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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Phase Diagram of a Deep Potential Water Model

Using the Deep Potential methodology, we construct a model that reproduces accurately the potential energy surface of the SCAN approximation of density functional theory for water, from low temperature and pressure to about 2400 K and 50 GPa, excluding the vapor stability region. The computational efficiency of the model makes it possible to predict its phase diagram using molecular dynamics. Satisfactory overall agreement with experimental results is obtained. Here, the fluid phases, molecular and ionic, and all the stable ice polymorphs, ordered and disordered, are predicted correctly, with the exception of ice III and XV that are stable in experiments, but metastable in the model. The evolution of the atomic dynamics upon heating, as ice VII transforms first into ice VII" and then into an ionic fluid, reveals that molecular dissociation and breaking of the ice rules coexist with strong covalent fluctuations, explaining why only partial ionization was inferred in experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Genomes of multicellular algal sisters to land plants illuminate signaling network evolution

Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum . We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fast Proton Transfer and Hydrogen Evolution Reactivity Mediated by [Co 13 C 2 (CO) 24 ] 4–

A common approach to speeding up proton transfer (PT) by molecular catalysts is manipulation of the secondary coordina-tion sphere with proton relays and these enhance overall reaction rates by orders of magnitude. In contrast, heterogenous electrocatalysts have band structures that promote facile PT concerted with electron transfer (ET), known as the Volmer mechanism. Here in this paper, we show that [Co 13 C 2 (CO) 24 ] 4– , containing multiple Co-Co bonds to statistically enhance observed rates of PT, promotes PT on the order of 2.3 × 10 9 M -1 s -1 which suggests a diffusion-limited rate. The fast ET and PT chemistry is at-tributed to the delocalized electronic structure of [Co 13 C 2 (CO) 24 ] 4– . Electrochemical characterization of [Co 13 C 2 (CO) 24 ] 4– in the presence and absence of protons reveals ET kinetics and diffusion behavior similar to other small clusters such as nano-materials and fullerenes.

08 HYDROGEN↗
DOE OSTI2021

Cobalt Carbonyl Clusters Enable Independent Control of Two Proton Transfer Rates in the Mechanism for Hydrogen Evolution

Abstract Metal carbonyl clusters (MCC's) are atomically defined nanomaterials which can be characterized using the precise tools of molecular (electro)chemistry. HER mechanisms involve two proton transfer (PT) steps in the catalytic cycle. For HER catalyzed by [Co 11 C 2 (CO) 23 ] 3− ( 1 3− ), cyclic voltammetry measurements were used to determine the rate for PT1 as k PT1 =3×10 8 M −1 s −1 , whereas the rate for PT2 is k PT2 =3.7×10 3 M −1 s −1 . The fast, diffusion‐limited rate for PT1 is consistent with a previous report describing [Co 13 C 2 (CO) 24 ] 4− ( 2 4− ), with PT=2.9×10 9 M −1 s −1 . In both cases rate enhancement in PT1 is promoted by the many Co−Co bonds on the surface of the MCC that serve as PT sites: a statistical enhancement of rate akin to the effects of proton relays. In contrast, k PT2 varies and is five orders of magnitude slower for 1 2− compared with 2 4− . Thus, MCC's and nanomaterials offer an opportunity to enhance the rate for PT1 while maintaining thermochemical or kinetic control of PT2.

Pattanayak, Santanu↗
DOE OSTI2023

The homogeneous mixing of MgO and H 2 O at extreme conditions

Investigating water worlds presents a unique opportunity to understand the fundamental processes of planetary formation and evolution. One key aspect is characterizing the interactions between water and rock under the pressures and temperatures present within these worlds. Investigating the conditions for the homogeneous mixing of these materials is imperative to characterizing bulk properties and evolution of water-rich exoplanets. Here, in this study, we use density functional molecular dynamics simulations to study MgO-H 2 O mixtures at high pressure–temperature conditions where H 2 O occurs in solid, superionic, or liquid form. MgO, the representative rocky material, can be either solid or liquid. We start from 500 K at 120 GPa, increasing the temperature step by step up to 8000 K. By inspection, we determine the temperature at which MgO-HO homogeneously mix in our simulations. At 6000 K and 174 GPa is when we find the system to homogeneously mix. This heat-until-it-mixes approach provides us with an upper bound on the temperature for the mixing of MgO and H 2 O. We find that homogeneous mixing occurs at sufficiently low temperatures to be relevant for the collisional growth of a water-rich planet.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

The origin and evolution of viruses inferred from fold family structure

The canonical frameworks of viral evolution describe viruses as cellular predecessors, reduced forms of cells, or entities that escaped cellular control. The discovery of giant viruses has changed these standard paradigms. Their genetic, proteomic and structural complexities resemble those of cells, prompting a redefinition and reclassification of viruses. In a previous genome-wide analysis of the evolution of structural domains in proteomes, with domains defined at the fold superfamily level, we found the origins of viruses intertwined with those of ancient cells. In this review, we extend these data-driven analyses to the study of fold families confirming the co-evolution of viruses and ancient cells and the genetic ability of viruses to foster molecular innovation. The results support our suggestion that viruses arose by genomic reduction from ancient cells and validate a co-evolutionary ‘symbiogenic’ model of viral origins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Distinguishing Electron and Hole Dynamics in Functionalized CdSe/CdS Core/Shell Quantum Dots Using Complementary Ultrafast Spectroscopies and Kinetic Modeling

The evolution of excitation energy and photogenerated charges in semiconductor quantum dots (QDs) functionalized with molecular acceptors can be probed on ultrafast time scales using techniques such as transient absorption (TA) spectroscopy. However, historical interpretations that the 1S(e)-1S 3/2 (h) transition in Cd-chalcogenide QDs is fully attributable to electrons may be misleading, and multiexponential models used to fit TA kinetics do not correspond directly to specific photophysical processes. Here, we present visible-wavelength and mid-IR TA and time-resolved photoluminescence measurements to inform a comprehensive kinetic model of the photoexcited CdSe/CdS core/shell QDs functionalized with passivating oleic acid (OA), hole-accepting ferrocene, or electron-accepting naphthalene bisimide (NBI). We show that ~30% of the 1S signal and 72% of the IR signal can originate from holes in well-passivated core/shell QDs. We also demonstrate evidence of electron trapping in OA-capped core/shell QDs, with additional electron transfer and hole trapping in the QDs functionalized with NBI. Electron (hole) trapping and detrapping occur in 450 ± 100 ps (430 ± 70 ps) and 340 ± 100 ps (1.1 ± 0.4 ns) respectively, while the time constant for electron transfer to NBI is ~1.8 ns. The comprehensive picture of photophysical processes provided by the complementary ultrafast techniques and kinetic modeling can accelerate both the fundamental science and application development of nanostructured and molecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers

Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Optimal control of coupled quantum systems based on the first-order Magnus expansion: Application to multiple dipole-dipole-coupled molecular rotors

This paper presents a method for performing approximate optimal control simulations for quantum systems with multiple coupled degrees of freedom. In this work, the time evolution is simulated using the first-order Magnus expansion in the interaction picture, where the couplings between different degrees of freedom are treated as the perturbation. A numerical implementation procedure is presented that leverages upon pairwise couplings and the separability of the zeroth-order time evolution operator to achieve a reduced computational cost, which is analyzed with respect to the number of degrees of freedom. The formulation is compatible with gradient-free methods to optimize the control field, and a stochastic hill climbing algorithm is adopted for this purpose. As illustrations, optimal control simulations are performed for systems of two and three dipole-dipole-coupled molecular rotors under the influence of a control field. For the two-rotor system, the field is optimized to achieve either orientation or entanglement objectives. For the three-rotor system, the field is optimized either to orient all three rotors in the same direction or to orient one rotor in a particular direction while the other two rotors point in the opposite direction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Spatial influence of paramagnetic molecules on magnetic tunnel junction-based molecular spintronic devices (MTJMSD)

Magnetic Tunnel Junction-Based Molecular Spintronic Devices (MTJMSDs) are potential candidates for inventing highly correlated systems. Understanding MTJMSD's magnetic behavior is essential to designing and fabricating practical devices. This paper investigates the effect of two contributing factors on MTJMSD's magnetic properties via Monte Carlo Simulation. Here, we have systematically studied coupling strengths and nature between magnetic molecules and ferromagnetic electrodes at various temperatures. We have also investigated the effect of length and thickness increase on MTJMSD temporal and spatial evolution of magnetic moment, magnetic correlation, and magnetic susceptibility. Our results showed that thermal energy increase significantly affects molecular devices.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Effects of dimensionality on the electronic structure of Ruddlesden-Popper chromates Sr n+1 ⁢Cr n ⁢O 3⁢n+1

Transition-metal oxides host a wide variety of electronic phenomena that can be significantly influenced by the effective dimensionality of the system under consideration. These include charge, spin, and orbital orderings, as well as unconventional superconductivity. In this context, the Ruddlesden-Popper chromates Sr n+1 Cr n O 3n+1 emerge as a particularly intriguing series of materials. Formally, the chromium atom displays a rather special 4+ oxidation state throughout the entire series. However, the effective dimensionality changes from quasi-2D to 3D as n increases from 1 to ∞. As a result, the insulating antiferromagnetic behavior observed for n = 1, 2, 3 transforms into itinerant antiferromagnetism with reduced transition temperature for the n = ∞ end member of the series, i.e., the perovskite SrCrO 3 . Further, distinct orbital orderings with exotic singlet states have been predicted for these systems. However, the lack of single-crystal bulk or thin-film samples has made experimental progress difficult. Here we demonstrate the synthesis of thin films of the perovskite SrCrO 3 and the associated layered chromates via oxide molecular beam epitaxy for n = 1 to n = 5. Our electrical transport measurements reveal a gradual evolution from a strongly insulating state in Sr 2 CrO 4 to a metallic state in the end member SrCrO 3 . X-ray absorption spectroscopy measurements demonstrate a varying hybridization strength of the Cr 4+ valence electrons across the series, helping to explain the trend in conduction. Finally, density functional theory calculations further confirm the observed transport trend and identify additional distortions present in the system.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Disentangling the evolution of electrons and holes in photoexcited ZnO nanoparticles

The evolution of charge carriers in photoexcited room temperature ZnO nanoparticles in solution is investigated using ultrafast ultraviolet photoluminescence spectroscopy, ultrafast Zn K-edge absorption spectroscopy, and ab initio molecular dynamics (MD) simulations. The photoluminescence is excited at 4.66 eV, well above the band edge, and shows that electron cooling in the conduction band and exciton formation occur in <500 fs, in excellent agreement with theoretical predictions. The x-ray absorption measurements, obtained upon excitation close to the band edge at 3.49 eV, are sensitive to the migration and trapping of holes. They reveal that the 2 ps transient largely reproduces the previously reported transient obtained at 100 ps time delay in synchrotron studies. In addition, the x-ray absorption signal is found to rise in ∼1.4 ps, which we attribute to the diffusion of holes through the lattice prior to their trapping at singly charged oxygen vacancies. Indeed, the MD simulations show that impulsive trapping of holes induces an ultrafast expansion of the cage of Zn atoms in <200 fs, followed by an oscillatory response at a frequency of ∼100 cm−1, which corresponds to a phonon mode of the system involving the Zn sub-lattice.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Fermentation Practices Select for Thermostable Endolysins in Phages

Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular form that combines different catalytic and cell wall-binding domains, even in phages infecting the same species. Yet, our current understanding lacks insight into how environmental factors and ecological niches may have influenced the evolution of these enzymes. In this study, we focused on phages infecting Streptococcus thermophilus, as this bacterial species has a well-defined and narrow ecological niche, namely, dairy fermentation. Among the endolysins found in phages targeting this species, we observed limited diversity, with a singular structural type dominating in most of identified S. thermophilus phages. Within this prevailing endolysin type, we discovered a novel and highly conserved calcium-binding motif. This motif proved to be crucial for the stability and activity of the enzyme at elevated temperatures. Ultimately, we demonstrated its positive selection within the host's environmental conditions, particularly under the temperature profiles encountered in the production of yogurt, mozzarella, and hard cheeses that rely on S. thermophilus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Unfaulting mechanisms of interstitial Frank loops in fluorite-structured ThO 2

Unfaulting of Frank loops in irradiated fluorite-structured oxides is of significance for understanding microstructural evolution. However, the mechanisms have not yet been directly observed. To this end, we utilize molecular dynamics to reveal the atomistic details related to the unfaulting process of interstitial Frank loops in ThO 2 , which involve a single pair or multiple pairs of co-propagating Shockley partials to annihilate the stacking faults. Here, we find that the unfaulting is achieved via a synchronous shear of the partial pairs to remove the extrinsic stacking fault in the cation sublattice and the intrinsic stacking fault in the anion sublattice. The high mobility of oxygen at the dislocation core may reduce the activation barriers of dislocation nucleation and migration. These findings provide a fundamental understanding of the transformation of faulted loops in irradiated ThO 2 , and could be transferable to other fluorite-structured oxides.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Time-Evolving Chirality Loss in Molecular Photodissociation Monitored by X-ray Circular Dichroism Spectroscopy

In this work, the ultrafast photoinduced chirality loss of 2-iodobutane is studied theoretically by time- and frequency-resolved X-ray circular dichroism (TRXCD) spectroscopy. Following an optical excitation, the iodine atom dissociates from the chiral center, which we capture by quantum non-adiabatic molecular dynamics simulations. At variable time delays after the pump, the resonant X-ray pulse selectively probes the iodine and carbon atom involved in the chiral dissociation through a selected core-to-valence transition. The TRXCD signal at the iodine L 1 edge accurately captures the timing of C–I photodissociation and thereby chirality loss, c.a 70 fs. The strong electric dipole–electric quadrupole (ED–EQ) response makes this signal particularly sensitive to vibronic coherence at the high X-ray regime. At the carbon K-edges, the signals monitor the molecular chirality of the 2-butyl radical photoproduct and the spin state of the iodine atom. The ED–EQ response is masked under the strong electric dipole-magnetic dipole response, making this signal intuitive for the electronic population. The evolution of the core electronic states and its chiral sensitivity is discussed. Overall, the element-specific TRXCD signal provides a detailed picture of molecular dynamics and offers a unique sensitive window into the time-dependent chirality of molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Tetracene Functionalized Si(111) Achieves Enhanced Solar-to-Chemical Energy Conversion via Molecular Acceptor States

The properties of semiconductor|liquid interfaces play a critical role in determining the efficiency of solar-to-hydrogen (STH) conversion. Here, we investigate how molecular functionalization of Si(111) and Si(111)|TiO 2 surfaces impacts photoelectrochemical (PEC) hydrogen production efficiency. We find that functionalization of ∼3% of the atop sites of Si(111) with either 9-anthracene (Anth) or 5-tetracene (Tet), with the remaining sites passivated by methyl groups, provides substrates with high electronic quality and low surface oxide densities, as determined by X-ray photoelectron spectroscopy (XPS) measurements. Surface photovoltage (SPV) spectroscopy shows that surfaces modified with Anth or Tet exhibit an increased photovoltage, with Tet-functionalized surfaces yielding an additional 192 meV relative to methyl-terminated Si(111), indicating improved charge separation for Si-Tet. Further improvement in onset potential was achieved by replacing a nitrogen-containing TiO 2 atomic layer deposition (ALD) precursor (TDMAT) with a precursor lacking nitrogen (TTIP), which eliminates the parasitic defect band in the TiO 2 overlayer (p-Si(111)-Tet|TTIP-TiO 2 |Pt: V OC = +0.283 ± 0.041 V vs RHE). Density functional theory (DFT) analysis demonstrates that compared with Anth-modified Si(111), the Tet-modified surface exhibits more hybridized Si(111)-Tet states closer to the silicon band edges. Mercury contact current–voltage (I–V, dark) measurements quantified the relative interfacial density of states of Si-Tet, Si-Anth and Si-Me surfaces─revealing that the interfacial state density was highest for Si-Tet. This suggests that such hybridized interfaces serve to capture better photoexcited charge, which enables facile electron transfer to molecular acceptors in solution. Altogether, the data indicate that beneficial hybrid molecular LUMO surface states interacting with the Si conduction band edge results in improved hydrogen evolution (HER) performance for p-Si devices.

Group theory↗
DOE OSTI2023

Interface microstructure effects on dynamic failure behavior of layered Cu/Ta microstructures

Abstract Structural metallic materials with interfaces of immiscible materials provide opportunities to design and tailor the microstructures for desired mechanical behavior. Metallic microstructures with plasticity contributors of the FCC and BCC phases show significant promise for damage-tolerant applications due to their enhanced strengths and thermal stability. A fundamental understanding of the dynamic failure behavior is needed to design and tailor these microstructures with desired mechanical responses under extreme environments. This study uses molecular dynamics (MD) simulations to characterize plasticity contributors for various interface microstructures and the damage evolution behavior of FCC/BCC laminate microstructures. This study uses six model Cu/Ta interface systems with different orientation relationships that are as- created, and pre-deformed to understand the modifications in the plasticity contributions and the void nucleation/evolution behavior. The results suggest that pre-existing misfit dislocations and loading orientations (perpendicular to and parallel to the interface) affect the activation of primary and secondary slip systems. The dynamic strengths are observed to correlate with the energy of the interfaces, with the strengths being highest for low-energy interfaces and lowest for high-energy interfaces. However, the presence of pre-deformation of these interface microstructures affects not only the dynamic strength of the microstructures but also the correlation with interface energy.

42 ENGINEERING↗
DOE OSTI2023

Entropic control of the free-energy landscape of an archetypal biomolecular machine

Biomolecular machines are complex macromolecular assemblies that utilize thermal and chemical energy to perform essential, multistep, cellular processes. Despite possessing different architectures and functions, an essential feature of the mechanisms of action of all such machines is that they require dynamic rearrangements of structural components. Surprisingly, biomolecular machines generally possess only a limited set of such motions, suggesting that these dynamics must be repurposed to drive different mechanistic steps. Although ligands that interact with these machines are known to drive such repurposing, the physical and structural mechanisms through which ligands achieve this remain unknown. Using temperature-dependent, single-molecule measurements analyzed with a time-resolution-enhancing algorithm, here, we dissect the free-energy landscape of an archetypal biomolecular machine, the bacterial ribosome, to reveal how its dynamics are repurposed to drive distinct steps during ribosome-catalyzed protein synthesis. Specifically, we show that the free-energy landscape of the ribosome encompasses a network of allosterically coupled structural elements that coordinates the motions of these elements. Moreover, we reveal that ribosomal ligands which participate in disparate steps of the protein synthesis pathway repurpose this network by differentially modulating the structural flexibility of the ribosomal complex (i.e., the entropic component of the free-energy landscape). Here, we propose that such ligand-dependent entropic control of free-energy landscapes has evolved as a general strategy through which ligands may regulate the functions of all biomolecular machines. Such entropic control is therefore an important driver in the evolution of naturally occurring biomolecular machines and a critical consideration for the design of synthetic molecular machines.

Science & Technology - Other Topics↗