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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids

Human biofluids, especially blood plasma or serum, hold great potential as the sources of potential biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge to detect promising low-abundance protein biomarkers. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high and moderate-abundance proteins, thus enabling more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomics applications of different human biofluids. The limitations and future perspective of immunoaffinity separation methods are also discussed.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Molecular Dynamics Study of Fe(II) Adsorption, Electron Exchange, and Mobility at Goethite (α-FeOOH) Surfaces

We present classical molecular simulations of the adsorption free energy profiles for the aqueous Fe(II) ion approaching key low index crystal faces of goethite at neutral surface charge conditions. Calculated profiles show minima corresponding to stable outer- and inner-sphere adsorbed structures. We analyzed the energetics and kinetics of most possible interfacial electron transfer reactions, as well as analyzing the same for subsurface migration pathways of injected electrons through calculating the Marcus free energy surfaces. We conclude that inner-sphere Fe(II)-complex formation is required for the interfacial electron transfer to occur, but the energetic cost of moving from the outer-sphere to inner-sphere geometry may prevent electron injection at some faces. We also show that some surfaces, especially (101), (100) and (001), are more energetically prone toward reduction than others. We demonstrate that subsurface charge migration in directions parallel to the surface, which run along the iron chains, is more energetically plausible than conduction through the resistive crystal bulk phase. Collectively this leads to the conclusion that Fe(II)-catalyzed recrystallization of goethite most likely proceeds by short path length electron migration through specific goethite surfaces along specific directions, until capture at Fe sites structurally susceptible to reduction and release.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Improving the Physical Basis for Updraft Dynamics in Deep Convection Parameterizations

This article presents a new deep convective parameterization that determines cloud characteristics based on a specified cloud size distribution. The vertical profiles of cloud properties are determined by analytic equations, which formulate entrainment with an inverse relationship to cloud width. In line with recent studies of large eddy simulations (LES), cloud widths are assumed to be constant with height and vertical mass flux (M) characteristics of the clouds are therefore regulated by the vertical velocity profile. The parameterization is configured to work with existing cloud base M closure formulations, with the closure predicting the total cloud area rather than the cloud base M directly. Analytic formula are also used to connect the vertical wind shear magnitude to the cloud size distribution, wherein larger shear magnitudes result in more numerous large updrafts than weaker shear magnitudes, which is in line with recent research results. The parameterization is compared against 10 deep convective LES with varying thermodynamic and vertical wind shear profiles. Results show dramatic improvements in the prediction of normalized M, detrainment, and the properties of detrained air over the existing Zhang and McFarlane (1995) scheme. In particular, the new model is able to correctly portray the transition from a bottom-heavy M profile in weakly sheared environments, to a top-heavy M profile in strongly sheared environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

In-situ piezoresponse force microscopy cantilever mode shape profiling

The frequency-dependent amplitude and phase in piezoresponse force microscopy (PFM) measurements are shown to be a consequence of the Euler-Bernoulli (EB) dynamics of atomic force microscope (AFM) cantilever beams used to make the measurements. Changes in the cantilever mode shape as a function of changes in the boundary conditions determine the sensitivity of cantilevers to forces between the tip and the sample. Conventional PFM and AFM measurements are made with the motion of the cantilever measured at one optical beam detector (OBD) spot location. A single OBD spot location provides a limited picture of the total cantilever motion, and in fact, experimentally observed cantilever amplitude and phase are shown to be strongly dependent on the OBD spot position for many measurements. In this work, the commonly observed frequency dependence of PFM response is explained through experimental measurements and analytic theoretical EB modeling of the PFM response as a function of both frequency and OBD spot location on a periodically poled lithium niobate sample. One notable conclusion is that a common choice of OBD spot location—at or near the tip of the cantilever—is particularly vulnerable to frequency dependent amplitude and phase variations stemming from dynamics of the cantilever sensor rather than from the piezoresponse of the sample.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms

We employed QM/MM molecular dynamics (MD) simulations to characterize the rate-limiting step of the glycosylation reaction of pancreatic α-amylase with combined DFT/molecular dynamics methods (PBE/def2-SVP : AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1 -2 kcal · mol -1 . Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.0 to 16.8 kcal · mol -1 and -6.3 to +3.8 kcal · mol -1 depending on the starting conformations, showing that despite significant state-of-the-art QM/MM MD sampling (0.5 ns/profile) the result still depends on the starting structure. In conclusion, the results supported the one step dissociative mechanism of Asp197 glycosylation preceded by an acid-base reaction by the Glu233, which are qualitatively similar to those from multi-PES QM/MM studies, and thus support the use of the latter to determine enzyme reaction mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments

Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Modeling of Electric Water Heaters for Demand Response: A Baseline PDE Model

Demand response (DR)control can effectively relieve balancing and frequency regulation burdens on conventional generators, facilitate integrating more renewable energy, and reduce generation and transmission investments needed to meet peak demands. Electric water heaters (EWHs) have a great potential in implementing DR control strategies because: (a) the EWH power consumption has a high correlation with daily load patterns; (b) they constitute a significant percentage of domestic electrical load; (c) the heating element is a resistor, without reactive power consumption; and (d) they can be used as energy storage devices when needed. Accurately modeling the dynamic behavior of EWHs is essential for designing DR controls. Various water heater models, simplified to different extents, were published in the literature; however, few of them were validated against field measurements, which may result in inaccuracy when implementing DR controls. In this paper, a partial differential equation physics-based model, developed to capture detailed temperature profiles at different tank locations, is validated against field test data for more than 10 days. The developed model shows very good performance in capturing water thermal dynamics for benchmark testing purposes

Balancing service, demand response, electric water↗
DOE OSTI2020

Antibody dynamics to SARS‐CoV‐2 in asymptomatic COVID‐19 infections

Abstract Background The missing asymptomatic COVID‐19 infections have been overlooked because of the imperfect sensitivity of the nucleic acid testing (NAT). Globally understanding the humoral immunity in asymptomatic carriers will provide scientific knowledge for developing serological tests, improving early identification, and implementing more rational control strategies against the pandemic. Measure Utilizing both NAT and commercial kits for serum IgM and IgG antibodies, we extensively screened 11 766 epidemiologically suspected individuals on enrollment and 63 asymptomatic individuals were detected and recruited. Sixty‐three healthy individuals and 51 mild patients without any preexisting conditions were set as controls. Serum IgM and IgG profiles were further probed using a SARS‐CoV‐2 proteome microarray, and neutralizing antibody was detected by a pseudotyped virus neutralization assay system. The dynamics of antibodies were analyzed with exposure time or symptoms onset. Results A combination test of NAT and serological testing for IgM antibody discovered 55.5% of the total of 63 asymptomatic infections, which significantly raises the detection sensitivity when compared with the NAT alone (19%). Serum proteome microarray analysis demonstrated that asymptomatics mainly produced IgM and IgG antibodies against S1 and N proteins out of 20 proteins of SARS‐CoV‐2. Different from strong and persistent N‐specific antibodies, S1‐specific IgM responses, which evolved in asymptomatic individuals as early as the seventh day after exposure, peaked on days from 17 days to 25 days, and then disappeared in two months, might be used as an early diagnostic biomarker. 11.8% (6/51) mild patients and 38.1% (24/63) asymptomatic individuals did not produce neutralizing antibody. In particular, neutralizing antibody in asymptomatics gradually vanished in two months. Conclusion Our findings might have important implications for the definition of asymptomatic COVID‐19 infections, diagnosis, serological survey, public health, and immunization strategies.

Lei, Qing↗
DOE OSTI2018

Motion of W and He atoms during formation of W fuzz

Measurements are conducted to identify the motion of tungsten and helium atoms during the formation of tungsten fuzz. In a first series of experiments the mobility of helium within the growing fuzz was measured by adding 3 He to the different stages of plasma exposure under conditions that promoted tungsten fuzz growth. Ion beam analysis was used to quantify the amount of 3 He remaining in the samples following the plasma exposure. The results indicate that the retention of helium in bubbles within tungsten is a dynamic process with direct implantation rather than diffusion into the bubbles, best describing the motion of the helium atoms. In the second experiment, an isotopically enriched layer of tungsten (~92.99% 182 W) is deposited on the surface of a bulk tungsten sample with the natural abundance of the isotopes. This sample is then exposed to helium plasma at the conditions necessary to support the formation of tungsten 'fuzz'. Depth profiles of the concentration of each of the tungsten isotopes are obtained using secondary ion mass spectrometry (SIMS) before and after the plasma exposure. The depth profiles clearly show mixing of tungsten atoms from the bulk sample toward the surface of the fuzz. Lastly, this supports a physical picture of the dynamic behavior of helium bubbles which, also, causes an enhanced mixing of tungsten atoms.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Real-Time Ecodriving Control in Electrified Connected and Autonomous Vehicles Using Approximate Dynamic Programing

Connected and automated vehicles (CAVs), particularly those with a hybrid electric powertrain, have the potential to significantly improve vehicle energy savings in real-world driving conditions. In particular, the ecodriving problem seeks to design optimal speed and power usage profiles based on available information from connectivity and advanced mapping features to minimize the fuel consumption over an itinerary. This paper presents a hierarchical multilayer model predictive control (MPC) approach for improving the fuel economy of a 48 V mild-hybrid powertrain in a connected vehicle environment. Approximate dynamic programing (DP) is used to solve the receding horizon optimal control problem, whose terminal cost is approximated with the base policy obtained from the long-term optimization. The controller was tested virtually (with deterministic and Monte Carlo simulation) across multiple real-world routes, demonstrating energy savings of more than 20%. The controller was then deployed on a test vehicle equipped with a rapid prototyping embedded controller. In-vehicle testing confirm the energy savings obtained in simulation and demonstrate the real-time ability of the controller.

Automation & Control Systems↗
DOE OSTI2021

Dynamic Transcriptomic and Phosphoproteomic Analysis During Cell Wall Stress in Aspergillus nidulans

The fungal cell-wall integrity signaling (CWIS) pathway regulates cellular response to environmental stress to enable wall repair and resumption of normal growth. This complex, interconnected, pathway has been only partially characterized in filamentous fungi. To better understand the dynamic cellular response to wall perturbation, a β-glucan synthase inhibitor (micafungin) was added to a growing A. nidulans shake-flask culture. From this flask, transcriptomic and phosphoproteomic data were acquired over 10 and 120 min, respectively. To differentiate statistically-significant dynamic behavior from noise, a multivariate adaptive regression splines (MARS) model was applied to both data sets. Over 1800 genes were dynamically expressed and over 700 phosphorylation sites had changing phosphorylation levels upon micafungin exposure. Twelve kinases had altered phosphorylation and phenotypic profiling of all non-essential kinase deletion mutants revealed putative connections between PrkA, Hk-8–4, and Stk19 and the CWIS pathway. Our collective data implicate actin regulation, endocytosis, and septum formation as critical cellular processes responding to activation of the CWIS pathway, and connections between CWIS and calcium, HOG, and SIN signaling pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

CROCUS Urban Canyons - Space Science and Engineering Center (SPARC) Doppler lidar data

This is the netCDF format output from the Halo Photonics Streamline XR Doppler lidar that was deployed next to the Space Science and Engineering Center (SPARC) trailer at the University of Illnois-Chicago greenhouse parking lot during CROCUS Urban Canyons. The purpose of collecting this dataset is to provide vertical and horizontal wind profiles for studying the characteristics of turbulence over the urban canyon of Chicago. This data contains the radial velocity, intensity, and backscatter from the vertical profile, range height indicator, and sector scans that were performed over both Intensive Operating Period 1 and 2 of CROCUS Urban Canyons. There are four different types of files: * The Range Height Indicator (RHI) files contain scans that are along a constant azimuth, spanning the entire hemisphere of elevation values above the surface. * The Velocity Azimuth Display (VAD) files contain the raw radial velocity data from the 6-beam, 60 degree scans. * The User1 files contain stacked Plan Position Indicator scans over a 45 degree quadrant over downtown Chicago. * The Stare files contain vertically pointing scans. These are standard netCDF files that can be opened using xarray. The VAD scans can be processed from their raw radial velocities to horizontal wind speeds with the Atmospheric data Community Toolkit (https://arm-doe.github.io/ACT/).

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC WINDS↗
DOE OSTI2023

Towards generic memory forensic framework for programmable logic controllers

A Programmable Logic Controller (PLC) is a microprocessor-based controller that is used to automate physical processes in critical infrastructure and various other industries and manufacturing sectors. Initially, PLCs were completely isolated from the Internet, and cyber security was not incorporated at the time of development. The introduction of industry 4.0 and the evolution of ICS systems to communicate over public IP addresses from the Internet enhanced productivity and efficiency, but Internet connectivity exposed the systems and their vulnerabilities, which led to an increase in cyber attacks. When a system is sabotaged/compromised, security analysts need to get to the root cause of the attack as quickly as possible to recover the system. To do so, memory forensic analysis is critical to provide a unique insight into the run-time memory activities and extract a reliable source of evidence. In this paper, we analyze the memory structure of the Schneider Electric Modicon M221 PLC. To build a memory profile, we reverse engineer the communication protocol and conduct differential analysis to gain knowledge about the structure of the memory and the low-level representation of control logic instructions. We then identify dynamic and static memory regions by modifying different project fields and conducting differential analysis, which allows us to identify boundaries of critical memory structures and extract important forensic artifacts that can be found in the memory. The Python implementation of the memory profile can help reduce the time and effort required for manual analysis in case of cyber incident or system failure.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

A FEATURE OF STELLAR DENSITY DISTRIBUTION WITHIN THE TIDAL RADIUS OF GLOBULAR CLUSTER NGC 6626 (M28) IN THE GALACTIC BULGE

Using wide-field J, H, and K{sub s} images obtained with the WIRCam near-infrared camera on the Canada-France-Hawaii Telescope, we investigated the spatial density configuration of stars within the tidal radius of metal-poor globular cluster NGC 6626, which is known to be located near the bulge region and have a thick-disk orbit motion. In order to trace the stellar density around a target cluster, we sorted the cluster's member stars using a mask-filtering algorithm and weighted the stars on the color-magnitude diagram. From the weight-summed surface density map, we found that the spatial density distribution of stars within the tidal radius is asymmetric with distorted overdensity features. The extending overdensity features are likely associated with the effects of the dynamic interaction with the Galaxy and the cluster's space motion. An interesting finding is that the prominent overdensity features extend toward the direction of the Galactic plane. This orientation of stellar density distribution can be interpreted with the result of the disk-shock effect of the Galaxy, previously experienced by the cluster. Indeed, the radial surface density profile accurately describes this overdensity feature with a break in the slope inside the tidal radius. Thus, the observed results indicate that NGC 6626 experienced a strong dynamical interaction with the Galaxy. Based on the result of strong tidal interaction with the Galaxy and previously published results, we discussed possible origins and evolutions of the cluster: (1) the cluster might have formed in satellite galaxies that were merged and created the Galactic bulge region in the early universe, after which time its dynamical properties were modified by dynamical friction, or (2) the cluster might have formed in primordial and rotationally supported massive clumps in the thick disk of the Galaxy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Magnetic Convection in a Nonuniformly Rotating Electroconducting Medium

We study the stability of a convective flow in a nonuniformly rotating plasma layer in an axially uniform magnetic field. The stationary and oscillating regimes of magnetic convection are considered depending on the angular velocity profile (Rossby number Ro) of the electroconducting medium. Using the Galerkin method for describing the weakly nonlinear stage of evolution of convection, we have obtained a nonlinear dynamic system of Lorentz-type equations. Numerical analysis of these equations has revealed the chaotic behavior of convective flows. The criteria for the emergence of chaotic flows are obtained depending on parameters of convection (Rayleigh number Ra), magnetic field (Chandrasekhar number Q), and rotation (Taylor number Ta) for the Rayleigh (Ro = –1) and Kepler (Ro = –3/4) angular velocity profiles of the medium.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Energy-Storage Fed Smart Inverters for Mitigation of Voltage Fluctuations in Islanded Microgrids

The continuous integration of intermittent low-carbon energy resources makes islanded microgrids vulnerable to voltage fluctuations. Besides, different dynamic response of synchronous-based and inverter-based distributed generation (DG) units can result in an instantaneous power imbalance between supply and demand during transients. As a result, the ac-bus voltage of microgrid starts oscillating which might have severe consequences such as blackouts. This paper modifies the conventional control scheme of battery energy storage systems (BESSs) to participate in improving the dynamic behavior of islanded microgrids by mitigating the voltage fluctuations. A piecewise linear-elliptic (PLE) droop is proposed and employed in BESS to achieve an enhanced voltage profile by injecting/absorbing reactive power during transients. In this way, the conventional inverter implemented in BESS turns into a smart inverter to cope with fast transients. Using the proposed approach in this paper, any linear droop curve with a specified coefficient can be replaced by a PLE droop curve. Compared with linear droop, an enhanced dynamic response is achieved by utilizing the proposed PLE droop. Case study results are presented using PSCAD/EMTDC to demonstrate the superiority of the proposed approach in improving the dynamic behavior of islanded microgrids.

Pilehvar, Mohsen S.↗
DOE OSTI2014

Self-shadowing effects of slim accretion disks in active galactic nuclei: the diverse appearance of the broad-line region

Supermassive black holes in active galactic nuclei (AGNs) undergo a wide range of accretion rates, which lead to diversity of appearance. We consider the effects of anisotropic radiation from accretion disks on the broad-line region (BLR) from the Shakura-Sunyaev regime to slim disks with super-Eddington accretion rates. The geometrically thick funnel of the inner region of slim disks produces strong self-shadowing effects that lead to very strong anisotropy of the radiation field. We demonstrate that the degree of anisotropy of the radiation fields grows with increasing accretion rate. As a result of this anisotropy, BLR clouds receive different spectral energy distributions depending on their location relative to the disk, resulting in the diverse observational appearance of the BLR. We show that the self-shadowing of the inner parts of the disk naturally produces two dynamically distinct regions of the BLR, depending on accretion rate. These two regions manifest themselves as kinematically distinct components of the broad Hβ line profile with different line widths and fluxes, which jointly account for the Lorentzian profile generally observed in narrow-line Seyfert 1 galaxies. In the time domain, these two components are expected to reverberate with different time lags with respect to the varying ionizing continuum, depending on the accretion rate and the viewing angle of the observer. The diverse appearance of the BLR due to the anisotropic ionizing energy source can be tested by reverberation mapping of Hβ and other broad emission lines (e.g., Fe II), providing a new tool to diagnose the structure and dynamics of the BLR. Other observational consequences of our model are also explored.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Field validation of an actuated convergent-beam acoustic Doppler profiler for high resolution flow mapping

Abstract Energetic river and tidal flow environments feature complex hydrodynamic conditions. Conventional acoustic Doppler profiling instrumentation typically requires assumptions of flow homogeneity over the spatial scales of the divergent beam separation. This removes the ability to measure spatio-temporal variability within the flow. However, velocity variability within these spatial scales is often important in the design of structures and devices exposed to such flow, informing dynamic and peak hydrodynamic load predictions. The research presented outlines the development and testing of a flow measurement instrument consisting of multiple spatially-separated single beam acoustic Doppler profilers converging on a remote focal point, the location of which can be programmatically adjusted through actuation. This increases the spatial resolution at which remote field measurements can be made in energetic flow environments. Field testing of the instrument was conducted in a tidal channel at Sequim Bay Inlet, WA, USA. Results are compared with independent reference measurements made by a co-located, motion-corrected acoustic Doppler velocimeter. This comparison, across tidal velocities of 0.4–0.7 m s −1 , showed a mean velocity error of 0.5%–13.2% across nine sample locations within a 3.00 m × 2.25 m plane. To the authors’ knowledge, this is the first publication of flow velocity results from non-intrusive acoustic measurements at an off-axis, focal point location that features 3D positional control.

13 HYDRO ENERGY↗