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At least 1,801 records · Page 100

Foundational Science to Accelerate Nuclear Energy Innovation [Brochure]

The foundational science gaps inhibiting the advancement of nuclear energy technologies are identified and tackled in five priority research opportunities. These opportunities pave the way to accelerate the development and ultimately the adoption of new nuclear energy systems. They include the fundamental aspects of ion-electron interactions; novel properties of next-generation coolants and solvents; interfacial dynamics, not only in solids, but in other aspects of nuclear reactors; novel operando and in-situ monitoring and sensing; and artificial intelligence to accelerate condensed phases discovery. Building on the foundation established by previous BES workshops, these opportunities encompass recent advances in fundamental knowledge and focus on the experimental and computational methods needed to resolve major technical challenges for nuclear energy technologies. Through developing fundamental scientific insight as well as pushing the frontiers of modeling complex systems and probing the operation of materials and chemical systems in extreme environments, research motivated by the priorities identified here will further develop the promise, potential, and utilization of nuclear energy for a clean energy future. The PROs are as follows: (1) Master complex electronic structures to tailor thermochemical reactivity, transport, and microstructural evolution; (2) Interrogate and direct the physics and chemistry underpinning next-generation coolants and solvents; (3) Elucidate and control the underlying physics and chemistry of interfaces in complex nuclear environments; (4) Bridge multi-fidelity multi-resolution experiments, computational modeling, and data science to control dynamic behavior; and (5) Harness artificial intelligence to design inherently resilient condensed phases.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Modal Analysis and Testing of a Cantilever Beam: Results and Guide

This report discusses modal analysis and testing of a cantilever beam including an introduction to modal testing, simulation, analysis, and a comparison of results. An accompanying presentation can be found from the LLNL CASIS website. Modal testing and analysis are essential for characterizing the response of a structure during vibration environments. Determining natural frequencies and mode shapes helps determine whether resonances will be reached during operations and if so, how the structure will respond and how the response can be tuned. The goal of this work is to convey the basics of modal testing and analysis through a simple project. This can be applied later to more complex, applicable structures. This includes a variety of work including data collection, finite element analysis and data processing. For this project a cantilever beam was chosen because it is a simple, well-characterized structure.

42 ENGINEERING↗

A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models

Interactions between WD40 repeat domain protein 5 (WDR5) and its various partners such as mixed lineage leukemia (MLL) and c-MYC are essential for sustaining oncogenesis in human cancers. However, inhibitors that block protein-protein interactions (PPIs) between WDR5 and its binding partners exhibit modest cancer cell killing effects and lack in vivo efficacy. Here, we present pharmacological degradation of WDR5 as a promising therapeutic strategy for treating WDR5-dependent tumors and report two high-resolution crystal structures of WDR5-degrader-E3 ligase ternary complexes. We identified an effective WDR5 degrader via structure-based design and demonstrated its in vitro and in vivo antitumor activities. On the basis of the crystal structure of an initial WDR5 degrader in complex with WDR5 and the E3 ligase von Hippel–Lindau (VHL), we designed a WDR5 degrader, MS67, and demonstrated the high cooperativity of MS67 binding to WDR5 and VHL by another ternary complex structure and biophysical characterization. MS67 potently and selectively depleted WDR5 and was more effective than WDR5 PPI inhibitors in suppressing transcription of WDR5-regulated genes, decreasing the chromatin-bound fraction of MLL complex components and c-MYC, and inhibiting the proliferation of cancer cells. In addition, MS67 suppressed malignant growth of MLL-rearranged acute myeloid leukemia patient cells in vitro and in vivo and was well tolerated in vivo. Collectively, our results demonstrate that structure-based design can be an effective strategy to identify highly active degraders and suggest that pharmacological degradation of WDR5 might be a promising treatment for WDR5-dependent cancers.

99 GENERAL AND MISCELLANEOUS↗

Thermodynamic, structural and magnetic studies of phase transformations in MnAl nanocomposite alloys

Highlights: • Small changes in MnAl stoichiometry (5 at.%) produce different phase structure. • In Mn{sub 60}Al{sub 40} as-cast alloy only hcp ε phase can be found • In Mn{sub 55}Al{sub 45} as-cast alloy, there is a mixture of γ{sub 2} (Al{sub 8}Mn{sub 5}) and ε as well as ferromagnetic MnAl τ-phase. • Energies of phase transformation of about 165 kJ/mol for Mn{sub 60}Al{sub 40} and 290 kJ/mol for Mn{sub 55}Al{sub 45} alloys are found. • hcp ε phase decomposes through the migration of interphase interfaces. - Abstract: We have undertaken a temperature-dependent, investigation of the thermodynamics, structure, morphology and magnetism of two MnAl nanocomposite alloys (Mn{sub 60}Al{sub 40} and Mn{sub 55}Al{sub 45}). Differential scanning calorimetry (DSC) studies allowed the determination of the exo-effects occurring in the structural phase transformation of MnAl, while by using temperature-dependent X-ray diffraction of synchrotron radiation we were able to monitor the phase transformation effects and the evolution with temperature of various structural phases occurring in the samples. We have shown that slight changes in stoichiometry (5 at.%) give rise to different phase structure in the as-cast state. While in Mn{sub 60}Al{sub 40} only hcp ε phase can be found, in Mn{sub 55}Al{sub 45} as-cast alloy, there is a quite complex phase structure with a mixture of γ{sub 2} (Al{sub 8}Mn{sub 5}) and ε as well as ferromagnetic MnAl τ-phase. Activation energies of about 165 kJ/mol and 290 kJ/mol have been calculated from the Ozawa-Flynn-Wall analysis of DSC experimental data. These findings are in good agreement with the results obtained from XRD. For the Mn{sub 55}Al{sub 45} as-cast alloy, we have confirmed by temperature-dependent synchrotron XRD that the hcp ε phase decomposes through the migration of interphase interfaces with the transformation rate controlled by boundary diffusion processes. High-resolution transmission electron microscopy have confirmed the phase structure obtained by XRD, while magnetic properties, obtained for the as-cast alloys are consistent with the multiphase character of the samples and in good agreement with previously reported results. The magnetization does not saturate for the maximum applied field of about 4 × 10{sup 6} A/m and a marked coercivity of about 160 kA/m is obtained for the Mn{sub 55}Al{sub 45} as-cast alloy.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Photodissociation and Theory to Investigate Uranium Oxide Cluster Cations

Uranium oxide cluster cations of the form U n O m + are produced by laser vaporization of a depleted uranium rod in a pulsed supersonic expansion. Ions are mass-analyzed and mass-selected with a time-of-flight spectrometer and studied with UV laser multiphoton dissociation. Cations of the stoichiometry UO 2 (UO 3 ) n + were observed as photofragments from all photodissociated cluster cations. (UO 3 ) n + clusters were also observed to result from dissociation of larger (UO 3 ) n + clusters, with UO 3 neutral as a common leaving group. Electronic structure calculations were used to investigate the stability of the prominent uranium oxide cluster cations using density functional theory (DFT) with the hybrid B3LYP exchange-correlation functional and at the CCSD(T) level and cc-pVnZ-PP basis sets (n = D,T), including diffuse orbitals as computational expense and availability permitted. Clustering energies, relative energies and dissociation energies of the cations are reported. The lowest energy neutral (UO 3 ) n clusters up to n = 3 are rings, n = 4 and 5 are chains with very low energy rings, and n = 6 is 3D. Finally, the lowest energy structures for UO 2 (UO 3 ) n + are composed of uranyl-like UO 2 + units bound by bridging oxygens to other UO 2 2+ units for n = 2 and 3, and for n = 4 a more complex 3D structure is predicted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology

Type A γ-aminobutyric acid receptors (GABA A Rs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants. However, our understanding of GABA A R pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABA A R assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABA A Rs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABA A R assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed.

59 BASIC BIOLOGICAL SCIENCES↗

Acceleration of heavy ions in inverse free electron laser

In conventional linear accelerators, the beam is accelerated with a synchronous harmonic of the radio frequency field where the electric field component is collinear with the beam direction. This approach requires the design of complex accelerating structures, especially for low-energy heavy ions. If the beam motion were sustainably coupled to transverse electromagnetic fields, this could significantly simplify the accelerating structure design, and even allow acceleration with free-space waves. However, despite the long history of the proposed concept for accelerating low-velocity ion beams, it has not found practical application, partially because of the complexity of the technical design. In this paper, we present a practical design approach for this undulator-based accelerator for low-energy heavy-ions, reminiscent of the inverse free electron laser operating principle, but in a different parameter space.

47 OTHER INSTRUMENTATION↗

Interface-driven mechanisms in cubic/noncubic nanolaminates at different scales

Superior structural properties of materials are generally desired in harsh environments, such as elevated temperatures, high rates of impact, and radiation. Composite nanolaminates, built with alternating stacks of crystalline layers, each with nanoscale individual thickness, are proving to exhibit many of these target properties. In principle, the nanolaminate concept can be applied to any twophase, bimetallic system; however, for a number of reasons, they have been limited to combinations of metals with a cubic crystal structure. There is growing demand to increase the number of advanced material systems containing noncubic metals, since these metals bear several desirable intrinsic properties. In this article, we cover recent modeling and experimental efforts to understand the complexity in structure, mechanisms, and behavior of noncubic/cubic nanolaminates. We hope this article will facilitate and encourage future studies in this promising area.

36 MATERIALS SCIENCE↗

Structure of a benzylidene derivative of 9(10H)-anthracenone in complex with tubulin provides a rationale for drug design

Highlights: • The first crystal structure of an anthracenone family agent complexed with tubulin. • Comparison of the binding mode between different agents reveals the inhibition mechanism. • This structure helps understand the results of the structure-activity-relationship (SAR) studies. Microtubules are composed of αβ-tubulin heterodimers and have been treated as highly attractive targets for antitumor drugs. A broad range of agents bind to tubulin and interfere with microtubule assembly, including colchicine binding site inhibitors (CBSIs). Tubulin Polymerization Inhibitor I (TPI1), a benzylidene derivative of 9(10H)-anthracenone, is a CBSI that inhibits the assembly of microtubules. However, for a long time, the design and development of anthracenone family drugs have been hindered by the lack of structural information of the tubulin-agent complex. Here we report a 2.3 Å crystal structure of tubulin complexed with TPI1, the first structure of anthracenone family agents. This complex structure reveals the interactions between TPI1 and tubulin, and thus provides insights into the development of new anthracenone derivatives targeting the colchicine binding site.

60 APPLIED LIFE SCIENCES↗

Determining the Three-Dimensional Structures of Silica-Supported Metal Complexes from the Ground Up

The immobilization of molecularly precise metal complexes to substrates, such as silica, provides an attractive platform for the design of active sites in heterogeneous catalysts. Specific steric and electronic variations of the ligand environment enable the development of structure–activity relationships and the knowledge-driven design of catalysts. At present, however, the three-dimensional environment of the precatalyst, much less the active site, is generally not known for heterogeneous single-site catalysts. We explored the degree to which NMR-based surface-to-complex interatomic distances could be used to solve the three-dimensional structures of three silica-supported metal complexes. Furthermore, the structure solution revealed unexpected features related to the environment around the metal that would be difficult to discern otherwise. This approach appears to be highly robust and, due to its simplicity, is readily applied to most single-site catalysts with little extra effort.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reimagining watershed restoration: a call for new investment and support structures for greater resiliency and long‐term impact

Hundreds of locally based watershed initiatives have mobilized stakeholders to take voluntary action to restore the ecological conditions of North America's watersheds. Lead organizations rely on project‐based grant funding, alignment with government programs, and volunteerism to incrementally restore what is ultimately a vast and complex ecosystem. Structurally, the vision and goals of these initiatives often exceed available resources and capacity. In 1999, the Bonneville Environmental Foundation began to test ways by which a funder might increase the capacity of local watershed organizations to achieve long‐term watershed restoration goals through a 10‐year commitment of funding and technical support. We partnered with other funders, collectively seeking solutions to increase the impact of this work. Reflecting on 13 years experience across 21 watersheds in 7 western states ( USA ), we have concluded that the scale of ecological change desired requires a time frame for planning, implementation, and public engagement that is inconsistent with present‐day approaches. This has left us asking how can the capacity and impact of a watershed initiative be sustained over many decades—a time frame that exceeds the tenure of any individual leader, the proven life cycles of many nonprofit organizations, and the commitment of most funders? Clear themes have emerged: (1) engaging diverse stakeholders in planning, (2) orienting the work around broader goals, (3) emphasizing human well‐being, and (4) developing resilient partnerships. Reimagining watershed restoration in this context, we suggest a new agenda for action and research that emphasizes a multidecadal planning horizon integrating climate change projections and changing demographics and social values. WIREs Water 2017, 4:e1174. doi: 10.1002/wat2.1174 This article is categorized under: Water and Life > Conservation, Management, and Awareness Engineering Water > Planning Water Human Water > Water Governance

Warren, Robert F.↗

Synthesis and spectral study of new azo dye and its iron complexes derived from 2-naphthol and 2-amino-3-hydroxypyridine

An azodye C{sub 5}H{sub 12}N{sub 3}O{sub 2} [LH] is synthesised by coupling diazotised 2-amino-3-hydroxy pyridine with 2-naphthol in ice cold condition. The Fe(II)and Fe(III) complexes were prepared by mixing ethanol solution of metal salt and azodye in 1:2 molar ratio. The dye and metal complexes are structurally characterised by elemental analysis, molar conductance, magnetic susceptibility measurements and spectral techniques like IR, UV-Vis, and Mössbauer analysis. Analytical data suggests the stoichiometry as [FeL{sub 2}Cl(H{sub 2}O)] for Fe(III) complex and [FeL{sub 2}(H{sub 2}O)] for Fe(II) complex. The IR spectral data suggests that [L{sup −}] is acting as a uninegative bidentate ligand. A high spin octahedral geometry is tentatively proposed for both the complexes with respect to the above studies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structural characterization of nonactive site, TrkA-selective kinase inhibitors

Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. Furthermore, these structures illustrate the flexibility of binding to sequences outside of—but adjacent to—the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Scattering Amplitudes and QFT Insight (Final Scientific Report)

The calculation of scattering amplitudes provides an invariant window into the physical dynamic content of relativistic quantum field theory. Yet with traditional methods, for empirically relevant theories, these calculations scale with a factorial complexity in external particles and precision. If we aspire to collapse the theoretical uncertainty obscuring new physics hidden at all scales from the microscopic probed at high energy colliders to the largest effective field theory in the universe governing the evolution of large scale structure, this complexity challenge necessitates new ideas and methods in calculation. Novel approaches like the color-kinematics duality and the associated double-copy construction have drastically simplified the situation, relating both gauge and gravity theory predictions to a much smaller kernel of invariant kinematic data. This project supporting research by the PI's Amplitudes and Insights group at Northwestern University looked to push insight deep into both the IR and the UV by establishing how novel structures must constrain the predictions of counterterms in both gauge and gravity theories, setting the groundwork to exploring the high energy behavior of particular gravity theories via constituent gauge-theory calculations, and confronting fundamental challenges at the interface between QFT amplitudes analysis and next generation gravitational wave science as well as well as inflationary and large scale structure cosmology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Unraveling nonperturbative QCD with transverse momentum hadronic structures

The main purpose of this thesis is to investigate the theoretical foundations of the factorization theorems that involve transverse quark and gluon momentum distributions, and to better understand the interface between foundational questions and phenomenological applications. Many of these applications involve using transverse parton momentum dependent (TMD) correlation functions as tools for probing the complex nonperturbative structures of the hadrons. We first introduce the concepts of collinear and TMD factorization in a toy-model theory and, by leveraging the comparative simplicity of such a model, we test the range of validity and limitations of the factorization approach. At the same time, we introduce the conventional approaches that are adopted for the phenomenological extractions of the TMD distributions, and catalog the advantages and disadvantages. Following the general theoretical framework of factorization, we then develop a different approach to TMD phenomenology that is able to systematically integrate the perturbative and non perturbative information in parametrizations of TMD distributions, while being completely consistent with their operator definitions and the predictions of QCD, including their nontrivial evolution. The name Hadron Structure Oriented approach, or HSO, is coined in order to emphasize the central role of the nonperturbative nature of QCD and its relation to the partonic structure of hadrons. Finally, we provide a first phenomenological implementation of the HSO approach by extracting TMD distributions relying on low-to-moderate energy Drell-Yan data. The quality and robustness of the results are then compared against higher energy processes like high-Q2 Z0 boson production. Our analysis demonstrates the feasibility of this novel approach and points the way toward the improvements it can achieve in future applications.

Rainaldi, Tommaso [Old Dominion Univ., Norfolk, VA↗

Complexation behavior of oppositely charged polyelectrolytes: Effect of charge distribution

Complexation behavior of oppositely charged polyelectrolytes in a solution is investigated using a combination of computer simulations and experiments, focusing on the influence of polyelectrolyte charge distributions along the chains on the structure of the polyelectrolyte complexes. The simulations are performed using Monte Carlo with the replica-exchange algorithm for three model systems where each system is composed of a mixture of two types of oppositely charged model polyelectrolyte chains (EGEG){sub 5}/(KGKG){sub 5}, (EEGG){sub 5}/(KKGG){sub 5}, and (EEGG){sub 5}/(KGKG){sub 5}, in a solution including explicit solvent molecules. Among the three model systems, only the charge distributions along the chains are not identical. Thermodynamic quantities are calculated as a function of temperature (or ionic strength), and the microscopic structures of complexes are examined. It is found that the three systems have different transition temperatures, and form complexes with different sizes, structures, and densities at a given temperature. Complex microscopic structures with an alternating arrangement of one monolayer of E/K monomers and one monolayer of G monomers, with one bilayer of E and K monomers and one bilayer of G monomers, and with a mixture of monolayer and bilayer of E/K monomers in a box shape and a trilayer of G monomers inside the box are obtained for the three mixture systems, respectively. The experiments are carried out for three systems where each is composed of a mixture of two types of oppositely charged peptide chains. Each peptide chain is composed of Lysine (K) and glycine (G) or glutamate (E) and G, in solution, and the chain length and amino acid sequences, and hence the charge distribution, are precisely controlled, and all of them are identical with those for the corresponding model chain. The complexation behavior and complex structures are characterized through laser light scattering and atomic force microscopy measurements. The order of the apparent weight-averaged molar mass and the order of density of complexes observed from the three experimental systems are qualitatively in agreement with those predicted from the simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A statistical and simulation-informed model for estimating permeability from pore size distribution in saturated geomaterials

Accurate permeability estimation is essential across subsurface engineering applications but remains challenging due to the complex pore structures of natural geomaterials. Traditional empirical methods and simplified theoretical models often inadequately capture the role of pore size distribution and connectivity. Here, this study develops a statistical and simulation-informed permeability model that collapses pore-scale complexity into a compact scaling of the form k = αϕμ d 2 , where ϕ is porosity, μ d is mean pore size, and α is a weakly varying coefficient. By combining pore network simulations with statistical analysis of unimodal and bimodal pore size distributions, we identify three key findings: (i) permeability is much more sensitive to mean pore size than to porosity; (ii) across extensive datasets, the ratio σ d /μ d (standard deviation to mean) clusters around a characteristic value ∼0.4, allowing the effects of the full pore size distribution to be represented by μ d and a narrowly varying α ≈ 0.05; and (iii) for bimodal systems, there exists a critical fraction of small pores ∼0.78 above which flow becomes small-pore dominated, enabling the definition of an effective flow-controlling pore population and facilitating simplified permeability estimation for such systems. The resulting model, which requires only porosity and a representative mean pore size as inputs, is validated against comprehensive experimental datasets (>1700 samples) spanning diverse soils and rocks and achieves good predictive accuracy. Overall, this work provides a physically grounded yet practically simple permeability estimator suitable for subsurface engineering, environmental protection, and resource management applications.

Permeability↗

PAK4 crystal structures suggest unusual kinase conformational movements

In order for protein kinases to exchange nucleotide they must open and close their catalytic cleft. These motions are associated with rotations of the N-lobe, predominantly around the ‘hinge region’. Here, we conducted an analysis of 28 crystal structures of the serine-threonine kinase, p21-activated kinase 4 (PAK4), including three newly determined structures in complex with staurosporine, FRAX486, and fasudil (HA-1077). We find an unusual motion between the N-lobe and C-lobe of PAK4 that manifests as a partial unwinding of helix αC. Principal component analysis of the crystal structures rationalizes these movements into three major states, and analysis of the kinase hydrophobic spines indicates concerted movements that create an accessible back pocket cavity. The conformational changes that we observe for PAK4 differ from previous descriptions of kinase motions, and although we observe these differences in crystal structures there is the possibility that the movements observed may suggest a diversity of kinase conformational changes associated with regulation. Author summary: Protein kinases are key signaling proteins, and are important drug targets, therefore understanding their regulation is important for both basic research and clinical points of view. In this study, we observe unusual conformational ‘hinging’ for protein kinases. Hinging, the opening and closing of the kinase sub-domains to allow nucleotide binding and release, is critical for proper kinase regulation and for targeted drug discovery. We determine new crystal structures of PAK4, an important Rho-effector kinase, and conduct analyses of these and previously determined structures. We find that PAK4 crystal structures can be classified into specific conformational groups, and that these groups are associated with previously unobserved hinging motions and an unusual conformation for the kinase hydrophobic core. Our findings therefore indicate that there may be a diversity of kinase hinging motions, and that these may indicate different mechanisms of regulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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