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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation

Cyanophycin is a bacterial biopolymer used for storage of fixed nitrogen. It is composed of a backbone of L-aspartate residues with L-arginines attached to each of their side chains. Cyanophycin is produced by cyanophycin synthetase 1 (CphA1) using Arg, Asp and ATP, and is degraded in two steps. First, cyanophycinase breaks down the backbone peptide bonds, releasing β-Asp-Arg dipeptides. Then, these dipeptides are broken down into free Asp and Arg by enzymes with isoaspartyl dipeptidase activity. Two bacterial enzymes are known to possess promiscuous isoaspartyl dipeptidase activity: isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA). We performed a bioinformatic analysis to investigate whether genes for cyanophycin metabolism enzymes cluster together or are spread around the microbial genomes. Many genomes showed incomplete contingents of known cyanophycin metabolizing genes, with different patterns in various bacterial clades. Cyanophycin synthetase and cyanophycinase are usually clustered together when recognizable genes for each are found within a genome. Cyanophycinase and isoaspartyl dipeptidase genes typically cluster within genomes lacking cphA1. About one-third of genomes with genes for CphA1, cyanophycinase and IaaA show these genes clustered together, while the proportion is around one-sixth for CphA1, cyanophycinase and IadA. We used X-ray crystallography and biochemical studies to characterize an IadA and an IaaA from two such clusters, in Leucothrix mucor and Roseivivax halodurans, respectively. The enzymes retained their promiscuous nature, showing that being associated with cyanophycin-related genes did not make them specific for β-Asp-Arg dipeptides derived from cyanophycin degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Real-time degradation dynamics of hydrated per- and polyfluoroalkyl substances (PFASs) in the presence of excess electrons

Per- and polyfluoroalkyl substances (PFASs) are synthetic chemicals that are harmful to both the environment and human health. In this work, using self-interaction-corrected Born–Oppenheimer molecular dynamics simulations, we provide the first real-time assessment of PFAS degradation in the presence of excess electrons. In particular, we show that the initial phase of the degradation involves the transformation of an alkane-type C–C bond into an alkene-type C[double bond, length as m-dash]C bond in the PFAS molecule, which is initiated by the trans elimination of fluorine atoms bonded to these adjacent carbon atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

First principles modeling of polymer encapsulant degradation in Si photovoltaic modules

An outstanding issue in the longevity of photovoltaic (PV) modules is the accelerated degradation caused by the presence of moisture. Moisture leads to interfacial instability, de-adhesion, encapsulant decomposition, and contact corrosion. However, experimental characterization of moisture in PV modules is not trivial and its impacts can take years or decades to establish in the field, presenting a major obstacle to designing high-reliability modules. First principles calculations provide an alternative way to study the ingress of water and its detrimental effect on the structure and decomposition of the polymer encapsulant and interfaces between the encapsulant and the semiconductor, the metal contacts, or the dielectric layer. Here, we use density functional theory (DFT) computations to model single chain, crystalline and cross-linked structures, infrared (IR) signatures, and degradation mechanisms of ethylene vinyl acetate (EVA), the most common polymer encapsulant used in Si PV modules. IR-active modes computed for low energy EVA structures and possible decomposition products match well with reported experiments. The EVA decomposition energy barriers computed using the Nudged Elastic Band (NEB) method show a preference for acetic acid formation as compared to acetaldehyde, are lowered in the presence of a water solvent or hydroxyl ion catalyst, and match well with reported experimental activation energies. This systematic study leads to a clear picture of the hydrolysis-driven decomposition of EVA in terms of energetically favorable mechanisms, possible intermediate structures, and IR signatures of reactants and products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Understanding multi-scale battery degradation with a macro-to-nano zoom through its hierarchy

Lithium-ion batteries (LIBs) feature structural and chemical complexities across a broad range of length scales. It is the hierarchy of the battery structure that determines its functionality. An in-depth understanding of the battery function, degradation, and failure mechanisms requires a thorough and systematic investigation from structural, chemical, mechanical, and dynamic perspectives. Here we present a macro-to-nano zoom through the hierarchy of a commercial 18650 type LIB using a suite of state-of-the-art X-ray microscopy techniques. Damage, deformation, and heterogeneity at different length scales are visualized and are associated with different degradation phenomena and mechanisms. Our results highlight the importance of the mechanical properties of the cathode material, which could impact both the immediate and the long-term cell behaviors significantly. While this study focuses on a commercial lithium cell with a standard configuration, our findings can be extrapolated and are applicable to the development of next-generation energy storage technology, e.g. solid-state batteries.

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

Light-enhanced oxygen degradation of MAPbBr 3 single crystal

Organometal halide perovskites are promising materials for optoelectronic applications, whose commercial realization depends critically on their stability under multiple environmental factors. In this study, a methylammonium lead bromide (MAPbBr 3 ) single crystal was cleaved and exposed to simultaneous oxygen and light illumination under ultrahigh vacuum (UHV). The exposure process was monitored using X-ray photoelectron spectroscopy (XPS) with precise control of the exposure time and oxygen pressure. It was found that the combination of oxygen and light accelerated the degradation of MAPbBr 3 , which could not be viewed as a simple addition of that by oxygen-only and light-only exposures. The XPS spectra showed significant loss of carbon, bromine, and nitrogen at an oxygen exposure of 10 10 Langmuir with light illumination, approximately 17 times of the additive effects of oxygen-only and light-only exposures. It was also found that the photoluminescence (PL) emission was much weakened by oxygen and light co-exposure, while previous reports had shown that PL was substantially enhanced by oxygen-only exposure. Measurements using a scanning electron microscope (SEM) and focused ion beam (FIB) demonstrated that the crystal surface was much roughened by the co-exposure. Furthermore, Density functional theory (DFT) calculations revealed the formation of superoxide and oxygen induced gap state, suggesting the creation of oxygen radicals by light illumination as a possible microscopic driving force for enhanced degradation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Insights into catalyst degradation during alkaline water electrolysis under variable operation

Energy conversion technologies that are key to decarbonization efforts face significant durability challenges due to variable operation. Understanding the impact of variable operation on catalytic stability and identifying the key variables that dictate degradation is crucial for developing robust technologies. Here, we present a comprehensive investigation of the effects of variable operation on liquid alkaline water electrolysis. Our findings reveal that variable operation induces severe degradation of Ni, Fe, and Co catalytic films that is not observed during steady-state operation. By systematically interrogating the electrode discharge during simulated shutdown tests using Raman spectroscopy and mass spectrometry techniques, we uncover significant alterations caused by reverse currents in real time. These include changes in crystal structure, composition, film thickness, electronic conductivity, and dissolution rates. Lab-scale electrolyzer experiments further highlight the impact of variable operation on catalyst materials under relevant conditions. Finally, we provide guidelines for leveraging these insights to advance electrocatalysis research. This work underscores the importance of integrating realistic stressors into stability testing and offers practical guidelines for catalyst design, performance evaluation, and industrial implementation. Collectively, insights from this study will drive the development of more resilient energy conversion technologies.

Marquez, Raul A. [Univ. of Texas, Austin, TX (Unit↗
DOE OSTI2026

Molecularly engineered Li compensation agent-integrated separator enabling regeneration of degraded LiFePO 4

Lithium replenishment separators (LRSs) integrating pre-lithiation agents can regenerate degraded lithium cathodes via facile reassembly with a fresh anode and the LRS. A persistent challenge is the formation of gas or solid residues during pre-lithiation. To address this, for the first time, we develop an LRS based on a molecularly engineered dilithium salt of tetrafluorohydroquinone, which compensates for lithium loss while generating decomposition products that dissolve in the electrolyte as a favorable additive, without forming gas or solid residues, thus offering a green route for lithium compensation. A pristine LiFePO 4 ‖graphite full cell with the LRS exhibits 9.3% higher overall capacity than a polypropylene separator (PPS) cell after 50 cycles at 0.5C, and the degraded LiFePO 4 ‖graphite full cell incorporating this LRS achieves a 44.9% higher capacity than the PPS-based cell after 200 cycles at 0.5C. Our LRS demonstrates strong potential for high-performance lithium-ion batteries and spent battery regeneration.

Tao, Fujun [Worcester Polytechnic Institute, MA (U↗
DOE OSTI2024

Degradation of performance in ICF implosions due to Rayleigh–Taylor instabilities: A Hamiltonian perspective

The Rayleigh–Taylor instability (RTI) is an ubiquitous phenomenon that occurs in inertial-confinement-fusion (ICF) implosions and is recognized as an important limiting factor of ICF performance. To analytically understand the RTI dynamics and its impact on ICF capsule implosions, we develop a first-principle variational theory that describes an imploding spherical shell undergoing RTI. The model is based on a thin-shell approximation and includes the dynamical coupling between the imploding spherical shell and an adiabatically compressed fluid within its interior. Using a quasilinear analysis, we study the degradation trends of key ICF performance metrics (e.g., stagnation pressure, residual kinetic energy, and areal density) as functions of initial RTI parameters (e.g., the initial amplitude and Legendre mode), as well as the 1D implosion characteristics (e.g., the convergence ratio). We compare analytical results from the theory against nonlinear results obtained by numerically integrating the governing equations of this reduced model. Our findings emphasize the need to incorporate polar flows in the calculation of residual kinetic energy and demonstrate that higher convergence ratios in ICF implosions lead to significantly greater degradation of key performance metrics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

The mechanism of hydroxyapatite coatings degradation at high substrate temperatures

Physical vapor deposition methods used for hydroxyapatite (HA) coatings typically require elevated substrate temperatures and post-deposition annealing to induce crystallization. However, such thermal treatments can degrade both the mechanical integrity and bioactivity of the coating, particularly when substrate temperatures exceed 500 °C. The mechanisms underlying these phenomena remain insufficiently understood. In this study, HA thin films were deposited on silicon and Ti6Al4V substrates using pulsed laser deposition and were systematically characterized to elucidate these mechanisms. XPS and SIMS analyses revealed a temperature-dependent loss of OH − and PO 4 3− groups, an increased Ca/P ratio, and the formation of interfacial oxides, all of which contribute to weakened adhesion. To clarify the temperature-dependent decline in bioactivity, protein adsorption behavior was analyzed using a Kramers-type kinetic framework; the fitted desorption kinetics indicate that coatings deposited near ∼500 °C provide the most stable protein attachment, whereas higher temperatures accelerate desorption due to dehydroxylation and carbonate substitution. Together, these findings provide mechanistic insight into the thermal degradation of HA coatings and offer a framework for optimizing deposition parameters to preserve stoichiometry, adhesion, and bioactivity for long-term biomedical applications.

Kylychbekov, Salizhan [Univ. of Oxford (United Kin↗
DOE OSTI2020

Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary

Significance Biomolecules, such as proteins or nucleic acids, can condense into liquid droplets whose biological or technological function depends on interactions with other solutes. We explore such interactions using a system of self-assembled DNA particles that forms liquid droplets which are degraded by an active solute, a restriction enzyme. We find that enzymes are able to penetrate the droplets when the liquid is poised near the phase boundary, enhancing the degradation rate and, in certain cases, causing internal bubbling. These results point to a complex interplay of phase stability and solute transport in liquid–liquid phase-separating macromolecular systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Vibrio MARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy

Vibrio vulnificus causes life-threatening wound and gastrointestinal infections, mediated primarily by the production of a Multifunctional-Autoprocessing Repeats-In-Toxin (MARTX) toxin. The most commonly present MARTX effector domain, the Makes Caterpillars Floppy-like (MCF) toxin, is a cysteine protease stimulated by host adenosine diphosphate (ADP) ribosylation factors (ARFs) to autoprocess. Here, we show processed MCF then binds and cleaves host Ra s-related proteins in b rain (Rab) guanosine triphosphatases within their C-terminal tails resulting in Rab degradation. We demonstrate MCF binds Rabs at the same interface occupied by ARFs. Moreover, we show MCF preferentially binds to ARF1 prior to autoprocessing and is active to cleave Rabs only subsequent to autoprocessing. We then use structure prediction algorithms to demonstrate that structural composition, rather than sequence, determines Rab target specificity. We further determine a crystal structure of aMCF as a swapped dimer, revealing an alternative conformation we suggest represents the open, activated state of MCF with reorganized active site residues. The cleavage of Rabs results in Rab1B dispersal within cells and loss of Rab1B density in the intestinal tissue of infected mice. Collectively, our work describes an extracellular bacterial mechanism whereby MCF is activated by ARFs and subsequently induces the degradation of another small host guanosine triphosphatase (GTPase), Rabs, to drive organelle damage, cell death, and promote pathogenesis of these rapidly fatal infections.

Science & Technology - Other Topics↗
DOE OSTI2025

Resolving electrochemically triggered topological defect dynamics and structural degradation in layered oxides

Understanding topological defects-controlled structural degradation of layered oxides—a key cathode material for high-performance lithium-ion batteries—plays a critical role in developing next-generation cathode materials. Here, by constructing a nanobattery in an electron microscope enabling atomic-scale monitoring of electrochemcial reactions, we captured the electrochemically driven atomistic dynamics and evolution of dislocations—a most important topological defect in material. We deciphered how dislocations nucleate, move, and annihilate within layered cathodes at the atomic scale. Specifically, we found two types of dislocation configurations, i.e., single dislocations and dislocation dipoles. Both pure dislocation glide/climb and mixed motions were captured, and the dislocation glide and climb velocities were first experimentally measured. Moreover, dislocation activity-mediated structural degradation such as crack nucleation, phase transformation, and lattice reorientation was unraveled. Our work provides deep insights into the atomistic dynamics of electrochemically driven dislocation activities in layered oxides.

Wang, Chunyang (ORCID:0000000184613952)↗
DOE OSTI2024

Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader

Abstract Bacteria that are chronically exposed to high levels of pollutants demonstrate genomic and corresponding metabolic diversity that complement their strategies for adaptation to hydrocarbon-rich environments. Whole genome sequencing was carried out to infer functional traits of Serratia marcescens strain SMTT recovered from soil contaminated with crude oil. The genome size (Mb) was 5,013,981 with a total gene count of 4,842. Comparative analyses with carefully selected S. marcescens strains, 2 of which are associated with contaminated soil, show conservation of central metabolic pathways in addition to intra-specific genetic diversity and metabolic flexibility. Genome comparisons also indicated an enrichment of genes associated with multidrug resistance and efflux pumps for SMTT. The SMTT genome contained genes that enable the catabolism of aromatic compounds via the protocatechuate para-degradation pathway, in addition to meta-cleavage of catechol (meta-cleavage pathway II); gene enrichment for aromatic compound degradation was markedly higher for SMTT compared to the other S. marcescens strains analysed. Our data presents a valuable genetic inventory for future studies on strains of S. marcescens and provides insights into those genomic features of SMTT with industrial potential.

Genetics & Heredity↗
DOE OSTI2025

Sustainable production of plastic-degrading enzymes in Chlamydomonas pacifica

AbstractThe discovery of a new extremophile alga,Chlamydomonas pacifica, provides an opportunity to expand on heterologous protein expression beyond the traditionalChlamydomonas reinhardtii. C. pacificais a unicellular extremophile capable of surviving at high pH, high temperatures, and high salinity. These various growth conditions allow C. pacifica to outcompete any invading contaminants in open-air environments. Developing this novel species as a platform for recombinant protein production could significantly advance commercial microalgal recombinant protein production. We have previously shown thatC. reinhardtiican secrete a plastic-degrading enzyme: a PETase known as PHL7. This PETase is capable of cleaving ester bonds and has been used commercially for the degradation of PET plastics. However, the expression of such an enzyme has yet to be done in open raceway ponds and on a large scale. Here, we describe the culturing of PHL7 transgenic C. pacifica strain in three 80L raceway ponds and the measurements of recombinant enzymatic expression and activity found in the culture media. Our work provides proof of concept that this new organism can produce functional PHL7 enzymes in addition to producing the valuable components that inherently exist in theC. pacificaalgae biomass.Graphical Abstract

Diaz, Crisandra Jade (ORCID:0000000173429041)↗
DOE OSTI2021

Interfacial Characterization of Positive Bias Voltage Degradation in PV Modules

Degradation from high system voltage is a prevailing failure mode in fielded photovoltaic modules, and the degradation mechanism is inherently dependent on the bias polarity. Here we report the effects of positive bias. Modules under positive bias demonstrated a significant photocurrent loss caused by two routes. First, delamination and discoloration of the silicon nitride layer, leading to optical loss determined by reflectance measurements. Second, chemical discoloration of the cell gridlines and encapsulant (EVA), which is linked to an electrochemical reaction at the silver electrodes. Chemical compositional analysis using X-ray photoemission spectroscopy demonstrated that the discoloration is attributed to Ag 2 S and/or Ag 2 O. Evidence of Ag ion migration from the cell grid into the encapsulant is observed after shallow depth profiling on the EVA surface. However, Ag was not detected at the EVA/glass interface, inferring limited Ag ion transport through the EVA. The source of sulfur is believed to be ambient air, which diffused into the module through the breathable backsheet.

characterization↗
DOE OSTI2026

Disruption of starch biosynthesis and triacylglycerol degradation impairs growth but improves photosynthesis in Arabidopsis

Enhancing lipid accumulation by redirecting carbon from starch to triacylglycerol (TAG) in vegetative tissues is a promising strategy for developing high-energy-density crops for bioenergy production. However, our understanding of how starch and TAG metabolism interact and how this interaction affects growth and photosynthesis is incomplete. Here, we investigated the metabolic and physiological consequences of disrupting starch biosynthesis and TAG turnover in Arabidopsis thaliana by generating single, double, and triple mutants involving ADG1 (starch biosynthesis), TGD1 (lipid trafficking), and SDP1\\\\\\\\r\\\\\\\\n(TAG lipase). Unexpectedly, elimination of starch biosynthesis lowered TAG levels in the high-TAG-accumulating tgd1 mutant, primarily through enhanced TAG breakdown. This decline was completely reversed by sucrose supplementation, suggesting that TAG degradation was induced by carbon limitation.\\\\\\\\r\\\\\\\\nGenetic suppression of TAG turnover via SDP1 disruption in the starchless tgd1 adg1-1 background led to a nine-fold rise in leaf TAG accumulation in the tgd1 sdp1 adg1-1 triple mutant, together with enhanced photosynthetic performance. However, this metabolic reprogramming incurred growth penalties.\\\\\\\\r\\\\\\\\nOur results highlight the role of dynamic TAG turnover in maintaining metabolic balance and photosynthesis in starch-deficient backgrounds. These findings underscore the need for refined metabolic engineering strategies that coordinate TAG biosynthesis and degradation to optimize lipid accumulation in bioenergy crops.

59 BASIC BIOLOGICAL SCIENCES↗