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At least 505 records · Page 28

A subsequent closed-form description of propagated signaling phenomena in the membrane of an axon

I recently introduced a closed-form description of propagated signaling phenomena in the membrane of an axon [R.F. Melendy, Journal of Applied Physics 118, 244701 (2015)]. Those results demonstrate how intracellular conductance, the thermodynamics of magnetization, and current modulation, function together in generating an action potential in a unified, closed-form description. At present, I report on a subsequent closed-form model that unifies intracellular conductance and the thermodynamics of magnetization, with the membrane electric field, E{sub m}. It’s anticipated this work will compel researchers in biophysics, physical biology, and the computational neurosciences, to probe deeper into the classical and quantum features of membrane magnetization and signaling, informed by the computational features of this subsequent model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The design space of E(3)-equivariant atom-centred interatomic potentials

Abstract Molecular dynamics simulation is an important tool in computational materials science and chemistry, and in the past decade it has been revolutionized by machine learning. This rapid progress in machine learning interatomic potentials has produced a number of new architectures in just the past few years. Particularly notable among these are the atomic cluster expansion, which unified many of the earlier ideas around atom-density-based descriptors, and Neural Equivariant Interatomic Potentials (NequIP), a message-passing neural network with equivariant features that exhibited state-of-the-art accuracy at the time. Here we construct a mathematical framework that unifies these models: atomic cluster expansion is extended and recast as one layer of a multi-layer architecture, while the linearized version of NequIP is understood as a particular sparsification of a much larger polynomial model. Our framework also provides a practical tool for systematically probing different choices in this unified design space. An ablation study of NequIP, via a set of experiments looking at in- and out-of-domain accuracy and smooth extrapolation very far from the training data, sheds some light on which design choices are critical to achieving high accuracy. A much-simplified version of NequIP, which we call BOTnet (for body-ordered tensor network), has an interpretable architecture and maintains its accuracy on benchmark datasets.

Computer Science↗

A SUITE OF SNS NEUTRON INSTRUMENT MODELS

MCSTAS models of the Spallation Neutron Source (SNS) neutron scattering instruments are being developed in a unified approach. Models aid performance assessment of the instruments, diagnosis of the component setup, and provide a tool for experiment planning and evaluation for the user community. The MCSTAS code has become a standard tool for neutron optics simulations in the neutron scattering community. Neutrons are tracked through the instrument model starting from moderator emission profiles through beam shaping components to the scattering at the sample and neutron detection. Models for the POWGEN, TOPAZ, VULCAN, and NOMAD instruments were completed utilizing as-built information as much as possible. Simulation results with the models are validated with measured data. While measurements and simulations of the neutron spectra incident to the sample location can agree within 10%, as for VULCAN, discrepancies have been identified for POWGEN and TOPAZ that indicate misalignment of components as neutron guide segments. Ideally, these misalignments are traced down and corrected as found.

Geoghegan, Ceris↗

Unified Creep Plasticity Damage (UCPD) Model for Rigid Polyurethane Foams

Numerous experiments were performed to characterize the mechanical response of several different rigid polyurethane foams (FR3712, PMDI10, PMDI20, and TufFoam35) to large deformation. In these experiments, the effects of load path, loading rate, and temperature were investigated. Results from these experiments indicated that rigid polyurethane foams exhibit significant volumetric and deviatoric plasticity when they are compressed. Rigid polyurethane foams were also found to be very strain-rate and temperature dependent. These foams are also rather brittle and crack when loaded to small strains in tension or to larger strains in compression. Thus, a new Unified Creep Plasticity Damage (UCPD) model was developed and implemented into SIERRA with the name Foam Damage to describe the mechanical response of these foams to large deformation at a variety of temperatures and strain rates. This report includes a description of recent experiments and experimental findings. Next, development of a UCPD model for rigid, polyurethane foams is described. Selection of material parameters for a variety of rigid polyurethane foams is then discussed and finite element simulations with the new UCPD model are compared with experimental results to show behavior that can be captured with this model.

36 MATERIALS SCIENCE↗

Seismicity-constrained fault detection and characterization with a multitask machine learning model

Geological fault detection and characterization are crucial for understanding subsurface dynamics across scales. While methods for fault delineation based on either seismicity location analysis or seismic image reflector discontinuity are well-established, a systematic approach that integrates both data types remains absent. We develop a novel machine learning model that unifies seismic reflector images and seismicity location information to automatically identify geological faults and characterize their geometrical properties. The model encodes a seismic image and a seismicity location image separately, and fuses the encoded features with a spatial-channel attention fusion module to improve the learning of important features in both inputs. We design an automated strategy to generate high-quality synthetic training data and labels. To improve the realism of the seismicity location image, we include random seismicity noise and missing seismicity location associated with some of the faults. We validate the model’s efficacy and accuracy using synthetic data examples and two field data examples. Moreover, we show that fine-tuning the trained model with a small, domain-specific dataset enhances its fidelity for field data applications. The results demonstrate that integrating seismicity location and seismic images into a unified framework allows the end-to-end neural network to achieve higher fidelity and accuracy in delineating subsurface faults and their geometrical properties compared with image-only fault detection methods. Our approach offers an adaptive data-driven tool for geological fault characterization and seismic hazard mitigation, bridging the gap between seismicity location and image-based fault detection methods.

58 GEOSCIENCES↗

Finite element model for piles in liquefiable ground

This paper develops a three dimensional finite element modelling method for piles in liquefiable ground and applies it to the analysis of seismic pile responses. A unified plasticity model for large post-liquefaction shear deformation of sand provides the basis for the effective and efficient modelling of liquefiable ground. Special attention is dedicated towards the modelling of piles and soil-pile interface to accurately reflect the behaviour of piles. A staged modelling procedure is adopted to appropriately generate the initial conditions for the soil and piles and achieve hydrostatic pore pressure prior to seismic loading. Three centrifuge shaking table tests on single piles, both with and without pile cap and superstructure, in level and inclined liquefiable ground are conducted and simulated in validation and application of the proposed method. Further studies to investigate the effects of pile cap, lateral spreading, and non-liquefiable surface layer are undertaken numerically using the validated method. The results show these aforementioned factors to be influential in the dynamic and residual response of piles in liquefiable ground.

Centrifuge test↗

High temperature inelastic deformation under uniaxial loading - Theory and experiment

The elevated-temperature uniaxial inelastic deformation behavior of an Ni-base alloy, B1900 + Hf, is investigated by performing isothermal tensile, creep, cyclic, stress relaxation, and thermomechanical fatigue tests. The range of strain rates examined is from 10 to the -7th to 100 per sec, while the test temperatures range from 25 to 1093 C. This extensive constitutive data base has been used for evaluating the unified constitutive models of Bodner and Partom (1972) and of Walker (1972) which apply for the small-strain regime. Comparison of test results with independent model predictions indicates good agreement over a broad range of loading conditions, demonstrating the applicability of the unified-constitutive-equation approach for describing the strongly nonlinear and temperature-dependent response of meals under a wide range of deformation and thermal histories. Thus the results give confidence that the unified approach is an effective and efficient approach in which complex history-dependent thermoviscoplastic flow can be represented within a single inelastic strain-rate term.

Chan, K. S.↗

Boreal Winter MJO Teleconnection in the Community Atmosphere Model Version 5 with the Unified Convection Parameterization

The Madden-Julian Oscillation (MJO), the dominant mode of tropical intraseasonal variability, influences weather and climate in the extratropics through atmospheric teleconnection. In this study, two simulations using the Community Atmosphere Model version 5 (CAM5) - one with the default shallow and deep convection schemes and the other with the Unified Convection scheme (UNICON) - are employed to examine the impacts of cumulus parameterizations on the simulation of the boreal wintertime MJO teleconnection in the Northern Hemisphere. We demonstrate that the UNICON substantially improves the MJO teleconnection. When the UNICON is employed, the simulated circulation anomalies associated with the MJO better resemble the observed counterpart, compared to the simulation with the default convection schemes. Quantitatively, the pattern correlation for the 300-hPa geopotential height anomalies between the simulations and observation increases from 0.07 for the default schemes to 0.54 for the UNICON. These circulation anomalies associated with the MJO further help to enhance the surface air temperature and precipitation anomalies over North America, although room for improvement is still evident. Initial value calculations suggest that the realistic MJO teleconnection with the UNICON is not attributed to the changes in the background wind, but primarily to the improved tropical convective heating associated with the MJO.

Yoo, Changhyun↗

Addressing the Big-Earth-Data Variety Challenge with the Hierarchical Triangular Mesh

We have implemented an updated Hierarchical Triangular Mesh (HTM) as the basis for a unified data model and an indexing scheme for geoscience data to address the variety challenge of Big Earth Data. We observe that, in the absence of variety, the volume challenge of Big Data is relatively easily addressable with parallel processing. The more important challenge in achieving optimal value with a Big Data solution for Earth Science (ES) data analysis, however, is being able to achieve good scalability with variety. With HTM unifying at least the three popular data models, i.e. Grid, Swath, and Point, used by current ES data products, data preparation time for integrative analysis of diverse datasets can be drastically reduced and better variety scaling can be achieved. In addition, since HTM is also an indexing scheme, when it is used to index all ES datasets, data placement alignment (or co-location) on the shared nothing architecture, which most Big Data systems are based on, is guaranteed and better performance is ensured. Moreover, our updated HTM encoding turns most geospatial set operations into integer interval operations, gaining further performance advantages.

SciDB↗

Design and Impacts of Land-Biogenic-Atmosphere Coupling in the NASA-Unified WRF (NU-WRF) Modeling System

Land-Atmosphere coupling is typically designed and implemented independently for physical (e.g. water and energy) and chemical (e.g. biogenic emissions and surface depositions)-based models and applications. Differences in scale, data requirements, and physics thus limit the ability of Earth System models to be fully coupled in a consistent manner. In order for the physical-chemical-biological coupling to be complete, treatment of the land in terms of surface classification, condition, fluxes, and emissions must be considered simultaneously and coherently across all components. In this study, we investigate a coupling strategy for the NASA-Unified Weather Research and Forecasting (NU-WRF) model that incorporates the traditionally disparate fluxes of water and energy through NASA's LIS (Land Information System) and biogenic emissions through BEIS (Biogenic Emissions Inventory System) and MEGAN (Model of Emissions of Gases and Aerosols from Nature) into the atmosphere. In doing so, inconsistencies across model inputs and parameter data are resolved such that the emissions from a particular plant species are consistent with the heat and moisture fluxes calculated for that land cover type. In turn, the response of the atmospheric turbulence and mixing in the planetary boundary layer (PBL) acts on the identical surface type, fluxes, and emissions for each. In addition, the coupling of dust emission within the NU-WRF system is performed in order to ensure consistency and to maximize the benefit of high-resolution land representation in LIS. The impacts of those self-consistent components on' the simulation of atmospheric aerosols are then evaluated through the WRF-Chem-GOCART (Goddard Chemistry Aerosol Radiation and Transport) model. Overall, this ambitious project highlights the current difficulties and future potential of fully coupled. components. in Earth System models, and underscores the importance of the iLEAPS community in supporting improved knowledge of processes and innovative approaches for models and observations.

Tan, Qian↗

Strategic Analysis of Complex Security Scenarios

Many advanced technical tools are available to prevent attacks on national infrastructure. Nevertheless, while traditional analyses of security problems have succeeded in producing good technical solutions, they have often ignored the human factor integral to these problems. Human attackers (who may be individuals or state-level attackers) expend substantial effort to breach security because they have the incentive for doing so. People involved in implementing security follow individual incentives, which need not align with global security concerns; consequently, desired security solutions are often implemented poorly, or not at all. This complex interplay between individual incentives and global (organizational and/or national) goals can be modeled and analyzed using game theoretic techniques. By analyzing not only what is possible, but also what is motivated, a holistic approach to security problems can be developed, informing policy and providing tools to policy makers. We study game theoretic models that unify several current incentive-based approaches to security, and develop simulation-based and mathematical optimization methods for analyzing such models that exploit the high-performance computing capabilities at Sandia. Our first model studies security in interdependent settings, offering a scalable local search heuristic to approximate optimal security decisions in general, and a linear programming approach, coupled with simulations of consequences, to optimally compute security in an important special case. Our second class of models addresses security patrolling problems when an adversary gets to observe the patrol location. We present a general framework, based on stochastic games, for computing optimal security policies in such settings, and present more scalable tools that apply in the important special cases. Our third contribution is a model of security that involves many defenders, but only models non-adaptive attackers (or natural disasters, inadvertent errors, etc). In this model, we demonstrate that the security decisions of many players result in global security configuration that is not very far from optimal, and is much more resilient to environment changes that an optimal solution. This positive effect dissipates, however, when the number of decision makers becomes too large.

Vorobeychik, Yevgeniy↗

An Integrated Model of RAF Inhibitor Action Predicts Inhibitor Activity against Oncogenic BRAF Signaling

The complex biochemical effects of RAF inhibitors account for both the effectiveness and mechanisms of resistance to these drugs, but a unified mechanistic model has been lacking. Here we show that RAF inhibitors exert their effects via two distinct allosteric mechanisms. Drug resistance due to dimerization is determined by the position of the αC helix stabilized by inhibitor, whereas inhibitor-induced RAF priming and dimerization are the result of inhibitor-induced formation of the RAF/RAS-GTP complex. The biochemical effect of RAF inhibitor in cells is the combined outcome of the two mechanisms. Therapeutic strategies including αC-helix-IN inhibitors are more effective in multiple mutant BRAF-driven tumor models, including colorectal and thyroid BRAFV600E cancers, in which first-generation RAF inhibitors have been ineffective.

60 APPLIED LIFE SCIENCES↗

Modeling of pressure spectra in a turbulent shear flow

The development of the pressure spectrum has been followed from its separation into turbulent-turbulent and turbulent-mean square contributions to a unified spectral model. The model is obtained by Fourier transforming the integral solution to Poisson's equation for an isotropic, homogeneous, constant mean shear flow. The variations in the asymptotic form for the mean-shear spectrum is discussed. It is noted that the spectra are associated with the particular velocity field selected, and that by an appropriate choice of spectral forms, the mean-square pressure of the flow may be calculated.

Beuther, P.↗

Overview of NASA's Integrated Design and Engineering Analysis (IDEA)Environment

Historically, the design of subsonic and supersonic aircraft has been divided into separate technical disciplines (such as propulsion, aerodynamics and structures) each of which performs their design and analysis in relative isolation from others. This is possible in most cases either because the amount of interdisciplinary coupling is minimal or because the interactions can be treated as linear. The design of hypersonic airbreathing vehicles, like NASA s X-43, is quite the opposite. Such systems are dominated by strong non-linear interactions between disciplines. The design of these systems demands that a multi-disciplinary approach be taken. Furthermore, increased analytical fidelity at the conceptual design phase is highly desirable as many of the non-linearities are not captured by lower fidelity tools. Only when these systems are designed from a true multi-disciplinary perspective can the real performance benefits be achieved and complete vehicle systems be fielded. Toward this end, the Vehicle Analysis Branch at NASA Langley Research Center has been developing the Integrated Design & Engineering Analysis (IDEA) Environment. IDEA is a collaborative environment for parametrically modeling conceptual and preliminary launch vehicle configurations using the Adaptive Modeling Language (AML) as the underlying framework. The environment integrates geometry, configuration, propulsion, aerodynamics, aerothermodynamics, trajectory, closure and structural analysis into a generative, parametric, unified computational model where data is shared seamlessly between the different disciplines. Plans are also in place to incorporate life cycle analysis tools into the environment which will estimate vehicle operability, reliability and cost. IDEA is currently being funded by NASA s Hypersonics Project, a part of the Fundamental Aeronautics Program within the Aeronautics Research Mission Directorate. The environment is currently focused around a two-stage-to-orbit configuration with a turbine based combined cycle (TBCC) first stage and reusable rocket second stage. This paper provides an overview of the development of the IDEA environment, a description of the current status and detail of future plans.

Robinson, Jeffrey S.↗

Reconstruction framework advancements to support streaming for the ePIC detector at the EIC

The ePIC collaboration adopted the JANA2 framework to manage its reconstruction algorithms. This framework has since evolved substantially in response to ePIC’s needs. There have been three main design drivers: integrating cleanly with the Podio-based data models and other layers of the key4hep stack, enabling external configuration of existing components, and supporting timeframe splitting for streaming readout. The result is a unified component model featuring a new declarative interface for specifying inputs, outputs, parameters, services, and resources. This interface enables the user to instantiate, configure, and wire components via an external file. One critical new addition to the component model is a hierarchical decomposition of data boundaries into levels such as Run, Timeframe, PhysicsEvent, and Subevent. Two new component abstractions, Folder and Unfolder, are introduced in order to traverse this hierarchy, e.g. by splitting or merging. The pre-existing components can now operate at different event levels, and JANA2 will automatically construct the corresponding parallel processing topology. This means that a user may write an algorithm once, and configure it at runtime to operate on timeframes or on physics events. Overall, these changes mean that the user requires less knowledge about the framework internals, obtains greater flexibility with configuration, and gains the ability to reuse the existing abstractions in new streaming contexts.

Brei, Nathan [Thomas Jefferson National Accelerato↗

SeeQ: A Programming Model for Portable Data-Driven Building Applications

This paper introduces SeeQ, a programming model and an abstraction framework that facilitates the development of portable data- driven building applications. Data-driven approaches can provide insights into building operations and guide decision-making to achieve operational objectives. Yet the configuration of such applications per building requires extensive effort and tacit knowledge. In SeeQ, we propose a portable programming model and build a software system that enables self-configuration and execution across diverse buildings. The configuration of each building is captured in a unified data model - in this paper, we work with the Brick ontology without loss of generality. SeeQ focuses on the distinction between the application logic and the configuration of an application against building-specific data inputs and systems. We test the proposed approach by configuring and deploying a diverse range of applications across five heterogeneous real-world buildings. The analysis shows the potential of SeeQ to significantly reduce the efforts associated with the delivery of building analytics.

analytics↗

Optimization and Evaluation of Stochastic Unified Convection Using Single-Column Model Simulations at Multiple Observation Sites

We extend the previously developed stochastic unified convection scheme (UNICON) for shallow convection to deep convection by parameterizing the impact of mesoscale organized flow on updraft properties. The extended stochastic UNICON parameterizes thermodynamic properties of updrafts at the near-surface as a multivariate Gaussian distribution, where the variances of the distribution are the summation of variances from non-organized turbulence and mesoscale organized flow. The distribution of updraft radius is parameterized as a power-law distribution with a scale break which is parameterized as a linear function of the strength of mesoscale organized flow. The proposed parameterization is validated using a series of large-eddy simulations of deep convection. The free parameters introduced in the formulation of stochastic UNICON are optimized using 10 cases of single-column model simulations over the ocean. Stochastic UNICON with the optimized parameters significantly reduces the biases of thermodynamic profiles and surface precipitation rates simulated in the original UNICON for tropical convection cases. The simulation of the variation in anomalies of temperature and moisture associated with the Madden-Julian oscillation is also improved. The overall improvements in simulated thermodynamic profiles are found to be due to the increased heating and drying tendencies by convective processes in stochastic UNICON. An additional simulation of an idealized deep convection case shows that stochastic UNICON produces enhanced cloud variabilities with dependency on updraft radius, indicating its ability to represent the coexistence of shallow and deep convection.

54 ENVIRONMENTAL SCIENCES↗