Workflow automation in liquid chromatography mass spectrometry

We describe the fully automated workflow path developed for the ingest and analysis of liquid chromatography mass spectrometry (LCMS) data. With the help of this computational workflow, we were able to replace two human work days to analyze data with two hours of unsupervised computation time. In addition, this tool also can compute confidence intervals for all its results, based on the noise level present in the data. We leverage only open source tools and libraries in this workflow

SPARCS: Stream-processing architecture applied in real-time cyber-physical security

In this paper, we showcase a complete, end-To-end, fault tolerant, bandwidth and latency optimized architecture for real time utilization of data from multiple sources that allows the collection, transport, storage, processing, and display of both raw data and analytics. This architecture can be applied for a wide variety of applications ranging from automation/control to monitoring and security. We propose a practical, hierarchical design that allows easy addition and reconfiguration of software and hardware components, while utilizing local processing of data at sensor or field site ('fog computing') level to reduce latency and upstream bandwidth requirements. The system supports multiple fail-safe mechanisms to guarantee the delivery of sensor data. We describe the application of this architecture to cyber-physical security (CPS) by supporting security monitoring of an electric distribution grid, through the collection and analysis of distribution-grid level phasor measurement unit (PMU) data, as well as Supervisory Control And Data Acquisition (SCADA) communication in the control area network

On the noise-induced passage through an unstable periodic orbit II: General case

Consider a dynamical system given by a planar differential equation, which exhibits an unstable periodic orbit surrounding a stable periodic orbit. It is known that under random perturbations, the distribution of locations where the system's first exit from the interior of the unstable orbit occurs, typically displays the phenomenon of cycling: The distribution of first-exit locations is translated along the unstable periodic orbit proportionally to the logarithm of the noise intensity as the noise intensity goes to zero. We show that for a large class of such systems, the cycling profile is given, up to a model-dependent change of coordinates, by a universal function given by a periodicised Gumbel distribution. Our techniques combine action-functional or large-deviation results with properties of random Poincar\'e maps described by continuous-space discrete-time Markov chains.Comment: 44 pages, 4 figure

Membrance interface evaluations for underwater mass spectrometers.

A component that has enabled the development of underwater mass spectrometry is a mechanically supported membrane interface probe. Our two research groups have used metallic porous frits that support polydimethyl siloxane (PDMS) membranes embedded in a heated membrane probe assembly, allowing the deployment of the underwater membrane introduction mass spectrometer (MIMS) instruments to ocean depths of 2000 meters. The fabrication of such frits has consisted of shaping larger Hastalloy C porous frits to the size required to support a PDMS capillary of 0.64 mm ID and 1.19 mm OD using a diamond‐coated wheel and Dremel tool. This procedure is time‐consuming and cumbersome, and the porosity of the final frits is likely not reproducible. To facilitate the fabrication of the membrane assembly, we report on the use of new porous metallic structures. Frits with diameters of approximately 3.0 mm (1/8”) and known porosities (48.3 % and 32.5%) were produced by the Fraunhofer Institute in Dresden, Germany, using powder metallurgical processes. We used these frits to fabricate new membrane interface assemblies. Using a new custom‐heated membrane probe with the new porous frits, we performed calibrations relating dissolved methane concentrations to mass spectrometer response (m/z 15) using linear least‐squares fitting procedures. Both the limit of detection (methane concentration in the tens of nanomolars) and the sensitivity (on the order of 10‐1 pico‐amps/nanomole of methane) were found to be comparable with those obtained with the previously fabricated Hastelloy C frits. The calibration parameters for the new assembly were also found to be a function of the flow rate, temperature, and sample hydrostatic pressure

Metastability in Interacting Nonlinear Stochastic Differential Equations II: Large-N Behaviour

We consider the dynamics of a periodic chain of N coupled overdamped particles under the influence of noise, in the limit of large N. Each particle is subjected to a bistable local potential, to a linear coupling with its nearest neighbours, and to an independent source of white noise. For strong coupling (of the order N^2), the system synchronises, in the sense that all oscillators assume almost the same position in their respective local potential most of the time. In a previous paper, we showed that the transition from strong to weak coupling involves a sequence of symmetry-breaking bifurcations of the system's stationary configurations, and analysed in particular the behaviour for coupling intensities slightly below the synchronisation threshold, for arbitrary N. Here we describe the behaviour for any positive coupling intensity \gamma of order N^2, provided the particle number N is sufficiently large (as a function of \gamma/N^2). In particular, we determine the transition time between synchronised states, as well as the shape of the "critical droplet", to leading order in 1/N. Our techniques involve the control of the exact number of periodic orbits of a near-integrable twist map, allowing us to give a detailed description of the system's potential landscape, in which the metastable behaviour is encoded

Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells

Reliable methods to determine the subcellular localization of bacterial proteins are needed for the study of prokaryotic cell biology. We describe here a simple and general technique for imaging of bacterial proteins in situ by fluorescence microscopy. The method uses the eukaryotic enzyme N-myristoyltransferase to modify the N-terminus of the protein of interest with an azido fatty acid. Subsequent strain-promoted azide–alkyne cycloaddition allows conjugation of dyes and imaging of tagged proteins by confocal fluorescence microscopy. We demonstrate the method by labeling the chemotaxis proteins Tar and CheA and the cell division proteins FtsZ and FtsA in Escherichia coli. We observe distinct spatial patterns for each of these proteins in both fixed and live cells. The method should prove broadly useful for protein imaging in bacteria

Pitting and Repair of the Space Shuttle's Inconel(Registered TradeMark) Honeycomb Conical Seal Panel

During return to flight servicing of the rudder speed brake (RSB) for each Space Shuttle Orbiter, inspectors discovered numerous small pits on the surface of the #4 right hand side honeycomb panel that covers the rudder speed brake actuators. Shortly after detection of the problem, concurrent investigations were initiated to determine the extent of damage, the root cause, and to develop a repair plan, since fabrication of a replacement panel is impractical for cost, schedule, and sourcing considerations. This paper describes the approach, findings, conclusions and recommendations associated with the investigation of the conical seal pitting. It documents the cause and contributing factors of the pitting, the means used to isolate each contributor, and the supporting evidence for the primary cause of the pitting. Finally, the selection, development and verification of the repair procedure used to restore the conical seal panel is described with supporting process and metallurgical rationale for selection

Universality of residence-time distributions in non-adiabatic stochastic resonance

We present mathematically rigorous expressions for the residence-time and first-passage-time distributions of a periodically forced Brownian particle in a bistable potential. For a broad range of forcing frequencies and amplitudes, the distributions are close to periodically modulated exponential ones. Remarkably, the periodic modulations are governed by universal functions, depending on a single parameter related to the forcing period. The behaviour of the distributions and their moments is analysed, in particular in the low- and high-frequency limits.Comment: 8 pages, 1 figure New version includes distinction between first-passage-time and residence-time distribution

A study of microstructural characteristics and differential thermal analysis of Ni-based superalloys

The objective of this work is to correlate the mechanical properties of the Ni-based superalloy MAR M246(Hf) used in the Space Shuttle Main Engine with its structural characteristics by systematic study of optical photomicrographs and differential thermal analysis. The authors developed a method of predicting the liquidus and solidus temperature of various nickel based superalloys (MAR-M247, Waspaloy, Udimet-41, polycrystalline and single crystals of CMSX-2 and CMSX-3) and comparing the predictions with the experimental differential thermal analysis (DTA) curves using Perkin-Elmer DTA 1700. The method of predicting these temperatures is based on the additive effect of the components dissolved in nickel. The results were compared with the experimental values