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DOE OSTI2025

The microbiologist's guide to metaproteomics

Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.

bioinformatics↗

DOE OSTI2021

Stress- and Time-Dependent Formation of Self-Lubricating In Situ Carbon (SLIC) Films on Catalytically-Active Noble Alloys

Abstract Low shear strength (30 MPa) organic films were grown in situ on Pt 0.9 Au 0.1 surfaces via cyclic sliding contact in dry N 2 with trace concentrations of ambient hydrocarbons. We present a systematic investigation of the stress- and time-dependent film formation. Steady-state friction coefficients were found to be as low as µ ~ 0.015 and inversely proportional to contact pressure, revealing non-Amontonian behavior. Above a Hertzian contact pressure of ~500 MPa, shear strength dropped, indicating an activated process. Raman spectroscopy identified non-uniformity in areal coverage and relative order with contact pressure. Regions of steady-state low-friction behavior exhibited spectra similar to DLC coatings. Atomic force microscopy was used to study the formation and growth of films at the nanoscale. Stress- and time-dependent measurements suggested a sublinear increase of film volume with time, and a transition from growth to wear at a Hertzian contact pressure of ~1.2 GPa.

Jones, Morgan R.↗

DOE OSTI2021

Investigations on the effect of current density on SiO/Si composite electrodes

An oxide layer on the surface of silicon particles is inevitable and is necessary for their application as anode materials for lithium ion batteries with high capacity and durability. However, a thick surficial oxide layer could significantly reduce the capacity of a Si anode. Here, Si nanoparticles with a thick surficial oxide layer of ~20 nm (Si@SiO x ) were fabricated through thermal oxidation and investigated electrochemically. The results revealed that very low current density is needed to activate Si@SiO x anodes during the first formation cycle. Once activated, the Si@SiO x anode can deliver reversible capacity as high as ~1000 mAh/g with low current density. Then, the Si@SiO x can be cycled at higher current densities of >700 mAh/g. Electrochemical impedance spectroscopy (EIS) shows that the lower current density results in lower charge-transfer resistance of the Si@SiO x anode, suggesting a higher degree of lithiation of the surficial oxide layer during low-current activation. EIS analysis also reveals that the lithiation of the surficial oxide is irreversible. We believe that the surface silicon oxide layer is lithiated and forms lithium silicate during the initial activation process. Lithium silicate has high conductivity and allows the lithiation/delithiation of Si core under the oxide layer during following charge and discharge.

25 ENERGY STORAGE↗

DOE OSTI2021

Organometallic complexes as preferred precursors to form molecular Ir(pyalk) coordination complexes for catalysis of oxygen evolution

Our previously reported ‘blue solution’ oxygen-evolution catalyst consists of an isomeric mixture of coordination complexes containing the (pyalk)Ir IV –O–Ir IV (pyalk) core unit and is thus entirely molecular but only when formed from organometallic precursors such as Cp*Ir(pyalk)Cl or Ir(pyalk)(CO) 2 (pyalk = (2-pyridyl)-2-propanolate). We now show that attempts to form it from such obvious coordination precursors as Na[Ir(pyalk)Cl 4 ] or Na[IrCl 2 (pyalk)(O 2 CPh) 2 ], under a variety of conditions, always fail in our hands, leading to a mixture of molecular ‘blue solution’ species and IrO x nanoparticles, rather than the purely homogeneous catalyst formed from organometallic precursors. The loss of the pyalk ligand during the oxidative activation is associated with the nanoparticle generation. External chelating ligands also failed to stop the nanoparticle formation. This work implies the paradoxical conclusion that organometallic complexes are effective as catalyst precursors, even when coordination complexes are the catalytically active species, since the inner-sphere organometallic ligands, although ultimately lost or degraded, may nevertheless have a stabilizing effect sufficient to suppress undesirable nanoparticle production pathways in the activation of the catalyst precursor. Finally, a key aspect of the present study is that organometallic complexes in general may be useful catalyst precursors even if the organometallic ligands are lost in the activation process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

In-situ kinetic study of irradiation induced crystallization in amorphous Al 2 O 3

In the last ten years amorphous alumina coatings, deposited by Pulsed Laser Deposition, emerged as potential key enabling technology in the fields of heavy liquid metal fast reactors (lead and lead-bismuth) and fusion. In the former, as coating of the steel fuel cladding and in the latter as multifunctional coating providing a barrier against tritium permeation, steel corrosion and electrical insulation. Nevertheless, a detailed knowledge of the behavior of this thermodynamically metastable material at high temperatures and under neutron irradiation is still unknown. A knowledge gap that is mandatory to fill up for the deployment of this barrier technology. In the present work, we present a first step towards this goal, by the in-situ dynamic observation of the radiation induced crystallization processes of thin films of amorphous Al 2 O 3 , induced by ion-irradiation over an extensive range of temperatures (400-800 °C). The study was performed at the Intermediate Voltage Electron Microscope (IVEM)-Tandem Facility at Argonne National Laboratory. The experimental findings allow to elucidate the dependence of the grain growth on ion dose and temperature. A kinetic approach has been used to derive the process activation energies and other important parameters.

36 MATERIALS SCIENCE↗

DOE OSTI2023

SootLib: A soot model library for combustion simulation

Soot formation in combustion is an important process that affects radiative heat transfer, flame temperatures, and emissions with health and environmental impacts. Soot formation involves complex chemistry for nucleation, growth, oxidation, and coagulation processes. The soot particles vary widely in size and accurate modeling requires representation of the particle size distribution (PSD). Modeling soot is not trivial, and is only one of several physical processes active in combustion systems. This paper presents a software package called SootLib, which is an open-source library for modeling soot formation and other aerosol systems. SootLib is written in C++, is documented with Doxygen, and is available on GitHub. The library includes several models for soot chemistry and coagulation, and it represents the PSD using either a sectional model or the method of moments (MOM). Four closure approaches for the MOM are implemented allowing up to eight moments: monodispersed, an assumed-shape lognormal distribution, the quadrature method of moments, and the method of moments with interpolative closure. SootLib provides an interface for inclusion in other combustion packages including CFD or reacting flow solvers. The range of models allows comparisons and sensitivity studies, and the modularity facilitates extension to other soot models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Effects of Structural Constraints on Excited-State Properties in Dimeric Cu(I) Diimine Complexes

Copper(I) bis-diimine complexes have played important roles in light-activated processes that can lead to their potential applications in photocatalysis and chemical sensing. Their metal-to-ligand charge-transfer (MLCT) excited-state properties are tunable by various structural factors. Dimeric Cu(I) complexes with connecting diimine derivative ligands offer another structural tuning platform for the excited-state properties. Here, we investigate excited-state properties in two covalently connected dimeric Cu(I)'s with varying structural constraints exerted by the number of carbons in the polyethylene bridge (C0 and C4) connecting the two copper(I) diimine moieties. An interesting feature of Cu(I) diimine complexes is their ability to flatten following a photoinduced structural change. Herein, we observe larger structural constraints and more structural rearrangement required upon excitation of the longer bridged complex C4 to achieve a conformation toward a more flattened tetrahedral coordination geometry compared to the shorter bridged C0. Vibrational wavepacket analysis of these complexes further supports the effect of these structural constraints where we observe a more rapid dephasing of the C0 complex, as opposed to the C4 complex, despite similar normal mode vibrations. The experimental results were supplemented by TDDFT calculations. In conclusion, the studies provide insight into using metal-metal interactions through constraints to tune excited-state dynamics and pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Arctic Cloud‐Base Ice Precipitation Properties Retrieved Using Bayesian Inference

Abstract Cloud‐climate feedbacks are still the greatest source of uncertainty in current climate projections. Arctic clouds, which are predominantly stratiform and supercooled, often long‐lived, and nearly continuously precipitate ice particles, contribute roughly 10% of the uncertainty attributed to the global cloud feedback. This Arctic cloud uncertainty is driven by incomplete observational and theoretical knowledge required to estimate and explain the state and active processes occurring in those clouds. A focus on ice precipitation properties at Arctic cloud base rather than the surface deconfounds the product of cloud condensate sink processes from the influence of the atmospheric thermodynamic state below cloud base, rendering cloud‐base properties a more appealing target for inference and evaluation of model simulations. Here I describe an inverse model for the estimation of cloud base ice precipitation properties over Utqiagvik, North Slope of Alaska, using the synthesis of ground‐based radar and lidar measurements. By leveraging a Markov Chain Monte Carlo algorithm as the core of the inverse model, a wide range of particle size distributions are sampled, and different combinations of ice habit models are examined, both of which are typically fixed in other retrieval methods. Results show intriguing links between different cloud base thermodynamic and ice precipitation properties. Apparent ice number concentration enhancements at temperatures of −5 and −15°C suggest possible secondary ice production (SIP). The analysis alludes to an overestimation of SIP occurrence and intensity, especially in studies relying only on radar or lidar measurements. Finally, reflectivity‐dependent ice precipitation rate and ice water content parameterizations are presented.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Experimental Observation of a New Attenuation Mechanism in hcp ‐Metals That May Operate in the Earth's Inner Core

Abstract Seismic observations show the Earth's inner core has significant and unexplained variation in seismic attenuation with position, depth and direction. Interpreting these observations is difficult without knowledge of the visco‐ or anelastic dissipation processes active in iron under inner core conditions. Here, a previously unconsidered attenuation mechanism is observed in zinc, a low pressure analog ofhcp‐iron, during small strain sinusoidal deformation experiments. The experiments were performed in a deformation‐DIA combined with X‐radiography, at seismic frequencies (∼0.003–0.1 Hz), high pressure and temperatures up to ∼80% of melting temperature. Significant dissipation (0.077 ≤ Q −1 (ω) ≤ 0.488) is observed along with frequency dependent softening of zinc's Young's modulus and an extremely small activation energy for creep (⩽7 kJ mol −1 ). In addition, during sinusoidal deformation the original microstructure is replaced by one with a reduced dislocation density and small, uniform, grain size. This combination of behavior collectively reflects a mode of deformation called “internal stress superplasticity”; this deformation mechanism is unique to anisotropic materials and activated by cyclic loading generating large internal stresses. Here we observe a new form of internal stress superplasticity, which we name as “elastic strain mismatch superplasticity.” In it the large stresses are caused by the compressional anisotropy. If this mechanism is also active inhcp‐iron and the Earth's inner‐core it will be a contributor to inner‐core observed seismic attenuation and constrain the maximum inner‐core grain‐size to ≲10 km.

Geochemistry & Geophysics↗

DOE OSTI2024

Photoinitiated thermoset polymerization through controlled release of metathesis catalysts encapsulated in poly(phthalaldehyde)

Photoinitiated polymerization enables spatiotemporal control of reaction conditions and can thereby generate materials with high complexity while consuming minimal energy. Where ring opening metathesis polymerization (ROMP) is concerned, photo-activated processes are typically enabled by chemical inhibition of ruthenium carbenes via the careful design of complexed ligands such that photoactivation can proceed through an isomerization or ligand dissociation event. In this contribution, we have explored a new approach to photoinitiation of ROMP based on physical inhibition through microencapsulation and controlled release of metathesis catalysts. Micron-sized particles of poly(phthalaldehyde) (PPA), catalyst, and photoacid generator were fabricated by spray drying. The particles were dispersed in dicyclopentadiene monomer, after which polymerization was initiated through temperature or UV exposure, both inducing depolymerization of the PPA particles and in situ catalyst release. The monomer/particle dispersions were found to be stable and reproducibly polymerizable with 3 weeks of storage at room temperature. Furthermore, the dispersions can be used for both photo- and thermal-initiated frontal ROMP, yielding a polymerized thermoset of equivalent properties to conventional bulk- and frontally-polymerized analogues. In conclusion, this work will ultimately enable new manufacturing techniques for ROMP-based materials, due to the modular, easily tunable nature of the underlying initiating system and its unparalleled stability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

The role of collective elasticity on activated structural relaxation, yielding, and steady state flow in hard sphere fluids and colloidal suspensions under strong deformation

In this work, we theoretically study the effect of external deformation on activated structural relaxation and aspects of the nonlinear mechanical response of glassy hard sphere fluids in the context of elastically collective nonlinear Langevin equation theory. This microscopic force-based approach describes activated relaxation as a coupled local–nonlocal event involving caging and longer range collective elasticity, with the latter becoming more important and ultimately dominant with increasing packing fraction under equilibrium conditions. The central new question we address is how this physical picture of activated relaxation, and the relative importance of local caging vs collective elasticity physics, depends on external deformation. Theoretical predictions are presented for deformation-induced enhancement of mobility, the onset of relaxation speed up at remarkably low values of stress, strain, or shear rate, apparent power law thinning of the steady state structural relaxation time and viscosity, a non-vanishing activation barrier in the shear thinning regime, an apparent Herschel–Bulkley form of the rate dependence of the steady state shear stress, exponential growth of different measures of a dynamic yield or flow stress with the packing fraction, and reduced fragility and dynamic heterogeneity under deformation. The results are contrasted with experiments and simulations, and qualitative or better agreement is found. An overarching conclusion is that deformation strongly reduces the importance of longer range collective elastic effects relative to the local caging aspect for most, but not all, physical questions, with deformation-dependent fragility and dynamic heterogeneity phenomena being qualitatively sensitive to collective elasticity. Overall, nonlinear rheology is predicted to be a more local problem than quiescent structural relaxation, albeit with deformation-modified activated processes still important.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Nonadiabatic transition paths from quantum jump trajectories

We present a means of studying rare reactive pathways in open quantum systems using transition path theory and ensembles of quantum jump trajectories. This approach allows for the elucidation of reactive paths for dissipative, nonadiabatic dynamics when the system is embedded in a Markovian environment. Here, we detail the dominant pathways and rates of thermally activated processes and the relaxation pathways and photoyields following vertical excitation in a minimal model of a conical intersection. We find that the geometry of the conical intersection affects the electronic character of the transition state as defined through a generalization of a committor function for a thermal barrier crossing event. Similarly, the geometry changes the mechanism of relaxation following a vertical excitation. Relaxation in models resulting from small diabatic coupling proceeds through pathways dominated by pure dephasing, while those with large diabatic coupling proceed through pathways limited by dissipation. The perspective introduced here for the nonadiabatic dynamics of open quantum systems generalizes classical notions of reactive paths to fundamentally quantum mechanical processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Quantifying trapped magnetic vortex losses in niobium resonators at mK temperatures

Trapped magnetic vortices in niobium introduce microwave losses that degrade the performance of superconducting resonators. While such losses have been extensively studied above 1 K, we report here their direct quantification in the millikelvin and low-photon regime relevant to quantum devices. Using a high-quality factor 3D niobium cavity cooled through its superconducting transition in controlled magnetic fields, we isolate vortex-induced losses and find the resistive component of the sensitivity to trapped flux S to be approximately 2 n Ω/mG at 10 mK and 6 GHz. The decay rate is initially dominated by two-level system (TLS) losses from the native niobium pentoxide, with vortex-induced degradation of T 1 occurring above B trap ∼ 50 mG. In the absence of the oxide, even 10 mG of trapped flux limits performance, Q 0 ∼ 10 10 , or T 1 ∼ 350 ms, underscoring the need for stringent magnetic shielding. The resistive sensitivity, S, decreases with temperature and remains largely field-independent, whereas the reactive component, S′, exhibits a maximum near 0.8 K. These behaviors are well modeled within the Coffey–Clem framework in the zero-creep limit, under the assumption that vortex pinning is enhanced by thermally activated processes. Our results suggest that niobium-based transmon qubits can tolerate vortex-induced dissipation at trapped field levels up to several hundred mG, but achieving long coherence times still requires careful magnetic shielding to suppress lower-field losses from other mechanisms.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Crystal structure and catalytic mechanism of drimenol synthase, an unusual bifunctional terpene cyclase–phosphatase

Drimenol synthase fromAquimarina spongiae(AsDMS) is a highly unusual chimera that integrates two distinct, sequential isoprenoid processing activities within a single polypeptide chain. AsDMS catalyzes the class II cyclization of farnesyl diphosphate (FPP) to form drimenyl diphosphate, which then undergoes enzyme-catalyzed hydrolysis to yield drimenol, a bioactive sesquiterpene alcohol with antifungal and anticancer properties. Here, we report the X-ray crystal structures of AsDMS and its complex with a sesquiterpene thiol. The AsDMS structure exhibits a didomain architecture consisting of a terpene cyclase β domain and a haloacid dehalogenase-like phosphatase domain, with two distinct active sites located on opposite sides of the protein. Mechanistic studies show that dephosphorylation of the drimenyl diphosphate intermediate proceeds through stepwise hydrolysis such that two equivalents of inorganic phosphate rather than inorganic pyrophosphate are coproducts of the reaction sequence. When the AsDMS reaction is performed in H 2 18 O, 18 O is not incorporated into drimenol, indicating that the hydroxyl oxygen of drimenol originates from the prenyl oxygen of FPP rather than a water molecule from bulk solution. These results correct a mechanistic proposal previously advanced by another group. Surprisingly, AsDMS exhibits substrate promiscuity, catalyzing the conversion of the slowly reactive substrate mimic farnesyl-S-thiolodiphosphate into cyclic and linear sesquiterpene products. Structural and mechanistic insights gained from AsDMS illustrate the functional diversity of terpene biosynthetic enzymes and provide a foundation for engineering “designer cyclase” assemblies capable of generating a wide variety of terpenoid products.

Science & Technology - Other Topics↗

DOE OSTI2023

HCOO - aq Degradation in Droplets by OH aq in an Atmospheric Pressure Glow Discharge

Plasmas in contact with liquids can degrade organic molecules in solution, as reactive oxygen and nitrogen species produced in the plasma solvate into the liquid. Immersing small droplets (tens of microns in diameter) in the plasma can more rapidly activate the liquid compared to treating a large volume of liquid with a smaller surface-to-volume ratio. The interactions between a radio frequency glow discharge sustained in He/H 2 O and a water droplet containing formate (HCOO - aq ) immersed in and flowing through the plasma were modeled using a 0-dimensional global plasma chemistry model to investigate these activation processes. HCOO - aq interacts with OH aq , produced from solvation of OH from the gas phase. HCOO - aq concentrations were benchmarked with previously reported experimental measurements. The diameter of the droplet, initial HCOO - aq concentration, and gas flow rate affect only the HCOO - aq concentration and OH aq density, leaving the OH density in the gas phase unaffected. Power deposition and gas mixture (e.g., percentage of H 2 O) change both the gas and liquid phase chemistry. A general trend was observed – during the first portion of droplet exposure to the plasma, OH aq primarily consumes HCOO - aq . However, O2 - aq , a byproduct of HCOO - aq consumption, consumes OH aq once O2 - aq reaches a critically large density. Using HCOO - aq as a surrogate for OH aq sensitive contaminants, combinations of residence time, droplet diameter, water vapor density, and power will determine the optimum remediation strategy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Helium bubble size effects on the surface morphological response of plasma-facing tungsten

Abstract We report a simulation study on the effects of helium (He) bubble size on the morphological evolution and pattern formation on the surface of tungsten used as a plasma-facing component (PFC) in nuclear fusion devices. We have carried out a systematic investigation based on self-consistent dynamical simulations of surface morphological evolution according to an atomistically-informed, 3D continuum-scale model that captures well the relevant length and time scales of surface nanostructure formation in PFC tungsten. The model accounts for PFC surface diffusion, driven by the biaxial compressive stress originating from the over-pressurized He bubbles in the near-surface region of PFC tungsten as a result of He plasma exposure, combined with the formation of self-interstitial atoms in tungsten that diffuse toward the PFC surface and the flux of surface adatoms generated as a result of surface vacancy-adatom pair formation upon He implantation; this transport of surface adatoms contributes to the anisotropic growth of surface nanostructural features due to the different rates of adatom diffusion along and across step edges of islands on the tungsten surface. Our detailed analysis reveals that varying the average He bubble size plays an important role in the PFC surface growth kinetics as well as the resulting surface topography. Specifically, we find that an increase in the He bubble size leads to a deceleration in the growth rate of the tungsten nanotendrils that emanate from the PFC surface. We also find that the separation distance between the resulting surface features increases with increasing He bubble size, as well as over time. This coarsening effect is a thermally activated process resulting in an accurate description of the temperature dependence of the average surface feature separation by an Arrhenius relation.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Physics makes the difference: Bayesian optimization and active learning via augmented Gaussian process

Abstract Both experimental and computational methods for the exploration of structure, functionality, and properties of materials often necessitate the search across broad parameter spaces to discover optimal experimental conditions and regions of interest in the image space or parameter space of computational models. The direct grid search of the parameter space tends to be extremely time-consuming, leading to the development of strategies balancing exploration of unknown parameter spaces and exploitation towards required performance metrics. However, classical Bayesian optimization (BO) strategies based on the Gaussian process (GP) do not readily allow for the incorporation of the known physical behaviors or past knowledge. Here we explore a hybrid optimization/exploration algorithm created by augmenting the standard GP with a structured probabilistic model of the expected system’s behavior. This approach balances the flexibility of the non-parametric GP approach with a rigid structure of physical knowledge encoded into the parametric model. The fully Bayesian treatment of the latter allows additional control over the optimization via the selection of priors for the model parameters. The method is demonstrated for a noisy version of a standard univariate test function used to evaluate optimization algorithms and further extended to physical lattice models. This methodology is expected to be universally suitable for injecting prior knowledge in the form of physical models and past data in the BO framework.

42 ENGINEERING↗

DOE OSTI2023

Reminiscence of Classical Chaos in Driven Transmons

Transmon qubits are ubiquitously used in superconducting quantum information processor architectures. Strong drives are required to realize fast, high-fidelity, gates and measurements, including parametrically activated processes. Here, we show that even off-resonant drives, in regimes routinely used in experiments, can cause strong modifications to the structure of the transmon spectrum rendering a large part of it chaotic. Accounting for the full nonlinear dynamics of the transmon in a Floquet-Markov formalism, we find that these chaotic states, often neglected through the hypothesis that the anharmonicity is weak, strongly impact the lifetime of the transmon’s computational states. In particular, we observe that chaos-assisted quantum phase slips greatly enhance band dispersions. In the presence of a measurement resonator, we find that approaching chaotic behavior correlates with strong transmon-resonator hybridization, and an average resonator response centered on the bare resonator frequency. These results lead to a photon-number threshold characterizing the appearance of chaos-induced quantum demolition effects during strong-drive operations, such as dispersive qubit readout. The phenomena described here are expected to be present in all circuits based on low-impedance Josephson junctions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗