Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “biological processing”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Crystallization pathways and interfacial drivers for the formation of hierarchical architectures

The development of structural hierarchy on various length scales during crystallization process is ubiquitous in biological systems and is also observed in synthetic nanomaterials. The driving forces for the formations of complex architectures range from local interfacial interactions, that modify interfacial speciation, local supersaturation, and nucleation barriers, to macroscopic interparticle forces. Although it is enticing to interpret the formation of hierarchical architectures as the assembly of independently nucleated building blocks, often crystallization pathways follow monomer-by-monomer addition with structural complexity arising from interfacial chemical coupling and strongly correlated fluctuation dynamics in the electric double layers. Here, the mechanism of the development of structural hierarchy through heterogeneous nucleation, coupled interfacial nucleation and assembly, and oriented attachment of independently nucleated particles is discussed. In this article, the emphasis is made on the discussion of the underlying interfacial forces and chemical coupling that drives crystallization pathways towards the formation of structural hierarchy.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Natural Abundance Isotope Ratio Measurements of Organic Molecules Using 21 T FTICR MS

Subtle variations in stable isotope ratios at natural abundance are challenging to measure but can yield critical insights into biological, physical, and geochemical processes. Well established methods, particularly multi-collector, gas-source or plasma isotope ratio mass spectrometry (IRMS) are the gold standard for stable isotope measurement but inherent limitations in these approaches make them ill-suited to determining site-specific and multiply substituted isotopic abundances of all but a few compounds, or to characterizing mixtures or larger intact molecules. Additionally, Fourier transform mass spectrometry (FTMS), namely Orbitrap mass spectrometry, has recently demonstrated the ability to measure natural abundance isotope ratios with chemically informative accuracy and precision. Here, we report the first use of Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for the accurate (<1‰) and precise (<1‰ standard error) simultaneous determination of $δ$ 13 C and $δ$ 15 N in caffeine isotopologues and provide a discussion of the critical instrumental parameters necessary to make such measurements. Finally, we report the ability to make these measurements with online liquid chromatography, expanding the ability of this technique to explore mixtures in the future.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2017

Imaging Nutrient Distribution in the Rhizosphere Using FTIR Imaging

Symbiotic associations in the rhizosphere between plants and microorganisms lead to efficient changes in the distribution of nutrients that promote growth and development for each organism involved. Understanding these nutrient fluxes provides insight into the molecular dynamics involved in nutrient transport from one organism to the other. Here, to study such a nutrient flow, a new application of Fourier transform infrared imaging (FTIRI) was developed that entailed growing Populus tremulodes seedlings on a thin, nutrient-enriched Phytagel matrix that allows pixel to pixel measurement of the distribution of nutrients, in particular, nitrate, in the rhizosphere. The FTIR spectra collected from ammonium nitrate in the matrix indicated the greatest changes in the spectra at 1340 cm -1 due to the asymmetric stretching vibrations of nitrate. For quantification of the nitrate concentration in the rhizosphere of experimental plants, a calibration curve was generated that gave the nitrate concentration at each pixel in the chemical image. These images of the poplar rhizosphere showed evidence for symbiotic sharing of nutrients between the plant and the fungi, Laccaria bicolor, where the nitrate concentration was five times higher near mycorrhizal roots than further out into the rhizosphere. This suggested that nitrates are acquired and transported from the media toward the plant root by the fungi. Similarly, the sucrose used in the growth media as a carbon source was depleted around the fungi, suggesting its uptake and consumption by the system. In conclusion, this study is the first of its kind to visualize and quantify the nutrient availability associated with mycorrhizal interactions, indicating that FTIRI has the ability to monitor nutrient changes with other microorganisms in the rhizosphere as a key step for understanding nutrient flow processes in more diverse biological systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

HEPOM: Using Graph Neural Networks for the Accelerated Predictions of Hydrolysis Free Energies in Different pH Conditions

Hydrolysis is a fundamental family of chemical reactions where water facilitates the cleavage of bonds. The process is ubiquitous in biological and chemical systems, owing to water’s remarkable versatility as a solvent. However, accurately predicting the feasibility of hydrolysis through computational techniques is a difficult task, as subtle changes in reactant structure like heteroatom substitutions or neighboring functional groups can influence the reaction outcome. Furthermore, hydrolysis is sensitive to the pH of the aqueous medium, and the same reaction can have different reaction properties at different pH conditions. In this work, we have combined reaction templates and high-throughput ab initio calculations to construct a diverse data set of hydrolysis free energies. The developed framework automatically identifies reaction centers, generates hydrolysis products, and utilizes a trained graph neural network (GNN) model to predict ΔG values for all potential hydrolysis reactions in a given molecule. The long-term goal of the work is to develop a data-driven, computational tool for high-throughput screening of pH-specific hydrolytic stability and the rapid prediction of reaction products, which can then be applied in a wide array of applications including chemical recycling of polymers and ion-conducting membranes for clean energy generation and storage.

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

Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments

The excited-state dynamics of chromophores in complex environments determine a range of vital biological and energy capture processes. Time-resolved, multidimensional optical spectroscopies provide a key tool to investigate these processes. Although theory has the potential to decode these spectra in terms of the electronic and atomistic dynamics, the need for large numbers of excited-state electronic structure calculations severely limits first-principles predictions of multidimensional optical spectra for chromophores in the condensed phase. In this work, we leverage the locality of chromophore excitations to develop machine learning models to predict the excited-state energy gap of chromophores in complex environments for efficiently constructing linear and multidimensional optical spectra. By analyzing the performance of these models, which span a hierarchy of physical approximations, across a range of chromophore–environment interaction strengths, we provide strategies for the construction of machine learning models that greatly accelerate the calculation of multidimensional optical spectra from first principles.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Nuclear–Electronic Orbital Quantum Mechanical/Molecular Mechanical Real-Time Dynamics

Simulating the nuclear–electronic quantum dynamics of large-scale molecular systems in the condensed phase is key for studying biologically and chemically important processes such as proton transfer and proton-coupled electron transfer reactions. Herein, the real-time nuclear–electronic orbital time-dependent density functional theory (RT-NEO-TDDFT) approach is combined with a hybrid quantum mechanical/molecular mechanical (QM/MM) strategy to enable the accurate description of coupled nuclear–electronic quantum dynamics in the presence of heterogeneous environments such as solvent or proteins. The densities of the electrons and quantum protons are propagated in real time, while the other nuclei are propagated classically on the instantaneous electron–proton vibronic surface. This approach is applied to phenol bound to lysozyme, intramolecular proton transfer in malonaldehyde, and nonequilibrium excited-state intramolecular proton transfer in o-hydroxybenzaldehyde. Furthermore, these examples illustrate that the RT-NEO-TDDFT framework, coupled with an atomistic representation of the environment, allows the simulation of condensed-phase systems that exhibit significant nuclear quantum effects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Ion-Specific Effects of Divalent Ions on the Structure of Polyelectrolyte Brushes

Polyelectrolyte brushes consist of charged polymer chains attached on one end to a surface at high densities. They are relevant for many practical applications ranging from biosensors to drug delivery to colloidal stability. Their structure and functionality can be dramatically influenced by multivalent counterions in the solution environment. In this work, the surface forces apparatus (SFA) and atomic force microscopy (AFM) were used to investigate the effects of three alkaline earth divalent cations, Mg 2+ , Ca 2+ , and Ba 2+ , on the structures of polystyrenesulfonate (PSS) brushes tethered to mica and silicon oxide surfaces. While all these ions caused significant shrinkage of the height of the PSS brushes, strong ion-specific effects were observed. Mg 2+ and C 2+ , caused homogeneous shrinkage; Ba 2+ led to pinned-micelle like inhomogeneous structures. Isothermal titration calorimetry (ITC) demonstrated that this ion specificity was mainly caused by the difference in binding energy between sulfonate groups and the divalent cations. Considering the abundance of divalent cations in industrial processes, natural environments, and biological systems, the understanding of strong ion-specific effects of divalent counterions is of great importance for theoretical studies and various applications involving polyelectrolytes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Crystal Structure of the Ergothioneine Sulfoxide Synthase from Candidatus Chloracidobacterium thermophilum and Structure-Guided Engineering To Modulate Its Substrate Selectivity

Ergothioneine is a thiohistidine derivative with potential benefits on many aging-related diseases. The central step of aerobic ergothioneine biosynthesis is the oxidative C–S bond formation reaction catalyzed by mononuclear nonheme iron sulfoxide synthases (EgtB and Egt1). Thus far, only the Mycobacterium thermoresistibile EgtB (EgtB Mth ) crystal structure is available, while the structural information for the more industrially attractive Egt1 enzyme is not. In this paper, we reported the crystal structure of the ergothioneine sulfoxide synthase (EgtB Cth ) from Candidatus Chloracidobacterium thermophilum . EgtB Cth has both EgtB- and Egt1-type of activities. Guided by the structural information, we conducted Rosetta Enzyme Design calculations, and we biochemically demonstrated that EgtB Cth can be engineered more toward Egt1-type of activity. This study provides information regarding the factors governing the substrate selectivity in Egt1- and EgtB-catalysis and lays the groundwork for future sulfoxide synthase engineering toward the development of an effective ergothioneine process through a synthetic biology approach.

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

Ultrafast Proton-Coupled Electron Transfer Reactions at Unit Quantum Yield

Proton-coupled electron transfer (PCET) reactions mediate essential biological energy-conversion processes, yet dynamical experiments that distinguish concerted electron/proton motion from sequential electron-transfer/proton-transfer pathways are unprecedented on ultrafast time scales. Here we report a tightly coupled donor–spacer–acceptor assembly, NDI-Sp-PhOH/BI, that enables direct interrogation of light-triggered and ultrafast PCET dynamics. Photoexcitation of the naphthalene diimide chromophore drives charge separation forming NDI radical anion and benzimidazolium phenoxy radical (PhO●/BIH+) products with a 440 fs time constant, followed by thermal charge recombination on a 5 ps time scale. Transient visible/near-infrared and mid-infrared spectroscopies independently track electron and proton motion and reveal coincident formation and decay of the charge-separated PCET products, excluding detectable phenol radical cation or phenoxide intermediates expected for sequential electron transfer-proton transfer (ET-PT) pathways. Surface-hopping quasiclassical trajectory simulations demonstrate rapid proton relocation coupled to evolution from locally excited to charge-transfer states, congruent with a concerted mechanism. These combined spectroscopic and computational results establish NDI-Sp-PhOH/BI as an archetype for ultrafast, concerted PCET occurring with unit quantum yield; further, because this platform provides distinct electronic and vibrational spectroscopic handles in its ground, electronically excited, and charge-separated states, it provides new opportunities to characterize mechanistic crossover in biomimetic PCET systems.

10 SYNTHETIC FUELS↗
DOE OSTI2019

Iron(III) Speciation Observed at Aqueous and Glycerol Surfaces: Vibrational Sum Frequency and X-ray

Aqueous solutions of FeCl 3 have been widely studied to shed light on a number of processes from dissolution, mineralization, biology, electrocatalysis, corrosion, to microbial biomineralization. Yet there are little to no molecular level studies of the air–liquid FeCl 3 interface. Here, both aqueous and glycerol FeCl 3 solution surfaces are investigated with polarized vibrational sum frequency generation (SFG) spectroscopy. We also present the first ever extreme ultraviolet reflection–absorption (XUV-RA) spectroscopy measurements of solvated ions and complexes at a solution interface, and observe with both X-ray photoelectron spectroscopy (XPS) and XUV-RA the existence of Fe(III) at the surface and in the near surface regions of glycerol FeCl 3 solutions, where glycerol is used as a high vacuum compatible proxy for water. XPS showed Cl - and Fe(III) species with significant Fe(III) interfacial enrichment. In aqueous solutions, an electrical double layer (EDL) of Cl - and Fe(III) species at 0.5 m FeCl 3 concentration is observed as evidenced from an enhancement of molecular ordering of water dipoles, consistent with the observed behavior at the glycerol surface. At higher concentrations in water, the EDL appears to be substantially repressed, indicative of further Fe(III) complex enrichment and dominance of a centrosymmetric Fe(III) species that is surface active. In addition, a significant vibrational red-shift of the dangling OH from the water molecules that straddle the air–water interface reveals that the second solvation shell of the surface active Fe(III) complex permeates the topmost layer of the aqueous interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.

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

Atomic dynamics of electrified solid–liquid interfaces in liquid-cell TEM

Electrified solid–liquid interfaces (ESLIs) play a key role in various electrochemical processes relevant to energy, biology and geochemistry. The electron and mass transport at the electrified interfaces may result in structural modifications that markedly influence the reaction pathways. For example, electrocatalyst surface restructuring during reactions can substantially affect the catalysis mechanisms and reaction products. Despite its importance, direct probing the atomic dynamics of solid–liquid interfaces under electric biasing is challenging owing to the nature of being buried in liquid electrolytes and the limited spatial resolution of current techniques for in situ imaging through liquids. Here, with our development of advanced polymer electrochemical liquid cells for transmission electron microscopy (TEM), we are able to directly monitor the atomic dynamics of ESLIs during copper (Cu)-catalysed CO 2 electroreduction reactions (CO 2 ERs). Our observation reveals a fluctuating liquid-like amorphous interphase. It undergoes reversible crystalline–amorphous structural transformations and flows along the electrified Cu surface, thus mediating the crystalline Cu surface restructuring and mass loss through the interphase layer. Furthermore, the combination of real-time observation and theoretical calculations unveils an amorphization-mediated restructuring mechanism resulting from charge-activated surface reactions with the electrolyte. Our results open many opportunities to explore the atomic dynamics and its impact in broad systems involving ESLIs by taking advantage of the in situ imaging capability.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Solvation directed morphological control in metal oxide nanostructures

The development of structural hierarchy on various length scales during the crystallization process is ubiquitous in biological systems and minerals and is common in synthetic nanomaterials. The driving forces for the formation of complex architectures range from local interfacial interactions, that modify interfacial speciation, local supersaturation, and nucleation barriers, to macroscopic interparticle forces. Although it is enticing to interpret the formation of hierarchical architectures as the assembly of independently nucleated building blocks, crystallization pathways often follow monomer-by-monomer addition with structural complexity arising from interfacial chemical coupling and strongly correlated fluctuation dynamics in the electric double layers. Here, we show that the development of structural hierarchy through heterogeneous nucleation is driven by dipolar and solvation forces. Specifically, coupled simulations and experimental studies revealed that dipole build-up along the slow growth direction can trigger twinning and the development of branched architectures. Enthalpic solvation interactions were shown to either enhance or reduce the dipole moment of the nanoparticles and, thereby, control crystal morphology and architecture. The systematic studies of chemical coupling between different solvents and undercoordinated surface atoms of the growing nanocrystals revealed the mechanism of dimensionality control and the development of structural hierarchy without ligands or structure-directing agents.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

Sub-millitesla magnetic field effects on the recombination reaction of flavin and ascorbic acid radicals

Even though the interaction of a <1 mT magnetic field with an electron spin is less than a millionth of the thermal energy at room temperature (k{sub B}T), it still can have a profound effect on the quantum yields of radical pair reactions. We present a study of the effects of sub-millitesla magnetic fields on the photoreaction of flavin mononucleotide with ascorbic acid. Direct control of the reaction pathway is achieved by varying the rate of electron transfer from ascorbic acid to the photo-excited flavin. At pH 7.0, we verify the theoretical prediction that, apart from a sign change, the form of the magnetic field effect is independent of the initial spin configuration of the radical pair. The data agree well with model calculations based on a Green’s function approach that allows multinuclear spin systems to be treated including the diffusive motion of the radicals, their spin-selective recombination reactions, and the effects of the inter-radical exchange interaction. The protonation states of the radicals are uniquely determined from the form of the magnetic field-dependence. At pH 3.0, the effects of two chemically distinct radical pair complexes combine to produce a pronounced response to ∼500 μT magnetic fields. These findings are relevant to the magnetic responses of cryptochromes (flavin-containing proteins proposed as magnetoreceptors in birds) and may aid the evaluation of effects of weak magnetic fields on other biologically relevant electron transfer processes.

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

Controlled molecule injector for cold, dense, and pure molecular beams at the European x-ray free-electron laser

A permanently available molecular-beam injection setup for controlled molecules (COMO) was installed and commissioned at the small quantum systems (SQS) instrument at the European x-ray free-electron laser (EuXFEL). A b-type electrostatic deflector allows for pure state-, size-, and isomer-selected samples of polar molecules and clusters. The source provides a rotationally cold (T ≈ 1 K) and dense (ρ ≈ 10 8 cm −3 ) molecular beam with pulse durations up to 100 µs generated by a new version of the Even-Lavie valve. Here, a performance overview of the COMO setup is presented along with characterization experiments performed both with an optical laser at the Center for Free-Electron-Laser Science and with x rays at EuXFEL under burst-mode operation. COMO was designed to be attached to different instruments at the EuXFEL, in particular, the SQS and single particles, clusters, and biomolecules (SPB) instruments. This advanced controlled-molecules injection setup enables x-ray free-electron laser studies using highly defined samples with soft and hard x-ray FEL radiation for applications ranging from atomic, molecular, and cluster physics to elementary processes in chemistry and biology.

He, Lanhai↗
DOE OSTI2023

Microbially mediated climate feedbacks from wetland ecosystems

Wetlands are crucial nodes in the carbon cycle, emitting approximately 20% of global CH4 while also sequestering 20%–30% of all soil carbon. Both greenhouse gas fluxes and carbon storage are driven by microbial communities in wetland soils. However, these key players are often overlooked or overly simplified in current global climate models. Here, we first integrate microbial metabolisms with biological, chemical, and physical processes occurring at scales from individual microbial cells to ecosystems. This conceptual scale-bridging framework guides the development of feedback loops describing how wetland-specific climate impacts (i.e., sea level rise in estuarine wetlands, droughts and floods in inland wetlands) will affect future climate trajectories. Furthermore, these feedback loops highlight knowledge gaps that need to be addressed to develop predictive models of future climates capturing microbial contributions. We propose a roadmap connecting environmental scientific disciplines to address these knowledge gaps and improve the representation of microbial processes in climate models. Together, this paves the way to understand how microbially mediated climate feedbacks from wetlands will impact future climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Field‐scale analysis of miscanthus production indicates climate change may increase the opportunity for water quality improvement in a key Iowa watershed

Abstract The Raccoon River Basin is the primary source for drinking water in Iowa's largest city and plays a major role in the Mississippi River Basin's high nutrient exports. Future climate change may have major impacts on the biological, physiological, and agronomic processes imposing a threat to ecosystem services. Efforts to reduce nitrogen (N) loads within this basin have included local litigation and the implementation of the Iowa Nutrient Reduction Strategy, which suggest incorporating bioenergy crops (i.e., miscanthus) within the current corn–soybean landscape to reach a 41% reduction in nitrate loads. This study focuses on simulating N export for historical and future land use scenarios by using an agroecosystem model (Agro‐IBIS) and a hydrology model (THMB) at the 500‐m resolution, similar to the scale of agricultural fields. Model simulations are driven by CMIP5 climate data for historical, mid‐century, and late‐century under the RCP 4.5 and 8.5 warming projections. Using recent crop profit analyses for the state of Iowa, profitability maps were generated and nitrogen leaching thresholds were used to determine where miscanthus should replace corn–soybean area to maximize reductions in N pollution. Our results show that miscanthus inclusion on low profit and high N leaching areas can result in a 4% reduction of N loss under current climate conditions and may reduce N loss by 21%–26% under future climate conditions, implying that water quality has the potential continue to improve under future climate conditions when strategically implemented conservation practices are included in future farm management plans.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Correlation-driven attosecond photoemission delay in the plasmonic excitation of C60 fullerene

Extreme light confinement in plasmonic nanosystems enables novel applications in photonics, sensor technology, energy harvesting, biology, and quantum information processing. Fullerenes represent an extreme case for nanoplasmonics: they are sub-nanometer carbon- based molecules showing high-energy and ultrabroad plasmon resonances, however the fundamental mechanisms driving the plasmonic response and the corresponding collective electron dynamics are still elusive. Here, we uncover the dominant role of electron correlations in the dynamics of the giant plasmon resonance (GPR) of the sub-nanometer system C60 by employing attosecond photoemission chronoscopy. We find a characteristic photoemission delay of up to about 300 attoseconds that is purely induced by coherent large-scale electron correlations in the plasmonic potential. These results provide novel insights into the nature of the plasmon resonances in sub-nanometer systems and open new perspectives for advancing nanoplasmonic applications.

Biswas, Shubhadeep [SLAC National Accelerator Labo↗