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Results for “dynamic profiling”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

ProteoSign: an end-user online differential proteomics statistical analysis platform

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a userfriendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ ProteoSign.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Magnetic Signatures of Radiation-Driven Double Ablation Fronts

In experiments performed with the OMEGA EP laser system, magnetic field generation in double ablation fronts was observed. Proton radiography measured the strength, spatial profile, and temporal dynamics of self-generated magnetic fields as the target material was varied between plastic (CH), aluminum, copper, and gold. Two distinct regions of magnetic field are generated in mid-Z targets -- one produced by gradients from electron thermal transport and the second from radiation-driven gradients. Extended magnetohydrodynamic simulations including radiation transport reproduced key aspects of the experiment, including field generation and double ablation front formation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κB signaling networks

Background: Gene expression profiles and protein dynamics in single cells have a large cell-to-cell variability due to intracellular noise. Intracellular fluctuations originate from two sources: intrinsic noise due to the probabilistic nature of biochemical reactions and extrinsic noise due to randomized interactions of the cell with other cellular systems or its environment. Presently, there is no systematic parameterization and modeling scheme to simulate cellular response at the single cell level in the presence of extrinsic noise. Results: In this paper, we propose a novel statistical ensemble method to simulate the distribution of heterogeneous cellular responses in single cells. We capture the effects of extrinsic noise by randomizing values of the model parameters. In this context, a statistical ensemble is a large number of system replicates, each with randomly sampled model parameters from biologically feasible intervals. We apply this statistical ensemble approach to the well-studied NF-κB signaling system. We predict several characteristic dynamic features of NF-κB response distributions; one of them is the dosage-dependent distribution of the first translocation time of NF-κB. Conclusion: The distributions of heterogeneous cellular responses that our statistical ensemble formulation generates reveal the effect of different cellular conditions, e.g., effects due to wild type versus mutant cells or between different dosages of external stimulants. Distributions generated in the presence of extrinsic noise yield valuable insight into underlying regulatory mechanisms, which are sometimes otherwise hidden.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Coherent homodyne detection for amplified cross-beam electric-field induced second harmonic

The electric-field induced second harmonic (E-FISH) signal sensing is commonly used as a nonlinear optical technique to probe electric fields inside a plasma region. Cross-beam E-FISH is being investigated to improve spatial resolution by defining the interaction volume via a controlled geometry of two overlapping noncolinear optical beams. This drastic reduction in interaction length of the electric field and laser region results in a significant signal reduction. Here, to overcome this signal reduction, we introduce coherent amplification of the cross-beam E-FISH signal by mixing the low E-FISH signal with a phase-locked bright local oscillator. We demonstrate enhancement of the signal. By introducing a local oscillator we can now derive the polarity of the measured electric field through the phase of the homodyne signal. To illustrate the technique, we, for the first time, to the best of our knowledge, measure the magnitude and the direction of the electric field in a cold atmospheric pressure plasma jet, which dynamically follows the profile of the applied bias current.

42 ENGINEERING↗
DOE OSTI2023

Power management for hybrid electric vehicles

A system and method for power management of hybrid electric vehicles is provided. In some implementations, a plug-in series hybrid electric vehicle may include an engine, a motor/generator (MG), a traction motor, an energy storage device, and a controller. The controller is coupled to the engine and the MG to control operation of the engine and the MG such that a state-of-charge (SOC) of the energy storage device tracks a dynamic reference SOC profile during a trip and an average engine power (AEP) is maintained above a threshold. In some instances, maintaining AEP above a threshold supports emission control of the vehicle.

Le, Dat Duc↗
DOE OSTI2015

Molecular dynamic simulation of Ar-Kr mixture across a rough walled nanochannel: Velocity and temperature profiles

This paper presents the results from a molecular dynamics simulation of mixture of argon and krypton in the Poiseuille flow across a rough walled nanochannel. The roughness effect on liquid nanoflows has recently drawn attention The computational software used for carrying out the molecular dynamics simulations is LAMMPS. The fluid flow takes place between two parallel plates and is bounded by horizontal rough walls in one direction and periodic boundary conditions are imposed in the other two directions. Each fluid atom interacts with other fluid atoms and wall atoms through Leenard-Jones (LJ) potential with a cut off distance of 5.0. To derive the flow a constant force is applied whose value is varied from 0.1 to 0.3 and velocity profiles and temperature profiles are noted for these values of forces. The velocity profile and temperature profiles are also looked at different channel widths of nanochannel and at different densities of mixture. The velocity profile and temperature profile of rough walled nanochannel are compared with that of smooth walled nanochannel and it is concluded that mean velocity increases with increase in channel width, force applied and decrease in density also with introduction of roughness in the walls of nanochannel mean velocity again increases and results also agree with the analytical solution of a Poiseuille flow.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

High Dynamic Range Beam Imaging with Two Simultaneously Sampling CCDs

Transverse beam profile measurement with sufficiently high dynamic range (HDR) is a key diagnostic to measure the beam halo, understand its sources and evolution. In this contribution we describe our initial experience with the HDR imaging of the electron beam at the JLab FEL. On contrary to HDR measurements made with wire scanners in counting mode, which provide only two or three 1D projections of transverse beam distribution, imaging allows to measure the distribution itself. That is especially important for non-equilibrium beams in the LINACs. The measurements were made by means of simultaneous imaging with two CCD sensors with different exposure time. Two images are combined then numerically in to one HDR image. The system works as an online tool providing HDR images at 4 Hz. An optically polished YAG:Ce crystal with the thickness of 100 {micro}m was used for the measurements. When tested with a laser beam images with the DR of about 10{sup 5} were obtained. With the electron beam the DR was somewhat smaller due to the limitations in the time structure of the tune-up beam macro pulse.

43 PARTICLE ACCELERATORS↗
DOE OSTI2013

High Dynamic Range Beam Imaging with Two Simultaneously Sampling CCDs

Transverse beam profile measurement with sufficiently high dynamic range (HDR) is a key diagnostic to measure the beam halo, understand its sources and evolution. In this contribution we describe our initial experience with the HDR imaging of the electron beam at the JLab FEL. On contrary to HDR measurements made with wire scanners in counting mode, which provide only two or three 1D projections of transverse beam distribution, imaging allows to measure the distribution itself. That is especially important for non-equilibrium beams in the LINACs. The measurements were made by means of simultaneous imaging with two CCD sensors with different exposure time. Two images are combined then numerically in to one HDR image. The system works as an online tool providing HDR images at 4 Hz. An optically polished YAG:Ce crystal with the thickness of 100 {micro}m was used for the measurements. When tested with a laser beam images with the DR of about 10{sup 5} were obtained. With the electron beam the DR was somewhat smaller due to the limitations in the time structure of the tune-up beam macro pulse.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Project Dinos I: A joint lensing–dynamics constraint on the deviation from the power law in the mass profile of massive ellipticals

The mass distribution in massive elliptical galaxies encodes their evolutionary history, thus providing an avenue to constrain the baryonic astrophysics in their evolution. The power-law assumption for the radial mass profile in ellipticals has been sufficient to describe several observables to the noise level, including strong lensing and stellar dynamics. In this paper, we quantitatively constrained any deviation, or the lack thereof, from the power-law mass profile in massive ellipticals through joint lensing–dynamics analysis of a large statistical sample with 77 galaxy–galaxy lens systems. We performed an improved and uniform lens modelling of these systems from archival Hubble Space Telescope imaging using the automated lens modelling pipeline dolphin. We combined the lens model posteriors with the stellar dynamics to constrain the deviation from the power law after accounting for the line-of-sight lensing effects, a first for analyses on galaxy–galaxy lenses. We find that the Sloan Lens ACS Survey lens galaxies with a mean redshift of 0.2 are consistent with the power-law profile within 1.1σ (2.8σ) and the Strong Lensing Legacy Survey lens galaxies with a mean redshift of 0.6 are consistent within 0.8σ (2.1σ), for a spatially constant (Osipkov–Merritt) stellar anisotropy profile. We adopted the spatially constant anisotropy profile as our baseline choice based on previous dynamical observables of local ellipticals. However, spatially resolved stellar kinematics of lens galaxies are necessary to differentiate between the two anisotropy models. Future studies will use our lens models to constrain the mass distribution individually in the dark matter and baryonic components.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Length scales and scale-free dynamics of dislocations in dense solid solutions

The fundamental interactions between an edge dislocation and a random solid solution are studied by analyzing dislocation line roughness profiles obtained from molecular dynamics simulations of Fe 0.70 Ni 0.11 Cr 0.19 over a range of stresses and temperatures. These roughness profiles reveal the hallmark features of a depinning transition. Namely, below a temperature-dependent critical stress, the dislocation line exhibits roughness in two different length scale regimes which are divided by a so-called correlation length. This correlation length increases with applied stress and at the critical stress (depinning transition or yield stress) formally goes to infinity. Above the critical stress, the line roughness profile converges to that of a random noise field. Motivated by these results, a physical model is developed based on the notion of coherent line bowing over all length scales below the correlation length. Above the correlation length, the solute field prohibits such coherent line bow outs. Using this model, we identify potential gaps in existing theories of solid solution strengthening and show that recent observations of length-dependent dislocation mobilities can be rationalized.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Heat transport in confined strongly coupled two-dimensional dust clusters

Dusty plasmas are a model system for studying strong correlation. The dust grains’ size of a few micro-meters and their characteristic oscillation frequency of a few hertz allow for an investigation of many-particle effects on an “atomic” level. In this article, we model the heat transport through an axially confined 2D dust cluster from the center to the outside. The system behaves particularly interesting since heat is not only conducted within the dust component but also transferred to the neutral gas. Fitting the analytical solution to the radial temperature profiles obtained in molecular dynamics simulations allows to determine the heat conductivity k. The heat conductivity is found to be constant over a wide range of coupling strengths even including the phase transition from solid to liquid here, as it was also found in extended systems by Nosenko et al.[Phys. Rev. Lett. 100, 025003 (2008)].

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Bistable dynamics of turbulence spreading in a corrugated temperature profile

We present a new model of turbulence spreading in magnetically confined plasma. A basic question in turbulence spreading is how to sustain finite amplitude fluctuations in a stable subcritical region, where linear dissipation of the turbulence is strong? The answer to this question relies on a consistent treatment of mesoscale temperature profile corrugation and microscale turbulence. We argue that inhomogeneous mixing of the turbulence corrugates the mean temperature profile and that the temperature corrugation then induces subcritical bifurcation of the turbulence. Thus, the system will transition from a metastable “laminar” state to an absolutely stable, excited state. Incorporating spatial coupling of the locally excited turbulent regions, a front forms. This front connects the excited and laminar states and penetrates the linear stable region efficiently. Here, we argue that such bistable turbulence spreading can explain observations of hysteresis in the intensity of L-mode core turbulence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2011

Quantum dynamics of hard-core bosons in tilted bichromatic optical lattices

We study the dynamics of strongly repulsive Bose gas in tilted or driven bichromatic optical lattices. Using the Bose-Fermi mapping and exact numerical method, we calculate the reduced single-particle density matrices, and study the dynamics of the density profile, the momentum distribution, and the condensate fraction. We show the oscillating and breathing mode of the dynamics, and the depletion of condensate for short-time dynamics. For long-time dynamics, we clearly show the reconstruction of system at integer multiples of Bloch-Zener time. We also show how to achieve clear Bloch oscillation and Landau-Zener tunneling for many-particle systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

SU-E-T-178: Clinical Feasibility of Multi-Leaf Collimator Based Dynamic Wedge

Purpose: A multi-leaf collimator (MLC) based dynamic wedge (MDW), which provide similar dose profile of physical wedge (PW) along x-jaw direction while significant monitor unit (MU) reduction, was developed and investigated for clinical use. Methods: A novel technique was used to create the wedge profile using MLC. A modification was applied to the DICOM-RT format file of the plan made with the PW to replace PW with MDW. The Varian enhanced dynamic wedge profile was used to produce MLC sequence, while the MU of the wedged field was recalculated using PW factor and fluence map. The profiles for all possible MDWs to substitute PWs were verified in 6/15 MV x-ray irradiations. New plans with MDWs were compared with the original plans in 5 rectal, 5 RT breast and 5 liver cases. Results: The wedge profile of the MDW fields were well matched with those of PWs inside the fields while less scatter than PW out of the fields. For plan comparisons of the clinical cases no significant dose discrepancy was observed between MDW plan and PW’s with the dose volume histograms. The maximum and mean doses in PTVs are agreed within 1.0%. The Result of OARs of MDW plans are slightly improved in the maximum doses (3.22 ∼ 150.4 cGy) and the mean doses (17.18 ∼ 85.52 cGy) on average for all cases while the prescribed doses are 45 Gy for rectal cases, 40 or 45 Gy for liver cases and 50 Gy for breast cases. The MUs of the fields which replace PW with MDW are reduced to 68% of those of PW. Conclusion: We developed a novel dynamic wedge technique with MLC that shows clinical advantage compared to PW.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A data-independent acquisition-based global phosphoproteomics system enables deep profiling

Phosphoproteomics can provide insights into cellular signaling dynamics. To achieve deep and robust quantitative phosphoproteomics profiling for minute amounts of sample, we here develop a global phosphoproteomics strategy based on data-independent acquisition (DIA) mass spectrometry and hybrid spectral libraries derived from data-dependent acquisition (DDA) and DIA data. Benchmarking the method using 166 synthetic phosphopeptides shows high sensitivity (<0.1 ng), accurate site localization and reproducible quantification (~5% median coefficient of variation). As a proof-of-concept, we use lung cancer cell lines and patient-derived tissue to construct a hybrid phosphoproteome spectral library covering 159,524 phosphopeptides (88,107 phosphosites). Based on this library, our single-shot streamlined DIA workflow quantifies 36,350 phosphosites (19,755 class 1) in cell line samples within two hours. Application to drug-resistant cells and patient-derived lung cancer tissues delineates site-specific phosphorylation events associated with resistance and tumor progression, showing that our workflow enables the characterization of phosphorylation signaling with deep coverage, high sensitivity and low between-run missing values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Mineral properties, microbes, transport, and plant-input profiles control vertical distribution and age of soil carbon stocks

The role of organo-mineral interactions, microbial dynamics, and vertical plant input profiles are hypothesized to be important in controlling soil organic matter (SOM) stocks and dynamics. In this paper, to test this hypothesis, we enhanced and applied a model (Biotic and Abiotic Model of SOM – BAMS1) that represents microbial dynamics and organo-mineral interactions integrated with a multiphase reactive transport solver for variably saturated porous media. The model represents aqueous chemistry, aqueous advection and diffusion, gaseous diffusion, sorption processes, bacterial and fungal activity, and archetypal monomer- and polymer-carbon substrate groups, including dead cell wall material. This model structure is fundamentally different, and produces different SOM dynamics, than the pseudo-first order relationships that are used in most site- and global-scale terrestrial SOM models. We simulated two grasslands, a seven-site chronosequence (~3.9–240 Ky) in Northern California, and a Russian Chernozem site where soils were sampled 100 years apart. We calibrated the model's vertically-resolved soil bulk specific surface area (SBSSA) using observed bulk SOM content, and then tested the model against observed Δ 14 C profiles. The modeled microbial processes, organo-mineral interactions, and vertical aqueous transport produced realistic vertically-resolved predictions of bulk SOM content, Δ 14 C values of SOM, lignin content, and fungi-to-aerobic bacteria biomass ratios. Using sensitivity analyses, we found that vertical carbon input profiles were important controls over the Δ 14 C depth distribution. Shallower carbon input profiles lead to older carbon at depth. In addition, the SBSSA was the dominant control over the magnitude and vertical distribution of SOM stocks. Finally, the findings of this study demonstrate the value of explicitly incorporating microbial activity, sorption, and vertical transport into land models to predict SOM dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Nonlinear Alfvén instability simulation and EP transport for ITER reversed shear (steady-state) and monotonic q-profile regimes *

The nonlinear evolution and dynamics of energetic particle (EP) driven instabilities in both steady-state (reversed shear q-profile) and monotonic q-profile regimes of ITER are examined using the global gyro-Landau closure model FAR3d. Both neutral beam and alpha components are included, leading to synergistic effects between the two populations. In order to maintain computational feasibility, the present nonlinear simulation includes all toroidal mode numbers ranging from n = 0 to 15. It cannot be excluded that n’s above this range could introduce larger linear growth rates; however, as indicated from the results, the n = 0 to 15 range is sufficient to provide a strong linear drive and significant nonlinear transport effects. While the toroidal mode numbers n = 6,13 dominate the linear instability growth phase, nonlinear energy transfers in the saturated phase reverse this trend, leading to the dominance of lower n’s in the saturated phase of the simulation. Zonal flow structure generation and EP density flattening are further consequences of the nonlinear phase. The density profile flattening is caused by collectively driven EP radial transport fluxes, which have non-local characteristics. Instantaneous alpha particle transport fluxes are significant (Γ α ~ 2 x 10 20 m –2 s –1 ) for the reversed shear regime and lower (Γ α ~ 1.1 x 10 20 m –2 s –1 ) for the monotonic q-profile case.

AE↗