Organization of the genome into euchromatin and heterochromatin appears to be evolutionarily conserved and relatively stable during lineage differentiation. In an effort to unravel the basic principle underlying genome folding, here we focus on the genome itself and report a fundamental role for L1 (LINE1 or LINE-1) and B1/Alu retrotransposons, the most abundant subclasses of repetitive sequences, in chromatin compartmentalization. We find that homotypic clustering of L1 and B1/Alu demarcates the genome into grossly exclusive domains, and characterizes and predicts Hi-C compartments. Spatial segregation of L1-rich sequences in the nuclear and nucleolar peripheries and B1/Alu-rich sequences in the nuclear interior is conserved in mouse and human cells and occurs dynamically during the cell cycle. In addition, de novo establishment of L1 and B1 nuclear segregation is coincident with the formation of higher-order chromatin structures during early embryogenesis and appears to be critically regulated by L1 and B1 transcripts. Importantly, depletion of L1 transcripts in embryonic stem cells drastically weakens homotypic repeat contacts and compartmental strength, and disrupts the nuclear segregation of L1- or B1-rich chromosomal sequences at genome-wide and individual sites. Mechanistically, nuclear co-localization and liquid droplet formation of L1 repeat DNA and RNA with heterochromatin protein HP1α suggest a phase-separation mechanism by which L1 promotes heterochromatin compartmentalization. Taken together, we propose a genetically encoded model in which L1 and B1/Alu repeats blueprint chromatin macrostructure. Our model explains the robustness of genome folding into a common conserved core, on which dynamic gene regulation is overlaid across cells.

An ElectroMagnetic Solver (EMS) [Chen et al , Phys. Plasmas, 13, 123507 (2006)] is employed to model a spectral gap and a gap eigenmode in a periodic structure in the whistler frequency range. A Radially Localised Helicon (RLH) mode [Breizman and Arefiev, Phys. Rev. Lett, 84, 3863 (2000)] is considered. We demonstrate that the computed gap frequency and gap width agree well with a theoretical analysis, and find a discrete eigenmode inside the gap by introducing a defect to the system's periodicity. The axial wavelength of the gap eigenmode is close to twice the system's periodicity, which is consistent with Bragg's law. Such an eigenmode could be excited by energetic electrons, similar to the excitation of Toroidal Alfvén Eigenmodes (TAE) by energetic ions in tokamaks.

A radio frequency (RF) field solver based on Maxwell's equations and a cold plasma dielectric tensor is employed to describe wave phenomena observed in a cylindrical non-uniform helicon discharge. The experiment is carried out on a recently built linear plasma-material interaction machine: the MAGnetized Plasma Interaction Experiment (MAGPIE) [B. D. Blackwell, J. F. Caneses, C. Samuell, J. Wach, J. Howard, and C. S. Corr, submitted on 25 March 2012 to Plasma Sources Science and Technology], in which both plasma density and static magnetic field are functions of axial position. The field strength increases by a factor of 15 from source to target plate, and plasma density and electron temperature are radially non-uniform. With an enhancement factor of 9.5 to the electron-ion Coulomb collision frequency, 12% reduction in the antenna radius, and the same other conditions as employed in the experiment, the solver produces axial and radial profiles of wave amplitude and phase that are consistent with measurements. Ion-acoustic turbulence, which can happen if electron drift velocity exceeds the speed of sound in magnetized plasmas, may account for the factor of 9.5 used to match simulated results with experimental data. To overcome the single m vacuum solution limitations of the RF solver, which can only compute the glass response to the same mode number of the antenna, we have adjusted the antenna radius to match the wave field strength in the plasma. A numerical study on the effects of axial gradient in plasma density and static magnetic field on wave propagations is performed, revealing that the helicon wave has weaker attenuation away from the antenna in a focused field compared to a uniform field. This may be consistent with observations of increased ionization efficiency and plasma production in a non-uniform field. We find that the relationship between plasma density, static magnetic field strength and axial wavelength agrees well with a simple theory developed previously. A numerical scan of the enhancement factor to the electron-ion Coulomb collision frequency from 1 to 15 shows that the wave amplitude is lowered and the power deposited into the core plasma decreases as the enhancement factor increases, possibly due to the stronger edge heating for higher collision frequencies.

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