Random close packing of semi-flexible polymers in two dimensions: Emergence of local and global order.

Through extensive Monte Carlo simulations, we systematically study the effect of chain stiffness on the packing ability of linear polymers composed of hard spheres in extremely confined monolayers, corresponding effectively to 2D films. First, we explore the limit of random close packing as a function of the equilibrium bending angle and then quantify the local and global order by the degree of crystallinity and the nematic or tetratic orientational order parameter, respectively. A multi-scale wealth of structural behavior is observed, which is inherently absent in the case of athermal individual monomers and is surprisingly richer than its 3D counterpart under bulk conditions.

Fine-tuning of colloidal polymer crystals by molecular simulation.

Through extensive molecular simulations we determine a phase diagram of attractive, fully flexible polymer chains in two and three dimensions. A rich collection of distinct crystal morphologies appear, which can be finely tuned through the range of attraction. In three dimensions these include the face-centered cubic, hexagonal close packed, simple hexagonal, and body-centered cubic crystals and the Frank-Kasper phase.

Densest packing of flexible polymers in 2D films.

How dense objects, particles, atoms, and molecules can be packed is intimately related to the properties of the corresponding hosts and macrosystems. We present results from extensive Monte Carlo simulations on maximally compressed packings of linear, freely jointed chains of tangent hard spheres of uniform size in films whose thickness is equal to the monomer diameter. We demonstrate that fully flexible chains of hard spheres can be packed as efficiently as monomeric analogs, within a statistical tolerance of less than 1%.

Polymorph Stability and Free Energy of Crystallization of Freely-Jointed Polymers of Hard Spheres.

The free energy of crystallization of monomeric hard spheres as well as their thermodynamically stable polymorph have been known for several decades. In this work, we present semianalytical calculations of the free energy of crystallization of freely-jointed polymers of hard spheres as well as of the free energy difference between the hexagonal closed packed (HCP) and face-centered cubic (FCC) polymorphs. The phase transition (crystallization) is driven by an increase in translational entropy that is larger than the loss of conformational entropy of chains in the crystal with respect to chains in the initial amorphous phase.

Local and Global Order in Dense Packings of Semi-Flexible Polymers of Hard Spheres.

The local and global order in dense packings of linear, semi-flexible polymers of tangent hard spheres are studied by employing extensive Monte Carlo simulations at increasing volume fractions. The chain stiffness is controlled by a tunable harmonic potential for the bending angle, whose intensity dictates the rigidity of the polymer backbone as a function of the bending constant and equilibrium angle. The studied angles range between acute and obtuse ones, reaching the limit of rod-like polymers.

Polymorphism and Perfection in Crystallization of Hard Sphere Polymers.

We present results on polymorphism and perfection, as observed in the spontaneous crystallization of freely jointed polymers of hard spheres, obtained in an unprecedentedly long Monte Carlo (MC) simulation on a system of 54 chains of 1000 monomers. Starting from a purely amorphous configuration, after an initial dominance of the hexagonal closed packed (HCP) polymorph and a transitory random hexagonal close packed (rHCP) morphology, the system crystallizes in a final, stable, face centered cubic (FCC) crystal of very high perfection. An analysis of chain conformational characteristics, of the spatial distribution of monomers and of the volume accessible to them shows that the phase transition is caused by an increase in translational entropy that is larger than the loss of conformational entropy of the chains in the crystal, compared to the amorphous state.

Crystallization of Flexible Chains of Tangent Hard Spheres under Full Confinement.

We present results from extensive Monte Carlo simulations on the crystallization of athermal polymers under full confinement. Polymers are represented as freely jointed chains of tangent hard spheres of uniform size. Confinement is applied through the presence of flat, parallel, and impenetrable walls in all dimensions.

Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions.

We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include localized, chain-connectivity-altering, identity-exchange, and cluster-based moves. The approach focuses on alleviating one of the main disadvantages of Monte Carlo algorithms, which is the general applicability under a wide range of conditions.

Entropy-Driven Heterogeneous Crystallization of Hard-Sphere Chains under Unidimensional Confinement.

We investigate, through Monte Carlo simulations, the heterogeneous crystallization of linear chains of tangent hard spheres under confinement in one dimension. Confinement is realized through flat, impenetrable, and parallel walls. A wide range of systems is studied with respect to their average chain lengths ( = 12 to 100) and packing densities ( = 0.

Crystal, Fivefold and Glass Formation in Clusters of Polymers Interacting with the Square Well Potential.

We present results, from Monte Carlo (MC) simulations, on polymer systems of freely jointed chains with spherical monomers interacting through the square well potential. Starting from athermal packings of chains of tangent hard spheres, we activate the square well potential under constant volume and temperature corresponding effectively to instantaneous quenching. We investigate how the intensity and range of pair-wise interactions affected the final morphologies by fixing polymer characteristics such as average chain length and tolerance in bond gaps.

Self-Avoiding Random Walks as a Model to Study Athermal Linear Polymers under Extreme Plate Confinement.

Monte Carlo (MC) simulations, built around chain-connectivity-altering moves and a wall-displacement algorithm, allow us to simulate freely-jointed chains of tangent hard spheres of uniform size under extreme confinement. The latter is realized through the presence of two impenetrable, flat, and parallel plates. Extreme conditions correspond to the case where the distance between the plates approaches the monomer size.

Confined Polymers as Self-Avoiding Random Walks on Restricted Lattices.

Polymers in highly confined geometries can display complex morphologies including ordered phases. A basic component of a theoretical analysis of their phase behavior in confined geometries is the knowledge of the number of possible single-chain conformations compatible with the geometrical restrictions and the established crystalline morphology. While the statistical properties of unrestricted self-avoiding random walks (SAWs) both on and off-lattice are very well known, the same is not true for SAWs in confined geometries.

The role of bond tangency and bond gap in hard sphere crystallization of chains.

We report results from Monte Carlo simulations on dense packings of linear, freely-jointed chains of hard spheres of uniform size. In contrast to our past studies where bonded spheres along the chain backbone were tangent, in the present work a finite tolerance in the bond is allowed. Bond lengths are allowed to fluctuate in the interval [σ, σ + dl], where σ is the sphere diameter.

Spontaneous crystallization in athermal polymer packings.

We review recent results from extensive simulations of the crystallization of athermal polymer packings. It is shown that above a certain packing density, and for sufficiently long simulations, all random assemblies of freely-jointed chains of tangent hard spheres of uniform size show a spontaneous transition into a crystalline phase. These polymer crystals adopt predominantly random hexagonal close packed morphologies.

Fivefold symmetry as an inhibitor to hard-sphere crystallization.

Through molecular simulations we investigate the dynamics of crystallization of hard spheres of uniform size from dense amorphous states and the role that hidden structures in an otherwise disordered medium might have on it. It is shown that short-range order in the form of sites with fivefold symmetry acts as a powerful inhibitor to crystal growth. Fivefold sites not only retard crystallization, but can self-assemble into organized structures that arrest crystallization at high densities or lead to the formation of defects in a crystal.

Numerical simulation of bubble dynamics in a Phan-Thien-Tanner liquid: non-linear shape and size oscillatory response under periodic pressure.

We study non-linear bubble oscillations driven by an acoustic pressure with the bubble being immersed in a viscoelastic, Phan-Thien-Tanner liquid. Solution is provided numerically through a method which is based on a finite element discretization of the Navier-Stokes flow equations. The proposed computational approach does not rely on the solution of the simplified Rayleigh-Plesset equation, is not limited in studying only spherically symmetric bubbles and provides coupled solutions for the velocity, stress fields and bubble interface.

Entropy-driven crystallization in dense systems of athermal chain molecules.

We describe the direct observation of entropy-driven crystallization in simulations of dense packings of linear hard-sphere chains. Crystal nuclei form spontaneously in the phase coexistence region independently of chain length. Incipient nuclei consistently develop well defined, stack-faulted layered morphologies with a single stacking direction.

Contact network in nearly jammed disordered packings of hard-sphere chains.

We present salient results of the analysis of the geometrical structure of a large fully equilibrated ensemble of nearly jammed packings of linear freely jointed chains of tangent hard spheres generated via extensive Monte Carlo simulations. In spite the expected differences due to chain connectivity, both the pair-correlation function and the contact network for chain packings are found to strongly resemble those in packings of monomeric hard spheres at the maximally random jammed (MRJ) state. A remarkable finding of the present work is the tendency of chains to form closed loops at the MRJ state as a consequence of chain collapse.

Universal scaling, entanglements, and knots of model chain molecules.

By identifying the maximally random jammed state of freely jointed chains of tangent hard spheres we are able to determine the distinct scaling regimes characterizing the dependence of chain dimensions and topology on volume fraction. Calculated distributions of (i) the contour length of the primitive paths and (ii) the number of entanglements per chain agree remarkably well with recent theoretical predictions in all scaling regimes. Furthermore, our simulations reveal a hitherto unsuspected connection between purely intramolecular (knots) and intermolecular (entanglements) topological constraints.

The structure of random packings of freely jointed chains of tangent hard spheres.

We analyze the structure of dense random packings of freely jointed chains of tangent hard spheres as a function of concentration (packing density) with particular emphasis placed on the behavior in the vicinity of their maximally random jammed (MRJ) state. Representative configurations over the whole density range are generated through extensive off-lattice Monte Carlo simulations on systems of average chain lengths ranging from N=12 to 1000 hard spheres. Several measures of order are used to quantitatively describe either local structure (sphere arrangements and bonded geometry) or global behavior (chain conformations and statistics).

Detailed atomistic molecular dynamics simulations of alpha-conotoxin AuIB in water.

We present results about the shape, size, structure, conformational stability, and hydrodynamics of alpha-conotoxin AuIB (a disulfide-rich peptide from the venom of Conus aulicus, recognized as a nicotinic acetylcholine antagonist with great pharmaceutical potential) from very long (0.5 mus) massively parallel molecular dynamics (MD) simulations in full atomistic detail. We extract coarse-grained descriptors of protein shape (ellipsoid), and of translational and rotational mobilities, i.

The characteristic crystallographic element norm: A descriptor of local structure in atomistic and particulate systems.

We introduce the characteristic crystallographic element (CCE) norm as a powerful descriptor of local structure in atomistic and particulate systems. The CCE-norm is sensitive both to radial and orientational deviations from perfect local order. Unlike other measures of local order, the CCE-norm decreases monotonically with increasing order, is zero for a perfectly ordered environment, and is strictly discriminating among different, competing crystal structures in imperfectly ordered systems.

Structure, dimensions, and entanglement statistics of long linear polyethylene chains.

This work elucidates the effect of both temperature and molecular length on the conformational and structural properties as well as on the entanglement statistics of long amorphous, polydisperse, and molten linear polyethylene (PE). A large number of PE samples are modeled in atomistic detail, with average molecular lengths ranging from C24 up to C1,000 over a wide range of temperatures in the interval of 300 View Article and Find Full Text PDF

Modeling the effect of cell-associated polymeric fluid layers on force spectroscopy measurements. Part I: model development.

The mechanical response, the force-indentation relationship, in normal force spectroscopy measurements carried out on individual polysaccharide encapsulated bacteria is modeled using three increasingly refined approaches that consider the elastic response of the bacterium and cantilever in combination with a fluid (hydrodynamic) model for the polysaccharide layer. For the hydrodynamic description of the polysaccharide layer, several increasingly realistic models are described in detail, together with numerical solution techniques. These models range from one-dimensional, Newtonian, to two-dimensional, axisymmetric, fully viscoelastic (Phan-Thien/Tanner).

Modeling the effect of cell-associated polymeric fluid layers on force spectroscopy measurements. Part II: experimental results and comparison with model predictions.

In this paper, experimentally obtained force curves on Staphylococcus aureus are compared with a previously developed model that incorporates hydrodynamic effects of extracellular polysaccharides together with the elastic response of the bacterium and cantilever. Force-displacement curves were predicted without any adjustable parameters. It is demonstrated that experimental results can be accurately described by our model, especially if viscoelastic effects of the extracellular polysaccharide layer are taken into account.