Considering Fluctuation Energy as a Measure of Gyrokinetic Turbulence

In gyrokinetic theory there are two quadratic measures of fluctuation energy, left invariant under nonlinear interactions, that constrain the turbulence. The recent work of Plunk and Tatsuno [Phys. Rev. Lett. 106, 165003 (2011)] reported on the novel consequences that this constraint has on the direction and locality of spectral energy transfer. This paper builds on that work. We provide detailed analysis in support of the results of Plunk and Tatsuno but also significantly broaden the scope and use additional methods to address the problem of energy transfer. The perspective taken here is that the fluctuation energies are not merely formal invariants of an idealized model (two-dimensional gyrokinetics) but are general measures of gyrokinetic turbulence, i.e. quantities that can be used to predict the behavior of the turbulence. Though many open questions remain, this paper collects evidence in favor of this perspective by demonstrating in several contexts that constrained spectral energy transfer governs the dynamics.Comment: Final version as published. Some cosmetic changes and update of reference

Angular momenta creation in relativistic electron-positron plasma

Creation of angular momentum in a relativistic electron-positron plasma is explored. It is shown that a chain of angular momentum carrying vortices is a robust asymptotic state sustained by the generalized nonlinear Schrodinger equation characteristic to the system. The results may suggest a possible electromagnetic origin of angular momenta when it is applied to the MeV epoch of the early Universe.Comment: 20 pages, 6 figure

Characterization of the SIDDHARTA-2 second level trigger detector prototype based on scintillators coupled to a prism reflector light guide

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Linearized model Fokker-Planck collision operators for gyrokinetic simulations. II. Numerical implementation and tests

A set of key properties for an ideal dissipation scheme in gyrokinetic simulations is proposed, and implementation of a model collision operator satisfying these properties is described. This operator is based on the exact linearized test-particle collision operator, with approximations to the field-particle terms that preserve conservation laws and an H-Theorem. It includes energy diffusion, pitch-angle scattering, and finite Larmor radius effects corresponding to classical (real-space) diffusion. The numerical implementation in the continuum gyrokinetic code GS2 is fully implicit and guarantees exact satisfaction of conservation properties. Numerical results are presented showing that the correct physics is captured over the entire range of collisionalities, from the collisionless to the strongly collisional regimes, without recourse to artificial dissipation.Comment: 13 pages, 8 figures, submitted to Physics of Plasmas; typos fixe

Effects of thermal fluctuation and the receptor-receptor interaction in bacterial chemotactic signalling and adaptation

Bacterial chemotaxis is controlled by the conformational changes of the receptors, in response to the change of the ambient chemical concentration. In a statistical mechanical approach, the signalling due to the conformational changes is a thermodynamic average quantity, dependent on the temperature and the total energy of the system, including both ligand-receptor interaction and receptor-receptor interaction. This physical theory suggests to biology a new understanding of cooperation in ligand binding and receptor signalling problems. How much experimental support of this approach can be obtained from the currently available data? What are the parameter values? What is the practical information for experiments? Here we make comparisons between the theory and recent experimental results. Although currently comparisons can only be semi-quantitative or qualitative, consistency is clearly shown. The theory also helps to sort a variety of data.Comment: 26 pages, revtex. Journal version. Analysis on another set of data on adaptation time is adde

Gyrokinetic turbulence: a nonlinear route to dissipation through phase space

This paper describes a conceptual framework for understanding kinetic plasma turbulence as a generalized form of energy cascade in phase space. It is emphasized that conversion of turbulent energy into thermodynamic heat is only achievable in the presence of some (however small) degree of collisionality. The smallness of the collision rate is compensated by the emergence of small-scale structure in the velocity space. For gyrokinetic turbulence, a nonlinear perpendicular phase mixing mechanism is identified and described as a turbulent cascade of entropy fluctuations simultaneously occurring at spatial scales smaller than the ion gyroscale and in velocity space. Scaling relations for the resulting fluctuation spectra are derived. An estimate for the collisional cutoff is provided. The importance of adequately modeling and resolving collisions in gyrokinetic simulations is biefly discussed, as well as the relevance of these results to understanding the dissipation-range turbulence in the solar wind and the electrostatic microturbulence in fusion plasmas.Comment: iop revtex style, 14 pages, 1 figure; submitted to PPCF; invited talk for EPS Conference on Plasma Physics, Crete, June 2008; Replaced to match published versio

The host metabolite D-serine contributes to bacterial niche specificity through gene selection

Escherichia coli comprise a diverse array of both commensals and niche-specific pathotypes. The ability to cause disease results from both carriage of specific virulence factors and regulatory control of these via environmental stimuli. Moreover, host metabolites further refine the response of bacteria to their environment and can dramatically affect the outcome of the host–pathogen interaction. Here, we demonstrate that the host metabolite, D-serine, selectively affects gene expression in E. coli O157:H7. Transcriptomic profiling showed exposure to D-serine results in activation of the SOS response and suppresses expression of the Type 3 Secretion System (T3SS) used to attach to host cells. We also show that concurrent carriage of both the D-serine tolerance locus (dsdCXA) and the locus of enterocyte effacement pathogenicity island encoding a T3SS is extremely rare, a genotype that we attribute to an ‘evolutionary incompatibility’ between the two loci. This study demonstrates the importance of co-operation between both core and pathogenic genetic elements in defining niche specificity

Vortex solitons - Mass, Energy and Angular momentum bunching in relativistic electron-positron plasmas

It is shown that the interaction of large amplitude electromagnetic waves with a hot electron-positron (e-p) plasma (a principal constituent of the universe in the MeV epoch) leads to a bunching of mass, energy, and angular momentum in stable, long-lived structures. Electromagnetism in the MeV epoch, then, could provide a possible route for seeding the observed large-scale structure of the universe.Comment: 17 pages with 2 figure

Measurement of the strong interaction induced shift and width of the 1s state of kaonic deuterium at J-PARC

The antikaon-nucleon interaction close to threshold provides crucial information on the interplay between spontaneous and explicit chiral symmetry breaking in low-energy QCD. In this context the importance of kaonic deuterium X-ray spectroscopy has been well recognized, but no experimental results have yet been obtained due to the difficulty of the measurement. We propose to measure the shift and width of the kaonic deuterium 1s state with an accuracy of 60 eV and 140 eV respectively at J-PARC. These results together with the kaonic hydrogen data (KpX at KEK, DEAR and SIDDHARTA at DAFNE) will then permit the determination of values of both the isospin I=0 and I=1 antikaon-nucleon scattering lengths and will provide the most stringent constraints on the antikaon-nucleon interaction, promising a breakthrough. Refined Monte Carlo studies were performed, including the investigation of background suppression factors for the described setup. These studies have demonstrated the feasibility of determining the shift and width of the kaonic deuterium atom 1s state with the desired accuracy of 60 eV and 140 eV.Comment: 12 pages, 9 figure