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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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All sourcesNASA NTRSDOE OSTI
NASA NTRS1972

Feasibility study: Replacement of the inoperative decommutating buffer subsystem for the instrumentation checkout complex in the Quality and Reliability Assurance Laboratory

A general purpose computer system, that is necessary for replacement of the present inoperative signal decommutator special purpose computer subsystem is described. The present decommutator subsystem has a very poor history of reliability and since April 1970, it has become inoperative because the core memory cannot be repaired. Functions of the present signal, decommutator subsystem are to receive, demultiplex, record in real time, playback in real time, and output to the SDS-930 control computer for analysis of the telemetry data. Recommendations for replacement of the inoperative telemetry decommutator subsystem are for the purchase of a mini-computer.

Hilliard, J. W.↗
NASA NTRS1977

Design, fabrication, and evaluation of charge-coupled devices with aluminum-anodized-aluminum gates

A 4-phase, 49 1/2 bit CCD shift register was designed and fabricated using two levels of aluminum metallization with anodic Al2O3 insulation separating the layers. Test circuitry was also designed and constructed. A numerical analysis of an MOS-RC transmission line was made and results are given to characterize performance for various conductivities. The electrical design of the CCD included a low-noise dual-gate input and a balanced floating diffusion output circuit. Metallization was accomplished both by low voltage DC sputtering and thermal evaporation. The audization was according to published procedures using a buffered tartaric acid bath. Approximately 20 wafers were processed with 50 complete chips per wafer. All devices failed by shorting between the metal levels at some point. Experimental procedures eliminated temperature effects from sintering and drying, anodic oxide thickness, edge effects, photoresist stripping procedures, and metallization techniques as the primary causes of failure. It was believed from a study of SEM images that protuberances (hillocks) grow up from the first level metal through the oxide either causing a direct short or producing a weak, highly stressed insulation point which fails at low voltage. The cause of these hillocks is unknown; however, they have been observed to grow during temperature excursions to 470 C.

Gassaway, J. D.↗
NASA NTRS1989

Analysis of random drop for gateway congestion control

Lately, the growing demand on the Internet has prompted the need for more effective congestion control policies. Currently No Gateway Policy is used to relieve and signal congestion, which leads to unfair service to the individual users and a degradation of overall network performance. Network simulation was used to illustrate the character of Internet congestion and its causes. A newly proposed gateway congestion control policy, called Random Drop, was considered as a promising solution to the pressing problem. Random Drop relieves resource congestion upon buffer overflow by choosing a random packet from the service queue to be dropped. The random choice should result in a drop distribution proportional to the bandwidth distribution among all contending TCP connections, thus applying the necessary fairness. Nonetheless, the simulation experiments demonstrate several shortcomings with this policy. Because Random Drop is a congestion control policy, which is not applied until congestion has already occurred, it usually results in a high drop rate that hurts too many connections including well-behaved ones. Even though the number of packets dropped is different from one connection to another depending on the buffer utilization upon overflow, the TCP recovery overhead is high enough to neutralize these differences, causing unfair congestion penalties. Besides, the drop distribution itself is an inaccurate representation of the average bandwidth distribution, missing much important information about the bandwidth utilization between buffer overflow events. A modification of Random Drop to do congestion avoidance by applying the policy early was also proposed. Early Random Drop has the advantage of avoiding the high drop rate of buffer overflow. The early application of the policy removes the pressure of congestion relief and allows more accurate signaling of congestion. To be used effectively, algorithms for the dynamic adjustment of the parameters of Early Random Drop to suite the current network load must still be developed.

Hashem, Emam Salaheddin↗
DOE OSTI2026

RU-net for automatic characterization of TRISO fuel cross sections

During irradiation, phenomena such as kernel swelling and buffer densification may impact the performance of tristructural isotropic (TRISO) particle fuel. Post-irradiation microscopy is often used to identify these irradiation-induced morphologic changes. However, each fuel compact generally contains thousands of TRISO particles. Manually performing the work to get statistical information on these phenomena is cumbersome and subjective. Here, to reduce the subjectivity inherent in that process and to accelerate data analysis, we used convolutional neural networks (CNNs) to automatically segment cross-sectional images of microscopic TRISO layers. CNNs are a class of machine-learning algorithms specifically designed for processing structured grid data. They have gained popularity in recent years due to their remarkable performance in various computer vision tasks, including image classification, object detection, and image segmentation. In this research, we generated a large irradiated TRISO layer dataset with more than 2,000 microscopic images of cross-sectional TRISO particles and the corresponding annotated images. Based on these annotated images, we used different CNNs to automatically segment different TRISO layers. These CNNs include RU-Net (developed in this study), as well as three existing architectures: U-Net, Residual Network (ResNet), and Attention U-Net. The preliminary results show that the model based on RU-Net performs best in terms of Intersection over Union (IoU). Using CNN models, we can expedite the analysis of TRISO particle cross sections, significantly reducing the manual labor involved and improving the objectivity of the segmentation results.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS2020

A New Method to Correct the Electrochemical Concentration Cell (ECC) Ozonesonde Time Response and its Implications for "Background Current" and Pump Efficiency

The electrochemical concentration cell (ECC) ozonesonde has been the main instrument for in situ profiling of ozone worldwide; yet, some details of its operation, which contribute to the ozone uncertainty budget, are not well understood. Here, we investigate the time response of the chemical reactions inside the ECC and how corrections can be used to remove some systematic biases. The analysis is based on the understanding that two reaction pathways involving ozone occur inside the ECC that generate electrical currents on two very different timescales. The main fast-reaction pathway with a time constant of about 20 s is due the conversion of iodide to molecular iodine and the generation of two free electrons per ozone molecule. A secondary slow-reaction pathway involving the buffer generates an excess current of about 2 %–10 % with a time constant of about 25 min. This excess current can be interpreted as what has conventionally been considered the “background current”. This contribution can be calculated and removed from the measured current instead of the background current. Here we provide an algorithm to calculate and remove the contribution of the slow-reaction pathway and to correct for the time lag of the fast-reaction pathway. This processing algorithm has been applied to ozonesonde profiles at Costa Rica and during the Central Equatorial Pacific Experiment (CEPEX) as well as to laboratory experiments evaluating the performance of ECC ozonesondes. At Costa Rica, where a 1 % KI, 1/10th buffer solution is used, there is no change in the derived total ozone column; however, in the upper troposphere and lower stratosphere, average reported ozone concentrations increase by up to 7 % and above 30 km decrease by up to 7 %. During CEPEX, where a 1 % KI, full-buffer solution was used, ozone concentrations are increased mostly in the upper troposphere, with no change near the top of the profile. In the laboratory measurements, the processing algorithms have been applied to measurements using the majority of current sensing solutions and using only the stronger pump efficiency correction reported by Johnson et al. (2002). This improves the accuracy of the ECC sonde ozone profiles, especially for low ozone concentrations or large ozone gradients and removes systematic biases relative to the reference instruments. In the surface layer, operational procedures prior to launch, in particular the use of filters, influence how typical gradients above the surface are detected. The correction algorithm may report gradients that are steeper than originally reported, but their uncertainty is strongly influenced by the prelaunch procedures.

electrochemical concentration cell (ECC) ozonesond↗
NASA NTRS1987

The corrosion mechanisms for primer coated 2219-T87 aluminum

To investigate metal surface corrosion and the breakdown of metal protective coatings, the ac Impedance Method was applied to zinc chromate primer coated 2219-T87 aluminum. The EG&GPARC Model 368 ac Impedance Measurement System, along with dc measurements with the same system using the Polarization Resistance Method, was used to monitor changing properties of coated aluminum disks immersed in 3.5 percent NaCl solutions buffered at pH 5.5 and pH 8.2 over periods of 40 days each. The corrosion system can be represented by an electronic analog called an equivalent circuit consisting of resistors and capacitors in specific arrangements. This equivalent circuit parallels the impedance behavior of the corrosion system during a frequency scan. Values for resistances and capacitances, that can be assigned in the equivalent circuit following a least squares analysis of the data, describe changes occurring on the corroding metal surface and in the protective coatings. A suitable equivalent circuit has been determined which predicts the correct Bode phase and magnitude for the experimental sample. The dc corrosion current density data are related to equivalent circuit element parameters.

Danford, Merlin D.↗
NASA NTRS1988

An electrochemical study of corrosion protection by primer-topcoat systems on 4130 steel with ac impedance and dc methods

To investigate metal surface corrosion and the breakdown of metal protective coatings, the ac impedance method is applied to six systems of primer coated and primer topcoated 4130 steel. Two primers were used: a zinc-rich epoxy primer and a red lead oxide epoxy primer. The epoxy-polyamine topcoat was used in four of the systems. The EG and G-PARC Model 368 ac impedance measurement system, along with dc measurements with the same system using the polarization resistance method, were used to monitor changing properties of coated 4230 steel disks immersed in 3.5 percent NaCl solutions buffered at pH 5.4 over periods of 40 to 60 days. The corrosion system can be represented by an electronic analog called an equivalent circuit consisting of resistors and capacitors in specific arrangements. This equivalent circuit parallels the impedance behavior of the corrosion system during a frequency scan. Values for the resistors and capacitors, that can be assigned in the equivalent circuit following a least-squares analysis of the data, describe changes that occur on the corroding metal surface and in the protective coatings. Two equivalent circuits have been determined that predict the correct Bode phase and magnitude of the experimental sample at different immersion times. The dc corrosion current density data are related to equivalent circuit element parameters. Methods for determining corrosion rate with ac impedance parameters are verified by the dc method.

Mendrek, M. J.↗
DOE OSTI2025

Evaluation of a high-throughput method for processing sponge-stick samples to detect viable, non-spore-forming biothreat agents

After a bioterrorism incident, surface sampling is often used to determine the extent of contamination and exposure, guiding decontamination efforts and decisions for re-occupancy of affected sites. The sponge-stick (SS) is a preferred and commonly used device for sample collection to detect both spore-forming and non-spore-forming biothreat agents from non-porous surfaces. Here, in this study, a recently developed high-throughput method (HTM) for processing SS samples to detect viable Bacillus anthracis spores was adapted for detection of non-spore-forming biothreat agents, Yersinia pestis and Francisella tularensis. The scalable HTM was used to process up to 20 SS samples simultaneously, compared to the current stomacher-based method which processes one SS at a time. Comparisons of the HTM and the stomacher-based method were statistically indistinguishable for most experiments (P > 0.05) with HTM recoveries of 37–60 % for Y. pestis inoculated at 102–103 cells/SS and held 48 h at 4 °C to mimic sample transport/storage. The HTM was integrated with Rapid Viability-Polymerase Chain Reaction (RV-PCR) analysis to detect viable Y. pestis in the presence of particulate contamination (Arizona Test Dust, ATD). This approach detected Y. pestis inoculated at 20 cells/SS and ATD did not impact detection (P > 0.05). F. tularensis showed significantly lower recoveries between no-hold time and 48-h hold time (4 °C, P < 0.05) using the HTM, which further testing showed could be due to toxicity of the neutralizing buffer used for SS pre-wetting. With modifications, this method could enhance throughput capacity while maintaining similar recovery efficiencies to current methods for other non-spore-forming bacterial pathogens.

Biological and medical sciences↗
NASA NTRS1985

Analysis of free zone electrophoresis of fixed erythrocytes performed in microgravity

A free fluid zone electrophoresis experiment was performed in the microgravity environment of Space Shuttle flight STS-3 (March 1983). The experiment was designed to confirm observations made on the Apollo-Soyuz mission of 1975 and to test the effect of high red blood cell (RBC) concentration on free fluid electrophoresis. Photographic documentation of cell zone progression in one-hour separations of mixtures of formaldehyde-fixed human and rabbit erythrocytes, which were subjected to a field of approximately 13 V/cm in low ionic strength buffer, was analyzed. One of two columns contained 2 x 10 to the 8th RBC/ml; (low concentration), and the other contained 1 x 10 to the 9th RBC/ml (high concentration). The observed and calculated leading edge displacements of the RBC in the two columns were in agreement, indicating the absence of unexpected effects of the reduced gravity environment. Post-flight analyses of the contents of the columns was not possible, and additional microgravity experiments are needed to evaluate the role of particle-particle interactions in concentrated suspensions undergoing electrophoresis.

Snyder, Robert S.↗
NASA NTRS2001

Model study of ATP and ADP buffering, transport of Ca(2+) and Mg(2+), and regulation of ion pumps in ventricular myocyte

We extended the model of the ventricular myocyte by Winslow et al. (Circ. Res 1999, 84:571-586) by incorporating equations for Ca(2+) and Mg(2+) buffering and transport by ATP and ADP and equations for MgATP regulation of ion transporters (Na(+)-K(+) pump, sarcolemmal and sarcoplasmic Ca(2+) pumps). The results indicate that, under normal conditions, Ca(2+) binding by low-affinity ATP and diffusion of CaATP may affect the amplitude and time course of intracellular Ca(2+) signals. The model also suggests that a fall in ATP/ADP ratio significantly reduces sarcoplasmic Ca(2+) content, increases diastolic Ca(2+), lowers systolic Ca(2+), increases Ca(2+) influx through L-type channels, and decreases the efficiency of the Na(+)/Ca(2+) exchanger in extruding Ca(2+) during periodic voltage-clamp stimulation. The analysis suggests that the most important reason for these changes during metabolic inhibition is the down-regulation of the sarcoplasmic Ca(2+)-ATPase pump by reduced diastolic MgATP levels. High Ca(2+) concentrations developed near the membrane might have a greater influence on Mg(2+), ATP, and ADP concentrations than that of the lower Ca(2+) concentrations in the bulk myoplasm. The model predictions are in general agreement with experimental observations measured under normal and pathological conditions.

NASA Discipline Cardiopulmonary↗
NASA NTRSDate not supplied

Nanopore Sequencing-Based Microbial Air Profiling Method for Crewed Spacecraft

Microbial monitoring of the International Space Station (ISS) atmosphere is vital to maintaining the health of the spacecraft and crew. Key to NASA’s microbial risk assessment is the identity of contaminating microorganisms in the environment. Historically, this has been achieved through impaction-based air sampling followed by culture. Identification of the microorganisms present requires sample return to Earth and lab-based analyses. While this culture-based approach has served to provide alerts to anomalies and overall confidence in the controls in place, it is not suitable for exploration missions with no sample return. Recently, significant advancements in molecular-based microbial monitoring via nanopore sequencing have been implemented onboard the ISS. Building on this work, multiple commercially available air samplers, compatible with downstream molecular analysis, were evaluated for use in the spaceflight environment. Through this assessment, the Coriolis Compact (Bertin Technologies), which uses cyclonic technology to collect bioaerosols onto the surface of a sterile cone, was selected for a larger-scale comparison to the current culture-based monitoring method. Using the Coriolis Compact, 1000 L of air was collected from the breakroom of an office building and a fitness center. The buffer used to dissociate the microbial cells from the surface of the cone was split between the NASA Microbiology Laboratory’s standard culture and Sanger sequencing-based method and the culture-independent nanopore sequencing method. The bacteria identified through culture were present in the nanopore data, with Micrococcus, Staphylococcus, and Moraxella being the most common cultured isolates, which is expected based on the media and growth conditions. Not surprisingly, the nanopore data yielded much higher diversity and paralleled that of previous atmospheric microbiome studies of human-occupied built environments. As compared to the culture-based data where the breakroom and fitness center data sets cluster in proximity, the nanopore data depicts the contrast of these atmospheric microbiomes. Moreover, the nanopore data were sufficient to meet NASA’s risk assessment needs and noted the culturable isolates routinely observed. This nanopore-based atmospheric microbial profiling method will enable near real-time environmental monitoring of crewed spacecraft as future missions extend beyond low-Earth orbit.

Brandon Dunbar↗
NASA NTRS2021

Waypoint Following Dynamics of a Quaternion Error Feedback Attitude Control System

Closed-loop attitude steering can be used to implement alternative attitude maneuvers by using a conventional attitude control system to track a non-standard attitude profile sampled as a series of sequential commands. The idea has been employed in practice to perform zero-propellant maneuvers on the International Space Station and minimum time maneuvers on NASA’s TRACE space telescope. A challenge for operational implementation of the idea is the finite capacity of a space vehicle’s command storage buffer. One approach to mitigate the problem is to downsample-and-hold the attitude commands so that the attitude control system to follows a set of waypoints. This paper explores the waypoint following dynamics of a quaternion error feedback control law for downsample-and-hold. It is shown that downsample-and-hold induces a ripple between downsamples that causes the satellite angular rate to significantly overshoot the desired limit. Analysis in the z-domain is carried out in order to understand the phenomenon. An interpolating Chebyshev-type filter is proposed that allows attitude commands to be encoded in terms of a small set of filter coefficients. Using the interpolating filter, commands can be issued at the ACS rate but with significantly reduced memory requirements. The attitude control system of NASA’s Lunar Reconnaissance Orbiter is used as an example to illustrate the behavior of a practical attitude control system.

Mark Karpenko↗
NASA NTRS1991

Determination of cytoplasmic calcium concentration in Dryopteris spores: a developmentally non-disruptive technique for loading of the calcium indicator fura-2

Germination of Dryopteris spores is mediated by the physiologically active, far-red-absorbing form of phytochrome, Pfr, and external Ca2+ is necessary for the transduction of the light signal. Because knowledge about the cytoplasmic calcium ion concentration, [Ca2+]i, is of great importance for understanding the role of calcium during signal transduction, this value was measured using fura-2 in fern spores undergoing the normal developmental progression into germination. Fura-2 was loaded into the spores by electroporation, which does not disrupt the normal process of germination. The intensity of the fluorescence emission of the loaded fura-2 was analysed by a microspectrophotometric assay of single spores, and successful loading could be obtained by the application of ten electrical pulses (field strength 7.5 kV cm-1, half-life (time constant) 230 microseconds). Fura-2 was alternately excited by light of wavelengths 355 and 385 nm through an inverted fluorescence microscope, and the emitted fura-2 fluorescence was collected by a silicon-intensified video camera. The cytoplasmic calcium ion concentration was calculated from the ratio of the camera output obtained for both wavelengths and displayed by a pseudo-color technique. Spores responded to changes of the extracellular Ca2+ concentration, and this observation is considered as evidence that fura-2 is loaded into the cytoplasm. The substitution of a low external [Ca2+] (1 mM ethyleneglycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA)) by 1 mM CaCl2 caused a fast increase of [Ca2+]i from approx. 50 nM to above 500 nM. In contrast, the subsequent substitution of CaCl2 by EGTA decreased [Ca2+]i again below 100 nM within 0.5 h. Furthermore, the application of ionomycin could initiate a change in [Ca2+]i according to the Ca2+ gradient established between the extracellular medium and cytoplasm. In spores sown on a Ca(2+) -free medium, [Ca2+]i, analysed in a buffer containing EGTA, was found to be around 50 nM during the first days of cultivation, independent of the irradiation protocol. However, if spores were grown in darkness on a Ca(2+) -containing medium and analysed in EGTA, [Ca2+]i was significantly higher (> or = 500 nM). In red-light-irradiated spores, [Ca2+]i was found to decrease with increasing time after irradiation, and was determined to be less than 100 nM when analysis was done 44 h after germination was initiated by the light treatment.

NASA Discipline Plant Biology↗
NASA NTRS1994

Radiation effects in nematodes: Results from IML-1 experiments

The nematode Caenorhabditis elegans was exposed to natural space radiation using the ESA biorack facility aboard Spacelab on International Microgravity Laboratory 1, STS-42. For the major experimental objective dormant animals were suspended in buffer or on agar or immobilized next to CR-39 plastic nuclear track detectors to correlate fluence of HZE particles with genetic events. This configuration was used to isolate mutations in a set of 350 essential genes as well as in the unc-22 structural gene. From flight samples 13 mutants in the unc-22 gene were isolated along with 53 lethal mutations from autosomal regions balanced by a translocation eT1(III;V). Preliminary analysis suggests that mutants from worms correlated with specific cosmic ray tracks may have a higher proportion of rearrangements than those isolated from tube cultures on a randomly sampled basis. Flight sample mutation rate was approximately 8-fold higher than ground controls which exhibited laboratory spontaneous frequencies.

Nelson, G. A.↗
NASA NTRS2016

Traffic Modeling for Deep Space Network in the Human Mars Exploration Era

In this article we describe the analysis and simulation effort of the end-to-end traffic flow for the Deep Space Network (DSN) in the Human Exploration Era, when DSN will provide communication and navigation services for human missions to distant celestial objects like the Moon, asteroids, and Mars. Using the network traffic derived for the 30-day period within July/August 2039 from the Space Communications Mission Model (SCMM), we simulate the bandwidths of the ground links and the buffer profiles of the network nodes. We also use a 2-state Markov scheme that models the store-and-forward mechanism that regulates the ground network traffic. The network traffic modeling and simulation generates ground bandwidth and buffer statistics, which in turn are used to formulate the future DSN ground network bandwidth and storage requirements.

Cheung, Kar-ming↗
NASA NTRS2004

Toward Synthesis, Analysis, and Certification of Security Protocols

Implemented security protocols are basically pieces of software which are used to (a) authenticate the other communication partners, (b) establish a secure communication channel between them (using insecure communication media), and (c) transfer data between the communication partners in such a way that these data only available to the desired receiver, but not to anyone else. Such an implementation usually consists of the following components: the protocol-engine, which controls in which sequence the messages of the protocol are sent over the network, and which controls the assembly/disassembly and processing (e.g., decryption) of the data. the cryptographic routines to actually encrypt or decrypt the data (using given keys), and t,he interface to the operating system and to the application. For a correct working of such a security protocol, all of these components must work flawlessly. Many formal-methods based techniques for the analysis of a security protocols have been developed. They range from using specific logics (e.g.: BAN-logic [4], or higher order logics [12] to model checking [2] approaches. In each approach, the analysis tries to prove that no (or at least not a modeled intruder) can get access to secret data. Otherwise, a scenario illustrating the &tack may be produced. Despite the seeming simplicity of security protocols ("only" a few messages are sent between the protocol partners in order to ensure a secure communication), many flaws have been detected. Unfortunately, even a perfect protocol engine does not guarantee flawless working of a security protocol, as incidents show. Many break-ins and security vulnerabilities are caused by exploiting errors in the implementation of the protocol engine or the underlying operating system. Attacks using buffer-overflows are a very common class of such attacks. Errors in the implementation of exception or error handling can open up additional vulnerabilities. For example, on a website with a log-in screen: multiple tries with invalid passwords caused the expected error message (too many retries). but let the user nevertheless pass. Finally, security can be compromised by silly implementation bugs or design decisions. In a commercial VPN software, all calls to the encryption routines were incidentally replaced by stubs, probably during factory testing. The product worked nicely. and the error (an open VPN) would have gone undetected, if a team member had not inspected the low-level traffic out of curiosity. Also, the use secret proprietary encryption routines can backfire, because such algorithms often exhibit weaknesses which can be exploited easily (see e.g., DVD encoding). Summarizing, there is large number of possibilities to make errors which can compromise the security of a protocol. In today s world with short time-to-market and the use of security protocols in open and hostile networks for safety-critical applications (e.g., power or air-traffic control), such slips could lead to catastrophic situations. Thus, formal methods and automatic reasoning techniques should not be used just for the formal proof of absence of an attack, but they ought to be used to provide an end-to-end tool-supported framework for security software. With such an approach all required artifacts (code, documentation, test cases) , formal analyses, and reliable certification will be generated automatically, given a single, high level specification. By a combination of program synthesis, formal protocol analysis, certification; and proof-carrying code, this goal is within practical reach, since all the important technologies for such an approach actually exist and only need to be assembled in the right way.

Schumann, Johann↗
NASA NTRS1986

Development of AC impedance methods for evaluating corroding metal surfaces and coatings

In an effort to investigate metal surface corrosion and the breakdown of metal protective coatings the AC Impedance Method was applied to zinc chromate primer coated 2219-T87 aluminum. The model 368-1 AC Impedance Measurement System recently acquired by the MSFC Corrosion Research Branch was used to monitor changing properties of coated aluminum disks immersed in 3.5% NaCl buffered at ph 5.5 over three to four weeks. The DC polarization resistance runs were performed on the same samples. The corrosion system can be represented by an electronic analog called an equivalent circuit that consists of transistors and capacitors in specific arrangements. This equivalent circuit parallels the impedance behavior of the corrosion system during a frequency scan. Values for resistances and capacities that can be assigned in the equivalent circuit following a least squares analysis of the data describe changes that occur on the corroding metal surface and in the protective coating. A suitable equivalent circuit was determined that predicts the correct Bode phase and magnitude for the experimental sample. The DC corrosion current density data are related to equivalent circuit element parameters.

Knockemus, Ward↗
DOE OSTI2026

Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy

Accurate representation of metal ions in macromolecular structures is critical for chemical interpretation, computational modeling, and machine-learning methods that rely on Protein Data Bank (PDB) entries. However, the elemental identity of metals modeled in crystallographic structures is often inferred indirectly and rarely validated experimentally. Here, we combine Particle Induced X-ray Emission (PIXE) and X-ray Fluorescence Spectroscopy (XRFS) to determine the elemental composition of protein samples used to generate 70 deposited metalloprotein crystal structures. By analyzing the original protein material employed for crystallization, but before the addition of crystallization buffer solutions, we assess whether the modeled metal ions in deposited structures are consistent with experimentally detectable elemental content. We find that in a majority of cases, the metals modeled in the corresponding PDB entries are inconsistent with the metals present in the protein samples before crystallization, or that additional metals are present but not represented in the structural models. Spectroscopic results were integrated with automated crystallographic validation metrics, including real-space Z-difference (RSZD) analysis and systematic rerefinement, to evaluate atomic-number mismatch at metal sites. PIXE and XRFS show strong agreement for dominant elemental signals and provide complementary, scalable approaches for identifying suspect metal assignments. This work does not address physiological or functional metalation but instead highlights a widespread data integrity issue in deposited macromolecular structures, PDB-wide. These results establish an experimentally corroborated link between elemental identity and crystallographic validation metrics, enabling the large-scale detection of chemically inconsistent annotations in structural databases used for computational modeling and machine learning.

Crystallization↗