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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Point Defects Control Guest Molecule Diffusion in the 1D Pores of Zn(tbip)

Molecular diffusion plays a critical role in metal-organic frameworks (MOFs) within the application of kinetic chemical separations. We carefully study in this work the unexpected role of point defects for short-chain alkanes diffusing in Zn(tbip), an MOF with rigid one-dimensional (1D) channels. Inside a defect-free Zn(tbip), guest molecules are expected to follow single-file diffusion along 1D channels. It has been found previously by Heinke et al. that these parallel 1D channels are connected for molecular diffusion. Our density functional theory (DFT) calculations suggest that linker vacancy defects could arise under experimentally relevant conditions by removing a pair of linkers. Further climbing-image nudged elastic band (cNEB) DFT calculations indicate that hopping of short-chain alkanes between adjacent 1D channels over defect windows can occur at moderate temperatures. In addition to providing insights into connected adjacent 1D channels in Zn(tbip), Heinke et al. also inferred that most 1D pores are blocked from a microkinetic model. Additionally, we explored the influence of hydrolyzed linker created by the formation of linker removal inside 1D pores. Our DFT calculations show that the linkers can effectively block the pores and the linker diffusion in 1D channels is slow. Our results, for the first time, offer a mechanistic explanation of the unexpected molecular diffusion behavior in this MOF with 1D channels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Dynamics of Product Branching from Radical Intermediates in Elementary Combustion Reactions (Final Technical Report)

While the total rate constant for many elementary reactions is well-characterized, understanding the product branching in complex reactions presents a formidable challenge. To gain an incisive probe of such reactions, our experiments investigate the dynamics of the product channels that arise from transient radical intermediates along the bimolecular reaction coordinates. Our recent published work uses the methodology developed in my group in the last fifteen years, using both imaging and scattering apparatuses. The experiments generate a particular isomeric form of an unstable radical intermediate along a bimolecular reaction coordinate and study the branching between the ensuing product channels of the energized radical as a function of its internal rotational and vibrational energy under collision-less conditions. The experiments use a combination of: 1) measurement of product velocity and angular distributions in a crossed laser-molecular beam apparatus, with electron bombardment detection in my lab in Chicago or 2) with tunable vacuum ultraviolet photoionization detection at Taiwan's National Synchrotron Radiation Research Center (NSRRC), and 3) velocity map imaging using state-selective REMPI and single photon VUV ionization of radical intermediates and reaction products. We also employ tunable VUV photoionization detection in our imaging apparatus, using difference frequency four-wave mixing to produce photoionization light tunable from 8 to 10.8 eV. This year of support funded our work to photolytically generate the radical intermediate important in the OH + propene reaction when OH adds to an end carbon. Our other major result this past year was on the photoionization detection of vinoxy radicals. Our experiments at the NSRRC definitively show that vinoxy dissociatively ionizes to both CH 3 + and HCO + , and establishes the absolute partial photoionization cross section of vinoxy to CH 3 + at 10.5 and 11.44 eV. This should allow experimentalists detecting vinoxy radicals produced in bimolecular reactions such as OH + propene to get good branching fractions to that product channel. Finally we initiated studies of the photodissociation of 1-bromo-2-chloroethane and 1,1-bromochloroethane at 193 nm at the NSRRC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1992

The nearby 2-solar mass Bok globule LBN 11 - Sub-sonic molecular clumps in a magnetic environment

A multiwavelength study of the nearby small Bok globule LBN 11 is performed in order to investigate the relationship between embedded magnetic fields, cloud structure, and star formation. Optical polarimetry of background stars is used to characterize and trace the embedded magnetic field direction. High-dispersion CO isotopic mapping is employed to determine the radial density distribution of the gas, measure cloud rotation, and identify individual gas clumps. CS and SO mapping revealed dense cores within the (C-13)O clumps. Analysis of coadded IRAS images reveal the cloud to be free of current or recent star formation: there are no IR point sources of sufficient flux or proper colors to signify young stars associated with the cloud. The molecular line maps show the cloud to be extremely clumpy. Clumps are found to range in size from 0.2 pc for the largest CO clump to about 0.04 pc for the smallest CS feature. It is concluded that, at least in the envelope of the cloud, the magnetic field and the CO clumps are coupled.

Clemens, Dan P.↗
DOE OSTI2021

The Role of Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology: Proceedings of a Workshop

Quantum concepts hold the potential to enable significant advances in sensing and imaging technologies that could be vital to the study of biological systems. The workshop Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology, held online March 8–10, 2021, was organized to examine the research and development needs to advance biological applications of quantum technology. Hosted by the National Academies of Sciences, Engineering, and Medicine, the event brought together experts working on state-of-the-art, quantum-enabled technologies and scientists who are interested in applying these technologies to biological systems. Through talks, panels, and discussions, the workshop facilitated a better understanding of the current and future biological applications of quantum-enabled technologies in fields such as microbiology, molecular biology, cell biology, plant science, mycology, and many others. The workshop was organized around three main themes. The first, quantum in biology, examined quantum concepts that are hypothesized to be important for life processes and that researchers are working to observe through biological imaging and sensing. The second, quantum for biology, addressed ways to use quantum concepts to enhance technologies for biological imaging and sensing. The third, biology for quantum, offered a wider discussion of how the frontiers of biological imaging and sensing could enable future study using quantum concepts, tools, or technologies. Throughout the workshop, participants identified a wide range of emerging approaches and opportunities at the intersection of quantum physics and biological sensing and imaging. During the workshop, there were some differences in how each speaker defined the term quantum. During one of the panels, Prem Kumar offered thoughts on what phenomena are classical versus quantum, explaining that techniques get progressively more quantum as you move from just having superposition to having superposition with measurement and entanglement. Another explanation from Clarice Aiello delineates the definition into several levels. This includes a base level of “quantum-ness,” which reflects that all matter is made of atoms, and when these particles are isolated they behave based on quantum mechanical principles. A second level is related to quantum coherence, where a single quantum object might be found in a coherent superposition state. A final level, which she described as the quantum-entangled level, involves multiple quantum systems which are entangled among themselves. Overall, the workshop touched on concepts such as superposition, entanglement, and squeezing and their potential implications for communication, computing, and simulation, in addition to the workshop’s main focal area, biological sensing and imaging. At the opening of the workshop, Thorsten Ritz of the University of California, Irvine, identified two questions at the heart of quantum biology: Is the machinery of life quantum mechanical, and can quantum mechanics be used to study the machinery of life in new ways? Participants highlighted systems in which researchers have explored these questions, from the vast array of molecular interactions involved in biological processes such as photosynthesis, to the mechanics involved in cellular functions such as differentiation and aggregation, to the role of oscillating magnetic fields in flight orientation among birds. Sensing and imaging technologies are crucial to biological research; these technologies could both enhance the study of quantum effects and be enhanced by quantum concepts. A critical challenge in biological research is to develop imaging and sensing tools that do not damage or interfere with the often fragile and fleeting systems being studied. Attendees discussed a variety of established and emerging technologies that could enhance noninvasive biological imaging, including single- and two-photon spectroscopy, single-molecule spectroscopy, quantum illumination, ghost imaging, and cryo-electron microscopy. One example came from Marlan Scully who gave a keynote address on the first day of the workshop. Scully emphasized the use of different laser technologies, which exhibit coherence and other quantum properties, in moving toward real-world biological applications, such as the detection of SARS-CoV-2. Both tools and theory will play an important role in advancing quantum biology research and applications. Several participants suggested theorists and experimentalists should work in tandem to understand and model biological processes. While physics often reduces systems to their simplest forms for fundamental insights, participants also noted the value of observing and understanding biological systems in all their “messiness,” capturing both the inner workings of biological systems and the complex interactions that occur within and between organisms. In discussions among participants, several attendees stressed the need to match emerging tools with the right scientific questions. Rather than developing quantum technologies as “a hammer looking for a nail,” participants emphasized a focus on exploring the problems these technologies are best suited to address. For example, it is important to consider the size of the phenomenon being studied, the timescales that are important in answering the scientific question, and other relevant considerations. Every tool along the spectrum from classical to quantum involves its own set of trade-offs. For example, Ted Laurence of the Lawrence Livermore National Laboratory said that quantum measurements, such as single photon counting, fluorescence transitions, and lasers, can take longer to produce the same results as classical measurements. These quantum measurements, however, do not require calibration and can enable new research questions to be answered. Prem Kumar, Northwestern University, noted that, despite their promise, quantum approaches should not be used simply for the sake of using quantum, especially in situations where classical approaches better meet the needs of the researcher. Understanding and applying quantum concepts could enable advances in a wide range of application areas including energy, synthetic biology, medicine, and sustainability. For example, Michelle O’Malley, University of California, Santa Barbara, described how improved noninvasive imaging approaches could help capture the complex interactions and functions involved in the breakdown of organic matter by microbial communities and lead to new technologies for capturing valuable products from plant waste. Several other participants discussed needs in tracking the movement of metabolites and molecules in microbial communities for insights into nutrient cycling in environments such as soil. Margaret Ahmad, Sorbonne University, discussed potential opportunities to leverage the magnetic properties of cryptochromes to advance new treatment approaches for diseases such as COVID-19 and cancer. Looking toward the future development of the field, participants discussed challenges to advancing quantum biology that arise from disciplinary disconnects between physicists and biologists. The siloing of academic research disciplines represents a significant barrier to progress. Disconnects in terminology, motivations and priorities, and structural barriers to collaborative work underscore the need for concerted efforts to bridge these divides. Attendees and speakers offered suggestions for resolving these divergences, establishing a shared language, moving the field forward, and fostering meaningful feedback between disciplines. Overall, participants stressed a need for balance, open communication, collaboration, unity, and clear dialogue on trade-offs between quantum and classical approaches. Keiko Torii, The University of Texas at Austin, said that the best collaborations happen when the project provides mutual advantages that can show off everyone’s talents, each team finds the work interesting, and partners develop a camaraderie to pursue new knowledge. To enable near- and long-term opportunities in this space, participants suggested that exploratory, high-risk funding could improve existing instrumentation to explore quantum enhancement collaboratively. They also emphasized the need for collaboration between quantum physicists and sensing/imaging scientists, which could be advanced through a dedicated quantum biology investigator program. People, even more than technology, will be crucial to the future of quantum biology. Participants explored training, education, and workforce needs to further develop this burgeoning field and cultivate the next generation of scientists. While many programs are still in their nascent stages, participants highlighted examples of approaches and programs being developed at various types of institutions to engage students and professional scientists in quantum biology research. Several participants stressed the need for an inclusive approach, spanning disciplines as well as communities to foster a diverse field fueled by the intellectual contributions of a wide range of people, including historically under-resourced schools and students. To increase awareness and excitement about quantum physics and related areas of biology, attendees suggested capitalizing on the “buzz” around quantum. Several participants emphasized the need to start early, introducing students to quantum concepts and their appealing “weirdness” in K–12 education. Engaging students early—before they become entrenched in traditional disciplinary siloes as typically happens in graduate school—could help to galvanize interest in the area and foster a generation of scientists with the interdisciplinary mindset and skills needed to advance this interdisciplinary field. While these efforts could be advanced at many levels and across multiple sectors, several participants suggested a national quantum biology center could be a valuable hub to coordinate and support quantum biology education and workforce development across academia, industry, and government.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2018

Design and Development of Modules to Support Live Microscopic Imaging on Ground-Based Microgravity Simulators

In space, astronauts are exposed to environmental stressors that often result in physiological changes. One prominent stressor in spaceflight is microgravity, and research has shown that long term microgravity exposure causes muscle atrophy, bone loss, cardiovascular concerns, and vision impairment. It is critical to understand how altered gravity affects physiology on the cellular, molecular, and gene level in order to accurately assess health risks and to develop effective countermeasures. Ground-based microgravity simulators such as random positioning machines (RPMs) are used to produce some of the biological effects of altered gravity on different cell types and organisms. Real-time imaging during simulations are of particular interest as we can study how basic cell functions such as cell division, cell migration, and proliferation progress under microgravity conditions. However, design limitations of present microgravity simulators such as susceptibility to parasitic vibration and displacement of the sample from the center of rotation challenge the accuracy of experiment results and live images. We have developed a cell culture sample holder module suitable for live microscopic imaging on an RPM. CAD modeling and 3D printing technology were used to implement modifications to the sample holder and to install a digital microscope to perform live bright-field and fluorescent imaging. Vibration damping materials were also investigated to allow for stable imaging while the microgravity simulator was within a cell culture incubator. Novel methods and hardware modifications for improving live cell imaging on ground-based microgravity simulators were proposed and discussed.

3D printing↗
NASA NTRSDate not supplied

Enabling Space Biological Knowledge Discovery Through Image and Video Data Sharing

Increased biomedical risks associated with deep space crewed missions (cis-Lunar, Mars transit/surface) require development of health countermeasures, novel ecosystem support, risk modeling, and fundamental space biological knowledge discovery. Molecular-omics, physiological-phenotypic-behavioral, and environmental-radiation telemetry data from space biological and health studies are needed for reuse by scientists to address these tasks. The data as well as space-relevant biospecimens are being made more findable, accessible, interoperable, and reusable through NASA’s Open Science Data Repository (OSDR). This new OSDR umbrella grouping includes NASA GeneLab, the NASA Ames Life Sciences Data Archive (ALSDA), and the NASA Biological Institutional Scientific Collection. The OSDR system design appropriately handles metadata and processed-tabular results from ALSDA studies collected from space experiments. But raw and processed ALSDA bioimage and video datasets require an expansion of OSDR’s data architecture to handle ingestion, curation, and egress. The academic-industry bioimaging field saw a scientific renaissance in the past several years through leveraging open-source software, international collaborations, machine learning, and other open science/programming approaches. As crewed missions and more biological experiments are on the deep space horizon, OSDR is embracing data stewardship through listening to feedback from subject matter experts and designing an expanded architecture which is appropriate for NASA’s goals to enable analysis and reuse of bioimaging and video data for the public science community.Discovery Through Image and Video Data Sharing

space biology↗
NASA NTRS1998

Determining the Molecular Growth Mechanisms of Tetragonal Lysozyme Crystals

Studies of the growth of tetragonal lysozyme crystals employing atomic force microscopy (AFM) have shown the advantages of this technique in investigating the growth mechanisms of protein crystals [1]. The resolution of these studies was in the micron range, which revealed surface features such as the occurrence of dislocations and 2D nucleation islands, similar to those found in inorganic systems. They clearly showed that the crystals grew by these surface growth mechanisms. However, the studies also revealed some surprising features, such as bimolecular growth step heights and pronounced growth anisotropies on the (110) face, which could not be explained. In previous studies we employed Periodic Bond Chain (PBC) theory to tetragonal lysozyme crystal growth and found that the crystals were constructed by strongly bonded molecular chains forming helices about the 43 axes [2,3]. The helices were connected to each other with weaker bonds. The growth process was shown to proceed by the formation of these 43 helices, resulting in bimolecular growth steps on the (110) face. It was also shown to explain many other observations on tetragonal lysozyme crystal growth. Although PBC analysis is not a new technique [4], it has not been widely used as the mechanisms predicted from it could not be experimentally verified. In this study the growth process of these crystals was investigated, particularly for the (110) face, employing some newly developed high resolution AFM techniques. These techniques allowed individual lysozyme molecules on the crystal faces to be resolved and predictions from PBC analyses to be tested. The analyses had shown that of the two possible packing arrangements on (110) faces, only one would actually occur. Employing the first of the newly developed techniques, these faces were scanned by high resolution AFM. The resulting images were then compared with the theoretically constructed images for the two possible packing arrangements on the (110) face. The theoretical images were constructed by convolution of the crystal surface shape obtained from crystallographic data with the AFM tip shape. The comparison confirmed the prediction that the molecular packing arrangement of these faces corresponded to that for complete 43 helices. The second AFM technique that was developed was used to follow the growth process by measuring the dimensions of individual growth units on the (110) face. Linescans across a growth step, performed near the saturation limit of the crystals, allowed the growth unit dimensions to be measured. These measurements showed that growth on the (110) face proceeded by the formation of new 43 helices from the addition of at least tetramer units in the [110] direction. In the [001] direction growth proceeded by the addition of various aggregate units corresponding to the 4(sub 3) helices.

Li, Huayu↗
DOE OSTI2022

Luxury iron uptake and storage in pennate diatoms from the equatorial Pacific Ocean

Abstract Iron is a key micronutrient for ocean phytoplankton, and the availability of iron controls primary production and community composition in large regions of the ocean. Pennate diatoms, a phytoplankton group that responds to iron additions in low-iron areas, can have highly variable iron contents, and some groups such as Pseudo-nitzschia, are known to use ferritin to store iron for later use. We quantified and mapped the intracellular accumulation of iron by a natural population of Pseudo-nitzschia from the Fe-limited equatorial Pacific Ocean. A total of 48 h after iron addition, nearly half of the accumulated iron was localized in storage bodies adjacent to chloroplasts believed to represent ferritin. Over the subsequent 48 h, stored iron was distributed to the rest of the cell through subsequent growth and division, partially supporting the iron contents of the daughter cells. This study provides the first quantitative view into the cellular trafficking of iron in a globally relevant phytoplankton group and demonstrates the unique capabilities of synchrotron-based element imaging approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dissecting subcycle interference in photoelectron holography

Multipath holographic interference in strong-field quantum tunnel ionization is key to revealing subangstrom attosecond dynamics for molecular movies. This critical subcycle motion is often obscured by longer timescale effects such as ring-shaped patterns that appear in above-threshold ionization (ATI). In the present work, we overcome this problem by combining two techniques in theory and experimental analysis: unit-cell averaging and time-filtering data and simulations. Together these suppress ATI rings and enable an unprecedented highly detailed quantitative match between strong-field ionization experiments in argon and the Coulomb-quantum orbit strong-field approximation (CQSFA) theory. Velocity map images reveal fine modulations on the holographic spiderlike interference fringes that form near the polarization axis. CQSFA theory traces this to the interference of three types of electron pathways. The level of agreement between experiment and theory allows sensitive determination of quantum phase differences and symmetries, providing an important tool for quantitative dynamical imaging in quantum systems.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRSDate not supplied

PRIMA: The PRobe Far-Infrared Mission for Astrophysics

PRIMA is a far-infrared observatory concept being developed to address timely and fundamental questions about the growths of galaxies and solar systems and their constituents. It will observe the build-up of heavy elements, dust, stars, and black holes in galaxies and their interrelationships, and trace the masses and water contents of protoplanetary disks to probe the growths of solar systems. The majority of observing time will be devoted to Guest Observer programs to enable the astrophysics community to identify and plan the most critical observations, with focused PI programs to address key science with rapid releases of data to inform community planning. PRIMA will have spectral, hyperspectral imaging, and polarimetric capabilities, enabled now for the first time by extraordinary progress in kinetic inductance detector (KID) array technology over the last two decades. The 2.0-meter telescope will be cooled to < 5 K to take maximum advantage of the KID sensitivities. For observations of atomic fine-structure lines, molecular lines, and solid-state emission and absorption bands, R = 200 spectral coverage will range from approximately 25 µm to 200 µm, with a high-resolution mode across the entire band that will have a spectral resolving power of a few thousand at 100 µm. R ~ 10 moderate-resolution (hyperspectral) imaging will range from 25 to 80 µm for rest-frame, mid- and far-infrared spectral energy distribution measurements to probe dust grain composition and disambiguate star formation and active galactic nuclei in galaxies. Polarimetric observations of large areas of Galactic molecular clouds and the Magellanic Clouds from 80 to ~200 µm will bridge between the large-scale polarimetry of the interstellar medium from cosmic microwave background observatories and protostellar disk-scale interferometric observations to probe magnetic fields at the critical scales at which clouds collapse to form stars. An overview of PRIMA’s basic design and capabilities will be presented. Other posters in this session describe PRIMA science, technology, and instrumentation in greater depth.

Jason Glenn↗
DOE OSTI2024

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Imaging of the PAH Emission Bands in the Orion Bar

The infrared spectrum of many planetary nebulae, HII regions, galactic nuclei, reflection nebulae, and WC stars are dominated by a set of narrow and broad features which for many years were called the "unidentified infrared bands". These bands have been attributed to several carbon-rich molecular species which all contain only carbon and hydrogen atoms, and fall into the class of PAH molecules or are conglomerates of PAH skeletons. If these bands are from PAHs, then PAHs contain 1-10% of the interstellar carbon, making them the most abundant molecular species in the interstellar medium after CO. From ground based telescopes, we have studied the emission bands assigned to C-H bond vibrations in PAHs (3.3, 11.3 microns) in the Orion Bar region, and showed that their distribution and intensities are consistent with a quantitative PAH model. We have recently obtained spectral images of the Orion Bar from the KAO at 6.2 and 7.7 microns using a 128 x 128 Si:Ga array camera in order to study the C-C modes of the PAH molecules. We will show these new data along with our existing C-H mode data set, and make a quantitative comparison of the data with the existing PAH model.

Bregman, Jesse↗
DOE OSTI2020

Imaging hole-density inhomogeneity in arsenic-doped CdTe thin films by scanning capacitance microscopy

We report nanometer-scale hole-density imaging in As-doped CdTe films by scanning capacitance microscopy (SCM). The hole-density profiling is validated by contrasting a CdTe cross-section sample made by molecular-beam epitaxy with systematically increased As doping in a staircase pattern over the range of 10 15 -10 18 /cm 3 within a single film. In polycrystalline films, the carrier distribution is significantly nonuniform, with inhomogeneity ranging from several hundred nm to several um and hole density varying by one order of magnitude (low 10^16 to low 10 17 /cm 3 ). This nonuniformity is distributed randomly, independent of the grain structure and grain boundaries (GBs). Kelvin probe force microscopy (KPFM) maps the surface potential and is correlated to cathodoluminescence (CL) and SCM by imaging over identical areas. Higher potential and lower CL intensity are found on GBs but not by SCM contrast; this indicates positive GB charging and recombination, but not GB-specific hole-density changes. The overall KPFM potential image is in rough agreement with the SCM carrier distribution and indicates band-edge potential fluctuations. Nonuniform carrier concentration, potential fluctuations, and defect recombination can all cause voltage and performance loss in As-doped CdTe solar technology.

14 SOLAR ENERGY↗
DOE OSTI2021

Interfacial intermixing and anti-phase boundaries in GaP/Si(0 0 1) heterostructures

Epitaxial GaP/Si heterostructures grown by molecular beam epitaxy (MBE) and migration-enhanced epitaxy (MEE) have been studied, primarily using aberration-corrected scanning transmission electron microscopy (AC-STEM). Atomically-resolved structure images, which are sensitive to atomic-column intensity revealed the detailed geometry of antiphase boundaries that were both parallel and also inclined to the growth direction. The polar/non-polar GaP/Si interfaces were neither atomically flat laterally nor abrupt vertically. Measurements of intensity profiles using both bright-field and dark-field AC-STEM images, as well as chemically-sensitive g 002 dark-field imaging, indicated substantial interfacial intermixing, which increased significantly from ~1.3 nm (MEE growth at 440 °C) to ~2.1 nm (MBE growth at 600 °C). The finite interface width will impact theoretical predictions of charge imbalance and strong electric fields across the heterointerface.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Self‐Assembly Methods Induce Different Individual‐Polymer‐Block Solvation Responses

An understanding of block-specific responses to stimuli in self-assembled copolymers is essential for the effective design of responsive materials. Here, materials formed from different post-reaction processing methods of the same ROMP block copolymer exhibit different block-specific solvent responses, as characterized in situ by fluorescence lifetime imaging microscopy (FLIM). FLIM data were acquired by tagging the polar or nonpolar block separately with a covalently incorporated viscosity-sensitive fluorescent molecular rotor to measure the changing tightness or looseness of assembly upon changes in solvent composition. Rapid precipitation from an insoluble solvent to form a film results in tighter assembly and less difference in tightness/looseness between the two blocks. Further, it interrupts individual block-solvent response behavior. Both results indicate an apparent disruption of the core–shell assembly. This model from FLIM is further supported by differential scanning calorimetry (DSC) and small-angle X-ray scattering (SAXS) data from isolated solids, which show tighter long-range interactions and more long-range order in these kinetically trapped states. Here, the experiments develop FLIM as a method for pinpointing stimuli-responsive behaviors from different processing methods to individual blocks. Together these outcomes provide a future handle for tailoring solvent-triggered assembly/disassembly behavior.

López, Pía A. [University of California, Irvine, C↗
DOE OSTI2022

Overexpression of phospholipid: diacylglycerol acyltransferase in Brassica napus results in changes in lipid metabolism and oil accumulation

The regulation of lipid metabolism in oil seeds is still not fully understood and increasing our knowledge in this regard is of great economic, as well as intellectual, importance. Oilseed rape (Brassica napus) is a major global oil crop where increases in triacylglycerol (TAG) accumulation have been achieved by overexpression of relevant biosynthetic enzymes. In this study, we expressed Arabidopsis phospholipid: diacylglycerol acyltransferase (PDAT1), one of the two major TAG-forming plant enzymes in B. napus DH12075 to evaluate its effect on lipid metabolism in developing seeds and to estimate its flux control coefficient. Despite several-fold increase in PDAT activity, seeds of three independently generated PDAT transgenic events showed a small but consistent decrease in seed oil content and had altered fatty acid composition of phosphoglycerides and TAG, towards less unsaturation. Mass spectrometry imaging of seed sections confirmed the shift in lipid compositions and indicated that PDAT overexpression altered the distinct heterogeneous distributions of phosphatidylcholine (PC) molecular species. Similar, but less pronounced, changes in TAG molecular species distributions were observed. Our data indicate that PDAT exerts a small, negative, flux control on TAG biosynthesis and could have under-appreciated effects in fine-tuning of B. napus seed lipid composition in a tissue-specific manner. This has important implications for efforts to increase oil accumulation in similar crops.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Structure of RADX and mechanism for regulation of RAD51 nucleofilaments

Replication fork reversal is a fundamental process required for resolution of encounters with DNA damage. A key step in the stabilization and eventual resolution of reversed forks is formation of RAD51 nucleoprotein filaments on exposed single strand DNA (ssDNA). To avoid genome instability, RAD51 filaments are tightly controlled by a variety of positive and negative regulators. RADX (RPA-related RAD51-antagonist on the X chromosome) is a recently discovered negative regulator that binds tightly to ssDNA, directly interacts with RAD51, and regulates replication fork reversal and stabilization in a context-dependent manner. Here, we present a structure-based investigation of RADX’s mechanism of action. Mass photometry experiments showed that RADX forms multiple oligomeric states in a concentration-dependent manner, with a predominance of trimers in the presence of ssDNA. The structure of RADX, which has no structurally characterized orthologs, was determined ab initio by cryo-electron microscopy (cryo-EM) from maps in the 2 to 4 Å range. The structure reveals the molecular basis for RADX oligomerization and the coupled multi-valent binding of ssDNA binding. The interaction of RADX with RAD51 filaments was imaged by negative stain EM, which showed a RADX oligomer at the end of filaments. Based on these results, we propose a model in which RADX functions by capping and restricting the end of RAD51 filaments.

Science & Technology - Other Topics↗