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At least 73 records · Page 4

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DOE OSTI2020

Solvation at metal/water interfaces: An ab initio molecular dynamics benchmark of common computational approaches

Determining the influence of the solvent on electrochemical reaction energetics is a central challenge in our understanding of electrochemical interfaces. To date, it is unclear how well existing methods predict solvation energies at solid/liquid interfaces, since they cannot be assessed experimentally. Ab initio molecular dynamics (AIMD) simulations present a physically highly accurate, but also a very costly approach. In this work, we employ extensive AIMD simulations to benchmark solvation at charge-neutral metal/water interfaces against commonly applied continuum solvent models. We consider a variety of adsorbates including *CO, *CHO, *COH, *OCCHO, *OH, and *OOH on Cu, Au, and Pt facets solvated by water. The surfaces and adsorbates considered are relevant, among other reactions, to electrochemical CO 2 reduction and the oxygen redox reactions. We determine directional hydrogen bonds and steric water competition to be critical for a correct description of solvation at the metal/water interfaces. As a consequence, we find that the most frequently applied continuum solvation methods, which do not yet capture these properties, do not presently provide more accurate energetics over simulations in vacuum. We find most of the computed benchmark solvation energies to linearly scale with hydrogen bonding or competitive water adsorption, which strongly differ across surfaces. Furthermore, we determine solvation energies of adsorbates to be non-transferable between metal surfaces, in contrast to standard practice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2012

PMA-Linked Fluorescence for Rapid Detection of Viable Bacterial Endospores

The most common approach for assessing the abundance of viable bacterial endospores is the culture-based plating method. However, culture-based approaches are heavily biased and oftentimes incompatible with upstream sample processing strategies, which make viable cells/spores uncultivable. This shortcoming highlights the need for rapid molecular diagnostic tools to assess more accurately the abundance of viable spacecraft-associated microbiota, perhaps most importantly bacterial endospores. Propidium monoazide (PMA) has received a great deal of attention due to its ability to differentiate live, viable bacterial cells from dead ones. PMA gains access to the DNA of dead cells through compromised membranes. Once inside the cell, it intercalates and eventually covalently bonds with the double-helix structures upon photoactivation with visible light. The covalently bound DNA is significantly altered, and unavailable to downstream molecular-based manipulations and analyses. Microbiological samples can be treated with appropriate concentrations of PMA and exposed to visible light prior to undergoing total genomic DNA extraction, resulting in an extract comprised solely of DNA arising from viable cells. This ability to extract DNA selectively from living cells is extremely powerful, and bears great relevance to many microbiological arenas.

LaDuc, Myron T.↗

DOE OSTI2025

Algae Asphalt to Enhance Pavement Sustainability and Performance at Subzero Temperatures

This paper evaluates the potential of algae-derived biobinders as sustainable alternatives for pavement construction. It specifically examines the physicochemical and rheological properties of biomodified binders and their potential to offset carbon emissions when used as partial replacements for conventional petroleum-based asphalt binders. Biosequestration of CO 2 using microalgal cell factories is a promising way of recycling CO 2 into biomass via photosynthesis. Our study demonstrates that incorporating algae-derived binders into asphalt can significantly reduce carbon emissions. Each 1% increase in algae-based biobinder leads to an approximate 4.5% decrease in net carbon emissions. This indicates that a blend containing about 22% biobinder has the potential to achieve carbon neutrality. Blends with higher proportions may even result in net-negative emissions, highlighting a promising strategy for environmentally responsible road construction. In terms of performance, the study shows that certain algae-derived biobinders significantly enhance the cracking resistance of asphalt, particularly under subzero temperatures, by improving its stress-relief capacity. A key contribution of this work is the introduction of polarizability as a novel molecular-level parameter for assessing the compatibility of algae-derived bio-oils with asphalt. By capturing the electronic responsiveness of bio-oil molecules, polarizability serves as a predictive indicator of their interaction potential with asphalt components, providing a new dimension for evaluating the binder performance at the molecular scale. Among the tested materials, the biobinder derived from Haematococcus pluvialis demonstrated particularly strong improvements in resistance to permanent deformation under repeated loading conditions analogous to traffic-induced stress, as well as enhanced resistance to moisture-induced damage. In conclusion, these findings advance the chemistry-driven design of biomass-based binders and highlight a promising pathway toward the development of low-carbon, high-performance, and sustainable infrastructure materials.

Algae↗

NASA NTRSDate not supplied

NASA Omics Archive Project

The space environment consists of a complex set of hazards including altered gravity, radiation, psychological/physiological stress, isolation, and confinement leading to complex biological responses. Advances in biotechnology capabilities offer considerable potential to provide novel insight into those responses as well as innovative diagnostic, treatment, and countermeasure solutions for astronauts as NASA begins to travel beyond low Earth orbit. Omics data (genomics, transcriptomics, proteomics, etc.) is one example that can provide NASA with critical knowledge of how a crewmember’s genetics, environment, and lifestyle can be used to develop individualized approaches for disease prevention, advance diagnostics, and improve treatment strategies. NASA ventured into the field of omics on human subjects with the successful completion of the NASA Twins Study which was the first step in mapping the multi-omic profile of astronauts to understand and mitigate the health consequences of spaceflight. The Human Research Program aims to build upon the success of the Twins Study with the NASA Omics Archive flight study, establishing a longitudinal biospecimen archive and efficiently generating a comprehensive high-quality multi-omic dataset from astronauts for the purpose of studying molecular, metabolic, and microbial changes associated with longduration spaceflight missions. The goal is to facilitate scientific and medical research community efforts to characterize and mitigate spaceflight health and performance risks. In this presentation, we will review details regarding the biospecimen and data archive to be generated by the NASA Omics Archive flight study. Data generated as part of this project will be archived in the NASA Life Sciences Portal (NLSP) and be made available for future hypothesis-driven research efforts or occupational surveillance through Institutional Review Board-approved data sharing and retrospective data requests submitted to the Life Sciences Data Archive (LSDA) team. We will also present results of a ground study performed to evaluate in-house procedures, new sample collection hardware, and vendor capabilities. The data repository generated and the samples to be archived by this study will enable future research efforts to assess an astronauts’ unique molecular and genetic profile with respect to individual spaceflight responses. Results of which will be instrumental in enabling precision health capabilities to better assess and mitigate spaceflight risks, detect disease states earlier, and actively monitor countermeasure treatments, ultimately improving clinical outcomes during future exploration class missions.

C. A. Theriot↗

NASA NTRS1972

Transient variation of martian ground-atmosphere thermal boundary layer structure.

Results of a numerical simulation of the diurnal redistribution of temperature by radiative and molecular-conductive processes in the Martian soil-atmosphere system. An attempt is made to assess the importance of atmospheric molecular conduction near the surface and to estimate the characteristic depth of the diurnal temperature wave. The computational results are found to indicate a dual structure in the diurnal temperature wave propagation pattern, with a diffusive-type wave in the lowest 150 m superimposed on a radiatively induced disturbance with a characteristic scale of 1.8 km. Atmospheric molecular thermal conduction typically accounts for about 15% of the total heating/cooling in the lowest 25 m. Thermal conduction in both the soil and atmosphere appears to be an important factor in the thermal coupling of these subsystems. A free-convection regime in the conduction layer is predicted by the model for about five hours of the Martian day.

Pallmann, A. J.↗

NASA NTRSDate not supplied

Molecular Accumulation during JWST’s Optical Telescope Cryogenic Thermal Vacuum Testing

Maintaining molecular cleanliness during the JWST’s Optical Telescope/Instrument Module (OTIS) Cryogenic Thermal Vacuum (TV) test campaign was critical to the success of its optical mission on orbit. In the thermal vacuum tests leading up to the final cryogenic test to validate the OTIS flight hardware, NASA Johnson Space Center’s (JSC’s) TV Chamber A was fully characterized for molecular contamination. It was found to contain common volatile condensable materials (VCM), including hydrocarbons, plasticizers, and silicones, all of which absorb in JWST’s infrared wavelength region. Due to the risks involved, cleaning molecular contamination from the OTIS mirrors was not an option and heating the Primary Mirror (PM) segments would have also been a risky and expensive endeavor. As a result, a monitoring process was developed and implemented during four different Pathfinder or risk reduction tests that were scheduled to occur prior to the flight hardware test. The goal was to quantify and assess the risk of molecular contamination depositing on the PM resulting from relatively warm chamber shrouds “leading” colder PM mirrors during warmup, by a margin of 10-50 Kelvin (K). This was accomplished using Cryogenic Quartz Crystal Microbalances (CQCMs), held at temperatures slightly cooler than the segments to signal the onset of contamination events. Per the JWST Contamination Control Plan (CCP)1, the total Primary Mirror molecular allocation requirement was 50 angstroms. In all tests, the results showed an average accumulated molecular contamination of <10 angstroms.

optics↗

NASA NTRSDate not supplied

Molecular Accumulation during JWST’s Optical Telescope Cryogenic Thermal Vacuum Testing

molecular, contamination, thermal vacuum, cryogeni↗

DOE OSTI2021

The relaxation behavior of supercooled and glassy imidacloprid

Employing dielectric spectroscopy, oscillatory shear rheology, and calorimetry, the present work explores the molecular dynamics of the widely used insecticide imidacloprid above and below its glass transition temperature. In its supercooled liquid regime, the applied techniques yield good agreement regarding the characteristic structural (alpha) relaxation times of this material. In addition, the generalized Gemant–DiMarzio–Bishop model provides a good conversion between the frequency-dependent dielectric and shear mechanical responses in its viscous state, allowing for an assessment of imidacloprid’s molecular hydrodynamic radius. In order to characterize the molecular dynamics in its glassy regime, we employ several approaches. These include the application of frequency–temperature superposition (FTS) to its isostructural dielectric and rheological responses as well as use of dielectric and calorimetric physical aging and the Adam–Gibbs–Vogel model. While the latter approach and dielectric FTS provide relaxation times that are close to each other, the other methods predict notably longer times that are closer to those reflecting a complete recovery of ergodicity. In conclusion, this seemingly conflicting dissimilarity demonstrates that the molecular dynamics of glassy imidacloprid strongly depends on its thermal history, with high relevance for the use of this insecticide as an active ingredient in technological applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Synergetic Effects of Soil Organic Matter Components During Interactions with Minerals

Mineral-associated soil organic matter (SOM) is critical for stabilizing organic carbon and mitigating climate change. However, mineral-SOM interactions at the molecular scale, particularly synergetic adsorption through organic-organic interaction on the mineral surface known as organic multilayering, remain poorly understood. This study investigates the impact of organic multilayering on mineral-SOM interactions, by integrating macroscale experiments and molecular-scale simulations that assess the individual and sequential adsorption of major SOM compounds – lauric acid (lipid), pentaglycine (amino acid), trehalose (carbohydrate), and lignin onto soil minerals. Ferrihydrite, Al-hydroxide, and calcite are exposed to SOM compounds to determine adsorption affinities and binding energies. Results show that lauric acid has 20-40 times higher K d than pentaglycine, following the order K d (ferrihydrite) > K d (Al-hydroxide) >> K d (calcite). Molecular-scale simulations confirm that lauric acid has a higher binding energy (30.8 kcal/mol) on ferrihydrite than pentaglycine (6.0 kcal/mol), attributed to lipid hydrophobicity. The lower binding energy of pentaglycine results from its hydrophilic amide groups, facilitating partitioning into water. Sequential experiments examine how the first layer of lipid or amino acid affects the adsorption of carbohydrate/lignin, which show little or no individual adsorption affinities. Macroscale results reveal that lipid and amino acid adsorption induce ferrihydrite particle repulsion increasing reactive surface area and enhancing carbohydrate/lignin adsorption independently and synergistically through organic multilayering. Molecular-scale results reveal that amino acid adsorbed on ferrihydrite interacts more readily with lignin macroaggregates (preformed in solution) than with individual lignin units, indicating organic multilayering via H-bonding. Further, these findings reveal the molecular mechanisms of SOM-mineral interactions, crucial for enhancing soil carbon stabilization.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Parallel molecular mechanisms for enzyme temperature adaptation

The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. Furthermore, we identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Assessing electrogenetic activation via a network model of biological signal propagation

Introduction: Molecular communication is the transfer of information encoded by molecular structure and activity. We examine molecular communication within bacterial consortia as cells with diverse biosynthetic capabilities can be assembled for enhanced function. Their coordination, both in terms of engineered genetic circuits within individual cells as well as their population-scale functions, is needed to ensure robust performance. We have suggested that “electrogenetics,” the use of electronics to activate specific genetic circuits, is a means by which electronic devices can mediate molecular communication, ultimately enabling programmable control. Methods: Here, we have developed a graphical network model for dynamically assessing electronic and molecular signal propagation schemes wherein nodes represent individual cells, and their edges represent communication channels by which signaling molecules are transferred. We utilize graph properties such as edge dynamics and graph topology to interrogate the signaling dynamics of specific engineered bacterial consortia. Results: We were able to recapitulate previous experimental systems with our model. In addition, we found that networks with more distinct subpopulations (high network modularity) propagated signals more slowly than randomized networks, while strategic arrangement of subpopulations with respect to the inducer source (an electrode) can increase signal output and outperform otherwise homogeneous networks. Discussion: We developed this model to better understand our previous experimental results, but also to enable future designs wherein subpopulation composition, genetic circuits, and spatial configurations can be varied to tune performance. We suggest that this work may provide insight into the signaling which occurs in synthetically assembled systems as well as native microbial communities.

Chun, Kayla↗

DOE OSTI2026

Stoichiometry dependent properties of cerium hydride: An active learning developed interatomic potential study

Cerium hydride has a variety of interesting properties, including a known lattice contraction and densification with increasing hydrogen content. However, precise stoichiometric control is not experimentally straightforward and ab initio approaches are not computationally feasible for many properties such as melting and low temperature diffusion. Therefore, we develop a machine-learned interatomic potential for cerium hydride that is valid for H to Ce ratios from 2.0 to 3.0. A query-by-committee active learning approach is used to develop the training set. Leveraging classical molecular dynamics simulations, we assess a range of properties and provide fundamental mechanisms for the trends with stoichiometry. Finally, a majority of the properties follow the trend of lattice contraction, being governed by the stronger lattice binding induced by adding octahedral atoms.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Connecting suborganismal data to bioenergetic processes: killifish embryos exposed to a dioxin-like compound

A core challenge for ecological risk assessment is to integrate molecular responses into a chain of causality to organismal or population level outcomes. Bioenergetic theory may be a useful approach for integrating suborganismal responses to predict organismal level responses that influence population dynamics. In this work, we describe a novel application of Dynamic Energy Budget (DEB), theory in the context of a toxicity framework (Adverse Outcome Pathways, AOP) to make quantitative predictions of chemical exposures to individuals, starting from suborganismal data. We use early life stage exposure of Fundulus heteroclitus to dioxin-like chemicals (DLCs) and connect AOP Key Events (KEs) to DEB processes through “damage” that is produced at a rate proportional to the internal toxicant concentration. We use transcriptomic data of fish embryos exposed to DLCs to translate molecular indicators of damage into changes in DEB parameters (damage increases somatic maintenance costs) and use DEB models to predict sublethal and lethal effects of young fish. By changing a small subset of model parameters, we predict the evolved tolerance to DLCs in some wild F. heteroclitus populations, a data set not used in model parameterization. The differences in model parameters points to reduced sensitivity and altered damage repair dynamics as contributing to this evolved resistance. Our methodology has potential extrapolation to untested chemicals of ecological concern.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2025

Thermal Gradient Effects on Local Hotspot Ignition in 1,3,5,7‐Tetranitro‐1,3,5,7‐tetrazocane (HMX)

Understanding hotspot ignition, growth, and criticality, as well as the timescales of each, is crucial for parameterizing mesoscale and continuum‐level models that rely on a statistical understanding of hotspots. However, these models often consider hotspots to have uniform temperatures or for hotspots of a given temperature and size to always behave the same. Therefore, using molecular dynamics simulations, we assess the influence of thermal distribution effects on hotspot local ignition and time to ignition in 1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocane (HMX) nanoscale hotspots. Finally, by assessing hotspots with a gradient driven from an initial two‐temperature core–shell setup, we show that small increases in the core temperature under a constant average temperature can lead to order‐of‐magnitude effects on reaction and local ignition timescales.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Subdiffusive High-Pressure Hydrogen Gas Dynamics in Elastomers

We report elastomeric rubber materials serve a vital role as sealing materials in the hydrogen storage and transport infrastructure. With applications including O-rings and hose liners, these components are exposed to pressurized hydrogen at a range of temperatures, cycling rates, and pressure extremes. High-pressure exposure and subsequent rapid decompression often lead to cavitation and stress-induced damage of the elastomer due to localization of the hydrogen gas. Here, we use all-atom classical molecular dynamics simulations to assess the impact of compositional variations on gas diffusion within the commonly used elastomer ethylene–propylene–diene monomer (EPDM). With the aim to build a predictive understanding of precursors to cavitation and to motivate material formulations that are less sensitive to hydrogen-induced failure, we perform systematic simulations of gas dynamics in EPDM as a function of temperature, gas concentration, and cross-link density. Our simulations reveal anomalous, subdiffusive hydrogen motion at pressure and intermediate times. We identify two groups of gas with different mobilities: one group exhibiting high mobility and one group exhibiting low mobility due to their motion being impeded by the polymer. With decreasing temperatures, the low-mobility group shows increased gas localization, the necessary precursor for cavitation damage in these materials. At lower temperatures, increasing cross-link density led to greater hydrogen gas mobility and a lower fraction of caged hydrogen, indicating that increasing cross-link density may reduce precursors to cavitation. Finally, we use a two-state kinetic model to determine the energetics associated with transitions between these two mobility states.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Elemental zoning enhances mass transport in zeolite catalysts for methanol to hydrocarbons

Mass transport limitations in zeolite catalysts pose major hurdles for their optimal performance in diverse chemical reactions. Most approaches to reduce these restrictions focus on the synthesis of either hierarchical or nanosized zeolites. Here we demonstrate that the existence of a siliceous, catalytically inactive exterior rim on ZSM-5 particles dramatically reduces the diffusion limitations, which leads to an enhanced catalyst lifetime for the methanol-to-hydrocarbon reaction. In this study, our findings reveal that binary inorganic and organic structure-directing agents enable a one-pot synthesis of Si-zoned ZSM-5 catalysts with diffusion properties that are characteristic of particles with a much smaller size. Operando ultraviolet–visible light diffuse reflectance spectroscopy reveals a marked reduction in external coking among Si-zoned samples. Molecular dynamics simulations to assess the diffusion of methanol and benzene in siliceous pores and in those with Brønsted acids reveal substantially reduced transport limitations in zoned regions, consistent with the improved catalyst activity of Si-zoned zeolites relative to that of ZSM-5 with a homogeneous acid-site distribution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Active learning of neural network potentials for rare events

Developing an automated active learning framework for Neural Network Potentials, focusing on accurately simulating bond-breaking in hexane chains through steered molecular dynamics sampling and assessing model transferability.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1976

Data reduction and evaluation procedures

The computational procedures that are involved in exhaust emissions data reduction and the use of these computational procedures for determining the quality of the data that is obtained from exhaust measurements were considered. Four problem areas were calculated: (1) the various methods for performing the carbon balance, (2) the method for calculating water correction factors, (3) the method for calculating the exhaust molecular weight, and (4) assessing the quality of the data.

Mirsky, W.↗