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At least 127 records · Page 7

Smart culture medium optimization for recombinant protein production: Experimental, modeling, and AI/ML-driven strategies

Recombinant protein production (RPP) is central to biotechnology, where recombinant proteins are used as either end products or catalysts in the synthesis of chemicals, fuels, and materials. Among the major cost drivers, culture medium plays a pivotal role in determining protein yield and quality. This review presents a comprehensive perspective on the critical stages of “smart” culture medium optimization: planning, screening, modeling, optimization, and validation. In the planning stage, we examine the nutritional and energetic roles of medium components, including carbon, nitrogen, amino acids, salts, and trace metals, and their impacts on culture parameters such as pH, oxidative state, and osmolality. We highlight the variability in trace metal content due to water sources, culture vessels, and raw materials, which can substantially influence RPP. The screening stage covers Design of Experiments (DoE) approaches, assessing their theoretical basis, implementation, and limitations. For modeling, we describe methods that integrate experimental data to develop predictive models for smart medium formulation. Model-based optimization strategies can then be employed to select optimal media compositions for a given application. The validation stage aims to evaluate model predictions and provide feedback for model training and refinement. Finally, we survey mechanistic and artificial intelligence/machine learning (AI/ML)-driven models as integrated, transformational tools for predictive modeling of bioprocess conditions, nutrient availability, cellular metabolism, and protein quality, with the goal of optimizing culture media to enhance protein yields while reducing costs and environmental impact. We conclude by addressing the challenges of translating laboratory-scale medium optimization to industrial-scale settings and exploring future AI/ML-driven approaches that may overcome current bottlenecks and accelerate medium design for RPP. Overall, this review provides a unified framework for advancing smart medium design in RPP.

Artificial Intelligence/Machine Learning (AI/ML)↗

Structural and Mechanical Analysis of Individual Mineralized Collagen Fibrils Using In Situ Transmission Electron Microscopy

Bone serves as an example of nature’s architectured material with its characteristic blend of strength and toughness, all at a lightweight design. Given the hierarchical nature of these materials, it is essential to understand the governing mechanisms and organization of their constituents across length scales for bioinspired structural design. Despite recent advances in transmission electron microscopy (TEM) that have allowed us to witness the hierarchical arrangement of bone at micro-down to the nanoscale, we are still missing the details about the structural organization and mechanical properties of the main building blocks of bone─mineralized collagen fibrils (MCFs). Here, we present a method to extract individual MCFs from nature’s model material, mineralized turkey leg tendon, using a dropcasting procedure. By isolating the MCFs onto TEM supporting grids, we visualized the arrangement of organic and mineral phases within individual MCFs at the nanoscale. Using a four-dimensional scanning transmission electron microscopy (4D-STEM) approach, the orientation of individual mineral crystals within the MCFs was examined. Furthermore, we conducted in situ tensile experiments, revealing exceptional tensile strains of at least 8%, demonstrating the intricate relationship between structural organization and the mechanical behavior of MCFs. These insights into the ultrastructure of mineralized tissue building blocks, as well as the proposed sample-extraction method compatible with in situ mechanical testing, provide a strong basis for research into nature-inspired material design.

4D-STEM↗

The shear Alfvén continuum of quasisymmetric stellarators

The shear Alfvén wave (SAW) continuum plays a critical role in the stability of energetic particle-driven Alfvén eigenmodes. We develop a theoretical framework to analyze the SAW continuum in three-dimensional (3-D) quasisymmetric magnetic fields, focusing on its implications for stellarator design. By employing a near-axis model and degenerate perturbation theory, the continuum equation is solved, highlighting unique features in 3-D configurations, such as the interactions between spectral gaps. Numerical examples validate the theory, demonstrating the impact of flux-surface shaping and quasisymmetric field properties on continuum structure. The results provide insights into optimizing stellarator configurations to minimize resonance-driven losses of energetic particles. This work establishes a basis for incorporating Alfvénic stability considerations into the stellarator design process, demonstrated through optimization of a quasihelical configuration to avoid high-frequency spectral gaps.

fusion plasma↗

Predictive Phenomics Initiative Project Dataset Catalog Collection

The Predictive Phenomics Science & Technology Initiative (PPI) at Pacific Northwest National Laboratory are tackling the grand challenge of understanding and predicting phenotype by identifying the molecular basis of function and enable function-driven design and control of biological systems. Research projects within this initiative are divided into three Thrust Areas (TAs): TA1) Enhancing Multi-Scale Phenomics Measurements, TA2) Identifying Molecular Patterns of Biological Function, and TA3) Computational Methods - Phenotypic Signatures. In efforts to enable discovery, reproducibility, and reuse of PPI-funded digital research data generated or used through the course of the proposed research-funded lifecycles, all corresponding digital data assets conducted under the Laboratory Directed Research and Development Program at PNNL are linked to this PPI dataset catalog collection.

59 BASIC BIOLOGICAL SCIENCES↗

Predictive Phenomics Initiative Project Dataset Catalog Collection

The Predictive Phenomics Science & Technology Initiative (PPI) at Pacific Northwest National Laboratory are tackling the grand challenge of understanding and predicting phenotype by identifying the molecular basis of function and enable function-driven design and control of biological systems. Research projects within this initiative are divided into three Thrust Areas (TAs): TA1) Enhancing Multi-Scale Phenomics Measurements, TA2) Identifying Molecular Patterns of Biological Function, and TA3) Computational Methods - Phenotypic Signatures. In efforts to enable discovery, reproducibility, and reuse of PPI-funded digital research data generated or used through the course of the proposed research-funded lifecycles, all corresponding digital data assets conducted under the Laboratory Directed Research and Development Program at PNNL are linked to this PPI dataset catalog collection.

59 BASIC BIOLOGICAL SCIENCES↗

Pivotal trial characteristics and types of endpoints used to support Food and Drug Administration rare disease drug approvals between 2013 and 2022

Background/aims Rare disease drug development faces unique challenges, such as genotypic and phenotypic heterogeneity within small patient populations and a lack of established outcome measures for conditions without previously successful drug development programs. These challenges complicate the process of selecting the appropriate trial endpoints and conducting clinical trials in rare diseases. In this descriptive study, we examined novel drug approvals for non-oncologic rare diseases by the U.S. Food and Drug Administration’s Center for Drug Evaluation and Research over the past decade and characterized key regulatory and trial design elements with a focus on the primary efficacy endpoint utilized as the basis of approval. Methods Using the Food and Drug Administration’s Data Analysis Search Host database, we identified novel new drug applications and biologics license applications with orphan drug designation that were approved between 2013 and 2022 for non-oncologic indications. From Food and Drug Administration review documents and other external databases, we examined characteristics of pivotal trials for the included drugs, such as therapeutic area, trial design, and type of primary efficacy endpoints. Differences in trial design elements associated with primary efficacy endpoint type were assessed such as randomization and blinding. Then, we summarized the primary efficacy endpoint types utilized in pivotal trials by therapeutic area, approval pathway, and whether the disease etiology is well defined. Results One hundred and seven drugs that met our inclusion criteria were approved between 2013 and 2022. Assessment of the 107 drug development programs identified 150 pivotal trials that were subsequently analyzed. The pivotal trials were mostly randomized (80%) and blinded (69.3%). Biomarkers (41.1%) and clinical outcomes (42.1%) were commonly utilized as primary efficacy endpoints. Analysis of the use of clinical trial design elements across trials that utilized biomarkers, clinical outcomes, or composite endpoints did not reveal statistically significant differences. The choice of primary efficacy endpoint varied by the drug’s therapeutic area, approval pathway, and whether the indicated disease etiology was well defined. For example, biomarkers were commonly selected as primary efficacy endpoints in hematology drug approvals (70.6%), whereas clinical outcomes were commonly selected in neurology drug approvals (69.6%). Further, if the disease etiology was well defined, biomarkers were more commonly used as primary efficacy endpoints in pivotal trials (44.7%) than if the disease etiology was not well defined (27.3%). Discussion In the past 10 years, numerous novel drugs have been approved to treat non-oncologic rare diseases in various therapeutic areas. To demonstrate their efficacy for regulatory approval, biomarkers and clinical outcomes were commonly utilized as primary efficacy endpoints. Biomarkers were not only frequently used as surrogate efficacy endpoints in accelerated approvals, but also in traditionally approved rare disease drugs. The choice of primary efficacy endpoints varied by therapeutic area, approval pathway, and understanding of disease etiology.

Hong, Kyungwan [Rare Diseases Team, Office of New ↗

An experimental study on gas-liquid phase fluid migration in hydrate-bearing sediments during hydrate dissociation

Natural gas hydrate production tests face problems such as severe sand blockage, poor gas-liquid phase separation, and significant land subsidence. This is because of the insufficient understanding of the complex phase transition and gas-liquid multi-phase fluid migration during hydrate dissociation. In hydrate-bearing sediment systems, hydrate phase transition couples with gas-liquid fluid migration. The phase transition causes changes in pore structure, which in turn modifies porous infiltration parameters and fluid flow capacity. Meanwhile, alterations in phase interfaces affect key parameters like surface tension and wettability. Gas-liquid fluid migration influences heat and mass transfer, thus affecting phase equilibrium and dissociation rates. To bridge the gap in describing gas-liquid fluid migration during hydrate dissociation in experiments, this research innovatively integrated an unsteady-state gas displacement by water and a quantitative hydrate dissociation process, independently developed a multi-phase seepage experimental system suitable for hydrate dissociation and determined the relationship between seepage parameters and hydrate saturation under different porosity. The results are as follows: a) Core samples with higher initial porosity show a greater recovery rate of fluid flow capacity. b) The retarding effect of multi-phase fluid has a more significant impact on the migration of the wetting phase fluid (water) than that of the non-wetting phase fluid (methane). c) During hydrate dissociation, the evolution of absolute permeability shows an “S-shaped” pattern, and the evolution of relative permeability shows a “wiring-harness” pattern. In conclusion, the findings can provide a theoretical basis for preventing geological disasters and for geotechnical engineering design during hydrate production.

58 GEOSCIENCES↗

Superstructure Optimization of Waste Plastic Pyrolysis, Integrating Thermal, Catalytic, and Plasma Technologies with Machine Learning

Global plastic waste generation exceeds 430 million tonnes per year, yet fewer than 9% are recycled in the United States. Pyrolysis offers a chemical recycling route at scale, but existing techno-economic and life cycle assessments fix product yields to single pure polymers, producing economic and environmental outputs that break down when the feed composition changes. Here, we present a superstructure optimization framework that addresses this by embedding a composition-aware random forest yield predictor, trained on 566 pyrolysis experiments, within a full-scale process simulation. Product distributions update automatically as feed allocation shifts across four reactor chemistries: conventional thermal, catalytic (HZSM-5), thermal oxo-degradation, and nonequilibrium CO2 plasma. The optimal superstructure achieves minimum selling prices of −0.56 to −0.76/kg feed and global warming potentials of −0.276 to −0.322 kg CO2-eq/kg feed across four commodity price scenarios, confirming profitable, carbon-negative operation without tipping fees. Carbon abatement costs of $\$$0.46 to $\$$1.25/kg CO2-eq are competitive with direct air capture. Sensitivity analysis shows that the catalytic-plasma split fraction is the single largest driver of both economic and climate performance, while hydrocracking allocation in the wax upgrading stage is emission-neutral across the full variable range. Mixed plastic waste streams, evaluated as composition-variable feedstocks rather than pure resins, are profitable and carbon-negative across realistic market conditions. These results give a quantitative basis for reactor selection, circular economy investment, and policy design targeting chemical recycling on a large scale.

Life cycle assessment↗

Prototype Hanford Barrier Performance Monitoring Report: Fiscal Year 2024

This report provides an annual update on performance monitoring of the Prototype Hanford Barrier (PHB) at the Hanford Site. The PHB is part of a long-term study that serves as the scientific basis for many of the evapotranspiration-capillary barrier designs currently used globally and for future engineered barrier designs planned for remedial actions over waste and demolition sites at the Hanford Site. The PHB allows us to identify potential future issues and develop better monitoring techniques before these engineered barriers are constructed. Surface barriers like the PHB are essential for preventing water infiltration and curbing the spread of contaminants to groundwater. Effective monitoring of soil moisture levels above and below these barriers is crucial given that performance metrics could span up to 1,000 years. From July 2023 to June 2024, the water flux (as measured by tipping buckets) through the 2-m-thick silt loam layer of the PHB – a fine silty material that stores water under high capillary tension – remained well below the 0.5-mm-per-year performance threshold, demonstrating its effectiveness in preventing water penetration. In 2024, degraded tipping bucket gauges were replaced to ensure the accuracy of future data. Additionally, neutron probes revealed that the wetting front from the rainy season only penetrated to a maximum depth of 1.2 m into the silt loam. This further demonstrated the barrier's efficiency, as the wetting front did not fully penetrate the 2-m-thick capillary barrier. The western gravel slope of the PHB, composed of Hanford Site pit gravel of varying sizes, demonstrated low flux rates. In contrast, the eastern riprap slope exhibited higher flux rates. Zhang (2017) found that the riprap side slope of the PHB had the highest drainage rates in January and the lowest in late summer or early fall, indicating significant summer evaporation. Drainage rates increased significantly under enhanced precipitation conditions, far exceeding the design criterion, which could lead to water infiltration into the waste zone. The study introduced the “edge effect,” where elevated drainage rates from the riprap may migrate laterally beneath the barrier, compromising its ability to isolate waste, and recommended expanding the barrier and conducting further research to mitigate this issue. This report provides a review on surface barrier edge effects and their potential impact to subsurface contaminant migration.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Conceptual Design of a Water Tank Critical Facility for SPARC

Critical experiments, sometimes referred to zero-power reactors, are crucial tools in developing and validating nuclear physics predictions and thus an indispensable capability to ensure criticality safety during all parts of the nuclear fuel cycle and in reducing uncertainties in reactor physics predictions toward optimizing nuclear energy production. The System Physics Advanced Reactor Facility (SPARC) project was recently initiated to enable large-scale criticality experiments using a horizontal split table machine well suited toward solid core materials systems (fuel, moderator, reflector). The facility selected for this mission was a former pool-type research reactor building and thus also well suited toward a second critical experiment capability able to house full-size light-water reactor (LWR) fuel bundles. A conceptual design study was undertaken to review past water tank critical experiments used for LWR physics experiments and to develop an early engineering design for a new critical assembly tank (CAT). The work described here shows that a relatively simple CAT concept can be constructed and deployed in the SPARC facility to meet the urgent demands for new critical experiments on advanced LWR fuel bundles designs. The SPARC facility layout is conducive to the receipt and upending of LWR fuel bundles using existing containers and equipment from the LWR industry. The facility’s overhead crane can then be used to handle fuel bundles and place them in a vertical storage rack or in the CAT for critical experiments, both of which fit within the building’s “open basement” alongside other equipment planned for SPARC and the horizontal split table. A slightly lower area in the basement can serve as a large drain tank so that fail-safe valves drain the CAT reactor tank for safe shutdown. Neutronic configurations were determined where a 3 × 3 array of fuel bundles can be surrounded by full-length “loose rods” to adjust reactivity so that critical is achieved when the bundles are fully submerged. Viable configurations were determined for both pressurized- and boiling-water-reactor-type fuel bundles. This design concept was used to develop an early planning basis for establishing the CAT capability alongside the otherwise planned SPARC project in order to help streamline the process. Recent presidential executive orders have highlighted the need to achieve power uprates in LWR plants and the CAT capability will be a crucial element of these initiatives. Based on the work described herein, it is recommended that an earnest and timely project begin in order to establish this urgently needed capability.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

BIL High Speed Fuel Cell Stack Manufacturing

General Motors LLC (GM) was awarded a project to develop and implement technologies for manufacturing 20,000 units of Fuel Cell Stacks per year on two shifts per day basis. GM leveraged prior in-house expertise in designing the Fuel Cells, deploying the manufacturing process steps in the laboratory environment as well as the deployment in the industrial environment on a smaller scale. The project focus was to design, build, and deploy a manufacturing line consisting of an anode and cathode electrode processing, unitized electrode assembly, fuel cell stacking, compression, testing, and final assembly of the fuel cell stack. The project was terminated in the first budget period.

08 HYDROGEN↗

Economic and Jobs Impacts of Point-Source Carbon Capture in Cement Industry – Case Study

The cement industry accounts for an estimated 8% of global CO2 emissions, which surpasses that of the entire aviation sector. In contrast with other industries, where CO2 emissions can be drastically reduced via electrification or fuels substitution, cement production releases CO2 as part of its process, during the calcination of carbonates to yield oxides. Thus, point-source carbon capture has become a key technology in the cement industry’s decarbonization. Apart from the expected environmental benefits, point-source carbon capture in the cement industry can yield important economic benefits and create jobs. The objective of this study was to perform a preliminary assessment of the economic and workforce impacts associated with the construction and operation of a point-source carbon capture retrofit of an existing cement production facility, using as a basis the data from a front-end engineering design (FEED) study to install a 3.9 million metric tons per year (Mtpy) CO2 capture facility at Holcim Ste Genevieve cement plant in Missouri, United States of America. The advanced carbon capture technology used in this FEED study was Air Liquide’s Cryocap™ FG carbon capture technology. The study evaluated the direct, indirect, and induced economic impacts of the construction, operation, and maintenance activities of the project over its lifespan. It also covered how the project will generate new jobs, their nature, and quantity, along with strategies to prepare the workforce. To perform this study, construction, operation, and maintenance cost estimates, as well as construction and operation staffing plans from the FEED study were input into IMPLAN version 7.5 software, licensed by IMPLAN Group LLC (Huntersville, VC), to predict the direct, indirect and induced economic impacts of the project using industry multipliers from the software. Additionally, recruitment strategies were developed for hiring individuals who belong to groups that are historically underserved or underrepresented, as well as anticipated recruitment of workers from the local community (whether training will be required or if the skills are associated with an existing labor force). The analysis estimated that the construction and operation of the carbon capture at Holcim Ste. Genevive will result in over 24 thousand work-years of job opportunities, close to USD 10 billion of economic impacts, including over USD 460 million of tax revenue. These results encompass the direct, indirect, and induced effects. A strategy to maximize hiring from the project and neighboring counties was developed, leveraging training agreements with local trade groups and universities. The result of this study can be used for a strategic preliminary assessment of the potential regional economic and job impacts of retrofitting existing cement plants with point source carbon systems, and its methodology can be replicated to individual projects to aid in planning and workforce development.

01 COAL, LIGNITE, AND PEAT↗

Adaptive Stiffness Power Take-Off System for a Hydraulic Hose-Pump Point Absorber Wave Energy Converter

Two crucial challenges faced in the design of ocean wave energy converters (WECs) are maintaining high capacity factors and remaining robust in everchanging, harsh ocean environments. This study introduces a novel mechanism for achieving reactive WEC control with a soft hydraulic power take-off, thereby addressing both challenges. The device of interest involves a hydraulic pump, constructed from a fluidic flexible matrix composite (F2MC), which is cyclically stretched by driving waves and pressurizes working fluid through a turbine-generator. This class of fiber-reinforced stretch hoses is established for ocean use as robust moorings and shock absorbers. The dynamic properties of the F2MC pump depend on internal pressure, which can be controlled by a continuously variable transmission between the turbine and generator, allowing the system to be adapted for better performance over a wide range of wave conditions. This work presents a dynamic model for operation and adaptive behavior of this power take-off system, experimentally validates components of the model, and performs dynamic simulations of the system that show increases in power production and capacity factor compared to non-adaptive operation for a variety of driving wave conditions. This work develops the basis for future large-scale experimental testing and controller design of this system.

Wave energy conversion, fluidic flexible matrix co↗

Red Hills Storage Hub Feasibility Study - Summary of Milestone 2 - Conceptual Basis of Plants and Pipeline Infrastructure

This document provides the first conceptual-level design of plants and pipeline infrastructure, including maps showing the project location, the potential footprint of the carbon capture and storage plant, the potential site of the capture and compression unit, and the conceptual pipeline layout for transporting the CO2 product from the capture facility to the future potential injection sites.

Carbon Capture and Storage,CarbonSAFE↗

Error-controlled Progressive Retrieval of Scientific Data under Derivable Quantities of Interest

The unprecedented amount of scientific data has introduced heavy pressure on the current data storage and transmission systems. Progressive compression has been proposed to mitigate this problem, which offers data access with on-demand precision. However, existing approaches only consider precision control on primary data, leaving uncertainties on the quantities of interest (QoIs) derived from it. In this work, we present a progressive data retrieval framework with guaranteed error control on derivable QoIs. Our contributions are three-fold. (1) We carefully derive the theories to strictly control QoI errors during progressive retrieval. Our theory is generic and can be applied to any QoIs that can be composited by the basis of derivable QoIs proved in the paper. (2) We design and develop a generic progressive retrieval framework based on the proposed theories, and optimize it by exploring feasible progressive representations. (3) We evaluate our framework using five real-world datasets with a diverse set of QoIs. Experiments demonstrate that our framework can faithfully respect any user-specified QoI error bounds in the evaluated applications. This leads to over 2.02× performance gain in data transfer tasks compared to transferring the primary data while guaranteeing a QoI error that is less than 1E-5.

Wu, Xuan↗

Luminescent Zr Complexes with Long-lived Intraligand Charge Transfer Excited States

Understanding and establishing design principles to tune the excited states of earth-abundant sensitizers is crucial for identifying new photosensitizers for sustainable technological advancements. Here, we report a series of three bis Zr (IV) complexes of tridentate, dianionic ligands incorporating two phenoxide donors and aza arene acceptors of increasing electron affinity (pyridine < pyrimidine < pyrazine ) that are air and water-stable. These complexes emit via thermally assisted delayed fluorescence from an intraligand charge transfer excited state with varying metal contributions. The electronic structural changes from different acceptors vary the excited state character and the photophysical properties significantly between the complexes. The variation in photophysics that includes emission lifetime (76 μs to 265 ns), intersystem crossing (ISC) lifetime ( 390 – 290 ps), and the energy difference between the singlet and triplet excited states (∆EST. 170 -100 meV). We observe solvent-independent ISC rates when the excited state has metal contributions (acceptor = pyridine), and the ISC rates vary significantly with solvent polarity when the excited state is an intra-ligand charge transfer state (acceptor = pyrimidine and pyrazine). Transient absorption measurements provided the basis spectra and verified the metal contribution in the excited state. This work provides a basis for developing new sensitizers based on Zr (IV) by providing design principles that can be used to modulate the character of the excited state and its photophysics.

Nattikallungal, Thabassum A. [University of Southe↗

EIC ESR beam position monitors thermal and thermomechanical study preliminary design

The Electron Ion Collider (EIC) Electron Storage Ring (ESR) Beam Position Monitors (BPM) are designed to monitor the electron beam orbit position on a turn-by-turn and bunch-by-bunch basis in the vacuum chamber. Large variations in ESR fill pattern and bunch intensity imposes a large dynamic range on the BPM system design. And given the large ESR beam current - up to 2.5 A with 1160 x 20 nC bunches – the heating by synchrotron radiation (SR) and beam impedance is a significant concern. The high energy of the electrons – up to 18 GeV – leads to scat tering of the SR that produces high radiation doses and as sociated heating of structures away from the SR impact area. Because of this intense heating, and stringent position stability requirements, an in-depth engineering analysis was carried out. This paper will review the analysis made of the preliminary design and its main outcomes.

43 PARTICLE ACCELERATORS↗

Web-Based Tools for Data-Informed Remedy Optimization: Software Theory and User Guide

This report documents the development and application of two web-based decision-support tools for pump-and-treat (P&T) groundwater remediation systems: PTOLEMY (Pump-and-Treat Optimized Location Evaluation to Maximize Yields) and OPTIMA (Optimization for Pump-and-Treat Implementation, Management, & Assessment). These tools enhance remedy design and management by leveraging advanced computational methods – specifically deep learning and multi-objective optimization – within a user-friendly platform. By integrating data-driven models with established hydrogeological knowledge, PTOLEMY and OPTIMA enable more efficient evaluation of well placement and operational strategies, helping site managers balance multiple remediation objectives under complex conditions. Both tools are implemented as modules within the SOCRATES (Suite Of Comprehensive Rapid Analysis Tools for Environmental Sites) web platform, which provides data access, visualization, and analytics to support remedy optimization across sites in the U.S. Department of Energy Office of Environmental Management complex. PTOLEMY is a rapid screening module designed to identify promising locations for new extraction wells. It employs a multi-channel three-dimensional convolutional neural network (MC3D-CNN) trained on high-fidelity simulation data to predict the relative performance (in terms of contaminant mass recovery) of potential well sites. Through an interactive web interface, PTOLEMY visualizes the probability of high performance across a site, highlighting areas where an extraction well is likely to yield above-threshold contaminant removal over a multi-year period. PTOLEMY’s map-based displays and exportable results support transparent communication of screening analyses. By focusing attention on the most favorable candidate locations, the tool augments traditional engineering judgment and physics-based modeling, providing a data informed basis for subsequent detailed evaluations. OPTIMA is a multi objective optimization module designed to find wellfield layouts and operating schedules that meet various cleanup goals. It quickly evaluates thousands of candidate setups – combinations of well locations, timing, and rates – and returns a small set of best trade-off options for comparison. At its core, OPTIMA uses a U-Net-based surrogate model – a deep-learning emulator of a groundwater flow and transport simulator – to dramatically accelerate scenario evaluations. Coupling this fast surrogate with the NSGA-II (Non-dominated Sorting Genetic Algorithm II) evolutionary algorithm, OPTIMA explores a wide decision space of well locations and schedules to identify Pareto-optimal solutions that trade off key objectives (e.g., minimizing cleanup time, maximizing contaminant mass removal, and minimizing plume extent). The tool outputs a family of optimal configurations and visualizes their trade-offs (Pareto frontiers of cleanup metrics and maps of optimized well placements). Site managers can use these results to understand the range of viable strategies and to select candidate designs for more detailed verification. OPTIMA is currently under active development and not yet fully released; this guide provides early documentation to support planning and gather user feedback.

54 ENVIRONMENTAL SCIENCES↗