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At least 253 records · Page 14

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Monte Carlo study of electron-beam penetration and backscattering in multi-walled carbon nanotube materials: The effect of different scattering models

A systematic study of electron-beam penetration and backscattering in multi-walled carbon nanotube (MWCNT) materials for beam energies of {approx}0.3 to 30 keV is presented based on event-by-event Monte Carlo simulation of electron trajectories using state-of-the-art scattering cross sections. The importance of different analytic approximations for computing the elastic and inelastic electron-scattering cross sections for MWCNTs is emphasized. We offer a simple parameterization for the total and differential elastic-scattering Mott cross section, using appropriate modifications to the Browning formula and the Thomas-Fermi screening parameter. A discrete-energy-loss approach to inelastic scattering based on dielectric theory is adopted using different descriptions of the differential cross section. The sensitivity of electron penetration and backscattering parameters to the underlying scattering models is examined. Our simulations confirm the recent experimental backscattering data on MWCNT forests and, in particular, the steep increase of the backscattering yield at sub-keV energies as well as the sidewalls escape effect at high-beam energies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Autonomous Operations for Advanced Reactors Utilizing Supervisory Control

Automation is a critical tenet of reactor plant operations as reliance on nuclear energy increases. Nuclear power plants require a large workforce which does not scale with output; that is, the cost per megawatt increases as reactor output becomes smaller. The economic viability of advanced reactors, particularly small modular reactors (SMRs) and microreactors, requires a significantly reduced onsite workforce. The logical solution is establishing a systematic process of elimination of reliance on human operators, and to the extent possible, replacing these actions with automated functions. In this paper, we propose a method for such transformation to establish a robust technical basis to enable transition to autonomy. Our method is based on finite state automata (FSA)—also known as finite state machines (FSMs). Relying on this method allows us to exploit the rich set of mathematical proofs available in the field of regular languages. FSA are one of the mathematical tools to model discrete event systems (DES). These properties are applied to produce an automated startup controller for the Massachusetts Institute of Technology Research Reactor (MITR). The startup procedure is captured in terms of discrete changes from one state to another while an independent supervisory control system directs the sequence of states and alerts a human in the event of an abnormal operation. First, the design and behavior of the MITR rod control system were modeled in Simulink. Then, the startup procedure was applied to the rod control system and the DES performed a startup by procedurally withdrawing rods to the subcritical position. The simulation also stops rod motion in response to an uncontrollable event and restarts rod motion once the event has been cleared.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

Conditioned quantum-assisted deep generative surrogate for particle-calorimeter interactions

Particle collisions at accelerators like the Large Hadron Collider (LHC), recorded by experiments such as ATLAS and CMS, enable precise standard model measurements and searches for new phenomena. Simulating these collisions significantly influences experiment design and analysis but incurs immense computational costs, projected at millions of CPU-years annually during the high luminosity LHC (HL-LHC) phase. Currently, simulating a single event with Geant4 consumes around 1000 CPU seconds, with calorimeter simulations especially demanding. To address this, we propose a conditioned quantum-assisted generative model, integrating a conditioned variational autoencoder (VAE) and a conditioned restricted Boltzmann machine (RBM). Our RBM architecture is tailored for D-Wave’s Pegasus-structured advantage quantum annealer for sampling, leveraging the flux bias for conditioning. This approach combines classical RBMs as universal approximators for discrete distributions with quantum annealing’s speed and scalability. We also introduce an adaptive method for efficiently estimating effective inverse temperature, and validate our framework on Dataset 2 of CaloChallenge.

97 MATHEMATICS AND COMPUTING↗

Enabling event-by-event precision in γ-ray cascades for neutron-induced reactions

Neutron-induced γ-ray spectra provide key inputs for modern active interrogation applications. A precise modeling of the nuclear reaction and subsequent emission of γ rays is challenging and often impossible due to limitations on evaluated data file formats and nuclear transport simulation codes. We present a framework that addresses these challenges by combining experimental data and reaction-model calculation outputs into an extended candidate version of the Generalized Nuclear Data Structure (GNDS) file, the successor format for the legacy Evaluated Nuclear Data File (ENDF-6). This proposed GNDS hierarchical format contains all the necessary ingredients for inline γ-ray cascade reproduction with event-by-event precision, including continuum–continuum and continuum–discrete transitions following neutron-capture and inelastic neutron scattering reactions. Cascade-event generation based on our approach demonstrates improved energy conservation on an event-by-event basis and permits the use of γ-γ coincidences in applications. This work offers, for the first time, a method to generate neutron-capture and inelastic neutron-scattering γ-ray cascades where energy conservation, correlations, and experimental primaries are fully accounted for.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Simulating Fracture Sealing by Granular LCM Particles in Geothermal Drilling

Lost circulation occurs when the returned fluid is less than what is pumped into the well due to loss of fluid to pores or fractures. A lost-circulation event is a common occurrence in a geothermal well. Typical geothermal reservoirs are often under-pressured and have larger fracture apertures. A severe lost-circulation event is costly and may lead to stuck pipe, well instability, and well abandonment. One typical treatment is adding lost-circulation materials (LCMs) to seal fractures. Conventional LCMs fail to properly seal fractures because their mechanical limit is exceeded at elevated temperatures. In this paper, parametric studies in numerical simulations are conducted to better understand different thermal effects on the sealing mechanisms of LCMs. The computational fluid dynamics (CFDs) and the discrete element method (DEM) are coupled to accurately capture the true physics of sealing by granular materials. Due to computational limits, the traditional Eulerian–Eulerian approach treats solid particles as a group of continuum matter. With the advance of modern computational power, particle bridging is achievable with DEM to track individual particles by modeling their interactive forces between each other. Particle–fluid interactions can be modeled by coupling CFD algorithms. Fracture sealing capability is investigated by studying the effect of four individual properties including fluid viscosity, particle size, friction coefficient, and Young’s modulus. It is found that thermally degraded properties lead to inefficient fracture sealing.

15 GEOTHERMAL ENERGY↗

Exploration of High-Dimensional Scalar Function for Nuclear Reactor Safety Analysis and Visualization

The next generation of methodologies for nuclear reactor Probabilistic Risk Assessment (PRA) explicitly accounts for the time element in modeling the probabilistic system evolution and uses numerical simulation tools to account for possible dependencies between failure events. The Monte-Carlo (MC) and the Dynamic Event Tree (DET) approaches belong to this new class of dynamic PRA methodologies. A challenge of dynamic PRA algorithms is the large amount of data they produce which may be difficult to visualize and analyze in order to extract useful information. We present a software tool that is designed to address these goals. We model a large-scale nuclear simulation dataset as a high-dimensional scalar function defined over a discrete sample of the domain. First, we provide structural analysis of such a function at multiple scales and provide insight into the relationship between the input parameters and the output. Second, we enable exploratory analysis for users, where we help the users to differentiate features from noise through multi-scale analysis on an interactive platform, based on domain knowledge and data characterization. Our analysis is performed by exploiting the topological and geometric properties of the domain, building statistical models based on its topological segmentations and providing interactive visual interfaces to facilitate such explorations. We provide a user’s guide to our software tool by highlighting its analysis and visualization capabilities, along with a use case involving dataset from a nuclear reactor safety simulation.

97 MATHEMATICS AND COMPUTING↗

Exploration of high-dimensional scalar function for nuclear reactor safety analysis and visualization

The next generation of methodologies for nuclear reactor Probabilistic Risk Assessment (PRA) explicitly accounts for the time element in modeling the probabilistic system evolution and uses numerical simulation tools to account for possible dependencies between failure events. The Monte-Carlo (MC) and the Dynamic Event Tree (DET) approaches belong to this new class of dynamic PRA methodologies. A challenge of dynamic PRA algorithms is the large amount of data they produce which may be difficult to visualize and analyze in order to extract useful information. We present a software tool that is designed to address these goals. We model a large-scale nuclear simulation dataset as a high-dimensional scalar function defined over a discrete sample of the domain. First, we provide structural analysis of such a function at multiple scales and provide insight into the relationship between the input parameters and the output. Second, we enable exploratory analysis for users, where we help the users to differentiate features from noise through multi-scale analysis on an interactive platform, based on domain knowledge and data characterization. Our analysis is performed by exploiting the topological and geometric properties of the domain, building statistical models based on its topological segmentations and providing interactive visual interfaces to facilitate such explorations. We provide a user's guide to our software tool by highlighting its analysis and visualization capabilities, along with a use case involving data from a nuclear reactor safety simulation. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Memoirs of Mass Accretion: Probing the Edges of Intracluster Light in Simulated Galaxy Clusters

The diffuse starlight extending throughout massive galaxy clusters, known as intracluster light (ICL), has the potential to be read as a memoir of mass accretion: informative, individual, and yet imperfect. Here, we combine dark-matter-only zoom-in simulations from the Symphony suite with the Nimbus “star-tagging” model of the stellar halo to assess how much information about the mass assembly of an individual galaxy cluster can be gleaned from idealized measurements of ICL outskirts. We show that the edges of a cluster’s stellar profile—the primary (R sp⋆,1 ) and secondary (R sp⋆,2 ) stellar “splashback” radii—are sensitive to both continuous mass accretion histories (MAHs) and discrete merger events, making them potentially powerful probes of a cluster’s past. We find that R sp⋆,1 strongly correlates with the cluster’s mass ∼1 dynamical time ago, while R sp⋆,2 traces more recent MAH to a slightly lesser degree. In combination, these features can further distinguish between clusters that have and have not undergone a major merger within the past dynamical time. We use both to predict realistic cluster MAHs with the MultiCAM framework. These outer ICL features are significantly more sensitive to mass accretion and merger histories than the stellar mass gap and halo concentration, and perform comparably to the commonly used X-ray-based tracer of relaxedness, x off . While our analysis is idealized, the relevant ICL features are potentially detectable in next-generation deep imaging of nearby clusters. This work highlights the promise of ICL measurements and lays the groundwork for more detailed forecasts of their power.

79 ASTRONOMY AND ASTROPHYSICS↗

Resistive magnetohydrodynamic reconnection: Resolving long-term, chaotic dynamics

In this paper, we address the long-term evolution of an idealised double current system entering reconnection regimes where chaotic behavior plays a prominent role. Our aim is to quantify the energetics in high magnetic Reynolds number evolutions, enriched by secondary tearing events, multiple magnetic island coalescence, and compressive versus resistive heating scenarios. Our study will pay particular attention to the required numerical resolutions achievable by modern (grid-adaptive) computations, and comment on the challenge associated with resolving chaotic island formation and interaction. We will use shock-capturing, conservative, grid-adaptive simulations for investigating trends dominated by both physical (resistivity) and numerical (resolution) parameters, and confront them with (visco-)resistive magnetohydrodynamic simulations performed with very different, but equally widely used discretization schemes. This will allow us to comment on the obtained evolutions in a manner irrespective of the adopted discretization strategy. Our findings demonstrate that all schemes used (finite volume based shock-capturing, high order finite differences, and particle in cell-like methods) qualitatively agree on the various evolutionary stages, and that resistivity values of order 0.001 already can lead to chaotic island appearance. However, none of the methods exploited demonstrates convergence in the strong sense in these chaotic regimes. At the same time, nonperturbed tests for showing convergence over long time scales in ideal to resistive regimes are provided as well, where all methods are shown to agree. Both the advantages and disadvantages of specific discretizations as applied to this challenging problem are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Pinning time statistics for vortex lines in disordered environments

We study the pinning dynamics of magnetic flux (vortex) lines in a disordered type-II superconductor. Using numerical simulations of a directed elastic line model, we extract the pinning time distributions of vortex line segments. We compare different model implementations for the disorder in the surrounding medium: discrete, localized pinning potential wells that are either attractive and repulsive or purely attractive, and whose strengths are drawn from a Gaussian distribution; as well as continuous Gaussian random potential landscapes. Here, we find that both schemes yield power-law distributions in the pinned phase as predicted by extreme-event statistics, yet they differ significantly in their effective scaling exponents and their short-time behavior.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Point cloud-based diffusion models for the Electron-Ion Collider

At high-energy collider experiments, generative models can be used for a wide range of tasks, including fast detector simulations, unfolding, searches of physics beyond the Standard Model, and inference tasks. In particular, it has been demonstrated that score-based diffusion models can generate high-fidelity and accurate samples of jets or collider events. This work expands on previous generative models in three distinct ways. First, our model is trained to generate entire collider events, including all particle species with complete kinematic information. We quantify how well the model learns event-wide constraints such as the conservation of momentum and discrete quantum numbers. We focus on the events at the future Electron-Ion Collider, but we expect that our results can be extended to proton-proton and heavy-ion collisions. Second, previous generative models often relied on image-based techniques. The sparsity of the data can negatively affect the fidelity and sampling time of the model. We address these issues using point clouds and a novel architecture combining edge creation with transformer modules called Point Edge Transformers. Third, we adapt the foundation model OmniLearn, to generate full collider events. This approach may indicate a transition toward adapting and fine-tuning foundation models for downstream tasks instead of training new models from scratch.

Araz, Jack Y. [Stony Brook Univ., NY (United State↗

Determination of the effective diffusivity of water in a poly (methyl methacrylate) membrane containing carbon nanotubes using kinetic Monte Carlo simulations

A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrix and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, D{sub eff}, of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, D{sub eff} is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for D{sub eff} as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on D{sub eff} (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and correlated them with the time needed for penetrant water molecules to explore the available large, fast-diffusing CNT pores before Fickian diffusion is reached.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analyzing the impact of modeling choices and assumptions in compartmental epidemiological models

In this study, computational models have become increasingly used as part of modeling, predicting, and understanding how infectious diseases spread within large populations. These models can be broadly classified into differential equation-based models (EBM) and agent-based models (ABM). Both types of models are central in aiding public health officials design intervention strategies in case of large epidemic outbreaks. We examine these models in the context of illuminating their hidden assumptions and the impact these may have on the model outcomes. Very few ABM/EBMs are evaluated for their suitability to address a particular public health concern, and drawing relevant conclusions about their suitability requires reliable and relevant information regarding the different modeling strategies and associated assumptions. Hence, there is a need to determine how the different modeling strategies, choices of various parameters, and the resolution of information for EBMs and ABMs affect outcomes, including predictions of disease spread. In this study, we present a quantitative analysis of how the selection of model types (i.e., EBM vs. ABM), the underlying assumptions that are enforced by model types to model the disease propagation process, and the choice of time advance (continuous vs. discrete) affect the overall outcomes of modeling disease spread. Our study reveals that the magnitude and velocity of the simulated epidemic depends critically on the selection of modeling principles, various assumptions of disease process, and the choice of time advance.

60 APPLIED LIFE SCIENCES↗

Benchmarking numerical methods for impact and cratering applications

Large scale computational models are important for studying impact cratering events that are prevalent both on Earth and, more broadly, in this solar system. To address these problems, models must reliably account for both large length scales (e.g., kilometers) and relatively long time scales (hundreds of seconds). This work benchmarks two such approaches, a more traditional hydrodynamics approach and a finite-discrete element method (FDEM), for impact cratering applications. Both 2D and 3D results are discussed for two different impact velocities, 5 km/s and 20 km/s, striking normal to the target and, for 3D simulations, 45° from vertical. In addition, comparisons to previously published data are presented. Finally, differences in how these methods model damage are discussed. Ultimately, both approaches show successful modeling of several different impact scenarios.

58 GEOSCIENCES↗

A Simulation Modeling Approach to Optimizing Nuclear Waste Dispositioning

The dispositioning of nuclear waste generated at facilities across the country is an ongoing battle that affects us all. National laboratories and research centers dealing in medical research, clean energy, and other nuclear activities such as the Department of Energy (DOE) facilities face the need to properly manage and dispose of nuclear waste. A dynamic modeling solution would enable the DOE and others to make decisions on waste disposal and technological options. In doing so, this research explores modeling techniques using available data to address these situations. The focus being on developing an initial robust and adaptable discrete event model using the ExtendSim tool. This modeling effort will target the dispositioning of transuranic waste at the Savannah River National Laboratory (SRNL) which can be expanded to represent the current state of disposition process for waste generated at other DOE facilities. The model aims to assess resource allocation and waste processing options to stabilize productivity and cut the backlog of nuclear waste. By assessing the results of different scenarios, this research aims to provide actionable insights for the DOE. This approach has the potential to significantly improve the management of radioactive waste, offering the capability of evaluating options for optimizing the process for nuclear waste disposal. The findings of this study can serve as a valuable resource for decision-makers and other national laboratories, or research entities engaged in nuclear operations by enabling them to make more informed choices.

Andaverde, Alexis↗

An Implicit Correlation Method for Cross-Correlation Sampling, with MCNPX-PoliMi Validation

Monte Carlo particle transport codes used to model detector response are traditionally run in analog mode. However, analog simulations of cross-correlation measurements are extremely time-consuming because the probability of coincident detection is small, approximately equal to the product of the probabilities of a single detection in each detector. The new “implicit correlation” method described here increases the number of correlated event scores, thereby reducing variance and required computation times. The cost of the implicit correlation method is comparable to the cost of simulating single-event detection for the lowest absolute detector efficiency in the problem. The new method is especially useful in the nuclear nonproliferation and safeguards fields for simulating correlation measurements of shielded special nuclear material. The new method was implemented in MCNPX-PoliMi for neutron-neutron cross-correlations with a Cf-252 spontaneous fission source measured by 14 detectors at various angles. The method demonstrated good agreement with analog simulation and reference measurement results. Small differences between nonanalog and analog cross-correlation distributions are attributed to discretization errors that are often not present in practical applications. Improvement in the figure of merit was greater than a factor of 100 in all tested cases.

Marcath, Matthew J.↗