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At least 703 records · Page 39

Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase

Although Elvitegravir (EVG) is a newly developed antiretrovirals drug to treat the acquired immunodeficiency syndrome (AIDS), drug resistance has already been found in clinic, such as E92Q/N155H and Q148H/G140S. Several structural investigations have already been reported to reveal the molecular mechanism of the drug resistance. As full length crystal structure for HIV-1 integrase is still unsolved, we use in this paper the crystal structure of the full length prototype foamy virus (PFV) in complex with virus DNA and inhibitor Elvitegravir as a template to construct the wild type and E92Q/N155H mutant system of HIV-1 integrase. Molecular dynamic simulations was used to revel the binding mode and the drug resistance of the EVG ligand in E92Q/N155H. Several important interactions were discovered between the mutated residues and the residues in the active site of the E92Q/N155H double mutant pattern, and cross correlation and clustering methods were used for detailed analysis. The results from the MD simulation studies will be used to guide the experimental efforts of developing novel inhibitors against drug-resistant HIV integrase mutants.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling Systematic Discrepancies in Nuclear-Data Measurements with Machine Learning

Nuclear data and their associated co-variances are constantly being reevaluated as techniques improve and as new experimental data, as well as nuclearmodel developments, emerge. A standard technique used to evaluate mean values in nuclear data, and their associated covariances, is the generalized linear least squares (GLLS) method. Aligning with recent efforts to incorporate measurement features into nuclear data evaluation, we augment GLLS by including a linear term which attempts to predict potential systematic discrepancies in experimental data as related to the measurement features. Due to the general nature of this augmentation, we are able to apply this evaluation to three key observables: neutroninduced fission cross sections, the average prompt neutron multiplicity, and the prompt-fission neutron spectrum of ²³⁹Pu.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

ITAR: A modified TAR method to determine depth dose distribution for an ophthalmic device that performs kilovoltage x-ray pencil-beam stereotaxy

Purpose: New technology has been developed to treat age-related macular degeneration (AMD) using 100 kVp pencil-beams that enter the patient through the radio-resistant sclera with a depth of interest between 1.6 and 2.6 cm. Measurement of reference and relative dose in a kilovoltage x-ray beam with a 0.42 cm diameter field size and a 15 cm source to axis distance (SAD) is a challenge that is not fully addressed in current guidelines to medical physicists. AAPM's TG-61 gives dosimetry recommendations for low and medium energy x-rays, but not all of them are feasible to follow for this modality. Methods: An investigation was conducted to select appropriate equipment for the application. PTW's Type 34013 Soft X-Ray Chamber (Freiburg, Germany) and CIRS's Plastic Water LR (Norfolk, VA) were found to be the best available options. Attenuation curves were measured with minimal scatter contribution and thus called Low Scatter Tissue Air Ratio (LSTAR). A scatter conversion coefficient (C{sub scat}) was derived through Monte Carlo radiation transport simulation using MCNPX (LANL, Los Alamos, NM) to quantify the difference between a traditional TAR curve and the LSTAR curve. A material conversion coefficient (C{sub mat}) was determined through experimentation to evaluate the difference in attenuation properties between water and Plastic Water LR. Validity of performing direct dosimetry measurements with a source to detector distance other than the treatment distance, and therefore a different field size due to a fixed collimator, was explored. A method—Integrated Tissue Air Ratio (ITAR)—has been developed that isolates each of the three main radiological effects (distance from source, attenuation, and scatter) during measurement, and integrates them to determine the dose rate to the macula during treatment. Results: LSTAR curves were determined to be field size independent within the range explored, indicating that direct dosimetry measurements may be performed with a source to detector distance of 20 cm even though the SAD is 15 cm during treatment. C{sub scat} varied from 1.102 to 1.106 within the range of depths of interest. The experimental variance among repeated measurements of C{sub mat} was larger than depth dependence, so C{sub mat} was estimated as1.019 for all depths of interest. Conclusions: Equipment selection, measurement techniques, and formalism for the determination of dose rate to the macula during stereotaxy for AMD have been determined and are strongly recommended by the authors of this paper to be used by clinical medical physicists.

61 RADIATION PROTECTION AND DOSIMETRY↗

Optical tweezer measurements of asymptotic nonlinearities in complex fluids

This article presents micro-medium-amplitude oscillatory shear (μMAOS), a method to measure the frequency-dependent micromechanical properties of soft materials in the asymptotically nonlinear regime using optical tweezers. For this work, we have developed a theoretical framework to extract these nonlinear mechanical properties of the material from experimental measurements and also proposed a physical interpretation of the third-order nonlinearities measured in single-tone oscillatory tests. We validate the method using a well-characterized surfactant solution of wormlike micelles, and subsequently employ this technique to demonstrate that the cytoplasm of a living cell undergoes strain softening and shear thinning when locally subjected to weakly nonlinear oscillatory deformations.

59 BASIC BIOLOGICAL SCIENCES↗

Experimental Investigation of Hydrodynamic Response of an Ocean Uranium Extraction Machine Attached to a Floating Wind Turbine

With conventional sources of uranium forecasted to be depleted within a century, developing methods to cost-effectively harvest uranium from seawater, which is estimated to contain 1000 times more uranium than on land, are crucial to the continued viability of nuclear power generation. Studies have shown that coupling a uranium harvester system with an existing offshore structure, such as a floating wind turbine (FWT), could greatly reduce the cost of harvesting uranium from seawater as it eliminates the need for dedicated moorings and increases the overall energy-gathering ability of the offshore wind farm. This study explores the hydrodynamic effects of adding a uranium harvester to an offshore floating wind turbine. The experimentally determined hydrodynamic responses of two designs of a Symbiotic Machine for Ocean uRanium Extraction (SMORE) are compared with that of an unmodified FWT. Both SMORE designs utilize adsorbent filament that is enclosed in a hard permeable shell to decouple the mechanical and chemical requirements of the device. In this work, it was found that both SMORE designs do not significantly shift the resonant peaks of the FWT.

42 ENGINEERING↗

Computer Simulation and Experimental Validation on the Oxidation and Sulfate Corrosion Resistance of Novel Chromium Based High Temperature Alloys

This report summarizes our recent works of ab initio molecular dynamics inter-atomic potentials development on dilute rare earth element yttrium (Y) etc. doped chromium (Cr) alloy systems, its applications in oxidation and corrosion resistance simulation, and experiment validation on the candidate systems. The simulation methods, experimental validation techniques, achievements already reached, students training, and future improvement are briefly introduced.

36 MATERIALS SCIENCE↗

High temperature high velocity direct power extraction using an open-cycle oxy-combustion system

The implementation of oxy-fuel technology in fossil-fuel power plants may contribute to increased system efficiencies and a reduction of pollutant emissions. One technology that has potential to utilize the temperature of undiluted oxy-combustion flames is open-cycle magnetohydrodynamic (MHD) power generators. These systems can be configured as a topping cycle and provide high enthalpy, electrically conductive flows for direct conversion of electricity. This report presents the design and modeling strategies of a MHD combustor operating at temperatures exceeding 3000 K. Throughout the study, computational fluid dynamics (CFD) models were extensively used as a design and optimization tool. A lab-scale 60 kWth model was designed, manufactured and tested as part of this project. A fully-coupled numerical method was developed in ANSYS FLUENT to characterize the heat transfer in the system. This study revealed that nozzle heat transfer may be predicted through a 40% reduction of the semi-empirical Bartz correlation. Experimental results showed good agreement with the numerical evaluation, with the combustor exhibiting a favorable performance when tested during extended time periods. A transient numerical method was employed to analyze fuel injector geometries for the 60-kW combustor. The ANSYS FLUENT study revealed that counter-swirl inlets achieve a uniform pressure and velocity ratio when the ports of the injector length to diameter ratio (L/D) is 4. An angle of 115 degrees was found to increase distribution efficiency. The findings show that this oxy-combustion concept is capable of providing a high-enthalpy environment for seeding, in order to render the flow to be conductive. Based on previous findings, temperatures in the range of 2800-3000 K may enable magnetohydrodynamic power extraction. The heat loss fraction in this oxy-combustion system, based on CFD and analytical calculations, at optimal operating conditions, was estimated to be less than 10 percent. Furthermore, the heat transfer design removed approximately 7 MW/m2. The results observed in the lab-scale system were employed to develop a 1-MW scaled prototype. Scaling methods were based on critical design criteria found in similar systems, aimed at replicating combustion flow fields and reducing possible instabilities. A numerical simulation of the combustor wall was developed for a combined thermal steady model and static structural model. This combined model was developed predict combined stress parameters within the wall during testing conditions. Both models were developed within ANSYS FEA software package. The relative accuracy presented as well major performance parameters are discussed to assess the design's validity and ensure safety. The scaled prototype was manufactured through selective laser melting (SLM)-based additive manufacturing to reduce lead times and increase geometrical complexity. Additional CFD models were developed to optimize coolant manifold system parameters and perform a parametric study on channel geometry. An investigation on coolant manifold geometry demonstrated improvements in channel flow distribution when enlarging manifold lengths and increasing the number of tubes feeding into the flow. A three-dimensional model based on a single channel was developed to capture the effect of variable properties and thermal stratification. All cases in the simulation exhibited higher wall temperatures and lower convective coefficients than those determined through 1-D analytical equations. This implies that pressure and velocity safety factors must be implemented during system operation. Overall, the findings made in this investigation are thought to be of value to researchers and industrial practitioners when designing oxy-fuel direct power extraction systems operating at temperatures exceeding 3000 K. In addition to this, the implementation of the developed technology at pilot and commercial scales could result in a significant improvement in the efficiencies of heritage and next-generation power cycles.

03 NATURAL GAS↗

Hydrogen-induced degradation dynamics in silicon heterojunction solar cells via machine learning

Abstract Among silicon-based solar cells, heterojunction cells hold the world efficiency record. However, their market acceptance is hindered by an initial 0.5% per year degradation of their open circuit voltage which doubles the overall cell degradation rate. Here, we study the performance degradation of crystalline-Si/amorphous-Si:H heterojunction stacks. First, we experimentally measure the interface defect density over a year, the primary driver of the degradation. Second, we develop SolDeg, a multiscale, hierarchical simulator to analyze this degradation by combining Machine Learning, Molecular Dynamics, Density Functional Theory, and Nudged Elastic Band methods with analytical modeling. We discover that the chemical potential for mobile hydrogen develops a gradient, forcing the hydrogen to drift from the interface, leaving behind recombination-active defects. We find quantitative correspondence between the calculated and experimentally determined defect generation dynamics. Finally, we propose a reversed Si-density gradient architecture for the amorphous-Si:H layer that promises to reduce the initial open circuit voltage degradation from 0.5% per year to 0.1% per year.

14 SOLAR ENERGY↗

Acquisition of Real-Time Operation Analytics for an Automated Serial Sectioning System

Mechanical serial sectioning is a highly repetitive technique employed in metallography for the rendering of 3D reconstructions of microstructure. While alternate techniques such as ultrasonic detection, micro-computed tomography, and focused ion beam milling have progressed much in recent years, few alternatives provide equivalent opportunities for comparatively high resolutions over significantly sized cross-sectional areas and volumes. To that end, the introduction of automated serial sectioning systems has greatly heightened repeatability and increased data collection rates while diminishing opportunity for mishandling and other user-introduced errors. Unfortunately, even among current, state-of-the-art automated serial sectioning systems, challenges in data collection have not been fully eradicated. Therefore, this paper highlights two specific advances to assist in this area; a non-contact laser triangulation method for assessment of material removal rates and a newly developed graphical user interface providing real-time monitoring of experimental progress. Furthermore, both are shown to be helpful in the rapid identification of anomalies and interruptions, while also providing comparable and less error-prone measures of removal rate over the course of these long-term, challenging, and innately destructive characterization experiments.

36 MATERIALS SCIENCE↗

Hybrid machine learning/physics-based approach for predicting oxide glass-forming ability

Predicting the liquid compositions that will vitrify at experimentally accessible quench rates remains one of the grand challenges in the field of condensed matter physics. This glass-forming ability can be quantified as the critical quench rate needed to suppress crystallization. Knowledge of this critical quench rate also informs which glass composition could be used for new applications. There have been several physical and empirical models presented in the literature to predict the critical quench rate/glass forming ability. These models range from those theoretically derived to those quantified only through experimental characterization. In this work, we instead propose a new method to calculate the critical quench rate using the recently developed toy landscape model combined with machine learning. The toy landscape model accesses the underlying physics that control the vitrification behavior by directly simulating the liquid thermodynamics and kinetics. In conclusion, the results are discussed in terms of industrial impact, physical insights, and how the glass science community can develop improved predictions of glass-forming ability.

Crystallization↗

A novel 3D heterotypic spheroid model for studying extracellular vesicle-mediated tumour and immune cell communication

Highlights: • A novel model for studying prostate cancer-derived EV mediated effects in human immune cells was developed. • The majority of EVs are not internalised but rather remain bound at the surface of B cells. • Various T cell subsets differ in their ability to interact with cancer-derived EVs. • A fraction of EVs are internalised in CD3{sup +} T cells via macropinocytosis. Cancer-derived extracellular vesicles (EVs) have emerged as important mediators of tumour-host interactions, and they have been shown to exert various functional effects in immune cells. In most of the studies on human immune cells, EVs have been isolated from cancer cell culture medium or patients' body fluids and added to the immune cell cultures. In such a setting, the physiological relevance of the chosen EV concentration is unknown and the EV isolation method and the timing of EV administration may bias the results. In the current study we aimed to develop an experimental cell culture model to study EV-mediated effects in human T and B cells at conditions mimicking the tumour microenvironment. We constructed a human prostate cancer cell line PC3 producing GFP-tagged EVs (PC3-CD63-GFP cells) and developed a 3D heterotypic spheroid model composed of PC3-CD63-GFP cells and human peripheral blood mononuclear cells (PBMCs). The transfer of GFP-tagged EVs from PC3-CD63-GFP cells to the lymphocytes was analysed by flow cytometry and fluorescence imaging. The endocytic pathway was investigated using three endocytosis inhibitors. Our results showed that GFP-tagged EVs interacted with a large fraction of B cells, however, the majority of EVs were not internalised by B cells but rather remained bound at the cell surface. T cell subsets differed in their ability to interact with the EVs - 15.7–24.1% of the total CD3{sup +} T cell population interacted with GFP-tagged EVs, while only 0.3–5.8% of CD8{sup +} T were GFP positive. Furthermore, a fraction of EVs were internalised in CD3{sup +} T cells via macropinocytosis. Taken together, the heterotypic PC3-CD63-GFP and PBMC spheroid model provides the opportunity to study the interactions and functional effects of cancer-derived EVs in human immune cells at conditions mimicking the tumour microenvironment.

60 APPLIED LIFE SCIENCES↗

Tensile performance of sustainable Strain-Hardening Cementitious Composites with hybrid PVA and recycled PET fibers

Highlights: • SHCCs with hybrid PVA/PET fibers are theoretically and experimentally studied. • A semi-empirical way to predict strain capacity of hybrid-fiber SHCCs is proposed. • The impacts of PET fiber surface treatment and curing time are explored. • SHCCs achieve satisfactory performance even 50% PVA fibers are replaced by PET fibers. • Using PET fibers in SHCCs effectively reduces material cost and environmental impact. - Abstract: Strain-Hardening Cementitious Composite (SHCC) is a type of advanced construction material that can enhance the resiliency and durability of structures. However, the high cost of the constituents limits the wide application of SHCCs. To reduce the material cost and improve the sustainability, this study explores the potential of replacing commonly-used polyvinyl alcohol (PVA) fibers by recycled polyethylene terephthalate (PET) fibers. The potential of fiber hybridization was first evaluated using micromechanical modeling, and the ultimate tensile strain of hybrid-fiber SHCCs was estimated using a semi-empirical method. Then the tensile performance of SHCCs after standard curing and accelerated aging was experimentally evaluated, and the crack pattern development with increasing tensile strain was recorded. Satisfactory mechanical performance can be achieved even when 50% of PVA fibers are replaced by recycled PET fibers with surface treatment. In addition, using recycled PET fibers in SHCCs can significantly reduce the material cost and environmental impact.

36 MATERIALS SCIENCE↗

Field measurement of moisture-buffering model inputs for residential buildings

Moisture adsorption and desorption in building materials impact indoor humidity. This effect should be included in building-energy simulations, particularly when humidity is being investigated or controlled. Several models can calculate this moisture-buffering effect, but accurate ones require model inputs that are not always known to the user of the building-energy simulation. This research developed an empirical method to extract whole-house model inputs for the effective moisture penetration depth (EMPD) model. The experimental approach was to subject the materials in the house to a square-wave relative-humidity profile, measure all of the moisture-transfer terms (e.g., infiltration, air-conditioner condensate), and calculate the only unmeasured term—the moisture sorption into the materials. We validated this method with laboratory measurements, which we used to measure the EMPD model inputs of two houses. After deriving these inputs, we measured the humidity of the same houses during tests with realistic latent and sensible loads and demonstrated the accuracy of this approach. Furthermore, these results show that the EMPD model, when given reasonable inputs, is an accurate moisture-buffering model.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Microkinetic Modeling: A Tool for Rational Catalyst Design

The design of heterogeneous catalysts relies on understanding the fundamental surface kinetics that controls catalyst performance, and microkinetic modeling is a tool that can help the researcher in streamlining the process of catalyst design. Microkinetic modeling is used to identify critical reaction intermediates and rate-determining elementary reactions, thereby providing vital information for designing an improved catalyst. In this review, we summarize general procedures for developing microkinetic models using reaction kinetics parameters obtained from experimental data, theoretical correlations, and quantum chemical calculations. We examine the methods required to ensure the thermodynamic consistency of the microkinetic model. We describe procedures required for parameter adjustments to account for the heterogeneity of the catalyst and the inherent errors in parameter estimation. We discuss the analysis of microkinetic models to determine the rate determining reactions using the degree of rate control and reversibility of each elementary reaction. We introduce incorporation of Brønsted–Evans–Polanyi relations and scaling relations in microkinetic models and the effects of these relations on catalytic performance and formation of volcano curves. We review the analysis of reaction schemes in terms of the maximum rate of elementary reactions, and we outline a procedure to identify kinetically significant transition states and adsorbed intermediates. Here, we explore the application of generalized rate expressions for the prediction of optimal binding energies of important surface intermediates and to estimate the extent of potential rate improvement. We also explore the application of microkinetic modeling in homogeneous catalysis, electro-catalysis, and transient reaction kinetics. We conclude by highlighting the challenges and opportunities in the application of microkinetic modeling for catalyst design.

42 ENGINEERING↗

Biopolymer-Templated Titania Film Formation for Nanostructured Coatings Revealed by Machine Learning-Supported Time-Resolved Analysis

This study presents a machine learning approach to derive the film formation of biopolymer-templated titania nanostructures during spray deposition, in combination with in situ grazing-incidence small-angle X-ray scattering (GISAXS). A neural network trained on synthetic GISAXS data directly predicts domain-size distributions from experimental two-dimensional scattering patterns, capturing the full kinetics of nanostructure evolution with high temporal resolution. The predictions reveal hierarchical size distributions and periodic growth features, consistent with layer-by-layer spray deposition and validated by complementary scanning electron microscopy (SEM) imaging. Quantitative comparison with conventional parametric GISAXS fits shows good qualitative agreement, with systematic differences explained by domain-shape assumptions and resolved by applying a geometric scaling factor. Simulated SEM-like surfaces derived from neural network outputs reproduce the porous, foam-like nanoscale morphology observed experimentally, reinforcing the method’s credibility. This integrated approach enables real-time, nondestructive, statistically averaged monitoring of bulk nanostructure development in functional coatings, offering a scalable methodology to accelerate the characterization and process control of sustainably manufactured nanostructured titania films for energy-related applications such as photocatalysis and photovoltaics.

Heger, JulianEliah↗

Quantum many-body physics from a gravitational lens

The past two decades have seen the emergence of remarkable interconnections among previously remotely related disciplines, such as condensed matter, nuclear physics, gravity and quantum information, fuelled both by experimental advances and by the new powerful theoretical methods offered by holographic duality. In this Review, we sample some recent developments in holographic duality in connection with quantum many-body dynamics. These include insights into strongly correlated phases without quasiparticles and their transport properties, quantum many-body chaos and the scrambling of quantum information. We also discuss recent progress in understanding the structure of holographic duality itself using quantum information, including a ‘local’ version of the duality, as well as the quantum error-correction interpretation of quantum many-body states with a gravity dual, and how such notions help to demonstrate the unitarity of black hole evaporation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Jumping-droplet electronics hot-spot cooling

Demand for enhanced cooling technologies within various commercial and consumer applications has increased in recent decades due to electronic devices becoming more energy dense. This study demonstrates jumping-droplet based electric-field-enhanced (EFE) condensation as a potential method to achieve active hot spot cooling in electronic devices. To test the viability of EFE condensation, we developed an experimental setup to remove heat via droplet evaporation from single and multiple high power gallium nitride (GaN) transistors acting as local hot spots (4.6 mm x 2.6 mm). An externally powered circuit was developed to direct jumping droplets from a copper oxide (CuO) nanostructured superhydrophobic surface to the transistor hot spots by applying electric fields between the condensing surface and the transistor. Heat transfer measurements were performed in ambient air (22-25°C air temperature, 20-45% relative humidity) to determine the effect of gap spacing (2-4 mm), electric field (50-250 V/cm), and heat flux (demonstrated to 13 W/cm 2 ). EFE condensation was shown to enhance the heat transfer from the local hot spot by ≈ 200% compared to cooling without jumping and by 20% compared to non-EFE jumping. Dynamic switching of the electric field for a two-GaN system reveals the potential for active cooling of mobile hot spots. The opportunity for further cooling enhancement by the removal of non-condensable gases promises hot spot heat dissipation rates approaching 120 W/cm 2 . Finally, this work provides a framework for the development of active jumping droplet based vapor chambers and heat pipes capable of spatial and temporal thermal dissipation control.

36 MATERIALS SCIENCE↗

The conversion of CESR to operate as the Test Accelerator, CesrTA. Part 3: Electron cloud diagnostics

Cornell's electron/positron storage ring (CESR) was modified over a series of accelerator shutdowns beginning in May 2008, which substantially improves its capability for research and development for particle accelerators. CESR's energy span from 1.8 to 5.6 GeV with both electrons and positrons makes it ideal for the study of a wide spectrum of accelerator physics issues and instrumentation related to present light sources and future lepton damping rings. Additionally a number of these are also relevant for the beam physics of proton accelerators. This paper is the third in a series of four describing the conversion of CESR to the test accelerator, CESRTA. The first two papers discuss the overall plan for the conversion of the storage ring to an instrument capable of studying advanced accelerator physics issues [1] and the details of the vacuum system upgrades [2]. This paper focuses on the necessary development of new instrumentation, situated in four dedicated experimental regions, capable of studying such phenomena as electron clouds (ECs) and methods to mitigate EC effects. The fourth paper in this series describes the vacuum system modifications of the superconducting wigglers to accommodate the diagnostic instrumentation for the study of EC behavior within wigglers. Lastly, while the initial studies of CESRTA focused on questions related to the International Linear Collider damping ring design, CESRTA is a very versatile storage ring, capable of studying a wide range of accelerator physics and instrumentation questions.

43 PARTICLE ACCELERATORS↗