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Python Library for Monte Carlo Simulations with Ab Initio and Machine-Learned Interatomic Potentials

There is a growing need in the simulation community for software that provides a transparent, reproducible, usable, and extensible (TRUE) Monte Carlo (MC) simulation framework employing energies from ab initio methods and machine-learning interatomic potentials (MLIPs). We introduce a Python library (ASE-MC) that adds Monte Carlo functionality to the Atomic Simulation Environment (ASE) package. Now, we can combine the powerful tools used to build systems and perform ab initio and MLIP in ASE with MC simulation algorithms to sample the configurational space with a concise Python script. After presenting the design philosophy, we demonstrate the flexibility of our approach using selected examples. These example simulations include liquid water described with a message-passing MLIP in the canonical and isothermal–isobaric ensembles, sampling the characteristic dihedral angle of biphenyl and comparing an MLIP to first-principles calculations, and a grand canonical Monte Carlo simulation of ammonia adsorption on Pt(111). These examples showcase the main features of the software, which include flexibility in the choice of ab initio or MLIP engine, ab initio or MLIP grand canonical MC with cavity bias insertions and deletions, the ability to add custom MC moves to the move set, and how users can condense complex MC workflows into a single Python script. Finally, this library serves as a framework for reproducible Monte Carlo simulations, facilitating easy reproduction of the work and application to new systems.

97 MATHEMATICS AND COMPUTING

Dataset for Cruz-O'Byrne et al (2026): "Divergent biogeochemical responses in upland coastal forest soils to repeated flooding and shifts in water chemistry"

Hydrologic disturbances from accelerated sea-level rise and the increasing frequency and intensity of storms and tidal flooding are altering biogeochemical processes in upland coastal forests, transforming these ecosystems into wetlands. However, the initial effects of flooding on belowground biogeochemistry and the mechanisms driving greenhouse gas dynamics and soil organic matter stability during the early stages of this transition remain poorly understood. This dataset presents the results of a mesocosm experiment conducted in a controlled, highly instrumented laboratory environment, in which freshwater and brackish water pulses were applied to intact soil monoliths from a temperate upland coastal forest to examine how floodwater chemistry influences soil biogeochemistry and organo-mineral interactions. All data files are plain-text CSV (comma-separated value), and no special software is required to read them. Details about the content of each file are available in the document “Dataset_readme”. The dataset consists of the following data: • rcruzobyrne_moisture: Soil volumetric water content (VWC) • rcruzobyrne_GHG: Headspace greenhouse gas (GHG) concentration and fluxes • rcruzobyrne_methane_isotopes: Headspace methane isotope signature • rcruzobyrne_porewater: Porewater chemistry • rcruzobyrne_CDOM: Porewater colored dissolved organic matter (CDOM) • rcruzobyrne_FTIR: Soil Fourier-transform infrared (FTIR) spectroscopy Details of the experimental setup, data collection, and data analysis are provided in the manuscript by Cruz-O’Byrne et al (2026) Divergent biogeochemical responses in upland coastal forest soils to repeated flooding and shifts in water chemistry. Biogeochemistry. https://doi.org/10.1007/s10533-026-01340-0

EARTH SCIENCE > ATMOSPHERE > GREENHOUSE GAS

Integrated Spatial, Spectral, & Temporal Optical Reflectance System for Precision Occupancy & Location Sensing to Improve Building Energy Efficiency

Buildings consume approximately 35% of the electricity used in the U.S. and building owners can significantly reduce this energy use by providing services like heating, electrical power and lighting only when people are present. The ARPAe funded program titled “INTEGRATED SPATIAL, SPECTRAL, & TEMPORAL OPTICAL REFLECTANCE SYSTEM FOR PRECISION OCCUPANCY & LOCATION SENSING TO IMPROVE BUILDING ENERGY EFFICIENCY” demonstrates how a low cost sensor technology developed for measuring distances can be used to count and locate occupants with a high degree of precision with a very low error rates. This platform tells a building control system where occupants are located (but not who they are) so that energy consuming services can be provided only when the services are needed by building occupants. The original proof of concept involved using low cost, commercially available time-of-flight (TOF) sensors that measure distance, but the performance of these existing sensors was lacking, as they could not operate properly in the presence of sunlight, which blinded the simple TOF sensors and limited their utility in buildings. This project proposed a powerful new class of TOF sensors that used state-of-the-art integrated circuit (IC) fabrication processes that combined advanced photonics with conventional silicon chip circuitry for improved sensor performance. An equally important part of this project was to find ways to maximize occupant count and location accuracy while using the fewest number of sensors possible, in order to keep costs low. By using building blueprints to create digital twins of commercial building spaces, the team developed new algorithms to maximize occupant count and tracking accuracy by properly locating the minimum number of sensors at just the right spots in the building. This capability not only minimizes system costs but also simplified sensor installation and system commissioning. Our simulations of our sensor networks for a range of commercial floorplan designs demonstrated that our installed cost target of $0.08/sqft was attainable, though not fully demonstrated during the project. Finally, we noted that the TOF sensor concept could provide a valuable role in health and eldercare by tracking patients without the need for worn sensors and would be useful for fall detection and other patient safety metrics, including tracking healthcare/patient interactions. We feel that, when fully developed, this new class of sophisticated TOF sensors and support software will be a powerful new approach to improving building energy efficiency based on occupant centric control platforms and will also open new levels of patient safety in healthcare operations. To realize this potential, the team formed the Troy Sensor Company LLC to oversee licensing of the programs patents and continue to seek commercialization of this program’s activity sensing technologies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

Light Water Reactor Sustainability Program: Upgrade of EMRALD to a Modern JavaScript-based Framework

Event Modeling Risk Assessment using Linked Diagrams (EMRALD) is a software tool developed at Idaho National Laboratory for researching the capabilities of dynamic probabilistic risk assessment. It provides a simple interface to represent complex interactions often seen when developing dynamic models. EMRALD can also interface with other applications by modifying inputs, running, and using their results within EMRALD for dynamic and integrated assessment. This report goes over the work performed as part of the Risk-Informed Systems Analysis Pathway under the Light Water Reactor Sustainability program to upgrade the EMRALD software.

97 MATHEMATICS AND COMPUTING

Lamellar: A Rust-based Asynchronous Tasking and PGAS Runtime for High Performance Computing

Cybersecurity is one of the largest concerns in modern computing, impacting and dictating how governments, private corporations, and individuals interact with and live in an increasingly digital world. The NSA has recently released a memo [ 1] on “Software Memory Safety” where they highlight that both Microsoft and Google have stated around 70% of software vulnerabilities were due to memory safety issues. Although languages such as C and C++ provide freedom and flexibility with memory management, guaran- teeing safety falls mostly on the developer. The NSA recommends using “memory safe” languages whenever possible. In this paper we introduce Lamellar, an asynchronous tasking and PGAS HPC runtime written in Rust, one such "memory safe" language. We describe the entire Lamellar stack, from network interfaces to high- level abstractions such as distributed LamellarArrays and Active Messages. We conclude by showing comparable performance to legacy PGAS runtimes (e.g. OpenSHMEM) on a subset of the BALE kernel suite while maintaining strong memory safety principles.

HPC Software Systems, Rust Programming Language, P

GenomeFace v1.0

GenomeFace is meta-genome binning software. Metagenomic binning, the process of grouping DNA sequences into taxonomic units, is critical for understanding the functions, interactions, and evolutionary dynamics of microbial communities. We propose a deep learning approach to binning using two neural networks, one based on composition and another on environmental abundance, dynamically weighting the contribution of each based on characteristics of the input data. Trained on over 43,000 prokaryotic genomes, our network for composition-based binning is inspired by metric learning techniques used for facial recognition. Using a task-specific, multi-GPU accelerated algorithm to cluster the embeddings produced by our network, our binner leverages marker genes observed to be universally present in nearly all taxa to grade and select optimal clusters of sequences from a hierarchy of candidates. We evaluate our approach on four simulated datasets with known ground truth. Our linear time integration of marker genes recovers more near complete genomes than state of the art but computationally infeasible solutions using them, while being over an order of magnitude faster. Finally, we demonstrate the scalability and acuity of our approach by testing it on three of the largest metagenome assemblies ever performed. Compared to other binners, we produced 47%-183% more near complete genomes. From these datasets, we find over the genomes of over 3000 new candidate species which have never been previously cataloged, representing a potential 4% expansion of the known bacterial tree of life.

Lettich, Richard [Lawrence Berkeley National Labor

Evaluation of In-Situ AM Process Monitoring Techniques and Potential for Detecting Process Anomalies and Undesirable Microstructures

The US Department of Energy’s Advanced Materials and Manufacturing Technologies (AMMT) program is pursuing rapid qualification of new materials for fabrication of nuclear relevant components using advanced manufacturing techniques. Particular interest is placed on code-qualifying stainless steel (SS) 316H processed by laser powder bed fusion (LPBF) additive manufacturing. A paradigm that incorporates data from in-situ sensing during the printing, ex-situ characterization, and advanced artificial intelligence–based models was established under the Transformation Challenge Reactor (TCR) program to develop a pedigree for each fabricated component that could be tracked from the feedstock to the component’s release for application. Under the TCR program, the Peregrine software was developed as a tool for incorporating the vast amounts of in-situ and ex-situ characterization data collected; all data stored on a rapidly growing digital platform. The digital platform allows for users to link site-specific process anomalies to the macro- and microstructure. The platform will eventually be able to predict component performance, which will be crucial to qualifying materials and components in risk-averse industries such as those supporting and building nuclear reactors. Current in-situ process monitoring techniques that are already integrated with software like Peregrine are advantageous for identifying process anomalies including powder spatter, component edge swelling, recoating-build interactions, and so on. However, additional data are required to fully predict the resulting microstructures needed for identifying relationships to component performance. The rapid cooling rates observed in LPBF are some of the highest of any bulk manufacturing process, resulting in heterogenous microstructures and typically causing anisotropy in mechanical properties. Moreover, evolved residual thermal stresses are high, which can cause severe defects such as delamination or cracking. Therefore, other in-situ monitoring methods are warranted for exploration to measure and map the thermal history, and potentially the stress state, of each build. This report summarizes different in-situ monitoring strategies proposed for LPBF with a focus on the more developed sensor systems. Novel capabilities for measuring melt pool temperatures are also addressed to better inform modeling efforts.

36 MATERIALS SCIENCE

Modeling Partial Reflection Paths for Infrasound Analysis

Numerical methods enabling simulation of scattered and partially reflected infrasonic propagation paths produced by interaction with fine-scale structure in the middle atmosphere have been implemented in the infraGA ray tracing software. This capability enables simulation of ensonification in the classical stratospheric “shadow zone” that has been observed during the Humming Roadrunner and LSECE surface explosion campaigns as well as in other data sets. In the case of LSECE, a pair of stations roughly 140 kilometers east of the source location observed arrivals with celerities (horizontal group velocities) slightly slower than observed stratospheric paths at similar azimuths. The arrivals exhibited increasing trace velocity later in the wavetrain indicating a steepening of the arrival path for longer or slower propagation paths. Simulation of partially reflected paths using the updated infraGA software methods finds good agreement between observed and predicted infrasonic ensonification at these locations within the stratospheric shadow zone. Further development of the partial reflection physics and comparison with other data sets is needed to more robustly understand how such anomalous infrasonic signals can be predicted; however, the demonstration of this capability is a promising first step in such analyses.

97 MATHEMATICS AND COMPUTING

Physics model enhancements in MARLEY version 2

Large next-generation neutrino detectors, such as those designed for accelerator-based oscillation experiments, are expected to have impressive sensitivity to MeV astrophysical neutrinos generated by the Sun and by supernovae. There are also numerous related prospects to search for MeV-scale phenomena beyond the Standard Model. In contrast to detectors constructed with water and hydrocarbon targets, which will be primarily sensitive to electron antineutrinos via inverse beta decay, the upcoming Deep Underground Neutrino Experiment (DUNE) will provide unparalleled capabilities to measure low-energy electron neutrinos from cosmic sources. Interpreting such future measurements in DUNE will require a high-quality simulation of MeV interaction physics in the argon nucleus. The MARLEY (Model of Argon Reaction Low Energy Yields) neutrino event generator has been designed with the goal of delivering the needed simulation capabilities for DUNE and other argon-based neutrino detectors. In this poster, I will present recent improvements to MARLEY's suite of interaction models, which will be released for general use by the neutrino community in version 2 of the software.

Gardiner, Steven James [Fermilab] (ORCID:000000028

RAG for FLAG: AI Assistance for a Physics Code

Artificial intelligence (AI) has quickly become an important tool in scientific research, where significant efforts are underway to develop tools that will expedite the research process. One area of particular impact is scientific software, which can be particularly complex, and therefore time consuming to learn and use effectively. AI assistants are increasingly helping to streamline the process by performing tasks such as interactively answering user questions or suggesting solutions. Los Alamos National Laboratory (LANL) develops several advanced scientific codes, such as FLAG, which can be used to run multiphysics simulations. With this study, our goal was to develop an AI assistant for FLAG that could help make the process of understanding the software and running physics simulations more efficient. To develop an AI assistant for FLAG, we used a method called retrieval-augmented generation (RAG), which is a technique that uses information from relevant data sources to enhance the accuracy of large language models (LLMs). We used the FLAG user manual and other FLAG documentation as the knowledge base for the RAG system. When a user provides a query, RAG retrieves relevant sections from the knowledge base in response, then uses those excerpts to generate grounded and contextually rich answers. We found that our AI assistant was able to provide context aware answers and source references to user queries. To evaluate performance, we developed a set of 40 benchmark questions and compared the accuracy of the responses to those of two standard LLMs without retrieval. Our AI assistant significantly outperformed the standard LLMs at answering FLAG-related questions, with an 82.5% accuracy rate, compared to 47.5% for both of the standard LLMs. This has the potential to make the process of learning and using FLAG much easier, especially for new users. Ultimately, it supports LANL’s broader mission by empowering scientists and engineers to focus more on discovery and analysis rather than on navigating complex software systems.

97 MATHEMATICS AND COMPUTING

Scaling Ultrahigh-Resolution E3SM Land Model for Leadership-Class Supercomputers

This paper presents advancements in scaling the ultrahigh-resolution E3SM Land Model (uELM) for deployment on leadership-class supercomputers, addressing the increased demand for km-scale Earth system modeling. By focusing on km-scale ELM simulations, we enhance predictive capabilities for climate interactions, facilitating improved responses to climate change impacts on energy systems, agriculture, and water resources. Our approach leverages innovative software architecture optimizations, sophisticated data handling techniques, and advanced parallel processing, achieving strong scalability on two leadership supercomputers (2400 nodes (105,600 cores) on Summit, and 1200 nodes (76,800 cores) on Frontier). Results from extensive scalability assessments on the Summit and Frontier also demonstrate outstanding I/O performance (close to 400 GB/s write throughput) and the model's ability to efficiently handle increasing computational demands. This study not only establishes uELM's capability for high-resolution simulations over vast geographical domains, but also sets a foundation for future Earth system modeling breakthroughs.

Wang, Dali [ORNL] (ORCID:0000000168065108)

Models and Algorithms for Equilibrium Analysis of Mixed-Material Nucleic Acid Systems

Dynamic programming algorithms within the NUPACK software suite enable analysis of equilibrium base-pairing properties for complex and test tube ensembles containing arbitrary numbers of interacting nucleic acid strands. Currently, calculations are limited to single-material systems that are either all-RNA or all-DNA. Here, to enable analysis of mixed-material systems that are critical for modern applications in vitro, in situ, and in vivo, we develop physical models and dynamic programming algorithms that allow the material of the system to be specified at nucleotide resolution. Free energy parameter sets are constructed for both RNA/DNA and RNA/2'OMe-RNA mixed-material systems by combining available empirical mixed-material parameters with single-material parameter sets to enable treatment of the full complex and test tube ensembles. New dynamic programming recursions account for the material of each nucleotide throughout the recursive process. For a complex with N nucleotides, the mixed-material dynamic programming algorithms maintain the O(N 3 ) time complexity of the single-material algorithms, enabling efficient calculation of diverse physical quantities over complex and test tube ensembles (e.g., complex partition function, equilibrium complex concentrations, equilibrium base-pairing probabilities, minimum free energy secondary structure(s), and Boltzmann-sampled secondary structures) at a cost increase of roughly 2.0-3.5×. The results of existing single-material algorithms are exactly reproduced when applying the new mixed-material algorithms to single-material systems. Accuracy is significantly enhanced using mixed-material models and algorithms to predict RNA/DNA and RNA/2'OMe-RNA duplex melting temperatures from the experimental literature as well as RNA/DNA melt profiles from new experiments. In conclusion, mixed-material analyses can be performed online using the NUPACK web app (www.nupack.org) or locally using the NUPACK Python module.

2′OMe-RNA

Advanced Transmission Technologies – GETs and HPCs Session 2: Advanced Power Flow Control and Transmission Topology Optimization

The INL TADA GETs Cohort Session 2, held on November 7, 2025, conducted in collaboration with ScottMadden, focused on two core Advanced Transmission Technologies (ATTs): Advanced Power Flow Control (APFC) and Transmission Topology Optimization (TTO). These technologies are pivotal in enhancing grid flexibility, reliability, and cybersecurity resilience. APFC, particularly through modular FACTS devices like Modular Static Synchronous Series Compensators (M-SSSCs), enables dynamic voltage injection to reroute power flows. The session highlighted the deployment benefits of APFC, such as rapid installation, minimal civil works, and re-deployability. Regulatory drivers like FERC Order 2023 mandate the inclusion of Grid-Enhancing Technologies (GETs) in interconnection studies. Case studies from Central Hudson, CAISO, and National Grid (UK) demonstrated APFC’s effectiveness in congestion relief and cost savings. The session also addressed cybersecurity concerns, including firmware vulnerabilities, SCADA integration risks, and supply chain dependencies. Participants engaged in interactive exercises to rank cybersecurity and supply chain risks, emphasizing the need for robust digital assurance strategies. TTO involves software-based reconfiguration of transmission networks to optimize power flow without new infrastructure. The session showcased its operational value, with examples from SPP, PJM, and MISO showing significant congestion cost reductions. Cybersecurity vulnerabilities were discussed, particularly in API security and software supply chains, referencing incidents like SolarWinds and attacks on Danish utilities. Digital assurance exercises explored worst-case scenarios, attack paths, and mitigation responsibilities between vendors and utilities. Reliability challenges such as algorithm stability, vendor dependency, and operator trust were also examined. Cross-cutting themes emphasized the importance of digital assurance tools, including Software Bills of Materials (SBOMs) and hardware-in-loop testing. Human performance, training, and operational confidence were identified as critical enablers of technology adoption. The session concluded with a preview of Session 3, which will focus on High Performance Conductors (HPCs) and risk-based cybersecurity tools. Session 2 of 3.

24 - POWER TRANSMISSION AND DISTRIBUTION

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.

59 BASIC BIOLOGICAL SCIENCES

PySIDT: Subgraph Isomorphic Decision Trees for Molecular Property Prediction

Accurate molecular property prediction is important across all fields of chemistry. Deep neural networks (DNNs) have become increasingly popular due to their ability to train automatically, avoiding the incredibly tedious process of constructing and extending traditional property estimation schemes. However, DNNs require large amounts of training data, are challenging to interpret, require large amounts of memory to load even during inference, and have severe difficulties incorporating qualitative chemical knowledge, which are often desired for molecular property prediction tasks. Here, in this study, we present PySIDT (https://github.com/zadorlab/PySIDT), a software for training and running inference on Subgraph Isomorphic Decision Trees (SIDTs). SIDTs are graph-based decision trees made of nodes associated with molecular substructures. Inference is done by descending target molecular structures down the decision tree to nodes with matching subgraph isomorphic substructures and making predictions based on the final (most specific) nodes matched. SIDTs scale down well to dataset sizes much smaller than is feasible for DNNs. As trees of molecular substructures, SIDTs are inherently readable and easy to visualize, making them easy to analyze. They are also straightforward to extend and retrain, facilitate uncertainty estimation, and enable easy integration of expert knowledge. We demonstrate the SIDT approach discussing its application to a diverse range of molecular prediction tasks: rate coefficient estimation, diffusion coefficient estimation, thermochemistry estimation, transition state bond stretch prediction, p K a prediction, stability of molecular structures, stability of surface structures, and prediction of surface lateral interaction energetics. Additionally, we demonstrate the power of the SIDT algorithms in two direct learning curve vanilla comparisons with the popular DNN-based software Chemprop and the popular gradient boosted trees-based software XGBoost on enthalpy of formation and rate coefficient prediction tasks. In particular, in the enthalpy of formation case, vanilla PySIDT is able to outperform vanilla Chemprop and XGBoost across the full range of training/validation set sizes out to 11,560 data points.

Johnson, Matthew Sean [Sandia National Laboratorie

Hybrid-BPR (Bayesian Personalized Ranking with Feature Embeddings and Explicit Negative Sampling) [SWR-26-039]

Hybrid-BPR is a Python library for Bayesian Personalized Ranking (BPR) with two key capabilities that go beyond standard BPR implementations: 1. User and item feature embeddings - incorporate content-based signals (genres, tags, metadata) alongside collaborative filtering. 2. Implicit negative interactions - use observed non-interactions (e.g. viewed-but-not-clicked) as negative training signal instead of random sampling from the full item space. The software is built for recommender systems research with MLflow experiment tracking, parallel hyperparameter sweeps, and standard ranking metrics.

Sandhu, Rimple [National Laboratory of the Rockies

Electromagnetic shower reconstruction in the ICARUS liquid argon time projection chamber detector

The ICARUS-T600 liquid argon time projection chamber (LArTPC) detector is taking data at shallow depth as the far detector of the Short Baseline Neutrino (SBN) program at Fermilab, to search for a possible sterile neutrino signal at $\Delta m^{2} \approx 1~\text{eV}^{2}$ with the Booster (BNB) and Main Injector (NuMI) neutrino beams at $\GeV{\sim 0.8}$ and $\GeV{\sim 2}$ average energies respectively. The LArTPC technology, developed by the ICARUS collaboration and now a standard in neutrino physics, offers impressive charged-particle imaging capabilities with $\sim1 \ \text{mm}$ spatial resolution, enabling efficient discrimination between track-like signatures (e.g., from muons, pions, and protons) and electromagnetic showers (from electrons and photons). Moreover, electron and photon signatures can be distinguished both with the calorimetric measurement of local energy depositions at the shower start and with the cm-scale conversion gap signature of photons. This contribution discusses event reconstruction at ICARUS focusing on Pandora, a multi-algorithm pattern recognition software widely used in LArTPC experiments. Over a hundred Pandora algorithms and tools are used to reconstruct cosmic rays and neutrino interactions in the ICARUS detector. Recent developments have focused on the reconstruction of electromagnetic shower signatures, crucial to ensure a robust and efficient reconstruction of charged-current $\nu_e$ interactions, which serve as a key signature of sterile neutrino oscillations at SBN. In this contribution, recent improvements to the reconstruction are discussed, focusing on the discrimination between tracks and electromagnetic showers using neutrino simulations and data.

Triozzi, Riccardo [Padua U.; INFN, Padua] (ORCID:0

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