Semiflexible Polymer Confined to a Spherical Surface

We develop a formalism for describing the kinematics of a wormlike chain confined to the surface of a sphere that simultaneously satisfies the spherical confinement and the inextensibility of the chain contour. We use this formalism to study the statistical behavior of the wormlike chain on a spherical surface. In particular, we provide an exact, closed-form expression for the mean square end-to-end distance that is valid for any value of chain length L, persistence length lp, and sphere radius R. We predict two qualitatively different behaviors for a long polymer depending on the ratio R/lp. For R/lp>4, the mean square end-to-end distance increases monotonically with the chain length, whereas for R/lp<4, a damped oscillatory behavior is predicted

Semiflexible polymer solutions. I. Phase behavior and single-chain statistics

We study the thermodynamics and single-chain statistics of wormlike polymer solutions with Maier–Saupe-type interactions using self-consistent-field (SCF) theory. The SCF equations are derived using a systematic field-theoretical approach which yields the SCF equations as the lowest order approximation, but permits fluctuation corrections to be incorporated. We solve the SCF equations using the spheroidal functions, which provides a nonperturbative description of the thermodynamics and single-chain statistics in the nematic state for arbitrary degrees of nematic order. Several types of phase diagrams are predicted, with an emphasis on the limit of metastability (spinodal) associated with each phase. The shape and location of these spinodals suggest interesting scenarios for the phase transition kinetics. A large but finite persistence length is shown to significantly decrease the isotropic–nematic transition temperature relative to that for rigid rods. In the nematic state, the mean-square end-to-end distance in the parallel and perpendicular directions are governed by two separate correlation lengths. An exact relationship between these correlation lengths and the eigenvalues of the spheroidal functions is provided, which reproduces the analytical expressions predicted from earlier studies in the limit of large nematic strength. The dominant contribution to the single-chain thermodynamics is shown to arise from small amplitude undulations in the directions perpendicular to the nematic direction; the presence of hairpins, though crucial for determining the dimensions of the polymer, has insignificant consequences on the single-chain thermodynamics

End-to-end distance vector distribution with fixed end orientations for the wormlike chain model

We find exact expressions for the end-to-end distance vector distribution function with fixed end orientations for the wormlike chain model. This function in Fourier-Laplace space adopts the form of infinite continued fractions, which emerges upon exploiting the hierarchical structure of the moment-based expansion. Our results are used to calculate the root-mean-square end displacement in a given direction for a chain with both end orientations fixed. We find that the crossover from rigid to flexible chains is marked by the root-mean-square end displacement slowly losing its angular dependence as the coupling between chain conformation and end orientation wanes. However, the coupling remains strong even for relatively flexible chains, suggesting that the end orientation strongly influences chain conformation for chains that are several persistence lengths long. We then show the behavior of the distribution function by a density plot of the probability as a function of the end-to-end distance vector for a wormlike chain in two dimensions with one end pointed in a fixed direction and the other end free (in its orientation). As we progress from high to low rigidity, the distribution function shifts from being peaked at a location near the full contour length of the chain in the forward direction, corresponding to a straight configuration, to being peaked near zero end separation, as in the Gaussian limit. The function exhibits double peaks in the crossover between these limiting behaviors

Closing the loop between microstructure and charge transport in conjugated polymers by combining microscopy and simulation.

A grand challenge in materials science is to identify the impact of molecular composition and structure across a range of length scales on macroscopic properties. We demonstrate a unified experimental-theoretical framework that coordinates experimental measurements of mesoscale structure with molecular-level physical modeling to bridge multiple scales of physical behavior. Here we apply this framework to understand charge transport in a semiconducting polymer. Spatially-resolved nanodiffraction in a transmission electron microscope is combined with a self-consistent framework of the polymer chain statistics to yield a detailed picture of the polymer microstructure ranging from the molecular to device relevant scale. Using these data as inputs for charge transport calculations, the combined multiscale approach highlights the underrepresented role of defects in existing transport models. Short-range transport is shown to be more chaotic than is often pictured, with the drift velocity accounting for a small portion of overall charge motion. Local transport is sensitive to the alignment and geometry of polymer chains. At longer length scales, large domains and gradual grain boundaries funnel charges preferentially to certain regions, creating inhomogeneous charge distributions. While alignment generally improves mobility, these funneling effects negatively impact mobility. The microstructure is modified in silico to explore possible design rules, showing chain stiffness and alignment to be beneficial while local homogeneity has no positive effect. This combined approach creates a flexible and extensible pipeline for analyzing multiscale functional properties and a general strategy for extending the accesible length scales of experimental and theoretical probes by harnessing their combined strengths

Modulation of DNA loop lifetimes by the free energy of loop formation

Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for transcriptional regulation in both prokaryotes and eukaryotes, and the speed of such regulations affects the fitness of individuals. Here, we examine the in vitro looping dynamics of the classic Lac repressor gene-regulatory motif. We show that both loop association and loop dissociation at the DNA-repressor junctions depend on the elastic deformation of the DNA and protein, and that both looping and unlooping rates approximately scale with the looping J factor, which reflects the system's deformation free energy. We explain this observation by transition state theory and model the DNA-protein complex as an effective worm-like chain with twist. We introduce a finite protein-DNA binding interaction length, in competition with the characteristic DNA deformation length scale, as the physical origin of the previously unidentified loop dissociation dynamics observed here, and discuss the robustness of this behavior to perturbations in several polymer parameters

Free expansion of elastic filaments

The dynamics of an elastic polymer filament undergoing contour length expansion is studied using computer simulation. The expansion occurs by development of transverse buckling waves that grow through a coarsening process. The growing buckles locally organize into a helical structure with a characteristic persistence length. The helical domain boundaries are eliminated from the relaxing structure by unwinding through the ends of the rod. The growth of the helical domains results in self-propulsive motion of the expanding rod, as one large helix spanning the entire chain relaxes during the late stages of the dynamics. Stability analyses and scaling arguments are provided to explain the simulation results