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At least 703 records · Page 39

Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.

Cell mechanics↗

Sachdev-Ye-Kitaev model on a noisy quantum computer

Here we study the SYK model -- an important toy model for quantum gravity on IBM's superconducting qubit quantum computers. By using a graph-coloring algorithm to minimize the number of commuting clusters of terms in the qubitized Hamiltonian, we find the gate complexity of the time evolution using the first-order product formula for N Majorana fermions is $\mathscr{O}$(N 5 J 2 t 2 /ε) where J is the dimensionful coupling parameter, t is the evolution time, and ε is the desired precision. With this improved resource requirement, we perform the time evolution for N=6,8 with maximum two-qubit circuit depth of 343. We perform different error mitigation schemes on the noisy hardware results and find good agreement with the exact diagonalization results on classical computers and noiseless simulators. In particular, we compute return probability after time t and out-of-time order correlators (OTOC) which is a standard observable of quantifying the chaotic nature of quantum systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Digital quantum magnetism on a trapped-ion quantum computer

Digital quantum matter—realized when discrete quantum gates approximate continuous time evolution—is susceptible to heating into chaotic, structureless states. If digitization errors are adequately suppressed, a long-lived transient regime of approximately energy-conserving dynamics can be observed on gate-based quantum computers. Conservation of energy, in turn, enables the exploration of a wide variety of complex behaviours observed in equilibrium systems, ranging from the non-trivial microscopic origins of thermalization itself to the stabilization of effective models hosting exotic emergent properties. Here we use Quantinuum’s H2 quantum computer to simulate digitized dynamics of the quantum Ising model, suppressing digitization errors well enough to observe thermalization on timescales that severely challenge classical simulation methods. Relaxation of an inhomogeneous state reveals an emergent hydrodynamics owing to approximate energy conservation and we compute the associated diffusion constant. By reprogramming our simulations to take place on a triangular lattice with periodic boundary conditions, we observe thermalization consistent with emergent gauge and topological constraints resulting from lattice frustration. Furthermore, our results were enabled by continued advances in two-qubit gate quality (native partial entangler fidelities of 99.94(1)%) and establish digital quantum computers as powerful tools for studying (effectively) continuous-time dynamics.

Information theory and computation↗

Simulation-aided occupant-centric building design: A critical review of tools, methods, and applications

Occupants are active participants in their built environment, affecting its performance while simultaneously being affected by its design and indoor environmental conditions. With recent advances in computer modeling, simulation tools, and analysis techniques, topics such as human-building interactions and occupant behavior have gained significant interest in the literature given their premise of improving building design processes and operating strategies. In practice, the focus of occupant-centric literature has been mostly geared towards the latter (i.e., operation), leaving the implications on building design practices underexplored. This paper fills the gap by providing a critical review of existing studies applying computer-based modeling and simulation to guide occupant-centric building design. The reviewed papers are organized along four main themes, namely occupant-centric: (i) metrics of building performance, (ii) modeling and simulation approaches, (iii) design methods and applications, and (iv) supporting practices and mechanisms. Important barriers are identified for a more effective application of occupant-centric building design practices, including the limited consideration of metrics beyond energy efficiency (e.g., occupant well-being and space planning), the limited implementation and validation of the proposed methods, and the lack of integration of occupant behavior modeling in existing building performance simulation tools. Finally, future research directions are discussed, covering large-scale international data collection efforts to move from generic assumptions about occupant behavior to specific/localized knowledge, improved metrics of measuring building performance, and improved industry practices, such as building codes, to promote an occupant-in-the-loop approach to the building design process.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Enhanced accuracy through ensembling of randomly initialized auto-regressive models for dynamical systems

Computational mechanics simulations using traditional finite element methods (FEM) require prohibitively expensive computational resources for real-time engineering applications, design optimization, and digital twin implementations. While machine learning (ML) surrogate models offer significant computational speedups, autoregressive ML models for time-dependent mechanical systems suffer from error accumulation that compromises long-term prediction reliability - a critical concern for engineering applications where accuracy over extended time horizons is essential for safety and performance assessments. Here, we propose a deep ensemble framework specifically designed to address this challenge in computational mechanics applications, where multiple ML surrogate models with random weight initializations are trained in parallel and their predictions aggregated during inference. This approach leverages statistical diversity to maximize information gain from a fixed set of training data and to mitigate error propagation, while maintaining the computational efficiency that makes ML surrogates attractive for engineering practice. We validate the framework on three representative problems spanning critical areas of computational mechanics: stress field evolution in heterogeneous microstructures under complex loading (relevant to advanced materials design and composite analysis), planetary-scale shallow water dynamics (applicable to environmental and geotechnical engineering), and Gray-Scott reaction-diffusion systems (relevant to mass transport and chemical process engineering). Across all test cases, the ensemble approach demonstrates consistent error reduction of 15-33% compared to individual models. The codes for this work are available on GitHub (https://github.com/Graham-Brady-Research-Group/AutoregressiveEnsemble_SpatioTemporal_Evolution).

autoregressive prediction↗

Machine learning surrogates for ion energy–angle distributions in thermal and RF plasma sheaths

Ion energy–angle distributions (IEADs) at material surfaces are a critical input for plasma–material interaction (PMI) studies in fusion devices, yet they are computationally expensive to obtain using particle-in-cell (PIC) simulations. In this work, we develop a machine learning surrogate based on a deep deconvolutional neural network (DDeCNN) trained on large databases generated with the hPIC2 code. The surrogate is capable of reconstructing IEADs from sheath parameters for both thermal and radio-frequency (RF) plasmas, including cases with multiple ion species. Across thousands of test cases, the model achieves high accuracy, with over 97 % of predictions classified as good or average based on standard error metrics (MAE, MSE, L2). Even in the more challenging RF and multi-species regimes, the surrogate reliably captures the multi-peak structure of PIC results. Once trained, the surrogate produces IEADs in milliseconds on a common workstation, yielding speedups of six to seven orders of magnitude compared with running a full PIC simulation. This computational gain enables dense parameter scans and direct coupling of IEAD predictions with PMI and erosion models on whole-device scales in fusion-relevant conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

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↗

An Atmospheric Aerosol Short Course for Early Career Scientists

The first Department of Energy (DOE) Environmental and Molecular Science Laboratory (EMSL)/Atmospheric Radiation Measurement (ARM) aerosol summer school was held July 15-19, 2019 at the EMSL user facility located at Pacific Northwest National Laboratory. The school set out to provide graduate students and early-career scientists an overview of atmospheric aerosol science and an introduction to the measurement techniques available through the EMSL and ARM user facilities to address current aerosol science issues. Instructors for the course were drawn from scientists from the EMSL (Laskin et al., 2016; China et al., 2018) and ARM facilities (McComiskey and Ferrare, 2016) as well as from the DOE Atmospheric System Research (ASR) program. Student support for the summer school was also jointly provided by EMSL, ARM, and ASR. The school spanned five days with each day covering a particular theme. 25 students from 21 institutions attended morning lectures on aerosol composition, properties, theory, measurements, and modeling. During afternoons, the students explored instruments that collect and analyze aerosol samples at EMSL and PNNL’s Atmospheric Measurements Laboratory. They also tested relevant computer modeling simulations and learned about NWChem, EMSL’s open-source computational chemistry software suite.

54 ENVIRONMENTAL SCIENCES↗

Sensitivity of Simulations of Double-detonation Type Ia Supernovae to Integration Methodology

Abstract We study the coupling of hydrodynamics and reactions in simulations of the double-detonation model for Type Ia supernovae. When assessing the convergence of simulations, the focus is usually on spatial resolution; however, the method of coupling the physics together as well as the tolerances used in integrating a reaction network also play an important role. In this paper, we explore how the choices made in both coupling and integrating the reaction portion of a simulation (operator/Strang splitting versus the simplified spectral deferred corrections method we introduced previously) influences the accuracy, efficiency, and nucleosynthesis of simulations of double detonations. We find no need to limit reaction rates or reduce the simulation time step to the reaction timescale. The entire simulation methodology used here is GPU-accelerated and made freely available as part of the Castro simulation code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Constructing a Simulation Surrogate with Partially Observed Output

Gaussian process surrogates are a popular alternative to directly using computationally expensive simulation models. When the simulation output consists of many responses, dimension-reduction techniques are often employed to construct these surrogates. However, surrogate methods with dimension reduction generally rely on complete output training data. This article proposes a new Gaussian process surrogate method that permits the use of partially observed output while remaining computationally efficient. The new method involves the imputation of missing values and the adjustment of the covariance matrix used for Gaussian process inference. The resulting surrogate represents the available responses, disregards the missing responses, and provides meaningful uncertainty quantification. In conclusion, the proposed approach is shown to offer sharper inference than alternatives in a simulation study and a case study where an energy density functional model that frequently returns incomplete output is calibrated.

42 ENGINEERING↗

Iodine recombination in xenon solvent: Clusters in the gas to liquid-like state transition

Supercritical fluids (SCFs) have attracted significant attention as solvents for chemical reactions due to their unique properties, such as high diffusivity, low viscosity, and tunable solvation properties. These properties profoundly influence reaction kinetics and are often attributed to the formation of molecular clusters within SCFs. To study the effect of supercritical solvent on chemical reactivity and dynamics of reactions, one needs to understand the dynamics of clusters in supercritical fluid. Extensive experiments on the photodissociation and recombination of iodine in supercritical fluids served as a model system for understanding these effects. Experimental studies have been complemented by theoretical and computational investigations, which mostly employ Monte Carlo or empirical molecular dynamics simulations. However, computational studies using non-reactive force fields and ab initio approaches present challenges in capturing reactive processes at larger scales within supercritical fluids. Here, in this work, we developed the ReaxFF parameters by training against quantum mechanics data. ReaxFF reactive force field based molecular dynamics simulations were performed, studying the dynamics of a xenon solvent and cage effect at different thermodynamic conditions for the iodine recombination reaction. We show that the conditions near the critical point are the optimal conditions to study the cage effect. We show that the average lifetime of xenon clusters ranging between 5 and 11 ps is comparable to iodine geminate recombination. Our simulation results of iodine recombination in xenon solvent demonstrate the higher probability of iodine molecule formation in the presence of xenon clusters. Finally, we show that the supercritical condition exhibits the highest recombination rate for iodine atoms.

Cage effect↗

Performance Testing and Assessment of Protection Scheme Using Real-Time Hardware-in-the-Loop and IEC 61850 Standard

The main challenge of the microgrid is to design a suitable protection scheme due to the complexity of the architecture of the microgrid. The importance of the proposed protection technique is threefold. First, it presents a co-simulation platform to integrate between a simulated model on power system computer aided design (PSCAD)/real time digital simulator computer aided design (RSCAD) software’s and physical devices schweitzer engineering laboratories (SEL) 421-7 relays to protect the microgrid that includes different resources connected based on inverter interface. Second, it presents a comprehensive hardware/software setup to test the protective relays in a closed loop system and shows how to configure the protective relay’s International Electrotechnical Commission 61850 communications. Third, IEEE 1588 standard is used to provide sub nanoseconds latency between the simulated model that emulated on real time digital simulator (RTDS) and the external devices. Also, the measurement signals are synchronized between RTDS and the external devices using giga-transceiver synchronization card (GTSYNC) interface card and SEL-2488 satellite-synchronized network clock. The results showed that the co-simulation infrastructure introduces a highly dependable design, analysis, and testing environment for cyber and physical data flow in the system. Besides that, the voltages at ac/dc sides and frequency at fault condition were maintained due to the energy storage device contributions at different modes of operation.

42 ENGINEERING↗

Forecasting Dynamic Line Rating with Spatial Variation Considerations

Dynamic line rating (DLR) is a technology that allows the ampacity of an electrical conductor to be calculated using real-time or forecasted weather conditions. Historically, the ampacity of a conductor has been determined using a static line rating method which assumes conservative weather assumptions. Therefore, not only can DLR give a more accurate measurement of the true ampacity of a conductor, but it can also increase its ampacity during weather conditions with greater thermal mitigations. The two primary cooling factors in the ampacity calculations are wind speed and direction. In complex terrain, wind speed and direction can have large variations over short distances. Therefore, accurately identifying the limiting span of a transmission line requires high spatial resolution of the wind along its path. One solution is to install dense weather stations along their path, though this can become costly over long distances. Therefore, researchers have investigated the use of Computation Fluid Dynamic (CFD) simulations to accurately compute the wind field along the path of a transmission line and use these results to identify the limiting section of the conductor. This work presents a case study that evaluates the coupling of CFD simulations and forecasted weather simulations using the High-Resolution Rapid Refresh (HRRR) model points over a 2-year span within a region in south eastern Idaho. The primary goal of the work is the evaluation of the number of HRRR model points used, i.e., weather stations, along the path of the line and the accuracy of the resulting ampacity. This was done using 4, 10, 17, 26, and 35 HRRR model points along two transmission line paths. The results indicate that as the number of model points are increased, the DLR ampacity of the lines decrease, yet converge as more points are added and demonstrate little change with additional HRRR points. It is expected that these results can help transmission line operators identify the number of weather stations that must be installed when coupled with CFD simulations and DLR ampacity to ensure accurate ratings and safe operations.

17 WIND ENERGY↗

New basis for Hamiltonian SU(2) simulations

Due to rapidly improving quantum computing hardware, Hamiltonian simulations of relativistic lattice field theories have seen a resurgence of attention. This computational tool requires turning the formally infinite-dimensional Hilbert space of the full theory into a finite-dimensional one. For gauge theories, a widely used basis for the Hilbert space relies on the representations induced by the underlying gauge group, with a truncation that keeps only a set of the lowest dimensional representations. This works well at large bare gauge coupling, but becomes less efficient at small coupling, which is required for the continuum limit of the lattice theory. In this work, we develop a new basis suitable for the simulation of an SU(2) lattice gauge theory in the maximal tree gauge. In particular, we show how to perform a Hamiltonian truncation so that the eigenvalues of both the magnetic and electric gauge-fixed Hamiltonian are mostly preserved, which allows for this basis to be used at all values of the coupling. Little prior knowledge is assumed, so this may also be used as an introduction to the subject of Hamiltonian formulations of lattice gauge theories. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Quantum computing for fusion energy science applications

This is a review of recent research exploring and extending present-day quantum computing capabilities for fusion energy science applications. We begin with a brief tutorial on both ideal and open quantum dynamics, universal quantum computation, and quantum algorithms. Then, we explore the topic of using quantum computers to simulate both linear and nonlinear dynamics in greater detail. Because quantum computers can only efficiently perform linear operations on the quantum state, it is challenging to perform nonlinear operations that are generically required to describe the nonlinear differential equations of interest. In this work, we extend previous results on embedding nonlinear systems within linear systems by explicitly deriving the connection between the Koopman evolution operator, the Perron–Frobenius evolution operator, and the Koopman–von Neumann evolution (KvN) operator. We also explicitly derive the connection between the Koopman and Carleman approaches to embedding. Extension of the KvN framework to the complex-analytic setting relevant to Carleman embedding, and the proof that different choices of complex analytic reproducing kernel Hilbert spaces depend on the choice of Hilbert space metric are covered in the appendixes. Finally, we conclude with a review of recent quantum hardware implementations of algorithms on present-day quantum hardware platforms that may one day be accelerated through Hamiltonian simulation. We discuss the simulation of toy models of wave–particle interactions through the simulation of quantum maps and of wave–wave interactions important in nonlinear plasma dynamics.

Joseph, I. (ORCID:0000000255400840)↗

Optimization of algorithmic errors in analog quantum simulations

Due to rapidly improving quantum computing hardware, Hamiltonian simulations of relativistic lattice field theories have seen a resurgence of attention. Furthermore, this computational tool requires turning the formally infinite-dimensional Hilbert space of the full theory into a finite-dimensional one. For gauge theories, a widely used basis for the Hilbert space relies on the representations induced by the underlying gauge group, with a truncation that keeps only a set of the lowest dimensional representations. This works well at large bare gauge coupling, but becomes less efficient at small coupling, which is required for the continuum limit of the lattice theory. In this work, we develop a new basis suitable for the simulation of an SU(2) lattice gauge theory in the maximal tree gauge. In particular, we show how to perform a Hamiltonian truncation so that the eigenvalues of both the magnetic and electric gauge-fixed Hamiltonian are mostly preserved, which allows for this basis to be used at all values of the coupling. Little prior knowledge is assumed, so this may also be used as an introduction to the subject of Hamiltonian formulations of lattice gauge theories.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Efficient emulation of relativistic heavy ion collisions with transfer learning

Measurements from the Large Hadron Collider (LHC) and the Relativistic Heavy Ion Collider (RHIC) can be used to study the properties of quark-gluon plasma. Systematic constraints on these properties must combine measurements from different collision systems and methodically account for experimental and theoretical uncertainties. Such studies require a vast number of costly numerical simulations. While computationally inexpensive surrogate models (“emulators”) can be used to efficiently approximate the predictions of heavy ion simulations across a broad range of model parameters, training a reliable emulator remains a computationally expensive task. We use transfer learning to map the parameter dependencies of one model emulator onto another, leveraging similarities between different simulations of heavy ion collisions. By limiting the need for large numbers of simulations to only one of the emulators, this technique reduces the numerical cost of comprehensive uncertainty quantification when studying multiple collision systems and exploring different models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Simulating dirty bosons on a quantum computer

Abstract Quantum computers hold the potential to unlock new discoveries in complex quantum systems by enabling the simulation of physical systems that have heretofore been impossible to implement on classical computers due to intractability. A system of particular interest is that of dirty bosons, whose physics highlights the intriguing interplay of disorder and interactions in quantum systems, playing a central role in describing, for instance, ultracold gases in a random potential, doped quantum magnets, and amorphous superconductors. Here, we demonstrate how quantum computers can be used to elucidate the physics of dirty bosons in one and two dimensions. Specifically, we explore the disorder-induced delocalized-to-localized transition using adiabatic state preparation. In one dimension, the quantum circuits can be compressed to small enough depths for execution on currently available quantum computers. In two dimensions, the compression scheme is no longer applicable, thereby requiring the use of large-scale classical state vector simulations to emulate quantum computer performance. In addition, simulating interacting bosons via emulation of a noisy quantum computer allowed us to study the effect of quantum hardware noise on the physical properties of the simulated system. Our results suggest that scaling laws control how noise modifies observables versus its strength, the circuit depth, and the number of qubits. Moreover, we observe that noise impacts the delocalized and localized phases differently. A better understanding of how noise alters the observed properties of the simulated system is essential for leveraging near-term quantum devices for simulation of dirty bosons, and indeed for condensed matter systems in general.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗