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DOE OSTI2018

Unfolding of IgG domains detected by non-reducing SDS-PAGE

Highlights: • Aberrant artefactual mAb masses and size heterogeneity noted by non-reducing SDS-PAGE. • This effect depends on pre-electrophoresis sample heating temperatures and conditions. • These phenomena are also observed for a commercial human IgG{sub 1} polyclonal antibody. • Multiple observed bands hypothesized to reflect IgG domain thermal unfolding in SDS. • These results are likely relevant to analyses of many monoclonal and polyclonal Abs. Monoclonal antibodies are very important in modern therapeutics and constitute a substantial percentage of newly approved drugs. Every therapeutic monoclonal antibody must be analyzed for structural and functional integrity, and all protein heterogeneities need to be identified and quantified. The conformational stabilities of the monoclonal antibodies are also important for antibody storage and handling stabilities. One of the first and simplest of the structural analysis techniques utilized is SDS-PAGE, which can be performed both with and without prior reduction to break disulfide bonds. This permits sizing of both heavy and light chains in the reduced condition, and sizing of the intact antibody and any disulfide aggregates in the non-reduced condition. Analyzing our human anti-cocaine monoclonal antibody, we noted unexpectedly larger apparent molecular weights and apparent protein size heterogeneities using non-reducing SDS-PAGE. These apparent molecular weight heterogeneities are not consistent with other analysis techniques. Heterogeneities were noted using several heating and pre-electrophoretic sample preparation protocols, and are modified by the inclusion of small concentrations of certain alcohols such as propanol and butanol. All of these unexpected results were also observed for a commercial human IgG{sub 1} antibody, suggesting that these observations are applicable to IgGs in general. Thus, careful attention must be paid to the interpretation of non-reducing SDS-PAGE results for IgGs. It is hypothesized that differential thermal unfolding of the Fab, CH2 and CH3 domains of the IgGs in SDS give rise to the stable, discrete bands observed using different heating protocols prior to non-reducing SDS-PAGE.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Automated label flows for excited states of correlation functions in lattice gauge theory

Extracting excited states from lattice gauge theory correlation functions can be achieved through $χ^2$ minimization fits or algebraic approaches such as the variational method and Prony's method. Performing any kind of error analysis often leads to overlapping confidence regions of model parameters, even when the spectrum is not particularly dense. To correctly estimate errors, one must beware of mislabeling the states. In this work, we provide an algorithm that we call automated label flows which consistently and systematically identifies a deterministic labeling of states. This is a black-box approach in the sense that it gives a sensible set of labels without user guidance. Further, as an example, we pair one black box method with another, analyzing a lattice correlation function from real data using automated label flows in the context of Prony's method.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Thermodynamics and kinetics of H adsorption and intercalation for graphene on 6 H -SiC(0001) from first-principles calculations

Previous experimental observations for H intercalation under graphene on SiC surfaces motivate the clarification of configuration stabilities and kinetic processes related to intercalation. From first-principles density-functional-theory calculations, we analyze H adsorption and intercalation for graphene on a 6H-SiC(0001) surface, where the system includes two single-atom-thick graphene layers: the top-layer graphene (TLG) and the underling buffer-layer graphene (BLG) above the terminal Si layer. Our chemical potential analysis shows that in the low-H coverage regime (described by a single H atom within a sufficiently large supercell), intercalation into the gallery between TLG and BLG or into the gallery underneath BLG is more favorable thermodynamically than adsorption on top of TLG. However, intercalation into the gallery between TLG and BLG is most favorable. We obtain energy barriers of about 1.3 and 2.3 eV for a H atom diffusing on and under TLG, respectively. From an additional analysis of the energy landscape in the vicinity of a step on the TLG, we assess how readily one guest H atom on the TLG terrace can directly penetrate the TLG into the gallery between TLG and BLG versus crossing a TLG step to access the gallery. Finally, we also perform density functional theory calculations for higher H coverages revealing a shift in favorability to intercalation of H underneath BLG and characterizing the variation with H coverage in interlayer spacings.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Density of States and Spectral Function of a Superconductor out of a Quantum-Critical Metal

We analyze the validity of a quasiparticle description of a superconducting state above a metallic quantum-critical point (QCP). A normal state at a QCP is a non-Fermi liquid with no coherent quasiparticles. A superconducting order gaps out low-energy excitations, except for a sliver of states for non-s-wave gap symmetry, and at a first glance, restores coherent quasiparticle behavior. We argue that this does not necessarily hold as the fermionic self-energy may remain singular above the gap edge. This singularity gives rise to markedly non-BCS behavior of the density of states and to the appearance of a nondispersing mode at the gap edge in the spectral function. We analyze the set of quantum-critical models with an effective dynamical four-fermion interaction V(Ω) ∝ 1/Ω γ , where Ω is a frequency of a boson, which mediates the interaction. We show that coherent quasiparticle behavior in a superconducting state holds for γ < 1/2, but breaks down for larger γ. Here, we discuss signatures of quasiparticle breakdown and compare our results with the photoemission data for Bi2201 and Bi2212.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Analysis of defects in In 2 O 3 :H synthesized in presence of water vapor and hydrogen gas mixture

Using hybrid functional-based density functional theory calculations, we analyze the structure and kinetics of defects formed in two competing synthesis routes to prepare hydrogen-doped In 2 O 3 films, using a hydrogen and oxygen gas mixture vs synthesis in the presence of water vapor. For both of these synthesis routes, we find that H + is the dominant defect species: when the Fermi level is close to the conduction band, H + has a lower formation energy than other intrinsic or extrinsic defects. Our results also suggest that water molecules spontaneously split into H + (which occupies octahedral voids) and OH – interstitials (which occupies vacant oxygen lattice sites or oxygen vacancies). From the analysis of the binding energies between these different defects, we conclude that these defects do not cluster and are most likely to stay spatially distributed throughout the films. In addition, the sum of formation energies of an oxygen (i.e., O$^{2–}_i$) and a H + interstitial is close to the formation energy of a OH – interstitial, meaning that water molecules are completely split into 2H + and O$^{2–}_i$ at the synthesis conditions. Further, in the presence of H 2 + O 2 gas mixture, oxygen interstitials occupy oxygen vacancies while hydrogen interstitials occupy vacant oxygen lattice sites and form bonds with lattice oxygens. Our analysis of the defect equilibria suggests that the hydrogen content in films synthesized in the presence of water vapor is higher than films synthesized in the presence of a hydrogen gas mixture. At high dopant concentrations, a hydrogen bond network is formed in the system and this leads to large distortions in the lattice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

On the Role of Interfacial Water Dynamics for Electrochemical Stability of RuO 2 and IrO 2

Abstract Based on the coincident onsets of oxygen evolution reaction (OER) and metal dissolution for many metal‐oxide catalysts it was suggested that OER triggers dissolution. It is believed that both processes share common intermediates, yet exact mechanistic details remain largely unknown. For example, there is still no clear understanding as to why rutile IrO 2 exhibits such an exquisite stability among water‐splitting electrocatalysts. Here, we employ density functional theory calculations to analyze interactions between water and the (110) surface of rutile RuO 2 and IrO 2 as a response to oxygen evolution involving lattice oxygen species. We observe that these oxides display qualitatively different interfacial behavior that should have important implications for their electrochemical stability. Specifically, it is found that IrO 2 (110) becomes further stabilized under OER conditions due to the tendency to form highly stable low oxidation state Ir(III) species. In contrast, Ru species at RuO 2 (110) are prone to facile reoxidation by solution water. This should facilitate the formation of high Ru oxidation state intermediates (>IV) accelerating surface restructuring and metal dissolution.

Evazzade, Iman↗

DOE OSTI2020

Perimatrix of middle ear cholesteatoma: A granulation tissue with a specific transcriptomic signature

Objectives/Hypothesis: To establish comprehensive transcriptomic profiles of cholesteatoma perimatrix tissue and granulation tissue from chronic otitis media (COM) that did not develop cholesteatoma, which can indicate molecular pathways involved in the cholesteatoma perimatrix pathology and invasiveness. Study Design: Retrospective Case Series. Methods: Transcriptome data were obtained from cholesteatoma perimatrix tissue and COM granulation tissue by an Illumina iScan microarray. Differentially expressed genes (DEGs) were subsequently analyzed using both bioinformatical functional annotation and network analysis. Expression of candidate genes (MMP9 and LCN2) was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on a larger group of samples. Results: Analysis of the transcriptome led to the identification of 169 differentially expressed genes between investigated tissues. Bioinformatic analysis suggested that most significant biological processes involving DEGs were previously described in cholesteatoma pathology. Network analysis identified ERBB2, TFAP2A, and TP63 as major hubs of the DEGs molecular network. Furthermore, it was observed that the cellular component most significantly enriched in DEGs was extracellular space containing 47 DEGs. Using qRT-PCR, it was confirmed that mRNA levels of the major extracellular hub (MMP9) are increased, whereas its interacting molecule (LCN2) mRNA levels were decreased in cholesteatoma perimatrix tissue compared to COM granulation tissue. Conclusions: The current study approach offers an overall look at molecular mechanisms that describe the cholesteatoma entity by focusing exclusively on the perimatrix processes in comparison to COM granulation tissue. The observed differences in gene expression between cholesteatoma perimatrix and COM granulation tissue could suggest novel markers potentially influenced by the perimatrix–matrix molecular interplay, which is not present in COM without cholesteatoma. Level of Evidence: NA. Laryngoscope, 130:E220–E227, 2020. © 2019 The American Laryngological, Rhinological and Otological Society, Inc.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

A study of mechanistic mapping of novel SNPs to male breast cancer

Alterations in BRCA2, PALB2, CHEK2, and p53 genes have been identified for their association with male breast cancer in various studies. The incidence of male breast cancer in India is consistent with its global rate. The present study was carried out with an aim to evaluate the genetic alterations in male breast cancer patients from Malwa region of Punjab, India. Four male breast cancer patients belonging to different families were recruited from Guru Gobind Singh Medical College and Hospital, Faridkot, India. A total of 51 genes reported with implications in the pathogenesis of breast cancer were screened using next generation sequencing. Germline variations were found in BRCA1, BRCA2, PMS2, p53, and PALB2 genes, previously reported to be associated with MBC as well as FBC. In addition to these, 13 novel missense alterations were detected in eight genes including STK11, FZR1, PALB2, BRCA2, NF2, BAP1, BARD1, and CHEK2. Impact of these missense alterations on structure and function of protein was also analyzed through molecular dynamics simulation. Structural analysis of these single nucleotide polymorphisms (SNPs) revealed significant impact on the encoded protein functioning.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2019

Z-Pinning approach for 3D printing mechanically isotropic materials

Conventional 3D printing approaches are restricted to building up material in a layer-by-layer format, which is more appropriately considered “2.5-D” printing. The layered structure inherently results in significant mechanical anisotropy in printed parts, causing the tensile strength in the build direction (z-axis) to be only a fraction of the in-plane strength – a decrease of 50–75% is common. In this study, a novel “z-pinning” approach is described that allows continuous material to be deposited across multiple layers within the volume of the part. Here, the z-pinning process is demonstrated using a Fused Filament Fabrication (FFF) printer for polylactic acid (PLA) and carbon fiber reinforced PLA. For both materials, z-pinning increased the tensile strength and toughness in the z-direction by more than a factor of 3.5. Direct comparisons to tensile strength in the x-axis showed a significant decrease in mechanical anisotropy as the volume of the pin was increased relative to the void in the rectilinear grid structure. In fact, the PLA sample with the largest pin volume demonstrated mechanically isotropic properties within the statistical uncertainty of the tests. Tensile test results were also analyzed relative to the functional area resisting deformation for each sample.

36 MATERIALS SCIENCE↗

DOE OSTI2021

FG nucleoporins feature unique patterns that distinguish them from other IDPs

FG nucleoporins (FG Nups) are intrinsically disordered proteins and are the putative regulators of nucleocytoplasmic transport. They allow fast, yet selective, transport of molecules through the nuclear pore complex, but the underlying mechanism of nucleocytoplasmic transport is not yet fully discovered. As a result, FG Nups have been the subject of extensive research in the past two decades. Although most studies have been focused on analyzing the conformation and function of FG Nups from a biophysical standpoint, some recent studies have investigated the sequence-function relationship of FG Nups, with a few investigating amino acid sequences of a large number of FG Nups to understand common characteristics that might enable their function. Previously, we identified an evolutionarily conserved feature in FG Nup sequences, which are extended subsequences with low charge density, containing only positive charges, and located toward the N-terminus of FG Nups. We named these patterns longest positive like charge regions (lpLCRs). These patterns are specific to positively charged residues, and negatively charged residues do not demonstrate such a pattern. In this study, we compare FG Nups with other disordered proteins obtained from the DisProt and UniProt database in terms of presence of lpLCRs. Our results show that the lpLCRs are virtually exclusive to FG Nups and are not observed in other disordered proteins. Also, lpLCRs are what differentiate FG Nups from DisProt proteins in terms of charge distribution, meaning that excluding lpLCRs from the sequences of FG Nups make them similar to DisProt proteins in terms of charge distribution. We also previously showed the biophysical effect of lpLCRs in conformation of FG Nups. The results of this study are in line with our previous findings and imply that lpLCRs are virtually exclusive and functionally significant characteristics of FG Nups and nucleocytoplasmic transport.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Improving air leakage prediction of buildings using the fan pressurization method with the Weighted Line of Organic Correlation

In many countries, the fan pressurization method is the most frequently chosen approach for measuring the air leakage of houses. The measurements are usually performed at pressures that far exceed pressures to which buildings are exposed to under normal conditions. A fit of these tests to the power-law formulation allows an extrapolation to data points outside the measured pressure range. With the Ordinary Least Square (OLS) fitting method, the pressure exponent and flow coefficient can be determined. However, the measurement results are highly sensitive to uncertainties induced by external factors like changing wind conditions during the tests, which is neglected by OLS. This may lead to errors in the prediction of flows at lower pressures. The Weighted Line of Organic Correlation (WLOC) is an alternative approach and takes measurement uncertainty into account. In this paper, a statistical analysis of an extensive data set of pressurization measurements has been performed. Both regression techniques have been compared for almost 7500 fan pressurization measurements of six houses in 109 different house leak configurations. The variability in predicting pressure exponent and flow coefficient for both WLOC and OLS regression was analyzed using probability density functions. It was found that the Weighted Line of Organic Correlation significantly decreases the uncertainty in predicting pressure exponent, flow coefficient, and other low-pressure air leakage metrics compared to the Ordinary Least Square fitting. Here, the authors highly recommend the implementation of WLOC in current measurement standards and test equipment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Reviewing flexibility in industrial electrification: Focusing on green ammonia and steel in the United States

The renewable energy transition in the power sector involves a paradigm shift for flexibility. Flexible demand is more attainable than before, while supply flexibility faces new constraints due to the increased share of variable renewable resources. Increased demand flexibility can allow less use of peaking power plants and avoid need for additional capacity. Industrial flexibility could be especially interesting in this regard, as industrial customers are larger on average than other customers and have typically provided the largest share of demand response in the United States. We consider industrial demand, studying characteristics of flexible industrial loads. We then examine the dynamics of change occurring around industrial load flexibility by focusing on two case studies: green ammonia and steel production via electric arc furnaces. Electric arc furnace steel production is an important component of current demand response programs, whereas green ammonia and green fuels offer new paradigms for flexibility. We analyze the structure and functions of the technological innovation systems of load flexibility in those two industries via interviews with twenty-two stakeholders. Here, we conclude that in the United States these technological innovation systems are not well-functioning for industry in general or for steel, but do seem to be present for green ammonia. Additionally, explicit connections between scope two greenhouse gas emissions (those from purchased energy) and flexibility are lacking, and likewise industry stakeholders do not appear to make a connection between decarbonization and load flexibility, thus flexible demand is not viewed as a tool in industrial decarbonization.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2023

Pressure-induced evolution of the lattice dynamics for selected UO 3 polymorphs

Uranium trioxide (UO 3 ) is a stable chemical form of uranium oxide with multiple polymorphs found throughout the nuclear fuel cycle. The pressure-induced changes in the structure and lattice dynamics of four of these polymorphs are simulated with density functional perturbation theory and analyzed. Two phases, α- and δ-UO 3 are found to exhibit an isotropic response to pressure and do not undergo any changes in coordination geometry up to ~40 GPa. In contrast, the other two phases investigated, β- and γ-UO 3 , exhibit an anisotropic response to pressure. Decomposition of the phonon eigenvectors allows us to assign specific pressure-induced structural changes to individual phonon modes. Here, this analysis has been performed on a per atom basis for the relatively simple α- and δ-UO 3 structures, which have one symmetrically unique uranium site, and on a per coordination environment basis for β- and γ-UO 3 , which have multiple U sites.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Understanding process-microstructure-property relationships in laser powder bed fusion of non-spherical Ti-6Al-4V powder

Powder feedstock is a major cost driver in metal additive manufacturing (AM). Replacing the spherical powder with the cost-efficient non-spherical one can reduce the feedstock cost up to 50% and attract more interest to adopt AM in production and new alloy development. Here, for this paper, a comprehensive study was conducted to understand process-microstructure-property relationships in laser powder bed fusion of hydride-dehydride Ti-6Al-4V powder. We demonstrated that variation of laser scan speed had a significant impact on the grain structure, pore evolution and properties compared to laser power. Dynamic X-ray radiography showed that with decreasing scan speed at a constant laser power, a transition from conduction to keyhole mode laser processing occurred, in which a deeper melt pool at lower scan speed intensified texture. In other words, an increase in laser scan speed resulted in formation of the refined prior β grains with shape factor of ~5, lowering the anisotropy. Furthermore, the degree of variant selection was evaluated based on the analyzed texture as a function of laser power and scan speed. With increasing laser scan speed, the dominant α/α boundary type was altered from type 2 to 4 and the degree of variant selection was noticeably decreased. On the other hand, increasing laser power left the morphology of prior β grains, their size, and the dominant α/α boundary (type 4) unchanged, while the texture and anisotropy were intensified, and the degree of variant selection was slightly decreased. Finally, dependency of surface roughness and microhardness were discussed as a function of laser processing parameters.

variant selection↗

DOE OSTI2019

A simultaneous understanding of jet and hadron suppression

In the context of the hybrid strong/weak coupling model for jet quenching, we perform a global fit to hadron and jet data in the most central bins both at RHIC and LHC. The qualitative and quantitative success of the analysis is attributed to the fact that the model correctly captures the fact that wider jets lose, on average, more energy than the narrower ones, to which high energy hadrons belong. We show how one can understand the relative jet and hadron suppression by analyzing the jet fragmentation functions, and also discuss the role of plasma finite resolution effects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Toward First-Principles Design of Organic Nonlinear Optical Materials: Crystal Structure Prediction and Halogen Bonding Impact on Hyperpolarizabilities of 2-Iodo-3-hydroxypyridine

Computational methods can potentially accelerate development of more efficient organic materials for second harmonic generation. Here, we test the method that includes the evolutionary algorithm for predicting crystal structure and prognosis of nonlinear optical properties based on the predicted structure. For this test, we selected 2-iodo-3-hydroxypyridine, which exhibits second harmonic generation intensity comparable to that of urea. We performed global minimization of the lattice energy and found the experimental structure when many-body dispersion correction is added to the density functional theory values. We analyzed geometric preferences of the halogen bonding in predicted virtual polymorphs. We also found linear correlation between the lengths of the iodine–iodine halogen bonds and calculated second order susceptibilities.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Joint Inversion of Body Wave Arrival Times, Surface Wave Dispersion Data and Receiver Functions: Method and Application to South China

In this work, we have developed a new joint inversion method that incorporates body wave arrival times, surface wave dispersion and receiver functions to simultaneously update earthquake locations and constrain three-dimensional P-wave (Vp) and S-wave velocity (Vs) models. Due to complementary sensitivities of the three types of data, the proposed joint inversion algorithm can reduce the intrinsic non-uniqueness of inversions using fewer types of data and better determine smooth velocity variations and velocity discontinuities. Synthetic tests demonstrate the advantages of this new joint inversion algorithm in resolving velocity structures, especially in constraining velocity gradients across the Moho interface. We have applied the proposed joint inversion algorithm to image the lithosphere velocity structure of south China. The inverted Vp and Vs models fit body wave arrival times, surface wave dispersion and receiver functions well. We further analyzed the distribution of Vs gradients across the Moho interface in detail, which helps us better understand tectonics in south China.

58 GEOSCIENCES↗

DOE OSTI2023

Electronic signatures of Lorentzian dynamics and charge fluctuations in lithiated graphite structures

Lithium graphite intercalation compounds (Li-GICs) are essential materials for modern day portable electronics and obtaining insights into their atomic structure and thermodynamics is of fundamental interest. Here we explore the electronic and atomic states of Li-GICs at varying degrees of Lithium loading (i.e., “staging”) by means of ab-initio molecular dynamics simulations and simulated X-ray adsorption spectroscopy (XAS). We analyze the atomic correlation functions and shows that the enhancements of the Li-ion entropy with increased staging result from Lorentzian lithium-ion dynamics and charge fluctuations, which activate low-energy phonon modes. The associated electronic signatures are modulations of the unoccupied π*/σ* orbital energy levels and unambiguous fingerprints in Carbon K-edge XAS spectra. Thus, we extend the canonical view of XAS, establishing that these “static” measurements in fact encode the signature of the thermodynamic response and relaxation dynamics of the system. This causal link between atomic structure, spectroscopy, thermodynamics, and information theory can be generally exploited to better understand stability in solid-state electrochemical systems.

25 ENERGY STORAGE↗