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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗
DOE OSTI2024

Adaptive nonequilibrium design of actin-based metamaterials: Fundamental and practical limits of control

The adaptive and surprising emergent properties of biological materials self-assembled in far-from-equilibrium environments serve as an inspiration for efforts to design nanomaterials. In particular, controlling the conditions of self-assembly can modulate material properties, but there is no systematic understanding of either how to parameterize external control or how controllable a given material can be. Here, we demonstrate that branched actin networks can be encoded with metamaterial properties by dynamically controlling the applied force under which they grow and that the protocols can be selected using multi-task reinforcement learning. These actin networks have tunable responses over a large dynamic range depending on the chosen external protocol, providing a pathway to encoding “memory” within these structures. Interestingly, we obtain a bound that relates the dissipation rate and the rate of “encoding” that gives insight into the constraints on control—both physical and information theoretical. Taken together, these results emphasize the utility and necessity of nonequilibrium control for designing self-assembled nanostructures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota)

Establishing a solid taxonomic framework is crucial for enabling discovery and documentation efforts. This ensures effective communication between scientists as well as reproducibility of results between laboratories, and facilitates the exchange and preservation of biological material. Such framework can only be achieved by establishing clear criteria for taxa characterization and rank assignment. Within the anaerobic fungi (phylum Neocallimastigomycota), the need for such criteria is especially vital. Difficulties associated with their isolation, maintenance and long-term storage often result in limited availability and loss of previously described taxa. To this end, we provide here a list of morphological, microscopic, phylogenetic and phenotypic criteria for assessment and documentation when characterizing newly obtained Neocallimastigomycota isolates. We also recommend a polyphasic rank-assignment scheme for novel genus-, species- and strain-level designations for newly obtained Neocallimastigomycota isolates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evaluation of Differential Peptide Loading on Tandem Mass Tag-Based Proteomic and Phosphoproteomic Data Quality

Global and phosphoproteome profiling has demonstrated great utility for the analysis of clinical specimens. One major barrier to the broad clinical application of proteomic profiling is the large amount of biological material required, particularly for phosphoproteomics—currently on the order of 25 mg wet tissue weight, depending on tissue type. For hematopoietic cancers such as acute myeloid leukemia (AML), the sample requirement is in excess of 10 million (1E7) peripheral blood mononuclear cells (PBMCs). Throughout the course of a prospective study, this requirement will certainly exceed what is obtainable from many of the individual patients/timepoints. For this reason, we were interested in examining the impact of differential peptide loading across multiplex channels on proteomic data quality. Methods: To achieve this, we tested a range of channel loading amounts (20, 40, 100, 200, and 400 µg of tryptic peptides, or approximately the material obtainable from 5E5, 1E6, 2.5E6, 5E6, and 1E7 AML patient cells) to assess proteome coverage, quantification reproducibility and accuracy in experiments utilizing isobaric tandem mass tag (TMT) labeling. As expected, we found that fewer missing values are observed in TMT channels with higher peptide loading amounts compared to those with lower loading. Moreover, channels with lower loading amounts have greater quantitative variability than channels with higher loading amounts. Statistical analysis of the differences in means among the five loading groups showed that the 20 µg loading group was significantly different from the 400 µg loading group. However, no significant differences were detected among the 40, 100, 200 and 400 µg loading groups. Conclusions: These assessment data demonstrate the practical limits of loading differential quantities of peptides across channels in TMT multiplexes, and provide a basis for designing the optimal clinical proteomics study when specimen quantities are limited.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Toward Multiscale, Multimaterial 3D Printing

Biological materials and organisms possess the fundamental ability to self-organize, through which different components are assembled from the molecular level up to hierarchical structures with superior mechanical properties and multifunctionalities. These complex composites inspire material scientists to design new engineered materials by integrating multiple ingredients and structures over a wide range. Additive manufacturing, also known as 3D printing, has advantages with respect to fabricating multiscale and multi-material structures. The need for multifunctional materials is driving 3D printing techniques toward arbitrary 3D architectures with the next level of complexity. In this paper, the aim is to highlight key features of those 3D printing techniques that can produce either multiscale or multimaterial structures, including innovations in printing methods, materials processing approaches, and hardware improvements. Several issues and challenges related to current methods are discussed. Ultimately, the authors also provide their perspective on how to realize the combination of multiscale and multimaterial capabilities in 3D printing processes and future directions based on emerging research.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Manipulating the Assembly and Architecture of Fibrillar Silk

Silk is a unique and exceptionally strong biological material. However, no synthetic method has yet come close to replicating the properties of natural silk. This shortfall is attributed to an insufficient understanding of both silk nanofibril structure and the mechanism of formation. Here in situ atomic force microscopy (AFM) and photo-induced force microscopy (PiFM) is utilized to investigate the formation process and define the basic structural paradigm of individual silk nanofibrils. By visualizing the multistage process of silk nanofibril formation, the importance of conformational transformations along the assembly pathway is revealed. Unfolded silk structures initially accumulate into amorphous clusters, which then evolve into crystal nuclei via conformational transformation into β-crystallites. Nanofibril elongation then occurs through the attachment of silk molecules at a single end of the nanofibril tip; this is facilitated through the formation of a new amorphous cluster that then repeats the aforementioned conformational transformation. However, enzymatic digestion of the amorphous regions leads to direct, rapid elongation of β-crystalline fibers. These findings imply that the energy landscape is characterized by shallow minima associated with intermediate states, which can be eliminated by introducing β-crystallites, and motivate research into the directed modification of the silk assembly pathway to select for features beneficial to specific applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Multispectral Quantitative Phase Imaging Using a Diffractive Optical Network

As a label‐free imaging technique, quantitative phase imaging (QPI) provides optical path length information of transparent specimens for various applications in biology, materials science, and engineering. Multispectral QPI measures quantitative phase information across multiple spectral bands, permitting the examination of wavelength‐specific phase and dispersion characteristics of samples. Herein, the design of a diffractive processor is presented that can all‐optically perform multispectral quantitative phase imaging of transparent phase‐only objects within a snapshot. The design utilizes spatially engineered diffractive layers, optimized through deep learning, to encode the phase profile of the input object at a predetermined set of wavelengths into spatial intensity variations at the output plane, allowing multispectral QPI using a monochrome focal plane array. Through numerical simulations, diffractive multispectral processors are demonstrated to simultaneously perform quantitative phase imaging at 9 and 16 target spectral bands in the visible spectrum. The generalization of these diffractive processor designs is validated through numerical tests on unseen objects, including thin Pap smear images. Due to its all‐optical processing capability using passive dielectric diffractive materials, this diffractive multispectral QPI processor offers a compact and power‐efficient solution for high‐throughput quantitative phase microscopy and spectroscopy.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Peptide-assisted supramolecular polymerization of the anionic porphyrin meso-tetra(4-sulfonatophenyl)porphine

Electronics made from biological materials are desirable for use in medical devices, biosensors, and soft robotics because they have properties inaccessible to current inorganic technologies. Here, a series of cationic peptides were developed to self-assemble with the anionic porphyrin meso-tetra(4-sulfonatophenyl)porphine (TPPS4) into supramolecular light-harvesting wires known as J-aggregates were developed. In addition to quantifying the binding events between each peptide and TPPS 4 , we found co-incubation with mixed peptides allowed TPPS 4 to bridge two different peptides at their terminal porphyrin-binding regions. The J-aggregates formed on macroscopic scale in near quantitative yield within similar to 3 h and readily interconverted with the soluble monomers upon cycling the pH; to our knowledge, this is the first report of a peptide-porphyrin system with such properties. This work has practical and conceptual relevance to the development of new bioelectronic materials.

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

Fed-batch production of deuterated protein in Escherichia coli for neutron scattering experimentation

Neutron scattering is a powerful technique for determining the structure and dynamics of biological materials in a variety of environmental conditions. A distinguishing property of the neutron is its sensitivity to detecting hydrogen and distinguishing it from its isotope deuterium. This enables unique types of experiments that take advantage of this differential sensitivity called isotopic contrast variation. Using this approach, the chemistry of the system is not changed, but the visibility of individual sample components can be tuned by varying the deuterium content of the system under investigation. Deuterated proteins are commonly produced in bacterial systems that are adapted to growth in D2O minimal media. To maximize the yield of deuterium-labeled protein and efficiently utilize D2O and occasionally the deuterated substrate, fed-batch processes are routinely used to maximize biomass production without compromising cell viability. A step-by-step procedure will be described along with a case study of the production of deuterated green fluorescent protein. Limitations of the process will also be discussed.

Weiss, Kevin L.↗
DOE OSTI2024

Phonons reveal coupled cholesterol-lipid dynamics in ternary membranes

Experimental studies of collective dynamics in lipid bilayers have been challenging due to the energy resolution required to observe these low-energy phonon-like modes. However, inelastic X-ray scattering (IXS) measurements — a technique for probing vibrations in soft and biological materials — are now possible with sub-meV resolution, permitting direct observation of low energy, phonon-like modes in lipid membranes. Here, in this study, IXS measurements with sub-meV energy resolution reveal a low-energy optic-like phonon mode at roughly 3 meV in the liquid-ordered (L o ) and liquid-disordered (L d ) phases of a ternary lipid mixture. This mode is only observed experimentally at momentum transfers greater than 5 nm -1 in the L o system. A similar gapped mode is also observed in all-atom molecular dynamics (MD) simulations of the same mixture, indicating that the simulations accurately represnt the fast, collective dynamics in the L o phase. It’s optical nature and the Q range of the gap together suggest that the observed mode is due to the coupled motion of cholesterol-lipid pairs, separated by several hydrocarbon chains within the membrane plane. Analysis of the simulations provide molecular insight into the origin of the mode in transient, nanoscale substructures of hexagonally packed hydrocarbon chains. This nanoscale hexagonal packing was previously reported based on molecular dynamics simulations and later by NMR measurements. Here, however, the integration of IXS and MD simulations identifies a new signature of the L o substructure in the collective lipid dynamics, thanks to the recent confluence of IXS sensitivity and MD simulation capabilities.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Programmable hydrogels by combining persistent and transient dynamic bonds

Out-of-equilibrium chemistry is currently being applied to polymer systems to mimic the autonomous behavior of biological materials. In this study, hydrogels with self-healing properties were developed that combine persistent crosslinks from dynamic metal-ligand coordination with transient crosslinks from dynamic anhydride bonds. Polymers containing terpyridine ligands and carboxylic acid groups were synthesized and crosslinked with divalent metal ions (Fe 2+ , Ni 2+ , Co 2+ , Zn 2+ , Cu 2+ ). The coordination bonds from terpyridine–metal coordination impart persistent stability, while transient anhydrides formed on treatment with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) temporarily increase crosslink density. Distinct behaviors are observed depending on the choice of metal, with Ni 2+ forming robust, stable networks; Zn 2+ creating moderately dynamic gels; and Cu 2+ yielding highly dynamic, soft materials. Treatment with EDC increased storage moduli significantly, with transient effects lasting up to 280 min depending on the metal ion. Self-healing experiments demonstrated independent contributions from metal coordination and transient anhydrides, enabling recovery of stress and strain under varying conditions. Additionally, complex and reversible 2D stiffness patterns were generated by spatially controlled EDC treatment of Zn 2+ and Cu 2+ hydrogel films, demonstrating programmability and reusability.

Rajawasam, Chamoni W. H. [Miami University, Oxford↗
DOE OSTI2023

Computational tools for the simulation and analysis of spin-polarized EPR spectra

The EPR spectra of paramagnetic species induced by photoexcitation typically exhibit enhanced absorptive and emissive features resulting from sublevel populations that differ from thermal equilibrium. The populations and the resulting spin polarization of the spectra are dictated by the selectivity of the photophysical process generating the observed state. Simulation of the spin-polarized EPR spectra is crucial in the characterization of both the dynamics of formation of the photoexcited state as well as its electronic and structural properties. EasySpin, the simulation toolbox for EPR spectroscopy, now includes extended support for the simulation of the EPR spectra of spin-polarized states of arbitrary spin multiplicity and formed by a variety of different mechanisms, including photoexcited triplet states populated by intersystem crossing, charge recombination or spin polarization transfer, spin-correlated radical pairs created by photoinduced electron transfer, triplet pairs formed by singlet fission and multiplet states arising from photoexcitation in systems containing chromophores and stable radicals. In this paper, we highlight EasySpin’s capabilities for the simulation of spin-polarized EPR spectra on the basis of illustrative examples from the literature in a variety of fields ranging across chemistry, biology, material science and quantum information science.

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

Ka-band linearizer for the Ultra-Compact X-ray free-electron laser at UCLA

There is a strong demand for accelerating structures able to achieve higher gradients and more compact dimensions for the next generation of linear accelerators for research, industrial and medical applications. Notably innovative technologies will permit compact and affordable advanced accelerators as the linear collider and X-ray free-electron lasers (XFELs) with accelerating gradients over twice the value achieved with current technologies. In particular XFELs are able to produce coherent X-ray pulses with peak brightness 10 orders of magnitude greater than preceding approaches, which has revolutionized numerous research fields through imaging of the nanoscopic world at the time and length scale of atom-based systems, that is of femtosecond and Angstrom. There is a strong interest for combining these two fields, to form a proper tool with the goal of producing a very compact XFEL in order to investigate multi-disciplinary topics in chemistry, biology, materials science, medicine and physics. In the framework of the Ultra-Compact XFEL project under study at the University of California, Los Angeles, a high gradient radio-frequency accelerating structure for the longitudinal phase-space linearization with an integrated voltage of at least 15 MV working on 6th harmonic of the main Linac frequency is required. We here present the electromagnetic design of a cryogenic normal-conducting 8 cm long Ka-band standing-wave linearizer working on π mode with a target accelerating gradient beyond 100 MV/m. The studies have been performed analytically and numerically to investigate the beam dynamics and electromagnetic issues.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Scanning Electrochemical Microscopy: An Evolving Toolbox for Revealing the Chemistry within Electrochemical Processes

The parallel development of ultramicroelectrodes (UMEs) and groundbreaking scanning probe microscopy techniques in the late 1980s led to the development of the scanning electrochemical microscope. Scanning electrochemical microscopy (SECM) was born from the idea of using a tiny electrode to measure the local electrochemical behavior at operating electrodes. From its foundations, the technique displayed an inherent versatility in measuring sample properties beyond topography. It allowed experimenters to measure and map chemical reactions occurring at diverse interfaces, from inspecting the reversibility of redox mediators at metal electrodes, to detecting the hallmarks of cellular respiration on living plant leaves. Related but distinct electrochemical scanning probe techniques, such as electrochemical atomic force microscopy (EC-AFM), scanning ion conductance microscopy (SICM), and scanning electrochemical cell microscopy (SECCM) have developed in parallel. These techniques have demonstrated exquisite spatial resolution down to the nanoscale regime. However, it is the proposition of this review that SECM remains unmatched at revealing the chemical aspects of electrochemistry. Furthermore, it is our intention to review and demonstrate that the versatile architecture of SECM continues to evolve and address fundamental and emerging challenges in the fields of energy storage and conversion, chemical biology, materials science, and environmental chemistry, among others.

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

Turning Outsiders into Insiders: A Call for Papers to Expand the Reach of National Laboratories’ Safety Successes, Challenges, Research, and Approaches

The most complex challenges facing the world today comprise the work of [Department of Energy’s] (DOE’s) 17 National Laboratories: [...] From furthering U.S. energy independence and leadership in clean technologies; to promoting innovation that advances U.S. economic competitiveness; to conducting research of the highest caliber in the physical, chemical, biological, materials, computational, and information sciences to advance understanding of the world around us-the Laboratories’ purview is expansive and further their contributions are indispensable.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Bioaerosol Emission Characteristics from Laboratory Burns

Combustion processes can aerosolize and transport particles both from nonbiological and biological origin, with the latter termed bioaerosol particle (BAP). Previous work has shown an increase in the level of BAP in smoke plumes. The mechanism of their emission, whether from combustion of biological material or coemission with dust and soil from fire-driven winds, has yet to be examined. Here, we carried out a series of controlled combustion experiments to understand the role of vegetation type and combustion conditions in the direct emission of BAP. The fuels we used included broadleaf, evergreen, and grass. We measured the emitted fluorescent BAP using a wideband integrated bioaerosol system (WIBS), and we measured the viability of filter-collected BAP using flow cytometry. Our measurements showed that the size and absolute concentration of the fluorescent BAP, and the viability of the BAP emitted during combustion, depend on the combustion conditions. In addition, the type of fuel impacted the type of emitted fluorescent BAP fraction relative to the total concentration of the emitted aerosol.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Role of the Mineral in the Self-Healing of Cracks in Human Enamel

Human enamel is an incredibly resilient biological material, withstanding repeated daily stresses for decades. The mechanisms behind this resilience remain an open question, with recent studies demonstrating a crack-deflection mechanism contributing to enamel toughness and other studies detailing the roles of the organic matrix and remineralization. Here, we focus on the mineral and hypothesize that self-healing of cracks in enamel nanocrystals may be an additional mechanism acting to prevent catastrophic failure. To test this hypothesis, we used a molecular dynamics (MD) approach to compare the fracture behavior of hydroxyapatite (HAP) and calcite, the main minerals in human enamel and sea urchin teeth, respectively. In this work, we find that cracks heal under pressures typical of mastication by fusion of crystals in HAP but not in calcite, which is consistent with the resilience of HAP enamel that calcite teeth lack. Scanning transmission electron microscopy (STEM) images of structurally intact ("sound") human enamel show dashed-line nanocracks that resemble and therefore might be the cracks healed by fusion of crystals produced in silico . The fast, self-healing mechanism shown here is common in soft materials and ceramics but has not been observed in single crystalline materials at room temperature. The crack self-healing in sound enamel nanocrystals, therefore, is unique in the human body and unique in materials science, with potential applications in designing bioinspired materials.

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

Structural Characterization of the Platinum Nanoparticle Hydrogen-Evolving Catalyst Assembled on Photosystem I by Light-Driven Chemistry

Directed assembly of abiotic catalysts onto biological redox protein frameworks is of interest as an approach for the synthesis of biohybrid catalysts that combine features of both synthetic and biological materials. In this report, we provide a multiscale characterization of the platinum nanoparticle (NP) hydrogen-evolving catalysts that are assembled by light-driven reductive precipitation of platinum from an aqueous salt solution onto the photosystem I protein (PSI), isolated from cyanobacteria as trimeric PSI. The resulting PSI-NP assemblies were analyzed using a combination of X-ray energy-dispersive spectroscopy (XEDS), high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), small-angle X-ray scattering (SAXS), and high-energy X-ray scattering with atomic pair distribution function (PDF) analyses. The results show that the PSI-supported NPs are approximately 1.8 nm diameter disk-shaped particles that assemble at discrete sites with 145 Å separation. This separation is too large to be consistent with NP nucleation and growth at a site adjacent to the F B cofactor site. Instead, we suggest a mechanism for NP growth at hydrophobic sites on the PSI stromal surface. The NPs photoreductively assembled on the PSI stromal surface are found to be analogous to the nanostructures produced by successive cycles of atomic layer deposition (ALD) of platinum onto 40 nm porous anodic alumina oxide supports, although the mechanisms for nucleation appear to differ. In conclusion, this work establishes a foundation for the investigation of the reductive assembly of abiotic metal catalysts at sites connected to photochemically reducing equivalent production in PSI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗