What Determines the fcc-bcc Structural Transformation in Shock Compressed Noble Metals?
Abstract not provided
Sharma, Surinder M.↗
SEARCH · Engineering Papers
Results for “Structure determination”
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CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM
Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.
47 OTHER INSTRUMENTATION↗
Determination of Molecular Structure and Dynamics of Molten Salts by Advanced Neutron and X-ray Scattering Measurements and Computer Modeling
The design and development of fully functional Molten-Salt Reactors (MSR) require detailed knowledge of the molten salt properties in order to understand and predict the salt’s behavior. Fundamental properties of interest include molecular structure, speciation, and dynamics (such as diffusion coefficients) of salt components and dissolved corrosion and fission products. Computer modeling is necessary to predict changes in physical and chemical properties due to irradiation, burning of dissolved fuel, and corrosion. The modeling requires experimental data, and advanced neutron and x-ray scattering and spectroscopy provide the most reliable and direct determination of the structure (Pair-Distribution Functions, PDF), and dynamics of ions in the melt. This project dealt with both fluoride and chloride salts. The PDFs have been measured by a combination of neutron and x-ray diffraction. We utilized the techniques of isotope substitutions, a very powerful tool available for neutron-scattering, to extract the details of the liquid structure. Although similar measurements have been done before, modern advanced neutron and x-ray-scattering techniques allow collecting the data at much higher resolution and in a wider range of temperatures. Importantly, we were among the first to study fluoride salts by neutron scattering. The importance of impurities and their effects on salt properties have become apparent recently and so new methods of salt purification were developed. We took advantage of these developments to produce reliable data, which have been used for computer simulations of both clean salts and those with added fission and corrosion products most relevant for MSRs. Ab initio molecular dynamics simulations have been performed to understand the multi-component liquid solution, in particular solubility of impurities and thermodynamic interactions in relation to the ionic-cluster structure of the fluid. We applied machine learning to regress from the simulation and experimental data in order to develop a fast-acting model that can handle molten salt with an arbitrary (≥ 10) number of chemical elements and be able to predict chemical potential as a function of composition and temperature. This project resulted in a number of experimental and computer-simulation publications, a patent application, and numerous conference presentations (American Physical Society, American Chemical Society, and The Electrochemical Society among others). Multiple students and postdocs participated and collaborated on aspects of this project. This project seeded new collaborations between MIT and other institutions, such as the University of Massachusetts Lowell, the University of Illinois Urbana-Champaign, the University of California Berkeley, and Oak Ridge and Los Alamos National Labs. As such, this project has had a broad and lasting impact beyond its original scientific scope.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Improved Predictive Tools for Structural Properties of Metal–Organic Frameworks
The accurate determination of structural parameters is necessary to understand the electronic and magnetic properties of metal–organic frameworks (MOFs) and is a first step toward accurate calculations of electronic structure and function for separations and catalysis. Theoretical structural determination of metal-organic frameworks is particularly challenging because they involve ionic, covalent, and noncovalent interactions, which must be treated in a balanced fashion. Here, we apply a diverse group of local exchange-correlation functionals (PBE, PBEsol, PBE-D2, PBE-D3, vdW-DF2, SOGGA, MN15-L, revM06-L, SCAN, and revTPSS) to a broad test set of MOFs to seek the most accurate functionals to study various structural aspects of porous solids, in particular to study lattice constants, unit cell volume, two types of pore size characteristics, bond lengths, bond angles, and torsional angles). The recently developed meta functionals revM06-L and SCAN, without adding any molecular mechanics terms, are able to predict more accurate structures than previously recommended functionals, both those without molecular mechanics terms (PBE, PBEsol, vdW-DF2, and revTPSS) and those with them (PBE-D2 and PBE-D3). To provide a broader test, these two functionals are also tested for lattice constants and band gaps of unary, binary, and ternary semiconductors.
36 MATERIALS SCIENCE↗
Atomic-Level Structure of Mesoporous Hexagonal Boron Nitride Determined by High-Resolution Solid-State Multinuclear Magnetic Resonance Spectroscopy and Density Functional Theory Calculations
Mesoporous hexagonal boron nitride (p-BN) has received significant attention over the last decade as a promising candidate for water cleaning/pollutant removal and hydrogen storage applications. In this work, high-resolution solid-state NMR spectroscopy and plane-wave density-functional theory (DFT) calculations are used to obtain an atomic-level description of p-BN. 1 H– 15 N or 1 H– 14 N heteronuclear (HETCOR) correlation experiments recorded with either conventional NMR at room temperature or dynamic nuclear polarization surface-enhanced spectroscopy (DNP-SENS) at ca. 100 K reveal NB 2 H, NBH 2 , NBH 3 + species residing on the edges of BN sheets. Ultra-high field 35.2 T 11 B NMR spectroscopy was used to resolve 11 B NMR signals from BN 3 , BN 2 O x (OH) 1–x (x = 0–1), BNO x (OH) 2–x (x = 0–2), BO x (OH) 3–x (x = 0–3), and BO x (OH) 4–x – (x = 0–4). Importantly, 2D 11 B dipolar double-quantum–single-quantum homonuclear correlation spectra reveal that many pore/defect sites are composed of boron oxide/hydroxide clusters connected to the BN framework through BN 2 O units. 1D and 2D 11 B{ 15 N} HETCOR NMR experiments, in addition to plane-wave DFT calculations of nine different structural models, further confirm the assignment of all NMR signals. The detailed structure determination of the pore and edge/defect sites within p-BN should further enable the rational design and development of next-generation p-BN-based materials. In addition, the techniques outlined here should be applicable to determine structure within other porous and/or boron-based materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Grain incompatibility determines the local structure of amorphous grain boundary complexions
Amorphous grain boundary complexions lack long-range crystalline order but are not featureless, as distinct gradients in structural short-range order have been reported through their thickness. In this work, we test the hypothesis that the distribution of short-range order is determined by the confining crystals using atomistic simulations of both Cu-Zr bicrystals and a random polycrystal. Voronoi polyhedra with structures similar to that of perfect face-centered cubic serve as signatures of high structural order and are only found at the amorphous-crystalline transition regions. The density of the ordered structural motifs within a specific amorphous-crystalline transition region is found to not be directly determined by the orientation and symmetry of the grain which touches it, but rather by the incompatibility between the two confining grains. Further, ordered polyhedra density is found to be inversely related to grain incompatibility, meaning that large incompatibilities between the confining crystals lead to less order in the amorphous-crystalline transition region. The finding that the entire grain-film-grain system must be considered to understand local structure unequivocally demonstrates that amorphous complexions are not simply a collection of independent phases which happen to nucleate at a grain boundary. Rather, an amorphous grain boundary complexion is a single entity that finds a local equilibrium configuration.
36 MATERIALS SCIENCE↗
Structure and functional determinants of Rad6–Bre1 subunits in the histone H2B ubiquitin-conjugating complex
The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 ‘backside’. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6–Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6–Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6–Bre1 interaction through a novel interface that is important for their biochemical and biological responses.
59 BASIC BIOLOGICAL SCIENCES↗
Electron Microscopy Approaches to Unraveling the Structure of Amorphous Materials
Determining atomic structures in crystalline materials—where atoms are arranged in rigid, periodic lattices—has been highly successful using probes such as electrons, X-rays, and neutrons. In contrast, amorphous materials, despite their ubiquity and technological importance, remain far more challenging to characterize with comparable accuracy and precision. This review highlights existing, emerging, and potential (scanning) transmission electron microscopy ((S)TEM) techniques for probing short- and medium-range order in amorphous materials. Approaches ranging from high-resolution (S)TEM imaging and selected electron diffraction pattern to four-dimensional STEM (4D-STEM) based pair distribution function, fluctuation electron microscopy, tomography, ptychography, and spectroscopic methods are discussed, emphasizing their ability to provide complementary insights across multiple length scales—from sub-angstrom local environments to nanometer-scale correlations. Here, we further explore the promise of multimodal and correlative strategies, as well as the growing role of machine learning and physics-informed AI in enabling real-time, quantitative interpretation of complex structural signatures. Together, these advances point toward a future where electron microscopy not only reveals the hidden order in amorphous systems but also establishes robust structure–property relationships, paving the way for materials innovation in disordered matter.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Stoichiometry of the Core Determines the Electronic Structure of Core-Shell III-V/II-VI Nanoparticles.
Recently, III-V quantum dots (QDs) emerged as an environmentally friendly alternative to CdSe; however, they exhibit broader emission spectra and inferior photoluminescence quantum yield. Here, we report a computational study of the optoelectronic properties of InxPz and InxGayPz QDs interfaced with zinc chalcogenide shells. Using density functional theory, we show that fine-tuning the composition of the core is critical to achieving narrow emission lines. We show that core-shell nanoparticles, where the core has the same diameter but different stoichiometries, may absorb and emit at different wavelengths, leading to broad absorption and emission spectra. The value of the fundamental gap of the core-shell particles depends on the ratio between the number of group III and P atoms in the core and is maximized for the 1:1 composition. We also show that the interplay between quantum confinement and strain determines the difference in the electronic properties of III-V QDs interfaced with ZnS or ZnSe shells.
Rusishvili, Mariami↗
Characterization of Interactions between CTX-M-15 and Clavulanic Acid, Desfuroylceftiofur, Ceftiofur, Ampicillin, and Nitrocefin
Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamases (ESBLs) are commonly associated with Gram-negative, hospital-acquired infections worldwide. Several beta-lactamase inhibitors, such as clavulanate, are used to inhibit the activity of these enzymes. To understand the mechanism of CTX-M-15 activity, we have determined the crystal structures of CTX-M-15 in complex with two specific classes of beta-lactam compounds, desfuroylceftiofur (DFC) and ampicillin, and an inhibitor, clavulanic acid. The crystal structures revealed that Ser70 and five other residues (Lys73, Tyr105, Glu166, Ser130, and Ser237) participate in catalysis and binding of those compounds. Based on analysis of steady-state kinetics, thermodynamic data, and molecular docking to both wild-type and S70A mutant structures, we determined that CTX-M-15 has a similar affinity for all beta-lactam compounds (ceftiofur, nitrocefin, DFC, and ampicillin), but with lower affinity for clavulanic acid. A catalytic mechanism for tested β-lactams and two-step inhibition mechanism of clavulanic acid were proposed. CTX-M-15 showed a higher activity toward DFC and nitrocefin, but significantly lower activity toward ampicillin and ceftiofur. The interaction between CTX-M-15 and both ampicillin and ceftiofur displayed a higher entropic but lower enthalpic effect, compared with DFC and nitrocefin. DFC, a metabolite of ceftiofur, displayed lower entropy and higher enthalpy than ceftiofur. This finding suggests that compounds containing amine moiety (e.g., ampicillin) and the furfural moiety (e.g., ceftiofur) could hinder the hydrolytic activity of CTX-M-15.
59 BASIC BIOLOGICAL SCIENCES↗
Determining the Electronic Structure and Thermoelectric Properties of MoS 2 /MoSe 2 Type‐I Heterojunction by DFT and the Landauer Approach
Abstract The electronic structure and thermoelectric properties of MoX 2 (X = S, Se) Van der Waals heterojunctions are reported, with the intention of motivating the design of electronic devices using such materials. Calculations indicate the proposed heterojunctions are thermodynamically stable and present a band gap reduction from 1.8 eV to 0.8 eV. The latter effect is highly related to interactions between metallic d‐character orbitals and chalcogen p‐character orbitals. The theoretical approach allows to predict a transition from semiconducting to semi‐metallic behavior. The band alignment indicates a type‐I heterojunction and band offsets of 0.2 eV. Transport properties show clear n‐type nature and a high Seebeck coefficient at 300 K, along with conductivity values (σ/τ) in the order of 10 20 . Lastly, using the Landauer approach and ballistic transport, the proposed heterojunctions can be modeled as a channel material for a typical one‐gate transistor configuration predicting subthreshold values of ≈60 mV dec −1 and field–effect mobilities of ≈160 cm −2 V −1 s −1 .
López‐Galán, Oscar A.↗
Determination of the Structures of Lignin Subunits and Nanoparticles in Solution by Small‐Angle Neutron Scattering: Towards Improving Lignin Valorization
Abstract Lignin nanoparticles (LNPs) are usually produced from lignin solution through supersaturation. The structure of the lignin in solution is still poorly understood due to structural variability of isolated lignins. Here, lignins were extracted from different plants to establish a general pattern of their structure in several lignin solvents. Lignin molecules (lignin subunits) and larger aggregates were observed in dimethyl sulfoxide (DMSO), ethylene glycol (EG) and 0.1 N NaOD solutions by small‐angle neutron scattering (SANS). It was proposed that the aggregates were composed of lignin subunits with a higher molecular weight and a higher ratio of the aliphatic to phenolic hydroxyl groups. The size, shape, and compactness are important factors that affect the uses of the LNPs, which were obtained from the SANS data for the first time. A discrepancy in the radius between SANS and DLS was discovered, pointing to a large hydration shell around the LNPs in aqueous solutions. The cytotoxicity of the corncob lignin, kraft lignin, and their LNPs were measured and compared.
Zhang, Xin↗
Determining the Electronic Structure of Paramagnetic Intermediates in membrane proteins: A high-resolution 2D 1H hyperfine sublevel correlation study of the redox-active tyrosines of photosystem II
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Determination of the structure of lithium niobosilicate glasses by molecular dynamics simulation with a new Nb-O potential
A partial charge empirical potential for the Nb-O pair has been developed based on existing parameters of other pairs in a Teter potential to enable molecular dynamics simulations of both lithium niobate crystal and lithium niobosilicate glasses. The developed potential is capable of describing structural features of lithium niobosilicate glasses in a wide composition range, including niobium coordination number and bond length, density, bond angle distribution, polyhedral distribution and fraction of bridging oxygen. Furthermore, the results obtained using this new potential show good agreement with experimental data of density and structure from Raman spectroscopy of lithium niobosilicate glasses and X-ray absorption spectroscopy near Nb K-edge.
36 MATERIALS SCIENCE↗
Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer
Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP + -dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.
60 APPLIED LIFE SCIENCES↗
Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to th
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Korasick, David A.↗
Potential pathogenicity determinants identified from structural proteomics of SARS-CoV and SARS-CoV-2
Despite SARS-CoV and SARS-CoV-2 being equipped with highly similar protein arsenals, the corresponding zoonoses have spread among humans at extremely different rates. The specific characteristics of these viruses that led to such distinct outcomes remain unclear. Here, we apply proteome-wide comparative structural analysis aiming to identify the unique molecular elements in the SARS-CoV-2 proteome that may explain the differing consequences. By combining protein modeling and molecular dynamics simulations, we suggest non-conservative substitutions in functional regions of the spike glycoprotein (S), nsp1, and nsp3 that are contributing to differences in virulence. Particularly, we explain why the substitutions at the receptor-binding domain of S affect the structure-dynamics behavior in complexes with putative host receptors. Conservation of functional protein regions within the two taxa is also noteworthy. We suggest that the highly conserved main protease, nsp5, of SARS-CoV and SARS-CoV-2 is part of their mechanism of circumventing the host interferon antiviral response. Overall, most substitutions occur on the protein surfaces and may be modulating their antigenic properties and interactions with other macromolecules. Our results imply that the striking difference in the pervasiveness of SARS-CoV-2 and SARS-CoV among humans seems to significantly derive from molecular features that modulate the efficiency of viral particles in entering the host cells and blocking the host immune response.
59 BASIC BIOLOGICAL SCIENCES↗
Determination of the structure of lithium niobosilicate glasses by molecular dynamics simulation with a new Nb-O potential
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99 GENERAL AND MISCELLANEOUS↗