Cosmological consequences of dark matter interactions and vacuum fluctuations

This thesis is divided into two parts: interacting dark matter and fluctuations in cosmology. There is an incongruence between the properties that dark matter is expected to possess between the early universe and the late universe. Weakly-interacting dark matter yields the observed dark matter relic density and is consistent with large-scale structure formation; however, there is strong astrophysical evidence in favor of the idea that dark matter has large self-interactions. The first part of this thesis presents two models in which the nature of dark matter fundamentally changes as the universe evolves. In the first model, the dark matter mass and couplings depend on the value of a chameleonic scalar field that changes as the universe expands. In the second model, dark matter is charged under a hidden SU(N) gauge group and eventually undergoes confinement. These models introduce very different mechanisms to explain the separation between the physics relevant for freezeout and for small-scale dynamics.

As the universe continues to evolve, it will asymptote to a de Sitter vacuum phase. Since there is a finite temperature associated with de Sitter space, the universe is typically treated as a thermal system, subject to rare thermal fluctuations, such as Boltzmann brains. The second part of this thesis begins by attempting to escape this unacceptable situation within the context of known physics: vacuum instability induced by the Higgs field. The vacuum decay rate competes with the production rate of Boltzmann brains, and the cosmological measures that have a sufficiently low occurrence of Boltzmann brains are given more credence. Upon further investigation, however, there are certain situations in which de Sitter space settles into a quiescent vacuum with no fluctuations. This reasoning not only provides an escape from the Boltzmann brain problem, but it also implies that vacuum states do not uptunnel to higher-energy vacua and that perturbations do not decohere during slow-roll inflation, suggesting that eternal inflation is much less common than often supposed. Instead, decoherence occurs during reheating, so this analysis does not alter the conventional understanding of the origin of density fluctuations from primordial inflation.

Advanced density functional theory methods for materials science

In this work we chiefly deal with two broad classes of problems in computational materials science, determining the doping mechanism in a semiconductor and developing an extreme condition equation of state. While solving certain aspects of these questions is well-trodden ground, both require extending the reach of existing methods to fully answer them. Here we choose to build upon the framework of density functional theory (DFT) which provides an efficient means to investigate a system from a quantum mechanics description.

Zinc Phosphide (Zn₃P₂) could be the basis for cheap and highly efficient solar cells. Its use in this regard is limited by the difficulty in n-type doping the material. In an effort to understand the mechanism behind this, the energetics and electronic structure of intrinsic point defects in zinc phosphide are studied using generalized Kohn-Sham theory and utilizing the Heyd, Scuseria, and Ernzerhof (HSE) hybrid functional for exchange and correlation. Novel 'perturbation extrapolation' is utilized to extend the use of the computationally expensive HSE functional to this large-scale defect system. According to calculations, the formation energy of charged phosphorus interstitial defects are very low in n-type Zn₃P₂ and act as 'electron sinks', nullifying the desired doping and lowering the fermi-level back towards the p-type regime. Going forward, this insight provides clues to fabricating useful zinc phosphide based devices. In addition, the methodology developed for this work can be applied to further doping studies in other systems.

Accurate determination of high pressure and temperature equations of state is fundamental in a variety of fields. However, it is often very difficult to cover a wide range of temperatures and pressures in an laboratory setting. Here we develop methods to determine a multi-phase equation of state for Ta through computation. The typical means of investigating thermodynamic properties is via ’classical’ molecular dynamics where the atomic motion is calculated from Newtonian mechanics with the electronic effects abstracted away into an interatomic potential function. For our purposes, a ’first principles’ approach such as DFT is useful as a classical potential is typically valid for only a portion of the phase diagram (i.e. whatever part it has been fit to). Furthermore, for extremes of temperature and pressure quantum effects become critical to accurately capture an equation of state and are very hard to capture in even complex model potentials. This requires extending the inherently zero temperature DFT to predict the finite temperature response of the system. Statistical modelling and thermodynamic integration is used to extend our results over all phases, as well as phase-coexistence regions which are at the limits of typical DFT validity. We deliver the most comprehensive and accurate equation of state that has been done for Ta. This work also lends insights that can be applied to further equation of state work in many other materials.

Regulation of the fitness of Atlantic salmon (Salmo salar) by intra-specific competition amongst the juveniles

Factors affecting the fitness of juvenile salmon are discussed. Although fitness from the genetic point of view is defined as the relative capacity of carriers of a given genotype to transmit their genes to the gene pool of the following generations, growth and survival of individuals are also components of fitness, and are influenced by responses to competition, which is the major topic of this article including implications for management. In order to better understand the relationships of density-dependent survival in Newfoundland, egg depositions were manipulated experimentally in the Freshwater River. Figures demonstrate the relationship between stock (number of eggs per 100 m2 of river) and recruitment (number of smolts per l00 m2 of Atlantic salmon, and also the percentage survival from egg to smolt stage related to potential egg depositions.

Studies of magnetic interactions in Ni-doped ZnO from first-principles calculations

The magnetic interactions in Ni-doped ZnO are calculated using GGA and GGA + U method of density functional theory. The following three cases: (i) Ni-doped ZnO, (ii) (Ni, Al)-codoped ZnO, and (iii) (Ni, Li)-codoped ZnO are studied. The ferromagnetic ordering is always favorable for the three cases within GGA method. However, the ferromagnetic state is sometimes favorable after treating within the method of GGA + U. The GGA underestimates the correlated interactions especially when the Ni ions align directly to each other. (C) 2007 Elsevier B.V. All rights reserved.

Concepts of spawning targets

This report discusses the concepts of spawning targets. Spawning target setting is based on the fact that the number of smolts produced by any given river is constrained by habitat availability. This means smolt numbers depend on spawner numbers up to a point, but thereafter smolt production reaches a ceiling. It has been shown, in some rivers at least, that the relationship between egg deposition and smolt production may approximately be described by a mathematical equation. The equation will vary between rivers and there is uncertainty over its exact form. The concept of Maximum Gain (MG) is explained and its application in fisheries management discussed. The author also critically examines the concept of Density Independent Mortality (DIM).

Estimating the abundance of clustered and cryptic marine macro-invertebrates in the Galápagos with particular reference to sea cucumbers

Estimating the abundance of marine macro-invertebrates is complicated by a variety of factors: 1) human factors, such as diver efficiency and diver error; and 2) biological factors, such as aggregation of organisms, crypsis, and nocturnal emergence behavior. Diver efficiency varied according to the detectability of an organism causing under-estimation of density by up to 50% in some species. All common species were aggregated at scales from 10-50 m. Transects need to be long enough to transcend the scale of patchiness to improve accuracy. Some species of sea urchins and sea cucumbers (pepinos) which are cryptic by day emerged at night so that daytime censuses underestimated their abundance by up to 10 times. In the sea cucumber fishery, estimates of abundance need to be made at the scale of the population, i.e. at hundreds of km. A strategy for this is proposed.

Ecological condition of coastal ocean waters of the northwestern Gulf of Mexico: 2011

In August 2011, the NOAA National Ocean Service (NOS) conducted an assessment of the status of ecological condition of soft-bottom habitat and overlying waters of the continental shelf in the northwestern Gulf of Mexico (GOM). The original sampling design included 50 randomly selected sites from the Mississippi River delta to the U.S./Mexican border, representing a total area of 111,162 square kilometers; however, vessel failures and inclement weather precluded sampling at 16 sites in the western-most part of the study region. Sampling was completed at the remaining 34 sites in offshore waters between the Mississippi River delta and Freeport, Texas, representing an estimated 75,591 square kilometers. Field sampling followed standard methods and indicators applied in prior NOAA coastal studies and EPA’s Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA). A key feature adopted from these studies was the incorporation of a random probabilistic sampling design. Such a design provides a basis for making unbiased statistical estimates of the spatial extent of ecological condition relative to various measured indicators and corresponding thresholds of concern. Indicators included multiple measures of water quality, sediment quality, and biological condition (benthic fauna, fish tissue contaminant levels). Water depths ranged from 13 – 83 m throughout the study area. About 9 % of the area had sediments composed of sands (< 20 % silt+clay), 47 % of the area was composed of intermediate muddy sands (20 – 80 % silt+clay), and 44 % of the sampled area consisted of mud (> 80 % silt+clay). About 50 % of the area (represented by 17 sites) had sediment total organic carbon (TOC) concentrations < 5 mg/g and all of the sites sampled had levels of TOC < 20 mg/g, well below the range associated with potentially harmful effects to benthic fauna (> 50 mg/g). Surface salinities ranged from 23.4 – 36.5 psu, with salinity generally increasing with distance west of the Mississippi River delta. Bottom salinities varied between 31.1 and 36.5 psu, with lowest values occurring at shallow, inner-shelf stations. Surface-water temperatures varied between 29.8 and 31.5 ºC, while near-bottom waters ranged in temperature from 19.4 – 31 ºC. An index of density stratification (Δσt) indicated that portions of coastal shelf waters in the northwestern GOM at the time of this sampling were strongly stratified. Values of Δσt at 19 of the 34 sites sampled in this study (56 % of the study area) ranged from 2.2 to 12.4, which is within the range considered to be indicative of strong vertical stratification (Δσt > 2). Stratification was strongest close to the Mississippi River delta, and decreased with distance west of the delta.

Ecological Condition of Coastal Ocean Waters within Stellwagen Bank National Marine Sanctuary: 2008

In June 2008, the NOAA National Ocean Service (NOS), in conjunction with the EPA National Health and Environmental Effects Laboratory (NHEERL), conducted an assessment of the status of ecological condition of soft-bottom habitat and overlying waters within the boundaries of Stellwagen Bank National Marine Sanctuary (SBNMS). The sanctuary lies approximately 20 nautical miles east of Boston, MA in the southwest Gulf of Maine between Cape Ann and Cape Cod and encompassing 638 square nautical miles (2,181 km2). A total of 30 stations were targeted for sampling using standard methods and indicators applied in prior NOAA coastal studies and EPA’s Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA). A key feature adopted from these studies was the incorporation of a random probabilistic sampling design. Such a design provides a basis for making unbiased statistical estimates of the spatial extent of ecological condition relative to various measured indicators and corresponding thresholds of concern. Indicators included multiple measures of water quality, sediment quality, and biological condition (benthic fauna, fish tissue contaminant levels). Depths ranged from 31 – 137 m throughout the study area. About 76 % of the area had sediments composed of sands (< 20 % silt-clay), 17 % of the area was composed of intermediate muddy sands (20 – 80 % silt-clay), and 7 % of the sampled area consisted of mud (> 80 % siltclay). About 70 % of the area (represented by 21 sites) had sediment total organic carbon (TOC) concentrations < 5 mg/g and all but one site (located in Stellwagen Basin) had levels of TOC < 20 mg/g, which is well below the range potentially harmful to benthic fauna (> 50 mg/g). Surface salinities ranged from 30.6 – 31.5 psu, with the majority of the study region (approximately 80 % of the area) having surface salinities between 30.8 and 31.4 psu. Bottom salinities varied between 32.1 and 32.5 psu, with bottom salinities at all sites having values above the range of surface salinities. Surface-water temperatures varied between 12.1 and 16.8 ºC, while near-bottom waters ranged in temperature from 4.4 – 6.2 ºC. An index of density stratification (Δσt) indicated that the waters of SBNMS were stratified at the time of sampling. Values of Δσt at 29 of the 30 sites sampled in this study (96.7 % of the study area) varied from 2.1 – 3.2, which is within the range considered to be indicative of strong vertical stratification (Δσt > 2) and typical of the western Gulf of Maine in summer. Levels of dissolved oxygen (DO) were confined to a fairly narrow range in surface (8.8 – 10.4 mg/L) and bottom (8.5 – 9.6 mg/L) waters throughout the survey area. These levels are within the range considered indicative of good water quality (> 5 mg/L) with respect to DO. None of these waters had DO at low levels (< 2 mg/L) potentially harmful to benthic fauna and fish.

Demersal groundfish densities in trawlable and untrawlable habitats off Washington: implications for the estimation of habitat bias in trawl surveys

Demersal groundfish densities were estimated by conducting a visual strip-transect survey via manned submersible on the continental shelf off Cape Flattery, Washington. The purpose of this study was to evaluate the statistical sampling power of the submersible survey as a tool to discriminate density differences between trawlable and untrawlable habitats. A geophysical map of the study area was prepared with side-scan sonar imagery, multibeam bathymetry data, and known locations of historical NMFS trawl survey events. Submersible transects were completed at randomly selected dive sites located in each habitat type. Significant differences in density between habitats were observed for lingcod (Ophiodon elongatus), yelloweye rockfish (Sebastes ruberrimus), and tiger rockfish (S. nigrocinctus) individually, and for “all rockfish” and “all flatfish” in the aggregate. Flatfish were more than ten times as abundant in the trawlable habitat samples than in the untrawlable samples, whereas rockfish as a group were over three times as abundant in the untrawlable habitat samples. Guidelines for sample sizes and implications for the estimation of the continental shelf trawl-survey habitat-bias are considered. We demonstrate an approach that can be used to establish sample size guidelines for future work by illustrating the interplay between statistical sampling power and 1) habitat specific-density differences, 2) variance of density differences, and 3) the proportion of untrawlable area in a habitat.

Phytoplankton communities of a floodplain lake of the Brahmaputra River basin, Upper Assam

Phytoplankton (52 species; Bacillariophyceae>Chlorophyceae>Cyanophyceae> Euglenophyceae=Dinophyceae) of Samuajan beel, a tropical floodplain lake, registered identical mean annual richness (30+4 species) in littoral and limnetic regions and depicted 33.3-77.2% and 31.4-81.1% community similarities respectively. Their abundance ranged between 137+54 n/l in littoral (Bacillariophyceae>Chlorophyceae) and 122 ± 45 n/l (Chlorophyceae>Bacillariophyceae) in limnetic communities, comprised about 46% of net plankton and indicated winter peaks. This study depicted moderate species diversity, high evenness and low dominance of phytoplankton; species diversity showed significant direct correlation with richness and evenness and an inverse relationship with dominance. Phytoplankton showed significant positive relationship with transparency and silicate and negative with water temperature, rainfall, chloride and nitrate. Multiple regression revealed that ten abiotic factors accounted for >80-98% of density variations of phytoplankton and the dominant groups. ANOVA depicted trends of significance in abundance of the biotic communities analysed.

Density stratified environments: The double-tank method

We present an alternative method of producing density stratifications in the laboratory based on the 'double-tank' method proposed by Oster (Sci Am 213:70-76, 1965). We refer to Oster's method as the 'forced-drain' approach, as the volume flow rates between connecting tanks are controlled by mechanical pumps. We first determine the range of density profiles that may be established with the forced-drain approach other than the linear stratification predicted by Oster. The dimensionless density stratification is expressed analytically as a function of three ratios: the volume flow rate ratio n, the ratio of the initial liquid volumes λ and the ratio of the initial densities ψ. We then propose a method which does not require pumps to control the volume flow rates but instead allows the connecting tanks to drain freely under gravity. This is referred to as the 'free-drain' approach. We derive an expression for the density stratification produced and compare our predictions with saline stratifications established in the laboratory using the 'free-drain' extension of Oster's method. To assist in the practical application of our results we plot the region of parameter space that yield concave/convex or linear density profiles for both forced-drain and free-drain approaches. The free-drain approach allows the experimentalist to produce a broad range of density profiles by varying the initial liquid depths, cross-sectional and drain opening areas of the tanks. One advantage over the original Oster approach is that density profiles with an inflexion point can now be established. © 2008 Springer-Verlag.

First-principles energetics of water: a many-body analysis

Standard forms of density-functional theory (DFT) have good predictive power for many materials, but are not yet fully satisfactory for solid, liquid and cluster forms of water. We use a many-body separation of the total energy into its 1-body, 2-body (2B) and beyond-2-body (B2B) components to analyze the deficiencies of two popular DFT approximations. We show how machine-learning methods make this analysis possible for ice structures as well as for water clusters. We find that the crucial energy balance between compact and extended geometries can be distorted by 2B and B2B errors, and that both types of first-principles error are important.

First-principles energetics of water clusters and ice: a many-body analysis.

Standard forms of density-functional theory (DFT) have good predictive power for many materials, but are not yet fully satisfactory for cluster, solid, and liquid forms of water. Recent work has stressed the importance of DFT errors in describing dispersion, but we note that errors in other parts of the energy may also contribute. We obtain information about the nature of DFT errors by using a many-body separation of the total energy into its 1-body, 2-body, and beyond-2-body components to analyze the deficiencies of the popular PBE and BLYP approximations for the energetics of water clusters and ice structures. The errors of these approximations are computed by using accurate benchmark energies from the coupled-cluster technique of molecular quantum chemistry and from quantum Monte Carlo calculations. The systems studied are isomers of the water hexamer cluster, the crystal structures Ih, II, XV, and VIII of ice, and two clusters extracted from ice VIII. For the binding energies of these systems, we use the machine-learning technique of Gaussian Approximation Potentials to correct successively for 1-body and 2-body errors of the DFT approximations. We find that even after correction for these errors, substantial beyond-2-body errors remain. The characteristics of the 2-body and beyond-2-body errors of PBE are completely different from those of BLYP, but the errors of both approximations disfavor the close approach of non-hydrogen-bonded monomers. We note the possible relevance of our findings to the understanding of liquid water.

Growth of Potamageton maackianus under low-light stress in eutrophic water

Decline of submersed macrophytes in Lake Donghu of China with the progress of eutrophication is assumedly due to low light stress by algae blooming. I conducted a laboratory experiment to study the impact of low-light stress on the growth of Potamogeton maackianus A. Been, a dominant submersed macrophyte of the lake before the 1970s. Plants were grown for six weeks in aquaria with Lake Donghu sediment and enriched water. Light delivered to aquaria was adjusted to simulate the typical Lake Donghu light intensities that exist at several water depths from 0.6m to 1.7m. Biomass growth of the plant was inversely related to light intensity at the simulated depths of greater than or equal to 1.0m (r = 0.96, p < 0.05, n=6) and was negative at the depths of greater than or equal to 1.4m. These results indicate that photosynthetic light saturation and compensation points of the plant in Lake Donghu should be ca. 0,9m and ca. 1.5m depths, respectively. Chlorophyll content, growth of main shoot, total shoot lengths and density of the plant all peaked at 1.2-1.3m simulated depths. These results indicate that P. maackianus responds to low light stress primarily by elongation of shoots, and increase of density. Its biomass growth and nutrient uptake rate did not correlate with the accelerated shoot growth. Below the light intensities of water deeper than 1.2-1.3m, shoot growth rate decreased. The flexible tolerant strategy of P. maackianus to low-light stress suggests that the disappearance of this plant from the lake was not mainly due to eutrophication-induced low-light stress.

Entrance-channel dependence of isospin effects on double n/p ratio in HIC

Within the hadronic transport model IBUU04, we investigate the effect of density-dependent symmetry energy on double neutron/proton (n/p) ratio of free nucleons in heavy ion collisions by taking four isotopic Sn+Sn reaction systems. Especially the entrance-channel asymmetry and impact-parameter dependence of the effect of symmetry energy are discussed. It is found that in both central and semi-central collisions the sensitivity of the double n/p ratio to the density-dependent symmetry energy is more pronounced in neutron-richer systems. Our results also indicate clearly that the effect of symmetry energy is stronger in central collisions than that in semi-central collisions.