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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Quantum optimal control for pure-state preparation using one initial state

This paper presents a framework for solving the pure-state preparation problem using numerical optimal control. As an example, we consider the case where a number of qubits are dispersively coupled to a readout cavity. Herein, we model open system quantum dynamics using the Markovian Lindblad master equation driven by external control pulses. The main result of this paper develops a basis of density matrices (a parameterization) where each basis element is a density matrix by itself. Utilizing a specific objective function, we show how an ensemble of the basis elements can be used as a single initial state throughout the optimization process—independent of the system dimension. We apply the general framework to the specific application of ground-state reset of one and two qubits coupled to a readout cavity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1994

Certification of tactics and strategies in aviation

The paper suggests that the 'tactics and strategies' notion is a highly suitable paradigm to describe the cognitive involvement of human operators in advanced aviation systems (far more suitable than classical functional analysis), and that the workload and situational awareness of operators are intimately associated with the planning and execution of their tactics and strategies. If system designers have muddled views about the collective tactics and strategies to be used during operation, they will produce sub-optimum designs. If operators use unproven and/or inappropriate tactics and strategies, the system may fail. The author wants to make a point that, beyond certification of people or system designs, there may be a need to go into more detail and examine (certify?) the set of tactics and strategies (i.e., the Operational Concept) which makes the people and systems perform as expected. The collective tactics and strategies determine the information flows and situational awareness which exists in organizations and composite human-machine systems. The available infrastructure and equipment (automation) enable these information flows and situational awareness, but are at the same time the constraining factor. Frequently, the tactics and strategies are driven by technology, whereas we would rather like to see a system designed to support an optimized Operational Concept, i.e., to support a sufficiently coherent, cooperative and modular set of anticipation and planning mechanisms. Again, in line with the view of MacLeod and Taylor (1993), this technology driven situation may be caused by the system designer's and operator job designer's over-emphasis on functional analysis (a mechanistic engineering concept), at the expense of a subject which does not seem to be well understood today: the role of the (human cognitive and/or automated) tactics and strategies which are embedded in composite human-machine systems. Research would be needed to arrive at a generally accepted 'planning theory' which can elevate the analysis, description and design of tactics and strategies from today's cottage industry methods to an engineering discipline. The available infrastructure and equipment (automation) enable these information flows and situational awareness, but are at the same time the constraining factor. Frequently, the tactics and strategies are driven by technology, whereas we would rather like to see a system designed to support an optimized Operational Concept, i.e., to support a sufficiently coherent, cooperative and modular set of anticipation and planning mechanisms. Again, in line with the view of MacLeod and Taylor (1993), this technology driven situation may be caused by the system designer's and operator job designer's over-emphasis on functional analysis (a mechanistic engineering concept), at the expense of a subject which does not seem to be well understood today: the role of the (human cognitive and/or automated) tactics and strategies which are embedded in composite human-machine systems. Research would be needed to arrive at a generally accepted 'planning theory' which can evaluate the analysis, description and design of tactics and strategies from today's cottage industry methods to an engineering discipline.

Koelman, Hartmut↗
DOE OSTI2025

Neural network approaches for parameterized optimal control

Here, we consider numerical approaches for deterministic, finite-dimensional optimal control problems whose dynamics depend on unknown or uncertain parameters. We seek to amortize the solution over a set of relevant parameters in an offline stage to enable rapid decision-making and be able to react to changes in the parameter in the online stage. To tackle the curse of dimensionality arising when the state and/or parameter are high-dimensional, we represent the policy using neural networks. We compare two training paradigms: First, our model-based approach leverages the dynamics and definition of the objective function to learn the value function of the parameterized optimal control problem and obtain the policy using a feedback form. Second, we use actor-critic reinforcement learning to approximate the policy in a data-driven way. Using an example involving a two-dimensional convection-diffusion equation, which features high-dimensional state and parameter spaces, we investigate the accuracy and efficiency of both training paradigms. While both paradigms lead to a reasonable approximation of the policy, the model-based approach is more accurate and considerably reduces the number of PDE solves.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2013

Science Opportunity Analyzer (SOA) Version 8

SOA allows scientists to plan spacecraft observations. It facilitates the identification of geometrically interesting times in a spacecraft s orbit that a user can use to plan observations or instrument-driven spacecraft maneuvers. These observations can then be visualized multiple ways in both two- and three-dimensional views. When observations have been optimized within a spacecraft's flight rules, the resulting plans can be output for use by other JPL uplink tools. Now in its eighth major version, SOA improves on these capabilities in a modern and integrated fashion. SOA consists of five major functions: Opportunity Search, Visualization, Observation Design, Constraint Checking, and Data Output. Opportunity Search is a GUI-driven interface to existing search engines that can be used to identify times when a spacecraft is in a specific geometrical relationship with other bodies in the solar system. This function can be used for advanced mission planning as well as for making last-minute adjustments to mission sequences in response to trajectory modifications. Visualization is a key aspect of SOA. The user can view observation opportunities in either a 3D representation or as a 2D map projection. Observation Design allows the user to orient the spacecraft and visualize the projection of the instrument field of view for that orientation using the same views as Opportunity Search. Constraint Checking is provided to validate various geometrical and physical aspects of an observation design. The user has the ability to easily create custom rules or to use official project-generated flight rules. This capability may also allow scientists to easily assess the cost to science if flight rule changes occur. Data Output allows the user to compute ancillary data related to an observation or to a given position of the spacecraft along its trajectory. The data can be saved as a tab-delimited text file or viewed as a graph. SOA combines science planning functionality unique to both JPL and the sponsoring spacecraft. SOA is able to ingest JPL SPICE Kernels that are used to drive the tool and its computations. A Percy search engine is then included that identifies interesting time periods for the user to build observations. When observations are then built, flight-like orientation algorithms replicate spacecraft dynamics to closely simulate the flight spacecraft s dynamics. SOA v8 represents large steps forward from SOA v7 in terms of quality, reliability, maintainability, efficiency, and user experience. A tailored agile development environment has been built around SOA that provides automated unit testing, continuous build and integration, a consolidated Web-based code and documentation storage environment, modern Java enhancements, and a focus on usability

Witoff, Robert J.↗
DOE OSTI2021

Data-driven chemical kinetic reaction mechanism for F-24 jet fuel ignition

A data-driven chemical kinetic mechanism for the military version of Jet A, F-24, is developed for numerical simulations of the ignition process. The main purpose of this study is to obtain a practical F-24 mechanism across wide temperature and equivalence ratio ranges, with a particular focus on the negative temperature coefficient and low temperature regions. The new mechanism (ARLMech-HC-F24) is based on the HyChem model of a similar fuel and optimized using a micro-genetic algorithm against an experimental ignition delay data set of the target fuel. The development and optimization processes include reaction selection, population creation, shuffled tournament implementation based on a merit function, and child-individual creation for the next generation. Several techniques and parameters are proposed to generate an accurate mechanism through an efficient process. The newly introduced data-driven mechanism based on these techniques shows better merit value convergence and represents the ignition behavior more accurately than that without the techniques. This practical mechanism is suitable for the numerical simulations of the F-24 or Jet A ignition problem, and the suggested strategies can be employed in similar problems of rate coefficients estimation.

42 ENGINEERING↗
DOE OSTI2022

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure --- this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗
DOE OSTI2022

SPATIAL GRAPH ATTENTION AND CURIOSITY-DRIVEN POLICY FOR ANTIVIRAL DRUG DISCOVERY

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure - this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Y↗
NASA NTRS1987

Investigation, development, and application of optimal output feedback theory. Volume 3: The relationship between dynamic compensators and observers and Kalman filters

Relationships between observers, Kalman Filters and dynamic compensators using feedforward control theory are investigated. In particular, the relationship, if any, between the dynamic compensator state and linear functions of a discrete plane state are investigated. It is shown that, in steady state, a dynamic compensator driven by the plant output can be expressed as the sum of two terms. The first term is a linear combination of the plant state. The second term depends on plant and measurement noise, and the plant control. Thus, the state of the dynamic compensator can be expressed as an estimator of the first term with additive error given by the second term. Conditions under which a dynamic compensator is a Kalman filter are presented, and reduced-order optimal estimaters are investigated.

Broussard, John R.↗
DOE OSTI2020

Revealing the Atomic Structures of Exposed Lateral Surfaces for Polymorphic Manganese Dioxide Nanowires

Polymorphic 1D MnO 2 nanostructures are widely applied in fields such as catalysis, sensing, and energy storage with the functionality mainly determined by the atomic patterns of their laterally exposed facets, which largely remain unclear so far. Herein, by high‐resolution transmission electron microscopy (HRTEM) imaging directly along their axial directions, the atomic structures of the outmost lateral facets of polymorphic MnO 2 nanowires are disclosed. To generalize the findings, four most commonly seen phases with characteristic tunnel structures are targeted, i.e., β‐, γ‐, α‐, and todorokite(t)‐MnO 2 , which are synthesized conventionally using a hydrothermal method reported in the literature. Axially imaging these MnO 2 nanowires via HRTEM, the {hkl} facets covering the lateral surfaces are accurately indexed, the atomic pattern of each {hkl} facet is revealed, and it is further coupled with the outmost tunnel configuration that can significantly affect the physicochemical property of MnO 2 materials via tunnel‐driven mass adsorption/transport. This work provides a reliable reference for atomic modeling of MnO 2 to benefit the pursuit of its structure–property relationship; in addition, it can benefit surface engineering strategies to better rationalize the facet growth control with optimized functionality.

Yuan, Yifei↗
DOE OSTI2024

Nanoporous Materials Genome Center Final Technical Report

Nanoporous materials (NPMs), including zeolites/zeotypes, metal-organic frameworks (MOFs), covalent organic frameworks, polymers with intrinsic microporosity, and molecular cages, possess enormous potential in diverse areas relevant to the DOE Office of Science Basic Energy Sciences (BES) mission and objectives. The Nanoporous Materials Genome Center (NMGC) has developed exascale-ready software, computational/theoretical chemistry methods, and data-driven science approaches that enable (i) the de-novo design of functional NPMs for chemical separation and catalysis tasks of increasing complexity, (ii) the discovery of the most promising functional NPMs from databases of synthesized and hypothetical adsorbent structures and the optimization of process conditions for specific applications, and (iii) the microscopic-level understanding of the fundamental interactions underlying the function of NPMs including hierarchical architectures, composite materials, responsive frameworks that may undergo phase transitions or post-synthetic modifications, and materials containing defects, partial disorder, or interfaces. A pivotal part of the NMGC project has been a tight collaboration between leading experimental groups for synthesis and characterization of NPMs and of computational groups that allowed for iterative feedback. The NMGC project has resulted in the publication of more than 290 research and review articles including more than 60 publications in high-impact journals and more than 15 journal covers. NMGC publications have already received more than 20,000 citations (with more than 3,000 citations per year in 2021, 2022, and 2023) and contribute to an h-index of more than 72. The NMGC award has supported collaborative research involving 28 research groups and contributed to the training of more than 40 postdocs, more than 60 graduate students, and more than 20 undergraduate students with broad expertise in data-driven science approaches, computational chemistry methods, and high-performance computing, in addition to the skills to thrive in an integrated experimental and computational research environment.

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

Simulation-driven optimization of high-order meshes in ALE hydrodynamics

Here we propose tools for high-order mesh optimization and demonstrate their benefits in the context of multi-material Arbitrary Lagrangian-Eulerian (ALE) compressible shock hydrodynamic applications. The mesh optimization process is driven by information provided by the simulation which uses the optimized mesh, such as shock positions, material regions, known error estimates, etc. These simulation features are usually represented discretely, for instance, as finite element functions on the Lagrangian mesh. The discrete nature of the input is critical for the practical applicability of the algorithms we propose and distinguishes this work from approaches that strictly require analytical information. Our methods are based on node movement through a high-order extension of the Target-Matrix Optimization Paradigm (TMOP). The proposed formulation is fully algebraic and relies only on local Jacobian matrices, so it is applicable to all types of mesh elements, in 2D and 3D, and any order of the mesh. We discuss the notions of constructing adaptive target matrices and obtaining their derivatives, reconstructing discrete data in intermediate meshes, node limiting that enables improvement of global mesh quality while preserving space-dependent local mesh features, and appropriate normalization of the objective function. The adaptivity methods are combined with automatic ALE triggers that can provide robustness of the mesh evolution and avoid excessive remap procedures. The benefits of the new high-order TMOP technology are illustrated on several simulations performed in the high-order ALE application BLAST.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Deep Learning–Assisted Multiobjective Optimization of Geological CO 2 Storage Performance under Geomechanical Risks

In geological CO 2 storage, designing the optimal well control strategy for CO 2 injection to maximize CO 2 storage while minimizing the associated geomechanical risks is not trivial. This challenge arises due to pressure buildup, CO 2 plume migration, the highly nonlinear nature of geomechanical responses to rock-fluid interaction, and the high computational cost associated with coupled flow and geomechanics simulations. In this paper, we introduce a novel optimization framework to address these challenges. The optimization problem is formulated as follows: maximize total CO 2 storage while minimizing geomechanical risks by adjusting the injection schedules within bounded constraints. The geomechanical risks are primarily driven by injection-induced pressure build-up, which is characterized by ground displacement and the induced microseismicity. We used the Fourier neural operator (FNO)-based deep learning model to construct surrogate models, replacing the time-consuming coupled flow and geomechanics simulations for evaluating the aforementioned objective functions. The developed surrogate models have been incorporated into a multiobjective optimization framework through a genetic algorithm to reduce the computational burden. The proposed optimization framework reduces the computational cost from approximately 2,400 hours, when using objective function evaluations based on physics-based simulations, to around 20 minutes. A set of Pareto-optimal solutions of the proposed workflow yields nontrivial optimal decisions, reducing the microseismicity potential and the vertical displacement. This Pareto front highlights the optimal trade-offs between CO 2 storage amount, safety, and ground displacement, emphasizing the need for careful optimization and management of injection strategies to achieve a balanced outcome. The novelty of this work is twofold. First, we demonstrate the importance of incorporating the minimization of the geomechanical risks as objective functions into the CO 2 storage optimization workflow to mitigate the potential risk of induced microseismicity and ground displacement. Second, we leverage the FNO-based surrogate models to optimize a real-field CO 2 storage operation.

42 ENGINEERING↗
DOE OSTI2026

Gearbox bearing crack growth prognostics and uncertainty quantification with physics-informed machine learning

This paper introduces the extreme theory of functional connections (X-TFC), a physics-informed machine learning algorithm, and tailors it to estimate the remaining useful life (RUL) of wind turbine gearbox bearings experiencing fatigue crack growth. Unlike purely data-driven methods, X-TFC embeds a physics model, based on Head's theory in this work, into its training objective. The core of X-TFC is a random-projection single-layer neural network trained via an extreme learning machine, which requires only limited damage progression data and solves for output weights with a least-squares optimization algorithm. A composite loss function balances the network's fit to observed degradation data against the residuals of the governing crack growth differential equation, ensuring the learned damage trajectory remains physically plausible. When applied to a vibration-based health-index (HI) dataset measured during the growth of a crack on the inner ring of a high-speed bearing in a wind turbine gearbox (Bechhoefer and Dubé, 2020), X-TFC achieves near-zero prediction bias. Even when trained on only the first 10 %–20 % of the damage progression data, with sufficient physics weighting its predictions remain monotonic and smooth, delivering high prognosability and trendability. To quantify the epistemic uncertainty, we employ a Monte Carlo ensemble of independently initialized X-TFC models trained on noise-perturbed data, which yields confidence intervals around each RUL estimate and captures both model-parameter and epistemic uncertainty. In addition to a vibration-based HI, we demonstrate that the proposed framework can be directly applied to a supervisory control and data acquisition (SCADA) data-based HI (Eftekhari Milani et al., 2026) measured during similar wind turbine gearbox bearing crack faults, preserving its accuracy and interpretability. This extension shows the versatility of our approach, which is applicable to bearings of multiple gearbox manufacturers, models, and ratings using only SCADA data. By integrating domain knowledge with machine learning, X-TFC offers a rapid, reliable tool for crack prognostics. Its adaptability to other bearing failure modes, such as pitch bearing ring cracks, positions X-TFC as a powerful enabler of data-driven, physics-informed asset management in the wind energy sector and beyond.

17 WIND ENERGY↗
DOE OSTI2026

Optimization techniques in self-similar compressible flow

We investigate the one-dimensional (1D) inviscid compressible flow equations for an ideal gas through the lens of optimization techniques. It is the case that, to our knowledge, optimization analysis applied to the so-called “linear velocity” solutions of the Euler compressible flow equations has not been previously conducted. Through both gradient-based and variational techniques, new variants of well-studied flow scenarios, i.e., self-similar, 1D, linear velocity solution class to idealized inviscid compressible flow equations, are determined, as encoded in both the kinematic and thermodynamic properties of this self-similar solution class. With the kinematics of the said solutions being driven by a self-similar “scale radius” and the thermodynamics being driven separately through the appearance of an arbitrary function, a myriad of new solution classes is possible. Acting as a guide to more realistic physical circumstances as well as discovery, it is the hope that the presented cases serve as the framework for future investigations into the intersection of self-similarity and optimization techniques. Fields of study that may find this work to be of interest include aerodynamic design, flow control, inertial confinement fusion, physics-informed neural networks, and other related areas of interest.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Modeling plasticity-mediated void growth at the single crystal scale: A physics-informed machine learning approach

Modeling the evolution of voids during plastic flow as well as their effects on plastic dissipation is critical for both component manufacturing and lifetime estimation purposes. To this end, we propose a rate-dependent constitutive model to homogenize the effects of semi-randomly distributed voids on single crystal plasticity whilst capturing void interaction and plastic anisotropy. Here, this present work focuses on the case of face centered cubic crystals to introduce an anisotropic gauge function applicable within the crystal plasticity formalism. The approach combines analytical methods to describe the micromechanics of the system in combination with symbolic regression to capture analytically intractable mechanisms from data. The hybrid framework uses a physics-informed genetic programming-based symbolic regression algorithm to solve a multiform optimization problem simultaneously producing a new gauge function and a new strain rate equation. This is also a multi-objective optimization problem with many competing objectives. A new search and selection step is introduced to the genetic algorithm that promotes convergence toward a global solution that better satisfies all the objectives. Overall, the symbolic equations produced leverage data-driven methods to achieve greater accuracy than comparable alternatives on an analytically intractable problem while maintaining model transparency.

36 MATERIALS SCIENCE↗
NASA NTRS1986

Unified control/structure design and modeling research

To demonstrate the applicability of the control theory for distributed systems to large flexible space structures, research was focused on a model of a space antenna which consists of a rigid hub, flexible ribs, and a mesh reflecting surface. The space antenna model used is discussed along with the finite element approximation of the distributed model. The basic control problem is to design an optimal or near-optimal compensator to suppress the linear vibrations and rigid-body displacements of the structure. The application of an infinite dimensional Linear Quadratic Gaussian (LQG) control theory to flexible structure is discussed. Two basic approaches for robustness enhancement were investigated: loop transfer recovery and sensitivity optimization. A third approach synthesized from elements of these two basic approaches is currently under development. The control driven finite element approximation of flexible structures is discussed. Three sets of finite element basic vectors for computing functional control gains are compared. The possibility of constructing a finite element scheme to approximate the infinite dimensional Hamiltonian system directly, instead of indirectly is discussed.

Mingori, D. L.↗
NASA NTRS2016

Closed Loop Control Compact Exercise Device for Use on MPCV

Long duration space travel to Mars or to an asteroid will expose astronauts to extended periods of reduced gravity. To combat spaceflight physiological deconditioning, astronauts will use resistive and aerobic exercise regimens for the duration of the space flight to minimize the loss of bone density, muscle mass and aerobic capacity that occurs during exposure to a reduced gravity environment. Unlike the International Space Station (ISS), the mass and volume available for an exercise device in the next generation of spacecraft is limited. Therefore, compact exercise device prototypes are being developed for human in the loop evaluations. The NASA Human Research Program (HRP) is managing Advanced Exercise Concepts (AEC) requirements development and candidate technology maturation for all exploration mission profiles from Multi-Purpose Crew Vehicle (MPCV) exploration missions (e.g., EM-2, up to 21 day) to Mars Transit (up to 1000 day) missions. Numerous technologies have been considered and evaluated against HRP-approved functional requirements and include flywheel, pneumatic and closed-loop microprocessor-controlled motor driven power plants. Motor driven technologies offer excellent torque density and load accuracy characteristics as well as the ability to create custom mechanical impedance (the dynamic relationship between force and velocity) and custom load versus position exercise algorithms. Further, closed-loop motor-driven technologies offer the ability to monitor exercise dose parameters and adapt to the needs of the crewmember for real time optimization of exercise prescriptions. A simple proportional-integral-derivative (PID) controller is demonstrated in a prototype motor driven exercise device with comparison to resistive static and dynamic load set points and aerobic work rate targets. The resistive load term in the algorithm includes a constant force component (Fcmg) as well as inertial component (Fima) and a discussion of system tuning is presented in terms of addressing key functional requirements and human interfaces. The device aerobic modality is modelled as a rowing exercise using ground data sets obtained from Concept 2 rowers as well as competitive rowing1. A discussion of software and electronic implementations are presented which demonstrate unique approaches to meeting the constrained mass, volume and power requirements of the MPCV. . In addition to utilizing traditional PID control, controllers utilizing state feedback with gains solved using a Linear Quadratic Regulator will be developed. Controllability and observability will be utilized to investigate the need for state measurement in the design. As the control system directly interacts with human test subjects, robust methods such as H-infinity are also being investigated.1. Kleshnev V. Biomechanics. In: Rowing, Handbook of Sports Medicine and Science. ed. by Secher N., Voliantis S. IOC Medical Commission, Blackwell Pub. pp. 22-34, 2007

microgravity↗
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↗