Rheology of Ring Polymer Melts: From Linear Contaminants to Ring/Linear Blends

Ring polymers remain a major challenge to our current understanding of polymer dynamics. Experimental results are difficult to interpret because of the uncertainty in the purity and dispersity of the sample. Using both equilibrium and non-equilibrium molecular dynamics simulations we have systematically investigated the structure, dynamics and rheology of perfectly controlled ring/linear polymer blends with chains of such length and flexibility that the number of entanglements is up to about 14 per chain, which is comparable to experimental systems examined in the literature. The smallest concentration at which linear contaminants increase the zero-shear viscosity of a ring polymer melt of these chain lengths by 10% is approximately one-fifth of their overlap concentration. When the two architectures are present in equal amounts the viscosity of the blend is approximately twice as large as that of the pure linear melt. At this concentration the diffusion coefficient of the rings is found to decrease dramatically, while the static and dynamic properties of the linear polymers are mostly unaffected. Our results are supported by a primitive path analysis.Comment: 5 pages, 4 figures, accepted by PR

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 was found to scale as N to the 4/5 power for an intermediate regime and N to the 2/3 power 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 following paper (DOI: 10.1063/1.3587138). 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.Comment: 15 pages, 14 figure

Persistent starspot signals on M dwarfs: multi-wavelength Doppler observations with the Habitable-zone Planet Finder and Keck/HIRES

Young, rapidly-rotating M dwarfs exhibit prominent starspots, which create quasiperiodic signals in their photometric and Doppler spectroscopic measurements. The periodic Doppler signals can mimic radial velocity (RV) changes expected from orbiting exoplanets. Exoplanets can be distinguished from activity-induced false positives by the chromaticity and long-term incoherence of starspot signals, but these qualities are poorly constrained for fully-convective M stars. Coherent photometric starspot signals on M dwarfs may persist for hundreds of rotations, and the wavelength dependence of starspot RV signals may not be consistent between stars due to differences in their magnetic fields and active regions. We obtained precise multi-wavelength RVs of four rapidly-rotating M dwarfs (AD Leo, G 227-22, GJ 1245B, GJ 3959) using the near-infrared (NIR) Habitable-zone Planet Finder, and the optical Keck/HIRES spectrometer. Our RVs are complemented by photometry from Kepler, TESS, and the Las Cumbres Observatory (LCO) network of telescopes. We found that all four stars exhibit large spot-induced Doppler signals at their rotation periods, and investigated the longevity and optical-to-NIR chromaticity for these signals. The phase curves remain coherent much longer than is typical for Sunlike stars. Their chromaticity varies, and one star (GJ 3959) exhibits optical and NIR RV modulation consistent in both phase and amplitude. In general, though, we find that the NIR amplitudes are lower than their optical counterparts. We conclude that starspot modulation for rapidly-rotating M stars frequently remains coherent for hundreds of stellar rotations, and gives rise to Doppler signals that, due to this coherence, may be mistaken for exoplanets.Comment: Accepted for publication in the Astrophysical Journa

First radial velocity results from the MINiature Exoplanet Radial Velocity Array (MINERVA)

The MINiature Exoplanet Radial Velocity Array (MINERVA) is a dedicated observatory of four 0.7m robotic telescopes fiber-fed to a KiwiSpec spectrograph. The MINERVA mission is to discover super-Earths in the habitable zones of nearby stars. This can be accomplished with MINERVA's unique combination of high precision and high cadence over long time periods. In this work, we detail changes to the MINERVA facility that have occurred since our previous paper. We then describe MINERVA's robotic control software, the process by which we perform 1D spectral extraction, and our forward modeling Doppler pipeline. In the process of improving our forward modeling procedure, we found that our spectrograph's intrinsic instrumental profile is stable for at least nine months. Because of that, we characterized our instrumental profile with a time-independent, cubic spline function based on the profile in the cross dispersion direction, with which we achieved a radial velocity precision similar to using a conventional "sum-of-Gaussians" instrumental profile: 1.8 m s$^{-1}$ over 1.5 months on the RV standard star HD 122064. Therefore, we conclude that the instrumental profile need not be perfectly accurate as long as it is stable. In addition, we observed 51 Peg and our results are consistent with the literature, confirming our spectrograph and Doppler pipeline are producing accurate and precise radial velocities.Comment: 22 pages, 9 figures, submitted to PASP, Peer-Reviewed and Accepte

Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome