The structure of the nematic-isotropic interface in polymer systems

The structure of the nematic-isotropic interfacial layer is studied theoretically for systems formed by rod-like and persistent macromolecules. It is shown that the width of interfacial layer is normally of the order of the straight part of a molecule. This allows us to use the approach which describes intermolecular interactions phenomenologically (i.e. it allows us to consider all interactions), at the same time this approach describes molecular flexibility microscopically (i.e. it allows us to study the effects of flexibility correctly). It was found, that non-monotonic gradient profiles in the surface layer of the order parameter or of the concentration of molecules as a function of the coordinate perpendicular to the interface are possible. For example, a thin layer with abnormal ordering of molecules along the surface may exist near the interface for some systems.     

Critical exponents for random knots

The size of a zero-thickness (no excluded volume) nonphantom polymer ring is shown to scale with chain length N in the same way as the size of the excluded-volume (self-avoiding) linear polymer, that is, as Nnu, where nu approximately 0.588. The consequences of this fact are examined, including the sizes of trivial and nontrivial knots.     

Ensembles of engineered cardiac tissues for physiological and pharmacological study: heart on a chip

Traditionally, muscle physiology experiments require multiple tissue samples to obtain morphometric, electrophysiological, and contractility data. Furthermore, these experiments are commonly completed one at a time on cover slips of single cells, isotropic monolayers, or in isolated muscle strips. In all of these cases, variability of the samples hinders quantitative comparisons among experimental groups. Here, we report the design of a "heart on a chip" that exploits muscular thin film technology--biohybrid constructs of an engineered, anisotropic ventricular myocardium on an elastomeric thin film--to measure contractility, combined with a quantification of action potential propagation, and cytoskeletal architecture in multiple tissues in the same experiment. We report techniques for real-time data collection and analysis during pharmacological intervention. The chip is an efficient means of measuring structure-function relationships in constructs that replicate the hierarchical tissue architectures of laminar cardiac muscle.     

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. II. Dynamics

Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. The ring melts were found to diffuse faster than their linear counterparts, with both architectures approximately obeying a D ～ N(-2.4) scaling law for large N. The mean-square displacement of the center-of-mass of the rings follows a sub-diffusive behavior for times and distances beyond the ring extension [linear span]R(g)(2)[linear span], neither compatible with the Rouse nor the reptation model. The rings relax stress much faster than linear polymers, and the zero-shear viscosity was found to vary as η(0) ～ N(1.4 ± 0.2) which is much weaker than the N(3.4) behavior of linear chains, not matching any commonly known model for polymer dynamics when compared to the observed mean-square displacements. These findings are discussed in view of the conformational properties of the rings presented in the preceding paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204904 (2011)].     

On the theory of the condensed states of heteropolymers

The collapse (globulization) of an ideal heteropolymer chain under the action of an external attractive field is considered. The problem of the collapse of different types of primary structures, including mobile, periodic, large-block, and statistical structures, is formulated. It is shown that for a random heteropolymer, the mathematical image of the globular state is the chain-length independence of the probability distribution of a random thermal distribution function of the end monomer coordinates. The free energy per monomer of a chain in a globular state and local densities of monomers of all types are shown to be a self-averaging quantities. An exactly solvable model is proposed for a globule formed by a statistical heteropolymer chain. In this model, different types of monomers are attracted to different centers by linear elastic forces with identical elastic constants. The modulus of elasticity is obtained for a heteropolymer globule with respect to the attraction of different types of monomers in different directions. It is shown that this modulus is higher for a short-periodic polymer than for a statistical one.     

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics

Molecular dynamics simulations were conducted to investigate the structural properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. For the rings, the radius of gyration squared, [linear span]R(g)(2)[linear span], was found to scale as N(4/5) for an intermediate regime and N(2/3) for the larger rings indicating an overall conformation of a crumpled globule. However, almost all beads of the rings are "surface beads" interacting with beads of other rings, a result also in agreement with a primitive path analysis performed in the next paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204905 (2011)]. Details of the internal conformational properties of the ring and linear polymers as well as their packing are analyzed and compared to current theoretical models.     

Random walks in the space of conformations of toy proteins

Monte Carlo dynamics of the lattice toy protein of 48 monomers is interpreted as a random walk in an abstract (discrete) space of conformations. To test the geometry of this space, we examine the return probability P(T), which is the probability to find the polymer in the native state after T Monte Carlo steps, provided that it starts from the native state at the initial moment. Comparing computational data with the theoretical expressions for P(T) for random walks in a variety of different spaces, we show that conformation spaces of polymer loops may have nontrivial dimensions and exhibit negative curvature characteristics of Lobachevskii (hyperbolic) geometry.     

A novel family of space-filling curves in their relation to chromosome conformation in eukaryotes

Spatial conformation of DNA chains during interphase in eukaryotic cell nucleus is relatively dense, yet unknotted and exhibits self-similar fractal properties. In this respect it resembles the space-filling curves of Hilbert, but differs in the experimentally accessible contact probability of distant loci. Here we construct space-filling curves with fractal domain boundaries of dimension close to that of the embedding space and show how these match the statistical properties and the contact probability of the DNA conformation. The present mathematical model should shed light on the statistical ensemble of unknotted dense polymers and ease the modeling of genome folding and related biological processes.