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All sources NASA NTRS DOE OSTI

DOE OSTI2022

From Qualitative to Quantitative AOP: A Case Study of Neurodegeneration

Adverse outcome pathways (AOPs) include a sequence of events that connect a molecular-level initiating event with an adverse outcome at the cellular level for human health endpoints, or at the population level for ecological endpoints. When there is enough quantitative understanding of the relationships between key events in an AOP, a mathematical model may be developed to connect key events in a quantitative AOP (qAOP). Ideally, a qAOP will reduce the time and resources spent for chemical toxicity testing and risk assessment and enable the extrapolation of data collected at the molecular-level by in vitro assays, for example, to predict whether an adverse outcome may occur. Here, we review AOPs in the AOPWiki, an AOP repository, to determine best practices that would facilitate conversion from AOP to qAOP. Then, focusing on a particular case study, acetylcholinesterase inhibition leading to neurodegeneration, we describe specific methods and challenges. Examples of challenges include the availability and collection of quantitative data amenable to model development, the lack of studies that measure multiple key events, and model accessibility or transferability across platforms. We conclude with recommendations for improving key event and key event relationship descriptions in the AOPWiki that facilitate the transition of qualitative AOPs to qAOPs.

Sinitsyn, Dennis↗

NASA NTRS1987

Numerical studies of collapsing interstellar clouds

Numerical simulation of the structure and evolution of interstellar clouds was conducted. Steps were taken toward an integrated treatment of the dynamical, thermal, and chemical processes entering model calculations, and a detailed study was made of radiative transfer in molecular lines to allow model predictions to be tested against empirical data. It is shown that the shapes of molecular lines are sensitive to details of the cloud structure and evolutionary state and are thus useful in inferring the cloud density, temperature, chemical composition, age, and initial conditions. The calculations have successfully reproduced and explained several observed cloud properties, including abundances of complex molecular species and the apparent depletion of CO in dense cores.

Bodenheimer, Peter↗

DOE OSTI2024

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

Mass spectrometry is broadly employed to study complex molecular mechanisms in various biological and environmental fields, enabling 'omics' research such as proteomics, metabolomics, and lipidomics. As study cohorts grow larger and more complex with dozens to hundreds of samples, the need for robust quality control (QC) measures through automated software tools becomes paramount to ensure the integrity, high quality, and validity of scientific conclusions from downstream analyses and minimize the waste of resources. Since existing QC tools are mostly dedicated to proteomics, automated solutions supporting metabolomics are needed. To address this need, we developed the software PeakQC, a tool for automated QC of MS data that is independent of omics molecular types (i.e., omics-agnostic). It allows automated extraction and inspection of peak metrics of precursor ions (e.g., errors in mass, retention time, arrival time) and supports various instrumentations and acquisition types, from infusion experiments or using liquid chromatography and/or ion mobility spectrometry front-end separations and with/without fragmentation spectra from data-dependent or independent acquisition analyses. Diagnostic plots for fragmentation spectra are also generated. Here, in this paper, we describe and illustrate PeakQC’s functionalities using different representative data sets, demonstrating its utility as a valuable tool for enhancing the quality and reliability of omics mass spectrometry analyses.

47 OTHER INSTRUMENTATION↗

NASA NTRS1978

Computer display and manipulation of biological molecules

This paper describes a computer model that was designed to investigate the conformation of molecules, macromolecules and subsequent complexes. Utilizing an advanced 3-D dynamic computer display system, the model is sufficiently versatile to accommodate a large variety of molecular input and to generate data for multiple purposes such as visual representation of conformational changes, and calculation of conformation and interaction energy. Molecules can be built on the basis of several levels of information. These include the specification of atomic coordinates and connectivities and the grouping of building blocks and duplicated substructures using symmetry rules found in crystals and polymers such as proteins and nucleic acids. Called AIMS (Ames Interactive Molecular modeling System), the model is now being used to study pre-biotic molecular evolution toward life.

Coeckelenbergh, Y.↗

DOE OSTI2023

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Pressure-temperature equation of state of Al 2 ⁢O 3 up to 14 Mbar and 40 kK

Sapphire (Al 2 ⁢O 3 ), known for its remarkable incompressibility at ambient conditions, plays a pivotal role in both static and dynamic compression research. Accurately characterizing its equation of state (EoS) is essential for these applications. Here, we present a complete Hugoniot of Al 2 ⁢ O 3 as locus of experimentally assessed, high-precision, pressure, density and temperature states up to 14 Mbar and 43 kK. The Hugoniot is established with single shock experiments using magnetically launched hyper velocity flyers on the Z Accelerator at Sandia National Laboratories. We explore principal Hugoniot states at very high shock 𝑇 and 𝑝 in the solid phase, tracking the solid-liquid boundary and culminating at 2.4-fold compression, where data provides a direct constraint on the liquid phase. Corresponding shock release data probe thermodynamic states complementary to the Hugoniot and place additional constraints on tabular EoS models. Our findings indicate a significant deviation from existing tabular EoS models for Al 2 ⁢ O 3 dictating a comprehensive overhaul. We develop two advanced EoSs for Al 2 ⁢ O 3 the SESAME 97412 model, featuring an extensive phase diagram that includes three solid phases and the liquid phase, and the updated LEOS 2200m2 model. EoS development is assisted with Quantum Molecular Dynamics simulations. Our experimental data allows for stringent testing of our EoSs. Both models accurately capture the Hugoniot of Al 2 ⁢O 3 up to the highest pressures and temperatures. Rigorous experimental determination of extreme pressures and temperatures, paired with sophisticated models, advances the frontier of EoS development beyond 1 terapascal.

Kalita, Patricia [Sandia National Laboratories (SN↗

DOE OSTI2022

Gas and Cosmic-Ray Properties in the MBM 53, 54, and 55 Molecular Clouds and the Pegasus Loops Revealed by H i Line Profiles, Dust, and Gamma-Ray Data

In studying the interstellar medium (ISM) and Galactic cosmic rays (CRs), uncertainty of the interstellar gas density has always been an issue. To overcome this difficulty, we used a component decomposition of the 21 cm H i emission line and used the resulting gas maps in an analysis of γ-ray data obtained by the Fermi Large Area Telescope (LAT) for the MBM 53, 54, and 55 molecular clouds and the Pegasus loop. We decomposed the ISM gas into intermediate-velocity clouds, narrow-line and optically thick H i, broad-line and optically thin H i, CO-bright H 2 , and CO-dark H 2 using detailed correlations with the H i line profiles from the HI4PI survey, the Planck dust-emission model, and the Fermi-LAT γ-ray data. We found the fractions of the optical depth correction to the H i column density and CO-dark H 2 to be nearly equal. We fitted the CR spectra directly measured at/near the Earth and the measured γ-ray emissivity spectrum simultaneously. We obtained a spectral break in the interstellar proton spectrum at ~7 GeV, and found that the γ-ray emissivity normalization agrees with the AMS-02 proton spectrum within 10%, relaxing the tension with the CR spectra previously claimed.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1984

Ultraviolet observations of interstellar extinction near the Cepheus OB3 molecular cloud

New IUE observations and available data for O and B stars new Cep OB3 are presented, and extinction curves for the stars are derived. The differences in those curves are examined in detail, showing that while the level of the far-UV extinction differs greatly throughout the region, the shape of the 2175 A bump does not. The different curves form a family which can be parametrized by the strength of the bump per E(B-V). This suggests that some single physical process dominates the modification of the grains in the region. Evidence is presented which indicates that this process is related to the evolution of the grains once they emerge from the Cep OB3 molecular cloud. The practicality of using the strength of the bump per E(B-V) for dereddening stars in a region where the form of the UV extinction differs from place to place is demonstrated.

Massa, D.↗

DOE OSTI2024

Manuscript Workflows from and Processed Organic Matter Composition of Experimentally Burned Open Air and Muffle Furnace Vegetation Chars across Differing Burn Severity and Feedstock Types from Pacific Northwest, USA (v3)

This dataset includes processed organic matter chemistry data from an experimental study designed to compare how the chemical composition of organic matter changes across different burn conditions and vegetation materials representative of major land cover types of the Pacific Northwest, USA. Chars were created in a closed muffle furnace or on an open burn table from four different feedstock species representing vegetation commonly impacted by fire regimes across the Pacific Northwest, USA. Source data and associated metadata (including methods and geospatial information) can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1894135 (Grieger et al. 2022). This dataset provides processing scripts and processed data for both solid and dissolved phase organic matter characterization data from experimentally generated chars. These processed data can be used to compare how different burn conditions may influence resultant organic matter chemistry and help further our understanding of potential biogeochemical impacts on river corridors post-fire. The processed data were subsequently analyzed; and the results and ecological implications of the findings were published in peer-reviewed manuscripts. The scripts and workflows used to develop the manuscripts are also included in this data package.This data package was originally published June 2024. It was updated September 2024 (new and modified files) and in January 2025 (modified files). See the change history section in the readme for more details.This dataset is comprised of one data package readme, one data dictionary (dd), one file level metadata (flmd), and folders containing (A) processed data; (B) general processing scripts; and (C) additional folders with specific manuscript analysis scripts and processed data. Step-by-step instructions to assist the user in recreating the workflow used to generate the results in the manuscripts is also provided. The processed data folder includes (1) a folder of processed Parallel Factor Analysis (PARAFAC) and spectra indices outputs from excitation emissions matrix (EEM) fluorescence and absorbance data; (2) a folder of processed solid state carbon-13 (13-C NMR) integrals; (3) folder of high resolution characterization of organic matter via 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory) processed data outputs from Formultitude (https://github.com/PNNL-Comp-Mass-Spec/Formultitude), blank corrections and data aggregation, and calculated molecular indices. All files are .pdf, .csv, .html, .Rmd, .R, or .RData.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Physicochemical control of solvation and molecular assembly of charged amphiphilic oligomers at air-aqueous interfaces

Hypothesis : Understanding the rules that control the assembly of nanostructured soft materials at interfaces is central to many applications. We hypothesize that electrolytes can be used to alter the hydration shell of amphiphilic oligomers at the air-aqueous interface of Langmuir films, thereby providing a means to control the formation of emergent nanostructures. Experiments : Three representative salts – (NaF, NaCl, NaSCN) were studied for mediating the self-assembly of oligodimethylsiloxane methylimidazolium (ODMS-MIM + ) amphiphiles in Langmuir films. The effects of the different salts on the nanostructure assembly of these films were probed using vibrational sum frequency generation (SFG) spectroscopy and Langmuir trough techniques. Experimental data were supported by atomistic molecular dynamic simulations. Findings : Langmuir trough surface pressure – area isotherms suggested a surprising effect on oligomer assembly, whereby the presence of anions affects the stability of the interfacial layer irrespective of their surface propensities. In contrast, SFG results implied a strong anion effect that parallels the surface activity of anions. These seemingly contradictory trends are explained by anion driven tail dehydration resulting in increasingly heterogeneous systems with entangled ODMS tails and appreciable anion penetration into the complex interfacial layer comprised of headgroups, tails, and interfacial water molecules. These findings provide physical and chemical insight for tuning a wide range of interfacial assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1985

Degradation studies of SMRM Teflon

A working group was organized to study materials and components of the Solar Max Satellite (SMS) that was returned by the STS 41C. These materials were exposed in space for 50 months and represent the only real time long term exposure data available to date. In the molecular modeling of material and energetic oxygen atom interaction, it is pointed out that the importance of developing correlation between accelerated exposure data from STS and some real time data. In particular, it was predicted that Teflon which showed no detectable degradation on various STS flights may be susceptible to atomic oxygen degradation under real time conditions. Initial inspection of returned SMS samples showed that Teflon suffered visual damage such as cracking and yellowing. The results of examination of these samples are given.

Liang, R. H.↗

DOE OSTI2022

Squeezing Out Interfacial Solvation: The Role of Hydrogen-Bonding in the Structural and Orientational Freedom of Molecular Self-Assembly

We report bioinspired membrane molecules with improved physical properties and enhanced stability can serve as functional models for conventional lipid or amphiphilic species. Importantly, these molecules can also provide new insights into emergent phenomena that manifest during self-assembly at interfaces. Here, we elucidate the structural response and mechanistic steps underlying the self-assembly of the amphiphilic, charged oligodimethylsiloxane imidazolium cation (ODMS-MIM+) at the air–aqueous interface using Langmuir trough methods with coincident surface-specific vibrational sum-frequency generation (SFG) spectroscopy. We find evidence for a new compression-induced desolvation step that precedes commonly known disordered-to-ordered phase transitions to form nanoscopic assemblies. The experimental data was supported by atomistic molecular dynamics (MD) simulations to provide a detailed mechanistic picture underlying the assembly and the role of water in these phase transitions. The sensitivity of the hydrophobic ODMS tail conformations to compression-owing to distinct water–ODMS interactions and tail–tail solvation properties-offers new strategies for the design of interfaces that can be further used to develop soft-matter electronics and low-dimensional materials using physical and chemical controls.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1990

Quantitative infrared spectroscopy of minor constituents of the Earth's atmosphere

We obtain quantitative laboratory spectroscopic measurements of molecular constituents which are of importance in understanding the health of the Earth's atmosphere, and, in particular, emphasize those species which are important for understanding stratospheric kinetics or are used for long term monitoring of the stratosphere. Our measurements provide: (1) line and band intensity values which are needed to establish limits of detectability for as yet unobserved species and to quantify the abundance of those species which are observed; (2) line-positions, -half widths and pressure induced shifts are all needed for remote sensing techniques, and (3) data on the above basic molecular parameters at temperatures and pressures appropriate for the real atmosphere.

Chackerian, C., Jr.↗

DOE OSTI2023

Electronic specific heat capacities and entropies from density matrix quantum Monte Carlo using Gaussian process regression to find gradients of noisy data

In this work, we present a machine learning approach to calculating electronic specific heat capacities for a variety of benchmark molecular systems. Our models are based on data from density matrix quantum Monte Carlo, which is a stochastic method that can calculate the electronic energy at finite temperature. As these energies typically have noise, numerical derivatives of the energy can be challenging to find reliably. In order to circumvent this problem, we use Gaussian process regression to model the energy and use analytical derivatives to produce the specific heat capacity. From there, we also calculate the entropy by numerical integration. We compare our results to cubic splines and finite differences in a variety of molecules in which Hamiltonians can be diagonalized exactly with full configuration interaction. We finally apply this method to look at larger molecules where exact diagonalization is not possible and make comparisons with more approximate ways to calculate the specific heat capacity and entropy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein

IGHV3-33 -encoded antibodies are prevalent in the human humoral response against the Plasmodium falciparum circumsporozoite protein (PfCSP). Among VH3-33 antibodies, cross-reactivity between PfCSP major repeat (NANP), minor (NVDP), and junctional (NPDP) motifs is associated with high affinity and potent parasite inhibition. However, the molecular basis of antibody cross-reactivity and the relationship with efficacy remain unresolved. Here, we perform an extensive structure-function characterization of 12 VH3-33 anti-PfCSP monoclonal antibodies (mAbs) with varying degrees of cross-reactivity induced by immunization of mice expressing a human immunoglobulin gene repertoire. We identify residues in the antibody paratope that mediate cross-reactive binding and delineate four distinct epitope conformations induced by antibody binding, with one consistently associated with high protective efficacy and another that confers comparably potent inhibition of parasite liver invasion. Our data show a link between molecular features of cross-reactive VH3-33 mAb binding to PfCSP and mAb potency, relevant for the development of antibody-based interventions against malaria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes

Higher plants synthesize cellulose using membrane-bound, six-lobed cellulose synthase complexes, each lobe containing trimeric cellulose synthases (CESAs). Although molecular biology reports support heteromeric trimers composed of different isoforms, a homomeric trimer was reported for in vitro studies of the catalytic domain of CESA1 of Arabidopsis (AtCESA1CatD) and confirmed in cryoEM structures of full-length CESA8 and CESA7 of poplar and cotton, respectively. In both structures, a small portion of the plant-conserved region (P-CR) forms the only contacts between catalytic domains of the monomers. Here, we report inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD. Molecular dynamics simulations for AtCESA1CatD trimers based on the CESA8 cryoEM structure were stable and dependent upon a small set of residue contacts. The results suggest that homomeric CESA trimers may be important for the synthesis of primary and secondary cell walls and identify key residues for future mutagenic studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

A Curated Experimental Compilation Analyzed by Theory Is More than a Review

Macromolecules is an exceptional resource in the field of polymer science and now publishes more than 1000 original articles a year that set the standard for scientific rigor and creative insights. Over the years, these individual contributions have combined to build the foundation of polymer science, broadly and inclusively defined. In addition to the individual articles, many of which are being celebrated in this series of editorials, Macromolecules has published invaluable reviews and perspectives. These scholarly contributions integrate the insights and results from numerous sources into a unified whole and often recommend future directions for the field. Novices and experts alike benefit from these works that capture topics from emerging discoveries to long-pondered topics and everything in between. To explore the importance of Macromolecules’ reviews and perspectives, we considered their influence on the field and found the 1994 review by Fetters et al. entitled “Connection between Polymer Molecular Weight, Density, Chain Dimensions, and Melt Viscoelastic Properties”1 to be a singularity. This review expertly curates and compiles a trove of data to build robust correlations between molecular characteristics and macroscopic viscoelastic properties of polymer melts, in the context of the tube model of entanglements.

36 MATERIALS SCIENCE↗

NASA NTRS1984

The formation of massive stars along the W5 ionization front

Far-infrared, near-infrared, millimeter-wave, and optical data are presented for two of the large molecular clouds which border the W5 (IC 1848) giant H II region. These data are combined to identify three B0-B2 zero-age main-sequence stars which are forming in these clouds and to study the density distribution and kinematic structure of their surrounding molecular gas. This investigation into the environment in which massive stars have formed in these clouds, when considered alongside similar studies of the W5A/S201 molecular cloud, leads to the conclusion that the expanding W5 H II region has played an important role in initiating the formation of these massive stars.

Wilking, B. A.↗