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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Tailoring the Interfacial Interactions of Porous Polymer Membranes to Accelerate Atomic Layer Deposition: The Latent Path to Antifouling Membranes

Atomic layer deposition (ALD) is a powerful strategy to engineer hybrid organic-inorganic membranes with emergent functionalities. The combination of atomic-level thickness control, a wide materials palette, and unprecedented conformality allows the physiochemical properties (e.g., hydrophilicity) of mesoporous polymer membranes to be precisely tuned. The nucleation of ALD material growth on polymer surfaces relies on Lewis acid-base interactions and remains an overlooked motif with tremendous potential to accelerate ALD nucleation and growth. Strategies to enhance these interactions could enable desirable properties such as antifouling behavior to be imparted on inert polymer surfaces that lack the necessary functional groups for ALD nucleation. Here, in this study, we demonstrate that the reactivity of polyacrylonitrile (PAN) membranes toward ALD metal oxide (MO) precursors with Lewis acid characteristics is enhanced by introducing strong Lewis base functional groups (amidoxime: Am) on the PAN backbone (Am-PAN). The resulting Lewis acid-base interactions accelerate the MO nucleation in Am-PAN and reduce the number of deposition cycles required to achieve hydrophilicity compared with the untreated PAN membrane. Unveiling the reaction mechanism, in situ Fourier transform infrared (FTIR) spectroscopy measurements established enhanced interaction dynamics between the ALD MO precursors and the Am-PAN membrane, unlike the PAN membrane. Spectroscopic ellipsometry and thermogravimetric analysis measurements revealed higher MO loadings in Am-PAN membranes compared to PAN membranes for the same number of ALD cycles. We found that strong Lewis acid-base interactions accelerated the ALD for a range of materials including Al 2 O 3 , TiO 2 , SnO 2 , and ZnO. More broadly, our work demonstrates that tailoring metal-precursor-polymer interactions is a powerful strategy to accelerate and modulate the ALD. We used this design strategy to fabricate Al 2 O 3 -Am-PAN hybrid membranes that showed 2-fold higher antifouling capability compared to pristine PAN membranes prepared with an equivalent number of Al 2 O 3 ALD cycles. Our approach expands the scope of design options for fouling-resistant porous hybrid inorganic-organic membranes and may ultimately reduce the operational costs of water treatment.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Bioimaging Science Program: 2022 Principal Investigator Meetings Proceedings

The mission of the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) program’s Bioimaging Science Program (BSP) is to understand the translation of genomic information into the mechanisms that power living cells, communities of cells, and whole organisms. The goal of BSP is to develop new imaging and measurement technologies to visualize the spatial and temporal relationships of key metabolic processes governing phenotypic expression in plants and microbes. The extended goal of dynamic imaging is to functionally connect cellular components and interdependent organisms. Information about the time and place of chemical reactions in situ can identify causal relationships between biological activators and downstream effectors. BSP held its annual PI meeting virtually February 28–March 1. Contributing investigators are convened to review progress and current state-of-the-art bioimaging research. Holding the 2022 BSP meeting as part of the broader Genomic Science Program (GSP) PI meeting allowed researchers to interact with the extended GSP community. This convergence provided a platform for networking and exchange of ideas with experts in other technologies and in target BSP application areas, helping to forge new multidisciplinary collaborations among investigators from the sister programmatic areas within BER’s Biological Systems Science Division. An important highlight of the BSP meeting was the keynote presentation by Nobel Laureate Dr. Joachim Frank on Time-Resolved Macromolecular Imaging using Cryo-EM. He discussed microfluidic mixing and fast freezing to capture nonequilibrium intermediate states during molecular binding and conformational changes. The action of molecular machines can be captured at nanometer resolution and millisecond discrimination. BSP PIs made presentations describing their research focus and progress in plenary sessions on bioimaging science and on quantum-enabled bioimaging science research projects. BSP research at universities and DOE laboratories is presented in this report. A final discussion of the BSP was organized by meeting plenary session chairs, who prepared the following Executive Summary of current BSP research, research challenges, future opportunities, and potential ideas for expanding the BSP’s impact and interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dynamic Mixing Behaviors of Ionically Tethered Polymer Canopy of Nanoscale Hybrid Materials in Fluids of Varying Physical and Chemical Properties

An emerging area of sustainable energy and environmental research is focused on the development of novel electrolytes that can increase the solubility of target species and improve subsequent reaction performance. Electrolytes with chemical and structural tunability have allowed for significant advancements in flow batteries and CO 2 conversion integrated with CO 2 capture. Liquid-like nanoparticle organic hybrid materials (NOHMs) are nanoscale fluids that are composed of inorganic nanocores and an ionically tethered polymeric canopy. NOHMs have been shown to exhibit enhanced conductivity making them promising for electrolyte applications, though they are often challenged by high viscosity in the neat state. In this study, a series of binary mixtures of NOHM-I-HPE with five different secondary fluids, water, chloroform, toluene, acetonitrile, and ethyl acetate, were prepared to reduce the fluid viscosity and investigate the effects of secondary fluid properties (e.g., hydrogen bonding ability, polarity, and molar volume) on their transport behaviors, including viscosity and diffusivity. We report our results revealed that the molecular ratio of secondary fluid to the ether groups of Jeffamine M2070 ($λ_{\text{SF}}$) was able to describe the effect that secondary fluid has on transport properties. Our findings also suggest that in solution, the Jeffamine M2070 molecules exist in different nanoscale environments, where some are more strongly associated with the nanoparticle surface than others, and the conformation of the polymer canopy was dependent on the secondary fluid. This understanding of the polymer conformation in NOHMs can allow for the better design of an electrolyte capable of capturing and releasing small gaseous or ionic species.

25 ENERGY STORAGE↗
DOE OSTI2022

Characterization of the Interfacial Orientation and Molecular Conformation in a Glass-Forming Organic Semiconductor

The ability to control structure in molecular glasses has enabled them to play a key role in modern technology; in particular, they are ubiquitous in organic light-emitting diodes. While the interplay between bulk structure and optoelectronic properties has been extensively investigated, few studies have examined molecular orientation near buried interfaces despite its critical role in emergent functionality. Direct, quantitative measurements of buried molecular orientation are inherently challenging, and many methods are insensitive to orientation in amorphous soft matter or lack the necessary spatial resolution. To overcome these challenges, we use polarized resonant soft X-ray reflectivity (pRSoXR) to measure nanometer-resolved, molecular orientation depth profiles of vapor-deposited thin films of an organic semiconductor Tris(4-carbazoyl-9-ylphenyl)amine (TCTA). Our depth profiling approach characterizes the vertical distribution of molecular orientation and reveals that molecules near the inorganic substrate and free surface have a different, nearly isotropic orientation compared to those of the anisotropic bulk. Comparison of pRSoXR results with near-edge X-ray absorption fine structure spectroscopy and optical spectroscopies reveals that TCTA molecules away from the interfaces are predominantly planar, which may contribute to their attractive charge transport qualities. Buried interfaces are further investigated in a TCTA bilayer (each layer deposited under separate conditions resulting in different orientations) in which we find a narrow interface between orientationally distinct layers extending across ≈1 nm. Coupling this result with molecular dynamics simulations provides additional insight into the formation of interfacial structure. This study characterizes the local molecular orientation at various types of buried interfaces in vapor-deposited glasses and provides a foundation for future studies to develop critical structure–function relationships.

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

Bond Length Alternation and Internal Dynamics in Model Aromatic Substituents of Lignin

In this report broadband microwave spectra were recorded over the 2-18 GHz frequency range for a series of four model aromatic components of lignin; namely, guaiacol (ortho-methoxy phenol, G), syringol (2,6-dimethoxy phenol, S), 4-methyl guaiacol (MG), and 4-vinyl guaiacol (VG), under jet-cooled conditions in the gas phase. Using a combination of 13 C isotopic data and electronic structure calculations, distortions of the phenyl ring by the substituents on the ring are identified. In all four molecules, the r C(1)-C(6) bond between the two substituted C-atoms lengthens, leading to clear bond alternation that reflects an increase in the phenyl ring resonance structure with double bonds at r C(1)-C(2) , r C(3)-C(4) and r C(5)-C(6) . Syringol, with its symmetric methoxy substituents, possesses a microwave spectrum with tunneling doublets in the a-type transitions associated with H-atom tunneling. These splittings were fit to determine a barrier to hindered rotation of the OH group of 1975 cm -1 , a value nearly 50% greater than that in phenol, due to the presence of the intramolecular OH…OCH 3 H-bonds at the two equivalent planar geometries. In 4-methyl guaiacol, methyl rotor splittings are observed and used to confirm and refine an earlier measurement of the three-fold barrier V 3 = 67 cm -1 . Finally, 4-vinyl guaiacol shows transitions due to two conformers differing in the relative orientations of the vinyl and OH groups.

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

Impact of Water Extraction on Malonamide Aggregation: A Molecular Dynamics and Graph Theoretic Approach

Solution structure in liquid-liquid extraction affects the efficacy of separation; however, even for simplified organic phases, structural characterization and attribution of aggregation to intermolecular interactions are fundamental challenges. We investigate water uptake into organic phases for two malonamides commonly applied to actinide and lanthanide separations. Extracted water induces reorganization of the amphiphilic extractant molecules, although we find this rearrangement is not strongly manifested in small-angle X-ray scattering making it challenging to probe without methods such as atomistic simulation. Using a graph theoretic approach to define hydrogen bonded water/malonamide aggregates from molecular dynamics simulations, we find evidence of a characteristic aggregate size by water number that results from geometric accommodation of the surrounding malonamide molecules. Furthermore, this implies a degree of size selectivity inherent to these water-in-oil aggregates. Conversely, we find no evidence of a characteristic size of the aggregates with respect to their malonamide number. By defining a separate graphical representation of self-association of the amphiphilic malonamides, we quantify how water affects the local and nonlocal topology of the malonamide network, providing a basis for characterization of the structure and impact of polar solutes in increasingly complex organic phases.

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

Determination of the Interfacial Energy between Graphene Nanoplatelets and Deuterated or Hydrogenated Polystyrene

The tracer diffusion coefficients of various graphene nanoplatelet-polystyrene (GNP-PS) systems were determined by using dynamic secondary ion mass spectrometry, which provided insights into the interactions within the polymer nanocomposite system. Bilayer films, where one contained trace amounts of deuterated polystyrene (dPS), were produced, and the interdiffusion was measured by detecting the position of the dPS interface. GNPs were placed in both or only one of the two layers. The diffusion coefficient was decreased when GNPs were present in both layers as compared to the samples without GNP, indicating an attractive interaction between GNP and polystyrene. Surprisingly, the coefficient increased relative to the control when GNPs were present only in the PS containing layer, whereas it decreased most strongly when GNP and dPS were present only in the same layer, indicating that an additional preference existed for GNPs and dPS. A significant difference in interfacial energies was measured using contact angle goniometry of PS or dPS droplets on flat GNP layers, confirming the preferential interaction. DFT calculations were used to calculate the interfacial interaction between GNP and dPS or PS, and they showed an attractive potential which was maximal when the PS rings were conformal with the GNP structure. Furthermore, the differential energy between PS and dPS at the GNP interface was in excellent agreement with the measured value. In contrast, contact angle goniometry indicated that the interaction between GNP and poly(methyl methacrylate) (PMMA) was unfavorable, and no difference in interfacial energy between dPMMA and PMMA was observed. Therefore, these techniques can provide a means for determining the relative affinity between GNP and different polymer hosts, which can be an important consideration in the mechanics and adhesion properties of the compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes

Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush-functionalized DNA nanostructures. Here we demonstrate that SI-TcEP can site-specifically pattern DONs with brushes containing both natural and non-natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse-grained simulations predict the conformation of the brush-functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush-functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site-specific growth of polynucleotide brushes. The ability to site-specifically decorate DONs with brushes of natural and non-natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.

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

Chapter 9: Human Behavior Dynamics in Sustainability

Human behavior dynamics and actions play a direct and significant role in shaping pathways toward sustainability, resulting in many sustainability challenges. A social dilemma arose when a hypothetical Colorado rural town closed down most of its medicine take-back stations as a result of reduced tax revenue. The current discourse discusses a scenario in which an individual "plays" against everyone else concerning whether to drive to the take-back station to dispose of unused medication (i.e., cooperating) or to flush it or throw it in the landfill (i.e., defecting). Using the structure of the pay-off matrix, this study analyzed unwanted medication disposal from a social dilemma perspective to provide insight into an individual's motivations to cooperate or defect and techniques for encouraging cooperation. The pay-off matrix encompasses four scenarios, namely, win-win when everyone cooperates, you're the sucker when only the individual cooperates, free rider when only the individual defects, and the tragedy of the commons when everyone defects. Reasons for an individual to cooperate include sharing the high moral value with everyone else, valuing social conformity, and taking great pride in doing the right thing, even when cooperating is costly. On the other hand, the individual who defects believes that cooperating will likely make little difference. The individual is selfish or insufficiently motivated by altruism and feels that the bad action will not get caught. When everyone defects, it likely results from participants not wanting to be a "sucker" and a lack of accountability (e.g., no punishment) associated with bad behavior. One solution to the free-rider problem is to appeal to the free rider's altruism. It is important to convince the individual that doing things for the benefit of others can also benefit themselves. Furthermore, a way to fix the social dilemma is to make the defectors pay for their actions that cause the negative externality (i.e., town water contaminated with pharmaceutical chemicals from unwanted medications). The higher the financial incentive for cooperative behavior, the lower the defecting propensity. By including punishment (e.g., discipline and penalty), people tend to defect less often, and highly cooperative outcomes emerge.

ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

Insights into the substrate specificity, structure, and dynamics of plant histidinol-phosphate aminotransferase (HISN6)

Histidinol-phosphate aminotransferase is the sixth protein (hence HISN6) in the histidine biosynthetic pathway in plants. HISN6 is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the reversible conversion of imidazole acetol phosphate into L-histidinol phosphate (HOLP). Here, we show that plant HISN6 enzymes are closely related to the orthologs from Chloroflexota. The studied example, HISN6 from Medicago truncatula (MtHISN6), exhibits a surprisingly high affinity for HOLP, which is much higher than reported for bacterial homologs. Moreover, unlike the latter, MtHISN6 does not transaminate phenylalanine. High-resolution crystal structures of MtHISN6 in the open and closed states, as well as the complex with HOLP and the apo structure without PLP, bring new insights into the enzyme dynamics, pointing at a particular role of a string-like fragment that oscillates near the active site and participates in the HOLP binding. When MtHISN6 is compared to bacterial orthologs with known structures, significant differences arise in or near the string region. The high affinity of MtHISN6 appears linked to the particularly tight active site cavity. Finally, a virtual screening against a library of over 1.3 mln compounds revealed three sites in the MtHISN6 structure with the potential to bind small molecules. Such compounds could be developed into herbicides inhibiting plant HISN6 enzymes absent in animals, which makes them a potential target for weed control agents.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Recombinant FimH Adhesin Demonstrates How the Allosteric Catch Bond Mechanism Can Support Fast and Strong Bacterial Attachment in the Absence of Shear

The FimH protein of Escherichia coli is a model two-domain adhesin that is able to mediate an allosteric catch bond mechanism of bacterial cell attachment, where the mannose-binding lectin domain switches from an ‘inactive’ conformation with fast binding to mannose to an ‘active’ conformation with slow detachment from mannose. Because mechanical tensile force favors separation of the domains and, thus, FimH activation, it has been thought that the catch bonds can only be manifested in a fluidic shear-dependent mode of adhesion. Here, we used recombinant FimH variants with a weakened inter-domain interaction and show that a fast and sustained allosteric activation of FimH can also occur under static, non-shear conditions. Moreover, it appears that lectin domain conformational activation happens intrinsically at a constant rate, independently from its ability to interact with the pilin domain or mannose. However, the latter two factors control the rate of FimH deactivation. Thus, the allosteric catch bond mechanism can be a much broader phenomenon involved in both fast and strong cell-pathogen attachments under a broad range of hydrodynamic conditions. In conclusion, this concept that allostery can enable more effective receptor-ligand interactions is fundamentally different from the conventional wisdom that allostery provides a mechanism to turn binding off under specific conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Unveiling horizons in quantum critical collapse

Critical gravitational collapse offers a unique window into regimes of arbitrarily high curvature, culminating in a naked singularity arising from smooth initial data — thus providing a dynamical counterexample to weak cosmic censorship. Near the critical regime, quantum effects from the collapsing matter are expected to intervene before full quantum gravity resolves the singularity. Despite its fundamental significance, a self-consistent treatment has so far remained elusive. In this work, we perform a one-loop semiclassical analysis using the robust anomaly-based method in the canonical setup of Einstein gravity minimally coupled to a free, massless scalar field. Focusing on explicitly solvable near-critical solutions in both 2 + 1 and 3 + 1 dimensions, we analytically solve the semiclassical Einstein equations and obtain controlled, quantitative results for several long-standing questions within the dominant s-wave sector. We find that regularity uniquely selects a Boulware-like quantum state, encoding genuine vacuum polarization effects from the collapsing matter. Remarkably, the resulting quantum corrections manifest as a growing mode. Horizon-tracing analyses, incorporating both classical and quantum modes, reveal the emergence of a finite mass gap, signaling a phase transition from classical Type II to quantum-modified Type I behavior, thereby providing a quantum enforcement of the weak cosmic censorship. The most non-trivial aspect of our analysis involves dealing with non-conformal matter fields in explicitly time-dependent critical spacetimes. Along the way, we uncover intriguing and previously underexplored features of quantum field theory in curved spacetime.

2D Gravity↗
DOE OSTI2025

Structural and Mechanistic Advances in the Chemistry of Methyl-Coenzyme M Reductase (MCR)

Methane represents 34% of U.S. energy consumption and is a major greenhouse gas related to the global carbon cycle and energy production. However, current industrial practices significantly increase atmospheric methane levels, necessitating a deeper understanding of its biosynthesis and oxidation. Methyl-coenzyme M reductase (MCR) is central to biological methane metabolism, catalyzing the final step of methanogenesis and the first step in anaerobic methane oxidation. It is also a key target for strategies to capture and transform methane into value-added chemicals.The active site of MCR is a buried Ni-based cofactor only accessible by the substrates via a 50 Å long tunnel. Although the Ni(I) state is required to initiate catalysis, capturing this state remains a challenge for the current structural techniques. Recent advances in structural biology using X-ray Free-Electron Laser serial crystallography have provided insights into MCR's inactive Ni(II) state at room temperature and show promise for capturing its active Ni(I) form.Our team has established several critical aspects of the MCR mechanism using a combination of experimental and computational studies. MCR uses CH 3 -SCoM and CoBSH as substrates, producing methane and a disulfide product CoMSSCoB. Kinetic analysis showed that productive substrate binding requires CH 3 -SCoM to bind first, inducing conformational changes that optimize the active site for subsequent CoBSH binding. Following substrate binding, four proposed methane production/oxidation mechanisms were examined, establishing whether the reaction proceeds through an organometallic methyl-nickel(III), methyl anion ion, or methyl radical intermediate. Experimental measurements using CoBSH analogs successfully slowed the reaction, allowing for mechanistic insight that demonstrated the methyl radical pathway, where the initial interactions involve homolytic cleavage of the methyl-sulfur bond, generating a methyl radical that quickly abstracts the thiol hydrogen atom of CoBSH to form methane. Computational studies further confirmed that, compared to other mechanisms, the methyl radical mechanism is thermodynamically more favorable and accessible under physiological conditions.Spectroscopic and computational studies challenged the conventional understanding of substrate binding in MCR by proposing an alternative positioning of CH 3 -SCoM and CoMSSCoB in the active site pocket. The research suggested that CH 3 -SCoM (substrate) and CoMSSCoB (product) bind via their sulfonate groups to the Ni(I) center of cofactor F 430 . This binding allows for the reaction without substrate reorganization in the pocket but would require a long-range electron transfer. Altogether, the work summarized in this review reflects our current understanding of the enzyme's catalytic mechanism and structural dynamics. This is essential for developing efficient methane conversion technologies that could mitigate its environmental impact while harnessing energy-storage properties.

03 NATURAL GAS↗
DOE OSTI2026

Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin

Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.

Amines↗
DOE OSTI2022

Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field

With the continual development of lanthanides (Ln) in current technological devices, an efficient separation process is needed that can recover greater amounts of these rare elements. Dicyclohexano-18-crown-6(DCH18C6) is a crown ether that may be a promising candidate for Ln separation, but additional research is required. As such, molecular dynamics(MD) simulations have been performed on four divalent lanthanide halide salts(Sm 2+ , Eu 2+ , Dy 2+ , and Yb 2+ ) and one divalent actinide halide salt (Cf 2+ ) bound to three diastereoisomers of DCH18C6. Dy 2+ , Yb 2+ , Cf 2+ , DCH18C6, and tetrahydrofuran (THF) solvent were parameterized for the AMOEBA polarizable force field for the first time, whereas existing parameters for Sm 2+ and Eu 2+ were utilized from our previous efforts. A coordination number (CN) of six for Ln 2+ /An 2+ –O solvated in THF indicated that the cations interacted almost entirely with the oxygens of the polyether ring. A CN of one for Ln 2+ /An 2+ -N solvated in acetonitrile for systems containing iodide suggested that theN atom of acetonitrile was competitive with I – for cation interactions. Fluctuation between five and six CNs for Dy 2+ and Yb 2+ suggested that although the cations remained in the polyether ring, the size of the ring may not be an ideal fit as these cations possess comparatively smaller ionic radii. Gibbs binding free energies of Sm 2+ in all DCH18C6 diastereoisomers solvated in THF were calculated. The binding free energy of the cis-syn-cis diastereoisomer was the most favorable, followed by cis-anti-cis, and then trans-anti-trans. Lastly, two major types of conformation were observed for each diastereoisomer that were related to the electrostatic interactions and charge density of the cations.

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

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure–function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

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

Tensionless strings on AdS 3 orbifolds

The bound state of one NS5 brane (wrapped on a T 4 ) and N NS1-branes has two dual descriptions: its low-energy dynamics is described by the symmetric orbifold of T 4 , while the near horizon geometry is captured by string theory on AdS 3 × S 3 × T 4 with one unit of NS flux. The latter theory is exactly solvable in the hybrid formalism, and this allows one to prove the equivalence of the two descriptions. In this paper we extend this duality to Z k orbifolds of this AdS 3 × S 3 background. In particular, we show that the corresponding worldsheet spectrum reproduces exactly the perturbative excitations on top of a certain non-perturbative state in the dual symmetric orbifold theory. Since the AdS/CFT duality map is exact for these models, we obtain an interesting picture of how the duality relates boundary and bulk descriptions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria that encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo , the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We used molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo . Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed the overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceu m model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗