Hamiltonian closures for fluid models with four moments by dimensional analysis

Fluid reductions of the Vlasov-Amp{\`e}re equations that preserve the Hamiltonian structure of the parent kinetic model are investigated. Hamiltonian closures using the first four moments of the Vlasov distribution are obtained, and all closures provided by a dimensional analysis procedure for satisfying the Jacobi identity are identified. Two Hamiltonian models emerge, for which the explicit closures are given, along with their Poisson brackets and Casimir invariants

Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of wire model vs. extended ladder model

We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of $N$ monomers (base pairs): (I) at the base-pair level, using the on-site energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the on-site energies of the bases and the hopping integrals between neighboring bases, i.e., an \textit{extended} ladder model since we also include diagonal hoppings. We solve a system of $MD$ ("matrix dimension") coupled equations [(I) $MD$ = $N$, (II) $MD$ = $2N$] for the time-independent problem, and a system of $MD$ coupled $1^\text{st}$ order differential equations for the time-dependent problem. We study the HOMO and the LUMO eigenspectra, the occupation probabilities, the Density of States (DOS) and the HOMO-LUMO gap as well as the mean over time probabilities to find the carrier at each site [(I) base pair or (II) base)], the Fourier spectra, which reflect the frequency content of charge transfer (CT) and the pure mean transfer rates from a certain site to another. The two TB approaches give coherent, complementary aspects of electronic properties and charge transfer in B-DNA monomer polymers and dimer polymers.Comment: 20 pages, 23 figure

Gyrofluid simulations of collisionless reconnection in the presence of diamagnetic effects

The effects of the ion Larmor radius on magnetic reconnection are investigated by means of numerical simulations, with a Hamiltonian gyrofluid model. In the linear regime, it is found that ion diamagnetic effects decrease the growth rate of the dominant mode. Increasing ion temperature tends to make the magnetic islands propagate in the ion diamagnetic drift direction. In the nonlinear regime, diamagnetic effects reduce the final width of the island. Unlike the electron density, the guiding center density does not tend to distribute along separatrices and at high ion temperature, the electrostatic potential exhibits the superposition of a small scale structure, related to the electron density, and a large scale structure, related to the ion guiding-center density

Gyrofluid simulations of collisionless reconnection in the presence of diamagnetic effects

The effects of the ion Larmor radius on magnetic reconnection are investigated by means of numerical simulations, with a Hamiltonian gyrofluid model. In the linear regime, it is found that ion diamagnetic effects decrease the growth rate of the dominant mode. Increasing ion temperature tends to make the magnetic islands propagate in the ion diamagnetic drift direction. In the nonlinear regime, diamagnetic effects reduce the final width of the island. Unlike the electron density, the guiding center density does not tend to distribute along separatrices and at high ion temperature, the electrostatic potential exhibits the superposition of a small scale structure, related to the electron density, and a large scale structure, related to the ion guiding-center density

Metriplectic framework for dissipative magneto-hydrodynamics

International audienceThe metriplectic framework, which allows for the formulation of an algebraic structure for dissipative systems, is applied to visco-resistive Magneto-Hydrodynamics (MHD), adapting what had already been done for non-ideal Hydrodynamics (HD). The result is obtained by extending the HD symmetric bracket and free energy to include magnetic field dynamics and resistive dissipation. The correct equations of motion are obtained once one of the Casimirs of the Poisson bracket for ideal MHD is identified with the total thermodynamic entropy of the plasma. The metriplectic framework of MHD is shown to be invariant under the Galileo Group. The metriplectic structure also permits us to obtain the asymptotic equilibria toward which the dynamics of the system evolves. This scheme is finally adapted to the two-dimensional incompressible resistive MHD, that is of major use in many applications

Gyrofluid simulations of collisionless reconnection in the presence of diamagnetic effects

The effects of the ion Larmor radius on magnetic reconnection are investigated by means of numerical simulations, with a Hamiltonian gyrofluid model. In the linear regime, it is found that ion diamagnetic effects decrease the growth rate of the dominant mode. Increasing ion temperature tends to make the magnetic islands propagate in the ion diamagnetic drift direction. In the nonlinear regime, diamagnetic effects reduce the final width of the island. Unlike the electron density, the guiding center density does not tend to distribute along separatrices and at high ion temperature, the electrostatic potential exhibits the superposition of a small scale structure, related to the electron density, and a large scale structure, related to the ion guiding-center density

Mode signature and stability for a Hamiltonian model of electron temperature gradient turbulence

Stability properties and mode signature for equilibria of a model of electron temperature gradient (ETG) driven turbulence are investigated by Hamiltonian techniques. After deriving the infinite families of Casimir invariants, associated with the noncanonical Poisson bracket of the model, a sufficient condition for stability is obtained by means of the Energy-Casimir method. Mode signature is then investigated for linear motions about homogeneous equilibria. Depending on the sign of the equilibrium "translated" pressure gradient, stable equilibria can either be energy stable, i.e.\ possess definite linearized perturbation energy (Hamiltonian), or spectrally stable with the existence of negative energy modes (NEMs). The ETG instability is then shown to arise through a Kre\u{\i}n-type bifurcation, due to the merging of a positive and a negative energy mode, corresponding to two modified drift waves admitted by the system. The Hamiltonian of the linearized system is then explicitly transformed into normal form, which unambiguously defines mode signature. In particular, the fast mode turns out to always be a positive energy mode (PEM), whereas the energy of the slow mode can have either positive or negative sign

Hamiltonian fluid closures of the Vlasov-Ampère equations: from water-bags to N moment models

International audienceMoment closures of the Vlasov-Ampère system, whereby higher moments are represented as functions of lower moments with the constraint that the resulting fluid system remains Hamiltonian, are investigated by using water-bag theory. The link between the water-bag formalism and fluid models that involve density, fluid velocity, pressure and higher moments is established by introducing suitable thermodynamic variables. The cases of one, two and three water-bags are treated and their Hamiltonian structures are provided. In each case, we give the associated fluid closures and we discuss their Casimir invariants. We show how the method can be extended to an arbitrary number of fields, i.e., an arbitrary number of water-bags and associated moments. The thermodynamic interpretation of the resulting models is discussed. Finally, a general procedure to derive Hamiltonian N-field fluid models is proposed