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At least 577 records · Page 32

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

pynucastro: A Python Library for Nuclear Astrophysics

We describe pynucastro 2.0, an open-source library for interactively creating and exploring astrophysical nuclear reaction networks. We demonstrate new methods for approximating rates and use detailed balance to create reverse rates, show how to build networks and determine whether they are appropriate for a particular science application, and discuss the changes made to the library over the past few years. Finally, we demonstrate the validity of the networks produced and share how we use pynucastro networks in simulation codes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Intern Abstract for Spring 2016

The Human Interface Branch - EV3 - is evaluating Organic lighting-emitting diodes (OLEDs) as an upgrade for current displays on future spacecraft. OLEDs have many advantages over current displays. Conventional displays require constant backlighting which draws a lot of power, but with OLEDs they generate light themselves. OLEDs are lighter, and weight is always a concern with space launches. OLEDs also grant greater viewing angles. OLEDs have been in the commercial market for almost ten years now. What is not known is how they will perform in a space-like environment; specifically deep space far away from the Earth's magnetosphere. In this environment, the OLEDs can be expected to experience vacuum and galactic radiation. The intern's responsibility has been to prepare the OLED for a battery of tests. Unfortunately, it will not be ready for testing at the end of the internship. That being said much progress has been made: a) Developed procedures to safely disassemble the tablet. b) Inventoried and identified critical electronic components. c) 3D printed a testing apparatus. d) Wrote software in Python that will test the OLED screen while being radiated. e) Built circuits to restart the tablet and the test pattern, and ensure it doesn't fall asleep during radiation testing. f) Built enclosure that will house all of the electronics Also, the intern has been working on a way to take messages from a simulated Caution and Warnings system, process said messages into packets, send audio packets to a multicast address that audio boxes are listening to, and output spoken audio. Currently, Cautions and Warnings use a tone to alert crew members of a situation, and then crew members have to read through their checklists to determine what the tone means. In urgent situations, EV3 wants to deliver concise and specific alerts to the crew to facilitate any mitigation efforts on their part. Significant progress was made on this project: a) Open channel with the simulated Caution and Warning system to acquire messages. b) Configure audio boxes. c) Grab pre-recorded audio files. d) Packetize the audio stream. A third project that was assigned to implement LED indicator modules for an Omnibus project. The Omnibus project is investigating better ways designing lighting for the interior of spacecraft-both spacecraft lighting and avionics box status lighting indication. The current scheme contains too much of the blue light spectrum that disrupts the sleep cycle. The LED indicator modules are to simulate the indicators running on a spacecraft. Lighting data will be gathered by human factors personal and use in a model underdevelopment to model spacecraft lighting. Significant progress was made on this project: Designed circuit layout a) Tested LEDs at LETF. b) Created GUI for the indicators. c) Created code for the Arduino to run that will illuminate the indicator modules.

Gibson, William↗

RhizoVision Explorer: open-source software for root image analysis and measurement standardization

Abstract Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo™, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo™. The two software showed general agreement, except that WinRhizo™ substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.

59 BASIC BIOLOGICAL SCIENCES↗

MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver

@e present MAESTROeX, a massively parallel solver for low Mach number astrophysical flows. The underlying low Mach number equation set allows for efficient, long-time integration for highly subsonic flows compared to compressible approaches. MAESTROeX is suitable for modeling full spherical stars as well as well as planar simulations of dynamics within localized regions of a star, and can robustly handle several orders of magnitude of density and pressure stratification. Previously, we have described the development of the predecessor of MAESTROeX, called MAESTRO, in a series of papers. Here, we present a new, greatly simplified temporal integration scheme that retains the same order of accuracy as our previous approaches. We also explore the use of alternative spatial mapping of the one-dimensional base state onto the full Cartesian grid. The code leverages the new AMReX software framework for block-structured adaptive mesh refinement (AMR) applications, allowing for scalability to large fractions of leadership-class machines. Finally, using our previous studies on the convective phase of single-degenerate progenitor models of SNe Ia as a guide, we characterize the performance of the code and validate the new algorithmic features. Like MAESTRO, MAESTROeX is fully open source.

79 ASTRONOMY AND ASTROPHYSICS↗

CLMM : a LSST-DESC cluster weak lensing mass modeling library for cosmology

ABSTRACT We present the v1.0 release of CLMM, an open source python library for the estimation of the weak lensing masses of clusters of galaxies. CLMM is designed as a stand-alone toolkit of building blocks to enable end-to-end analysis pipeline validation for upcoming cluster cosmology analyses such as the ones that will be performed by the Vera C. Rubin Legacy Survey of Space and Time-Dark Energy Science Collaboration (LSST-DESC). Its purpose is to serve as a flexible, easy-to-install, and easy-to-use interface for both weak lensing simulators and observers and can be applied to real and mock data to study the systematics affecting weak lensing mass reconstruction. At the core of CLMM are routines to model the weak lensing shear signal given the underlying mass distribution of galaxy clusters and a set of data operations to prepare the corresponding data vectors. The theoretical predictions rely on existing software, used as backends in the code, that have been thoroughly tested and cross-checked. Combined theoretical predictions and data can be used to constrain the mass distribution of galaxy clusters as demonstrated in a suite of example Jupyter Notebooks shipped with the software and also available in the extensive online documentation.

79 ASTRONOMY AND ASTROPHYSICS↗

Risk-Adaptive Experimental Design for High-Consequence Systems: LDRD Final Report

Constructing accurate statistical models of critical system responses typically requires an enormous amount of data from physical experiments or numerical simulations. Unfortunately, data generation is often expensive and time consuming. To streamline the data generation process, optimal experimental design determines the 'best' allocation of experiments with respect to a criterion that measures the ability to estimate some important aspect of an assumed statistical model. While optimal design has a vast literature, few researchers have developed design paradigms targeting tail statistics, such as quantiles. In this project, we tailored and extended traditional design paradigms to target distribution tails. Our approach included (i) the development of new optimality criteria to shape the distribution of prediction variances, (ii) the development of novel risk-adapted surrogate models that provably overestimate certain statistics including the probability of exceeding a threshold, and (iii) the asymptotic analysis of regression approaches that target tail statistics such as superquantile regression. To accompany our theoretical contributions, we released implementations of our methods for surrogate modeling and design of experiments in two complementary open source software packages, the ROL/OED Toolkit and PyApprox.

97 MATHEMATICS AND COMPUTING↗

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 2. Evaluating Controls on Flow Persistence in an Urbanized Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in an urbanized catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, distributed temperature sensing (DTS), continuous self-potential (SP) monitoring, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Field_Application subfolder contains the ATS XML input scripts, data files, output data for the SP site. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. The flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.m can only be used with COMSOL with MATLAB) is executed using the ATS output data to simulate the potential field. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) DTS Contains collated DTS data including raw Stokes and anti-Stokes measurement (provided as .h5 file). It also includes DTS processing.ipynb, a Jupyter notebook for calibrating the DTS data using dts_calibration Python package. cooler_calibration.csv is the DTS calibration CSV used in the calibration sequence. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion. 6) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 7) SP Contains the SP data collected in field at the SP sites (provided as CSV files). 8) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). Note: Code files (.ipynb, .py, .xml) can be opened in any standard code editor, .exo file can be viewed using Paraview, .h5 files can be opened using HDFView software and h5py Python package, and .resipy file can be opened with the open-source ResIPy software.

ATS↗

Automated Crystal Orientation Mapping in py4DSTEM using Sparse Correlation Matching

Crystalline materials used in technological applications are often complex assemblies composed of multiple phases and differently oriented grains. Robust identification of the phases and orientation relationships from these samples is crucial, but the information extracted from the diffraction condition probed by an electron beam is often incomplete. We have developed an automated crystal orientation mapping (ACOM) procedure which uses a converged electron probe to collect diffraction patterns from multiple locations across a complex sample. We provide an algorithm to determine the orientation of each diffraction pattern based on a fast sparse correlation method. We demonstrate the speed and accuracy of our method by indexing diffraction patterns generated using both kinematical and dynamical simulations. We have also measured orientation maps from an experimental dataset consisting of a complex polycrystalline twisted helical AuAgPd nanowire. From these maps we identify twin planes between adjacent grains, which may be responsible for the twisted helical structure. All of our methods are made freely available as open source code, including tutorials which can be easily adapted to perform ACOM measurements on diffraction pattern datasets.

36 MATERIALS SCIENCE↗

The Earth Model Column Collaboratory (EMC 2 ) v1.1: an open-source ground-based lidar and radar instrument simulator and subcolumn generator for large-scale models

Abstract. Climate models are essential for our comprehensive understanding of Earth's atmosphere and can provide critical insights on future changes decades ahead. Because of these critical roles, today's climate models are continuously being developed and evaluated using constraining observations and measurements obtained by satellites, airborne, and ground-based instruments. Instrument simulators can provide a bridge between the measured or retrieved quantities and their sampling in models and field observations while considering instrument sensitivity limitations. Here we present the Earth Model Column Collaboratory (EMC2), an open-source ground-based lidar and radar instrument simulator and subcolumn generator, specifically designed for large-scale models, in particular climate models, but also applicable to high-resolution model output. EMC2 provides a flexible framework enabling direct comparison of model output with ground-based observations, including generation of subcolumns that may statistically represent finer model spatial resolutions. In addition, EMC2 emulates ground-based (and air- or space-borne) measurements while remaining faithful to large-scale models' physical assumptions implemented in their cloud or radiation schemes. The simulator uses either single particle or bulk particle size distribution lookup tables, depending on the selected scheme approach, to perform the forward calculations. To facilitate model evaluation, EMC2 also includes three hydrometeor classification methods, namely, radar- and sounding-based cloud and precipitation detection and classification, lidar-based phase classification, and a Cloud Feedback Model Intercomparison Project Observational Simulator Package (COSP) lidar simulator emulator. The software is written in Python, is easy to use, and can be straightforwardly customized for different models, radars, and lidars. Following the description of the logic, functionality, features, and software structure of EMC2, we present a case study of highly supercooled mixed-phase cloud based on measurements from the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) West Antarctic Radiation Experiment (AWARE). We compare observations with the application of EMC2 to outputs from four configurations of the NASA Goddard Institute for Space Studies (GISS) climate model (ModelE3) in single-column model (SCM) mode and from a large-eddy simulation (LES) model. We show that two of the four ModelE3 configurations can form and maintain highly supercooled precipitating cloud for several hours, consistent with observations and LES. While our focus is on one of these ModelE3 configurations, which performed slightly better in this case study, both of these configurations and the LES results post-processed with EMC2 generally provide reasonable agreement with observed lidar and radar variables. As briefly demonstrated here, EMC2 can provide a lightweight and flexible framework for comparing the results of both large-scale and high-resolution models directly with observations, with relatively little overhead and multiple options for achieving consistency with model microphysical or radiation scheme physics.

58 GEOSCIENCES↗

Modern Design of Resonant Edge-Slot Array Antennas

Resonant edge-slot (slotted-waveguide) array antennas can now be designed very accurately following a modern computational approach like that followed for some other microwave components. This modern approach makes it possible to design superior antennas at lower cost than was previously possible. Heretofore, the physical and engineering knowledge of resonant edge-slot array antennas had remained immature since they were introduced during World War II. This is because despite their mechanical simplicity, high reliability, and potential for operation with high efficiency, the electromagnetic behavior of resonant edge-slot antennas is very complex. Because engineering design formulas and curves for such antennas are not available in the open literature, designers have been forced to implement iterative processes of fabricating and testing multiple prototypes to derive design databases, each unique for a specific combination of operating frequency and set of waveguide tube dimensions. The expensive, time-consuming nature of these processes has inhibited the use of resonant edge-slot antennas. The present modern approach reduces costs by making it unnecessary to build and test multiple prototypes. As an additional benefit, this approach affords a capability to design an array of slots having different dimensions to taper the antenna illumination to reduce the amplitudes of unwanted side lobes. The heart of the modern approach is the use of the latest commercially available microwave-design software, which implements finite-element models of electromagnetic fields in and around waveguides, antenna elements, and similar components. Instead of building and testing prototypes, one builds a database and constructs design curves from the results of computational simulations for sets of design parameters. The figure shows a resonant edge-slot antenna designed following this approach. Intended for use as part of a radiometer operating at a frequency of 10.7 GHz, this antenna was fabricated from dimensions defined exclusively by results of computational simulations. The final design was found to be well optimized and to yield performance exceeding that initially required.

Gosselin, R. B.↗

The Earth Model Column Collaboratory (EMC2) v1.1: An Open-Source Ground-Based Lidar and Radar Instrument Simulator and Subcolumn Generator for Large-Scale Models

Climate models are essential for our comprehensive understanding of Earth's atmosphere and can provide critical insights on future changes decades ahead. Because of these critical roles, today's climate models are continuously being developed and evaluated using constraining observations and measurements obtained by satellites, airborne, and ground-based instruments. Instrument simulators can provide a bridge between the measured or retrieved quantities and their sampling in models and field observations while considering instrument sensitivity limitations. Here we present the Earth Model Column Collaboratory (EMC2), an open-source ground-based lidar and radar instrument simulator and subcolumn generator, specifically designed for large-scale models, in particular climate models, but also applicable to high-resolution model output. EMC2 provides a flexible framework enabling direct comparison of model output with ground-based observations, including generation of subcolumns that may statistically represent finer model spatial resolutions. In addition, EMC2 emulates ground-based (and air- or space-borne) measurements while remaining faithful to large-scale models' physical assumptions implemented in their cloud or radiation schemes. The simulator uses either single particle or bulk particle size distribution lookup tables, depending on the selected scheme approach, to perform the forward calculations. To facilitate model evaluation, EMC2 also includes three hydrometeor classification methods, namely, radar- and sounding-based cloud and precipitation detection and classification, lidar-based phase classification, and a Cloud Feedback Model Intercomparison Project Observational Simulator Package (COSP) lidar simulator emulator. The software is written in Python, is easy to use, and can be straightforwardly customized for different models, radars, and lidars. Following the description of the logic, functionality, features, and software structure of EMC2, we present a case study of highly supercooled mixed-phase cloud based on measurements from the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) West Antarctic Radiation Experiment (AWARE). We compare observations with the application of EMC2 to outputs from four configurations of the NASA Goddard Institute for Space Studies (GISS) climate model (ModelE3) in single-column model (SCM) mode and from a large-eddy simulation (LES) model. We show that two of the four ModelE3 configurations can form and maintain highly supercooled precipitating cloud for several hours, consistent with observations and LES. While our focus is on one of these ModelE3 configurations, which performed slightly better in this case study, both of these configurations and the LES results post-processed with EMC2 generally provide reasonable agreement with observed lidar and radar variables. As briefly demonstrated here, EMC2 can provide a lightweight and flexible framework for comparing the results of both large-scale and high-resolution models directly with observations, with relatively little overhead and multiple options for achieving consistency with model microphysical or radiation scheme physics.

Earth Model Column Collaboratory↗

Quandary

Quandary numerically simulates and optimizes the time-evolution of open quantum systems. The underlying dynamics are modelled by Lindblad's master equation, a linear ordinary differential equation (ODE) describing quantum systems interacting with the environment. Quandary solves this ODE numerically by applying a time-stepping integration scheme, and utilizes a gradient-based optimization approach to determine optimal control pulses that drive the quantum system to a desired target state. Two optimization objectives are considered: (a) Unitary gate optimization that finds controls to realize a unitary gate transformation, and (b) optimal reset that aims to drive the quantum system to the ground states. Gradient-based optimization schemes utilizing Petsc's Tao optimization package are applied to generate control pulses that minimize the respective measure. To evaluate the gradient of the objective function, the discrete adjoint method is used while leveraging techniques from Algorithmic Differentiation to produce exact and consistent gradients. To mitigate excessive execution run times, the software can be build together with the XBraid software library which provides a parallelization strategy to distribute the time-evolution of the underlying dynamics onto multiple processor.

Petersson, NilsA.↗

A reactive electrochemomechanical theory for growth and remodeling of polyelectrolyte hydrogels and application to dynamic polymerization of $\text{DNA}$ hydrogels

Here this study develops a framework for growth and remodeling of active polyelectrolyte hydrogels that accounts for effects of compositional changes on the mechanical response. By developing a reactive electrochemomechanical theory, thermodynamical constraints upon reactive and remodeling processes are elucidated within a general framework that allows any number of chemical reactions to evolve the response of the gel and transfer mass and charge between constituents. Fully coupled, nonlinear constitutive relations are adopted for molar fluxes, allowing exploration of effects including cross-diffusion, electrophoresis, and electro-osmosis. A robust finite element implementation is developed in the open source FEBio software (febio.org) by exploiting an equivalence between electrochemomechanics and mixture theory. The implementation is verified against analytical solutions for free swelling, and a proper reduction to a prior chemomechanical theory is demonstrated for neutral gels swollen only by a solvent with no solutes. The theory and implementation are then applied to model the tunable large swelling achieved through dynamic polymerization of DNA crosslinkers seen in our recently developed experimental hydrogel system (Cangialosi et al., 2017). A novel constitutive model for reaction-driven evolution of the locking stretch λ L in a non-Gaussian mechanical free energy was developed, where the increasing concentration of DNA crosslinkers makes further swelling energetically favorable. With a single free parameter, excellent agreement was found between measured and predicted equilibrium swelling ratios. This study demonstrated the ability to extend the electrochemomechanical framework to include chemical reactions and composition-aware constitutive models, and showed that development of reactive models allows simulation of complex dynamic polymerization phenomena not treated before. The theoretical frame here can be further expanded in scope to incorporate additional non-ideal and nonlinear phenomena.

42 ENGINEERING↗

teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering

Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.

59 BASIC BIOLOGICAL SCIENCES↗

Status of SAS4A/SASSYS-1 Software Development and Application (FY2024)

SAS4A/SASSYS-1 is a simulation tool used to perform deterministic analysis of anticipated events as well as design basis and beyond design basis accidents for advanced liquid-metal-cooled nuclear reactors. With its origin as SAS1A in the late 1960s, the SAS series of codes has been under continuous use and development for over fifty years. It has been identified as a critical element of safety analysis capabilities for the U.S. Department of Energy and is utilized within industry to perform the transient safety analyses required to support the licensing of Liquid Metal-cooled Fast Reactors (LMFRs). This report summarizes the code development and update activities carried out during FY2024. In FY2024, programmatic activities focused on key improvements to software useability, such as enhanced user interfaces for reactivity feedback modeling, improvements in stability/useability of the Code Manual, and improvements to the acceptance testing infrastructure, including automation of acceptance testing and generation of the Acceptance Testing Report. To support end user applications, an open training was held, a semi-public forum was maintained, and a practical benchmarking and validation matrix was developed which allowed limitations of existing testing capabilities to be assessed. The existing fuel models were also enhanced with improved modeling capabilities and testing for the oxide and annular fuel models.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Tycho: Realistically Simulating Exoplanets within Stellar Clusters. I. Improving the Monte Carlo Approach

To fully understand the diverse population of exoplanets, we must study their early lives within open clusters, the birthplace of most stars with masses >0.5M {sub ⊙} (including those currently in the field). Indeed, when we observe planets within clustered environments, we notice highly eccentric and odd systems that suggest the importance of dynamical pathways created by interactions with additional bodies (as in the case of HD 285507b). However, it has proven difficult to investigate these effects, as many current numerical solvers for the multi-scale N-body problem are simplified and limited in scope. To remedy this, we aim to create a physically complete computational solution to explore the role of stellar close encounters and interplanetary interactions in producing the observed exoplanet populations for both open cluster stars and field stars. We present a new code, Tycho, which employs a variety of different computational techniques, including multiple N-body integration methods, close encounter handling, modified Monte Carlo scattering experiments, and a variety of empirically informed initial conditions. We discuss the methodology in detail, and its implementation within the AMUSE software framework. Approximately 1% of our systems are promptly disrupted by star-star encounters contributing to the rogue planets occurrence rate. Additionally, we find that close encounters which that perturb long-period planets lead to 38.3% of solar-system-like planetary systems becoming long-term unstable.

79 ASTRONOMY AND ASTROPHYSICS↗