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At least 1,261 records · Page 70

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗

A Simple Model of the Energy Threshold for Snowball Chambers

Cloud and bubble chambers have historically been used for particle detection, capitalizing on supersaturation and superheating, respectively. Here, we present new results from a prototype snowball chamber, in which an incoming particle triggers the crystallization of a purified, supercooled liquid. We demonstrate, for the first time, simulation agreement with our first results from 5 years ago: the higher temperature of the freezing of water and significantly shorter time spent supercooled compared to the control in the presence of a Cf-252 fission neutron source. This is accomplished by combining Geant4 modeling of neutron interactions with the Seitz nucleation model used in superheated bubble chambers, including those seeking dark matter. We explore the possible implications of using this new technology for GeV-scale WIMP searches, especially in terms of spin-dependent proton coupling, and report the first supercooling of WbLS (water-based liquid scintillator).

47 OTHER INSTRUMENTATION↗

A study of application of remote sensing to river forecasting. Volume 2: Detailed technical report, NASA-IBM streamflow forecast model user's guide

The Model is described along with data preparation, determining model parameters, initializing and optimizing parameters (calibration) selecting control options and interpreting results. Some background information is included, and appendices contain a dictionary of variables, a source program listing, and flow charts. The model was operated on an IBM System/360 Model 44, using a model 2250 keyboard/graphics terminal for interactive operation. The model can be set up and operated in a batch processing mode on any System/360 or 370 that has the memory capacity. The model requires 210K bytes of core storage, and the optimization program, OPSET (which was used previous to but not in this study), requires 240K bytes. The data band for one small watershed requires approximately 32 tracks of disk storage.

Source record↗

An assessment model for atmospheric composition

Predicting future perturbations to global air quality and climate requires, as a prerequisite, prognostic models for the composition of the Earth's atmosphere. Such assessment models are needed to evaluate the impact on our environment of different social choices that affect emissions of the photochemically and radiatively important trace gases. Our presentation here of a prototype assessment model is intended to encourage public scientific discussions of the necessary components of the model and their interactions, with the recognition that models similar to this will likely be used by the Environmental Protection Agency and other regulatory agencies in order to assess the effect of changes in atmospheric composition on climate over the next century.

Prather, Michael J.↗

Cirrus Simulations of CRYSTAL-FACE 23 July 2002 Case

A key objective of the Cirrus Regional Study of Tropical Anvils and Cirrus Layers - Florida Area Cirrus Experiment (CRYSTAL-FACE) is to understand relationships between the properties of tropical convective cloud systems and the properties and lifecycle of the extended cirrus anvils they produce. We report here on a case study of 23 July 2002 where a sequence of convective storms over central Florida produced an extensive anvil outflow. Our approach is to use a suitably-initialized cloud- system simulation with MM5 (Starr et al., companion paper in this volume) to define initial conditions and time-dependent forcing for a simulation of anvil evolution using a two-dimensional fine-resolution (100 m) cirrus cloud model that explicitly accounts for details of cirrus microphysical development (bin or spectra model) and fully interactive radiative processes. The cirrus model follows Lin (1997). The microphysical components are described in Lin et al. (2004) - see Lin et a1 (this volume). Meteorological conditions and observations for the 23 July case are described in Starr et al. (this volume). The goals of the present study are to evaluate how well we can simulate a cirrus anvil lifecycle, to evaluate the importance of various physical processes that operate within the anvil, and to evaluate the importance of environmental conditions in regulating anvil lifecycle. CRYSTAL-FACE produced a number of excellent case studies of anvil systems that will allow environmental factors, such as static stability or wind shear in the upper troposphere, to be examined. In the present study, we strive to assess the importance of propagating gravity waves, likely produced by the deep convection itself, and radiative processes, to anvil lifecycle and characteristics.

Starr, David↗

Cirrus Simulations of CRYSTAL-FACE 23 July 2002 Case

A key objective of the Cirrus Regional Study of Tropical Anvils and Cirrus Layers - Florida Area Cirrus Experiment (CRYSTAL-FACE) is to understand relationships between the properties of tropical convective cloud systems and the properties and lifecycle of the extended cirrus anvils they produce. We report here on a case study of 23 July 2002 where a sequence of convective storms over central Florida produced an extensive anvil outflow. Our approach is to use a suitably-initialized cloud-system simulation with MM5 to define initial conditions and time-dependent forcing for a simulation of anvil evolution using a two-dimensional fine-resolution (100 m) cirrus cloud model that explicitly accounts for details of cirrus microphysical development (bin or spectra model) and fully interactive radiative processes. The cirrus model follows Lin. Meteorological conditions and observations for the 23 July case are described in this volume. The goals of the present study are to evaluate how well we can simulate a cirrus anvil lifecycle, to evaluate the importance of various physical processes that operate within the anvil, and to evaluate the importance of environmental conditions in regulating anvil lifecycle. CRYSTAL-FACE produced a number of excellent case studies of anvil systems that will allow environmental factors, such as static stability or wind shear in the upper troposphere, to be examined. In the present study, we strive to assess the importance of propagating gravity waves, likely produced by the deep convection itself, and radiative processes, to anvil lifecycle and characteristics.

Starr, David↗

Shock Interaction Control for Scramjet Cowl Leading Edges

An experimental study was conducted to qualitatively determine the effectiveness of stagnation-region gas injection in protecting a scramjet cowl leading edge from the intense heating produced by Type III and Type IV shock interactions. The model consisted of a two-dimensional leading edge, representative of that of a scramjet cowl. Tests were conducted at a nominal freestream Mach number of 6. Gaseous nitrogen was supersonically injected through the leading-edge nozzles at various mass flux ratios and with the model pitched at angles of 0deg and -20deg relative to the freestream flow. Qualitative data, in the form of focusing and conventional schlieren images, were obtained of the shock interaction patterns. Results indicate that large shock displacements can be achieved and both the Type III and IV interactions can be altered such that the interaction does not impinge on the leading edge surface.

Albertson, Cindy W.↗

Formal Validation of Fault Management Design Solutions

The work presented in this paper describes an approach used to develop SysML modeling patterns to express the behavior of fault protection, test the model's logic by performing fault injection simulations, and verify the fault protection system's logical design via model checking. A representative example, using a subset of the fault protection design for the Soil Moisture Active-Passive (SMAP) system, was modeled with SysML State Machines and JavaScript as Action Language. The SysML model captures interactions between relevant system components and system behavior abstractions (mode managers, error monitors, fault protection engine, and devices/switches). Development of a method to implement verifiable and lightweight executable fault protection models enables future missions to have access to larger fault test domains and verifiable design patterns. A tool-chain to transform the SysML model to jpf-Statechart compliant Java code and then verify the generated code via model checking was established. Conclusions and lessons learned from this work are also described, as well as potential avenues for further research and development.

Statechart↗

Generation and Calibration of Linear Models of Aircraft with Highly Coupled Aeroelastic and Flight Dynamics

The lightweight structures and unconventional configurations being considered for the next generation of aircraft mean that any effort to predict or control the flight dynamics is impacted by the structural dynamics. One of the most severe forms of coupling between aeroelasticity and flight dynamics is an instability called body freedom flutter. The existing tools often assume a relatively weak effect of structural dynamics on the flight dynamics, and are therefore incapable of modeling strong interactions like body freedom flutter. A method of combining different sources of data traditionally used for aeroelasticity and flight dynamics is described by reconciling many of the differences between these models. By building upon past modeling efforts, a level of familiarity in the approach is achieved. Generally the differences from the traditional approaches are subtle but significant. The traditional frequency domain flutter model in a modal coordinate system is converted to a form consistent with a time domain flight dynamics model. The time domain rational function approximation about a non-inertial coordinate system and the unique constraints for the conversion between the inertial and non-inertial coordinate systems are discussed. A consistent transformation of the states of aeroelastic models to flight dynamics models is derived, which enables the integration of data from higher fidelity computational fluid dynamics models or wind-tunnel testing. The present method of integrating multidisciplinary data was used to create models that compare well with X-56A flight-test data, including conditions past the flutter speed.

Ouellette, Jeffrey↗

Preliminary 3D Simulations of Anomalous Thermocouple Coupling to Surface Electric Fields

Anomalous measurements from subsurface thermocouples have been observed during re-entry of the Orion capsule (EFT-1 plugs). These measurements are considered anomalous because the amplitude and frequency of the inferred temperature modulations are too large to be due to plausible heating processes. Consequently, it is believed the anomalies are caused by electrical interference generated by the re-entry plasma. Quantifying these effects requires several steps: modeling the external plasma flows, modeling the plasma-surface interaction, and finally modeling the surface-thermocouple coupling. This paper addresses this last step using 3D finite element simulations of a wire embedded in a weakly conductive medium.

thermocouple anomaly↗

Using XR for Improving Scientific Discovery With Numerical Weather Models

Our work explores the use of extended reality (XR) to im- prove scientific discovery with numerical weather/climate models that inform Earth science digital twins, specifically the NASA Goddard Earth Observing System (GEOS) global atmospheric model. The overall project is named the Vi- sualization And Lagrangian dynamics Immersive eXtended Reality Toolkit (VALIXR), which has two main areas of focus: (1) enhancing the understanding of and interaction with model output data through advanced visualizations in the XR environment, and (2) the integration of Lagrangian dynamics into the GEOS model, which allows a natural, feature-specific analysis of Earth science phenomena as op- posed to traditional, fixed-point Eulerian dynamics. Here, we report initial work on these focus areas.

Thomas Grubb↗

Methods for System-Level Multidisciplinary Uncertainty Analysis of Low-Boom Flight Vehicles

Current research supporting NASA’s Commercial Supersonic Technology project is focused on the efficient prediction of uncertainty in sonic boom loudness generated by low-boom aircraft concepts. This paper focuses on research incorporating aircraft trim and aerostructural analysis into a multidisciplinary system-level uncertainty analysis. This enables the modeling of a steady-state representation of a point in the uncertainty space, simulating the vehicle as it would be flown. This approach also enables multiple uncertain parameters defining the configuration of the vehicle to be reduced to three: Mach number, altitude, and aircraft weight. To demonstrate this methodology, a case study exploring a conceptual low-boom supersonic aircraft is performed. Two different approaches are used to model the interactions between nearfield pressure signature analysis and sonic boom propagation, and their performance is evaluated in terms of accuracy and computational expense. One method uses a set of local surrogate models to generate a large number of nearfield signatures and perform Monte Carlo analysis. This method is found to produce, at a lower expense, uncertainty metrics that are comparable to the second method, in which uncertainty metrics are computed based on loudness metric values obtained directly from simulated nearfield signatures.

UQ↗

Method for System-Level Multidisciplinary Uncertainty Analysis of Low-Boom Flight Vehicles

Current research supporting NASA’s Commercial Supersonic Technology project is focused on the efficient prediction of uncertainty in sonic boom loudness generated by low-boom aircraft concepts. This paper focuses on research incorporating aircraft trim and aerostructural analysis into a multidisciplinary system-level uncertainty analysis. This enables the modeling of a steady-state representation of a point in the uncertainty space, simulating the vehicle as it would be flown. This approach also enables multiple uncertain parameters defining the configuration of the vehicle to be reduced to three: Mach number, altitude, and aircraft weight. To demonstrate this methodology, a case study exploring a conceptual low-boom supersonic aircraft is performed. Two different approaches are used to model the interactions between nearfield pressure signature analysis and sonic boom propagation, and their performance is evaluated in terms of accuracy and computational expense. One method uses a set of local surrogate models to generate a large number of nearfield signatures and perform Monte Carlo analysis. This method is found to produce, at a lower expense, uncertainty metrics that are comparable to the second method, in which uncertainty metrics are computed based on loudness metric values obtained directly from simulated nearfield signatures.

Supersonics↗

QCD critical point from the Nambu–Jona-Lasino model with a scalar-vector interaction

We study the critical point in the QCD phase diagram in the Nambu–Jona-Lasino (NJL) model by including a scalar-vector coupled interaction. We find that varying the strength of this interaction, which has no effect on the vacuum properties of QCD, can significantly affect the location of the critical point in the QCD phase diagram, particularly the value of the critical temperature. This provides a convenient way to use the NJL-based transport or hydrodynamic model to extract information about the QCD phase diagram from relativistic heavy-ion collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Aβ [Eβ] in 37K decay: new physics with opposite β helicity

By extending our analysis and simulations of our K -decay data set to allow the asymmetry with respect to nuclear spin to vary with energy , we have gained sensitivity to new physics that depends on a helicity factor for the , . In particular, we constrain Lorentz scalar and tensor quark-lepton interaction strengths at a sensitivity complementary to the similar Fierz interference term in neutron decay. Our result for that new physics is = 0.033 0.084 (stat) 0.039 (syst), consistent with the standard model electroweak interaction value . We consider presently achieved complementarity to -decay and particle physics experiments, along with projectable technical improvements to our method.

Behr, J. A.↗

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.↗

Modeling the QBO and SAO Driven by Gravity Waves

Hines' Doppler spread parameterization (DSP) for small scale gravity waves (GW) is applied in a global scale numerical spectral model (NSM) to describe the semi-annual and quasi-biennial oscillations (SAO and QBO) as well as the long term interannual variations that are driven by wave mean flow interactions. This model has been successful in simulating the salient features observed near the equator at altitudes above 20 km, including the QBO extension into the upper mesosphere inferred from UARS measurements. The model has now been extended to describe also the mean zonal and meridional circulations of the upper troposphere and lower stratosphere that affect the equatorial QBO and its global scale extension. This is accomplished in part through tuning of the GW parameterization, and preliminary results lead to the following conclusions: (1) To reproduce the upwelling at equatorial latitudes associated with the Brewer/Dobson circulation that in part is modulated in the model by the vertical component of the Coriolis force, the eddy diffusivity in the lower stratosphere had to be enhanced and the related GW spectrum modified to bring it in closer agreement with the form recommended for the DSP. (2) To compensate for the required increase in the diffusivity, the observed QBO requires a larger GW source that is closer to the middle of the range recommended for the DSP. (3) Through global scale momentum redistribution, the above developments are conducive to extending the QBO and SAO oscillations to higher latitudes. Multi-year interannual oscillations are generated through wave filtering by the solar driven annual oscillation in the zonal circulation. (4) In a 3D version of the model, wave momentum is absorbed and dissipated by tides and planetary waves. Thus, a somewhat larger GW source is required to generate realistic amplitudes for the QBO and SAO.

Mayr, H. G.↗

Deployment Simulation Methods for Ultra-Lightweight Inflatable Structures

Two dynamic inflation simulation methods are employed for modeling the deployment of folded thin-membrane tubes. The simulations are necessary because ground tests include gravity effects and may poorly represent deployment in space. The two simulation methods are referred to as the Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method. They are available in the LS-DYNA nonlinear dynamic finite element code. Both methods are suitable for modeling the interactions between the inflation gas and the thin-membrane tube structures. The CV method only considers the pressure induced by the inflation gas in the simulation, while the ALE method models the actual flow of the inflation gas. Thus, the transient fluid properties at any location within the tube can be predicted by the ALE method. Deployment simulations of three packaged tube models; namely coiled, Z-folded, and telescopically-folded configurations, are performed. Results predicted by both methods for the telescopically-folded configuration are correlated and computational efficiency issues are discussed.

Wang, John T.↗