly, the correlations in dense three dimensional solutions are found to decay with a power law $C(s) \sim s^{-ω}$ with $ω=3/2$ and the exponential behavior commonly assumed is clearly ruled out for long chains. % In semidilute solutions, the density dependent scaling of $C(s) \approx g^{-ω_0} (s/g)^{-ω}$ with $ω_0=2-2ν=0.824$ ($ν=0.…
We perform simulations to compute the effective potential between the centers-of-mass of two polymers with reversible bonds. We investigate the influence of the topology of the unbonded precursor (linear or ring) and the specific sequence of the reactive groups (from purely random to periodic), establishing that both have a strong impact on the effective potential. When the reactive sites of both polymers are chemically orthogonal so that only intramolecular bonds are possible, the interactions become more repulsive the closer to periodic the sequence is. The opposite effect is found if both p…
Using non-equilibrium Brownian dynamics computer simulations, we have investigated the steady state statistics of a polymer chain under three different shear environments: i) linear shear flow in the bulk (no walls), ii) shear vorticity normal to the adsorbing wall, iii) shear gradient normal to the adsorbing wall. The statistical distribution of the chain end-to-end distance and its orientational angles are calculated within our monomer-resolved computer simulations. Over a wide range of shear rates, this distribution can be mapped onto a simple theoretical finite-extensible-nonlinear-elastic…
The classical bond-fluctuation model (BFM) is an efficient lattice Monte Carlo algorithm for coarse-grained polymer chains where each monomer occupies exclusively a certain number of lattice sites. In this paper we propose a generalization of the BFM where we relax this constraint and allow the overlap of monomers subject to a finite energy penalty $\overlap$. This is done to vary systematically the dimensionless compressibility $g$ of the solution in order to investigate the influence of density fluctuations in dense polymer melts on various s tatic properties at constant overall monomer dens…
We examine the thermally-induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of Molecular Dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped dynamics are investigated, and a comparison with recent studies of bond scission in model polymers with harmonic interactions is performed. We find that the polymer degradation changes qualitatively between the inertial regime and that of heavily damped dynamics. The role of bond healing (recombination) is also studied and probability distributions for the recom…
The breakage of a polymer chain of segments, coupled by anharmonic bonds with applied constant external tensile force is studied by means of Molecular Dynamics simulation. We show that the mean life time of the chain becomes progressively independent of the number of bonds as the pulling force grows. The latter affects also the rupture rates of individual bonds along the polymer backbone manifesting the essential role of inertial effects in the fragmentation process. The role of local defects, temperature and friction in the scission kinetics is also examined.
The relation between elasticity and yielding is investigated in a model polymer solid by Molecular-Dynamics simulations. By changing the bending stiffness of the chain and the bond length, semicrystalline and disordered glassy polymers - both with bond disorder - as well as nematic glassy polymers with bond ordering are obtained. It is found that in systems with bond disorder the ratio Ty/G between the shear yield strength Ty and the shear modulus G is close to the universal value of the atomic metallic glasses. The increase of the local nematic order in glasses leads to the increase of the sh…
By means of Langevin dynamics simulations, we investigate the gel formation of randomly functionalized polymers in solution, with the ability to form both intra- and intermolecular reversible bonds. Under highly dilute conditions, these polymers form soft nano-objects (so-called single-chain nanoparticles, SCNPs), resulting from the purely intramolecular cross-linking of the reactive functional groups. Here we show that the competition between intra- and intermolecular bonds at finite concentration is governed by a delicate balance of various entropic contributions and leads to a density depen…
The effect of a high Reynold's number, pressure-driven flow of a compressible gas on the conformation of an oligomer tethered to the wall of a square-channel is studied under both ideal solvent and poor solvent conditions using a hybrid multiparticle collision dynamics and molecular dynamics algorithm. Unlike previous studies, the flow field contains an elongational component in addition to a shear component as well as fluid slip near the walls and results in a Schmidt number for the polymer beads that is less than unity. In both solvent regimes the oligomer is found to extend in the direction…
In this paper, we study the equilibrium properties of polymer chains end-tethered to a fluid membrane. The loss of conformational entropy of the polymer results in an inhomogeneous pressure field that we calculate for gaussian chains. We estimate the effects of excluded volume through a relation between pressure and concentration. Under the polymer pressure, a soft surface will deform. We calculate the deformation profile for a fluid membrane and show that close to the grafting point, this profile assumes a cone-like shape, independently of the boundary conditions. Interactions between differe…
The dynamical response of a tethered semiflexible polymer with self-attractive interactions and subjected to an external force field is numerically investigated by varying stiffness and self-interaction strength. The chain is confined in two spatial dimensions and placed in contact with a heat bath described by the Brownian multiparticle collision method. For strong self-attraction the equilibrium conformations range from compact structures to double-stranded chains, and to rods when increasing the stiffness. Under the external field at small rigidities, the initial close-packed chain is conti…
It is commonly accepted that in concentrated solutions or melts high-molecular weight polymers display random-walk conformational properties without long-range correlations between subsequent bonds. This absence of memory means, for instance, that the bond-bond correlation function, $P(s)$, of two bonds separated by $s$ monomers along the chain should exponentially decay with $s$. Presenting numerical results and theoretical arguments for both monodisperse chains and self-assembled (essentially Flory size-distributed) equilibrium polymers we demonstrate that some long-range correlations remain…
The local glass transition temperature Tg of pyrene-labeled polystyrene (PS) chains intermixed with end-tethered PS chains grafted to a neutral silica substrate was measured by fluorescence spectroscopy. To isolate the impact of the grafted chains, the films were capped with bulk neat PS layers eliminating competing effects of the free surface. Results demonstrate that end-grafted chains strongly increase the local Tg of matrix chains by $\approx$45 K relative to bulk Tg, independent of grafted chain molecular weight from Mn = 8.6 to 212 kg/mol and chemical end-group, over a wide range of graf…
We study jamming in model freely rotating polymers as a function of chain length $N$ and bond angle $θ_0$. The volume fraction at jamming, $ϕ_J(θ_0)$, is minimal for rigid-rod-like chains ($θ_0 = 0$), and increases monotonically with increasing $θ_0 \leq π/2$. In contrast to flexible polymers, marginally jammed states of freely rotating polymers are highly hypostatic, even when bond and angle constraints are accounted for. Large aspect ratio (small $θ_0$) chains behave comparably to stiff fibers: resistance to large-scale bending plays a major role in their jamming phenomenology. Low aspect ra…
The non-equilibrium structural and dynamical properties of semiflexible polymers confined to two dimensions are investigated by molecular dynamics simulations. Three different scenarios are considered: The force-extension relation of tethered polymers, the relaxation of an initially stretched semiflexible polymer, and semiflexible polymers under shear flow. We find quantitative agreement with theoretical predictions for the force-extension relation and the time dependence of the entropically contracting polymer. The semiflexible polymers under shear flow exhibit significant conformational chan…
We examine nonequilibrium features of collapse behavior in model polymers with competing crystallization and glass transitions using extensive molecular dynamics simulations. By comparing to "colloidal" systems with no covalent bonds but the same non-bonded interactions, we find three principal results: (i) Tangent-sphere polymers and colloids, in the equilibrium-crystallite phase, have nearly identical static properties when the temperature T is scaled by the crystallization temperature T_{cryst}; (ii) Qualitative features of nonequilibrium relaxation below T_{cryst}, measured by the evolutio…
The bond fluctuation model with a bond potential has been applied to investigation of the glass transition of linear chains and chains with a regular disposition of small branches. Cooling and subsequent heating curves are obtained for the chain energies and also for the mean acceptance probability of a bead jump. In order to mimic different trends to vitrification, a factor B gauging the strength of the bond potential with respect to the long-range potential (i.e. the intramolecular or intermolecular potential between indirectly bonded beads) has been introduced. (A higher value of B leads to…
Associative polymers with sticker-and-spacer architectures undergo phase transitions that combine phase separation and bond percolation. Here, we generalize mean-field models for bond percolation and extract effective sticker interaction strengths from experimental data for specific proteins. We use graph-based Monte Carlo simulations to evaluate effects ignored by mean-field models. These include bond cooperativity defined as changes to strengths of new bonds (physical crosslinks) given the presence of a prior bond. We find that bond cooperativity fundamentally alters phase behavior, especial…
Using molecular simulations, we study the properties of a polymer brush in contact with an explicit solvent under Couette and Poiseuille flow. The solvent is comprised of chemically identical chains. We present evidence that individual, unentangled chains in the dense brush exhibit cyclic, tumbling motion and non-Gaussian fluctuations of the molecular orientations similar to the behaviour of isolated tethered chains in shear flow. The collective molecular motion gives rise to an inversion of hydrodynamic flow direction in the vicinity of the brush-coated surface. Utilising Couette and Poiseuil…
