Podcasts about isothermal

Finite Shock Model of Density Fluctuations in Isothermal Turbulence by Branislav Rabatin et al. on Monday 10 October The probability distribution of density in isothermal, supersonic, turbulent gas is approximately lognormal. This behaviour can be traced back to the shock waves travelling through the medium, which randomly adjust the density by a random factor of the local sonic Mach number squared. Provided a certain parcel of gas experiences a large number of shocks, due to the central limit theorem, the resulting distribution for density is lognormal. We explore a model in which parcels of gas undergo finite number of shocks before relaxing to the ambient density, causing the distribution for density to deviate from a lognormal. We confront this model with numerical simulations with various r.m.s. Mach numbers ranging from subsonic as low as 0.1 to supersonic at 25. We find that the fits to the finite formula are an order of magnitude better than a lognormal. The model naturally extends even to subsonic flows, where no shocks exist. arXiv: http://arxiv.org/abs/http://arxiv.org/abs/2210.03597v1

Finite Shock Model of Density Fluctuations in Isothermal Turbulence by Branislav Rabatin et al. on Monday 10 October The probability distribution of density in isothermal, supersonic, turbulent gas is approximately lognormal. This behaviour can be traced back to the shock waves travelling through the medium, which randomly adjust the density by a random factor of the local sonic Mach number squared. Provided a certain parcel of gas experiences a large number of shocks, due to the central limit theorem, the resulting distribution for density is lognormal. We explore a model in which parcels of gas undergo finite number of shocks before relaxing to the ambient density, causing the distribution for density to deviate from a lognormal. We confront this model with numerical simulations with various r.m.s. Mach numbers ranging from subsonic as low as 0.1 to supersonic at 25. We find that the fits to the finite formula are an order of magnitude better than a lognormal. The model naturally extends even to subsonic flows, where no shocks exist. arXiv: http://arxiv.org/abs/http://arxiv.org/abs/2210.03597v1

Density distribution function of a self-gravitating isothermal turbulent fluid in the context of molecular clouds ensembles -- III Virial analysis by S. Donkov et al. on Sunday 25 September In the present work we apply virial analysis to the model of self-gravitating turbulent cloud ensembles introduced by Donkov & Stefanov in two previous papers, clarifying some aspects of turbulence and extending the model to account not only for supersonic flows but for trans- and subsonic ones as well. Make use of the Eulerian virial theorem at an arbitrary scale, far from the cloud core, we derive an equation for the density profile and solve it in approximate way. The result confirms the solution $varrho(ell)=ell^{-2}$ found in the previous papers. This solution corresponds to three possible configurations for the energy balance. For trans- or subsonic flows, we obtain a balance between the gravitational and thermal energy (Case 1) or between the gravitational, turbulent and thermal energies (Case 2) while for supersonic flows, the possible balance is between the gravitational and turbulent energy (Case 3). In Cases 1 and 2 the energy of the fluid element can be negative or zero end thus the solution is dynamically stable and shall be long lived. In Case 3 the energy of the fluid element is positive or zero, i.e., the solution is unstable or at best marginally bound. At scales near the core, one cannot neglect the second derivative of the moment of inertia of the gas, which prevents derivation of an analytic equation for the density profile. However, we obtain that gas near the core is not virialized and its state is marginally bound since the energy of the fluid element vanishes. arXiv: http://arxiv.org/abs/http://arxiv.org/abs/2203.04005v3

Density distribution function of a self-gravitating isothermal compressible turbulent fluid in the context of molecular clouds ensembles -- III Virial analysis by S. Donkov et al. on Wednesday 21 September In the present work we apply virial analysis to the model of self-gravitating turbulent cloud ensembles introduced by Donkov & Stefanov in two previous papers, clarifying some aspects of turbulence and extending the model to account not only for supersonic flows but for trans- and subsonic ones as well. Make use of the Eulerian virial theorem at an arbitrary scale, far from the cloud core, we derive an equation for the density profile and solve it in approximate way. The result confirms the solution $varrho(ell)=ell^{-2}$ found in the previous papers. This solution corresponds to three possible configurations for the energy balance. For trans- or subsonic flows, we obtain a balance between the gravitational and thermal energy (Case 1) or between the gravitational, turbulent and thermal energies (Case 2) while for supersonic flows, the possible balance is between the gravitational and turbulent energy (Case 3). In Cases 1 and 2 the energy of the fluid element can be negative or zero end thus the solution is dynamically stable and shall be long lived. In Case 3 the energy of the fluid element is positive or zero, i.e., the solution is unstable or at best marginally bound. At scales near the core, one cannot neglect the second derivative of the moment of inertia of the gas, which prevents derivation of an analytic equation for the density profile. However, we obtain that gas near the core is not virialized and its state is marginally bound since the energy of the fluid element vanishes. arXiv: http://arxiv.org/abs/http://arxiv.org/abs/2203.04005v2

Our last episode of the year and we look back at the two big tornado outbreaks in the last ten days. The Storm Prediction Center in Norman, Oklahoma was once again spot on with the severe weather forecast. Bobby talks about the rare snow event in Portland with an "Anafront" and the atmosphere going "Isothermal". Going forward into 2022, B Squared will have a different format that we feel will better suit the show and our listeners. Merry Christmas and Happy New Year!

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.25.354415v1?rss=1 Authors: Heier, J. A., Pokutta, S., Dale, I. W., Kim, S. K., Hinck, A. P., Weis, W. I., Kwiatkowski, A. V. Abstract: Alpha-catenin binds directly to beta-catenin and connects the cadherin-catenin complex to the actin cytoskeleton. Tension regulates alpha-catenin conformation: actomyosin-generated force stretches the middle(M)-region to relieve autoinhibition and reveal a binding site for the actin-binding protein vinculin. Here we describe the biochemical properties of alpha-T(testes)-catenin, an alpha-catenin isoform critical for cardiac function, and how intramolecular interactions regulate vinculin binding autoinhibition. Isothermal titration calorimetry (ITC) showed that alpha-T-catenin binds the beta-catenin/N-cadherin complex with a similar low nanomolar affinity to that of alpha-E-catenin. Limited proteolysis revealed that the alpha-T-catenin M-region adopts a more open conformation than alpha-E-catenin. The alpha-T-catenin M-region binds the vinculin N-terminus with low nanomolar affinity, indicating that the isolated alpha-T-catenin M-region is not autoinhibited and thereby distinct from alpha-E-catenin. However, the alpha-T-catenin head (N- and M-regions) binds vinculin 1000-fold more weakly (low micromolar affinity), indicating that the N-terminus regulates M-region binding to vinculin. In cells, alpha-T-catenin recruitment of vinculin to cell-cell contacts requires the actin-binding domain and actomyosin-generated tension, indicating that force regulates vinculin binding. Together, our results indicate that the alpha-T-catenin N-terminus is required to maintain M-region autoinhibition and modulate vinculin binding. We postulate that the unique molecular properties of alpha-T-catenin allow it to function as a scaffold for building specific adhesion complexes. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.24.265165v1?rss=1 Authors: Busath, D. D., McGuire, K. L., Ess, D. H., Smit, P., Harrison, R. G., Hill, J. T. Abstract: Copper(II) is known to bind in the influenza virus His37 cluster in the homotetrameric M2 proton channel and block the proton current needed for uncoating. Copper complexes based on iminodiacetate also block the M2 proton channel and show reduced cytotoxicity and zebrafish-embryo toxicity. In voltage-clamp oocyte studies using the ubiquitous amantadine-insensitive M2 S31N variant, the current block showed fast and slow phases in contrast to the single phase found for amantadine block of WT M2. Here we evaluate the mechanism of block by copper adamantyl iminodiacitate (Cu(AMT-IDA)) and copper cyclooctyl iminodiacitate (Cu(CO-IDA)) complexes and address whether the complexes can covalently bind to one or more of the His37 imidazoles. The current traces were fitted to parametrized master equations. The energetics of binding and the rate constants suggest that the first step is copper-complex binding within the channel and the slow step in the current block is the covalent bond formation between copper complex and histidine. Isothermal titration calorimetry (ITC) indicates that a single imidazole binds strongly to the copper complexes. Structural optimization using density functional theory (DFT) reveals that the complexes fit inside the channel and project the Cu(II) towards the His37 cluster allowing one imidazole to form a covalent bond with the Cu(II). Electrophysiology and DFT studies also show that the complexes block the G34E amantadine-resistant mutant in spite of some crowding in the binding site by the glutamates. Copy rights belong to original authors. Visit the link for more info

The past decade has witnessed a dramatic increase of anti-retroviral treatment of Human Immunodeficiency Virus (HIV) infected patients in many African countries. Due to costs and sophistication of currently available commercial viral load assays, little attention has been paid to therapy monitoring through measurement of plasma viral load, a challenge that could reverse achievements already made against HIV/AIDS infection. Loop-mediated isothermal amplification (LAMP) has been shown to be simple, rapid and cost-effective, characteristics which make this assay ideal for viral load monitoring in resource limited settings. The aim of this study was to establish and evaluate LAMP for quantitative detection of HIV-1 group M virus in blood and plasma. Cell culture supernatants of HIV-1 subtype B (IIIB and MVP899-87) viruses were used to optimize reaction conditions and to test primer suitability. Together with HIV-1 M non-B subtypes, HIV-1 group O and HIV-2, the cell culture supernatants were used to evaluate the performance of LAMP, to generate a model for viral load estimation and to establish the limits of the assay. A panel of 467 clinical samples was analyzed (282 plasmas and 121 dry blood spots from Kenya and 112 plasmas from Germany) and the results obtained by LAMP were compared to those generated by the Abbott Real Time HIV-1 assay, an established commercial viral load quantification test. A linear regression equation was generated from time to detection values and used to estimate the viral loads of the samples by the LAMP assay. Kenyan samples were tested in Nairobi and Munich. LAMP primers targeting the integrase of the pol gene were found to be the most suitable compared to further 3 primer sets tested. Lower limit of detection (LLOD) of 1,200 copies/mL and lower limit of quantification (LLOQ) of 9,800 copies/mL were determined as suitable thresholds for quantitative estimations of the LAMP viral loads. Sensitivities of 82 and 86% (Kenyan samples) and 93% (German samples) and specificities of 99 and 100% were realized with plasma samples. The study also realized a sensitivity of 76% and specificity of 77% with dry blood spot samples from Kenya. In conclusion, LAMP assay shows obvious potential for diagnostic application in semi-quantification of HIV-1 group M viral load in resource limited countries. However there is a need for further improvement of primers in respect to detection of HIV-1 non-B viruses and evaluation of dry blood spot samples to ensure that more reliable results are obtained.

This is the 50th anniversary year for the North Carolina Community College System and we are profiling every member college to celebrate. Tonight Rick Sullivan visits Isothermal Community College… a school with a popular international business partner, and a different way of looking at its educational mission.

This is the 50th anniversary year for the North Carolina Community College System and we are profiling every member college to celebrate. Tonight Rick Sullivan visits Isothermal Community College… a school with a popular international business partner, and a different way of looking at its educational mission.

The volume of a tube is expanded stepwise, keeping the temperature constant. In a pV diagram, pressure is depicted as a function of volume.

The volume of a tube is expanded stepwise, keeping the temperature constant. In a pV diagram, pressure is depicted as a function of volume.

Loop-mediated isothermal amplification (LAMP) is a powerful, innovative gene amplification technique which is emerging as an easy to perform and rapid diagnostic tool for detection and identification of microbial diseases. Early and accurate detection is of paramount importance concerning the diagnosis of the highly contagious bacteria Yersinia ruckeri and Renibacterium salmoninarum. An easy to perform diagnostic technique is also required if assays should be carried out in field inquiries. The method provides a single step, reaction tube assay only requiring a temperature-controlled water bath. In the experiments of the presented study, LAMP assays were conducted for Y. ruckeri (the pathogen causing Enteric Redmouth Disease, ERM) and R. salmoninarum (the pathogen causing Bacterial Kidney Disease, BKD). In the case of ERM, the amplified target was a sequence stretch of the gene yruI/yruR encoding the quorum sensing system which controls the expression of virulence genes. In the case of BKD, a sequence stretch of the gene encoding the major soluble antigen protein (p57) in R. salmoninarum was amplified. This protein indicates an active infection because it is the predominant cell surface-associated and secreted protein by the bacterium. The newly established LAMP assays for ERM and BKD enabled amplification of a stretch of each target gene at a temperature of 63°C in less than one hour, with no need of thermal cycling. Assays are carried out with a reaction mix containing four specific primers, the sample and Bst DNA polymerase. Amplification products were detected by visual inspection, agarose gel electrophoresis, and in real-time using a turbidimeter. Assays specificity were demonstrated using DNAs from other related bacteria yielding no amplification product, and by restriction analysis with HphI and EcoRV enzymes producing a specific bands´ pattern of the amplified products. Compared to regular PCR-based detection methods, the developed LAMP assays were consistently faster and ten-fold more sensitive. A safe detection of the specific sequence stretches with high specificity and efficiency was possible using DNA isolated both from bacterial extracts and from clinical fish specimens. These findings showed that LAMP assays are more sensitive than other detection methods such as time consuming culture methods and PCR assays. In conclusion, for the first time LAMP assays developed and optimised to detect Y. ruckeri and R. salmoninarum were introduced as diagnostic tools. In comparison with the performance of already established diagnostic methods, LAMP assays are superior in sensitivity, rapidness, specificity, and cost-efficiency. Both assays are highly appropriate for application in field inquiries to monitor the spread of ERM and BKD.

Background: Koi Herpesvirus (KHV) affects both juvenile and adult common carp and koi, and is especially lethal to fry. The high mortalities caused by the disease have had a negative impact on the international koi trade. Different diagnostic techniques have been used to detect KHV, including: isolation of the virus in cell culture, electron microscopy, several PCR tests, ELISA and in situ hybridisation. All of these methods are time consuming, laborious and require specialised equipment. Results: A rapid field diagnosis of KHV in common and koi carp was developed using loop-mediated isothermal amplification (LAMP). The LAMP reaction rapidly amplified nucleic acid with high specificity and efficiency under isothermal conditions using a simple water bath. Two methods of extracting DNA from host tissue were compared: extraction by boiling and by using a commercial extraction kit. A set of six primers - two inner primers, two outer primers and two loop primers - was designed from a KHV amplicon. The reaction conditions were optimised for detection of KHV in 60 min at 65 degrees C using Bst (Bacillus stearothermophilus) DNA polymerase. When visualised by gel electrophoresis, the products of the KHV LAMP assay appeared as a ladder pattern, with many bands of different sizes from 50 base-pairs (bp) up to the loading well. The KHV LAMP product could also be simply detected visually by adding SYBR Green I to the reaction tube and observing a colour change from orange to green. All samples positive for KHV by visual detection were confirmed positive by gel electrophoresis. The KHV LAMP had the same sensitivity as a standard PCR assay for the detection of KHV. Conclusion: This paper describes an accelerated LAMP assay for diagnosis of KHV. The entire procedure took only 90 minutes to produce a result: 15 minutes for DNA extraction; 60 min for the LAMP reaction; 2 min for visual detection using SYBR Green I. The test can be used under field conditions because the only equipment it requires is a water bath.

The viscosity-temperature relationships of five melts on the join Na2Si2O2-Na4Al2O5 (5, 10, 20, 30 and 40 mole percent Na4Al2O5) have been measured in air, at 1 atm and 1000–1350°C with a concentric cylinder viscometer. All the melts on this join of constant bulk polymerization behave as Newtonian fluids, in the range of shear rates investigated, and the melts exhibit Arrhenian viscosity-temperature relationships. Isothermal viscosities on this join initially decrease and then increase with increasing mole percent Na4Al2O5. The minimum viscosity occurs near 20 mole percent Na4Al2O5 at 1000°C and moves to higher Na4Al2O5 content with increasing temperature. The observation of a viscosity minimum along the join Na2Si2-O5-Na4Al2O5 is not predicted based on earlier viscosity data for the system Na2O-Al2O3-SiO2 (RlEBLlNG, 1966) or based on calculation methods derived from this and other data (Bottinga and Weill, 1972). This unexpected behavior in melt viscosity-temperature relations emphasizes the need for a more complete data set in simple silicate systems. Previous spectroscopic investigation of melts on the join Na22Si2O5-Na4Al2O5 offer a structural explanation for the observed viscosity data in terms of a disproportionation reaction involving polyanionic units. Macroscopically, the viscosity data may be qualitatively reconciled with the configurational entropy model for viscous flow (Richet, 1984).