Radial distribution function of semiflexible polymers

We calculate the distribution function of the end--to--end distance of a semiflexible polymer with large bending rigidity. This quantity is directly observable in experiments on single semiflexible polymers (e.g., DNA, actin) and relevant to their interpretation. It is also an important starting point for analyzing the behavior of more complex systems such as networks and solutions of semiflexible polymers. To estimate the validity of the obtained analytical expressions, we also determine the distribution function numerically using Monte Carlo simulation and find good quantitative agreement.Comment: RevTeX, 4 pages, 1 figure. Also available at http://www.cip.physik.tu-muenchen.de/tumphy/d/T34/Mitarbeiter/frey.htm

A general theory of DNA-mediated and other valence-limited interactions

We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the configurational and combinatorial entropic factors that play a key role in valence-limited interactions. By rigorously enforcing self-consistency, it achieves near-quantitative accuracy with respect to detailed Monte Carlo calculations. With suitable approximations and in particular geometries, our theory reduces to previous successful treatments, which are now united in a common and extensible framework. We expect our tools to be useful to other researchers investigating ligand-mediated interactions. A complete and well-documented Python implementation is freely available at http://github.com/patvarilly/DNACC .Comment: 18 pages, 10 figure

Structure and dynamics of colloidal depletion gels: coincidence of transitions and heterogeneity

Transitions in structural heterogeneity of colloidal depletion gels formed through short-range attractive interactions are correlated with their dynamical arrest. The system is a density and refractive index matched suspension of 0.20 volume fraction poly(methyl methacyrlate) colloids with the non-adsorbing depletant polystyrene added at a size ratio of depletant to colloid of 0.043. As the strength of the short-range attractive interaction is increased, clusters become increasingly structurally heterogeneous, as characterized by number-density fluctuations, and dynamically immobilized, as characterized by the single-particle mean-squared displacement. The number of free colloids in the suspension also progressively declines. As an immobile cluster to gel transition is traversed, structural heterogeneity abruptly decreases. Simultaneously, the mean single-particle dynamics saturates at a localization length on the order of the short-range attractive potential range. Both immobile cluster and gel regimes show dynamical heterogeneity. Non-Gaussian distributions of single particle displacements reveal enhanced populations of dynamical trajectories localized on two different length scales. Similar dependencies of number density fluctuations, free particle number and dynamical length scales on the order of the range of short-range attraction suggests a collective structural origin of dynamic heterogeneity in colloidal gels.Comment: 14 pages, 10 figure

Electronic Structure of Charge- and Spin-controlled Sr_{1-(x+y)}La_{x+y}Ti_{1-x}Cr_{x}O_{3}

We present the electronic structure of Sr_{1-(x+y)}La_{x+y}Ti_{1-x}Cr_{x}O_{3} investigated by high-resolution photoemission spectroscopy. In the vicinity of Fermi level, it was found that the electronic structure were composed of a Cr 3d local state with the t_{2g}^{3} configuration and a Ti 3d itinerant state. The energy levels of these Cr and Ti 3d states are well interpreted by the difference of the charge-transfer energy of both ions. The spectral weight of the Cr 3d state is completely proportional to the spin concentration x irrespective of the carrier concentration y, indicating that the spin density can be controlled by x as desired. In contrast, the spectral weight of the Ti 3d state is not proportional to y, depending on the amount of Cr doping.Comment: 4 pages, 3 figures. Accepted for publication in Phys. Rev. Let

Quadrupole Susceptibility and Elastic Softening due to a Vacancy in Silicon Crystal

We investigate the electronic states around a single vacancy in silicon crystal by using the Green's function approach. The triply degenerate vacancy states within the band gap are found to be extended over a large distance $\sim20 {\rm \AA}$ from the vacancy site and contribute to the reciprocal temperature dependence of the quadrupole susceptibility resulting in the elastic softening at low temperture. The Curie constant of the quadrupole susceptibility for the trigonal mode ($O_{yz},O_{zx},O_{xy}$) is largely enhanced as compared to that for the tetragonal mode ($O_{2}^{0},O_{2}^{2}$). The obtained results are consistent with the recent ultrasonic experiments in silicon crystal down to 20 mK. We also calculate the dipole and octupole susceptibilities and find that the octupole susceptibilities are extremely enhannced for a specific mode.Comment: 6 pages, with 5 figure

Hawaiian Kalo, Past and Future

The arrival of taro in the Hawaiian Islands, its significance in Hawaiian culture, and the decline in its production since the early to mid-1800s is discussed. The university's role in preserving Hawaiian taro varieties is described, along with recent taro breeding programs conducted by its scientists

Shapes of Semiflexible Polymers in Confined Spaces

We investigate the conformations of a semiflexible polymer confined to a square box. Results of Monte Carlo simulations show the existence of a shape transition when the persistence length of the polymer becomes comparable to the dimensions of box. An order parameter is introduced to quantify this behavior. A simple mean-field model is constructed to study the effect of the shape transition on the effective persistence length of the polymer.Comment: 8 pages, 20 figure

A generalized theory of semiflexible polymers

DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a renewed interest in the polymer mechanics relevant for describing the conformational free energy of DNA bending induced by protein-DNA complexes. Recent experimental results from DNA cyclization studies have cast doubt on the applicability of the canonical semiflexible polymer theory, the wormlike chain (WLC) model, to DNA bending on biological length scales. This paper develops a theory of the chain statistics of a class of generalized semiflexible polymer models. Our focus is on the theoretical development of these models and the calculation of experimental observables. To illustrate our methods, we focus on a specific toy model of DNA bending. We show that the WLC model generically describes the long-length-scale chain statistics of semiflexible polymers, as predicted by the Renormalization Group. In particular, we show that either the WLC or our new model adequate describes force-extension, solution scattering, and long-contour-length cyclization experiments, regardless of the details of DNA bend elasticity. In contrast, experiments sensitive to short-length-scale chain behavior can in principle reveal dramatic departures from the linear elastic behavior assumed in the WLC model. We demonstrate this explicitly by showing that our toy model can reproduce the anomalously large short-contour-length cyclization J factors observed by Cloutier and Widom. Finally, we discuss the applicability of these models to DNA chain statistics in the context of future experiments

Renormalized one-loop theory of correlations in polymer blends

The renormalized one-loop theory is a coarse-grained theory of corrections to the self-consistent field theory (SCFT) of polymer liquids, and to the random phase approximation (RPA) theory of composition fluctuations. We present predictions of corrections to the RPA for the structure function $S(k)$ and to the random walk model of single-chain statics in binary homopolymer blends. We consider an apparent interaction parameter $\chi_{a}$ that is defined by applying the RPA to the small $k$ limit of $S(k)$. The predicted deviation of $\chi_{a}$ from its long chain limit is proportional to $N^{-1/2}$, where $N$ is chain length. This deviation is positive (i.e., destabilizing) for weakly non-ideal mixtures, with \chi_{a} N \alt 1, but negative (stabilizing) near the critical point. The positive correction to $\chi_{a}$ for low values of $\chi_{a} N$ is a result of the fact that monomers in mixtures of shorter chains are slightly less strongly shielded from intermolecular contacts. The depression in $\chi_{a}$ near the critical point is a result of long-wavelength composition fluctuations. The one-loop theory predicts a shift in the critical temperature of ${\cal O}(N^{-1/2})$, which is much greater than the predicted ${\cal O}(N^{-1})$ width of the Ginzburg region. Chain dimensions deviate slightly from those of a random walk even in a one-component melt, and contract slightly with increasing $\chi_{e}$. Predictions for $S(k)$ and single-chain properties are compared to published lattice Monte Carlo simulations.Comment: submitted to J. Chem. Phy

Consistent coarse-graining strategy for polymer solutions in the thermal crossover from Good to Theta solvent

We extend our previously developed coarse-graining strategy for linear polymers with a tunable number n of effective atoms (blobs) per chain [D'Adamo et al., J. Chem. Phys. 137, 4901 (2012)] to polymer systems in thermal crossover between the good-solvent and the Theta regimes. We consider the thermal crossover in the region in which tricritical effects can be neglected, i.e. not too close to the Theta point, for a wide range of chain volume fractions Phi=c/c* (c* is the overlap concentration), up to Phi=30. Scaling crossover functions for global properties of the solution are obtained by Monte-Carlo simulations of the Domb-Joyce model. They provide the input data to develop a minimal coarse-grained model with four blobs per chain. As in the good-solvent case, the coarse-grained model potentials are derived at zero density, thus avoiding the inconsistencies related to the use of state-dependent potentials. We find that the coarse-grained model reproduces the properties of the underlying system up to some reduced density which increases when lowering the temperature towards the Theta state. Close to the lower-temperature crossover boundary, the tetramer model is accurate at least up to Phi<10, while near the good-solvent regime reasonably accurate results are obtained up to Phi<2. The density region in which the coarse-grained model is predictive can be enlarged by developing coarse-grained models with more blobs per chain. We extend the strategy used in the good-solvent case to the crossover regime. This requires a proper treatment of the length rescalings as before, but also a proper temperature redefinition as the number of blobs is increased. The case n=10 is investigated. Comparison with full-monomer results shows that the density region in which accurate predictions can be obtained is significantly wider than that corresponding to the n=4 case.Comment: 21 pages, 14 figure