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At least 1,531 records · Page 85

Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease

Acute Lyme disease results from transmission of and infection by the bacterium Borrelia burgdorferi following a tick bite. During acute infection, bacteria can disseminate to the central nervous system (CNS) leading to the development of Lyme meningitis. Here we have analyzed pooled cerebrospinal fluid (CSF) allowing for a deep view into the proteome for a cohort of patients with early-disseminated Lyme disease and CSF inflammation leading to the identification of proteins that reflect host responses, which are distinct for subjects with acute Lyme disease. Additionally, we analyzed individual patient samples and quantified changes in protein abundance employing label-free quantitative mass spectrometry based methods. The measured changes in protein abundances reflect the impact of acute Lyme disease on the CNS as presented in CSF. We have identified 89 proteins that differ significantly in abundance in patients with acute Lyme disease. A number of the differentially abundant proteins have been found to be localized to brain synapse and thus constitute important leads for better understanding of the neurological consequence of disseminated Lyme disease.

Borreliosis, Lyme Megingitis↗

Statistical Inference Over Persistent Homology Predicts Fluid Flow in Porous Media

Here, we statistically infer fluid flow and transport properties of porous materials based on their geometry and connectivity, without the need for detailed We summarize structure by persistent homology and then determines the similarity of structures using image analysis and statistics. Longer term, this may enable quick and automated categorization of rocks into known archetypes. We first compute persistent homology of binarized 3D images of material subvolume samples. The persistence parameter is the signed Euclidean distance from inferred material interfaces, which captures the distribution of sizes of pores and grains. Each persistence diagram is converted into an image vector. Here, we infer structural similarity by calculating image similarity. For each image vector, we compute principal components to extract features. We fit statistical models to features estimates material permeability, tortuosity, and anisotropy. We develop a Structural SIMilarity index to determine statistical representative elementary volumes.

36 MATERIALS SCIENCE↗

From Fluid Flow to Coupled Processes in Fractured Rock: Recent Advances and New Frontiers

Abstract Quantitative predictions of natural and induced phenomena in fractured rock is one of the great challenges in the Earth and Energy Sciences with far‐reaching economic and environmental impacts. Fractures occupy a very small volume of a subsurface formation but often dominate fluid flow, solute transport and mechanical deformation behavior. They play a central role in CO 2 sequestration, nuclear waste disposal, hydrogen storage, geothermal energy production, nuclear nonproliferation, and hydrocarbon extraction. These applications require predictions of fracture‐dependent quantities of interest such as CO 2 leakage rate, hydrocarbon production, radionuclide plume migration, and seismicity; to be useful, these predictions must account for uncertainty inherent in subsurface systems. Here, we review recent advances in fractured rock research covering field‐ and laboratory‐scale experimentation, numerical simulations, and uncertainty quantification. We discuss how these have greatly improved the fundamental understanding of fractures and one's ability to predict flow and transport in fractured systems. Dedicated field sites provide quantitative measurements of fracture flow that can be used to identify dominant coupled processes and to validate models. Laboratory‐scale experiments fill critical knowledge gaps by providing direct observations and measurements of fracture geometry and flow under controlled conditions that cannot be obtained in the field. Physics‐based simulation of flow and transport provide a bridge in understanding between controlled simple laboratory experiments and the massively complex field‐scale fracture systems. Finally, we review the use of machine learning‐based emulators to rapidly investigate different fracture property scenarios and accelerate physics‐based models by orders of magnitude to enable uncertainty quantification and near real‐time analysis.

58 GEOSCIENCES↗

Extended harmonic mapping connects the equations in classical, statistical, fluid, quantum physics and general relativity

Abstract One potential pathway to find an ultimate rule governing our universe is to hunt for a connection among the fundamental equations in physics. Recently, Ren et al. reported that the harmonic maps with potential introduced by Duan, named extended harmonic mapping (EHM), connect the equations of general relativity, chaos and quantum mechanics via a universal geodesic equation. The equation, expressed as Euler–Lagrange equations on the Riemannian manifold, was obtained from the principle of least action. Here, we further demonstrate that more than ten fundamental equations, including that of classical mechanics, fluid physics, statistical physics, astrophysics, quantum physics and general relativity, can be connected by the same universal geodesic equation. The connection sketches a family tree of the physics equations, and their intrinsic connections reflect an alternative ultimate rule of our universe, i.e. , the principle of least action on a Finsler manifold.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter

We report a novel technical approach for subcritical fluid extraction (SFE) for organic matter characterization in complex matrices such as soil. The custom platform combines on-line SFE with micro-solid phase extraction, nano liquid chromatography (LC), electrospray ionization and Fourier transform mass spectrometry (SFE-LC-FTMS). We demonstrated the utility of SFE-LC-FTMS, including results from both Orbitrap and FTICR MS, for analysis of complex mixtures of organic compounds in a solid matrix by characterizing soil organic matter in peat, a high-carbon soil. For example, in a single experiment, >6000 molecular formulas can be assigned based upon FTICR MS data from 1–50 μL of soil samples (roughly 1–50 mg of soil, dependent on soil density), nearly twice that typically obtained from direct infusion liquid solvent extraction (LSE) from an order of magnitude larger volume of the same soil. The detected species consisted predominately of lipid-like, lignin-like and protein-like compounds, based on their O/C and H/C ratios, with predominantly CHO and CHONP molecular compositions. These results clearly demonstrate that SFE has the potential to effectively extract a variety of molecular species and could become an important member of a suite of extraction methods for studying SOM and other natural organic matter. This is especially true when comprehensive coverage, minimal sample volumes, and high sensitivity are required, or when the presence of organic solvent residue in residual soil is problematic. Lastly, the SFE based extraction protocol could potentially enable spatially resolved characterization of organic matter in soil with a resolution of ~1 mm3 to facilitate studies probing the spatial heterogeneity of soil.

54 ENVIRONMENTAL SCIENCES↗

Phase-shift effects on growth and transport of dust particles in VHF capacitively coupled silane discharges: Two dimensional fluid simulation

A two-dimensional (2D) self-consistent fluid model is developed to describe the formation, subsequent growth, transport, and charging mechanisms of nanoparticles in a capacitively coupled silane discharge applied by two very high frequency (VHF) sources with phase shift. In this discharge process, large anions are produced by a series of chemical reactions of anions with silane molecules, while the lower limit of the initial nanoparticles are taken as large anions (Si{sub 12}H{sub 25}{sup -} and Si{sub 12}H{sub 24}{sup -}) to directly link the coagulation module with the nucleation module. And then, by using the coagulation module, the particle number density quickly decreases over several orders of magnitude, whereas the particle size strongly increases. We investigate in particular the growth of the nanoparticles ranging in size from {approx}1 to 50 nm in coagulation processes. The influences of controlled phase shifts between VHF (50 MHz) voltages on the electron density, electron temperature, nanoparticle uniformity, and deposition rate, are carefully studied. It is found from our simulation that the plasma density and nanoparticle density become center high and more uniform as the phase shift increases from 0 to 180 deg. Moreover, the role of phase-shift control in the silane discharge diluted with hydrogen gas is also discussed.

36 MATERIALS SCIENCE↗

Reduced fluid-kinetic equations for low-frequency dynamics, magnetic reconnection, and electron heating in low-beta plasmas

A minimal model for magnetic reconnection and, generally, low-frequency dynamics in low-beta plasmas is proposed. The model combines analytical and computational simplicity with physical realizability: it is a rigorous limit of gyrokinetics for plasma beta of order the electron-ion mass ratio. The model contains collisions and can be used both in the collisional and collisionless reconnection regimes. It includes gyrokinetic ions (not assumed cold) and allows for the topological rearrangement of the magnetic field lines by either resistivity or electron inertia, whichever predominates. The two-fluid dynamics are coupled to electron kinetics--electrons are not assumed isothermal and are described by a reduced drift-kinetic equation. The model, therefore allows for irreversibility and conversion of magnetic energy into electron heat via parallel phase mixing in velocity space. An analysis of the exchanges between various forms of free energy and its conversion into electron heat is provided. It is shown how all relevant linear waves and regimes of the tearing instability (collisionless, semicollisional, and fully resistive) are recovered in various limits of our model. An efficient way to simulate our equations numerically is proposed, via the Hermite representation of the velocity space. It is shown that small scales in velocity space will form, giving rise to a shallow Hermite-space spectrum, whence it is inferred that, for steady-state or sufficiently slow dynamics, the electron heating rate will remain finite in the limit of vanishing collisionality.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A paradigm for the stability of the plasma sheath against fluid perturbations

The stability of the sheath created by a collisionless, unmagnetized plasma interacting with a material boundary at floating potential is studied with a fluid plasma model. In the limit where the sonic sheath ion flow is neglected, ion perturbations can be unstable to the Rayleigh-Taylor instability, driven by the sheath ion density gradient and electric field. The sonic sheath ion flow, however, is very effective in stabilizing these modes by convective stabilization. Therefore, within the assumptions of our model and the parameters considered, the sheath is stable.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fluid Model Analysis of the Distribution of the Negative Ion Density before the Extraction from a Tandem Type of a Plasma Source

Unified description of the expansion (through a magnetic filter) and extraction regions, including also the driver, of volume-production based sources of negative hydrogen ions is presented in the study. The model is one-dimensional, developed within the fluid plasma theory. It covers description of both the second chamber of the tandem sources and a single inductively-driven (with a planar coil) discharge of a matrix source. Four parameters have been varied in the analysis of the results: type, position and magnitude of the filter field and rf power applied for the discharge maintenance. The obtained results for the spatial distribution of the plasma parameters as well as for the electronegativity, for the negative ion beam current and its ratio to the electron current at the position of the extraction are discussed regarding optimum conditions for the source operation. The conclusion is that a magnetic field extended over a large region till the extraction favors locality in the discharge behavior and, respectively, the local production of the negative ions. This leads to high density of the extracted negative ion beam current at reasonable values of its ratio to the electron current density.

43 PARTICLE ACCELERATORS↗

Two-fluid electromagnetic simulations of plasma-jet acceleration with detailed equation-of-state

We describe a new particle-based two-fluid fully electromagnetic algorithm suitable for modeling high density (n{sub i} {approx} 10{sup 17} cm{sup -3}) and high Mach number laboratory plasma jets. In this parameter regime, traditional particle-in-cell (PIC) techniques are challenging due to electron timescale and lengthscale constraints. In this new approach, an implicit field solve allows the use of large timesteps while an Eulerian particle remap procedure allows simulations to be run with very few particles per cell. Hall physics and charge separation effects are included self-consistently. A detailed equation of state (EOS) model is used to evolve the ion charge state and introduce non-ideal gas behavior. Electron cooling due to radiation emission is included in the model as well. We demonstrate the use of these new algorithms in 1D and 2D Cartesian simulations of railgun (parallel plate) jet accelerators using He and Ar gases. The inclusion of EOS and radiation physics reduces the electron temperature, resulting in higher calculated jet Mach numbers in the simulations. We also introduce a surface physics model for jet accelerators in which a frictional drag along the walls leads to axial spreading of the emerging jet. The simulations demonstrate that high Mach number jets can be produced by railgun accelerators for a variety of applications, including high energy density physics experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

1-D fluid model of atmospheric-pressure rf He+O{sub 2} cold plasmas: Parametric study and critical evaluation

In this paper atmospheric-pressure rf He+O{sub 2} cold plasmas are studied by means of a 1-D fluid model. 17 species and 60 key reactions selected from a study of 250+ reactions are incorporated in the model. O{sub 2}{sup +}, O{sub 3}{sup -}, and O are the dominant positive ion, negative ion, and reactive oxygen species, respectively. Ground state O is mainly generated by electron induced reactions and quenching of atomic and molecular oxygen metastables, while three-body reactions leading to the formation of O{sub 2} and O{sub 3} are the main mechanisms responsible for O destruction. The fraction of input power dissipated by ions is {approx}20%. For the conditions considered in the study {approx}6% of the input power is coupled to ions in the bulk and this amount will increase with increasing electronegativity. Radial and electrode losses of neutral species are in most cases negligible when compared to gas phase processes as these losses are diffusion limited due to the large collisionality of the plasma. The electrode loss rate of neutral species is found to be nearly independent of the surface adsorption probability p for p > 0.001 and therefore plasma dosage can be quantified even if p is not known precisely.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Neutron field parameter measurements on the JET tokamak by means of super-heated fluid detectors

The neutron field parameters (fluence and energy distribution) at a specific location outside the JET Torus Hall have been measured by means of super-heated fluid detectors (or 'bubble detectors') in combination with an independent, time-of-flight, technique. The bubble detector assemblies were placed at the end of a vertical line of sight at about 16 m from the tokamak mid plane. Spatial distributions of the neutron fluence along the radial and toroidal directions have been obtained using two-dimensional arrays of bubble detectors. Using a set of three bubble detector spectrometers the neutron energy distribution was determined over a broad energy range, from about 10 keV to above 10 MeV, with an energy resolution of about 30% at 2.5 MeV. The very broad energy response allowed for the identification of energy features far from the main fusion component (around 2.45 MeV for deuterium discharges).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Computational fluid dynamics and frequency-dependent finite-difference time-domain method coupling for the interaction between microwaves and plasma in rocket plumes

Under certain conditions during rocket flights, ionized exhaust plumes from solid rocket motors may interfere with radio frequency transmissions. To understand the relevant physical processes involved in this phenomenon and establish a prediction process for in-flight attenuation levels, we attempted to measure microwave attenuation caused by rocket exhaust plumes in a sea-level static firing test for a full-scale solid propellant rocket motor. The microwave attenuation level was calculated by a coupling simulation of the inviscid-frozen-flow computational fluid dynamics of an exhaust plume and detailed analysis of microwave transmissions by applying a frequency-dependent finite-difference time-domain method with the Drude dispersion model. The calculated microwave attenuation level agreed well with the experimental results, except in the case of interference downstream the Mach disk in the exhaust plume. It was concluded that the coupling estimation method based on the physics of the frozen plasma flow with Drude dispersion would be suitable for actual flight conditions, although the mixing and afterburning in the plume should be considered depending on the flow condition.

42 ENGINEERING↗

Verification of electromagnetic fluid-kinetic hybrid electron model in global gyrokinetic particle simulation

The fluid-kinetic hybrid electron model is verified in global gyrokinetic particle simulation of linear electromagnetic drift-Alfvenic instabilities in tokamak. In particular, we have recovered the {beta}-stabilization of the ion temperature gradient mode, transition to collisionless trapped electron mode, and the onset of kinetic ballooning mode as {beta}{sub e} (ratio of electron kinetic pressure to magnetic pressure) increases.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Quantum fluid model of coherent stimulated radiation by a dense relativistic cold electron beam

Using a quantum fluid model, the linear dispersion relation for FEL pumped by a short wavelength laser wiggler is deduced. Subsequently, a new quantum corrected resonance condition is obtained. It is shown that, in the limit of low energy electron beam and low frequency pump, the quantum recoil effect can be neglected, recovering the classical FEL resonance condition, k{sub s}=4k{sub w}γ{sup 2}. On the other hand, for short wavelength and high energy electron beam, the quantum recoil effect becomes strong and the resonance condition turns into k{sub s}=2√(k{sub w}/λ{sub c})γ{sup 3/2}, with λ{sub c} being the reduced Compton wavelength. As a result, a set of nonlinear coupled equations, which describes the quantum FEL dynamics as a three-wave interaction, is obtained. Neglecting wave propagation effects, this set of equations is solved numerically and results are presented.

43 PARTICLE ACCELERATORS↗

Statistical thermodynamics for a self-gravitating fluid of rotating particles

Systems with long-range interactions (those which decay at large distances as r{sup -l}, with l≥d, where d is the dimensionality of the considered space), like gravitational or charged ones, present difficulties when treated by conventional statistical mechanics perturbation methods. In this work a self-gravitating fluid of rotating spherical particles is considered. The corresponding inter-particle potential model is a long-ranged one and was obtained from the application of the Newtonian limit to the Kerr metric. This potential has been expressed as a finite sum of hard-core Yukawa potentials. This new potential mimics the original long-ranged one and can be treated with conventional statistical mechanics methods. The first-order mean spherical approximation is applied to this potential to obtain the thermodynamic response functions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Properties of the Lennard-Jones dimeric fluid in two dimensions: An integral equation study

The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resummed thermodynamic perturbation theory for bond cooperativity in associating fluids with small bond angles: Effects of steric hindrance and ring formation

In this paper we develop a thermodynamic perturbation theory for two site associating fluids which exhibit bond cooperativity (system energy is non-pairwise additive). We include both steric hindrance and ring formation such that the equation of state is bond angle dependent. Here, the bond angle is the angle separating the centers of the two association sites. As a test, new Monte Carlo simulations are performed, and the theory is found to accurately predict the internal energy as well as the distribution of associated clusters as a function of bond angle.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗