Effect of chain stiffness on the competition between crystallization and glass-formation in model unentangled polymers.

We map out the solid-state morphologies formed by model soft-pearl-necklace polymers as a function of chain stiffness, spanning the range from fully flexible to rodlike chains. The ratio of Kuhn length to bead diameter (lK/r0) increases monotonically with increasing bending stiffness kb and yields a one-parameter model that relates chain shape to bulk morphology. In the flexible limit, monomers occupy the sites of close-packed crystallites while chains retain random-walk-like order.

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.

Combined molecular algorithms for the generation, equilibration and topological analysis of entangled polymers: methodology and performance.

We review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the implementation of both, the Monte Carlo (MC) procedure for the system generation and equilibration, and a postprocessing step, where we identify the underlying topological structure of the simulated systems in the form of primitive paths. In order to demonstrate our arguments, we study how molecular length and packing density (volume fraction) affect the performance of the MC scheme built around chain-connectivity altering moves.

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

Flexible chain molecules in the marginal and concentrated regimes: universal static scaling laws and cross-over predictions.

We present predictions for the static scaling exponents and for the cross-over polymer volumetric fractions in the marginal and concentrated solution regimes. Corrections for finite chain length are made. Predictions are based on an analysis of correlated fluctuations in density and chain length, in a semigrand ensemble in which mers and solvent sites exchange identities.

Dense and nearly jammed random packings of freely jointed chains of tangent hard spheres.

Dense packings of freely jointed chains of tangent hard spheres are produced by a novel Monte Carlo method. Within statistical uncertainty, chains reach a maximally random jammed (MRJ) state at the same volume fraction as packings of single hard spheres. A structural analysis shows that as the MRJ state is approached (i) the radial distribution function for chains remains distinct from but approaches that of single hard sphere packings quite closely, (ii) chains undergo progressive collapse, and (iii) a small but increasing fraction of sites possess highly ordered first coordination shells.

Determination of rotary diffusivity of poly(n-propyl isocyanate) by molecular dynamics.

The rotational dynamics of a nondilute solution of the rodlike polymer poly(n-propyl isocyanate) (PPIC) has been studied on an atomistic model by means of a large-scale classical molecular dynamics investigation. The rotary diffusivity of PPIC in toluene solution has been determined from the Einsteinian diffusion regime of the end-to-end vector on the surface of the unit sphere and has been found to be Dr=10.5x10(5)(+/-2.

Min-map bias Monte Carlo for chain molecules: biased Monte Carlo sampling based on bijective minimum-to-minimum mapping.

A novel Monte Carlo (MC) simulation scheme based on Theodorou's bijective mapping strategy [D. N. Theodorou, J.