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At least 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Dynamics-Based Peptide–MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO

An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen–major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we apply CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach, to identify per-residue antigen binding contributions and then design novel antigens of increased MHC-II binding affinity for a type 1 diabetes-implicated system. We build upon a small-molecule lead optimization algorithm by training a convolutional variational autoencoder (CVAE) on MD trajectories of 48 different systems across four antigens and four HLA serotypes. We develop several new machine learning metrics including a structure-based anchor residue classification model as well as cluster comparison scores. ML-MD predictions agree well with experimental binding results and free energy perturbation-predicted binding affinities. Moreover, ML-MD metrics are independent of traditional MD stability metrics such as contact area and root-mean-square fluctuations (RMSF), which do not reflect binding affinity data. Finally, our work supports the role of structure-based deep learning techniques in antigen-specific immunotherapy design.

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

Tunable Nanostructures from Inverse Surfactants

Hierarchical materials in the natural world are often made through the self-assembly of amphiphilic molecules. Achieving similar structural complexity in synthetic materials requires understanding how various molecular parameters affect assembly behavior. In recent years, inverse surfactants─molecules with hydrophobic head groups and hydrophilic macromolecular tails─have been shown to self-assemble into supramolecular assemblies in aqueous solutions that show promise for a number of applications, including drug delivery. Here, we build an understanding of the morphological phase diagram of inverse surfactants using insights from scattering experiments, computer simulations, and statistical mechanics. The scattering and simulation results reveal that changing the headgroup size is an important molecular knob in controlling morphological transitions. The molecular size ratio of the hydrophobic group to the hydrophilic group emerges as a crucial dimensionless quantity in our theory and plays a determining role in setting the micelle structure and the transition from mesoscale to macroscale aggregates. Our minimal theory is able to qualitatively explain the key features of the morphological phase diagram, including the prevalence of fiber-like structures in comparison to spherical and planar micelles. Together, these findings provide a more complete picture of the molecular dependencies of assemblies of inverse surfactants, which we hope may aid in the de novo design of supramolecular structures.

Christakopoulos, Panagiotis [ORNL] (ORCID:00090004↗
DOE OSTI2025

Long-Range Metal–Sorbent Interactions Determine CO 2 Capture and Conversion in Dual-Function Materials

Carbon capture and utilization involve multiple energy- and cost-intensive steps. Dual-function materials (DFMs) can reduce these demands by coupling CO 2 adsorption and conversion into a single material with two functionalities: a sorbent phase and a metal for catalytic CO 2 conversion. The role of metal catalysts in the conversion process seems salient from previous work, but the underlying mechanisms remain elusive and deserve deeper investigation to achieve maximum utilization of the two phases. Here, for this work, preformed colloidal Ru nanoparticles were deposited onto a “NaOx”/Al 2 O 3 sorbent to prepare prototypical DFMs with controlled phases for CO 2 capture and hydrogenation to CH 4 . Ru addition was found to double the high-temperature CO 2 adsorption capacity by activating the “NaOx”/Al 2 O 3 sorbent phase during a reductive pretreatment step. Most importantly, low Ru loadings were sufficient to ensure maximum CO 2 adsorption and conversion. This was attributed to the key role of the metal–sorbent interactions, wherein Ru was required to hydrogenate strongly bound CO 2 on the “NaO x ”/Al 2 O 3 sorbent to CH 4 via the H 2 activated on Ru. This interaction facilitated rate-determining carbonate migration and subsequent hydrogenation at the metal–sorbent interface. Overall, Ru controlled the CO 2 hydrogenation reaction rate, while the “NaO x ”/Al 2 O 3 sorbent dictated the CO 2 uptake capacity. By controlling metal–sorbent interactions at the molecular level, we demonstrate the critical role of the two phases and their synergy, facilitating the design of DFMs with maximum CO 2 capture and conversion efficiency.

carbon capture↗
DOE OSTI2023

Directing polymorph specific calcium carbonate formation with de novo protein templates

Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain largely unknown. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we design helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and find that both protein monomers and protein-C a2+ supramolecular assemblies directly nucleate nano-calcite with non-natural {110} or {202} faces while vaterite, which forms first in the absence of the proteins, is bypassed. These protein-stabilized nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.

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

The distinct trimeric structure of the immunodominant chlamydial antigen Major Outer Membrane Protein

The chlamydial Major Outer Membrane Protein (MOMP) is a promising subunit vaccine candidate due to its abundance in the outer membrane (OM), the presence of four surface-exposed variable domains (VDs) containing neutralizing and serotyping epitopes, and confirmed T-cell epitopes located in its constant domains (CDs). However, recombinant and denatured forms of MOMP have failed to elicit immune responses comparable to native preparations, indicating that conformation is critical for immunogenicity. Here, we present two cryo-EM structures of native Chlamydia muridarum MOMP, isolated from infectious elementary bodies (EBs). EB MOMP forms a distinct trimer with a stem of three narrow, non-permeable β-barrels and an extracellular, folded antigenic cap that displays VDs. In complex with a neutralizing Fab fragment of a conformational antibody, the cap undergoes structural reorganization that shows how epitope presentation is modulated by immune engagement. These structures reveal the molecular basis of MOMP’s serovar specificity and provide a template for structure-based vaccine design.

Guo, Yirui↗
DOE OSTI2025

Accurate Dehydrogenation Enthalpies Dataset for Liquid Organic Hydrogen Carriers

This contribution presents a comprehensive extension of the QM9 dataset (originally at 133 K molecules) with the calculation of G4MP2 enthalpies for 9,841 molecules, featuring up to nine heavy atoms. We present QM9-LOHC, a (de)hydrogenation dataset of 10,373 reactions, including a minimum of 5.5% weight hydrogen storage capacity in line with the Department of Energy standards for Liquid Organic Hydrogen Carriers (LOHC). By utilizing the accurate quantum chemical method G4MP2 we expand the QM9 database and explore new avenues for the exploration of hydrogen storage technologies (electrochemical LOHCs, alkali metal-LOHCs, and mixtures of LOHCs). The QM9-LOHC dataset, with its focus on reactions that vary only by hydrogen saturation levels, provides a needed data resource for advancing the design and optimization of both conventional and innovative LOHC systems, and high-fidelity data for molecular discovery.

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

Microporous metal–organic frameworks for the purification of propylene

Separation of propylene from its analogous hydrocarbons such as propane is of great importance in the petrochemical industry to produce valuable chemical feedstocks with desired purity. However, the well-established method currently used for industrial propane/propylene separation is energy intensive. It involves repeated cycling in the cryogenic and high-pressure distillation process and requires multiple columns and high reflux ratios because of the very similar physical properties of the two species. Thus, it is identified as one of the most capital- and energy-intensive processes. Adsorptive separation based on porous adsorbents is regarded as an alternative energy-efficient technology to replace or supplement the traditional heat-driven cryogenic distillation processes. In this context, metal–organic frameworks (MOFs) have emerged as the most promising candidates for propane/propylene separation, taking into consideration their unique tunability with respect to pore geometry and pore functionality. In this highlight, we summarize the latest advancement in developing MOFs as physisorbents for the separation and purification of propylene from propane, with a focus on those that demonstrate selective molecular exclusion and propane-selective adsorption. We discuss the adsorption preferences related to the material design and separation mechanisms, and review the existing challenges. Lastly, we offer our perspectives on various strategies for the future design of MOFs that hold true potential for propylene purification under industrial settings.

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

Raman Wavelength Conversion in Ionic Liquids

Here, we explore the use of room-temperature ionic liquids (ILs) as Raman wavelength converters. ILs provide an engineerable framework to design suitable liquids for wavelength conversion over a broad spectral range, through careful selection of the molecular structures of the IL anions and cations so that specific characteristics can be obtained, such as a desirable Raman shift, low Brillouin scattering, and good optical transmission in the pump and Stokes wavelengths. Applying such criteria, we demonstrate that 1-ethyl-3-methylimidazolium dicyanamide (EMIM DCA) is an effective medium for conversion of 532-nm pulses from a Q-switched Nd :YAG laser to 603 nm. This corresponds to an approximate 2200 cm –1 shift, which can be used to generate mid-infrared radiation through subsequent difference frequency generation for optical pumping of CO 2 lasers. Threefold-higher Raman conversion efficiency is obtained in EMIM DCA compared with water under identical conditions in a proof-of-principle single-pass conversion setup, resulting in an efficient generation of multimillijoule, <6 ns duration, high-quality orange laser pulses in a wavelength region that is difficult to access at high energies. Consequently, we examine ILs representing two other classes of Raman-active functional groups and obtain conversion up to the fifth-order Stokes shift and first anti-Stokes shift. Through the tunable selection of their components and their useful dynamical properties, ILs provide a platform for efficient, simple, and alignment-tolerant high-energy Raman shifting with numerous industrial and technological applications.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Novel small molecule FGF 23 inhibitors increase serum phosphate and improve skeletal abnormalities in Hyp mice

We report that excess fibroblast growth factor 23 (FGF23) causes hereditary hypophosphatemic rickets, such as X-linked hypophosphatemia (XLH) and tumor induced osteomalacia (TIO). A small molecule that specifically binds to FGF23 to prevent activation of the FGFR/a-Klotho complex has potential advantages over the currently approved systemically administered FGF23 blocking antibody. Using structure-based drug design we previously identified ZINC13407541 (N-[[2-(2-phenylethenyl)cyclopenten-1-yl]methylidene]hydroxylamine) as a small molecule antagonist for FGF23. Additional structure-activity studies developed a series of ZINC13407541 analogues with enhanced drug-like properties. In this study, we tested in a pre-clinical Hyp mouse homologue of XLH a direct connect analogue (8n) [(E)-2-(4-(tert-butyl)phenyl)cyclopent-1-ene-1-carbaldehyde oxime] that exhibited the greatest stability in microsomal assays, and 13a [(E)-2-((E)-4-methylstyryl)benzaldehyde oxime] that exhibited increased in vitro potency. Using cryo-electron microscopy (Cryo-EM) structure and computational docking, we identified a key binding residue (Q156) of the FGF23 antagonists, ZINC13407541 and its analogues (8n and 13a) in the N-terminal domain of FGF23 protein. Site-directed mutagenesis and bimolecular fluorescence complementation (BiFC)-fluorescence resonance energy transfer (FRET) assay confirmed the binding site of these three antagonists. We found that pharmacological inhibition of FGF23 with either of these compounds blocked FGF23 signaling and increased serum phosphate and 1,25(OH)2D concentrations in Hyp mice. Long-term parenteral treatment with 8n or 13a also enhanced linear bone growth, increased mineralization of bone, and narrowed the growth plate in Hyp mice. The more potent 13a compound had greater therapeutic effects in Hyp mice. Further optimization of these FGF23 inhibitors may lead to versatile drugs to treat excess FGF23-mediated disorders.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Capacitance of thin films containing polymerized ionic liquids

Electrode-polymer interfaces dictate many of the properties of thin films such as capacitance, the electric field experienced by polymers, and charge transport. However, structure and dynamics of charged polymers near electrodes remain poorly understood, especially in the high concentration limit representative of the melts. To develop an understanding of electric field–induced transformations of electrode-polymer interfaces, we have studied electrified interfaces of an imidazolium-based polymerized ionic liquid (PolyIL) using combinations of broadband dielectric spectroscopy, specular neutron reflectivity, and simulations based on the Rayleigh’s dissipation function formalism. Overall, we obtained the camel-shaped dependence of the capacitance on applied voltage, which originated from the responses of an adsorbed polymer layer to applied voltages. This work provides additional insights related to the effects of molecular weight in affecting structure and properties of electrode-polymer interfaces, which are essential for designing next-generation energy storage and harvesting devices.

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

Effects of Salt Aggregation in Perfluoroether Electrolytes

Electrolytes comprised of polymers mixed with salts have great potential for enabling the use of Li metal anodes in batteries for increased safety. Ionic conductivity is one of the key performance metrics of these polymer electrolytes and achieving high room-temperature conductivity remains a challenge to date. For a bottom-up design of the polymer electrolytes, we must first understand how the structure of polyelectrolytes on a molecular level determines their properties. Here, we use classical molecular dynamics to study the solvation structure and ion diffusion in electrolytes composed of a short-chain perfluoroether with LiFSI or LiTFSI salts. Density functional theory is also used to provide some insights into the structures and energies of the salt interactions with the perfluoroether. We observe the formation of aggregates of salts in the fluorinated systems even at low salt concentrations. The fluorine-fluorine attraction in the solvent is the governing factor for creating the salt aggregates. The aggregates’ size and lifetime change with concentration and anion. These simulations provide an insight into the structure and dynamics of perfluoroether based electrolytes that can be used to improve Li-ion batteries.

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

OpenFerro v0.1.0

OpenFerro is a Python package for on-lattice atomistic dynamics simulation of ferroic materials. OpenFerro is based on JAX, a high-performance linear algebra package supporting auto-differentiation and GPU acceleration. OpenFerro is designed to minimize the effort required to build on-lattice Hamiltonian models, and to perform molecular dynamics (MD) and Landau-Lifshitz-Gilbert simulations. Unlike existing codes, OpenFerro provides a unified interface to model different types of local order parameters.

Xie, Pinchen [Lawrence Berkeley National Laborator↗
NASA NTRS1977

Some basic mathematical methods of diffusion theory

An introductory treatment of the fundamentals of diffusion theory is presented, starting with molecular diffusion and leading up to the statistical methods of turbulent diffusion. A multilayer diffusion model, designed to permit concentration and dosage calculations downwind of toxic clouds from rocket vehicles, is described. The concepts and equations of diffusion are developed on an elementary level, with emphasis on atmospheric applications.

Giere, A. C.↗
NASA NTRS2000

8-9 and 14-15 Micron Two-Color 640x486 GaAs/AlGaAs Quantum Well Infrared Photodetector (QWIP) Focal Plane Array Camera

An optimized long-wavelength two-color Quantum Well Infrared Photodetector (QWIP) device structure has been designed. This device structure was grown on a three inch semi-insulating GaAs substrate by molecular beam epitaxy (MBE). This wafer was processed into several 640x486 format monolithically integrated 8-9 and 14-15 micron two color (or dual wavelength) QWIP focal plane arrays (FPAs). These FPAs were then hybridized to 640x486 silicon CMOS readout multiplexers. A thinned (i.e., substrate removed) FPA hybrid was integrated into a liquid helium cooled dewar to perform electrical and optical characterization and to demonstrate simultaneous two-color imagery. The 8-9 micron detectors in the FPA have shown background limited performance (BLIP) at 70 K operating temperature, at 300 K background with f/2 cold stop. The 14-15 micron detectors of the FPA have reached BLIP at 40 K operating temperature at the same background conditions. In this presentation we discuss the performance of this long-wavelength dualband QWIP FPA in quantum efficiency, detectivity, noise equivalent temperature difference (NEAT), uniformity, and operability.

Gunapala, S. D.↗
NASA NTRS2009

Synthesis of Submillimeter Radiation for Spectroscopy

The frequency-multiplier submillimeter spectrometer (FMSS) is a laboratory apparatus for far-infrared molecular spectroscopy, embodying several advances over prior such apparatuses. The most innovative part of the FMSS is a source of monochromatic submillimeter- wavelength radiation that can be tuned over a wide frequency range, as needed for trace gas analyses and molecular- structure studies for which such apparatuses are typically used. The radiation source features a modular design and is built mostly from commercially available components. It includes a computer-controlled radio-frequency synthesizer, amplifiers, and frequency multipliers of a type heretofore used in local oscillators for heterodyne far-infrared receivers. In conjunction with the rest of the apparatus, this source makes it possible to perform measurements over large portions of the submillimeter-wavelength spectrum with resolution, accuracy, and sensitivity greater than those achievable in Fourier-transform infrared spectroscopy. In comparison with prior laboratory submillimeter- wavelength radiation sources, this source is much lighter in weight, less cumbersome, less power-hungry, and capable of sustained operation with less intervention by laboratory personnel. Also, unlike some prior submillimeter-wavelength sources, this source does not require a high-voltage power source. As shown in more detail in the figure, the radiation source includes a sweep frequency synthesizer connected to an external waveform generator, the output of which is used as a reference signal. The synthesizer is computer-controlled through a standard general-purpose interface bus (GPIB) and is operated in phase-locked continuous- wave mode for all measurements. The synthesizer output ranges in frequency from 11 to 18 GHz. For suppression of frequency spurs and harmonics, the output of the frequency synthesizer is fed through a tunable yttrium iron garnet (YIG) filter, which is swept in frequency simultaneously with the frequency synthesizer.

Maiwald, Frank↗
NASA NTRS2008

The Orbiting Carbon Observatory: NASA's First Dedicated Carbon Dioxide Mission

The Orbiting Carbon Observatory is scheduled for launch from Vandenberg Air Force Base in California in January 2009. This Earth System Science Pathfinder (ESSP) mission carries and points a single instrument that incorporates 3 high-resolution grating spectrometers designed to measure the absorption of reflected sunlight by near-infrared carbon dioxide (CO2) and molecular oxygen bands. These spectra will be analyzed to retrieve estimates of the column-averaged CO2 dry air mole fraction, X(sub CO2). Pre-flight qualification and calibration tests completed in early 2008 indicate that the instrument will provide high quality X(sub CO2) data. The instrument was integrated into the spacecraft, and the completed Observatory was qualified and tested during the spring and summer of 2008, in preparation for delivery to the launch site in the fall of this year. The Observatory will initially be launched into a 635 km altitude, near-polar orbit. The on-board propulsion system will then raise the orbit to 705 km and insert OCO into the Earth Observing System Afternoon Constellation (A-Train). The first routine science observations are expected about 45 days after launch. Calibrated spectral radiances will be archived starting about 6 months later. An exploratory X(sub CO2) product will be validated and then archived starting about 3 months after that.

Carbon Cycle↗
DOE OSTI2021

Building Toward the Future in Chemical and Materials Simulation with Accessible and Intelligently Designed Web Applications

Over the last few decades, significant progress has been made in the development and use of electronic structure and other molecular simulation methods. As these methods become more mature and are able to simulate larger and more complex chemical simulations, the need for improvement in scientific visualization, molecular builders, simplified input to simulation methods, and the development of new approaches and languages to describe simulations, along with workflows to carry them out, becomes more apparent. In this chapter, we describe our recent efforts in developing a prototype open-source computational tool called Arrows that combines NWChem, SQL and NoSQL databases, email, web APIs, and web applications in a way that make molecular and materials modeling accessible to all scientists and engineers. At the same time, because of its simplified input, it provides a framework for expert users to carry out large numbers of calculations and run complex workflows.

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