Embedded Ribbons of Graphene Allotropes: An Extended Defect Perspective

Four fundamental dimer manipulations can be used to produce a variety of localized and extended defect structures in graphene. Two-dimensional templates result in graphene allotropes, here viewed as extended defects, which can exhibit either metallic or semiconducting electrical character. \emph{Embedded allotropic ribbons}--i.e. thin swaths of the new allotropes--can also be created within graphene. We examine these ribbons and find that they maintain the electrical character of their parent allotrope even when only a few atoms in width. Such extended defects may facilitate the construction of monolithic electronic circuitry.Comment: 24 pages, 21 figure

Electron Bernstein waves in spherical tokamak plasmas with "magnetic wells"

In addition to traditional regimes with monotonously increasing magnetic field, regimes with "magnetic wells" also occur in spherical tokamaks (STs). The magnetic field profile inversion modifies significantly the whole picture of the wave propagation and damping. Since the magnetic wells may become quite common with further improvement of ST performance, analysis of such configurations is of interest for assessment of EBW plasma heating an CD perspectives. In this paper the basic features of the EBWs propagation and damping for the second cyclotron harmonic in a slab model are considered.Comment: Proc. of 13-th Joint Workshop on ECE and ECRH, N.Novgorod, Russia May 17-20, 2004, 8 pages, 4 fig

Epigenetic Chromatin Silencing: Bistability and Front Propagation

The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side-chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally.Comment: 19 pages, 5 figure

Plasma Physics

Contains research objectives and reports on four research projects.U.S. Atomic Energy Commission (Contract AT(30-1)-1842)U.S. Atomic Energy Commission Contract W-7405-Eng-3

Microwave Gaseous Discharges

Contains reports on two research projects

OPERating ON Chromatin, a Colorful Language where Context Matters

Histones, the fundamental packaging elements of eukaryotic DNA, are highly decorated with a diverse set of post-translational modifications (PTMs) that are recognized to govern the structure and function of chromatin. Ten years ago, we put forward the histone code hypothesis, which provided a model to explain how single and/or combinatorial PTMs on histones regulate the diverse activities associated with chromatin (e.g. gene transcription). At that time, there was a limited understanding of both the number of PTMs that occur on histones as well as the proteins that place, remove and interpret them. Since the conception of this hypothesis, the field has witnessed an unprecedented advance in our understanding of the enzymes that contribute to the establishment of histone PTMs, as well as the diverse effector proteins that bind them. While debate continues as to whether histone PTMs truly constitute a strict “code”, it is becoming clear that PTMs on histone proteins function in elaborate combinations to regulate the many activities associated with chromatin. In this special issue, we celebrate the 50th anniversary of the landmark publication of the lac operon with a review that provides a current view of the histone code hypothesis, the lessons we have learned over the last decade, and the technologies that will drive our understanding of histone PTMs forward in the future

Microwave Gaseous Discharges

Contains reports on two research projects

Microwave Gaseous Disharges

Contains reports on seven research projects.Atomic Energy Commission under Contract AT(30-1)184