A Symbiotic View Of Life: We Have Never Been Individuals

The notion of the biological individual is crucial to studies of genetics, immunology, evolution, development, anatomy, and physiology. Each of these biological subdisciplines has a specific conception of individuality, which has historically provided conceptual contexts for integrating newly acquired data. During the past decade, nucleic acid analysis, especially genomic sequencing and high-throughput RNA techniques, has challenged each of these disciplinary definitions by finding significant interactions of animals and plants with symbiotic microorganisms that disrupt the boundaries that heretofore had characterized the biological individual. Animals cannot be considered individuals by anatomical or physiological criteria because a diversity of symbionts are both present and functional in completing metabolic pathways and serving other physiological functions. Similarly, these new studies have shown that animal development is incomplete without symbionts. Symbionts also constitute a second mode of genetic inheritance, providing selectable genetic variation for natural selection. The immune system also develops, in part, in dialogue with symbionts and thereby functions as a mechanism for integrating microbes into the animal-cell community. Recognizing the holobiont -the multicellular eukaryote plus its colonies of persistent symbionts-as a critically important unit of anatomy, development, physiology, immunology, and evolution opens up new investigative avenues and conceptually challenges the ways in which the biological subdisciplines have heretofore characterized living entities

Nonlinear polarisation and dissipative correspondence between low frequency fluid and gyrofluid equations

The correspondence between gyrofluid and low frequency fluid equations is examined. The lowest order conservative effects in ExB advection, parallel dynamics, and curvature match trivially. The principal concerns are polarisation fluxes, and dissipative parallel viscosity and parallel heat fluxes. The emergence of the polarisation heat flux in the fluid model and its contribution to the energy theorem is reviewed. It is shown that gyroviscosity and the polarisation fluxes are matched by the finite gyroradius corrections to advection in the long wavelength limit, provided that the differences between gyrocenter and particle representations is taken into account. The dissipative parallel viscosity is matched by the residual thermal anisotropy in the gyrofluid model in the collision dominated limit. The dissipative parallel heat flux is matched by the gyrofluid parallel heat flux variables in the collision dominated limit. Hence, the gyrofluid equations are a complete superset of the low frequency fluid equations.Comment: RevTeX 4, 28 pages, no figures, final revised version for Physics of Plasmas prior to proof stag

Energetic Consistency and Momentum Conservation in the Gyrokinetic Description of Tokamak Plasmas

Gyrokinetic field theory is addressed in the context of a general Hamiltonian. The background magnetic geometry is static and axisymmetric, and all dependence of the Lagrangian upon dynamical variables is in the Hamiltonian or in free field terms. Equations for the fields are given by functional derivatives. The symmetry through the Hamiltonian with time and toroidal angle invariance of the geometry lead to energy and toroidal momentum conservation. In various levels of ordering against fluctuation amplitude, energetic consistency is exact. The role of this in underpinning of conservation laws is emphasised. Local transport equations for the vorticity, toroidal momentum, and energy are derived. In particular, the momentum equation is shown for any form of Hamiltonian to be well behaved and to relax to its magnetohydrodynamic (MHD) form when long wavelength approximations are taken in the Hamiltonian. Several currently used forms, those which form the basis of most global simulations, are shown to be well defined within the gyrokinetic field theory and energetic consistency.Comment: RevTeX 4, 47 pages, no figures, revised version updated following referee comments (discussion more strictly correct/consistent, 4 references added, results unchanged as they depend on consistency of the theory), resubmitted to Physics of Plasma

Negative Differential Resistivity and Positive Temperature Coefficient of Resistivity effect in the diffusion limited current of ferroelectric thin film capacitors

We present a model for the leakage current in ferroelectric thin- film capacitors which explains two of the observed phenomena that have escaped satisfactory explanation, i.e. the occurrence of either a plateau or negative differential resistivity at low voltages, and the observation of a Positive Temperature Coefficient of Resistivity (PTCR) effect in certain samples in the high-voltage regime. The leakage current is modelled by considering a diffusion-limited current process, which in the high-voltage regime recovers the diffusion-limited Schottky relationship of Simmons already shown to be applicable in these systems

6 Batch Injection and Slipped Beam Tune Measurements in Fermilab's Main Injector

During Nova operations it is planned to run the Fermilab Recycler in a 12 batch slip stacking mode. In preparation for this, measurements of the tune during a six batch injection and then as the beam is slipped by changing the RF frequency, but without a 7th injection, have been carried out in the Main Injector. The coherent tune shifts due to the changing beam intensity were measured and compared well with the theoretically expected tune shift. The tune shifts due to changing RF frequency, required for slip stacking, also compare well with the linear theory, although some nonlinear affects are apparent at large frequency changes. These results give us confidence that the expected tunes shifts during 12 batch slip stacking Recycler operations can be accommodated.Comment: 3 pp. 3rd International Particle Accelerator Conference (IPAC 2012) 20-25 May 2012, New Orleans, Louisian

Time domain numerical calculations of unsteady vortical flows about a flat plate airfoil

A time domain numerical scheme is developed to solve for the unsteady flow about a flat plate airfoil due to imposed upstream, small amplitude, transverse velocity perturbations. The governing equation for the resulting unsteady potential is a homogeneous, constant coefficient, convective wave equation. Accurate solution of the problem requires the development of approximate boundary conditions which correctly model the physics of the unsteady flow in the far field. A uniformly valid far field boundary condition is developed, and numerical results are presented using this condition. The stability of the scheme is discussed, and the stability restriction for the scheme is established as a function of the Mach number. Finally, comparisons are made with the frequency domain calculation by Scott and Atassi, and the relative strengths and weaknesses of each approach are assessed