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At least 145 records · Page 8

KRAS4a and KRAS4b show distinct lipid-dependent regulation of RAS-RAF membrane dynamics

KRAS4a and KRAS4b are important regulators of signaling, and their interactions with the plasma membrane are dynamic and influenced by lipid composition. KRAS 4a and 4b have nearly identical globular domains but differ in their membrane-associated hyper variable region (HVR). The functional distinctions between these isoforms remain unclear, particularly with regards to their dependence on specific lipids and the membrane environment. Previous work showed that the membrane orientation of KRAS4b affects its ability to bind to RAF kinase RBDCRD and that the KRAS–RBDCRD complex adopts different poses on the membrane as well as influences the size and composition of the lipid environment. To model differences between KRAS 4a and 4b protein–lipid interactions, we extended the Multiscale Machine-Learned Modeling Infrastructure (MuMMI) to incorporate continuum simulations in the grand canonical ensemble, enabling sampling across macroscopic, coarse-grained, and all-atom resolutions. Using this framework, we systematically altered PIP2 concentrations, KRAS 4a versus 4b, and RAF RBDCRD complexation to assess impacts on membrane–protein interactions and dynamics. Our results reveal that reducing PIP2 shifts and broadens the membrane orientational preference of both KRAS 4b and 4a, with stronger effects on 4b HVR localization versus 4a. We demonstrate that with depletion of the strong negatively charged PIP2 lipid, the less charged phosphatidylserine replaces PIP2. Our findings highlight similarities and distinctions in the dynamics and lipid dependency of KRAS isoforms and suggest that ordering of the local lipid composition by HVRs is a shared property and key modulator of RAS-mediated signaling at the plasma membrane.

Biological and medical sciences↗

Effects of Galactic Irradiation on Thermal and Electronic Transport in Tungsten

The impact of irradiation on the thermal and electronic properties of materials is a persistent puzzle, particularly defect formation at the atomic and nanoscales. This work examines the nanoscale effects of low-energy irradiation on tungsten (W), focusing on defect-induced modifications to thermal and electronic transport. Using the site-projected thermal conductivity (SPTC) method [A. Gautam et al. PSS-RRL, 2400306, 2024], bulk and twin-grain boundary W with vacancy defects based on the Norgett–Robinson–Torrens displacements per atom model is analyzed. SPTC provides a detailed prediction of postcascade spatial thermal conductivity distribution. Electronic conductivity activity is estimated using the “N 2 method” [K. Nepal et al. Carbon, 119711, 2025] to explore the consequences of vacancies and grain boundaries, highlighting the defect-dependent nature of charge transport behavior. These findings offer high-resolution insights into irradiation-driven transport phenomena, with implications for space-exposed materials and nanoscale thermal/electronic management.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Particlization in fluid dynamical simulations of heavy-ion collisions: The IS3D module

The IS3D particlization module simulates the emission of hadrons from heavy-ion collisions via Monte-Carlo sampling of the Cooper–Frye formula which converts fluid dynamical information into local phase-space distributions for hadrons. The code package includes multiple choices for the non-equilibrium correction to these distribution functions: the 14-moment approximation, first-order Chapman–Enskog expansion, and two types of modified equilibrium distributions. This makes it possible to explore to what extent heavy-ion experimental data are sensitive to different choices for δf n , presently the main source of theoretical uncertainty in the particlization stage. Here, we validate our particle sampler with a high degree of precision by generating several million hadron emission events from a longitudinally boost-invariant hypersurface and comparing the event-averaged particle spectra and space–time distributions to the Cooper–Frye formula.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Record acceleration of the two-dimensional Ising model using a high-performance wafer-scale engine

The versatility and wide-ranging applicability of the Ising model, originally introduced to study phase transitions in magnetic materials, have made it a cornerstone in statistical physics and a valuable tool for evaluating the performance of emerging computer hardware. Here, we present a novel implementation of the two-dimensional Ising model on Cerebras Wafer-Scale Engine (WSE) – a revolutionary processor that is opening new frontiers in computing. In our deployment of the checkerboard algorithm, we optimized the Ising model to take advantage of the unique WSE architecture. Specifically, we employed a compressed bit representation storing 16 spins on each int16 word, and efficiently distributed the spins over the processing units enabling seamless weak scaling and limiting communications to only immediate neighboring units. Our implementation can handle up to 754 simulations in parallel, achieving an aggregate of over 61.8 trillion flip attempts per second for Ising models with up to 200 million spins. This represents a gain of up to 148 times over previously reported single-devices with a highly optimized implementation on NVIDIA V100 and up to 88 times in productivity compared to NVIDIA H100. Our findings highlight the significant potential of the WSE in scientific computing, particularly in the field of materials modeling.

Ising model↗

Large-Eddy Simulation of a wind turbine using a Filtered Actuator Line Model

When dealing with multirotor devices such as quadcopters or wind farms, the cost of blade-resolved large-eddy simulation (LES) becomes prohibitive. Combining LES with a family of lower-fidelity models, called actuator line models (ALMs), has grown in popularity in the past decade. ALM replaces full blade resolution with an array of actuator points or lines parameterized by aerodynamic lift/drag polar plots along the blades. Body forces computed based on these actuator points are then projected onto the LES flow mesh, mimicking the effect of rotating blades on the flow. However, the optimal projection radius and the associated LES grid size is often too restrictive for multirotor simulations. Recently, a new tip-correction-based filtered ALM (F-ALM) was proposed by Martinez-Tossas and Meneveau (2019), which allows coarser-than-optimal grids by avoiding the associated overprediction of thrust. In this work, F-ALM is implemented into a high-order, in-house LES code to simulate National Renewable Energy Laboratory Phase VI wind turbine. It is then followed by a comparison between the baseline ALM and the newly implemented F-ALM in terms of instantaneous and time-averaged flow fields and blade loads, revealing the advantages of F-ALM in preventing the overprediction of power on coarse grids. Finally, this encourages accurate and affordable simulations of multirotor devices in the future.

17 WIND ENERGY↗

Quantum simulation of excited states from parallel contracted quantum eigensolvers

Abstract Computing excited-state properties of molecules and solids is considered one of the most important near-term applications of quantum computers. While many of the current excited-state quantum algorithms differ in circuit architecture, specific exploitation of quantum advantage, or result quality, one common feature is their rooting in the Schrödinger equation. However, through contracting (or projecting) the eigenvalue equation, more efficient strategies can be designed for near-term quantum devices. Here we demonstrate that when combined with the Rayleigh–Ritz variational principle for mixed quantum states, the ground-state contracted quantum eigensolver (CQE) can be generalized to compute any number of quantum eigenstates simultaneously. We introduce two excited-state (anti-Hermitian) CQEs that perform the excited-state calculation while inheriting many of the remarkable features of the original ground-state version of the algorithm, such as its scalability. To showcase our approach, we study several model and chemical Hamiltonians and investigate the performance of different implementations.

Physics↗

Evaluation of SPARC divertor conditions in H-mode operation using SOLPS-ITER

The predicted divertor conditions for the SPARC tokamak are calculated using SOLPS-ITER for a range of scrape-off-layer (SOL) heat flux widths λ q , input powers, and particle fueling locations. Under H-mode scenario conditions with an upstream separatrix density of 1 x 10 20 m -3 , the most conservative range of λ q extrapolations ( 0.15 mm) results in extremely high unmitigated particle and energy fluxes to the divertor, both under full field (12.2 T) and power (P SOL = 29 MW) conditions, and 2/3 field with P SOL = 10 MW. Increasing the cross-field SOL diffusivities by 2–10× reduces the magnitude of the mitigation challenge, however strategies such as impurity seeding or strike-point-sweeping will likely still be required. A combination of steady-state and time-dependent SOLPS-ITER simulations are used to map out phase space diagrams of upstream and divertor conditions. The simulations include parallel currents but neglect cross-field drifts. At low upstream density the inner and outer divertor conditions are highly asymmetric, with a large temperature difference and significant heat fluxes driven by parallel currents. The solution has sharp bifurcations with a region of hysteresis, depending on whether the initial state is at a low or high density. This behavior is observed even when the fueling location, cross-field diffusivity, and impurity level is changed, although the density window with asymmetry is reduced with increasing diffusivity. The addition of neon impurity seeding reduces the divertor heat fluxes, but also causes a drop in the upstream electron density with fixed particle throughput. This drop can be counteracted by increased main ion throughput, however too much neon results in a back transition into the asymmetric divertor regimes suggesting a need for control of both main ion and impurity seeding levels to achieve a desired divertor state.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Distributed Stochastic Optimization of a Neural Representation Network for Time-Space Tomography Reconstruction

4D time-space reconstruction of dynamic events or deforming objects using X-ray computed tomography (CT) is an important inverse problem in non-destructive evaluation. Conventional back-projection based reconstruction methods assume that the object remains static for the duration of several tens or hundreds of X-ray projection measurement images (reconstruction of consecutive limited-angle CT scans). However, this is an unrealistic assumption for many in-situ experiments that causes spurious artifacts and inaccurate morphological reconstructions of the object. To solve this problem, we propose to perform a 4D time-space reconstruction using a distributed implicit neural representation (DINR) network that is trained using a novel distributed stochastic training algorithm. Our DINR network learns to reconstruct the object at its output by iterative optimization of its network parameters such that the measured projection images best match the output of the CT forward measurement model. Here, we use a forward measurement model that is a function of the DINR outputs at a sparsely sampled set of continuous valued 4D object coordinates. Unlike previous neural representation architectures that forward and back propagate through dense voxel grids that sample the object's entire time-space coordinates, we only propagate through the DINR at a small subset of object coordinates in each iteration resulting in an order-of-magnitude reduction in memory and compute for training. DINR leverages distributed computation across several compute nodes and GPUs to produce high-fidelity 4D time-space reconstructions. We use both simulated parallel-beam and experimental cone-beam X-ray CT datasets to demonstrate the superior performance of our approach.

36 MATERIALS SCIENCE↗

Evaluation of Impedance Measurement Using Spread Spectrum Time Domain Reflectometry

We evaluate the feasibility of spectral time domain reflectometry (STDR) and spread spectrum time domain reflectometry (SSTDR) as a new modality for impedance measurement to test energized/noisy systems over a very broad frequency spectrum (near dc to gigahertz) as well as multiple channels in parallel. We simulate how the S/SSTDR signal parameters (signal-to-noise ratio (SNR) frequency and length of the pseudo-noise (PN) signals) affect the accuracy and usable frequency band for reflection coefficient and impedance measurement. An initial measurement validation is included. Here, we conclude with a recommendation of what will be required for a viable multichannel impedance (and reflection, transmission coefficient) measurement system for either energized or nonenergized systems, in noisy environments, that can test multiple channels simultaneously.

14 SOLAR ENERGY↗

Virtual Time III, Part 2: Combining Conservative and Optimistic Synchronization

This is Part 2 of a trio of works intended to provide a unifying framework in which conservative and optimistic synchronization for parallel discrete event simulations can be freely and transparently combined in the same logical process on an event-by-event basis. Here, in this article, we continue the outline of an approach called Unified Virtual Time (UVT) that was introduced in Part 1, showing in detail via two extended examples how conservative synchronization can be refactored and combined with optimistic synchronization in the UVT framework. We describe UVT versions of both a basic time windowing algorithm called Unified Simple Time Windows and a refactored version of the Chandy-Misra-Bryant Null Message algorithm called Unified CMB.

97 MATHEMATICS AND COMPUTING↗

Control And Optimization Modular Modeling Application For Nuclear Deployment

The purpose of the COMMAND code is to provide a flexible, scalable tool for use in developing, integrating, and testing the technologies necessary for achieving autonomous operations of advanced nuclear reactors. The code enables users to efficiently implement custom simulations and experiments by combining key methods from different software modules. These modules are focused on: modeling and simulation tools, such as nuclear simulation tools used for high-fidelity modeling (e.g., Reactor Excursion and Leak Analysis Program [RELAP5-3D] and Monte Carlo N-Particle [MCNP]); machine learning and optimization tools (e.g., anomaly detection and data-driven modeling techniques); advanced control in its digital, high-performance, and supervisory control forms (e.g., proportional integral derivative (PID) control and model predictive control (MPC); and integration with hardware through industrial communication protocols. To ensure flexibility and scalability, COMMAND was designed to be both modular—the software “pieces” all inherit from generic building blocks and can be combined and connected to create complicated simulations—and high performing—designed for parallel processing, enabling simulations and experiments to take advantage of multi-core computers, servers, and nodes. The code is written in the Python programming language due to the language's popularity, active community, and open-source and cross-platform nature. Maintaining consistency with other simulation tools used within the nuclear energy community, users implement simulations and experiments through text input files, which define components, parameters, connections, etc., through lines of text. Given that COMMAND is written in Python, these input files are native Python scripts, and so use the standard Python structure and formatting. This also enables users to take advantage of Python's extensive package library to develop custom capabilities for their specific use cases.

Faber, Jacob [Idaho National Laboratory (INL), Ida↗

Black-box statistical prediction of lossy compression ratios for scientific data

Lossy compressors are increasingly adopted in scientific research, tackling volumes of data from experiments or parallel numerical simulations and facilitating data storage and movement. In contrast with the notion of entropy in lossless compression, no theoretical or data-based quantification of lossy compressibility exists for scientific data. Users rely on trial and error to assess lossy compression performance. As a strong data-driven effort toward quantifying lossy compressibility of scientific datasets, we provide a statistical framework to predict compression ratios of lossy compressors. Our method is a two-step framework where (i) compressor-agnostic predictors are computed and (ii) statistical prediction models relying on these predictors are trained on observed compression ratios. Proposed predictors exploit spatial correlations and notions of entropy and lossyness via the quantized entropy. We study 8+ compressors on 6 scientific datasets and achieve a median percentage prediction error less than 12%, which is substantially smaller than that of other methods while achieving at least a 8.8× speedup for searching for a specific compression ratio and 7.8× speedup for determining the best compressor out of a collection.

97 MATHEMATICS AND COMPUTING↗

Cyber Security Analysis for Nuclear Reactor Control Systems (Final Technical Report)

This project investigated the cyber-security impacts of moving from an all analog, point-to-point, instrumentation and control (I&C) system to a digital I&C system based on Modbus and a shared communication medium. A formalism called a hybrid attack graph was expanded to support the nuclear research reactor system. The hybrid attack graph allows one to check a system for vulnerabilities, in this case cyber-security vulnerabilities, and to document the attack vectors (scenarios) causing those vulnerabilities. In parallel, a simulation of the system was developed to model both the physical reactor parameters and operations, as well as the network interconnects and communications. This simulation platform was modeled on the nuclear research reactor located at Washington State University. The simulation platform provided a sandbox to evaluate and quantify the impact of identified and proposed vulnerabilities in the system and to determine the effectiveness of countermeasures at stopping these attacks. The simulation and hybrid attack graph tools were integrated to provide a streamlined process of generating attack scenarios, playing those scenarios out in the simulation, and then analyzing the results to correlate system state to states in the hybrid attack graph. This process was used to (1) quantify the impact of attack scenarios and (2) to determine if the system moved through the hybrid attack graph as anticipated. The hybrid attack graph tool was extended and customized to produce a tool to automatically identify critical assets (CAs) and critical digital assets (CDAs) as defined by NRC Regulatory Guide 5.71. This tool was verified using the nuclear research reactor at Washington State University. Finally, a series of educational modules covering the findings of the different aspects of this research have been created.

97 MATHEMATICS AND COMPUTING↗

Charon User Manual (V.2.1) (Rev.01)

This manual gives usage information for the Charon semiconductor device simulator. Charon was developed to meet the modeling needs of Sandia National Laboratories and to improve on the capabilities of the commercial TCAD simulators; in particular, the additional capabilities are running very large simulations on parallel computers and modeling displacement damage and other radiation effects in significant detail. The parallel capabilities are based around the MPI interface which allows the code to be ported to a large number of parallel systems, including linux clusters and proprietary "big iron" systems found at the national laboratories and in large industrial settings.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Misuse Detection for a Generalized SFR Test Reactor

Sodium-cooled Fast Reactors (SFRs) present unique challenges for international safeguards. SFRs possess neutron physics characteristics that if configured appropriately could produce more fissile material than consumed. An adversary state may choose to build an SFR, justified by a lack of domestic natural uranium and limited access or interest to procuring uranium from international markets. Once constructed, the state may choose to misuse the SFR for the purpose of diverting fissile plutonium from declared operation. This work shows that a demonstration SFR does not need to be configured as a plutonium breeder to create one Significant Quantity (SQ) of plutonium in a short amount of time (e.g., one to few years). However, such an extreme case of misuse would change the core reactivity in such a way as to be easily indicated by deviations of control rod position compared to declared operation. In this work a contrived SFR demonstration reactor was modeled for the purpose of exploring proliferation scenarios and how such misuse could be detected using the SFR's Reactor Data Acquisition System (RDAS). Typically, the International Atomic Energy Agency (IAEA) does not have access to the control rod position, power, thermal, pressure sensing and indicating systems of nuclear power plants. However, this work shows that such data streams can be compared against a parallel detailed simulation model (a Digital Twin) to detect possible misuse.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Charon User Manual: v. 2.2 (revision1)

This manual gives usage information for the Charon semiconductor device simulator. Charon was developed to meet the modeling needs of Sandia National Laboratories and to improve on the capabilities of the commercial TCAD simulators; in particular, the additional capabilities are running very large simulations on parallel computers and modeling displacement damage and other radiation effects in significant detail. The parallel capabilities are based around the MPI interface which allows the code to be ported to a large number of parallel systems, including linux clusters and proprietary “big iron” systems found at the national laboratories and in large industrial settings.

42 ENGINEERING↗