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Results for “molecular evolution”

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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The impact of the atmospheric turbulence-development tendency on new particle formation: a common finding on three continents

Abstract A new mechanism of new particle formation (NPF) is investigated using comprehensive measurements of aerosol physicochemical quantities and meteorological variables made in three continents, including Beijing, China; the Southern Great Plains site in the USA; and SMEAR II Station in Hyytiälä, Finland. Despite the considerably different emissions of chemical species among the sites, a common relationship was found between the characteristics of NPF and the stability intensity. The stability parameter (ζ = Z/L, where Z is the height above ground and L is the Monin–Obukhov length) is found to play an important role; it drops significantly before NPF as the atmosphere becomes more unstable, which may serve as an indicator of nucleation bursts. As the atmosphere becomes unstable, the NPF duration is closely related to the tendency for turbulence development, which influences the evolution of the condensation sink. Presumably, the unstable atmosphere may dilute pre-existing particles, effectively reducing the condensation sink, especially at coarse mode to foster nucleation. This new mechanism is confirmed by model simulations using a molecular dynamic model that mimics the impact of turbulence development on nucleation by inducing and intensifying homogeneous nucleation events.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Real-Time Monitoring of Strain Accumulation and Relief during Epitaxy of Ultrathin Co Ferrite Films with Varied Co Content

Ultrathin Co x Fe 3-x O 4 films of high structural quality and with different Co content (x = 0.6–1.2) were prepared by reactive molecular beam epitaxy on MgO(001) substrates. Epitaxy of these ferrite films is extensively monitored by means of time-resolved (operando) X-ray diffraction recorded in out-of-plane geometry to characterize the temporal evolution of the film structure. The Co ferrite films show high crystalline ordering and smooth film interfaces independent of their Co content. All Co x Fe 3-x O 4 films exhibit enhanced compressive out-of-plane strain during the early stages of growth, which partly releases with increasing film thickness. When the Co content of the ferrite films increases, the vertical-layer distances increase, accompanied by slightly increasing film roughnesses. The latter result is supported by surface-sensitive low-energy electron diffraction as well as X-ray reflectivity measurements on the final films. In contrast, the substrate–film interface roughness decreases with increasing Co content, which is confirmed with X-ray reflectivity measurements. In addition, the composition and electronic structure of the ferrite films is characterized by means of hard X-ray photoelectron spectroscopy performed after film growth. The experiments reveal the expected increasing Fe 3+ /Fe 2+ cation ratios for a higher Co content.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Bubble Relaxation Dynamics in Homopolymer DNA Sequences

Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard–Bishop–Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine–thymine (AT) and guanine–cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule’s dynamics, for times between 0.5–500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.

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

Hydration structure of flat and stepped MgO surfaces

We investigate the solvation structure of flat and stepped MgO(001) in neutral liquid water using ab initio molecular dynamics based on a hybrid density functional with dispersion corrections. Our simulations show that the MgO surface is covered by a densely packed layer of mixed intact and dissociated adsorbed water molecules in a planar arrangement with strong intermolecular H-bonds. The water dissociation fractions in this layer are >20% and >30% on the flat and stepped surfaces, respectively. Slightly above the first water layer, we observe metastable OH groups perpendicular to the interface, similar to those reported in low temperature studies of water monolayers on MgO. Here, these species receive hydrogen bonds from four nearby water molecules in the first layer and have their hydrophobic H end directed toward bulk water, while their associated protons are bound to surface oxygens. The formation of these OH species is attributed to the strong basicity of the MgO surface and can be relevant for understanding various phenomena from morphology evolution and growth of (nano)crystalline MgO particles to heterogeneous catalysis.

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

A collective elastic fluctuation mechanism for decoupling and stretched relaxation in glassy colloidal and molecular liquids

We propose a microscopic theory for the decoupling of self-diffusion and structural relaxation in glass-forming liquids within the Elastically Collective Nonlinear Langevin Equation (ECNLE) activated dynamics framework. Our central hypothesis is that the heterogeneity relevant to this problem is static fluctuations of local density on the scale of 3–4 particle diameters and how this changes local packing correlations. These fluctuations modify the degree of dynamical cage expansion that mechanistically couples intracage large amplitude hopping and longer range collective elasticity in ECNLE theory. Decoupling only emerges in the deeply supercooled regime where the strongly temperature dependent elastic barrier becomes non-negligible relative to its noncooperative local analog. The theory makes predictions for various aspects of the decoupling phenomenon, including apparent fractional power law Stokes-Einstein behavior, that appear to be consistent with experiments and simulations on hard sphere fluids and molecular liquids. Of central importance is a microscopic connection between the barrier fluctuation variance and most probable barrier height. Sensible results are also obtained for the nonexponential stretching of a generic relaxation time correlation function and its temperature evolution. Nonuniversality can arise from the relative importance of the local and collective barriers (related to fragility) and the precise magnitude of the length scale that defines the transition from local cage to elastic physics. Comparison is made with a traplike model based on a Gaussian distribution of barriers.

Xie, Shi-Jie (ORCID:0000000333174720)↗
DOE OSTI2023

Evolution of neuronal cell classes and types in the vertebrate retina

The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs1. Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. Here we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, a reptile, a teleost fish and a lamprey. We found high molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells (RGCs) and Müller glia), with transcriptomic variation across species related to evolutionary distance. Major subclasses were also conserved, whereas variation among cell types within classes or subclasses was more pronounced. However, an integrative analysis revealed that numerous cell types are shared across species, based on conserved gene expression programmes that are likely to trace back to an early ancestral vertebrate. The degree of variation among cell types increased from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified rodent orthologues of midget RGCs, which comprise more than 80% of RGCs in the human retina, subserve high-acuity vision, and were previously believed to be restricted to primates. By contrast, the mouse orthologues have large receptive fields and comprise around 2% of mouse RGCs. Projections of both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but are descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Atomically Dispersed CuN x Sites from Thermal Activation of Boron Imidazolate Cages for Electrocatalytic Methane Generation

Atomically dispersed metal sites (ADMSs) have been recognized as promising candidates for electrochemical conversion. Among a diverse range of molecular precursors for ADMS synthesis, framework materials are particularly interesting due to their high degree of tunability and control over the primary coordination sphere of the metal ions. In this work, we demonstrate that a copper boron imidazolate cage, BIF-29(Cu), is a convenient precursor for a competent catalyst with isolated Cu sites coordinated by N donors for carbon dioxide electroreduction (CO 2 RR). Although BIF-29(Cu) exhibited moderate methane selectivity over hydrogen evolution reaction (HER), the methane selectivity is significantly enhanced by 2 times (55% CH 4 at –1.25 V vs RHE) after mild thermal activation. Extensive characterization methods indicate the transformation of crystalline BIF-29(Cu) into an amorphous carbonaceous material comprising isolated CuN x sites. Moreover, in situ X-ray absorbance spectroscopy indicates stable CuN x sites that are reduced during CO 2 RR. This work encourages the discovery of single-site electrocatalytic systems through a rational selection of molecular precursor and calcination parameters for promoting product selectivity.

10 SYNTHETIC FUELS↗
DOE OSTI2020

2‐Aminobenzenethiol‐Functionalized Silver‐Decorated Nanoporous Silicon Photoelectrodes for Selective CO 2 Reduction

Abstract A molecularly thin layer of 2‐aminobenzenethiol (2‐ABT) was adsorbed onto nanoporous p‐type silicon (b‐Si) photocathodes decorated with Ag nanoparticles (Ag NPs). The addition of 2‐ABT alters the balance of the CO 2 reduction and hydrogen evolution reactions, resulting in more selective and efficient reduction of CO 2 to CO. The 2‐ABT adsorbate layer was characterized by Fourier transform infrared (FTIR) spectroscopy and modeled by density functional theory calculations. Ex situ X‐ray photoelectron spectroscopy (XPS) of the 2‐ABT modified electrodes suggests that surface Ag atoms are in the +1 oxidation state and coordinated to 2‐ABT via Ag−S bonds. Under visible light illumination, the onset potential for CO 2 reduction was −50 mV vs. RHE, an anodic shift of about 150 mV relative to a sample without 2‐ABT. The adsorption of 2‐ABT lowers the overpotentials for both CO 2 reduction and hydrogen evolution. A comparison of electrodes functionalized with different aromatic thiols and amines suggests that the primary role of the thiol group in 2‐ABT is to anchor the NH 2 group near the Ag surface, where it serves to bind CO 2 and also to assist in proton transfer.

Kan, Miao↗
DOE OSTI2023

Solar energy conversion by photosystem II: principles and structures

Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Evolution of Electronic Properties of Graphene Nanoribbons with Progressive Carving: From Straight to Porous to Chevron Ribbons

Graphene nanoribbons (GNRs) are highly versatile materials due to their unique electronic, magnetic, and optical properties, which can be precisely tuned by controlling their width, edge structure, and topology. Here, we report the on-surface synthesis and characterization of a straight N = 15 armchair GNR with periodic annulene nanopores (15-pGNR). It serves as a structural link between two well-established GNRs: the pristine N = 15 armchair GNR without pores (15-AGNR) and the chevron GNR (cGNR). With the addition of the 15-pGNR reported in this study, these three GNRs form a rare experimentally accessible series of ribbons, in which the evolution of electronic properties can be tracked upon progressive carving of a basic 15-AGNR: first, by creating periodic nanopores to form 15-pGNR and then by extending the pore area and producing meandering cGNR. We have designed a molecular precursor for the 15-pGNR and grown the nanoribbons on single-crystal gold substrates by on-surface synthesis in ultra-high vacuum (UHV) conditions. The atomically precise structure of 15-pGNR was confirmed by scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM). The band gap of 15-pGNR was studied by scanning tunneling spectroscopy (STS) and dI/dV mapping, and the occupied electronic levels were investigated by angle-resolved photoemission spectroscopy (ARPES). A theoretical and experimental comparison of 15-pGNRs, 15-AGNRs, and cGNRs demonstrates that the introduction of periodic nanopores into 15-AGNR leads to a more than 2-fold increase in its band gap. In contrast, the band gaps of 15-pGNR and cGNR differ only by about 15%. Such band gap increase can be qualitatively understood to arise from two combined effects, the periodic perforation of the graphene lattice and the confinement effect induced by the GNR width.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Radiation Damage in Materials—Helium Effects

Despite its scarcity in terrestrial life, helium effects on microstructure evolution and thermo-mechanical properties can have a significant impact on the operation and lifetime of applications, including: advanced structural steels in fast fission reactors, plasma facing and structural materials in fusion devices, spallation neutron target designs, energetic alpha emissions in actinides, helium precipitation in tritium-containing materials, and nuclear waste materials. The small size of a helium atom combined with its near insolubility in almost every solid makes the helium–solid interaction extremely complex over multiple length and time scales. This Special Issue, “Radiation Damage in Materials—Helium Effects”, contains review articles and full-length papers on new irradiation material research activities and novel material ideas using experimental and/or modeling approaches. These studies elucidate the interactions of helium with various extreme environments and tailored nanostructures, as well as their impact on microstructural evolution and material properties.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Atomistic simulations of nanoindentation on nanoglasses: Effects of grain size and gradient microstructure on the mechanical properties

The use of nanoglass (NG) microstructures has been shown as an effective strategy to improve the ductility of rather brittle metallic glass alloys. To evaluate the effects of grain size and gradient design on the mechanical properties of NGs, we perform molecular dynamics simulations of nanoindentation on Cu 64 Zr 36 NGs. We consider samples with uniform 3 and 7 nm grain sizes as well as gradient microstructures with gradient grain sizes varying from 3 to 7 nm. Here, the results show that the deformation mechanism in NGs with small grain sizes is dominated by the activation and evolution of multiple shear transformation zones. Increasing grain sizes enhances the elastic modulus and hardness at the cost of reduced abrasion resistance. Though the average grain size at the indentation surface plays a crucial role in the deformation behavior of gradient NG models, their strain localization and plastic deformation states are affected by the grain sizes far from the indenter. Desired combinations of mechanical properties can be realized by different NG microstructure designs.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Proton Relay for the Rate Enhancement of Electrochemical Hydrogen Reactions at Heterogeneous Interfaces

Proton transfer is critically important to many electrocatalytic reactions, and directed proton delivery could open new avenues for the design of electrocatalysts. However, although this approach has been successful in molecular electrocatalysis, proton transfer has not received the same attention in heterogeneous electrocatalyst design. Here, in this work, we report that a metal oxide proton relay can be built within heterogeneous electrocatalyst architectures and improves the kinetics of electrochemical hydrogen evolution and oxidation reactions. The volcano-type relationship between activity enhancement and pK a of amine additives confirms this improvement; we observe maximum rate enhancement when the pK a of a proton relay matches the pH of the electrolyte solution. Density-functional-theory-based reactivity studies reveal a decreased proton transfer energy barrier with a metal oxide proton relay. These findings demonstrate the possibility of controlling the proton delivery and enhancing the reaction kinetics by tuning the chemical properties and structures at heterogeneous interfaces.

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

Probing the active sites of oxide encapsulated electrocatalysts with controllable oxygen evolution selectivity

Electrocatalysts encapsulated by nanoscopic overlayers can control the rate of redox reactions at the outer surface of the overlayer or at the buried interface between the overlayer and the active catalyst, leading to complex behavior in the presence of two competing electrochemical reactions. This study investigated oxide encapsulated electrocatalysts (OECs) comprised of iridium (Ir) thin films coated with an ultrathin (2–10 nm thick) silicon oxide (SiO x ) or titanium oxide (TiO x ) overlayer. The performance of SiO x |Ir and TiO x |Ir thin film electrodes towards the oxygen evolution reaction (OER) and Fe(II)/Fe(III) redox reactions were evaluated. An improvement in selectivity towards the OER was observed for all OECs. Overlayer properties, namely ionic and electronic conductivity, were assessed using a combination of electroanalytical methods and molecular dynamics simulations. SiO x and TiO x overlayers were found to be permeable to H 2 O and O 2 such that the OER can occur at the MO x |Ir (M = Ti, Si) buried interface, which was further supported with molecular dynamics simulations of model SiO 2 coatings. In contrast, Fe(II)/Fe(III) redox reactions occur to the same degree with TiO x overlayers having thicknesses less than 4 nm as bare electrocatalyst, while SiO x overlayers inhibit redox reactions at all thicknesses. This observation is attributed to differences in electronic transport between the buried interface and outer overlayer surface, as measured with through-plane conductivity measurements of wetted overlayer materials. These findings reveal the influence of oxide overlayer properties on the activity and selectivity of OECs and suggest opportunities to tune these properties for a wide range of electrochemical reactions.

08 HYDROGEN↗
DOE OSTI2021

Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi

The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in Kalanchoë fedtschenkoi. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

On the evolution of scalar iso-surface area density in a turbulent mixing layer

In this paper, the transport equation for scalar iso-surface area density (Σ) in a turbulent, temporally developing mixing layer is examined. Exploring the spatial and temporal evolution of the terms in the Σ transport equation is vital to improving our understanding of turbulent flows characterized by distinct interfaces, e.g. the flame surface or the turbulent/non-turbulent interface. Previous work reported by the authors identified that Σ exhibits self-similar behaviour consistent with the development of the temporal mixing layer. Accordingly, each of the terms in the Σ transport equation is found to behave in a self-similar manner, though there are notable differences in the self-similar behaviours for each term. Based on the results presented herein, it is suggested that the rate of change of Σ (∂Σ/∂t) and the advection term scale with hλ Φ /ΔU, where h is the width of the mixing layer, λ Φ is the scalar Taylor length scale and ΔU is the velocity difference. The production and destruction terms are found to scale with an additional factor (ReSc) 1/2 . In contrast, the molecular diffusion term is found to scale with a factor (ReSc) –1/2 compared to ∂Σ/∂t. Importantly, it is found that the difference between the production and destruction terms, or net surface ‘stretch’, scales with the same factor as ∂Σ/∂t and the advection term, which may have a significant impact on how the evolution of Σ is understood and modelled in turbulent flows.

42 ENGINEERING↗