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Results for “Directed 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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

A macromolecular assembly directed ceramic aerogel monolith material

Ceramic aerogels exhibit remarkable thermal insulation for energy efficient building applications, while it is indispensable to understand their nanoporous structure evolution to control their thermal regulation performance. In this study, we design and synthesize a lightweight porous silica aerogel monolithic material, and demonstrate its thermal insulation performance regulated by the morphology of porous nanostructures controlled by surfactant induced self-assembly. The micelle networks and in situ gas bubble formation guide the formation of uniform pores in the as-synthesized monolith, which shows superior thermal and acoustic insulation and robust mechanical stability with a thermal conductivity of 0.032 W m –1 K –1 , a soundproof performance improvement by 17% at a frequency of 800 Hz, and a 1.3 MPa compressive strength with a Young's modulus of 15 MPa. Lastly, these findings provide a new route to manufacture low-cost aerogel monolithic insulation materials for energy efficient building applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Direct observation of the dead-cone effect in quantum chromodynamics

In particle collider experiments, elementary particle interactions with large momentum transfer produce quarks and gluons (known as partons) whose evolution is governed by the strong force, as described by the theory of quantum chromodynamics (QCD). These partons subsequently emit further partons in a process that can be described as a parton shower, which culminates in the formation of detectable hadrons. Studying the pattern of the parton shower is one of the key experimental tools for testing QCD. This pattern is expected to depend on the mass of the initiating parton, through a phenomenon known as the dead-cone effect, which predicts a suppression of the gluon spectrum emitted by a heavy quark of mass m Q and energy E, within a cone of angular size m Q /E around the emitter. Previously, a direct observation of the dead-cone effect in QCD had not been possible, owing to the challenge of reconstructing the cascading quarks and gluons from the experimentally accessible hadrons. We report the direct observation of the QCD dead cone by using new iterative declustering techniques to reconstruct the parton shower of charm quarks. This result confirms a fundamental feature of QCD. Furthermore, the measurement of a dead-cone angle constitutes a direct experimental observation of the non-zero mass of the charm quark, which is a fundamental constant in the standard model of particle physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Convoluted filtering for process cycle modeling

Principles of materials science and engineering, physics, mathematics, and information science are used to extract knowledge and insights from the process-structure–property-performance relationships hidden in materials data. The process-structure modeling can be accelerated without loss of interpretability, with artificial intelligence tools that mimic the salient features of the process and process-structure relations. In this work, a novel convoluted model-filtering technique was exploited to build and successfully train the Convoluted Filter (CoFi) artifacts for Fe-based alloy heat treatment cycles. The artifacts were pre-trained to filter out deep models that change the surrogate microstructure state after the heat treatment at ambient conditions. Direct representation of the thermal cycle features within knowledge Graph facilitated development of meaningful data models for microstructure evolution, which reduce overfitting to limited datasets.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Interface velocity dependent solute trapping and phase selection during rapid solidification of laser melted hypo-eutectic Al-11at.%Cu alloy

Microstructure formation of a hypo-eutectic Al-11Cu (atom percent) alloy during solidification after laser melting has been studied by transmission electron microscopy (TEM). The evolution of the solid-liquid-interface velocity, V SL , during the solidification process has been determined from direct observation by in-situ TEM. This enabled correlating V SL with development of four distinct microstructure zones. Crystal growth mode transitions from planar to cellular, cellular to dendritic, dendritic to cellular, and cellular to planar, have been observed for the accelerating solid-liquid-interface. The transition from coupled two-phase growth to the single-phase growth occurred for V SL = V a = (0.80±0.05) m/s, where V a is the velocity of absolute stability, at the onset of banded morphology grain formation. The in-situ and post-mortem TEM uniquely permitted determination of the non-equilibrium solidus for the rapidly solidifying Al-11Cu alloy. Experimental evidence for solute clustering and chemical ordering tendencies at length scales on the order of ≤ 5nm has been detected in the single-phase regions of the banded grains. The structural features of the single-phase bands have been interpreted as signatures of ‘frozen in’ configurations present in the liquid boundary layer adjacent to the growing crystal, which has a width of about 3nm. Finally, the nano-scale spatiotemporal resolution experimental TEM studies performed here provided quantitative metrics, e.g. the solidification interface velocity dependent solute concentration of the α-Al phase and the near-atomic scale structure in the single-phase bands, that are uniquely suitable for comparison with theory and model predictions for solidification microstructure development in multicomponent alloys after laser melting.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Atomistic Characterization of Gramicidin Channel Formation

We investigated gramicidin A (gA) subunit dimerization in lipid bilayers using microsecond-long replica-exchange umbrella sampling simulations, millisecond-long unbiased molecular dynamics simulations, and machine learning. Our simulations led to a dimer structure that is indistinguishable from the experimentally determined gA channel structures, with the two gA subunits joined by six hydrogen bonds (6HB). The simulations also uncovered two additional dimer structures, with different gA–gA stacking orientations that were stabilized by four or two hydrogen bonds (4HB or 2HB). When examining the temporal evolution of the dimerization, we found that two bilayer-inserted gA subunits can form the 6HB dimer directly, with no discernible intermediate states, as well as through paths that involve the 2HB and 4HB dimers.

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

Dynamic Ligand Surface Chemistry of Excited PbS Quantum Dots

The ligand shell around colloidal quantum dots mediates the electron and energy transfer processes that underpin their use in optoelectronic and photocatalytic applications. In this work, we show that the surface chemistry of carboxylate anchoring groups of oleate ligands passivating PbS quantum dots undergoes significant changes when the quantum dots are excited to their excitonic states. Additionally, we directly probe the changes of surface chemistry using time-resolved mid-infrared spectroscopy that records the evolution of the vibrational frequencies of carboxylate groups following excitation of the electronic states. The data reveal a reduction of the Pb-O coordination of carboxylate anchoring groups to lead atoms at the quantum dot surfaces. The dynamic surface chemistry of the ligands may increase their surface mobility in the excited state and enhance the ability of molecular species to penetrate the ligand shell to undergo energy and charge transfer processes that depend sensitively on distance.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Formation of Carbon–Carbon Interlinkage Bonds under High Pressure

The formation of carbon–carbon interlinkage bonds (CCIBs) via the chemical binding of interlayer carbon atoms of many sp 2 -bonded carbon precursors is an essential step for synthesizing various diamond and diamond-like materials. Although the existence of CCIBs may be reasonably assumed under high-pressure conditions, direct experimental evidence has been scarce. Micro-Raman spectroscopy is here employed to track in situ the evolution of C–C bonds in a pressure range from ambient to 54 GPa. A pressure-induced two-stage (polynomial and linear) shift of the G peak and new generation of the CCIB peak at about 1550 cm –1 are observed in multiple types of layer-structured carbon precursors, including glassy carbon, natural graphite, and carbon nanotubes. In conclusion, the experimental discovery of CCIBs holds significance in comprehending phase transitions of sp 2 -bonded carbon materials and has implications for the advancement of novel carbon structures.

Anode materials↗
DOE OSTI2026

Carbon doping in GeTe drives differences in local structure and properties

Advances in low-power, energy-efficient information storage and computing require understanding and controlling the atomic and nanoscale structures of functional materials, such as phase-change materials. Phase-change memory technology enables nonvolatile, low-power memory in devices by storing information through reversible changes in a phase-change material's atomic structure (i.e., transformations between amorphous and crystalline phases) that have corresponding changes in properties, including electronic resistivity and optical reflectivity. Here, we apply complementary X-ray absorption spectroscopy and X-ray pair distribution function analyses to experimentally identify the local- and medium-range atomic structure differences of GeTe and C-doped GeTe thin films. Upon controlled heating, composition- and temperature-dependent atomic structure evolution in GeTe and C-doped GeTe films shows differences in bonding behavior and local structure that directly influence crystallization onset temperature. We find that the introduction of C interrupts Ge–Ge bonds in amorphous GeTe, altering the as-deposited structure to be more similar to the distorted rocksalt structure of crystalline α–GeTe. The change alters the response of the amorphous atomic structure to heating and also lowers the crystallization onset temperature, from 230 °C in GeTe to 220 °C in the C-doped film. The combined insights from both X-ray techniques provide understanding of structural transformations that enables the development and optimization of next-generation memory and computing materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Drag reduction and the Vogel exponent of a flexible beam in transient shear flows

Interactions between a flexible beam and a fluid in a channel are of great relevance to biological hairy surfaces, aquatic vegetation, marine life (e.g., fish gills), and many industrial systems alike. While steady state response of a beam to such flows is fairly well-explored, their behavior in the transient regime is not fully understood. Here, a series of numerical simulations are performed to study the laminar Couette flow of an incompressible viscous fluid past an elastic beam in a two-dimensional channel. The flexible beam is perpendicular to the direction of flow, and its base is fixed to the stationary bottom of the channel. We measure the evolution of the Vogel exponent, drag reduction, and reconfiguration number during the transient and steady-state response of the fluid–structure system for different geometrical and physical properties. Our benchmark shows a good agreement between numerical and experimental observations. Our results show that the system's steady-state response at different bulk-fluid velocities can be reproduced by investigating the shear flow response during the transient regime. We define a new variable that characterizes the evolution of the local velocity profile in the proximity of the free end of the beam and use that to characterize the transient-regime response. The analysis yields insight into the competing effects of elasticity of the beam and non-linear flow response.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Tuning the band topology of GdSb by epitaxial strain

Rare-earth monopnictide (RE-V) semimetal crystals subjected to hydrostatic pressure have shown interesting trends in magnetoresistance, magnetic ordering, and superconductivity, with theory predicting pressure-induced band inversion. Yet, thus far, there have been no direct experimental reports of interchanged band order in RE-Vs due to strain. This work studies the evolution of band topology in biaxially strained GdSb(001) epitaxial films using angle-resolved photoemission spectroscopy (ARPES) and density functional theory (DFT). As biaxial strain is tuned from tensile to compressive strain, the gap between the hole and the electron bands dispersed along [001] decreases. The conduction and valence band shifts seen in DFT and ARPES measurements are explained by a tight-binding model that accounts for the orbital symmetry of each band. Finally, we discuss the effect of biaxial strain on carrier compensation and magnetic ordering temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Entropic formation of a thermodynamically stable colloidal quasicrystal with negligible phason strain

Quasicrystals have been discovered in a variety of materials ranging from metals to polymers. Yet, why and how they form is incompletely understood. In situ transmission electron microscopy of alloy quasicrystal formation in metals suggests an error-and-repair mechanism, whereby quasiperiodic crystals grow imperfectly with phason strain present, and only perfect themselves later into a high-quality quasicrystal with negligible phason strain. The growth mechanism has not been investigated for other types of quasicrystals, such as dendrimeric, polymeric, or colloidal quasicrystals. Soft-matter quasicrystals typically result from entropic, rather than energetic, interactions, and are not usually grown (either in laboratories or in silico) into large-volume quasicrystals. Consequently, it is unknown whether soft-matter quasicrystals form with the high degree of structural quality found in metal alloy quasicrystals. Here, we investigate the entropically driven growth of colloidal dodecagonal quasicrystals (DQCs) via computer simulation of systems of hard tetrahedra, which are simple models for anisotropic colloidal particles that form a quasicrystal. Using a pattern recognition algorithm applied to particle trajectories during DQC growth, we analyze phason strain to follow the evolution of quasiperiodic order. As in alloys, we observe high structural quality; DQCs with low phason strain crystallize directly from the melt and only require minimal further reduction of phason strain. Finally, we also observe transformation from a denser approximant to the DQC via continuous phason strain relaxation. Our results demonstrate that soft-matter quasicrystals dominated by entropy can be thermodynamically stable and grown with high structural quality––just like their alloy quasicrystal counterparts.

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

Modelling and assessing the near-wake representation and turbulence behaviour of control-oriented wake models

Due to the interaction between the wake of an upstream turbine on a downstream turbine, power losses and increased fatigue loads occur. By yawing the upstream turbine with regard to the wind direction, one can potentially reduce the power losses of the downstream turbine and reduce the fatigue loads. The evolution of the wake depends on the pressure gradient within the near-wake region and the turbulent kinetic energy and must be incorporated in existing wake steering algorithms to provide an accurate estimation of the wake flow. This paper will show a first approach to implement a near-wake model and a turbulence model in the curled wake model within the controls-oriented framework FLORIS. The near-wake model is based on an analytical expression of the velocity profile to model the pressure gradient. Furthermore, two turbulence models are incorporated within the curled wake model based on a Gaussian-distribution and a mixing length formulation. The adapted curled wake model is then assessed with the measurement data acquired in the wind tunnel at ForWind – University of Oldenburg. The evaluation of the models show good agreement for the velocity deficit and representation of the near-wake region. Furthermore, the turbulent kinetic energy behaved as expected in comparison to other work, showing a ring of high turbulent kinetic energy at non-yawed condition which is deflected to a curled shape at large yaw angles with the turbulence model based on a mixing length formulation.

FLORIS↗
DOE OSTI2022

The EBLM project – IX. Five fully convective M-dwarfs, precisely measured with CHEOPS and TESS light curves

ABSTRACT Eclipsing binaries are important benchmark objects to test and calibrate stellar structure and evolution models. This is especially true for binaries with a fully convective M-dwarf component for which direct measurements of these stars’ masses and radii are difficult using other techniques. Within the potential of M-dwarfs to be exoplanet host stars, the accuracy of theoretical predictions of their radius and effective temperature as a function of their mass is an active topic of discussion. Not only the parameters of transiting exoplanets but also the success of future atmospheric characterization relies on accurate theoretical predictions. We present the analysis of five eclipsing binaries with low-mass stellar companions out of a subsample of 23, for which we obtained ultra-high-precision light curves using the CHEOPS satellite. The observation of their primary and secondary eclipses are combined with spectroscopic measurements to precisely model the primary parameters and derive the M-dwarfs mass, radius, surface gravity, and effective temperature estimates using the PYCHEOPS data analysis software. Combining these results to the same set of parameters derived from TESS light curves, we find very good agreement (better than 1 per cent for radius and better than 0.2 per cent for surface gravity). We also analyse the importance of precise orbits from radial velocity measurements and find them to be crucial to derive M-dwarf radii in a regime below 5 per cent accuracy. These results add five valuable data points to the mass–radius diagram of fully convective M-dwarfs.

Sebastian, D. (ORCID:0000000222149258)↗
DOE OSTI2021

Theory of Trotter Error with Commutator Scaling

The Lie-Trotter formula, together with its higher-order generalizations, provides a simple approach to decomposing the exponential of a sum of operators. Despite significant effort, the error scaling of such product formulas remains poorly understood. We develop a theory of Trotter error that overcomes the limitations of truncating the Baker-Campbell-Hausdorff expansion. Our analysis directly exploits the commutativity of operator summands, producing tighter error bounds for both real- and imaginary-time evolutions. Whereas previous work achieves similar goals for systems with geometric locality or Lie-algebraic structure, our approach holds in general. We give a host of improved algorithms for digital quantum simulation and quantum Monte Carlo methods, nearly matching or even outperforming the best previous results. Our applications include: (i) a simulation of second-quantized plane-wave electronic structure, nearly matching the interaction-picture algorithm of Low and Wiebe; (ii) a simulation of $k$-local Hamiltonians almost with induced one-norm scaling, faster than the qubitization algorithm of Low and Chuang; (iii) a simulation of rapidly decaying power-law interactions, outperforming the Lieb-Robinson-based approach of Tran et al.; (iv) a hybrid simulation of clustered Hamiltonians, dramatically improving the result of Peng, Harrow, Ozols, and Wu; and (v) quantum Monte Carlo simulations of the transverse field Ising model and quantum ferromagnets, tightening previous analyses of Bravyi and Gosset. We obtain further speedups using the fact that product formulas can preserve the locality of the simulated system. Specifically, we show that local observables can be simulated with complexity independent of the system size for power-law interacting systems, which implies a Lieb-Robinson bound nearly matching a recent result of Tran et al. Our analysis reproduces known tight bounds for first- and second-order formulas. We further investigate the tightness of our bounds for higher-order formulas. For quantum simulation of a one-dimensional Heisenberg model with an even-odd ordering of terms, our result overestimates the complexity by only a factor of $5$. Our bound is also close to tight for power-law interactions and other orderings of terms. This suggests that our theory can accurately characterize Trotter error in terms of both the asymptotic scaling and the constant prefactor.

quantum computing, numerical analysis↗
DOE OSTI2021

Nonparallel transcriptional divergence during parallel adaptation

Abstract How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies ( Poecilia reticulata ) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high‐ and low‐predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity, as well as the evolution of expression plasticity itself, across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high‐ and low‐predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

Fischer, Eva K.↗
DOE OSTI2023

Direct Measurement of Small Particle Growth and Aging at the Atmospheric Radiation Measurement Southern Great Plains Observatory Field Campaign Report

Two identical Captive Aerosol Growth and Evolution (CAGE) chambers were operated at the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility’s Southern Great Plains (SGP) observatory in the late summer and fall of 2021. The field study was scheduled to begin in spring, 2020, but was delayed because of the pandemic. CAGE chambers are designed to expose particles to an environment that mirrors that of the surroundings with or without a controlled perturbation designed to assess a sensitivity. The analysis here focuses on roughly the last two months of the overall study period during which measurements were almost continuous and when several perturbation experiments were conducted. Though the utility of a dual-chamber system is the ability to measure the influence of a single change on top of ambient conditions, both chambers were initially operated in the same way, with ambient air pulled through the gas exchange channel in both and ammonium sulfate particles injected into both. The similar time-dependent particle growth observed in the chambers for those periods provides confidence in differences observed during the subsequent perturbation experiments. The growth rate of particles in the reference chamber into which only ammonium sulfate particles were injected and for which only ambient air was pulled through were used to describe time-of-day averages. The average growth rate was highest in the evening and in the morning after sunrise and lowest in the late afternoon. The sensitivity of particle growth to secondary aerosol precursor gases was studied by adding them at a controlled rate to the ambient air flow pulled through one of the two chambers. Addition of 5 ppb of α-pinene resulted in an average particle growth rate of 4.4 nm hr -1 , compared with that of just 0.8 nm hr -1 in the reference chamber. The added α-pinene also triggered one new particle formation (NPF) event in the early evening just before sunset and another in the morning just after sunrise. Similarly, addition of 5 ppb of SO 2 to one chamber led to a pair of NPF events and to increased particle growth rate, though unlike the impact of added α-pinene, growth was enhanced only during the daytime when OH concentration is highest. The influence of aerosol liquid water on secondary aerosol formation and particle growth was investigated by injecting ammonium sulfate seed particles into one chamber and potassium sulfate particles into the other. Particles were injected into the two chambers four times over a 1.5-day period. The chamber relative humidity (RH) history during and following each injection was used to determine whether each particle type was crystalline or aqueous. For the case when both particle types remained crystalline throughout the period, they were tracked and for the case when they remained aqueous, the magnitude and time-dependence of the growth of both were almost exactly the same. For the other two cases the ammonium sulfate particles deliquesced upon injection and remained aqueous, while the potassium sulfate particles remained crystalline. For those two cases, the aqueous particles grew substantially faster than did the crystalline particles, providing evidence of the role of aerosol liquid water on secondary aerosol formation and particle growth.

54 ENVIRONMENTAL SCIENCES↗