Saddles in the energy landscape: extensivity and thermodynamic formalism

We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system size, as well as several approximations for the properties of low-order saddles (i.e., those with only a few unstable directions). We then cast the canonical partition function in a saddle-explicit form and develop, for the first time, a rigorous energy landscape approach capable of reproducing trends observed in simulations, in particular the temperature dependence of the energy and fractional order of sampled saddles.Comment: 4 pages, 1 figur

Identification, Genotyping and Antimicrobial Susceptibility Testing of Brucella spp. Isolated from Livestock in Egypt

Brucellosis is a highly contagious zoonosis worldwide with economic and public health impacts. The aim of the present study was to identify Brucella (B.) spp. isolated from animal populations located in different districts of Egypt and to determine their antimicrobial resistance. In total, 34-suspected Brucella isolates were recovered from lymph nodes, milk, and fetal abomasal contents of infected cattle, buffaloes, sheep, and goats from nine districts in Egypt. The isolates were identified by microbiological methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Differentiation and genotyping were confirmed using multiplex PCR for B. abortus, Brucella melitensis, Brucella ovis, and Brucella suis (AMOS) and Bruce-ladder PCR. Antimicrobial susceptibility testing against clinically used antimicrobial agents (chloramphenicol, ciprofloxacin, erythromycin, gentamicin, imipenem, rifampicin, streptomycin, and tetracycline) was performed using E-Test. The antimicrobial resistance-associated genes and mutations in Brucella isolates were confirmed using molecular tools. In total, 29 Brucella isolates (eight B. abortus biovar 1 and 21 B. melitensis biovar 3) were identified and typed. The resistance of B. melitensis to ciprofloxacin, erythromycin, imipenem, rifampicin, and streptomycin were 76.2%, 19.0%, 76.2%, 66.7%, and 4.8%, respectively. Whereas, 25.0%, 87.5%, 25.0%, and 37.5% of B. abortus were resistant to ciprofloxacin, erythromycin, imipenem, and rifampicin, respectively. Mutations in the rpoB gene associated with rifampicin resistance were identified in all phenotypically resistant isolates. Mutations in gyrA and gyrB genes associated with ciprofloxacin resistance were identified in four phenotypically resistant isolates of B. melitensis. This is the first study highlighting the antimicrobial resistance in Brucella isolated from different animal species in Egypt. Mutations detected in genes associated with antimicrobial resistance unravel the molecular mechanisms of resistance in Brucella isolates from Egypt. The mutations in the rpoB gene in phenotypically resistant B. abortus isolates in this study were reported for the first time in Egypt

Enumeration of distinct mechanically stable disk packings in small systems

We create mechanically stable (MS) packings of bidisperse disks using an algorithm in which we successively grow or shrink soft repulsive disks followed by energy minimization until the overlaps are vanishingly small. We focus on small systems because this enables us to enumerate nearly all distinct MS packings. We measure the probability to obtain a MS packing at packing fraction $\phi$ and find several notable results. First, the probability is highly nonuniform. When averaged over narrow packing fraction intervals, the most probable MS packing occurs at the highest $\phi$ and the probability decays exponentially with decreasing $\phi$. Even more striking, within each packing-fraction interval, the probability can vary by many orders of magnitude. By using two different packing-generation protocols, we show that these results are robust and the packing frequencies do not change qualitatively with different protocols.Comment: 4 pages, 3 figures, Conference Proceedings for X International Workshop on Disordered System

Effects of Medication on Respiration Pattern of Tranquilized White Mice

White mice of varying ages were given a definite amount of the tranquilizer, reserpine, over a three-week period. At the end of this period, respiration rates were determined by use of a physiograph with impedance pneumograph and small animal attachments. Mice were given, in addition to the tranquilizer, varying dosages of different medicinals, and their respiratory pattern was recorded. Such medicinals as thyroxin, streptomycin, vitamins E and C were given and in combination with sulfanilamide, nicotinamide, neonal, kayquinone, hykenone. Effects of multiple medications were noted and recorded. Reserpine, when given in all combinations, lowered the respiratory rate from that recorded when each drug was given alone. Vitamin C gave a stabilizing effect to the respiratory pattern when given in combination with other medications

Model-based Probe State Estimation and Crack Inverse Methods Addressing Eddy Current Probe Variability

Recent work on model-based inverse methods with eddy current inspections of surface breaking discontinuities has shown some sizing error due to variability in probes with the same design specifications [1]. This is an important challenge for model-based inversion crack sizing techniques, to be robust to the varying characteristics of eddy current probes found in the field [1-2]. In this paper, a model-based calibration process is introduced that estimates the state of the probe. First, a carefully designed surrogate model was built using VIC-3D® simulations covering the critical range of probe rotation angles, tilt in two directions, and probe offset (liftoff) for both tangential and longitudinal flaw orientations. Some approximations and numerical compromises in the model were made to represent tilt in two directions and reduce simulation time; however, this surrogate model was found to represent the key trends in the eddy current response for each of the four probe properties in experimental verification studies well. Next, this model was incorporated into an iterative inversion scheme during the calibration process, to estimate the probe state while also addressing the gain/phase fit and centering the calibration notch indication. Results are presented showing several examples of the blind estimation of tilt and rotation angle for known experimental cases with good agreement within +/- 2.5 degrees. The RMS error was found to be significantly reduced by fitting the probe state and, in many instances, probe state estimation addresses the previously un-modelled characteristics (model error) with real probe inversion studies. Additional studies are presented comparing the size of the calibration notch and the quality of the calibration fit, where calibrating with too small or too large a notch can produce poorer inversion results. Once the probe state is estimated, the final step is to transform the base crack inversion surrogate model and apply it for crack characterization. Because of the dimensionality of this problem, simulations were made at a limited set of select flaw sizes with varying length, depth and width, and an interpolation scheme was used to address the effect of the probe state at intermediate solution points. Using this process, results are presented demonstrating improved crack inversion performance for extreme probe states

Molecular structural order and anomalies in liquid silica

The present investigation examines the relationship between structural order, diffusivity anomalies, and density anomalies in liquid silica by means of molecular dynamics simulations. We use previously defined orientational and translational order parameters to quantify local structural order in atomic configurations. Extensive simulations are performed at different state points to measure structural order, diffusivity, and thermodynamic properties. It is found that silica shares many trends recently reported for water [J. R. Errington and P. G. Debenedetti, Nature 409, 318 (2001)]. At intermediate densities, the distribution of local orientational order is bimodal. At fixed temperature, order parameter extrema occur upon compression: a maximum in orientational order followed by a minimum in translational order. Unlike water, however, silica's translational order parameter minimum is broad, and there is no range of thermodynamic conditions where both parameters are strictly coupled. Furthermore, the temperature-density regime where both structural order parameters decrease upon isothermal compression (the structurally anomalous regime) does not encompass the region of diffusivity anomalies, as was the case for water.Comment: 30 pages, 8 figure

EUV spectroscopy of highly charged Sn13+-Sn15+ ions in an electron-beam ion trap

Extreme-ultraviolet (EUV) spectra of Sn13+-Sn15+ ions have been measured in an electron-beam ion trap (EBIT). A matrix inversion method is employed to unravel convoluted spectra from a mixture of charge states typically present in an EBIT. The method is benchmarked against the spectral features of resonance transitions in Sn13+ and Sn14+ ions. Three new EUV lines in Sn14+ confirm its previously established level structure. This ion is relevant for EUV nanolithography plasma but no detailed experimental data currently exist. We used the Cowan code for first line identifications and assignments in Sn15+. The collisional-radiative modeling capabilities of the Flexible Atomic Code were used to include line intensities in the identification process. Using the 20 lines identified, we have established 17 level energies of the 4p44d configuration as well as the fine-structure splitting of the 4p5 ground-state configuration. Moreover, we provide state-of-the-art ab initio level structure calculations of Sn15+ using the configuration-interaction many-body perturbation code ambit. We find that the here-dominant emission features from the Sn15+ ion lie in the narrow 2% bandwidth around 13.5 nm that is relevant for plasma light sources for state-of-the-art nanolithography

Rapamycin-coated expanded polytetrafluoroethylene bypass grafts exhibit decreased anastomotic neointimal hyperplasia in a porcine model

ObjectiveWe tested the hypothesis that rapamycin coated onto, and eluted from, expanded polytetrafluoroethylene (ePTFE) grafts would diminish neointimal hyperplasia in a porcine model.MethodsRapamycin (also called sirolimus) was coated onto the luminal surface of 6-mm-internal-diameter thin-walled ePTFE grafts by using an adhesive polymer that allows timed release of the drug. An adhesive polymer that allows timed release of rapamycin from ePTFE was developed with commercially available chemicals and applied on 6-mm ePTFE grafts. Graft integrity was characterized by scanning electron microscopy, and rapamycin levels were quantified by using high-performance liquid chromatography. Twenty-two mongrel pigs were randomized into three groups: untreated ePTFE (n = 6), adhesive-only coated ePTFE (n = 6), or adhesive- and rapamycin-coated ePTFE (n = 10). End-to-side unilateral aortoiliac bypasses were performed by using 6-mm-internal-diameter ePTFE grafts and standardized anastomotic lengths. Unilateral end-to-side aortoiliac ePTFE grafts (6-mm internal diameter) were inserted by using polypropylene sutures, 6-0 proximally and 7-0 distally; all anastomoses were 12 mm long. All animals received aspirin (325 mg orally) daily. All animals were given oral aspirin (325 mg) daily beginning on the day before surgery. At 28 days, the animals were killed, and the grafts were explanted in continuity with the adjacent aortic cuff and the outflow iliac artery. Variables compared between groups included graft patency, distal anastomotic length and cross-sectional narrowing, and intimal thickness at the arterial-graft junction indexed to the adjacent graft thickness. Microscopic analysis was performed with hematoxylin and eosin and Masson trichrome stains on paraffin sections. A pathologist blinded to experimental groups graded sections for collagen deposition, neointima formation, inflammatory cellular infiltrates, medial necrosis, and aneurysmal degeneration.ResultsAll animals survived until they were killed without clinical evidence of limb ischemia or graft infection. Preplanned t tests in the context of one-way analysis of variance showed no difference in outcome measures between the untreated ePTFE and adhesive-only coated ePTFE groups; therefore, they were combined in further comparisons with the adhesive- and rapamycin-coated ePTFE group. The Rapamycine eluting expanded polytetrafluoroethylene group had longer anastomoses (85.6% vs 60.6% of the initial anastomotic length maintained; P < .0001) and less cross-sectional narrowing in the outflow graft (16.2% vs 28.5%; P = .0007) when compared with the other two groups by using two-tailed Student t tests. There was no evidence of medial necrosis or aneurysmal degeneration. All patent grafts had complete endothelialization on hematoxylin and eosin sections. Rapamycin was detectable and quantifiable in the arterial wall at 28 days after implantation.ConclusionsRapamycin can be coated onto and eluted from ePTFE by using a nonionic polymer and a simple coating technique. At 4 weeks after implantation, the rapamycin-eluting ePTFE grafts demonstrate gross, pathologic, and morphometric features of diminished neointimal hyperplasia when compared with non–drug-eluting ePTFE. Four weeks after implantation in a porcine model, rapamycin-eluting ePTFE grafts demonstrated gross, pathologic, and morphometric features of diminished neointimal hyperplasia when compared with untreated and adhesive-only coated ePTFE grafts.Clinical RelevanceRapamycin-eluting ePTFE grafts decrease neointimal hyperplasia in a porcine model. Further studies are needed to evaluate whether patency will be improved. Rapamycin-eluting ePTFE grafts may allow the use of prosthetic grafts in situations in which autologous vein is unavailable and in which neointimal hyperplasia is pronounced, such as in small-diameter (<6-mm) vessels typical of infrapopliteal interventions