New observations regarding deterministic, time reversible thermostats and Gauss's principle of least constraint

Deterministic thermostats are frequently employed in non-equilibrium molecular dynamics simulations in order to remove the heat produced irreversibly over the course of such simulations. The simplest thermostat is the Gaussian thermostat, which satisfies Gauss's principle of least constraint and fixes the peculiar kinetic energy. There are of course infinitely many ways to thermostat systems, e.g. by fixing $\sum\limits_i{|{p_i}|^{\mu + 1}}$. In the present paper we provide, for the first time, convincing arguments as to why the conventional Gaussian isokinetic thermostat ($\mu=1$) is unique in this class. We show that this thermostat minimizes the phase space compression and is the only thermostat for which the conjugate pairing rule (CPR) holds. Moreover it is shown that for finite sized systems in the absence of an applied dissipative field, all other thermostats ($\mu=1$) perform work on the system in the same manner as a dissipative field while simultaneously removing the dissipative heat so generated. All other thermostats ($\mu=1$) are thus auto-dissipative. Among all $\mu$-thermostats, only the $\mu=1$ Gaussian thermostat permits an equilibrium state.Comment: 27 pages including 10 figures; submitted for publication Journal of Chemical Physic

Exact and approximate many-body dynamics with stochastic one-body density matrix evolution

We show that the dynamics of interacting fermions can be exactly replaced by a quantum jump theory in the many-body density matrix space. In this theory, jumps occur between densities formed of pairs of Slater determinants, $D_{ab}=| \Phi_a > < \Phi_b |$, where each state evolves according to the Stochastic Schr\"odinger Equation (SSE) given in ref. \cite{Jul02}. A stochastic Liouville-von Neumann equation is derived as well as the associated Bogolyubov-Born-Green-Kirwood-Yvon (BBGKY) hierarchy. Due to the specific form of the many-body density along the path, the presented theory is equivalent to a stochastic theory in one-body density matrix space, in which each density matrix evolves according to its own mean field augmented by a one-body noise. Guided by the exact reformulation, a stochastic mean field dynamics valid in the weak coupling approximation is proposed. This theory leads to an approximate treatment of two-body effects similar to the extended Time-Dependent Hartree-Fock (Extended TDHF) scheme. In this stochastic mean field dynamics, statistical mixing can be directly considered and jumps occur on a coarse-grained time scale. Accordingly, numerical effort is expected to be significantly reduced for applications.Comment: 12 pages, 1 figur

Iron and Manganese in the Ross Sea, Antarctica: Seasonal Iron Limitation in Antarctic Shelf Waters

Dissolved iron and manganese and total dissolvable iron were measured in water column samples from the Polynya Region of the southern Ross Sea in cruises in Nov.-Dec. 1994 (spring 1994) and Dec. 1995 to Jan. 1996 (summer 1995). Iron and manganese addition bottle incubation experiments were also performed on these cruises to assess the nutritional sufficiency of ambient iron and manganese concentrations for phytoplankton growth. Generally high dissolved iron concentrations (\u3e0.5 nM) and relatively complex iron and manganese vertical profiles were obtained in spring 1994 vs. summer 1995. Dissolved iron concentrations in the upper water column averaged 1.0 nM in spring 1994 and 0.23 nM in summer 1995, excluding 2 stations where concentrations exceeding 1 nM were attributed to inputs from melting sea ice. The Observed differences in the iron and manganese distribution between spring 1994 and summer 1995 were attributed to seasonal decreases in bottom water upwelling and sea ice melting, which supplied these metals to the upper water column, combined with the cumulative removal of iron and manganese from the water column throughout the spring and summer, due to biological uptake, vertical export, and scavenging by suspended and sinking particles. Results of metal addition bottle incubation experiments indicated that ambient dissolved Iron concentrations were adequate for phytoplankton growth requirements in spring and early summer, when algal production is highest and Phaeocystis antarctica dominates the algal community, whereas low dissolved Iron concentrations limited algal community growth later in the summer, except in stratified, Iron enriched water near melting sea ice, where diatoms are able to bloom. Observations and inferred seasonal distribution of P. antarctica and diatoms in this water suggested that iron availability and vertical mixing (i.e., irradiance) exert the primary controls on phytoplankton growth and community structure in the southern Ross Sea in spring and summer

Separation of VUV/UV photons and reactive particles in the effluent of a He/O2 atmospheric pressure plasma jet

Cold atmospheric pressure plasmas can be used for treatment of living tissues or for inactivation of bacteria or biological macromolecules. The treatment is usually characterized by a combined effect of UV and VUV radiation, reactive species, and ions. This combination is usually beneficial for the effectiveness of the treatment but it makes the study of fundamental interaction mechanisms very difficult. Here we report on an effective separation of VUV/UV photons and heavy reactive species in the effluent of a micro scale atmospheric pressure plasma jet ($\mu$-APPJ). The separation is realized by an additional flow of helium gas under well-defined flow conditions, which deflects heavy particles in the effluent without affecting the VUV and UV photons. Both components of the effluent, the photons and the reactive species, can be used separately or in combination for sample treatment. The results of treatment of a model plasma polymer film and vegetative Bacillus subtilis and Escherichia coli cells are shown and discussed. A simple model of the He gas flow and reaction kinetics of oxygen atoms in the gas phase and at the surface is used to provide a better understanding of the processes in the plasma effluent. The new jet modification, called X-Jet for its appearance, will simplify the investigation of interaction mechanisms of atmospheric pressure plasmas with biological samples.Comment: 10 pages, 7 figures, submitted to Journal of Physics D: Applied Physic

Time-averaged MSD of Brownian motion

We study the statistical properties of the time-averaged mean-square displacements (TAMSD). This is a standard non-local quadratic functional for inferring the diffusion coefficient from an individual random trajectory of a diffusing tracer in single-particle tracking experiments. For Brownian motion, we derive an exact formula for the Laplace transform of the probability density of the TAMSD by mapping the original problem onto chains of coupled harmonic oscillators. From this formula, we deduce the first four cumulant moments of the TAMSD, the asymptotic behavior of the probability density and its accurate approximation by a generalized Gamma distribution

Ecological impacts of small dams on South African rivers Part 2: Biotic response – abundance and composition of macroinvertebrate communities

This paper investigates the cumulative impacts of small dams on invertebrate communities in 2 regions of South Africa – the Western Cape and Mpumalanga. Previous research found reduced discharge, increased total dissolved salts, and a decrease in average score per taxon (ASPT; collected using SASS4 methods) at sites with high density of small dams in their catchment. These changes in ASPT are investigated using the invertebrate abundance data available in the River Health Programme. Multivariate analyses found differences in invertebrate communities in rivers with high densities of small dams in their catchment in foothill-gravel streams (in both Western Cape and Mpumalanga) and in foothill-cobble streams (in Western Cape only). Opportunistic taxa that are tolerant of pollution, and capable of exploiting various habitats, and those that prefer slower currents increased in numbers, while other taxa that are sensitive to pollution and disturbance declined in numbers. Some regional differences were noted possibly reflecting climatic differences between the regions. Since the results of this study are correlative, it highlights the need for a systematic (by sites and seasons) and detailed (at species level) collection of data to verify the results of cumulative effects of small dams. This can further the development of a framework for small-dam construction and management that will limit their impact on river catchments

New and old N=8 superconformal field theories in three dimensions

We show that an infinite family of N=6 d=3 superconformal Chern-Simons-matter theories has hidden N=8 superconformal symmetry and hidden parity on the quantum level. This family of theories is different from the one found by Aharony, Bergman, Jafferis and Maldacena, as well as from the theories constructed by Bagger and Lambert, and Gustavsson. We also test several conjectural dualities between BLG theories and ABJ theories by comparing superconformal indices of these theories.Comment: 16 pages, late

Behavior of bulk high-temperature superconductors of finite thickness subjected to crossed magnetic fields

Crossed magnetic field effects on bulk high-temperature superconductors have been studied both experimentally and numerically. The sample geometry investigated involves finite-size effects along both (crossed) magnetic field directions. The experiments were carried out on bulk melt-processed Y-Ba-Cu-O (YBCO) single domains that had been pre-magnetized with the applied field parallel to their shortest direction (i.e. the c-axis) and then subjected to several cycles of the application of a transverse magnetic field parallel to the sample ab plane. The magnetic properties were measured using orthogonal pick-up coils, a Hall probe placed against the sample surface and Magneto-Optical Imaging (MOI). We show that all principal features of the experimental data can be reproduced qualitatively using a two-dimensional finite-element numerical model based on an E-J power law and in which the current density flows perpendicularly to the plane within which the two components of magnetic field are varied. The results of this study suggest that the suppression of the magnetic moment under the action of a transverse field can be predicted successfully by ignoring the existence of flux-free configurations or flux-cutting effects. These investigations show that the observed decay in magnetization results from the intricate modification of current distribution within the sample cross-section. It is also shown that the model does not predict any saturation of the magnetic induction, even after a large number (~ 100) of transverse field cycles. These features are shown to be consistent with the experimental data.Comment: 41 pages, 9 figures, accepted in Phys. Rev. B Changes : 8 references added, a few precisions added, some typos correcte

Reduced-symmetry two-dimensional solitons in photonic lattices

We demonstrate theoretically and experimentally a novel type of localized beams supported by the combined effects of total internal and Bragg reflection in nonlinear two-dimensional square periodic structures. Such localized states exhibit strong anisotropy in their mobility properties, being highly mobile in one direction and trapped in the other, making them promising candidates for optical routing in nonlinear lattices.Comment: 5 pages, 4 figure