Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “biophysical chemistry”

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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A DNA molecular printer capable of programmable positioning and patterning in two dimensions

Nanoscale manipulation and patterning usually require costly and sensitive top-down techniques such as those used in scanning probe microscopies or in semiconductor lithography. DNA nanotechnology enables exploration of bottom-up fabrication and has previously been used to design self-assembling components capable of linear and rotary motion. In this work, we combine three independently controllable DNA origami linear actuators to create a nanoscale robotic printer. The two-axis positioning mechanism comprises a moveable gantry, running on parallel rails, threading a mobile sleeve. We show that the device is capable of reversibly positioning a write head over a canvas through the addition of signaling oligonucleotides. We demonstrate “write” functionality by using the head to catalyze a local DNA strand–exchange reaction, selectively modifying pixels on a canvas. Furthermore, this work demonstrates the power of DNA nanotechnology for creating nanoscale robotic components and could find application in surface manufacturing, biophysical studies, and templated chemistry.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

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

Single-photon absorption and emission from a natural photosynthetic complex

Photosynthesis is generally assumed to be initiated by a single photon from the Sun, which, as a weak light source, delivers at most a few tens of photons per nanometre squared per second within a chlorophyll absorption band1. Yet much experimental and theoretical work over the past 40 years has explored the events during photosynthesis subsequent to absorption of light from intense, ultrashort laser pulses. Here, we use single photons to excite under ambient conditions the light-harvesting 2 (LH2) complex of the purple bacterium Rhodobacter sphaeroides, comprising B800 and B850 rings that contain 9 and 18 bacteriochlorophyll molecules, respectively. Excitation of the B800 ring leads to electronic energy transfer to the B850 ring in approximately 0.7 ps, followed by rapid B850-to-B850 energy transfer on an approximately 100-fs timescale and light emission at 850–875 nm. Using a heralded single photon source20,21 along with coincidence counting, we establish time correlation functions for B800 excitation and B850 fluorescence emission and demonstrate that both events involve single photons. We also find that the probability distribution of the number of heralds per detected fluorescence photon supports the view that a single photon can upon absorption drive the subsequent energy transfer and fluorescence emission and hence, by extension, the primary charge separation of photosynthesis. An analytical stochastic model and a Monte Carlo numerical model capture the data, further confirming that absorption of single photons is correlated with emission of single photons in a natural light-harvesting complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Elucidation of the physical factors that control activated transport of penetrants in chemically complex glass-forming liquids

Understanding the activated transport of penetrant or tracer atoms and molecules in condensed phases is a challenging problem in chemistry, materials science, physics, and biophysics. Many angstrom- and nanometer-scale features enter due to the highly variable shape, size, interaction, and conformational flexibility of the penetrant and matrix species, leading to a dramatic diversity of penetrant dynamics. Based on a minimalist model of a spherical penetrant in equilibrated dense matrices of hard spheres, a recent microscopic theory that relates hopping transport to local structure has predicted a novel correlation between penetrant diffusivity and the matrix thermodynamic dimensionless compressibility, S 0 ( T ) (which also quantifies the amplitude of long wavelength density fluctuations), as a consequence of a fundamental statistical mechanical relationship between structure and thermodynamics. Moreover, the penetrant activation barrier is predicted to have a factorized/multiplicative form, scaling as the product of an inverse power law of S 0 ( T ) and a linear/logarithmic function of the penetrant-to-matrix size ratio. This implies an enormous reduction in chemical complexity that is verified based solely on experimental data for diverse classes of chemically complex penetrants dissolved in molecular and polymeric liquids over a wide range of temperatures down to the kinetic glass transition. The predicted corollary that the penetrant diffusion constant decreases exponentially with inverse temperature raised to an exponent determined solely by how S 0 ( T ) decreases with cooling is also verified experimentally. Our findings are relevant to fundamental questions in glassy dynamics, self-averaging of angstrom-scale chemical features, and applications such as membrane separations, barrier coatings, drug delivery, and self-healing.

Science & Technology - Other Topics↗
DOE OSTI2020

Nano-FET-enabled biosensors: Materials perspective and recent advances in North America

Field-effect transistor (FET) is a very promising platform for biosensor applications due to its magnificent properties, including label-free detection, high sensitivity, fast response, real-time measurement capability, low running power, and the feasibility to miniaturize to a portable device. 1D (e.g. carbon nanotubes, Si nanowires, conductive polymer nanowires, 1D metal oxides, and others) and 2D (e.g. graphene materials, transition metal dichalcogenides, black phosphorus, and 2D metal oxides) materials, with their unique structural and electronic properties that are unavailable in bulk materials, have helped improve the sensitivity of FET biosensors and enabled detection down to single molecule. In this article, we give insights into the rapidly evolving field of 1D and 2D materials-based FET biosensors, with an emphasis on structure and electronic properties, synthesis, and biofunctionalization approaches of these nanomaterials. In addition, the progress in the 1D/2D-FET biosensors in North America, in the last decade, is summarized in tables. Moreover, challenges and future perspectives of 1D/2D-FET biosensors are covered.

1D materials↗
DOE OSTI2024

Deconvolution of dynamic heterogeneity in protein structure

Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution.

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

Two-component dynamics in supercritical $\text {CO}_2$ from inelastic X-ray scattering

Supercritical fluids are characterized by unique thermodynamic properties. One of these properties is the existence of two-component dynamics that is associated with distinct low-frequency and high-frequency vibrational responses of the fluid. However, the origin of this behavior remains unknown. By combining inelastic X-ray scattering and molecular dynamics simulations, we show that this behavior can be connected to density heterogeneities arising from molecular clusters. Analyses of measurements and molecular trajectories suggest that the two-component dynamics emerges due to distinct momentum fluctuations of clustered and unbound molecules. This connection between clusters and two-component dynamics highlights the importance of molecular-structural heterogeneities in supercritical fluids, colloids, and condensed-matter systems.

biophysics↗
DOE OSTI2024

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in viscoelastic biomaterials exhibiting fluid-like properties under rest and low shear, but solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly in a manner similar to formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Mathematical Model of ATM Activation and Chromatin Relaxation by Ionizing Radiation

We propose a comprehensive mathematical model to study the dynamics of ionizing radiation induced Ataxia-telangiectasia mutated (ATM) activation that consists of ATM activation through dual mechanisms: the initiative activation pathway triggered by the DNA damage-induced local chromatin relaxation and the primary activation pathway consisting of a self-activation loop by interplay with chromatin relaxation. The model is expressed as a series of biochemical reactions, governed by a system of differential equations and analyzed by dynamical systems techniques. Radiation induced double strand breaks (DSBs) cause rapid local chromatin relaxation, which is independent of ATM but initiates ATM activation at damage sites. Key to the model description is how chromatin relaxation follows when active ATM phosphorylates KAP-1, which subsequently spreads throughout the chromatin and induces global chromatin relaxation. Additionally, the model describes how oxidative stress activation of ATM triggers a self-activation loop in which PP2A and ATF2 are released so that ATM can undergo autophosphorylation and acetylation for full activation in relaxed chromatin. In contrast, oxidative stress alone can partially activate ATM because phosphorylated ATM remains as a dimer. The model leads to predictions on ATM mediated responses to DSBs, oxidative stress, or both that can be tested by experiments.

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

Electric fields imbue enzyme reactivity by aligning active site fragment orbitals

It is broadly recognized that intramolecular electric fields, produced by the protein scaffold and acting on the active site, facilitate enzymatic catalysis. This field effect can be described by several theoretical models, each of which is intuitive to varying degrees. In this contribution, we show that a fundamental effect of electric fields is to generate electrostatic potentials that facilitate the energetic alignment of reactant frontier orbitals. We apply this model to demystify the impact of electric fields on high-valent iron–oxo heme proteins: catalases, peroxidases, and peroxygenases/monooxygenases. Specifically, we show that this model easily accounts for the observed field-induced changes to the spin distribution within peroxidase active sites and explains the transition between epoxidation and hydroxylation pathways seen in Cytochrome P450 active site models. Thus, for the intuitive interpretation of the chemical effect of the field, the strategy involves analyzing the response of the orbitals of active site fragments, and their energetic alignment. We note that the energy difference between fragment orbitals involved in charge redistribution acts as a measure for the chemical hardness/softness of the reactive complex. This measure, and its sensitivity to electric fields, offers a single parameter model from which to quantitatively assess the effects of electric fields on reactivity and selectivity. Thus, the model provides an additional perspective to describe electrostatic preorganization and offers ways for its manipulation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1980

Life from a plantary perspective: Fundamental issues in global ecology

Twenty-three scientists from diverse disciplines met for one week at the University of California, Santa Barbara to discuss life from a planetary perspective. The scientists represented the major disciplines concerned with the Earth's biota, oceans, atmosphere and sediments, including geochemistry, atmospheric chemistry, chemical oceanography, limnology, forestry, terrestrial ecology, microbiology, biophysics, geography and remote sensing as well as mathematics. These twenty-three scientists met to discuss whether there was, at this time, a set of scientific issues concerning life and the entire Earth as a single unit, to set down the major tractable issues, and to suggest a set of activities that would promote the study of the issues identified. Their conclusions are summarized.

Botkin, D. B.↗
DOE OSTI2021

Understanding flavin electronic structure and spectra

Abstract Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

Physics through the 1990s: Scientific interfaces and technological applications

The volume examines the scientific interfaces and technological applications of physics. Twelve areas are dealt with: biological physics-biophysics, the brain, and theoretical biology; the physics-chemistry interface-instrumentation, surfaces, neutron and synchrotron radiation, polymers, organic electronic materials; materials science; geophysics-tectonics, the atmosphere and oceans, planets, drilling and seismic exploration, and remote sensing; computational physics-complex systems and applications in basic research; mathematics-field theory and chaos; microelectronics-integrated circuits, miniaturization, future trends; optical information technologies-fiber optics and photonics; instrumentation; physics applications to energy needs and the environment; national security-devices, weapons, and arms control; medical physics-radiology, ultrasonics, MNR, and photonics. An executive summary and many chapters contain recommendations regarding funding, education, industry participation, small-group university research and large facility programs, government agency programs, and computer database needs.

Source record↗
DOE OSTI2023

2023 SAGE-Camp Report

The 7 th Summer Physics Camp for Young Women was successfully held in person in 2023 from June 5 th to 16 th at the New Mexico School for the Arts in Santa Fe, NM at Hilo Intermediate School in Hawaii. This year’s camp was dedicated to the topic of Energy Security and was made possible thanks to the strong collaboration of Los Alamos, Sandia and Hawaii teams and the logistical and financial support of Los Alamos and Sandia National Laboratories, New Mexico Consortium, SAGE- Moore Foundation, LANL Foundation, ACS, IEE, APS four corners, N3B, Hawaii Museum of Science and Technology, New Mexico School for the Arts (NMSA) and Tech Source. The camp mobilized more than 120 volunteers who made the camp a success. The camp is free of charge to the students and included free lunch and snacks for the busy brains to have plenty of energy, also included all materials needed for the hands-on activities (like drone building, crystal structure, solar panels, wind turbine fabrication, soldering, coding etc) and also a stipend for students who attended for the full two weeks and for two educators and two student mentors in NM. The camp offered 32 high school students from New Mexico and 8 from Hawaii a unique opportunity to explore science topics and meet a broad range of role model professionals across STEM fields including astrophysics, cybersecurity, Energy fields, space science, engineering, biophysics, environmental science, robotics, computer science, nuclear engineering, radiological science, physics and chemistry. With nearly 120 volunteers who came mainly from Los Alamos National Laboratory (66%) and Sandia national laboratories (18%), two funded educators from NM, Dr. Weldon Beauchamp and Dr. Ellee Cook, and two educators from Hilo, Dr. Pascale Creek Pinner and LeAnn Ragasa, the camp was educationally sound and extremely varied. The collaboration with school educators is critical for the goal of this camp to not only impact students' lives but also improve STEM education in NM and Hawaii. The ultimate goal of the camp is to increase higher education aspirations of students, empower them to consider careers in STEM and learn more about the opportunities available to them in our local colleges and DOE National Laboratories. In addition, the camp also hired 2 past students as student mentors, Megan Odom and Elisea Jackson, who currently attend NMSA and were students at the camp in 2022 when it was virtual. The in-person camp which aims at empowering under-represented minorities in STEM in our community received more than 52 applications this year from all over NM and 8 applications from Hawaii. Our selection criteria are based on diversity, equity and inclusion, and students for whom the camp can be a life-changing opportunity are given a chance to attend the camp. During COVID, the camp was held virtually and gave the opportunity to students from remote areas in NM and Hawaii to attend from their homes. This year, fantastic families supported students everyday even when home was in remote areas in NM like Lea county, Sandoval county, Bernalillo or Mora county. The organizers hope next year they can offer a residential option for students from remote areas.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2020

Modeling Functional Organic Chemistry in Arctic Rivers: An Idealized Siberian System

Rivers of the Arctic will become ever more important for the global climate, since they carry a majority of continental dissolved organic carbon flux into the rapidly changing polar ocean. Aqueous organics comprise a wide array of functional groups, several of which are likely to impact coastal and open water biophysical properties. Light attenuation, interfacial films, aerosol formation, gas release and momentum exchange can all be cited. We performed Lagrangian kinetic modeling for the evolution of riverine organic chemistry as the molecules in question make their way from the highlands to Arctic outlets. Classes as diverse as the proteins, sugars, lipids, re-condensates, humics, bio-tracers and small volatiles are all included. Our reduced framework constitutes an idealized northward flow driving a major hydrological discharge rate and primarily representing the Russian Lena. Mountainous, high solute and tundra sources are all simulated, and they meet up at several points between soil and delta process reactors. Turnover rates are parameterized beginning with extrapolated coastal values imposed along a limited tributary network, with connections between different terrestrial sub-ecologies. Temporal variation of our total dissolved matter most closely resembles the observations when we focus on the restricted removal and low initial carbon loads, suggesting relatively slow transformation along the water course. Thus, channel combinations and mixing must play a dominant role. Nevertheless, microbial and photochemical losses help determine the final concentrations for most species. Chemical evolution is distinct for the various functionalities, with special contributions from pre- and post-reactivity in soil and delta waters. Several functions are combined linearly to represent the collective chromophoric dissolved matter, characterized here by its absorption. Tributaries carry the signature of lignin phenols to segregate tundra versus taiga sources, and special attention is paid to the early then marine behaviors of low molecular weight volatiles. Heteropolycondensates comprise the largest percentage of reactive carbon in our simulations due to recombination/accumulation, and they tend to be preeminent at the mouth. Outlet concentrations of individual structures such as amino acids and absorbers lie above threshold values for biophysical influence, on the monolayer and light attenuation. The extent of coastal spreading is examined through targeted regional box modeling, relying on salinity and color for calibration. In some cases, plumes reach the scale of peripheral arctic seas, and amplification is expected during upcoming decades. Conclusions are mapped from the Lena to other boreal discharges, and future research questions are outlined regarding the bonding type versus mass release as permafrost degrades. Dynamic aqueous organic coupling is recommended for polar system models, from headwaters to coastal diluent.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Ligand‐Mediated Quantum Yield Enhancement in 1‐D Silver Organothiolate Metal–Organic Chalcogenolates

X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. Here, the proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2013

Photosynthesis-dependent Isoprene Emission from Leaf to Planet in a Global Carbon-chemistry-climate Model

We describe the implementation of a biochemical model of isoprene emission that depends on the electron requirement for isoprene synthesis into the FarquharBallBerry leaf model of photosynthesis and stomatal conductance that is embedded within a global chemistry-climate simulation framework. The isoprene production is calculated as a function of electron transport-limited photosynthesis, intercellular and atmospheric carbon dioxide concentration, and canopy temperature. The vegetation biophysics module computes the photosynthetic uptake of carbon dioxide coupled with the transpiration of water vapor and the isoprene emission rate at the 30 min physical integration time step of the global chemistry-climate model. In the model, the rate of carbon assimilation provides the dominant control on isoprene emission variability over canopy temperature. A control simulation representative of the present-day climatic state that uses 8 plant functional types (PFTs), prescribed phenology and generic PFT-specific isoprene emission potentials (fraction of electrons available for isoprene synthesis) reproduces 50 of the variability across different ecosystems and seasons in a global database of 28 measured campaign-average fluxes. Compared to time-varying isoprene flux measurements at 9 select sites, the model authentically captures the observed variability in the 30 min average diurnal cycle (R2 6496) and simulates the flux magnitude to within a factor of 2. The control run yields a global isoprene source strength of 451 TgC yr1 that increases by 30 in the artificial absence of plant water stress and by 55 for potential natural vegetation.

photosynthesis↗