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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

Giant nonlinear optical responses from photon-avalanching nanoparticles

Avalanche phenomena use steeply nonlinear dynamics to generate disproportionately large responses from small perturbations, and are found in a multitude of events and materials. Photon avalanching enables technologies such as optical phase-conjugate imaging, infrared quantum counting and efficient upconverted lasing. However, the photon-avalanching mechanism underlying these optical applications has been observed only in bulk materials and aggregates, limiting its utility and impact. In this study we report the realization of photon avalanching at room temperature in single nanostructures-small, Tm 3+ -doped upconverting nanocrystals-and demonstrate their use in super-resolution imaging in near-infrared spectral windows of maximal biological transparency. Avalanching nanoparticles (ANPs) can be pumped by continuous-wave lasers, and exhibit all of the defining features of photon avalanching, including clear excitation-power thresholds, exceptionally long rise time at threshold, and a dominant excited-state absorption that is more than 10,000 times larger than ground-state absorption. Beyond the avalanching threshold, ANP emission scales nonlinearly with the 26th power of the pump intensity, owing to induced positive optical feedback in each nanocrystal. This enables the experimental realization of photon-avalanche single-beam super-resolution imaging with sub-70-nanometre spatial resolution, achieved by using only simple scanning confocal microscopy and without any computational analysis. Pairing their steep nonlinearity with existing super-resolution techniques and computational methods, ANPs enable imaging with higher resolution and at excitation intensities about 100 times lower than other probes. The low photon-avalanching threshold and excellent photostability of ANPs also suggest their utility in a diverse array of applications, including sub-wavelength imaging and optical and environmental sensing.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Exponential Escape Rate of Filamentary Incubation in Mott Spiking Neurons

Mott materials such as vanadium oxides, when subject to a strong applied voltage, present an inhomogeneous insulator-to-metal transition with formation of metallic filaments within the insulating bulk. This property is enabling the development of compact and power-efficient neuromorphic devices known as Mott neurons. However, the nature of the transition has not been fully understood yet, as it may be attributed to different effects, including Joule self-heating and hot-carrier injection. Moreover, the experimental determination of the threshold voltage needed to induce the transition has proven to be challenging, as the transition becomes increasingly unpredictable when the threshold is approached. The physical understanding of these issues would not only deepen our understanding of Mott insulators, but would also be an important step toward the realization of neuromorphic devices based on such materials. In this work we use numerical simulations based on the Mott resistor network model to study the nature of the filament incubation and formation process. Here, we show that both electronic and thermal effects, in the form of current density focusing and Joule self-heating, respectively, contribute to the filamentary incubation and growth. Remarkably, we find that the percolation of the metallic filaments near the threshold is intrinsically stochastic, qualitatively similar to the familiar Arrhenius activated behavior and to the stochastic firing of biological neurons. More precisely, we characterize the filament percolation as a Poisson point process, which has the same probability distribution as mathematical models of neuronal firing with an exponential escape rate. Finally, we support the numerical simulation results by performing experiments in VO 2 that are in agreement with the exponential escape rate behavior. Thus, we establish a functionality of Mott insulators that opens a path toward implementing neuromorphic hardware with quantum materials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Hydrodynamically Controlled Self‐Organization in Mixtures of Active and Passive Colloids

Abstract Active particles are known to exhibit collective behavior and induce structure in a variety of soft‐matter systems. However, many naturally occurring complex fluids are mixtures of active and passive components. The authors examine how activity induces organization in such multi‐component systems. Mixtures of passive colloids and colloidal micromotors are investigated and it is observed that even a small fraction of active particles induces reorganization of the passive components in an intriguing series of phenomena. Experimental observations are combined with large‐scale simulations that explicitly resolve the near‐ and far‐field effects of the hydrodynamic flow and simultaneously accurately treat the fluid–colloid interfaces. It is demonstrated that neither conventional molecular dynamics simulations nor the reduction of hydrodynamic effects to phoretic attractions can explain the observed phenomena, which originate from the flow field that is generated by the active colloids and subsequently modified by the aggregating passive units. These findings not only offer insight into the organization of biological or synthetic active–passive mixtures, but also open avenues to controlling the behavior of passive building blocks by means of small amounts of active particles.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid

Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydrogenase, which acts on the substrate CHMS. We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations, we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.

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

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance

By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car–Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson’s equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. Furthermore, this is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500–1000 atoms (e.g., (H₂O)₂₅₆) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.

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

Using phage display for rational engineering of a higher-affinity humanized 3’ phosphohistidine-specific antibody

Abstract Histidine phosphorylation is a non-canonical post-translational modification (PTM), with 1-phosphohistidine (1-pHis) and 3-phosphohistidine (3-pHis) isoforms, that is understudied due to a lack of robust reagents, including high-affinity pHis-specific antibodies. Engineering pHis antibodies is challenging due to the labile nature of its phosphoramidate (P-N) bond. We developed a strategy for in vitro engineering of antibodies for the detection of native 3-pHis targets, in which the rabbit SC44-8 anti-3-pTza mAb is humanized into a scaffold (hSC44) that is suitable for phage display. Six unique Fab phage-displayed hSC44 scaffold libraries were screened for antibodies that bound 3-pHis with higher affinity and had specificity for 3-pHis versus 3-pTza. hSC44.20N32F L , the best engineered antibody, has ~10-fold higher affinity for 3-pHis than parental hSC44. Eleven new Fab structures, including the first antibody-pHis peptide structures, together with structural and quantum mechanical calculations, provided molecular insights into 3-pHis and 3-pTza discrimination by hSC44.20N32F L and the increased affinity obtained through engineering. We demonstrated the utility of these high-affinity 3-pHis-specific antibodies for the recognition of pHis proteins in mammalian cells by immunoblotting and immunofluorescence staining. Our work describes a general method for engineering labile PTM-specific antibodies and provides novel antibodies for investigating the role of 3-pHis in cell biology.

Martyn, Gregory D.↗
DOE OSTI2021

Metal Chalcogenides for Neuromorphic Computing: Emerging Materials and Mechanisms

The approaching end of Moore's Law scaling has significantly accelerated multiple fields of research including neuromorphic-, quantum-, and photonic computing, each of which possesses unique benefits unobtained through conventional binary computers. One of the most compelling arguments for neuromorphic computing systems is power consumption, noting that computations made in the human brain are approximately 106 times more efficient than conventional CMOS logic. This review article focuses on the materials science and physical mechanisms found in metal chalcogenides that are currently being explored for use in neuromorphic applications. We begin by reviewing the key biological signal generation and transduction mechanisms within neuronal components of mammalian brains and subsequently compare with observed experimental measurements in chalcogenides. With robustness and energy efficiency in mind, we will focus on short-range mechanisms such as structural phase changes and correlated electron systems that can be driven by low-energy stimuli, such as temperature or electric field. We aim to highlight fundamental materials research and existing gaps that need to be overcome to enable further integration or advancement of metal chalcogenides for neuromorphic systems.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A New Theoretical Framework for Designing Ion Transport Pathways

The rapid transport of specific ions through matter is critical to energy storage, membrane separations, and health. However, commercial materials resist ion transport, lack specificity, or both, making ion transport costly and ineffective. Inspiration for new material designs can be taken from biology, where membrane transport proteins exert exquisite control over the specificity and rate of ion transport. The challenge in understanding and designing transport pathways is that ions often exchange their hydrating waters for direct contacts with atoms in the transport pathway. Despite intense study over decades, no theory exists to explain local ion binding and transport mechanisms and experiments cannot differentiate reliably between ions and water in binding sites. Here, we developed a new approach, based on quantum methods and extension of the quasi-chemical free energy theory, to understand and design pathways through materials for rapid transport of specific ions. Understanding ion transport mechanisms will significantly advance our nation’s ability to develop cost-effective materials for energy sustainability and therapeutics for health.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Density Functional Tight-Binding Simulations Reveal the Presence of Surface Defects on the Quartz (101)–Water Interface

Understanding the structure and reactivity of quartz–water interfaces is critical for numerous applications in the geological, environmental, and biological sciences. However, disagreements on the atomic-level structure of the interfaces between experiments and simulations are hampering our ability to predict the surface reactivity. Here, we used density functional tight-binding (DFTB)-based molecular dynamics to simulate a series of quartz (101) surfaces having different types and densities of surface defects in water and compared them with the structures determined by X-ray reflectivity measurements. The DFTB simulations are able to reproduce previous classical and quantum mechanical predictions of the pristine quartz (101)–water interface that disagree with experimental observations. To remedy this situation, a set of defective quartz surfaces having various surface silicon (Si) vacancies were built as indicated by recent experimental studies. We found that the rotation of surface [SiO 4 ] tetrahedra near Si vacancies can lead to outward displacements of Si atoms similar to those observed in the experiments. The presence of additional surface Si vacancies caused inward relaxations of terminal oxygens through the formation of hydrogen bonds. Finally, the overall results indicate that the quartz (101)–water interface may include a mixture of geminal (≡Si–(OH) 2 )- and vicinal (≡Si–OH)-type silanol groups together with the presence of surface Si vacancies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Potential Applications of Quantum Computing at Los Alamos National Laboratory, v0.3.0

Since the scientific revolution in the 16th and 17th centuries, the process of scientific discovery has followed an iterative feedback process of observation, hypothesis development and testing with physical experiments, which is widely referred to as the scientific method. This process remained largely unchanged until the middle of the 20th century, when the emergence of digital computers empowered scientist to build and inspect detailed simulations of physical phenomena. Over the last century, computational tools have transformed modern approaches to scientific discovery by enabling fast and affordable hypothesis testing before physical experiments are conducted, shown in Figure 1-1. Some notable examples include: global climate forecasts to understand how the environment may change over decades [130]; modeling the behavior of plasma to design fusion reactors [59]; and understanding the behavior of molecules in biological processes [161, 223].

36 MATERIALS SCIENCE↗
DOE OSTI2022

The impact of G-quadruplex dynamics on inter-tetrad electronic couplings: a hybrid computational study

The G-quadruplex is a fascinating nucleic acid motif with implications in biology, medicine, and nanotechnologies. G-quadruplexes can form in the telomeres at the edges of chromosomes and in other guanine-rich regions of the genome. They can also be engineered for exploitation as biological materials for nanodevices. Their higher stiffness and higher charge transfer rates make them better candidates in nanodevices than duplex DNA. For the development of molecular nanowires, it is important to optimize electron transport along the wire axis. One powerful basis to do so is by manipulating the structure, based on known effects that structural changes have on electron transport. Here, for this work, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. We find that this structure–function relationship is complex. A single helix shape parameter alone does not embody such complexity, but rather a combination of distances and angles between stacked bases influences charge transfer efficiency. By analyzing linear combinations of shape descriptors for different topologies, we identify the structural features that most affect charge transfer efficiency. We discuss the transferability of the proposed model and the limiting effects of inherent flexibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Photoelectron spectroscopy with entangled photons; enhanced spectrotemporal resolution

In this theoretical study, we show how photoelectron signals generated by time-energy entangled photon pairs can monitor ultrafast excited state dynamics of molecules with high joint spectral and temporal resolutions, not limited by the Fourier uncertainty of classical light. This technique scales linearly, rather than quadratically, with the pump intensity, allowing the study of fragile biological samples with low photon fluxes. Since the spectral resolution is achieved by electron detection and the temporal resolution by a variable phase delay, this technique does not require scanning the pump frequency and the entanglement times, which significantly simplifies the experimental setup, making it feasible with current instrumentation. Application is made to the photodissociation dynamics of pyrrole calculated by exact nonadiabatic wave packet simulations in a reduced two nuclear coordinate space. This study demonstrates the unique advantages of ultrafast quantum light spectroscopy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Nanophotonics for Chemical Imaging and Spectroscopy

The manipulation of light and light-matter interactions on the nanoscale is enabled by the unique optical properties of plasmonic metal nanostructures and nanoparticles. Indeed, engineered hybrid molecular-plasmonic nanostructures have enabled single molecule detection and identification via surface-enhanced Raman scattering (SERS). Further, the same effect is at the core of visualizing single molecules with sub-nanometer spatial resolution via tip-enhanced Raman scattering (TERS). More generally, modern applications of plasmon-enhanced spectroscopy and microscopy fueled advances in fields as diverse as quantum and semiconductor materials, heterogeneous catalysis, and the health sciences, to name a few. All these exciting developments and many more are touched in this virtual special issue (VSI) on nanophotonics. From ultra-precise chemical imaging measurements performed in a scanning tunneling microscope chamber to single molecule spectroscopic measurements performed at solid-air and solid-liquid interfaces, this VSI includes contributions from active practitioners that are all striving to better-understand increasingly complex interfaces encountered in the biological, materials, and chemical sciences.

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

Signatures of a liquid–liquid transition in an ab initio deep neural network model for water

Significance Water is central across much of the physical and biological sciences and exhibits physical properties that are qualitatively distinct from those of most other liquids. Understanding the microscopic basis of water’s peculiar properties remains an active area of research. One intriguing hypothesis is that liquid water can separate into metastable high- and low-density liquid phases at low temperatures and high pressures, and the existence of this liquid–liquid transition could explain many of water’s anomalous properties. We used state-of-the-art approaches in computational quantum chemistry, statistical mechanics, and machine learning and obtained evidence consistent with a liquid–liquid transition, supporting the argument for the existence of this phenomenon in real water.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Low-energy electron driven reactions in 2-bromo-5-nitrothiazole

Thiazole derivatives are biologically relevant molecules, used also in pharmaceutical applications. Herein, we report results for electron attachment to 2-bromo-5-nitrothiazole (BNT) in the gas phase. Employing two crossed electron–molecule beam experiments, we determined the efficiency curves of various fragment anions as a function of the initial electron energy between about 0 and 10 eV as well as the emission angle and kinetic energy distributions of Br− and NO2− ions formed from a resonance near 4 eV. The experiments were supported by quantum chemical calculations, exploring possible dissociation pathways along with their reaction energies. We also compared the electron attachment characteristics of BNT with those of the native thiazole molecule by performing electron attachment experiments and calculations for this molecule as well. Compared to thiazole, which is primarily degraded only by electrons with kinetic energies between about 5 and 10 eV, BNT is susceptible to low-energy electrons near 0 eV with enhanced cross section for (dissociative) electron attachment. However, although BNT offers two localization sites with high electron affinity (Br and NO2 moieties), we do not find the corresponding anions as the dominant negatively charged species formed upon electron attachment. Instead, the reaction channels with an abstraction of Br and NO2 as neutral radicals prevail, accompanied by the opening of the thiazole ring due to the relatively weak C–S bond.

Chen, Jiakuan (ORCID:0009000729608641)↗
DOE OSTI2020

Experimental and theoretical description of the process of contact laser surgery with a titanium-doped optothermal fibre converter

In an in vitro experiment simulating a surgeon’s actions in the process of contact laser surgery of soft biological tissue, the dependences of the temperature of a titanium-doped optothermal fibre converter (TOTFC) and the depths of coagulation and ablation of biological tissue on the average radiation power of a diode laser with a wavelength of 980 nm and on the speed of the converter movement along biological tissue are obtained. The structural, optical, and thermophysical models of TOTFC are discussed, as well as the thermophysical model of the interaction of a laser-heated converter with biological tissue, which takes into account the temperature dependences of the basic thermophysical parameters of the converter and biological tissue, as well as the contribution of the thickness h{sub int} of the water vapour layer between the converter and biotissue. It is shown that the proposed model allows describing the result of contact laser surgery of soft biotissue with TOTFC adequately to the experiment. (laser biophotonics)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Electrostatic control of photoisomerization pathways in proteins

Rotation around a specific bond after photoexcitation is central to vision and emerging opportunities in optogenetics, super-resolution microscopy, and photoactive molecular devices. Competing roles for steric and electrostatic effects that govern bond-specific photoisomerization have been widely discussed, the latter originating from chromophore charge transfer upon excitation. We systematically altered the electrostatic properties of the green fluorescent protein chromophore in a photoswitchable variant, Dronpa2, using amber suppression to introduce electron-donating and electron-withdrawing groups to the phenolate ring. Through analysis of the absorption (color), fluorescence quantum yield, and energy barriers to ground- and excited-state isomerization, we evaluate the contributions of sterics and electrostatics quantitatively and demonstrate how electrostatic effects bias the pathway of chromophore photoisomerization, leading to a generalized framework to guide protein design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cas9 deletion of lutein biosynthesis in the marine alga Picochlorum celeri reduces photosynthetic pigments while sustaining high biomass productivity

Domestication of algae for food and renewable biofuels remains limited by the low photosynthetic efficiencies of processes that have evolved to be competitive for optimal light capture, incentivizing the development of large antennas in light-limiting conditions, thus decreasing efficient light utilization in cultivated ponds or photobioreactors. Reducing the pigment content to improve biomass productivity has been a strategy discussed for several decades and the ability to reduce pigment significantly is now fully at hand thanks to the widespread use of genome editing tools. Picochlorum celeri is one of the fastest growing marine algae identified and holds particular promise for outdoor cultivation, especially in saline water and warm climates. We show that while chlorophyll b is essential to sustain high biomass productivities under dense cultivation, removing Picochlorum celeri’s main carotenoid, lutein, leads to a decreased total chlorophyll content, higher a/ b ratio, reduced functional LHCII cross section and higher maximum quantum efficiencies at lower light intensities, resulting in an incremental increase in biomass productivity and increased PAR-to-biomass conversion efficiency. These findings further strengthen the existing strategies to improve photosynthetic efficiency and biomass production in algae.

59 BASIC BIOLOGICAL SCIENCES↗