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At least 1,441 records · Page 80

Computational studies of Ras and PI3K

Until recently, experimental techniques in molecular cell biology have been the primary means to investigate biological risk upon space radiation. However, computational modeling provides an alternative theoretical approach, which utilizes various computational tools to simulate proteins, nucleotides, and their interactions. In this study, we are focused on using molecular mechanics (MM) and molecular dynamics (MD) to study the mechanism of protein-protein binding and to estimate the binding free energy between proteins. Ras is a key element in a variety of cell processes, and its activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. Different computational approaches for this particular study are presented to calculate the solvation energies and binding free energies of H-Ras and PI3K. The goal of this study is to establish computational methods to investigate the roles of different proteins played in the cellular responses to space radiation, including modification of protein function through gene mutation, and to support the studies in molecular cell biology and theoretical kinetics models for our risk assessment project.

Ren, Lei↗

Human factors model concerning the man-machine interface of mining crewstations

The U.S. Bureau of Mines is developing a computer model to analyze the human factors aspect of mining machine operator compartments. The model will be used as a research tool and as a design aid. It will have the capability to perform the following: simulated anthropometric or reach assessment, visibility analysis, illumination analysis, structural analysis of the protective canopy, operator fatigue analysis, and computation of an ingress-egress rating. The model will make extensive use of graphics to simplify data input and output. Two dimensional orthographic projections of the machine and its operator compartment are digitized and the data rebuilt into a three dimensional representation of the mining machine. Anthropometric data from either an individual or any size population may be used. The model is intended for use by equipment manufacturers and mining companies during initial design work on new machines. In addition to its use in machine design, the model should prove helpful as an accident investigation tool and for determining the effects of machine modifications made in the field on the critical areas of visibility and control reach ability.

Rider, James P.↗

Downscaling GISS ModelE Boreal Summer Climate over Africa

The study examines the perceived added value of downscaling atmosphere-ocean global climate model simulations over Africa and adjacent oceans by a nested regional climate model. NASA/Goddard Institute for Space Studies (GISS) coupled ModelE simulations for June- September 1998-2002 are used to form lateral boundary conditions for synchronous simulations by the GISS RM3 regional climate model. The ModelE computational grid spacing is 2deg latitude by 2.5deg longitude and the RM3 grid spacing is 0.44deg. ModelE precipitation climatology for June-September 1998-2002 is shown to be a good proxy for 30-year means so results based on the 5-year sample are presumed to be generally representative. Comparison with observational evidence shows several discrepancies in ModelE configuration of the boreal summer inter-tropical convergence zone (ITCZ). One glaring shortcoming is that ModelE simulations do not advance the West African rain band northward during the summer to represent monsoon precipitation onset over the Sahel. Results for 1998-2002 show that onset simulation is an important added value produced by downscaling with RM3. ModelE Eastern South Atlantic Ocean computed sea-surface temperatures (SST) are some 4 K warmer than reanalysis, contributing to large positive biases in overlying surface air temperatures (Tsfc). ModelE Tsfc are also too warm over most of Africa. RM3 downscaling somewhat mitigates the magnitude of Tsfc biases over the African continent, it eliminates the ModelE double ITCZ over the Atlantic and it produces more realistic orographic precipitation maxima. Parallel ModelE and RM3 simulations with observed SST forcing (in place of the predicted ocean) lower Tsfc errors but have mixed impacts on circulation and precipitation biases. Downscaling improvements of the meridional movement of the rain band over West Africa and the configuration of orographic precipitation maxima are realized irrespective of the SST biases.

Regional climate models↗

Exploring strongly correlated quantum spin systems with quantum computers

At inception, quantum annealing leveraged quantum mechanics for classical optimization tasks. However, as machine coherence increases, the realization of quantum spin systems has emerged as an even more fruitful application of this computational model. Alternatives to the standard gate model deserve exploration, to achieve useful quantum advantage via analog quantum computing. The recent demonstration of so-called coherent quantum annealing with 1,000s of qubits, further expands the potential for this hardware to explore quantum system dynamics where the effects of quantum fluctuations can be carefully controlled and observed directly. Implementing existing celebrated spin models—or in fact new and dedicated ones—into quantum annealers will lead to observation and detection of quantum phenomena not yet observed, or not visualized directly, in experimental physics laboratories. Rather than computing or simulating quantum systems, these quantum computers allow one to simply build quantum systems, and experiment on them in an uniquely controlled way, with characterization down to the constitutive degree of freedom. This provides an unprecedented opportunity for understanding the physics of quantum spin systems. Keywords: Theoretical physics currently abounds of interesting theoretical spin models to explore frustration, strongly correlated spins, spin liquids, fractionalized excitations, and topological matter. However enticing, such models are generally only weak proxies for the properties of actual materials. In quantum annealers these models could be realized and experimented upon. Moreover, many more realistic models of such materials could be realized in quantum annealers. Employed in this way, quantum annealers provide an extraordinary versatile platform to explore quantum effects that are hard to find, detect, and characterize in natural materials.

36 MATERIALS SCIENCE↗

A Realistic Full-Scale 3D Modeling of Turning Using Coupled Smoothed Particle Hydrodynamics and Finite Element Method for Predicting Cutting Forces

Computational modelling is an effective technique for understanding the complex physics of machining. Large deformations, material separation, and high computational requirements are the key challenges faced while simulating machining. This work introduces a full-scale three-dimensional model of turning operations using a combined approach based on the Smoothed Particle Hydrodynamics (SPH) and Finite Element (FE) methods. By exploiting the advantages of each method, this approach leads to high-fidelity coupled SPH-FE machining models. Cutting forces and chip morphology are the primary results of interest. The machining models are validated with the results of turning experiments. Two-dimensional machining model underpredicts the cutting force and feed force by approximately 49% and 70%, respectively. Moreover, passive force cannot be predicted using the two-dimensional model. On the other hand, with the three-dimensional models developed in this manuscript, the difference between the total simulated force and experimentally measured force is ∼17%. The chip morphologies correlate with experiments in terms of the direction of the chip movement and the “long” continuous chips observed while turning Al 6061. This work expands the realm of machining simulations from two-dimensional orthogonal machining or sectional three-dimensional model to a full-scale realistic simulation. The encouraging simulation results show the potential to study more complex phenomena, such as machining stability and tool path modulation.

42 ENGINEERING↗

Coupling a Computational Fluid Dynamics Model to a Spacecraft Thermal System Model for the DraMS Instrument Thermal Analysis

The Dragonfly Mass Spectrometer (DraMS) is an instrument on the Dragonfly mission, which will spend 7 years in deep space cruise before landing and operating on the surface of Titan. Vacuum thermal analyses are required for deep space cruise, and convection analyses are required for the Titan surface operations. Model exchanges across multiple thermal teams are needed for all phases of the mission. For DraMS, Thermal Desktop® (TD) has been the main thermal analytical tool of choice due to its capability in modeling complex thermal systems with relatively low computational power and for its availability across thermal teams. However, TD does not have computational fluid dynamics (CFD) capability and struggles to accurately capture complex convective behavior. DraMS has fans operating in tandem and gas flow behaviors are not easily predicted due to its complex flow paths. CFD software, such as Fluent, can model and predict such complex flow behaviors, but CFD models are computationally expensive, and its workflow processes are not tailored towards simulating large and complex systems. Therefore, a coupled modeling approach was chosen for DraMS: A TD model was used for simulating all the conductive, radiative, and source terms, while a Fluent CFD model was added on, as needed, to the TD model to provide the convective boundary conditions using the System Coupling software. The coupling software allows the TD and Fluent models to communicate data and arrive at a co-solved and co-converged solution. Furthermore, Thermal Iso-value Exchange (TIE) method was developed to facilitate and improve the TD-Fluent data exchange process. This paper will discuss the analytical studies that were done to verify the accuracy and usability of the coupled approach and the challenges associated, which lead to the development of the TIE approach. DraMS thermal design and co-solved analysis results will also be discussed.

Heat transfer↗

Moment method analysis of linearly tapered slot antennas: Low loss components for switched beam radiometers

A Moment Method Model for the radiation pattern characterization of single Linearly Tapered Slot Antennas (LTSA) in air or on a dielectric substrate is developed. This characterization consists of: (1) finding the radiated far-fields of the antenna; (2) determining the E-Plane and H-Plane beamwidths and sidelobe levels; and (3) determining the D-Plane beamwidth and cross polarization levels, as antenna parameters length, height, taper angle, substrate thickness, and the relative substrate permittivity vary. The LTSA geometry does not lend itself to analytical solution with the given parameter ranges. Therefore, a computer modeling scheme and a code are necessary to analyze the problem. This necessity imposes some further objectives or requirements on the solution method (modeling) and tool (computer code). These may be listed as follows: (1) a good approximation to the real antenna geometry; and (2) feasible computer storage and time requirements. According to these requirements, the work is concentrated on the development of efficient modeling schemes for these type of problems and on reducing the central processing unit (CPU) time required from the computer code. A Method of Moments (MoM) code is developed for the analysis of LTSA's within the parameter ranges given.

Koeksal, Adnan↗

Combustion Processes in Hybrid Rocket Engines

In recent years, there has been a resurgence of interest in the development of hybrid rocket engines for advanced launch vehicle applications. Hybrid propulsion systems use a solid fuel such as hydroxyl-terminated polybutadiene (HTPB) along with a gaseous/liquid oxidizer. The performance of hybrid combustors depends on the convective and radiative heat fluxes to the fuel surface, the rate of pyrolysis in the solid phase, and the turbulent combustion processes in the gaseous phases. These processes in combination specify the regression rates of the fuel surface and thereby the utilization efficiency of the fuel. In this paper, we employ computational fluid dynamics (CFD) techniques in order to gain a quantitative understanding of the physical trends in hybrid rocket combustors. The computational modeling is tailored to ongoing experiments at Penn State that employ a two dimensional slab burner configuration. The coordinated computational/experimental effort enables model validation while providing an understanding of the experimental observations. Computations to date have included the full length geometry with and with the aft nozzle section as well as shorter length domains for extensive parametric characterization. HTPB is sed as the fuel with 1,3 butadiene being taken as the gaseous product of the pyrolysis. Pure gaseous oxygen is taken as the oxidizer. The fuel regression rate is specified using an Arrhenius rate reaction, which the fuel surface temperature is given by an energy balance involving gas-phase convection and radiation as well as thermal conduction in the solid-phase. For the gas-phase combustion, a two step global reaction is used. The standard kappa - epsilon model is used for turbulence closure. Radiation is presently treated using a simple diffusion approximation which is valid for large optical path lengths, representative of radiation from soot particles. Computational results are obtained to determine the trends in the fuel burning or regression rates as a function of the head-end oxidizer mass flux, G=rho(e)U(e), and the chamber pressure. Furthermore, computation of the full slab burner configuration has also been obtained for various stages of the burn. Comparisons with available experimental data from small scale tests conducted by General Dynamics-Thiokol-Rocketdyne suggest reasonable agreement in the predicted regression rates. Future work will include: (1) a model for soot generation in the flame for more quantitative radiative transfer modelling, (2) a parametric study of combustion efficiency, and (3) transient calculations to help determine the possible mechanisms responsible for combustion instability in hybrid rocket motors.

Venkateswaran,S.↗

Computer display and manipulation of biological molecules

This paper describes a computer model that was designed to investigate the conformation of molecules, macromolecules and subsequent complexes. Utilizing an advanced 3-D dynamic computer display system, the model is sufficiently versatile to accommodate a large variety of molecular input and to generate data for multiple purposes such as visual representation of conformational changes, and calculation of conformation and interaction energy. Molecules can be built on the basis of several levels of information. These include the specification of atomic coordinates and connectivities and the grouping of building blocks and duplicated substructures using symmetry rules found in crystals and polymers such as proteins and nucleic acids. Called AIMS (Ames Interactive Molecular modeling System), the model is now being used to study pre-biotic molecular evolution toward life.

Coeckelenbergh, Y.↗

A structural dynamics investigation related to EIDI applications

A method for modeling the structural dynamics of electro-impulse deicing is presented. A guideline for building a representative finite element model is discussed together with the experimental determination of the force pulse parameters used in the computational model. The results from the computer solution are compared with experimental results for a semi-cylindrical shell. This preliminary comparison indicated that typical structural dynamic responses may be predicted in the near coil field for the duration of the forcing pulse. The sensitivity of the response to both geometric and electrical parameters is also discussed.

Bernhart, W. D.↗

AAPM Truth‐based CT (TrueCT) reconstruction grand challenge

Background: This Special Report summarizes the 2022, AAPM grand challenge on Truth-based CT image reconstruction. Purpose: To provide an objective framework for evaluating CT reconstruction methods using virtual imaging resources consisting of a library of simulated CT projection images of a population of human models with various diseases. Methods: Two hundred unique anthropomorphic, computational models were created with varied diseases consisting of 67 emphysema, 67 lung lesions, and 66 liver lesions. The organs were modeled based on clinical CT images of real patients. The emphysematous regions were modeled using segmentations from patient CT cases in the COPDGene Phase I dataset. For the lung and liver lesion cases, 1–6 malignant lesions were created and inserted into the human models, with lesion diameters ranging from 5.6 to 21.9 mm for lung lesions and 3.9 to 14.9 mm for liver lesions. The contrast defined between the liver lesions and liver parenchyma was 82 ± 12 HU, ranging from 50 to 110 HU. Similarly, the contrast between the lung lesions and the lung parenchyma was defined as 781 ± 11 HU, ranging from 725 to 805 HU. For the emphysematous regions, the defined HU values were −950 ± 17 HU ranging from −918 to −979 HU. The developed human models were imaged with a validated CT simulator. The resulting CT sinograms were shared with the participants. The participants reconstructed CT images from the sinograms and sent back their reconstructed images. Further, the reconstructed images were then scored by comparing the results against the corresponding ground truth values. The scores included both task-generic (root mean square error [RMSE] and structural similarity matrix [SSIM]), and task-specific (detectability index [d’] and lesion volume accuracy) metrics. For the cases with multiple lesions, the measured metric was averaged across all the lesions. To combine the metrics with each other, each metric was normalized to a range of 0 to 1 per disease type, with “0” and “1” being the worst and best measured values across all cases of the disease type for all received reconstructions. Results: The True-CT challenge attracted 52 participants, out of which 5 successfully completed the challenge and submitted the requested 200 reconstructions. Across all participants and disease types, SSIM absolute values ranged from 0.22 to 0.90, RMSE from 77.6 to 490.5 HU, d’ from 0.1 to 64.6, and volume accuracy ranged from 1.2 to 753.1 mm3. The overall scores demonstrated that participant “A” had the best performance in all categories, except for the metrics of d’ for lung lesions and RMSE for liver lesions. Participant “A” had an average normalized score of 0.41 ± 0.22, 0.48 ± 0.32, and 0.42 ± 0.33 for the emphysema, lung lesion, and liver lesion cases, respectively. Conclusions: The True-CT challenge successfully enabled objective assessment of CT reconstructions with the unique advantage of access to a diverse population of diseased human models with known ground truth. This study highlights the significant potential of virtual imaging trials in objective assessment of medical imaging technologies.

60 APPLIED LIFE SCIENCES↗

A methodology for evaluating the reliability and risk of structures under complex service environments

The theoretical basis and numerical implementation of NESSUS (Numerical Evaluation of Stochastic Structures Under Stress; Cruse et al., 1988), a computer code for probabilistic structural analyses of aerospace components, are described, with an emphasis on the use of NESSUS for reliability and risk assessment. Topics addressed include the structure of NESSUS, the material-properties model, computational procedures, probabilistic models of fatigue-crack initiation, risk/cost evaluation, fatigue-fracture analyses, and fatigue-crack propagation. Numerical results from typical applications are presented in extensive graphs and briefly characterized; the usefulness of NESSUS predictions for establishing inspection and retirement schedules and for component certification is indicated.

Shiao, Michael C.↗

Electronic transport in copper–graphene composites

In this work, we investigate electronic transport properties of copper–graphene (Cu–G) composites using a density-functional theory (DFT) framework. Conduction in composites is studied by varying the interfacial distance of copper/graphene/copper (Cu/G/Cu) interface models. Electronic conductivity of the models computed using the Kubo–Greenwood formula shows that the conductivity increases with decreasing Cu–G distance and saturates below a threshold Cu–G distance. The DFT-based Bader charge analysis indicates increasing charge transfer between Cu atoms at the interfacial layers and the graphene with decreasing Cu–G distance. The electronic density of states reveals increasing contributions from both copper and carbon atoms near the Fermi level with decreasing Cu–G interfacial distance. By computing the space-projected conductivity of the Cu/G/Cu models, we show that the graphene forms a bridge to the electronic conduction at small Cu–G distances, thereby enhancing the conductivity.

36 MATERIALS SCIENCE↗

Multiphase Modeling in a Parallel Plate Fluidized Bed Receiver for Concentrating Solar Power

A novel high temperature particle solar receiver is developed by using a light trapping planar cavity configuration. As particles fall through the cavity, the concentrated solar radiation warms the boundaries of the receiver and in turn heats the particles. Particles flow through the system, forming a packed bed at the lower end, leaving the system from the bottom at a constant flow rate. Air is introduced to the system as the fluidizing medium to improve particle heat transfer and mixing. A laboratory scale cavity receiver is built and a near IR quartz lamp is used to provide flux to the vertical wall of the heat exchanger. The system is modeled using a continuum two-fluid method. The computational model matches the experimental system size and the particle size distribution is assumed monodisperse. A conduction model that accounts for the effects of solid concentration is implemented, and the heat flux boundary condition matches the experimental setup. Radiative heat transfer is estimated using a widely used correlation during the post-processing step to determine an overall heat transfer coefficient. The model is validated against testing data and achieves less than 30% discrepancy and a heat transfer coefficient greater than 1000 W/m2K.

CSP↗

Understanding and controlling water-organic co-transport in amorphous microporous materials

The transport of molecules in microporous material is a significant and active area of research in separation applications. The movement of vapor/liquid molecules in a high-loading condition in microporous spaces is especially challenging to interrogate. This project aims to understand and control the transport of complex water and organic solvent mixtures in varying structures of microporous carbon molecular sieve (CMS) and activated carbon membranes. Modeling of transport behavior in such carbonaceous samples using computational modeling is difficult due to their amorphous structure. Therefore, this research intends to study the transport mechanism of water-organic mixtures by experimentally revealing fundamental transport properties, such as guest sorption amounts as well as diffusion and permeation rates. Considering the different size and guest-host affinity of water and organic solvent molecules, the objective of this research is to understand the structural conditions within the ultramicropores and micropores that generate different types of molecular transport and selection mechanisms within such complex systems. Carbonaceous materials are developed using tailored pyrolysis techniques to pyrolyze polymeric precursors, including polyvinylidene chloride (PVDC),polyvinylidene fluoride (PVDF), polymer of intrinsic microporosity (PIM) -1, and fully aromatic polyamide. The initial stage of the research will focus on the microscopic diffusion and sorption studies of pure component water, xylene isomers, and n,n- dimethylformamide within various carbons. Additional structural investigation on CMS, such as gas physisorption and neutron scattering studies, will be executed to gain deeper insight into these structure-transport relationships. Scanning electron microscopy and X-ray photoelectron microscopy are also used to further characterize these materials. The research will progress to probe mutual diffusion of complex water-organic mixtures within various CMS microstructures. Competitive sorption and permeation studies of the binary mixtures in different microstructural CMS will be followed. The obtained binary mixture transport parameters were used to predict binary water-organic mixtures transport.

36 MATERIALS SCIENCE↗

Finch: Toxicity Dose Response Curve Prediction of Chemical Compounds and Mixtures

A paradigm shift in chemical risk assessment is emphasizing mixture testing over single compound analysis, eliminating animal testing, and adopting advanced modeling approaches to understand mixture activity profiles. However, existing computational models largely focus on single chemicals, with few effective solutions for modeling complex mixtures that account for synergistic or antagonistic effects and multiple Modes of Action (MoA). Conventional methods like concentration addition (CA) and independent action (IA) are insufficient for this task as they are designed for simplistic interactions and struggle to account for the dynamic and multifaceted nature of chemical mixtures, such as overlapping MoA and non-linear interactions. Finch offers a novel approach utilizing deep learning (DL) embeddings and multi-task quantitative structure-activity relationship (QSAR) models to improve chemical exposure prediction. By leveraging molecular descriptors, physiochemical properties, and large language model (LLM) embeddings from SMILES inputs, Finch preserves critical information in a latent space thereby enhancing predictive accuracy. The multi-task learning aspect of Finch is highly advantageous, as it simultaneously optimizes multiple loss functions, leveraging all available data across tasks to develop generalized representations that effectively capture complex ingredient interactions within mixtures.

59 BASIC BIOLOGICAL SCIENCES↗

Impact of remote sensing upon the planning, management, and development of water resources

Principal water resources users were surveyed to determine the impact of remote data streams on hydrologic computer models. Analysis of responses demonstrated that: most water resources effort suitable to remote sensing inputs is conducted through federal agencies or through federally stimulated research; and, most hydrologic models suitable to remote sensing data are federally developed. Computer usage by major water resources users was analyzed to determine the trends of usage and costs for the principal hydrologic users/models. The laws and empirical relationships governing the growth of the data processing loads were described and applied to project the future data loads. Data loads for ERTS CCT image processing were computed and projected through the 1985 era.

Castruccio, P. A.↗