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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Optimizing Batch Crystallization with Model-based Design of Experiments

Poster for Foundations of Computer Aided Process Design (FOCAPD) 2024 describing the formality of model-based design of experiments for batch crystallization. This paper focuses on the implementation of model-based design of experiments for parameter precision, enabled by Pyomo.DoE, a package in Python. Specifically, this work outlines an identifiability analysis for the estimability of the model parameters in a batch crystallization system.

Lynch, Hailey↗
DOE OSTI2024

Optimizing Batch Crystallization with Model-based Design of Experiments

Adaptive and self-optimizing intelligent systems such as digital twins are increasingly important in science and engineering. Digital twins utilize mathematical models to provide added precision to decision-making. However, physics-informed models are challenging to build, calibrate, and validate with existing data science methods. Model-based design of experiments (MBDoE) is a popular framework for optimizing data collection to maximize parameter precision in mathematical models and digital twins. In this work, we apply MBDoE, facilitated by the open-source package Pyomo.DoE, to train and validate mathematical models for batch crystallization. We quantitatively examined the estimability of the model parameters for experiments with different cooling rates. This analysis provides a quantitative explanation for the heuristic of using multiple experiments at different cooling rates.

Lynch, Hailey↗
DOE OSTI2020

Feedback regulation of crystal growth by buffering monomer concentration

Abstract Crystallization is a ubiquitous means of self-assembly that can organize matter over length scales orders of magnitude larger than those of the monomer units. Yet crystallization is notoriously difficult to control because it is exquisitely sensitive to monomer concentration, which changes as monomers are depleted during growth. Living cells control crystallization using chemical reaction networks that offset depletion by synthesizing or activating monomers to regulate monomer concentration, stabilizing growth conditions even as depletion rates change, and thus reliably yielding desired products. Using DNA nanotubes as a model system, here we show that coupling a generic reversible bimolecular monomer buffering reaction to a crystallization process leads to reliable growth of large, uniformly sized crystals even when crystal growth rates change over time. Buffering could be applied broadly as a simple means to regulate and sustain batch crystallization and could facilitate the self-assembly of complex, hierarchical synthetic structures.

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

Viscosity of the Mercurian Magma Ocean: Implications of Sulfur-Free and Sulfur-Bearing Magma Oceans for Differentiation and Crustal Petrogenesis

Mercury is believed to have had a magma ocean in its early evolution whose solidification dynamics contributed to the planet’s present day surface composition. The surface is characterized by two main geological provinces; the Northern Smooth Plains (NSP),and the Heavily Cratered Terrain (HCT) and Intercratered Terrian (IcT). These provinces are defined by the differences in morphology, composition, and age. The NSP are located in the northern hemisphere and have low Mg/Si, Ca/Si, and S/Si ratios and high Al/Si ratios, and are compositionally analogous to a magnesian alkali basalt. The HCT/IcT cover the majority of the planet and are older than the NSP, and are characterized by high Mg/Si, Ca/Si, and S/Si ratios and low Al/Si ratios. The dichotomy in surface composition motivates the study into the structure of the mantle as a product of magma ocean solidification. Two important and interrelated parameters that determine the efficiency of crystal fractionation during magma ocean solidification are convection vigor and viscosity of the magma ocean. Crystal suspension in a cooling magma ocean could be efficient or inefficient which suggests two end member possibilities for magma ocean solidification. The first is the formation of a compositionally stratified mantle reflecting a cumulate sequence produced along a fractional liquid line of descent. The second is the formation of a well-mixed, batch crystallized mantle by high viscosity and/or vigorously convecting magma ocean. Determining which of these end members, or where on the spectrum between them is most relevant to Mercury’s magma ocean can be experimentally constrained through high P-T falling-sphere viscometry experiments.

Mouser, M. D.↗
DOE OSTI2021

Beyond single crystals: Imaging rubrene polymorphism across crystalline batches through lattice phonon Raman microscopy

Polymorphism is an issue troubling numerous scientific fields. A phenomenon where molecules can arrange in different orientations in a crystal lattice, polymorphism in the field of organic photovoltaic materials can dramatically change electronic properties of these materials. Rubrene is a benchmark photovoltaic material showing high carrier mobility in only one of its three polymorphs. To use rubrene in devices, it is important to quantify the polymorph distribution arising from a particular crystal growth method. However, current methods for characterizing polymorphism are either destructive or inefficient for batch scale characterization. Lattice phonon Raman spectroscopy has the ability to distinguish between polymorphs based on low frequency intermolecular vibrations. Here, we present here the addition of microscopy to lattice phonon Raman spectroscopy, which allows us to not only characterize polymorphs efficiently and nondestructively through Raman spectroscopy but also concurrently gain information on the size and morphology of the polymorphs. We provide examples for how this technique can be used to perform large, batch scale polymorph characterization for crystals grown from solution and physical vapor transport.We end with a case study showing how Raman microscopy can be used to efficiently optimize a green crystal growth method, selecting for large orthorhombic crystals desired for rubrene electronic device applications.

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

In situ counter-diffusion crystallization and long-term crystal preservation in microfluidic fixed targets for serial crystallography

Compared with batch and vapor diffusion methods, counter diffusion can generate larger and higher-quality protein crystals yielding improved diffraction data and higher-resolution structures. Typically, counter-diffusion experiments are conducted in elongated chambers, such as glass capillaries, and the crystals are either directly measured in the capillary or extracted and mounted at the X-ray beamline. Despite the advantages of counter-diffusion protein crystallization, there are few fixed-target devices that utilize counter diffusion for crystallization. In this article, different designs of user-friendly counter-diffusion chambers are presented which can be used to grow large protein crystals in a 2D polymer microfluidic fixed-target chip. Methods for rapid chip fabrication using commercially available thin-film materials such as Mylar, propylene and Kapton are also detailed. Rules of thumb are provided to tune the nucleation and crystal growth to meet users' needs while minimizing sample consumption. These designs provide a reliable approach to forming large crystals and maintaining their hydration for weeks and even months. This allows ample time to grow, select and preserve the best crystal batches before X-ray beam time. Importantly, the fixed-target microfluidic chip has a low background scatter and can be directly used at beamlines without any crystal handling, enabling crystal quality to be preserved. The approach is demonstrated with serial diffraction of photoactive yellow protein, yielding 1.32 Å resolution at room temperature. Fabrication of this standard microfluidic chip with commercially available thin films greatly simplifies fabrication and provides enhanced stability under vacuum. These advances will further broaden microfluidic fixed-target utilization by crystallographers.

Liu, Zhongrui↗
DOE OSTI2026

Stabilizing homogeneous CaMn6Sn6via oscillatory crystal growth: structural complexity in a kagome metal

CaMn6Sn6 is a member of the large family of Mn-based kagome metals derived by filling voids of the prototypical CoSn structure. We observed Ca-deficiency and structural complexity, with approximately 10% deficiency of calcium relative to the ideal 166 stoichiometry. These features are common in related Ca-based materials. We find that growth conditions stabilize different phases with varying Curie temperatures. Diffraction and magnetization measurements reveal that conventional growth profiles yield inhomogeneity both within and between crystals in a given batch, whereas an oscillatory temperature profile promotes homogeneous crystals that adopt a superstructure beyond the parent hexagonal structure type. We present the physical properties of crystals grown using the oscillatory approach. The crystals are highly conductive, with a c-axis residual resistivity ratio ρ(300 K)/ρ(2 K) exceeding 100 and a positive, linear magnetoresistance at base temperature. Magnetically, the crystals are quite similar to MgMn6Sn6, with easy-plane ferromagnetic behavior and a Curie temperature of TC ≈ 237 K. These results highlight the critical role of growth conditions in stabilizing homogeneous crystals of complex phases such as Ca0.9Mn6Sn6. The oscillatory growth approach provides an effective route for accessing the intrinsic properties of this complex material and may be broadly useful for the growth of related kagome systems.

May, Andrew [ORNL] (ORCID:0000000307778539)↗
DOE OSTI2022

Progress in Near-Equilibrium Ammonothermal (NEAT) Growth of GaN Substrates for GaN-on-GaN Semiconductor Devices

This paper reviews the near-equilibrium ammonothermal (NEAT) growth of bulk gallium nitride (GaN) crystals and reports the evaluation of 2″ GaN substrates and 100 mmbulk GaN crystal grown in our pilot production reactor. Recent progress in oxygen reduction enabled growing NEAT GaN substrates with lower residual oxygen, coloration, and optical absorption. The oxygen concentration was approximately 2 × 1018 cm−2, and the optical absorption coefficient was 1.3 cm−1 at 450 nm. Maps of full-width half maximum (FWHM) of X-ray diffraction rocking curveswere generated for grown crystals and finished wafers. The X-ray rocking curve maps confirmed high-quality and uniform microstructure across the entire surface of the bulk crystals and substrates. The average FWHM of the 50 best bulk crystals from the recent batch was 28 ± 4 arcsec for the 002 diffraction and 34 ± 5 arcsec for the 201 diffraction, with an average radius of curvature of 20 m. X-ray topography measured on both sides of the bulk crystals implied that the density of dislocations wasreduced by one order of magnitude during the NEAT growth. A typical NEAT GaN substrate shows dislocation density of about 2 × 105 cm−2.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison

For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A highly active Burkholderia polyketoacyl-CoA thiolase for production of triacetic acid lactone

Triacetic acid lactone (TAL) is a versatile platform chemical traditionally biosynthesized via decarboxylative Claisen condensation by 2-pyrone synthase. However, this route is limited by poor efficiency and dependence on malonyl-CoA. Here, we show that non-decarboxylative Claisen condensation by polyketoacyl-CoA thiolases offers a more efficient alternative. Through mining homologs of a previously reported enzyme from Cupriavidus necator, we identify five thiolases with TAL production activity. One candidate, BktBbr from Burkholderia sp. RF2-non_BP3, exhibits approximately 30-fold higher activity in vitro and supports 30-fold higher TAL titers in Escherichia coli compared to the original enzyme. Fed-batch fermentation achieves titers up to 2.8 g L⁻¹. Structural analysis of BktBbr co-crystallized with CoA esters guides rational engineering to further enhance performance. Our discovery of a highly active thiolase establishes an alternative enzymatic route to produce TAL efficiently, providing a scalable foundation for sustainable biomanufacturing.

Wang, Zilong [Joint BioEnergy Institute (JBEI), Em↗
DOE OSTI2022

RUScal : Software for the analysis of resonant ultrasound spectroscopy measurements

Resonant ultrasound spectroscopy is used to nondestructively measure the elastic resonances of small solids to elucidate the material's elastic properties or other qualities like size, shape, or composition. In this work, we introduce the software RUScal for the purpose of determining elastic properties by analyzing the eigenfrequencies of solid specimens with common shapes, such as rectangular parallelepipeds, cylinders (solid and hollow tube), ellipsoids, and octahedrons, as well as irregularly shaped ellipsoids that can be described analytically. All symmetry classes are supported, from isotropic to triclinic, along with the option to add or remove up to three orthogonal mirror planes as well as the ability to reorient the crystal axes with respect the sample edges via Euler angles. Additional features include tools to help find initial sets of elastic constants, including grid exploration and Monte Carlo methods, a tool to analyze frequencies as a function of sample length or crystal orientation, an error analysis tool to assess fit quality, and formatting of the input and output files for batch fitting, e.g., as a function of temperature. This software was validated with published resonant ultrasound spectroscopy data for various materials, shapes, and symmetries with noted improvements in calculation time compared to finite element methods.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Data for An End-to-End Pipeline for Succinic Acid Production at an Industrially Relevant Scale Using Issatchenkia orientalis

Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34–90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids.

Metabolomics↗
DOE OSTI2026

Crystal generation using the fully differentiable pipeline and latent space optimization

We present a materials generation framework that couples a symmetry-conditioned variational autoencoder with a differentiable SO(3) power spectrum objective to steer candidates toward a specified local environment under the crystallographic constraints. In particular, we implement a fully differentiable pipeline that performs batch-wise optimization on both direct and latent crystallographic representations. Using the GPU acceleration, the implementation achieves about fivefold speed compared to our previous CPU workflow, while yielding comparable outcomes. In addition, we introduce the optimization strategy that alternatively performs optimization on the direct and latent crystal representations. This dual-level relaxation approach can effectively escape local minima defined by different objective gradients, thus increasing the success rate of generating complex structures satisfying the target local environments. This framework can be extended to systems consisting of multi-components and multi-environments, providing a scalable route to generate material structures with the target local environment.

conditional VAE↗
DOE OSTI2021

Unsaturated Sulfur Crown Ethers Can Extract Mercury(II) and Show Promise for Future Copernicium(II) Studies: A Combined Experimental and Computational Study

The unsaturated hexathia-18-crown-6 (UHT18C6) molecule was investigated for the extraction of Hg(II) in HCl and HNO3 media. This extractant can be directly compared to the recently studied saturated hexathia-18-crown-6 (HT18C6). The default conformation of the S lone pairs in UHT18C6 is endodentate, where the pocket of the charge density, according to the crystal structures, is oriented toward the center of the ring, which should allow better extraction for Hg(II) compared to the exodentate HT18C6. Batch study experiments showed that Hg(II) had better extraction at low acid molarity (ca. 99% in HCl and ca. 95% in HNO 3 ), while almost no extraction was observed above 0.4 M HCl and 4 M HNO 3 (<5%). Speciation studies were conducted with the goal of delineating a plausible extraction mechanism. Density functional theory calculations including relativistic effects were carried out on both Hg(II)-encapsulated HT18C6 and UHT18C6 complexes to shed light on the binding strength and the nature of bonding. Our calculations offer insights into the extraction mechanism. In addition to Hg(II), calculations were performed on the hypothetical divalent Cn(II) ion, and showed that HT18C6 and UHT18C6 could extract Cn(II). Finally, the extraction kinetics were explored to assess whether this crown can extract the short-lived Cn(II) species in a future online experiment.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis

Abstract Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34–90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗