Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry

Motivation: We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations. Results: Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a dataset onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service

Measurement and Control of Oxygen Partial Pressure in an Electrostatic Levitator

Recently the NASA Marshall Space Flight Center electrostatic levitation (ESL) laboratory has been upgraded to include an oxygen control system. This system allows the oxygen partial pressure within the vacuum chamber to be measured and controlled, at elevated temperatures, theoretically in the range from 10(exp -36) to 10(exp 0) bar. The role of active surface agents in liquid metals is fairly well known; however, published surface tension data typically has large scatter, which has been hypothesized to be caused by the presence of oxygen. The surface tension of metals is affected by even a small amount of adsorption of oxygen. It has even been shown that oxygen partial pressures may need to be as low as 10(exp -24) bar to avoid oxidation. While electrostatic levitation is done under high vacuum, oxide films or dissolved oxygen may have significant effects on materials properties, such as surface tension and viscosity. Therefore, the ability to measure and control the oxygen partial pressure within the chamber is highly desirable. The oxygen control system installed at MSFC contains a potentiometric sensor, which measures the oxygen partial pressure, and an oxygen ion pump. In the pump, a pulse-width modulated electric current is applied to yttrium-stabilized zirconia, resulting in oxygen transfer into or out of the system. Also part of the system is a control unit, which consists of temperature controllers for the sensor and pump, PID-based current loop for the ion pump, and a control algorithm. This system can be used to study the effects of oxygen on the thermophysical properties of metals, ceramics, glasses, and alloys. It can also be used to provide more accurate measurements by processing the samples at very low oxygen partial pressures. The oxygen control system will be explained in more detail and an overview of its use and limitations in an electrostatic levitator will be described. Some preliminary measurements have been made, and the results to date will be provided

Electrostatic Levitation for Studies of Additive Manufacturing Materials for Extreme Environments

The electrostatic levitation (ESL) laboratory at NASA's Marshall Space Flight Center (MSFC) is a national resource for researchers developing advanced materials for new technologies. Electrostatic levitation minimizes gravitational effects and allows materials to be studied without contact with a container or data-gathering instrumentation

Electrostatic Levitation for Studies of Additive Manufactured Materials

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Electrostatic Levitation for Studies of Additive Manufactured Materials

The electrostatic levitation (ESL) laboratory at NASA's Marshall Space Flight Center is a unique facility for investigators studying high temperature materials. The laboratory boasts two levitators in which samples can be levitated, heated, melted, undercooled, and resolidified. Electrostatic levitation minimizes gravitational effects and allows materials to be studied without contact with a container or instrumentation. The lab also has a high temperature emissivity measurement system, which provides normal spectral and normal total emissivity measurements at use temperature. The ESL lab has been instrumental in many pioneering materials investigations of thermophysical properties, e.g., creep measurements, solidification, triggered nucleation, and emissivity at high temperatures. Research in the ESL lab has already led to the development of advanced high temperature materials for aerospace applications, coatings for rocket nozzles, improved medical and industrial optics, metallic glasses, ablatives for reentry vehicles, and materials with memory. Modeling of additive manufacturing materials processing is necessary for the study of their resulting materials properties. In addition, the modeling of the selective laser melting processes and its materials property predictions are also underway. Unfortunately, there is very little data for the properties of these materials, especially of the materials in the liquid state. Some method to measure thermophysical properties of additive manufacturing materials is necessary. The ESL lab is ideal for these studies. The lab can provide surface tension and viscosity of molten materials, density measurements, emissivity measurements, and even creep strength measurements. The ESL lab can also determine melting temperature, surface temperatures, and phase transition temperatures of additive manufactured materials. This presentation will provide background on the ESL lab and its capabilities, provide an approach to using the ESL in supporting the development and modeling of the selective laser melting process for metals, and provide an overview of the results to date

The NASA MSFC Electrostatic Levitation (ESL) Laboratory: Summary of Capabilities, Recent Upgrades, and Future Work

The NASA Marshall Space Flight Center (MSFC) electrostatic levitation (ESL) laboratory has a long history of providing materials research and thermophysical property data. A summary of the labs capabilities, recent upgrades, and ongoing and future work will be provided. The laboratory has recently added two new capabilities to its main levitation chamber: a rapid quench system and an oxygen control system. The rapid quench system allows samples to be dropped into a quench vessel that can be filled with a low melting point material, such as a gallium or indium alloy. Thereby allowing rapid quenching of undercooled liquid metals. The oxygen control system consists of an oxygen sensor, oxygen pump, and a control unit. The sensor is a potentiometric device that determines the difference in oxygen activity between two gas compartments separated by an electrolyte, which is yttria-stabilized zirconia. The pump utilizes coulometric titration to either add or remove oxygen. The system is controlled by a desktop control unit, which can also be accessed via a computer. This system allows the oxygen partial pressure within the vacuum chamber to be measured and controlled, theoretically in the range from 10-36 to 100 bar. The ESL laboratory also has an emissometer, called the High-Temperature Emissivity Measurement System (HiTEMS). This system measures the spectral emissivity of materials from 600degC to 3,000degC. The system consists of a vacuum chamber, a black body source, and a Fourier Transform Infrared Spectrometer (FTIR). The system utilizes optics to swap the signal between the sample and the black body. The system was originally designed to measure the hemispherical spectral emissivity of levitated samples, which are typically 2.5mm spheres. Levitation allows emissivity measurements of molten samples, but more work is required to develop this capability. The system is currently setup measure the near-normal spectral emissivity of stationary samples, which has been used to take measurements of ablative materials, rocket nozzle coating materials, and materials for spacecraft instruments

Autocatalytic plume pinch-off

A localized source of buoyancy flux in a non-reactive fluid medium creates a plume. The flux can be provided by either heat, a compositional difference between the fluid comprising the plume and its surroundings, or a combination of both. For autocatalytic plumes produced by the iodate-arsenous acid reaction, however, buoyancy is produced along the entire reacting interface between the plume and its surroundings. Buoyancy production at the moving interface drives fluid motion, which in turn generates flow that advects the reaction front. As a consequence of this interplay between fluid flow and chemical reaction, autocatalytic plumes exhibit a rich dynamics during their ascent through the reactant medium. One of the more interesting dynamical features is the production of an accelerating vortical plume head that in certain cases pinches-off and detaches from the upwelling conduit. After pinch-off, a new plume head forms in the conduit below, and this can lead to multiple generations of plume heads for a single plume initiation. We investigated the pinch-off process using both experimentation and simulation. Experiments were performed using various concentrations of glycerol, in which it was found that repeated pinch-off occurs exclusively in a specific concentration range. Autocatalytic plume simulations revealed that pinch-off is triggered by the appearance of accelerating flow in the plume conduit.Comment: 10 figures. Accepted for publication in Phys Rev E. See also http://www.physics.utoronto.ca/nonlinear/papers_chemwave.htm

A Global 86GHz VLBI Survey of Compact Radio Sources

We present results from a large 86GHz global VLBI survey of compact radio sources. The main goal of the survey is to increase by factors of 3--5 the total number of objects accessible for future 3-mm VLBI imaging. The survey observations reach the baseline sensitivity of 0.1Jy and image sensitivity of better than 10 mJy/beam. The total of 127 compact radio sources have been observed. The observations have yielded images for 109 sources, extending the database of the sources imaged at 86GHz with VLBI observation by a factor of 5, and only 6 sources have not been detected. The remaining 12 objects have been detected but could not be imaged due to insufficient closure phase information. Radio galaxies are less compact than quasars and BL Lacs on sub-milliarcsecond scale. Flux densities and sizes of core and jet components of all imaged sources have been estimated using Gaussian model fitting. From these measurements, brightness temperatures have been calculated, taking into account resolution limits of the data. The cores of 70% of the imaged sources are resolved. The core brightness temperatures of the sources peak at $\sim 10^{11}$ K and only 1% have brightness temperatures higher than $10^{12}$ K. Cores of Intraday Variable (IDV) sources are smaller in angular size than non-IDV sources, and so yield higher brightness temperatures.Comment: 72 pages, 12 figures, accepted for publication in the Astronomical Journa