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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Holistic Measurement Driven Resilience: Combining Operational Fault and Failure Measurements and Fault Injection for Quantifying Fault Detection, Propagation and Impact. Final report

For HPC systems to date, application resilience to faults and failures has been accomplished by the brute- force method of checkpoint/restart, which allows an application to make forward progress in the face of system and application faults, errors, and failures independent of root cause or end result. It has remained the primary resilience mechanism because we lack a way to identify faults and anticipate consequences early enough to take meaningful mitigating action. However, checkpoint/restart implementations put a tremendous burden on system resources and on the applications themselves and is becoming less feasible at scale. Because we have not yet operated at scales at which checkpoint/restart fails to provide forward progress, despite increasing costs, vendors have had little motivation to provide the instrumentation necessary for early identification of faults and failures. However, as we move from petascale to exascale, component mean time to failure (MTTF) will render the existing techniques ineffectual and/or too expensive. Furthermore, fault recovery mechanisms such as failover and/or error correction introduce performance inconsistency. Instrumentation allowing early indication of problems and tools to enable use of such information by systems, operating systems, and applications offer an alternative, more scalable and less costly solution. In the HMDR project, we built on our experience and expertise developed and accumulated over years of research on design, monitoring, measurement, and assessment of resilient computing systems. Analysis of field data on the current and past generations of extreme-scale systems revealed several challenges that, if not addressed in increasingly larger and more complex systems, may hinder the effectiveness of future exascale computing systems. Specifically, i) file systems and interconnects in current-generation large-scale systems already operate at the margins of resiliency, including consistent performance, and may not scale to larger deployments; ii) automated, software-based failover mechanisms are frequently inadequate and can introduce wider failures, such that failures during recovery may lead to system/application failures, including system-wide outages; and iii) silent data corruption represents a critical fault mode and will require efficient detection mechanisms if next-generation applications are to take full advantage of exascale hardware. To address the above challenges, we assembled a team of world-renowned experts in resilient extreme- scale computing from the University of Illinois (Electrical and Computer Engineering, Computer Science, and NCSA), SNL, LANL, NERSC, and Cray. Our team includes representatives from centers that house many of the largest HPC resources in the world, both today and over the coming years. The team has a unique track record of research in i) system and application failure characterization based on the analysis of field data, ii) data-driven design of fault/error detection mechanisms, and iii) experimental characterization of system/application resiliency. The team includes system owners/operators who provide continuous data collection and access and ensure installation of appropriate analysis tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Automated methods for scalable, parallelized enzymatic biopolymer synthesis and modification using microfluidic devices

Methods for the automated template-free synthesis of user-defined sequence controlled biopolymers using microfluidic devices are described. The methods facilitate simultaneous synthesis of up to thousands of uniquely addressed biopolymers from the controlled movement and combination of regents as fluid droplets using microfluidic and EWOD-based systems. In some forms, biopolymers including nucleic acids, peptides, carbohydrates, and lipids are synthesized from step-wise assembly of building blocks based on a user-defined sequence of droplet movements. In some forms, the methods synthesize uniquely addressed nucleic acids of up to 1,000 nucleotides in length. Methods for adding, removing and changing barcodes on biopolymers are also provided. Biopolymers synthesized according to the methods, and libraries and databases thereof are also described. Modified biopolymers, including chemically modified nucleotides and biopolymers conjugated to other molecules are described.

Banal, James↗
DOE OSTI2021

Exploring electron beam induced atomic assembly via reinforcement learning in a molecular dynamics environment

We report atom-by-atom assembly of functional materials and devices is perceived as one of the ultimate targets of nanotechnology. Recently it has been shown that the beam of a scanning transmission electron microscope can be used for targeted manipulation of individual atoms. However, the process is highly dynamic in nature rendering control difficult. One possible solution is to instead train artificial agents to perform the atomic manipulation in an automated manner without need for human intervention. As a first step to realizing this goal, we explore how artificial agents can be trained for atomic manipulation in a simplified molecular dynamics environment of graphene with Si dopants, using reinforcement learning. We find that it is possible to engineer the reward function of the agent in such a way as to encourage formation of local clusters of dopants under different constraints. This study shows the potential for reinforcement learning in nanoscale fabrication, and crucially, that the dynamics learned by agents encode specific elements of important physics that can be learned.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

United States Nuclear Power Reactor Used Nuclear Fuel Database and Applications

The Unified Database (UDB) within STANDARDS serves as the foundational data infrastructure for managing the United States' spent nuclear fuel inventory of 315,111 discharged assemblies totaling 91,036 metric tons of heavy metal. The database organizes this complex inventory through over 200 interconnected tables structured into eight primary attribute categories, supporting integrated analyses across storage, transportation, and disposal domains. Data enters the UDB through the GC-859 Nuclear Fuel Data Survey, which transitioned to web-based collection in 2023, improving data quality through real-time validation. The UDB enables automated generation of input files for nuclear safety analyses, reducing preparation time from weeks to hours while maintaining traceability. Applications include national inventory reporting, Certificate of Compliance assessments, and facility optimization. The three-tier distribution model balances accessibility with security requirements for federal agencies, national laboratories, and research organizations. The UDB provides essential data infrastructure as spent fuel management transitions from site-specific to integrated national campaigns.

Stefanovic, Peter↗
DOE OSTI2020

HERON

HERON is a modeling toolset and plugin for RAVEN to accelerate stochastic technoeconomic assessment of the economic viability of various grid-energy system configurations, especially with application to electrical grids and integrated energy systems (IES). The frameworks enabling this toolset are INL's RAVEN and its TEAL plugin. The toolset includes automated RAVEN workflow generation tools for performing stochastic analysis and optimization driven by technoeconomic factors. The workflows generated employ RAVEN for parametric or optimizing study of grid component characteristics, and again for stochastic sampling of regulated and deregulated markets, load, and weather histories. The toolset further provides methods for economically-optimal dispatch of system components given the stochastic samples of market, load, and weather histories. The toolset allows assembling of existing and new models through the RAVEN interface to the Modelica process modeling language.

Talbot, PaulW↗
DOE OSTI2024

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

The design of protein–protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. Deep learning methods promise to simplify protein–protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here, we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning–based methods to unlock the widespread application of designed protein–protein interfaces and self-assembling protein nanomaterials in biotechnology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Performing k eff Validation of As-Loaded Criticality Safety Calculations Using UNF-ST&DARDS: Applicable Experiment Selection [Slides]

This presentation discusses the UNF-ST&DARDS which performs many analyses for as-loaded SNF canisters, including criticality safety, shielding, thermal-hydraulic, and containment. It also discusses the experiment selection based on c k assessment of similarity and that the c k value of 0.8 or greater considered applicable for validation. 11 PWR SNF canisters (MPC-32) are used in this work. 1 model represents a failed fuel assembly as fresh, per the design basis and the remaining 10 models represent all 32 assemblies with depleted fuel. In conclusion, critical experiment selection can be performed with S/U techniques for as-loaded canisters in UNF-ST&DARDS. Sufficient benchmark experiments exist to support validation and additional MOX experiments that are a good match for commercial SNF would be a benefit to provide independent data. The presentations states that S/U techniques identify different pools of experiments for different systems and that the process is amenable to automation within UNF-ST&DARDS.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

An unstructured mesh based neutronics optimization workflow

We have developed a fully automated workflow to optimize the neutronics performance of the Second Target Station (STS) at the Oak Ridge National Laboratory’s Spallation Neutron Source. The optimization workflow starts with the parametrized solid CAD engineering models and converts them into the unstructured mesh (UM) models for the neutronics calculations with MCNP6.2. Calculations are executed and their results are loaded into the Dakota optimization toolkit. Dakota analyzes the results and proposes new geometry parameters for the next design iteration. The cycle repeats until the optimal parameters are found. The automated CAD to MCNP conversion, the use of high-fidelity UM models, and the use of modern optimizer are the key elements that advance the entire optimization workflow in comparison with the original workflow. The original workflow was based on a simplified constructive solid geometry (CSG) modeling with MCNPX, mcnp_pstudy tool, and an in-house optimizer. Herein to demonstrate the new workflow, we present a case of neutronics optimization of the moderator–reflector assembly (MRA). Apart from the MRA, the workflow can optimize other major STS components, such as the spallation target, neutron beamlines, radiation shielding, and various accelerator components. Importantly, the new workflow opens the door to the advanced multi-physics multi-parameter optimization and has the potential for use in other nuclear physics and accelerator applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

V-HAMSTeR v1.0.0

V-HAMSTeR is a bioinformatics software tool designed to predict the hosts of viruses directly from genomic sequences. It can be used by researchers to predict animal, prokaryotic, plant, protist or fungal viral hosts including viruses that may be fragmented or discovered in environmental metagenomic datasets. Features & Uses: The software employs a novel dual-stream deep learning architecture that dynamically fuses implicit sequence embeddings from a genomic foundation model with 13 explicit, handcrafted biological features (e.g., coding density and strand switch rates). To ensure maximum reliability, V=HAMSTeR deploys a 5-fold deep ensemble calibrated via Joint Temperature Scaling, providing users with statistically rigorous confidence probabilities. It also features an automated sequence chunking and mean-pooling module to seamlessly process variable-length contigs. Advantages Over Similar Technologies: Existing tools (e.g., IPEV, RNAVirHost) typically rely on either basic k-mers or isolated neural networks. V-HAMSTeR's hybrid architecture captures both broad genomic context and specific biological motifs that standalone foundation models often miss. Furthermore, unlike competitor tools that struggle with incomplete data or exhibit extreme overconfidence, V-HAMSTeR is explicitly benchmarked and mathematically calibrated for fragmented assemblies (1kb–10kb). This makes it uniquely robust, accurate, and trustworthy for the messy reality of real-world environmental viromics.

Grigson, Susie [Lawrence Berkeley National Laborat↗
DOE OSTI2024

Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

INTEGRATE - Inverse Network Transformations for Efficient Generation of Robust Airfoil and Turbine Enhancements

The INTEGRATE (Inverse Network Transformations for Efficient Generation of Robust Airfoil and Turbine Enhancements) project is developing a new inverse-design capability for the aerodynamic design of wind turbine rotors using invertible neural networks. This AI-based design technology can capture complex non-linear aerodynamic effects while being 100 times faster than design approaches based on computational fluid dynamics. This project enables innovation in wind turbine design by accelerating time to market through higher-accuracy early design iterations to reduce the levelized cost of energy. INVERTIBLE NEURAL NETWORKS Researchers are leveraging a specialized invertible neural network (INN) architecture along with the novel dimension-reduction methods and airfoil/blade shape representations developed by collaborators at the National Institute of Standards and Technology (NIST) learns complex relationships between airfoil or blade shapes and their associated aerodynamic and structural properties. This INN architecture will accelerate designs by providing a cost-effective alternative to current industrial aerodynamic design processes, including: - Blade element momentum (BEM) theory models: limited effectiveness for design of offshore rotors with large, flexible blades where nonlinear aerodynamic effects dominate - Direct design using computational fluid dynamics (CFD): cost-prohibitive - Inverse-design models based on deep neural networks (DNNs): attractive alternative to CFD for 2D design problems, but quickly overwhelmed by the increased number of design variables in 3D problems AUTOMATED COMPUTATIONAL FLUID DYNAMICS FOR TRAINING DATA GENERATION - MERCURY FRAMEWORK The INN is trained on data obtained using the University of Marylands (UMD) Mercury Framework, which has with robust automated mesh generation capabilities and advanced turbulence and transition models validated for wind energy applications. Mercury is a multi-mesh paradigm, heterogeneous CPU-GPU framework. The framework incorporates three flow solvers at UMD, 1) OverTURNS, a structured solver on CPUs, 2) HAMSTR, a line based unstructured solver on CPUs, and 3) GARFIELD, a structured solver on GPUs. The framework is based on Python, that is often used to wrap C or Fortran codes for interoperability with other solvers. Communication between multiple solvers is accomplished with a Topology Independent Overset Grid Assembler (TIOGA). NOVEL AIRFOIL SHAPE REPRESENTATIONS USING GRASSMAN SPACES We developed a novel representation of shapes which decouples affine-style deformations from a rich set of data-driven deformations over a submanifold of the Grassmannian. The Grassmannian representation as an analytic generative model, informed by a database of physically relevant airfoils, offers (i) a rich set of novel 2D airfoil deformations not previously captured in the data , (ii) improved low-dimensional parameter domain for inferential statistics informing design/manufacturing, and (iii) consistent 3D blade representation and perturbation over a sequence of nominal shapes. TECHNOLOGY TRANSFER DEMONSTRATION - COUPLING WITH NREL WISDEM Researchers have integrated the inverse-design tool for 2D airfoils (INN-Airfoil) into WISDEM (Wind Plant Integrated Systems Design and Engineering Model), a multidisciplinary design and optimization framework for assessing the cost of energy, as part of tech-transfer demonstration. The integration of INN-Airfoil into WISDEM allows for the design of airfoils along with the blades that meet the dynamic design constraints on cost of energy, annual energy production, and the capital costs. Through preliminary studies, researchers have shown that the coupled INN-Airfoil + WISDEM approach reduces the cost of energy by around 1% compared to the conventional design approach. This page will serve as a place to easily access all the publications from this work and the repositories for the software developed and released through this pr...

aerodynamics↗
DOE OSTI2025

Expansion of the tmRNA sequence database and new tools for search and visualization

Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Indoor Occupant Counting by RF Backscattering

Building HVAC (heating, ventilation and air conditioning) consumes approximately 13% of all energy consumption in USA. Motion detectors, cameras and user programmable thermostats have been shown to be ineffective for HVAC controls to save energy, mostly due to the user concerns of comfort, reliability and privacy. A new HVAC control system based on real-time occupant counting that is fully automated, highly accurate, economically sensible and preserving privacy and aesthetics can thus bring forth a disruptive impact to this large energy sector. Our indoor occupant monitoring technology is based on the radio-frequency identification system (RFID), deployed in the room, not on the occupants. One reader with four antennas can be deployed on the ceiling or behind the ceiling panels for every thousand square feet in home, office and assisted living, with or without room partitions. The sticker-like passive tag, 10 cents each and maintenance-free, are profusely hidden on the wall or inside the furniture at arbitrary position, preserving privacy and aesthetics. The large number of tags can realize diverse observation points to accommodate arbitrary room layouts, which is impractical by other active units of camera, infrared, radar or lidar. With 20 tags, the system can reliably detect the number of occupants. For 100 tags, occupant posture and location can be known. The technology has been verified in the research labs and test buildings with very high accuracy. When the real-time occupant number can be accurately known without assuming devices on occupants or occupant motion, the building HVAC system can be automated to achieve building energy saving without sacrificing occupant comfort. According to our limited testing in a few types of building models and the simplified cost calculation, the RFID system has low overall cost in production, deployment, operation and maintenance. The signal processing algorithm based on machine learning requires very small number of training cases as most learning is transferrable for various layouts, and very low computational needs during operation, according to our testing in four different room sizes and layouts. In our preliminary estimate from HVAC saving alone, the RFID system can potentially pay for itself within 1.5 years, in addition to the other enhancement in building automation systems (BAS). Our commercialization strategy and business pitch deck focus on venturing this Cornell occupant monitoring technology into BAS and energy management markets. We have identified three broad BAS market segments of senior living, residential buildings, and office buildings. We have put together the minimum viable product characteristics for these identified segments, including analyses on total cost and competing technologies, as well as the fit and technical gaps for these market segments. We intend to bring the technology to market by licensing or partnering with existing BAS vendors. A list of potential collaborators and licensing partner candidates was assembled for different aspects of integrating our technology into a potential product that can be used with BAS.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Core Design Optimization of the Westinghouse Lead Fast Reactor

Westinghouse is pursuing an advanced Nuclear Power Plant design based on Lead Fast Reactor (LFR) technology for global commercialization. To achieve an optimal combination of key attributes, such as safety, sustainability, and economic competitiveness, Westinghouse and ANL partnered in developing and applying a formalized core design optimization strategy. An LFR analysis workflow was developed to automate a suite of reactor physics, fuels performance, safety, and economics simulations on a selected LFR concept. The workflow streamlines analysis of a wide range of LFR designs with different dimensions and fuel types to assess their viability and economic performance, significantly reducing human processing time and risks of processing errors. The LFR optimization exercise was defined, resulting in selection of the design constraints (geometric, neutronics, thermo-mechanical, safety, thermal-hydraulics, and economics) and performance metrics researched (minimization of both the fuels LCOE and the first core inventory cost). A total of 14 varied design parameters were considered, including assembly dimensions, coolant temperature, and enrichment distribution throughout the core. The LFR analysis workflow was connected to DAKOTA for sensitivity and optimization analyses. Due to the extremely large size of the potential LFR optimization solution space relative to the computing time required to characterize one LFR solution, a multi-stage optimization approach was proposed to breakdown the problem into several stages with more reasonable sizes. This optimization approach enabled finding various viable core solutions with different cost tradeoffs that were considered by Westinghouse and justify selection of a smaller core with multi-batch 2-year cycle length.

Stauff, Nicolas E.↗
DOE OSTI2021

Cladding Profilometry Analysis of Experimental Breeder Reactor-II Metallic Fuel Pins with HT9, D9, and SS316 Cladding

BISON finite element method fuel performance simulations were conducted using an existing automated process that couples the Fuels Irradiation & Physics Database (FIPD) and the Integral Fast Reactor Materials Information System database by writing input files and comparing the BISON output to post-irradiation fuel pin profilometry measurements contained within the databases. The importance of this work is to demonstrate the ability to benchmark fuel performance metallic fuel models within BISON using Experimental Breeder Reactor-II fuel pin data for a number of similar pins, while building off previous modeling efforts. Changes to the generic BISON input file include implementing pin specific axial power and flux profiles, pin specific fluences, frictional contact, and irradiation-induced volumetric swelling models for cladding. A statistical analysis of irradiation-induced volumetric swelling models for HT9, D9, and SS316 was performed for experiments X421/X421A, X441/X441A, and X486. Between these three experiments, there were 174 post-irradiation examination (PIE) profilometries used for validating the swelling models presented using a standard error of the estimate (SEE) method. Implementation of the volumetric swelling models for D9 and SS316 claddings was found to have a significant impact on the BISON profilometry simulated, where HT9 clad pins had an insignificant change due to low fluence values. BISON profilometry simulated for HT9, D9, and SS316 fuel pins agreed with PIE profilometry measurements, with assembly SEE values being 4.4 × 10−3 for X421A, 2.0 × 10−3 for X441A, and 2.8 × 10−3 for X486. D9 clad pins in X421/X421A had the highest SEE values, which is due to the BISON simulated profilometry being shifted axially. While this work accomplished its purpose to demonstrate the modeling of multiple fuel pins from the databases to help validate models, the results suggest that the continued development of metallic fuel models is necessary for qualifying new metallic fuel systems to better capture some physical performance phenomena, such as the hot pressing of U-Pu-Zr and the fuel cladding chemical interaction.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Synthetic data-driven deep learning for label-free autonomous atomic force microscopy

Atomic force microscopy (AFM) is a widely used tool for nanoscale characterization across materials science, energy research, and biology. However, its adoption in high-throughput materials discovery and statistically driven studies remains limited by a strong dependence on expert operator input and by the scarcity of annotated experimental AFM datasets needed to enable data-driven automation. Here, we introduce SimuScan, a synthetic-data–driven framework that enables reliable AFM feature identification, segmentation, and targeted imaging without requiring large manually labeled experimental datasets. SimuScan generates tunable, high-fidelity synthetic AFM images of defined morphologies while incorporating realistic experimental artifacts, including tip–sample convolution, noise, flattening distortions, and surface debris. These datasets are shown to support scalable, label-free training of modern deep learning models for AFM analysis. When integrated into data-driven AFM workflows, SimuScan-trained models can locate and analyze nanoscale structures across large datasets and guide targeted follow-up imaging. We validate this approach on nanostructured surfaces, DNA assemblies, and bacterial cells, demonstrating robust generalization across diverse sample types with minimal operator intervention. More broadly, this work establishes a general strategy for generating explicitly conditioned, task-relevant synthetic data to improve the reliability of downstream models in autonomous microscopy.

Millan-Solsona, Ruben [Oak Ridge National Laborato↗
DOE OSTI2020

Patterning of magneto-optical nanomaterials

Patterning of colloidal particles in precisely organized architectures has attracted intense research interest for decades. This is due to their potential applications in flexible electronics, magnetic and optical devices, sensors, biotechnology, communications, etc. However, creation of mesoscale assemblies at commercial scale received less attention. The mesoscale systems reside between the micro- and macroscopic scales, with length dimensions from ≈ 100 um to 5mm. One way to create mesoscale materials is to leverage decades of experimental and theoretical research in nanomaterials field that allows us to precisely create and control the placement of nanoscale materials. We developed a versatile and automatic mesoscale patterning technology that provide precise and consistent control and special arrangement of functional nanomaterials. The versatility of the strategy is demonstrated by patterning nanoparticles with different dimensions, shapes and compositions, tethered with various functionalities and subjected to different external stimuli. Nanomaterials were created via the paten t pending automated flow-throughput domain process (AFTDP), aka nano-additive manufacturing approach, recently developed by us, based on a unique small-scale fluidics concept, that enables a uniform reaction environment for production of high-quality materials in large quantities.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Optimizing Cell-based Antimicrobials through Pooled Genomic Libraries

DNA synthesis and assembly technologies ushered in through synthetic biology have great promise for biomanufacturing, bioremediation, and the development of living therapeutics. Unfortunately, predicting sequence to function relationships, including for biosynthetic pathways expressed in a new host organism, is difficult and often requires many iterative cycles of design, construction, and testing. We are working to develop data-driven approaches to identify the genetic determinants of growth defects and productivity for the expression of a cell-based antimicrobial. We assayed the growth, pigment production, and antimicrobial activity of a collection of over 10,000 genetic mutants of the violacein biosynthetic pathway and sequenced the genetic variation of these mutants. Through this project, we have developed an innovative codebase to automate the determination of pigmentation and antimicrobial clearing diameter for tens of thousands of genetic mutants cultivated on agar dishes. Further, we have written DNA sequence analysis code to demultiplex & provide consensus sequences from high-throughput PacBio long-read circular consensus sequencing (CCS) datasets. From this foundation, we plan to map DNA sequence to function to predict an optimal genetic design to maximize antimicrobial activity while minimizing deleterious growth effects. The workflows and algorithms developed through this project can be broadly applied to other engineered functions in microbes, uncovering sequence to function relationships for complex phenotypes where function impacts fitness.

59 BASIC BIOLOGICAL SCIENCES↗