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DOE OSTI2025

Enabling Next Generation Reaction Injection Molding (RIM) for Lightweight Structures

Replacing metal components in trucks, trailers, and buses with lightweight polymer composites is challenging due to high temperatures and complex manufacturing. The Reaction Injection Molding (RIM) process using Dicyclopentadiene (DCPD) resin offers a solution by producing robust parts with excellent stiffness, impact strength, and resistance properties. Simulations are essential for optimizing this process, predicting defects, and improving quality. However, most commercial software is tailored for thermoplastics, requiring thermoset users to generate their own datasets. In this project, a material data card for DCPD was developed to perform RIM simulations. Design of Experiments (DOE) was used to identify key factors affecting filling, curing, and warpage, aiming to minimize cycle time and defects. The simulations explored varying injection gate parameters (size, location, number) and process conditions (mold/resin temperature, injection/curing pressure). Results showed that gate design significantly impacts filling behavior and defects. A single central gate provided balanced flow with fewer defects, while two corner gates led to more defects. Additionally, lower injection pressure increased filling time, while higher mold temperature accelerated curing but led to more warpage. This optimization framework aims to enhance DCPD part performance and promote sustainable manufacturing by reducing waste and energy consumption. This research has been performed in collaborations with McClarin Composites. The research outcome has been submitted to the Journal of Manufacturing Processes.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Digital Twin User Guide for Chelan County Public Utility District

This user manual offers a comprehensive guide for developing a Digital twin (DT) of a Kaplan turbine at Chelan County Public Utility District (Chelan PUD) using neural networks. As variable renewable generation expands, hydropower units must operate with optimal efficiency and stability. For Kaplan machines, this flexibility is achieved through coordinated control of guide vane (wicket gates) opening and runner blade pitch, which amplifies the plant’s inherent nonlinear behavior and challenges traditional physics-only modeling. The efficiency of the Kaplan turbine varies with different combinations of the guide vans (wicket gate) opening and the blade angle. Each guide van opening and blade angle has a corresponding highest efficiency point, forming a cam relationship that represents the optimal combination.The discharge of a hydraulic turbine is controlled by the opening angle of the guide vans. Therefore, for each value of head, there is a certain guide van opening and blade angle that corresponds to the highest efficiency. For a given head, different combinations of the guide van opening and blade angle have different efficiencies. Therefore, coordinate cam curves are used to describe the relationship between the wicket gate opening and blade angle with different water head. To address these challenges, the manual details a data-driven modeling and learning workflow centered on structured neural networks. The approach is designed to forecast critical operational variables—discharge flow, net head, penstock (or scroll-case) pressure, and generator electrical outputs—by leveraging real-time inputs such as the generator power control setpoint, exciter field current and field voltage, together with hydromechanical commands (e.g., gate position and, when available, runner blade-pitch angle). The neural models are trained and validated on operational data from a Kaplan unit operated by Chelan PUD, demonstrating that the structured NN architecture can learn the coupled gate–blade–electrical dynamics. The result is a robust DT that improves situational awareness and supports data-informed decision-making for Chelan PUD’s Kaplan turbine operations.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2026

Automated Membership Inference Attacks: Discovering MIA Signal Computations using LLM Agents

Membership inference attacks (MIAs), which enable adversaries to determine whether specific data points were part of a model's training dataset, have emerged as an important framework to understand, assess, and quantify the potential information leakage associated with machine learning systems. Designing effective MIAs is a challenging task that usually requires extensive manual exploration of model behaviors to identify potential vulnerabilities. In this paper, we introduce AutoMIA -- a novel framework that leverages large language model (LLM) agents to automate the design and implementation of new MIA signal computations. By utilizing LLM agents, we can systematically explore a vast space of potential attack strategies, enabling the discovery of novel strategies. Our experiments demonstrate AutoMIA can successfully discover new MIAs that are specifically tailored to user-configured target model and dataset, resulting in improvements of up to 0.18 in absolute AUC over existing MIAs. This work provides the first demonstration that LLM agents can serve as an effective and scalable paradigm for designing and implementing MIAs with SOTA performance, opening up new avenues for future exploration.

Tran, Toan Viet [Emory University]↗

DOE OSTI2024

INSPIRED: Inelastic neutron scattering prediction for instantaneous results and experimental design

Inelastic neutron scattering (INS) has unique advantages in probing how atoms vibrate and how the vibrations propagate and interact. Such dynamic information is crucial in understanding various material properties, from heat capacity, thermal conductivity, phase transitions, and chemical reactions to more exotic quantum behavior. The analysis and interpretation of the INS spectra often start from a model structure of the sample, followed by a series of calculations to obtain the simulated spectra to compare with experiments. The conventional way to perform such calculations usually requires significant time, computing resources, and specialized expertise. Here, we present a new program named INSPIRED (Inelastic Neutron Scattering Prediction for Instantaneous Results and Experimental Design), which enables users to perform rapid INS simulations in several different ways on their personal computers in just a few clicks, with the crystal structure as the only input file. Specifically, the users can choose a pre-trained symmetry-aware neural network (coupled with an autoencoder) to predict the phonon density of states (DOS), 1D S(E) and 2D S(|Q|,E) spectra for any given structure. One can also choose an existing density functional theory (DFT) calculation from a database (containing over 12,000 crystals), and quickly obtain the simulated INS spectra for single crystals and powders. It is also possible to use pre-trained universal machine learning force fields to relax a given crystal structure, calculate the phonon dispersion and DOS, and, subsequently, the INS spectra. All these functions are implemented with a PyQt graphic user interface. Finally, we expect these new tools will benefit broad user communities and significantly improve the efficiency of experiment design, execution, and data analysis for INS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

ComStock Measure Documentation: Fan Static Pressure Reset for Multizone Variable Air Volume Systems

This report assesses the potential for nationwide adoption of a duct static pressure reset in MZ VAV systems in appropriate applications. Building on the 3-year End-Use Load Profiles project to calibrate and validate the U.S. Department of Energy’s ResStock™ and ComStock™ models, this work produces national datasets that enable cities, states, utilities, and other stakeholders to answer a broad range of questions regarding their commercial building stock. ComStock is a highly granular, bottom-up model that uses various data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual sub-hourly energy consumption of the commercial building stock across the United States. The “baseline” model intends to represent the U.S. commercial building stock as it existed in 2018. The methodology of the baseline model is discussed in the ComStock Reference Documentation. The goal of this work is to develop energy efficiency and demand flexibility measures that cover market-ready technologies and study their mass-adoption impact on the baseline building stock. “Measures” refers to various “what-if” scenarios that can be applied to buildings. The results for the baseline and measure scenario simulations are published in public datasets that provide insights into building stock characteristics, operational behaviors, utility bill impacts, and annual and sub-hourly energy usage by fuel type and end use. This report describes the modeling methodology for a single ComStock measure scenario—Fan Static Pressure Reset for Multizone Variable Air Volume (VAV) Systems—and briefly introduces key results. The full public dataset can be accessed on the ComStock data lake or via the Data Viewer at comstock.nrel.gov. The public dataset enables users to create custom aggregations of results for their use case (e.g., filter to a specific county or building type).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Enhancing Cluster Identification in Atom Probe Tomography Data Using Transfer Learning

Atom probe tomography (APT) has enabled the direct visualization of solute clusters, providing valuable insights into material structures. This clustering is crucial for understanding the nanoscale composition and behavior of materials, which can significantly influence their mechanical and physical properties. However, the widely used clustering methods in the APT community face challenges such as subjective parametric selection and limited applicability, particularly in dealing with overlapping clusters, nested clusters, and artifacts across different scales, such as precipitates and dislocations. To address these challenges, we present a framework based on density-based cluster analysis that aims to be less dependent on user input, reproducible, and robust.

Density-based clustering↗

DOE OSTI2023

Stereo Camera Deployment in Support of TRACER (Field Campaign Report)

An improved understanding of the salient environmental controls on cloud formation, evolution, and eventual dissipation is critical to address ongoing challenges with cloud process and parameterization representations in global climate and Earth system models. One goal for the recent U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility’s Tracking Aerosol Convection Interactions Experiment (TRACER) campaign was to collect a comprehensive data set that enabled such convective cloud process studies and key demonstrations for those controls that influenced cloud life cycle (i.e., aerosols, thermodynamics) in the Houston, Texas region. To help accomplish this, ARM instrumentation during TRACER was tasked with tracking a large number of individual, isolated convective cells – and to follow the evolution of these cells at high spatiotemporal resolution to characterize changes in cloud dynamic and microphysical properties. Since Houston experiences a range of convective clouds, it was known that the standard ARM Mobile Facility (AMF) instruments may not be sufficient to completely document initiating, transient, or dissipating low- or shallow-cloud behaviors that were also expected during this campaign (in terms of sensitivity, resolution, and/or operational availability). As one partial solution, a supplemental stereo camera deployment (this sub-campaign) was requested to augment the ARM AMF instrumentation to better address shallow and shallow-to-deep transitional types of cloud process drivers during TRACER (ARM stereo cameras for clouds [STEREOCAM]; Romps and Öktem 2018). The primary scientific focus was the relationships between cloud properties and the ambient conditions, which points to several key TRACER science questions including: ‘What is the relationship between cloud size or updraft intensity to the environmental wind shear and/or humidity?’ Overall, the ARM TRACER stereo camera deployment demonstrated unique effectiveness in observing a wide range of critical shallow, congestus, and transitioning or time-evolving cloud characteristics. The data sets from these cameras include information on the clouds' horizontal dimensions, elevations, and depths, while also enabling potential products for cloud initiation and dissipation rates, and vertical velocities. Stereo cameras simultaneously inform on cloud life cycle stage and spatial properties such as cloud fractional coverage, which should provide complementary information for ARM users when combined with TRACER cloud radars, lidar, and/or other profiling sensors. Moreover, camera products offer large-eddy simulation (LES),-scale-appropriate cloud coverage, depth, and spatial variability estimates, while opening additional avenues to challenge difficult process questions on cloud updrafts/entrainment and their covariability with environmental controls such as wind shear and humidity.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Production of Germanium and Gallium Concentrates for Industrial Processes

A conceptual design of a process to produce germanium and gallium metal from mixed rare earth concentrates (consisting of oxides or carbonates) (MREC) produced from lignite carbon-ore was developed. The design was based on past work associated with the recovery of Ge from carbon-ore ash, modeling of the behavior of Ge and Ga in pyrometallurgical processes, and laboratory testing of the potential recovery of Ge and Ga from MREC. A teaming plan was developed that encompasses the entire supply chain that consisted of the Ge and Ga-rich carbon-ore resource, MREC pilot scale concentrate producer, MREC processing facility to produce Ge/Ga concentrates, refining of Ge and Ga concentrates to produce high purity metals (99.999+ purity), and Ge/Ga end users. A research plan was developed to transition the Ge and Ga separation from MREC, concentrating, and refining technology from a conceptual design to commercial scale. A technical and economic assessment of the conceptual design indicated that MREC derived from the UND process can produce 90 to 99% pure Ge and Ga concentrates at >20% lower costs.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2022

CTF Theory Manual: Version 4.3

Coolant-Boiling in Rod Arrays—Two Fluids (COBRA-TF) is a thermal/hydraulic (T/H) simulation code designed for light water reactor (LWR) vessel analysis. It uses a two-fluid, three-field (i.e., fluid film, fluid drops, and vapor) modeling approach. Both subchannel and three-dimensional Cartesian forms of its governing equations are available for the solution. The code was originally developed by Pacific Northwest Laboratory in 1980, and had been used and modified by several institutions over the last few decades. COBRA-TF also found use at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Modeling Group (RDFMG) and has been improved, updated, and subsequently rebranded as CTF. CTF was later adopted in the early 2010s by Oak Ridge National Laboratory (ORNL) for use in the Consortium for Advanced Simulation of Light Water Reactors (CASL) program, which led to a significant advancement of the code software quality, modeling accuracy, testing systems, and capabilities for improved support of modeling of common LWR nominal and transient behavior. As part of the improvement process, it was necessary to generate sufficient documentation for the public domain code which had lacked such material upon being adopted by RDFMG. This document serves as a theory manual for CTF, detailing the many two-phase heat transfer, drag, and important accident scenario models contained in the code, as well as the numerical solution process utilized. Additional documents available in the CTF documentation suite include the user manual and verification and validation manual.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

CTF Theory Manual: Version 4.4

Coolant-Boiling in Rod Arrays – Two Fluids (COBRA-TF) is a thermal/hydraulic (T/H) simulation code designed for light-water reactor (LWR) vessel analysis. It uses a two-fluid, three-field (i.e., fluid film, fluid drops, and vapor) modeling approach. Both subchannel and 3D Cartesian forms of its governing equations are available for the solution. The code was originally developed by Pacific Northwest Laboratory in 1980 and has been used and modified by several institutions over the last few decades. COBRA-TF also found use at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Modeling Group (RDFMG) and has been improved, updated, and subsequently rebranded as CTF. CTF was later adopted in the early 2010s by Oak Ridge National Laboratory (ORNL) for use in the Consortium for Advanced Simulation of Light Water Reactors (CASL) program, which led to a significant advancement of the code’s software quality, modeling accuracy, testing systems, and capabilities for improved support in modeling common LWR nominal and transient behavior. As part of the improvement process, it was necessary to generate sufficient documentation for the public domain code which had lacked such material upon being adopted by RDFMG. This document serves as a theory manual for CTF, detailing the many two-phase heat transfer, drag, and important accident scenario models contained in the code, as well as the numerical solution process utilized. Additional documents available in the CTF documentation suite include the user manual and the verification and validation manual.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Simplified inelastic constitutive models for ASME Section III, Division 5 design by inelastic analysis

This report describes the development of simplified, universal constitutive model that captures the high temperature monotonic and cyclic behavior of a range of commonly-used high temperature materials. The goal of the work is to provide a simple, universal constitutive model to replace the current bespoke models for Grade 91, 316H, and Alloy 617 included in Nonmandatory Appendix HBB-Z of the ASME Boiler & Pressure Vessel Code, and to extend this model to cover Alloy 800H. We initiated this work in response to feedback from reactor vendors and other Code users requesting simplified models, compared to the current models, that are easier to implement and use in commercial finite element analysis software. This report describes the completion of this effort by developing a model to correct the defects in standard model forms presently used for high temperature material modeling, described in past work, developing and implementing new numerical methods to train this model against test data, and then actually training the model for the four materials. The report provides a complete mathematical description of the model along with the tabulated material coefficients for the four materials. The final step will be to formulate an ASME Code change to introduce the new models into the Code.

36 MATERIALS SCIENCE↗

DOE OSTI2024

FORCE Update 2024

The Framework for Optimization of Resources and Economics (FORCE) tool suite is the U.S. Department of Energy’s Nuclear Integrated Energy Systems (IES) Program flagship tool suite for technoeconomic IES analysis of IES. This tool suite is useful for analysis designed to evaluate and improve the technoeconomics of energy production systems, particularly for systems including nuclear technology. In this report, we document the development activity for the FORCE tool suite to extend its capabilities as performed during fiscal year 2024. In addition to reliability and accessibility, capability is one of the three standards guiding the development of the FORCE tool suite and the software codes that are its constituent parts. Extending the capabilities of the FORCE tool suite allows analysis both within the IES program as well as industry, university, and laboratory partners to perform analysis with more accuracy, insight, and impactful narrative. Four areas of capability development were the focus of activity this year: economic parameter uncertainty quantification, multiresolution analysis, components-to-optimization workflow automation, and statespace construction workflows for real-time optimal control. In economic parameter uncertainty quantification, the ability of HERON to capture risk due to scenarios (weather and energy demand uncertainty) was expanded to also include uncertainties in financial parameters such as capital cost or operation and maintenance costs. By including these sources of uncertainty, which are sometimes very large compared with scenario uncertainty, HERON is better able to capture the risk posed by investment in various IES technology. Because of this, analysts can also consider the reduction in risks that can be realized by choice of some technologies. In multiresolution analysis, development activity extended on work completed previously. In fiscal year 2023, methods for decomposing time series signals, such as demand, solar and wind availability, and price profiles, were analyzed and down-selected to those most effective at splitting signals into different resolutions. These resolutions allow considering the influence of different energy demand and supply behaviors across different time scales. For example, energy demand might be divided into seasonal, weekly, and hourly profiles. In fiscal year 2024, this preliminary work was extended and implemented within the Risk Analysis Virtual Environment (RAVEN) risk and uncertainty analysis platform, which is used throughout the FORCE framework. This development of the “multi-resolution time series analysis” (MR-TSA) module in RAVEN allows training synthetic history generators on complex time series. These synthetic history generators can then be used in HERON for generating scenarios that represent possible market and weather scenarios that can be analyzed on different time scales. We envision completing this work in the future, implementing multiresolution dispatch optimization strategies that can make the most beneficial use of these stratified time histories. In components-to-optimization workflow development, workflows for translating user inputs of components into algorithms for algebraic optimization were selected and implemented. Similar algorithms within the Holistic Energy Resource Optimization Network (HERON) were separated from the main code base of HERON and gathered with the components-to-optimization workflows in the new Dispatch Optimization Variable Engine (DOVE) software library. This modularization allows FORCE users to analyze dispatch optimization and energy system duty cycles independently of HERON, which previously was a burdensome task. Additionally, these dispatch optimization algorithms, set up in an independent library, can now be used across all software applications within FORCE, especially including the real-time optimal control software Optimization of Real-time Capacity Allocation (ORCA). Allowing FORCE software to share dispatch optimization algorithms within a single library allows for improved software maintenance and reliability. In statespace characterization workflow development, alternative workflows for optimizing dispatch with additional technical accuracy was the focus, particularly to improve the real-time optimization decision making in ORCA. Using algorithms and workflows initially developed for the Feasible Actuator Range Modifier (FARM), workflows for determining the statespace representation of IES were identified and demonstrated. The resulting dispatch optimization required a more robust optimization algorithm than that originally used in HERON (and moved to DOVE), which required adding an alternate workflow to DOVE that can more accurately match the behavior of physical systems using a partial differential equation representation. In conclusion, capability developments in the FORCE tool suite in fiscal year 2024 have improved the ability of the FORCE tool suite to perform

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

Scalable line and plane relaxation in a parallel structured multigrid solver

The efficient solution of sparse, linear systems that arise through the discretization of partial differential equations remains a key challenge for a range of high performance scientific simulations. One approach for reducing data movement and improving performance is by exposing and exploiting structure in a problem through the use of robust structured multilevel solvers. By choosing coarsening that preserves the structure of the problem, these methods maintain efficient structured computation and communication throughout the multigrid hierarchy. However, when coarsening is not permitted to be dependent on the operator, anisotropy must be addressed by the smoother — producing error compatible for coarse-grid correction with structured coarsening. Here, the components required in a scalable parallel structured solver are described with a focus on memory and communication efficiency of robust smoothers. While the implementation of communication and memory reduction techniques in smoothers integrated in a complete 3D solver present a significant engineering challenge, a novel approach is proposed that addresses these challenges systematically through a change to the solver’s execution model. Enabled by user-level threading paired with a set of data and communication abstractions, this approach permits seamless aggregation of communication in plane smoothers — directly reusing code for a 2D distributed multilevel cycle. Results show an effective reduction in communication costs for coarse-grid problems, and result in a speedup of 8.7x in smoothing routines shown in Fig. 12 using this approach. This produces a significant improvement to strong scalability while maintaining favorable weak scaling behavior. Finally, a parallel scaling study using a series of refined meshes is included that demonstrates the effectiveness of this approach in an application of interest.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Turbo-Turtle v0.12.1

A collection of solid body modeling tools for 2D sketched, 2D axisymmetric, and 3D revolved models. It also contains general purpose meshing and image generation utilities appropriate for any model, not just those created with this package. Implemented for Abaqus and Cubit as backend modeling and meshing software. Orginal implementation targeted Abaqus so most options and descriptions use Abaqus modeling concepts and language. Turbo-Turtle makes a best effort to maintain common behaviors and features across each third-party software’s modeling concepts. As much as possible, the work for each subcommand is performed in Python 3 to minimize solution approach duplication in third-party tools. The third-party scripting interface is only accessed when creating the final tool specific objects and output. The tools contained in this project can be expanded to drive other meshing utilities in the future, as needed by the user community. This project derives its name from the origins as a sphere partitioning utility following the turtle shell (or soccer ball) pattern.s.

Brindley, Kyle↗

DOE OSTI2023

Cloud Atlas: An Interactive Apparatus for Air Quality Awareness

This paper introduces a research project of a kinetic apparatus that translates collected air quality data to users. The kinetic mechanical skeleton is embedded with processors and electronics, and constantly changes its form according to air quality data collected online via a web crawler. By translating invisible environmental conditions, such as air quality data into morphological, colorful, and acoustic changes for the device, the participants can be aware of the phenomenon of air pollution in real time. The interac- tions between participants' movements and the changes of the device imply how human behaviors can affect the state of the atmosphere. As a result, the device evokes public awareness and participation in environmental issues through tangible experiences. This research aims to explore a new kind of responsive architecture that acts as a medium between invisible environments and inhabitants.

Zhao, Xiaoxiao↗

DOE OSTI2023

Advanced Laboratory and Field Arrays: Technical Report for Performance Enhancement for Marine Energy Converter (MEC) Arrays (Task 5)

Task 5 consisted of two parts, wave energy converter (WEC) arrays and current energy converter (CEC) arrays. The two parts of the project were executed independently, and this report covers only the work on WECs. In this part of the task, the team characterized the behavior of and developed control schemes for wave energy converter (WEC) arrays that improved performance (i.e., maximized aggregate power generation and reduced the levelized cost of energy) over baseline, non-coordinated control approaches. Specifically, for WEC arrays: the team developed optimal layouts of arrays that considered the effect of WEC placement within an array on coordinated array control with real-time estimation schemes. The numerical codes developed through this task were made available to users for array design. These tools utilized existing commercial software as well as software developed within the project team.

13 HYDRO ENERGY↗

DOE OSTI2025

Improved Weld Residual Stress Modeling System in BlackBear

This report presents enhancements to the MOOSE-based BlackBear application aimed at improving its capability to simulate welding and other thermo-mechanical manufacturing processes. Two primary avenues of improvement are pursued. First, to enhance user accessibility, we introduce a centralized default block restriction mechanism that ensures coverage checks are performed within user-specified default blocks. This default setting is applied consistently to all block-describable objects, such as variables, kernels, and more. In addition, we develop a modular action for moving heat source simulations, which integrates path file parsing, subdomain modification, and heat source kernel enforcement into a single, streamlined configuration. Second, to improve solver robustness, we implement an alternative method for assigning initial conditions to the updated active domain during the simulation, thereby enhancing convergence behavior. To validate the framework, we design and conduct several benchmark simulations, including heat conduction with progressive material addition, linear elasticity with time-dependent material deposition, and viscoplasticity model with isotropic hardening under similar conditions. Finally, we demonstrate the effectiveness of the proposed framework through large-scale thermo-mechanical welding simulations in both two and three dimensions.

42 ENGINEERING↗

DOE OSTI2025

PERCEPTIVE: an R shiny $\underline{p}$ipelin$\underline{e}$ for the p$\underline{r}$edi$\underline{c}$tion of $\underline{ep}$igenetic modula$\underline{t}$ors $\underline{i}$n no$\underline{v}$el sp$\underline{e}$cies

Epigenetic processes are central to regulating gene expression, genome stability, and metabolic function across the tree of life; yet, their roles remain underexplored in microalgae, especially as new species continue to be identified and characterized. This is likely due to the cumbersome nature and species-dependent attributes of epigenetic wet-lab methodologies, which preclude the rapid identification of epigenetic modifications and modulators. However, there is high conservation of epigenetic processes from budding yeast to humans; in many cases, one may infer how behavior and function are epigenetically regulated in novel species by identifying epigenetic modulators, or the proteins responsible for conferring epigenetic modifications. Here, to this end, we have developed a graphical software package, titled PERCEPTIVE (pipeline for the prediction of epigenetic modulators in novel species). This platform solely uses the genomic sequence of an algal species, and preexisting information from other model organisms, to predict the epigenetic modulators and associated modifications in algae. Predictions are presented to the user in a graphical interface, which provides literature-based interpretation of results, enabling users to quickly understand potential epigenetic processes in their algal species of interest and plan follow-up experiments. To test PERCEPTIVE, we predicted epigenetic modulators in several feedstock candidate algae species. To validate these predictions, wet-lab studies were performed, including mass spectrometry; these results underscore the high accuracy of PERCEPTIVE predictions. Overall, PERCEPTIVE represents a powerful in silico tool for the research and manipulation of algal species, which does not require a priori knowledge of epigenetics and is accessible to a broad set of investigators.

59 BASIC BIOLOGICAL SCIENCES↗