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At least 649 records · Page 36

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DOE OSTI2024

p14 ARF forms meso-scale assemblies upon phase separation with NPM1

NPM1 is an abundant nucleolar chaperone that, in addition to facilitating ribosome biogenesis, contributes to nucleolar stress responses and tumor suppression through its regulation of the p14 Alternative Reading Frame tumor suppressor protein (p14 ARF ). Oncogenic stress induces p14 ARF to inhibit MDM2, stabilize p53 and arrest the cell cycle. Under non-stress conditions, NPM1 stabilizes p14 ARF in nucleoli, preventing its degradation and blocking p53 activation. However, the mechanisms underlying the regulation of p14 ARF by NPM1 are unclear because the structural features of the p14 ARF -NPM1 complex were elusive. Here we show that p14 ARF assembles into a gel-like meso-scale network upon phase separation with NPM1. This assembly is mediated by intermolecular contacts formed by hydrophobic residues in an α-helix and β-strands within a partially folded N-terminal portion of p14 ARF . These hydrophobic interactions promote phase separation with NPM1, enhance p14 ARF nucleolar partitioning, restrict NPM1 diffusion within condensates and nucleoli, and reduce cellular proliferation. Our structural analysis provides insights into the multifaceted chaperone function of NPM1 in nucleoli by mechanistically linking the nucleolar localization of p14 ARF to its partial folding and meso-scale assembly upon phase separation with NPM1.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Stereoselective synthesis of a 4-α-glucoside of valienamine and its X-ray structure in complex with Streptomyces coelicolor GlgE1-V279S

Glycoside hydrolases (GH) are a large family of hydrolytic enzymes found in all domains of life. As such, they control a plethora of normal and pathogenic biological functions. Thus, understanding selective inhibition of GH enzymes at the atomic level can lead to the identification of new classes of therapeutics. In these studies, we identified a 4-α-glucoside of valienamine (8) as an inhibitor of Streptomyces coelicolor (Sco) GlgE1-V279S which belongs to the GH13 Carbohydrate Active EnZyme family. The results obtained from the dose–response experiments show that 8 at a concentration of 1000 µM reduced the enzyme activity of Sco GlgE1-V279S by 65%. The synthetic route to 8 and a closely related 4-α-glucoside of validamine (7) was achieved starting from readily available D-maltose. A key step in the synthesis was a chelation-controlled addition of vinylmagnesium bromide to a maltose-derived enone intermediate. X-ray structures of both 7 and 8 in complex with Sco GlgE1-V279S were solved to resolutions of 1.75 and 1.83 Å, respectively. Structural analysis revealed the valienamine derivative 8 binds the enzyme in an E 2 conformation for the cyclohexene fragment. Also, the cyclohexene fragment shows a new hydrogen-bonding contact from the pseudo-diaxial C(3)–OH to the catalytic nucleophile Asp 394 at the enzyme active site. Asp 394, in fact, forms a bidentate interaction with both the C(3)–OH and C(7)-OH of the inhibitor. In contrast, compound 7 disrupts the catalytic sidechain interaction network of Sco GlgE1-V279S via steric interactions resulting in a conformation change in Asp 394. These findings will have implications for the design other aminocarbasugar-based GH13-inhibitors and will be useful for identifying more potent and selective inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

TRUST-EABM Contact Thermal Conductance (CTC) Report

(U) Single Feature Testbeds to Reduce Uncertainty in Simulations and Tests [3] provided an overview for the need of experiments, with accompanying models and simulations, specifically designed to reduce uncertainties and build confidence in complex testing and analysis applications. The Contact Thermal Conductance (CTC) testbed is a joint effort between W-13 (formerly E-13) and MST-8. The objective of this study was to design a testbed, with accompanying finite element models, to quantify, reduce, and propagate measurement uncertainties in contact thermal conductance measurements between two mating components in WR-like thermal environments. The knowledge gained through this simplified experiment would educate more complex assessments and interaction conditions with WR-like materials and geometries.

42 ENGINEERING↗

NASA NTRS1972

Adhesion and transfer of PTFE to metals studied by auger emission spectroscopy

The adhesion and transfer of polytetrafluoroethylene (PTFE) to metals in ultrahigh vacuum has been studied using Auger emission spectroscopy. The transfer was effected both by compressive static contact and by sliding contact. The transfer observed after static contact was independent of the chemical constitution of the substrate. Electron induced desorption of the fluorine in the transferred PTFE showed that the fluorine had no chemical interaction with the metal substrate. The coefficient of friction on metals was independent of the chemical constitution of the substrate. However, sliding PTFE on soft metals such as aluminum, generated wear fragments that lodged in the PTFE and machined the substrate.

Pepper, S. V.↗

NASA NTRS1972

Thermal properties of granulated materials.

Review of the thermophysical properties of granular materials or silicates believed to simulate the lunar surface layer. Emphasis is placed on thermal conductivity data and the effects of material and environmental variables on the thermal conductivity. There are three basic mechanisms of heat transfer in particulate materials: conduction by the gas contained in the void spaces between the particles; conduction within the solid particles and across the interparticle contacts; and thermal radiation within the particles, across the void spaces between particle surfaces, and between void spaces themselves. Gas and solid conduction, thermal radiation, and the interaction between conduction and radiation are considered.

Wechsler, A. E.↗

NASA NTRS1984

Interactions between volume and surface EM waves in layered structures

Using light scattering spectroscopy, the interaction of Surface Plasmon Polariton SPP in silver films on a glass substrate is with the incident radiation and with optical phonons of an external medium in contact with the film. The mean free path and the field strength of SPP are determined. The same SPP plays an important role in light emitting tunnel junctions (LETJ) in which an electrical current is converted into Volume Electromagnetic Wave VEW. The efficiency of light emission from LETJ through a prism coupler rather than through surface roughness is discussed. The coupling between phonon surface polaritons (PhSP) and optical guided waves (OGW) in thin films of GaP is also examined.

Ushioda, S.↗

DOE OSTI2024

MOOSE–Workbench Integration and MOOSE Meshing Capability Enhancements to Facilitate Inputs and Outputs for Multiphysics Modeling

The Multiphysics Object-Oriented Simulation Environment (MOOSE) is an open-source framework that supports many of the US Department of Energy’s (DOE’s) Nuclear Energy Advanced Modeling and Simulation (NEAMS) technical areas (TA). These TAs develop and use NEAMS physics and coupling modules in multiple ways to enable the research and development of complex physics models. In addition to the MOOSE framework, the NEAMS Workbench user interface provides a common analysis environment with user-interaction accelerators that streamline the tasks of model creation, review, execution, and output inspection. In FY 2024, objectives were realized in the MOOSE framework application development support and user-oriented improvements. Application development improvements support both developers and users with an expanded Reactor Module and Mesh System, stateful material property support for mortar contact, and customizable convergence criteria. Additionally, new user-oriented features were implemented in the MOOSE framework language server, including autocompletion snippets, definition from source and find reference navigations, and syntax overrides. Lastly, improvements were made to the input interpreter necessary to support the MOOSE language server and the NEAMS Workbench so that they can interact with syntactically incomplete user inputs. These improvements and more were intended to address stakeholder feedback and improve developer and user ability to conduct advanced nuclear energy modeling and simulation in support of DOE and industry needs.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2024

MOOSE-Workbench integration and MOOSE meshing capability enhancements to facilitate inputs and outputs for multiphysics modeling

The Multiphysics Object-Oriented Simulation Environment (MOOSE) is an open-source framework that supports many of the US Department of Energy’s (DOE’s) Nuclear Energy Advanced Modeling and Simulation (NEAMS) technical areas (TA). These TAs develop and use NEAMS physics and coupling modules in multiple ways to enable the research and development of complex physics models. In addition to the MOOSE framework, the NEAMS Workbench user interface provides a common analysis environment with user-interaction accelerators that streamline the tasks of model creation, review, execution, and out put inspection. In FY 2024, objectives were realized in the MOOSE framework application development support and user-oriented improvements. Application development improvements support both developers and users with an expanded Reactor Module and Mesh System, stateful material property support for mortar contact, and customizable convergence criteria. Additionally, new user-oriented features were implemented in the MOOSE framework language server, including autocompletion snippets, definition from source and find reference navigations, and syntax overrides. Lastly, improvements were made to the input interpreter necessary to support the MOOSE language server and the NEAMS Workbench so that they can interact with syntactically incomplete user inputs. These improvements and more were intended to address stakeholder feedback and improve developer and user ability to conduct advanced nuclear energy modeling and simulation in support of DOE and industry needs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

The Ephb2 Receptor Uses Homotypic, Head-to-Tail Interactions within Its Ectodomain as an Autoinhibitory Control Mechanism

The Eph receptor tyrosine kinases and their ephrin ligands direct axon pathfinding and neuronal cell migration, as well as mediate many other cell–cell communication events. Their dysfunctional signaling has been shown to lead to various diseases, including cancer. The Ephs and ephrins both localize to the plasma membrane and, upon cell–cell contact, form extensive signaling assemblies at the contact sites. The Ephs and the ephrins are divided into A and B subclasses based on their sequence conservation and affinities for each other. The molecular details of Eph–ephrin recognition have been previously revealed and it has been documented that ephrin binding induces higher-order Eph assemblies, which are essential for full biological activity, via multiple, distinct Eph–Eph interfaces. One Eph–Eph interface type is characterized by a homotypic, head-to-tail interaction between the ligand-binding and the fibronectin domains of two adjacent Eph molecules. While the previous Eph ectodomain structural studies were focused on A class receptors, we now report the crystal structure of the full ectodomain of EphB2, revealing distinct and unique head-to-tail receptor–receptor interactions. The EphB2 structure and structure-based mutagenesis document that EphB2 uses the head-to-tail interactions as a novel autoinhibitory control mechanism for regulating downstream signaling and that these interactions can be modulated by posttranslational modifications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Charge Separation at Organic Interfaces with Near-Zero Energy Offset: A Step toward Designing Inorganic-like Organic Semiconductors

For organic semiconductors, it is often presumed that an energy level offset at the donor–acceptor (D-A) interface is required to provide the driving force for charge separation (CS). This energy level offset unavoidably leads to a voltage loss in organic photovoltaics. In this work, by using zinc phthalocyanine (ZnPc) and fluorinated zinc phthalocyanine (F 4 ZnPc) as a model D/A interface, we found that spontaneous CS, with an enthalpy increase of ∼0.3–0.4 eV, can occur even with an interfacial energy offset as small as ∼0.1 eV. This enthalpy-increase CS process is driven by entropy. The entropic driving force can be enhanced by two factors: (1) a point-like spatial contact between the delocalized electron and hole wave function in the charge transfer exciton; (2) a small band bending near the interface originating from long-range electrostatic interaction. Our work demonstrates that effective CS can occur at interfaces with a near-zero energy level offset, which means that the energy loss at the D/A interface can be avoided.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Early immune response to Coccidioides is characterized by robust neutrophil and fibrotic macrophage recruitment and differentiation

Coccidioidomycosis, or Valley fever, is an emerging respiratory disease caused by soil-dwelling fungi of the Coccidioides genus that is expected to spread from the southwest into the central U.S. by 2050. While 60% of infections are asymptomatic, the other 40% of patients experience a range of symptoms, from self-limiting pneumonia to life-threatening disseminated disease. The immunological events that underlie the progression to severe disease remain underdefined. Here, we probed the early immune response to Coccidioides using a high dose of an attenuated strain of Coccidioides posadasii in a mouse model of infection coupled with single-cell RNA sequencing. At 24 h post-infection, robust immune infiltration is detected in the lung, marked by high levels of inflammatory PD-L1 + neutrophils and fungal-contact-dependent pro-fibrotic Spp1 + macrophages. These findings elucidate the early dynamics of the host response to Coccidioides and provide a deeper understanding of host-pathogen interactions in the lung.

Coccidioides↗

DOE OSTI2024

Deep Learning Prediction of Protein Complex Structures

Proteins interact to form protein complex to carry out biological functions such as catalytic chemical reaction. Therefore, it is important to develop computational methods to predict protein-protein interaction and the structures of protein complexes to study and enhance protein function. In this project, we successfully developed several deep learning methods to predict inter-protein contacts and the reinforcement learning and optimization methods to reconstruct protein complex structures from predicted inter-chain contacts. The methods were integrated with the MULTICOM protein complex structure prediction system and applied to predict the complex structures of biomass production-related proteins of green algae. During the two and a half years of research and development, all the specific milestones of the project were achieved successfully. 16 publications/manuscripts were produced. 10 software tools were developed. A patent application was submitted. Our MULTICOM predictors leveraging some tools developed in this project were ranked among the top predictors in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Aging of Limestones and Silane–Siloxane-Based Protective Hydrophobics: The Impact of Heating–Cooling and Freeze–Thaw Cycles

Stones are traditionally used in construction and architectural applications as building elements due to their aesthetic and technical/structural performance. Like other environmental factors (rain, humidity, moisture, salt presence, biological activity, etc.), heating–cooling and freeze–thaw cycles significantly threaten the longevity of stone materials. Hence, considering the socio-economic and cultural value of stones, preventive actions such as hydrophobic coatings are applied to prevent or mitigate damage. The scope of this study is the performance assessment of limestones with different characteristics and the efficiency of various commercial silane/siloxane-based hydrophobic coatings when exposed to thermal variation and freeze–thaw. For that purpose, the standards EN 14066:2013 (determination of resistance to aging by thermal shock) and EN 12371:2010 (determination of frost resistance) were followed. Open porosity and static contact angles were estimated to assess the stone durability and water protection capabilities of the hydrophobics. Additionally, sound speed propagation velocity, quality of building material index, elastic modulus and flexural strength were measured to evaluate the variation of mechanical properties. Static contact angle revealed that the coatings maintained an efficient level of hydrophobicity even after thermal-shock and freeze–thaw weathering tests. The study also revealed a critical interaction between freeze–thaw cycles, hydrophobic coatings and structural integrity of the stones, mostly on more porous ones. When they are subjected to harsh environmental conditions, untreated porous limestones keep structural cohesion, allowing for the natural absorption and release of water during freezing and thawing. On the contrary, when limestones are treated, the hydrophobic coatings can moderately obstruct the water release due to the partial saturation of the porous framework by the products. It also probably resulted from the different mechanical behavior between the inner matrix and layer of stone coated, resulting in a premature breakout and mechanical damage of the stone.

Lisci, Carla (ORCID:000000032179130X)↗

NASA NTRS1972

Adhesion and transfer of polytetrafluorethylene to metals studied by Auger emission spectroscopy

The adhesion and transfer of polytetrafluoroethylene (PTFE) to metals in ultrahigh vacuum were studied. The transfer was effected both by compressive static contact and by sliding contact. The transfer observed after static contact was independent of the chemical constitution of the substrate. Electron-induced desorption of the fluorine in the transferred PTFE showed that the fluorine had no chemical interaction with the metal substrate. The coefficient of friction on metals was independent of the chemical constitution of the substrate. However, sliding PTFE on soft metals, such as aluminum, generated wear fragments that lodged in the PTFE and machined the substrate.

Pepper, S. V.↗

NASA NTRS1989

Impact cratering: A geologic process

The mechanisms involved in the formation of impact craters are examined theoretically, reviewing the results of recent investigations. Topics addressed include crater morphology, stress waves in solids, the contact and compression stage, the excavation stage, and ejecta deposits. Consideration is given to the scaling of crater dimensions, the crater modification stage, multiring basins, cratered landscapes, atmospheric interactions, and the implications of impact cratering for planetary evolution. Extensive diagrams, graphs, tables, and images of typical craters are provided.

Melosh, H. J.↗

NASA NTRS1998

Numerical Modeling of Physical Vapor Transport in Contactless Crystal Growth Geometry

Growth from the vapor under conditions of limited contact with the walls of the growth ampoule is beneficial for the quality of the growing crystal due to reduced stress and contamination which may be caused by interactions with the growth container. The technique may be of a particular interest for studies on crystal growth under microgravity conditions: elimination of some factors affecting the crystal quality may make interpretation of space-conducted processes more conclusive and meaningful. For that reason, and as a part of our continuing studies on 'contactless' growth technique, we have developed a computational model of crystal growth process in such system. The theoretical model was built, and simulations were performed using the commercial computational fluid dynamics code, (CFD) ACE. The code uses an implicit finite volume formulation with a gray discrete ordinate method radiation model which accounts for the diffuse absorption and reflection of radiation throughout the furnace. The three-dimensional model computes the heat transfer through the crystal, quartz, and gas both inside and outside the ampoule, and mass transport from the source to the crystal and the sink. The heat transport mechanisms by conduction, natural convection, and radiation, and mass transport by diffusion and convection are modeled simultaneously and include the heat of the phase transition at the solid-vapor interfaces. As the thermal boundary condition, temperature profile along the walls of the furnace is used. For different thermal profiles and furnace and ampoule dimensions, the crystal growth rate and development of the crystal-vapor and source-vapor interfaces (change of the interface shape and location with time) are obtained. Super/under-saturation in the ampoule is determined and critical factors determining the 'contactless' growth conditions are identified and discussed. The relative importance of the ampoule dimensions and geometry, the furnace dimensions and its temperature, and the properties of the grown material are analyzed. The results of the simulations are compared with related experimental results on growth of CdTe, CdZnTe, ZnTe, PbTe, and PbSnTe crystals by this technique.

Palosz, W.↗

NASA NTRS1991

Optimization of transistor design including large signal device/circuit interactions at extremely high frequencies (20-100+GHz)

Transistor design for extremely high frequency applications requires consideration of the interaction between the device and the circuit to which it is connected. Traditional analytical transistor models are to approximate at some of these frequencies and may not account for variations of dopants and semiconductor materials (especially some of the newer materials) within the device. Physically based models of device performance are required. These are based on coupled systems of partial differential equations and typically require 20 minutes of Cray computer time for a single AC operating point. A technique is presented to extract parameters from a few partial differential equation solutions for the device to create a nonlinear equivalent circuit model which runs in approximately 1 second of personal computer time. This nonlinear equivalent circuit model accurately replicates the contact current properties of the device as computed by the partial differential solver on which it is based. Using the nonlinear equivalent circuit model of the device, optimization of systems design can be performed based on device/circuit interactions.

Levy, Ralph↗

DOE OSTI2020

Experimental and theoretical description of the process of contact laser surgery with a titanium-doped optothermal fibre converter

In an in vitro experiment simulating a surgeon’s actions in the process of contact laser surgery of soft biological tissue, the dependences of the temperature of a titanium-doped optothermal fibre converter (TOTFC) and the depths of coagulation and ablation of biological tissue on the average radiation power of a diode laser with a wavelength of 980 nm and on the speed of the converter movement along biological tissue are obtained. The structural, optical, and thermophysical models of TOTFC are discussed, as well as the thermophysical model of the interaction of a laser-heated converter with biological tissue, which takes into account the temperature dependences of the basic thermophysical parameters of the converter and biological tissue, as well as the contribution of the thickness h{sub int} of the water vapour layer between the converter and biotissue. It is shown that the proposed model allows describing the result of contact laser surgery of soft biotissue with TOTFC adequately to the experiment. (laser biophotonics)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗