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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The selective heating effect of microwave irradiation on a binary mixture of water and polyethylene oxide: a molecular dynamics simulation approach

In this study, we investigate the molecular mechanisms of a microwave-driven selective heating process by performing molecular dynamics simulations for three different systems including pure water, pure polyethylene oxide (PEO), and water-PEO mixed systems in the presence of a microwave with two different intensities of electric field such as 0.001 V/Å -1 and 0.01 V/Å -1 at a frequency of 100 GHz. First, from performing molecular dynamics simulations of CO and CO 2 in the presence of the microwave, it is confirmed that the molecular dipole moment is responsible for the rotational motion induced by the oscillating electric field. Second, by analyzing the MD simulations of the pure water system, we discover that the dipole moment of water exhibits a time lag with respect to the microwave. During the heating process, however, the temperature, kinetic, and potential energies increase synchronously with the oscillating electric field of the microwave, showing that the heating of the water system is caused by the molecular reaction of water to the microwave. Comparing the water-PEO mixed system to the pure water and pure PEO systems, the water-PEO mixed system has a higher heating rate than the pure PEO system but a lower heating rate than the pure water system. Therefore, we conclude that heating the water-PEO mixed system is driven by water molecules selectively activated by microwave irradiation. Furthermore, we also calculate the diffusion coefficients of water molecules and PEO chains by describing their mean square displacements, demonstrating that the diffusion coefficients are increased in the presence of microwaves for both water and PEO in pure and mixed systems. Lastly, during the microwave heating process, the structures of the water-PEO mixed system are altered as a function of the intensity of electric field, which is mainly driven by the response of water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Excited-state electronic structure of molecules using many-body Green’s functions: Quasiparticles and electron–hole excitations with VOTCA-XTP

Here, we present the open-source VOTCA-XTP software for the calculation of the excited-state electronic structure of molecules using many-body Green’s function theory in the GW approximation with the Bethe–Salpeter equation (BSE). This work provides a summary of the underlying theory and discusses the details of its implementation based on Gaussian orbitals, including resolution-of-identity techniques and different approaches to the frequency integration of the self-energy or acceleration by offloading compute-intensive matrix operations using graphics processing units in a hybrid OpenMP/Cuda scheme. A distinctive feature of VOTCA–XTP is the capability to couple the calculation of electronic excitations to a classical polarizable environment on an atomistic level in a coupled quantum- and molecular-mechanics (QM/MM) scheme, where a complex morphology can be imported from Molecular Dynamics simulations. The capabilities and limitations of the GW–BSE implementation are illustrated with two examples. First, we study the dependence of optically active electron–hole excitations in a series of diketopyrrolopyrrole-based oligomers on molecular-architecture modifications and the number of repeat units. Second, we use the GW–BSE/MM setup to investigate the effect of polarization on localized and intermolecular charge-transfer excited states in morphologies of low-donor content rubrene–fullerene mixtures. These showcases demonstrate that our implementation currently allows us to treat systems with up to 2500 basis functions on regular shared-memory workstations, providing accurate descriptions of quasiparticle and coupled electron–hole excited states of various characters on an equal footing.

74 ATOMIC AND MOLECULAR PHYSICS↗
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 OSTI2026

Molecular Dynamics Investigation of Oil Wetting on Synthetic Polymer Substrates

Understanding the interaction of polymer surfaces with nonpolar, low surface tension liquids, or whether a substrate is oleophobic versus oleophilic, is critical for applications ranging from antifingerprint coatings to oil–water separation membranes and oil spill remediation. Despite its technological importance, the molecular mechanisms underpinning polymer–oil wetting are not well characterized. Here, we employ molecular dynamics simulations to investigate the behavior of n-hexadecane in contact with chemically distinct polymer surfaces, spanning eight constitutional unit chemistries as well as amorphous and crystalline morphologies. This permits a critical examination of both thermodynamic and dynamic descriptors of oleophobicity, including oil contact angle, dewetting free energy, interfacial diffusivity, and a proposed “ghost probe energy,” which does not require explicit simulation of oil–polymer interactions. We find that the oil contact angle does not reliably distinguish oleophobic behavior across polymer chemistries, whereas other metrics provide clearer and more consistent differentiation. Analysis of the results reveals that polymer–oil wetting behavior is primarily governed by interfacial van der Waals interactions and modulated by surface flexibility and morphology. Collectively, this work establishes a computational framework for characterizing oil wetting and provides additional insight into what molecular-level factors dictate trends in oleophobicity.

lipids↗
DOE OSTI2023

Molecules Functionalized with Cycling Centers for Quantum Information Science

The ability for a single molecule to produce enough laser-induced fluorescence to control and detect its quantum state is known as optical cycling. This property has been used to great effect in atoms, where the relatively small number of states promotes their ability to repeatedly fluoresce, for applications such as laser cooling, precision measurement, atomic clocks, and quantum information processing. The extension of this capability to molecular species, however, has been difficult, primarily due to their propensity to become vibrationally excited during illumination. This project brought together experts from atomic physics, physical chemistry, and computational quantum chemistry to develop means to create molecules capable of optical cycling. In particular, this program sought to produce an optical cycling center (OCC), a quantum functional group capable of chemical attachment to a wide variety of molecular hosts while retaining (and thereby furnishing to its host) the ability to optically cycle. Following our team’s theoretical identification of promising species, including alkaline-earth phenoxides, we then created these species and in many cases confirmed their optical cycle closure. We now not only know of the existence of a handful of large, molecular species that can be deployed for applications in quantum technologies and measurement, but have improved our knowledge of the molecular mechanisms leading to this discovery, which will enable generalization in the future. The extension of these ideas for informed chemical design of cycling molecules with bespoke properties is now being pursued by multiple groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

Reverse transcription, an essential event in the HIV-1 life cycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral capsid. The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics (MD) simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetically favorable conditions for passive translocation of dNTPs into the HIV-1 capsid. Furthermore, binding of the host cell metabolite inositol hexakisphosphate (IP 6 ) enhances dNTP import, while binding of synthesized molecules like benzenehexacarboxylic acid (BHC) inhibits it. The enhancing effect on reverse transcription by IP 6 and the consequences of interactions between CA and nucleotides were corroborated using atomic force microscopy, transmission electron microscopy, and virological assays. Collectively, our results provide an atomistic description of the permeability of the HIV-1 capsid to small molecules and reveal a novel mechanism for the involvement of metabolites in HIV-1 capsid stabilization, nucleotide import, and reverse transcription.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Enhanced chloroplast FtsZ-ring constriction by the ARC6–ARC3 module in Arabidopsis

Chloroplast division, a process tightly linked to the energy demands of plants, is initiated by the formation of the stromal filamenting temperature-sensitive Z (FtsZ) ring. The Z ring is highly dynamic, and its constriction provides the essential force for chloroplast division. However, the regulatory mechanisms governing Z-ring dynamics and constriction remain poorly understood. Here, we report that the chloroplast inner envelope membrane (IEM) protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS6 (ARC6) interacts with the chloroplast stromal protein ARC3, and this interaction is negatively regulated by the conserved J-like domain of ARC6. ARC3 is found both distributed throughout the stroma and localized to a ring-like structure at the chloroplast division site. We demonstrate that ARC6 recruits ARC3 to the division site to form a ring-like structure, likely through direct interaction. This ARC6–ARC3 interaction enables ARC3 to bind FtsZs. Furthermore, we show that the ARC6–ARC3 complex significantly promotes the dynamics of chloroplast Z rings reconstituted in a heterologous system. Finally, the constriction of these reconstituted Z rings is markedly enhanced by ARC6–ARC3. Our findings reveal a regulatory mechanism that governs Z-ring dynamics and constriction, shedding light on the molecular mechanisms underlying chloroplast division.

Science & Technology - Other Topics↗
DOE OSTI2025

Binding and Translocation of Substrate Allosterically Promotes Functional Interactions Within the AlkB–AlkG Electron Transfer Complex

The alkane monooxygenase AlkB and rubredoxin AlkG form an electron transfer complex that hydroxylates terminal alkanes to produce alcohols. The recent cryoEM study of Fontimonas thermophila AlkB-AlkG complex revealed its architecture, including a dodecane (D12) substrate at the active site. However, FtAlkBG molecular mechanism of action of remains unknown. Here, in this study, we examined its dynamics and interactions by multiscale computations, including molecular dynamics simulations, elastic network models, and QM/MM of the oxygen activation mechanism at the AlkB catalytic site. D12 maintained stable interactions within the catalytic site during two MD runs, coordinated by hydrophobic residues L263-L264, I267, I133. A third extended run revealed that D12 could translocate to a membrane-exposed site near S49/F46 along a hydrophobic channel gated by I54. During this translocation, D12 was temporarily stabilized at intermediate sites IS1 (lined by I27/L30-G31/G50/L53-I54/P59/S124/A127-V128) and IS2 (I33-G34/L37/L45-F46/S49) before nearly exiting the protein, and diffused back to the active site, assisted by L30. Substrate binding and translocation across those intermediate sites affects the coupling between the iron centers in AlkBG, and interfacial interactions between AlkB-AlkG. The channel was further connected to the cytosol, near two surface-exposed arginines, potentially allowing for O 2 passage. The allosteric effects between D12 putative entry site, catalytic site and AlkB-AlkG interface were analyzed by ENM-based methods which confirmed the cooperative perturbation-responses and strongly correlated movements of residues belonging to those distal regions. Our study provides new mechanistic insights into key sites and their interactions that could be targeted for developing AlkB-variants with desirable alkane conversion functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

siRNA high throughput screening identifies regulators of chloropicrin and hydrogen fluoride injury in human corneal epithelial cell models

Corneal injuries induced by various toxicants result in similar clinical presentations such as corneal opacity and neovascularization. Many studies suggest that several weeks post-exposure a convergence of the molecular mechanisms drives these progressive pathologies. However, chemical agents vary in toxicological properties, and early molecular responses are anticipated to be somewhat dissimilar for different toxicants. In this report we chose 3120 targets from the Dharmacon Human Druggable genome to screen for chloropicrin (CP) and hydrogen fluoride (HF) corneal injury as we hypothesized that targets identified in vitro may be effective as therapeutic targets in future studies. Human immortalized corneal epithelial cells (SV40-HCEC) were used for screening. Cell viability and IL-8 were analyzed to down-select hits into validation studies, where multiplex cytokine analysis and high content analysis were performed to understand toxicant effect and target function. Some endpoints were also evaluated in a second human immortalized corneal epithelial cell line, TCEpi. Over 20 targets entered validation studies for CP and HF; of these, only three targets were shared: NR3C1, RELA, and KMT5A. These findings suggest that early molecular responses to different toxicants may be somewhat distinctive and present dissimilar targets for possible early intervention.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm

Neither the disease mechanism nor treatments for COVID-19 are currently known. Here, we present a novel molecular mechanism for COVID-19 that provides therapeutic intervention points that can be addressed with existing FDA-approved pharmaceuticals. The entry point for the virus is ACE2, which is a component of the counteracting hypotensive axis of RAS. Bradykinin is a potent part of the vasopressor system that induces hypotension and vasodilation and is degraded by ACE and enhanced by the angiotensin 1-9 produced by ACE2. Here, we perform a new analysis on gene expression data from cells in bronchoalveolar lavage fluid (BALF) from COVID-19 patients that were used to sequence the virus. Comparison with BALF from controls identifies a critical imbalance in RAS represented by decreased expression of ACE in combination with increases in ACE2, renin, angiotensin, key RAS receptors, kinogen and many kallikrein enzymes that activate it, and both bradykinin receptors. This very atypical pattern of the RAS is predicted to elevate bradykinin levels in multiple tissues and systems that will likely cause increases in vascular dilation, vascular permeability and hypotension. These bradykinin-driven outcomes explain many of the symptoms being observed in COVID-19.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2000

Molecular Modeling and Experimental Study of Nonlinear Optical Compounds: Mono-Substituted Derivatives of Dicyanovinylbenzene

A search for potential nonlinear optical (NLO) compounds has been performed using the Cambridge Structural Database and molecular modeling. We have studied a series of mono-substituted derivatives of dicyanovinylbenzene as the NLO properties of one of its derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were described earlier. The molecular geometry in the series of the compounds studied was investigated with an X- ray analysis and discussed along with results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the molecular planarity has been revealed. Two new compounds from the series studied were found to be active for second harmonic generation (SHG) in the powder. The measurements of SHG efficiency have shown that the o-F- and p-Cl-derivatives of dicyanovinylbenzene are about 10 and 20- times more active than urea, respectively. The peculiarities of crystal structure formation in the framework of balance between the van der Waals and electrostatic interactions have been discussed. The crystal morphology of DIVA and two new SHG-active compounds have been calculated on the basis of their known crystal structures.

Timofeeva, Tatyana V.↗
DOE OSTI2020

DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Physical insights into biological memory using phospholipid membranes

Electrical signals may propagate along neuronal membranes in the brain, thus enabling communication between nerve cells. In doing so, lipid bilayers, fundamental scaffolds of all cell membranes, deform and restructure in response to such electrical activity. These changes impact the electromechanical properties of the membrane, which then physically store biological memory. This memory can exist either over a short or long period of time. Traditionally, biological memory is defined by the strengthening or weakening of transmissions between individual neurons. In this report we show that electrical stimulation may also alter the properties of the lipid membrane, thus pointing toward a novel mechanism for memory storage. Furthermore, based on the analysis of existing electrophysiological data, we study molecular mechanisms underlying the long-term potentiation in phospholipid membranes. Finally, we examine possible relationships between the memory capacitive properties of lipid membranes, neuronal learning, and memory.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Optimized suspension culture: the rotating-wall vessel

Suspension culture remains a popular modality, which manipulates mechanical culture conditions to maintain the specialized features of cultured cells. The rotating-wall vessel is a suspension culture vessel optimized to produce laminar flow and minimize the mechanical stresses on cell aggregates in culture. This review summarizes the engineering principles, which allow optimal suspension culture conditions to be established, and the boundary conditions, which limit this process. We suggest that to minimize mechanical damage and optimize differentiation of cultured cells, suspension culture should be performed in a solid-body rotation Couette-flow, zero-headspace culture vessel such as the rotating-wall vessel. This provides fluid dynamic operating principles characterized by 1) solid body rotation about a horizontal axis, characterized by colocalization of cells and aggregates of different sedimentation rates, optimally reduced fluid shear and turbulence, and three-dimensional spatial freedom; and 2) oxygenation by diffusion. Optimization of suspension culture is achieved by applying three tradeoffs. First, terminal velocity should be minimized by choosing microcarrier beads and culture media as close in density as possible. Next, rotation in the rotating-wall vessel induces both Coriolis and centrifugal forces, directly dependent on terminal velocity and minimized as terminal velocity is minimized. Last, mass transport of nutrients to a cell in suspension culture depends on both terminal velocity and diffusion of nutrients. In the transduction of mechanical culture conditions into cellular effects, several lines of evidence support a role for multiple molecular mechanisms. These include effects of shear stress, changes in cell cycle and cell death pathways, and upstream regulation of secondary messengers such as protein kinase C. The discipline of suspension culture needs a systematic analysis of the relationship between mechanical culture conditions and biological effects, emphasizing cellular processes important for the industrial production of biological pharmaceuticals and devices.

Non-NASA Center↗
DOE OSTI2026

Role of Amorphous Chains in Nanoplastic Formation from Semicrystalline Polymers

Semicrystalline polymers, e.g., polyethylene terephthalate (PET), release micro- (100 nm to 1 mm) and nanoplastics (up to 100 nm) [MNPL] when they are degraded under quiescent conditions. However, the exact molecular mechanisms leading to material fragmentation into MNPL are unknown. Here, we monitor the evolution of chain molecular weight and the MNPL production kinetics during hydrolysis of PET pellets. We find that only ~0.6% of the amorphous phase ester bonds are hydrolyzed at the onset of MNPL release. Then, by combining a random scission model with measured amorphous spacings, we estimate that only ~15% of the stress transmitters in the amorphous phase, namely, bridges and entangled loops, have failed by this point. Thus, spontaneous fragmentation of the semicrystalline nanostructure occurs despite significant intercrystalline connectivity. We resolve this apparent contradiction by proposing that fragmentation can only occur when progressive tie-chain scission causes the material to undergo the ductile/brittle transition. Mechanistically, we speculate that the internal stresses responsible for material fragmentation are caused by processing (i.e., residual stresses) and/or sample densification induced by chemi-crystallization. We discuss additional factors that may affect our analysis and thus require further investigation, such as skin-core effects, preferential degradation of stress transmitters and/or recrystallization processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗