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At least 253 records · Page 14

Editorial: Advances in computational molecular biophysics

This special issue of BBA is dedicated to Dr. Jeremy C. Smith on the occasion of his 60th birthday and his more than three decades as a practitioner of computational molecular biophysics. The special issue showcases cutting-edge work in computational molecular biophysics. The senior authors of the manuscripts in this issue are Dr. Smith’s previous or present collaborators. Their articles reflect Dr. Smith’s distinguished career integrating experimental and molecular simulation approaches into a unified description of the function, structure, and dynamics of biomolecules. Each of the articles presented here illustrates one aspect of the broad nature of computational molecular biophysics.

59 BASIC BIOLOGICAL SCIENCES↗

SineKAN: Kolmogorov-Arnold Networks using sinusoidal activation functions

Recent work has established an alternative to traditional multi-layer perceptron neural networks in the form of Kolmogorov-Arnold Networks (KAN). The general KAN framework uses learnable activation functions on the edges of the computational graph followed by summation on nodes. The learnable edge activation functions in the original implementation are basis spline functions (B-Spline). Here, we present a model in which learnable grids of B-Spline activation functions are replaced by grids of re-weighted sine functions (SineKAN). We evaluate numerical performance of our model on a benchmark vision task. We show that our model can perform better than or comparable to B-Spline KAN models and an alternative KAN implementation based on periodic cosine and sine functions representing a Fourier Series. Further, we show that SineKAN has numerical accuracy that could scale comparably to dense neural networks (DNNs). Compared to the two baseline KAN models, SineKAN achieves a substantial speed increase at all hidden layer sizes, batch sizes, and depths. Current advantage of DNNs due to hardware and software optimizations are discussed along with theoretical scaling. Additionally, properties of SineKAN compared to other KAN implementations and current limitations are also discussed.

Reinhardt, Eric↗

Edge majorana quasiparticles and qubits

Various embodiments described herein provide for a topological quantum computer that uses edge Majorana quasi-particles to form qubits. An inverted Indium Arsenide (InAs) and Gallium Antimonide (GaSb) heterostructure is disclosed that is a quantum spin Hall insulator. A layer of aluminum can be deposited over a nanotube that is placed across the layers of the heterostructure. Once the nanotube is removed, and a gate is formed on the heterostructure and the heterostructure is cooled so that the aluminum becomes superconducting, helical edge states are formed at the junction of the super conducting aluminum, the InAs, and the GaSb which creates a Majorana zero modes (MZMs) at zero magnetic field. The MZMs can be used to construct a topological qubit for fault-resistant topological quantum computation.

Pan, Wei↗

Land use mapping using edge density texture measures on Thematic Mapper simulator data

Texture analysis was performed as part of an investigation of the information content of Thematic Mapper (TM) imagery. High altitude aircraft scanner imagery from the Airborne Thematic Mapper (ATM) instrument was acquired over central California and used to simulate TM data. Edge density texture images were constructed by computation of proportions of edge pixels in a 31 x 31 moving window on a near infrared ATM band. A training technique was employed to select computational parameters to maximize the difference between edge density measurements in urban and in rural areas. The results of classification of the texture images showed that urban and rural areas could be distinguished with texture alone, indicating that inclusion of texture in automated classification procedures could significantly improve their accuracy.

Hlavka, C. A.↗

In Search of the Physics: The Interplay of Experiment and Computation in Airframe Noise Research: Flap-Edge Noise

The LaRC investigative process for airframe noise has proven to be a useful guide for elucidation of the physics of flow-induced noise generation over the last five years. This process, relying on a close interplay between experiment and computation, is described and demonstrated here on the archetypal problem of flap-edge noise. Some detailed results from both experiment and computation are shown to illustrate the process, and a description of the multi-source physics seen in this problem is conjectured.

Streett, C. L.↗

2022 Agnew and Metropolis Postdoc Fellow Showcase Event Book

Agnew National Security Postdoc Fellows pursue cutting-edge experimental, theoretical, computational science, and engineering research aligned with the national security mission. Metropolis Postdoc Fellows pursue cutting-edge research in the areas of computational and computer science, physics, and engineering. Computer simulation capabilities are developed in support of the stockpile stewardship program together with broader national nuclear security needs. Fellows have access to some of the most powerful supercomputers in the world to perform pioneering research.

42 ENGINEERING↗

A Multi-Objective Approach for Optimizing Edge-Based Resource Allocation Using TOPSIS

Existing approaches for allocating resources on edge environments are inefficient and lack the support of heterogeneous edge devices, which in turn fail to optimize the dependency on cloud infrastructures or datacenters. To this extent, we propose in this paper OpERA, a multi-layered edge-based resource allocation optimization framework that supports heterogeneous and seamless execution of offloadable tasks across edge, fog, and cloud computing layers and architectures. By capturing offloadable task requirements, OpERA is capable of identifying suitable resources within nearby edge or fog layers, thus optimizing the execution process. Throughout the paper, we present results which show the effectiveness of our proposed optimization strategy in terms of reducing costs, minimizing energy consumption, and promoting other residual gains in terms of processing computations, network bandwidth, and task execution time. We also demonstrate that by optimizing resource allocation in computation offloading, it is then possible to increase the likelihood of successful task offloading, particularly for computationally intensive tasks that are becoming integral as part of many IoT applications such robotic surgery, autonomous driving, smart city monitoring device grids, and deep learning tasks. The evaluation of our OpERA optimization algorithm reveals that the TOPSIS MCDM technique effectively identifies optimal compute resources for processing offloadable tasks, with a 96% success rate. Moreover, the results from our experiments with a diverse range of use cases show that our OpERA optimization strategy can effectively reduce energy consumption by up to 88%, and operational costs by 76%, by identifying relevant compute resources.

97 MATHEMATICS AND COMPUTING↗

Diaspora: Resilience-enabling services for science from HPC to edge

Scientific applications of interest to DOE must increasingly engage distributed resources (e.g., instruments, remote computers, data stores, edge devices) and deliver more stringent levels of service (e.g., uninterrupted processing of experiment data streams). In such systems, state is distributed and components can fail in many ways, often silently, making application resilience a major concern. Addressing the resilience needs of such applications requires methods for gaining knowledge of resources and applications and for translating that knowledge into action. We are working on addressing these needs in the context of multi-messenger astronomy, where detecting and responding to unusual transient events in multiple cosmic messengers (gravitational wave, electromagnetic, high- energy particles) from different instruments leads to a federated learning problem.

47 OTHER INSTRUMENTATION↗

Edge geometry of turbomachine blades

Computer program calculates leading- and trailing-edge circle radii, tangency angles on leading- and trailing-edge circles, and stagger angle of turbomachinery blade sections, using only spline points defining blade surfaces.

Schumann, L. F.↗

Numerical simulation of the edge tone phenomenon

Time accurate Navier-Stokes computations were performed to study a class 2 (acoustic) whistle, the edge tone, and to gain knowledge of the vortex-acoustic coupling mechanisms driving production of these tones. Results were obtained by solving the full Navier-Stokes equations for laminar compressible air flow of a two dimensional jet issuing from a slit interacting with a wedge. Cases considered were determined by varying the distance from the slit to the wedge. Flow speed was kept constant at 1,750 cm/s as was the slit thickness of 0.1 cm, corresponding to conditions in the experiments of Brown. The analytical computations revealed edge tones to be present in four harmonic stages of jet flow instability over the wedge as the jet length was varied from 0.3 to 1.6 cm. Excellent agreement was obtained in all four edge tone stage cases between the present computational results and the experimentally obtained frequencies and flow visualization results of Brown. Specific edge tone generation phenomena and further confirmation of certain theories and empirical formulas concerning these phenomena were brought to light in this analytical simulation of edge tones.

Dougherty, N. S.↗

The globus compute dataset: An open function-as-a-service dataset from the edge to the cloud

Here we present a unique function-as-a-service (FaaS) dataset capturing the use of the Globus Compute (previously funcX) platform. Globus Compute implements a federated model via which users may deploy endpoints on arbitrary remote computers, from the edge to high performance computing (HPC) cluster, and they may then invoke Python functions on those endpoints via a reliable cloud -hosted service. The dataset covers 31 weeks and includes 2121472 task submissions from 252 users executed on 580 remote computing endpoints. It includes 277386 registered functions. We describe the dataset and various observations, some that are similar to other FaaS datasets, for example, that 74% of tasks run for less than 1 s, and some that are unique to Globus Compute, for example, that endpoints are used in different ways and that the majority of functions are related to scientific computing and machine learning. To the best of our knowledge, this dataset represents the first federated FaaS dataset that includes user workloads, distributed computing endpoints, and analysis of registered function bodies. We expect the dataset to be useful for researching FaaS architectures, workload modeling, container warming, and other distributed computing architectures.

97 MATHEMATICS AND COMPUTING↗

Synchrophasor Data Anomaly Detection on Grid Edge by 5G Communication and Adjacent Compute

The fifth-generation mobile communication (5G) technology offers the opportunities to enhance the grid real-time monitoring. The 5G-enabled phasor measurement units (PMUs) features flexible positioning and cost-effective long-term maintenance, without constraints of fixing wire. This paper is the first to demonstrate the applicability of 5G in PMU communication, and the experiment was carried out at Verizon non-standalone testbed at Pacific Northwest National Laboratory (PNNL) Advanced Wireless Communication lab. The performance of 5G-enabled PMU communication setup is reviewed and discussed in this paper, and the paper presents a real-time dynamic linear model (DML) based synchrophasor data anomaly detection application. Last but not least, the practicability of implementing 5G for wide-area protection strategies is explored and discussed by analyzing the experimental results.

5G, Synchrophasor data, machine learning, anomaly ↗

Relativistic nonorthogonal configuration interaction: application to L 2,3 -edge X-ray spectroscopy

In this article, we develop a relativistic exact-two-component nonorthogonal configuration interaction (X2C-NOCI) for computing L-edge X-ray spectra. This article to our knowledge is the first time NOCI has been used for relativistic wave functions. A set of molecular complexes, including SF 6 , SiCl 4 and [FeCl 6 ] 3– , are used to demonstrate the accuracy and computational scaling of the X2C-NOCI method. Here, our results suggest that X2C-NOCI is able to satisfactorily capture the main features of the L 2,3 -edge X-ray absorption spectra. Excitations from the core require a large amount of orbital relaxation to yield reasonable energies and X2C-NOCI allows us to treat orbital optimization explicitly. However, the cost of computing the nonorthogonal coupling is higher than in conventional CI. Here, we propose an improved integral screening using overlap-scaled density combined with a continuous measure of the generalized Slater–Condon rules that allows us to estimate if an element is zero before attempting a two-electron integral contraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Database of ab initio L-edge X-ray absorption near edge structure

Abstract The L-edge X-ray Absorption Near Edge Structure (XANES) is widely used in the characterization of transition metal compounds. Here, we report the development of a database of computed L-edge XANES using the multiple scattering theory-based FEFF9 code. The initial release of the database contains more than 140,000 L-edge spectra for more than 22,000 structures generated using a high-throughput computational workflow. The data is disseminated through the Materials Project and addresses a critical need for L-edge XANES spectra among the research community.

42 ENGINEERING↗

Integrated edge-to-exascale workflow for real-time steering in neutron scattering experiments

We introduce a computational framework that integrates artificial intelligence (AI), machine learning, and high-performance computing to enable real-time steering of neutron scattering experiments using an edge-to-exascale workflow. Focusing on time-of-flight neutron event data at the Spallation Neutron Source, our approach combines temporal processing of four-dimensional neutron event data with predictive modeling for multidimensional crystallography. At the core of this workflow is the Temporal Fusion Transformer model, which provides voxel-level precision in predicting 3D neutron scattering patterns. The system incorporates edge computing for rapid data preprocessing and exascale computing via the Frontier supercomputer for large-scale AI model training, enabling adaptive, data-driven decisions during experiments. This framework optimizes neutron beam time, improves experimental accuracy, and lays the foundation for automation in neutron scattering. Although real-time experiment steering is still in the proof-of-concept stage, the demonstrated potential of this system offers a substantial reduction in data processing time from hours to minutes via distributed training, and significant improvements in model accuracy, setting the stage for widespread adoption across neutron scattering facilities and more efficient exploration of complex material systems.

97 MATHEMATICS AND COMPUTING↗

Numerical and physical aspects of aerodynamic flows III; Proceedings of the Third Symposium, California State University, Long Beach, CA, January 21-24, 1985

The present symposium considers hydrodynamic stability and turbulent transition, transition calculations in three-dimensional flows, a quasi-simultaneous finite difference approach for strongly interacting flows, the significance of the thin layer Navier-Stokes approximation, unsteady airfoil boundary layers, predictions and experiments on airfoils at low Reynolds numbers, and a comparison of interactive boundary layer and thin layer Navier-Stokes procedures. Also discussed are a viscous-inviscid interaction method for computing unsteady transonic separation, massive separation and dynamic stall on a cusped trailing edge airfoil, the computation of turbulent separated flows over wings, an iterative scheme for three-dimensional transonic flows, and the computation of three-dimensional flows with shock wave/boundary layer interaction. Many of the papers in this symposium were abstracted previously (cf., A85-42951).

Cebeci, T.↗