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At least 145 records · Page 8

De Novo Design of Proteins That Bind Naphthalenediimides, Powerful Photooxidants with Tunable Photophysical Properties

De novo protein design provides a framework to test our understanding of protein function and build proteins with cofactors and functions not found in nature. Here, we report the design of proteins designed to bind powerful photooxidants and the evaluation of the use of these proteins to generate diffusible small-molecule reactive species. Because excited-state dynamics are influenced by the dynamics and hydration of a photooxidant’s environment, it was important to not only design a binding site but also to evaluate its dynamic properties. Thus, we used computational design in conjunction with molecular dynamics (MD) simulations to design a protein, designated NBP (NDI Binding Protein), that held a naphthalenediimide (NDI), a powerful photooxidant, in a programmable molecular environment. Solution NMR confirmed the structure of the complex. We evaluated two NDI cofactors in this de novo protein using ultrafast pump–probe spectroscopy to evaluate light-triggered intra- and intermolecular electron transfer function. Moreover, we demonstrated the utility of this platform to activate multiple molecular probes for protein labeling.

carbonyls↗

De novo design of transmembrane β barrels

Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a “hypothesis, design, and test” approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.

Vorobieva, Anastassia A.↗

A Solar Fuels Nexus: Molecules and Materials for Light-Driven Catalysis

The American Chemical Society (ACS) selects two groups of graduate students each year to plan and host a one-day symposium at each national meeting (both fall and spring).This year our Graduate Student Symposium Planning Committee (GSSPC), composed of seven students from four universities, proposal entitled “A Solar Fuels Nexus: Molecules and Materials for Light-Driven Catalysis” was selected for the “Crossroads in Chemistry” ACS Meeting that will take place March 23-26, 2023 in Indianapolis, IN. All members of our GSSPC are affiliated with the DOE Fuels from Sunlight Energy Innovation Hub, with two from the Liquid Sunlight Alliance (LiSA) and five from the Center for Hybrid Approaches in Solar Energy to Liquid Fuels (CHASE). Here we request funds to support this symposium. This symposium will highlight research progress and perspectives in the solar fuels generation field and seeks to advance the four priority research objectives (PROs) established by the Department of Energy’s Office of Basic Energy Sciences (DOE-BES) Roundtable Report that are also central to many research goals within LiSA and CHASE. The symposium will consist of research presentations from 10 invited senior researcher speakers on topics such as molecular catalyst design, computational modeling of electron transfer systems, microenvironmental effects on CO2 reduction and H2O oxidation catalysis, and intelligent design of semiconductor interfaces with ample time for discussions. These research topics fit very well with the Solar Photochemistry supported research areas of “light-driven electron and energy transfer in condensed phase and interfacial molecular systems,” “electrocatalysis and photocatalysis of solar fuels reactions,” and “semiconductor photoelectrochemistry.” More broadly, this symposium seeks to advance the DOE-BES’s mission to: “support fundamental research to understand, predict, and ultimately control matter and energy at the level of electrons, atoms, and molecules” by providing a diverse atmosphere where such research will be disseminated, discussed, and debated. There will be a strong focus on Diversity, Equity, and Inclusivity (DEI) in our symposium. Of our 10 speakers, 7 will be from underrepresented demographics in STEM, including 5 who identify as women. Furthermore, we have representatives from academia accompanied by one national lab scientist and one officer from the Office of Fossil Energy and Carbon Management at the DOE. All speakers will be holding a short DEI moment ahead of their talks. In order to support the career development of attending early career scientists, we will also be hosting a luncheon specifically for graduate students and postdocs to provide them opportunities to network with the distinguished speakers and other attendees. DOE funds for this symposium will be used to support the attendance and participation of 15 graduate students from US institutions by defraying travel and registration costs. These funds will promote engagement and conversation between early career scientists in the solar fuels field, while disseminating solar fuels research funded by and relevant to the DOE.

30 DIRECT ENERGY CONVERSION↗

Mixed Ionic Electronic Conducting Quaternary Perovskites: Materials by Design for Solar Thermochemical Hydrogen

The innovative research conducted by Arizona State University and Princeton University in the project "Mixed Ionic-Electronic Conducting Quaternary Perovskites: Materials by Design for Solar Thermochemical Hydrogen" marks a significant stride forward in thermochemical water splitting. Through an intricate blend of computational design and experimental validation, the project delved into the promising potential of Mixed Ionic Electronic Conducting (MIEC) perovskites. These complex materials, characterized by their unique redox-active nature and adaptability in stoichiometry, present a promising frontier for efficient solar thermochemical hydrogen production. Firstly, the research enhanced the science by utilizing state-of-the-art computational methodologies to unravel the nuanced chemical potentials of MIEC perovskites. By simulating various off-stoichiometric scenarios and redox conditions, the team was able to predict material behaviors under diverse environmental conditions, a feat unachievable through conventional experimental methodologies alone. This approach not only fast-tracks the material screening process, significantly reducing the time from laboratory re-search to practical application, but also uncovers trends and correlations that are pivotal for future materials innovation. Regarding technical effectiveness, the project stands out in its economic feasibility. Traditional methods of materials discovery are often marred by high costs and extensive timeframes, owing to the iterative nature of experimental processes. However, by employing theoretical computations and validating these findings with targeted experiments, the project introduced a cost-effective paradigm for materials discovery and the first ever prediction, synthesis, and preliminary validation of a material solely from computational and theoretical considerations. This synergy between computation and experimentation expedites the discovery of optimal materials conducive to high-efficiency solar-to-hydrogen conversion processes. Furthermore, the public stands to benefit substantially from this research. The success of MIEC perovskites in solar thermochemical applications heralds a shift towards lower cost and lower electricity input for clean hydrogen production, hence potentially impacting climate and energy resilience. By improving the efficiency of solar-to-hydrogen conversions, the research paves the way for reduced dependency on fossil fuels, addressing the urgent global need for accessible and renewable energy sources. Moreover, the project's advancements contribute to scientific literacy in renewable energy technologies, empowering society through knowledge and spurring future innovations. In essence, this research project demonstrates significant progress in the realm of advanced water splitting through solar thermochemistry. Through its groundbreaking approaches in computational materials science and its implications for real-world applications, it holds the promise of a cleaner, more energy-resilient future.

08 HYDROGEN↗

Immersive Visualization for Scientific Data Analysis

We will present the use of immersive visualization at the National Renewable Energy Laboratory (NREL), showcasing how immersive visualization is advancing scientific research and engineering practices and transforming our day-to-day operations. We are leveraging immersive visualization to support scientific discovery and engineering in various domains, including material design, computational fluid dynamics, immersive analytics, grid modernization, digital twins, and situated visualization. We have observed several benefits across four key areas: enhanced spatial judgments, improved understanding through interaction, increased capacity to embed high-dimensional data, and improved collaboration.

immersive analytics↗

Strategies for designing biocatalysts with new functions

Enzymes can be optimized to accelerate chemical transformations via a range of methods. In this review, we showcase how protein engineering and computational design techniques can be interfaced to develop highly efficient and selective biocatalysts.

09 BIOMASS FUELS↗

Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins

A challenge for design of protein–small-molecule recognition is that incorporation of cavities with size, shape, and composition suitable for specific recognition can considerably destabilize protein monomers. This challenge can be overcome through binding pockets formed at homo-oligomeric interfaces between folded monomers. Interfaces surrounding the central homo-oligomer symmetry axes necessarily have the same symmetry and so may not be well suited to binding asymmetric molecules. To enable general recognition of arbitrary asymmetric substrates and small molecules, we developed an approach to designing asymmetric interfaces at off-axis sites on homo-oligomers, analogous to those found in native homo-oligomeric proteins such as glutamine synthetase. We symmetrically dock curved helical repeat proteins such that they form pockets at the asymmetric interface of the oligomer with sizes ranging from several angstroms, appropriate for binding a single ion, to up to more than 20 Å across. Of the 133 proteins tested, 84 had soluble expression in E. coli, 47 had correct oligomeric states in solution, 35 had small-angle X-ray scattering (SAXS) data largely consistent with design models, and 8 had negative-stain electron microscopy (nsEM) 2D class averages showing the structures coming together as designed. Both an X-ray crystal structure and a cryogenic electron microscopy (cryoEM) structure are close to the computational design models. The nature of these proteins as homo-oligomers allows them to be readily built into higher-order structures such as nanocages, and the asymmetric pockets of these structures open rich possibilities for small-molecule binder design free from the constraints associated with monomer destabilization.

59 BASIC BIOLOGICAL SCIENCES↗

Real-time PCR assays that detect genes for botulinum neurotoxin A–G subtypes

The role of Real-Time PCR assays for surveillance and rapid screening for pathogens is garnering more and more attention because of its versatility and ease of adoption. The goal of this study was to design, test, and evaluate Real-Time TaqMan PCR assays for the detection of botulinum neurotoxin (bont/A-G) genes from currently recognized BoNT subtypes. Assays were computationally designed and then laboratory tested for sensitivity and specificity using DNA preparations containing bont genes from 82 target toxin subtypes, including nine bivalent toxin types; 31 strains representing other clostridial species; and an extensive panel that consisted of DNA from a diverse set of prokaryotic (bacterial) and eukaryotic (fungal, protozoan, plant, and animal) species. In addition to laboratory testing, the assays were computationally evaluated using in silico analysis for their ability to detect bont gene sequences from recently identified toxin subtypes. Seventeen specific assays (two for each of the bont/C, bont/D, bont/E, and bont/G subtypes and three for each of the bont/A, bont/B, and bont/F subtypes) were designed and evaluated for their ability to detect bont genes encoding multiple subtypes from all seven serotypes. These assays could provide an additional tool for the detection of botulinum neurotoxins in clinical, environmental and food samples that can complement other existing methods used in clinical diagnostics, regulatory, public health, and research laboratories.

59 BASIC BIOLOGICAL SCIENCES↗

A Computational Framework to design 3D stiffness gradient acoustic metamaterials for impedance matching

Acoustic waves play a crucial role in various applications, including medical imaging, non-destructive testing, and sonar systems. One of the significant challenges in these applications is impedance matching, which is essential for minimizing reflections and maximizing the transfer of acoustic energy between different media. Acoustic metamaterials offer a promising solution to this challenge. In addition to impedance control, gradient stiffness can enhance structural efficiency and enable spatial control of wave propagation, making it a valuable feature in acoustic metamaterial design. In this pa- per, we present our developed computational method to design 3D stiffness gradient acoustic metamaterials for impedance matching. The key steps in our approach include generating initial designs using a periodic covariance function to provide unit cells that are both periodic on the boundaries and randomly formed inside the unit cell. Furthermore, we integrated manufacturing constraints into the design process, ensuring that the structures are interconnected for fabrication. We propose two computational optimization algorithms: GenUnit, based on a non-dominated sorting genetic algorithm (NSGA-II), and MLMatch, which leverages differentiable machine learning. The two approaches are not separate contributions but complementary com- ponents of a unified framework. GenUnit requires no training data and directly interfaces with physics-based simulations, making it highly accurate but slower for large-scale exploration. In contrast, MLMatch is data-hungry during training but, once trained, enables near-instantaneous inference and broad design-space coverage. Together, they form a hybrid strategy: ML- Match rapidly explores the global design space, and GenUnit provides local refinement with high-fidelity accuracy. This balance between training cost, inference time, and precision is the motivation for including both methods in the same study. We applied this dual-algorithm framework to generate two metallic-based metamaterial designs that match the acoustic impedance of water while exhibiting a controlled gradient in stiffness (from stiff to soft). The stiffness gradient is particularly advantageous in applications where one side of the structure must interface with soft or sensitive surfaces, such as human tissue or delicate components. Here, this work paves the way for improved materials in various acoustic applications, particularly in ultrasound devices, by providing better impedance.

Metamaterial↗

Cooperative Education

Los Alamos National Laboratory (LANL) is a multidisciplinary national laboratory that conducts research and development in national security, engineering, materials science, computational modeling, and advanced manufacturing. The laboratory develops innovative technologies to address complex scientific and engineering challenges. This project focuses on the development and evaluation of high-performance absorbing structures through computational design, simulation, and engineering analysis. Absorbing structures are used in applications where damage mitigation, structural protection, and material efficiency are critical performance requirements. The increasing demand for lightweight, high-strength, and highly efficient structural systems has created a need for improved design methodologies capable of maximizing absorption while minimizing weight and material usage. The project utilizes advanced engineering software, including 3D CAD software and FEA, to generate and optimize structural concepts. Computational simulations are performed to evaluate structural behavior under loading conditions, while mathematical analyses are conducted using Python-based tools as well as established analytical equations from material and structural mechanics. The project benefits LANL by supporting the development of advanced design methodologies and improving the understanding of material and structural performance. During the internship term, a significant portion of the design development, simulation, and data analysis activities will be completed. Success of the project depends on collaboration among engineering mentors and technical staff members. Work will be conducted at Los Alamos National Laboratory using laboratory computing resources and engineering software.

42 ENGINEERING↗

NEXTorch: A Design and Bayesian Optimization Toolkit for Chemical Sciences and Engineering

Automation and optimization of chemical systems require well-informed decisions on what experiments to run to reduce time, materials, and/or computations. Data-driven active learning algorithms have emerged as valuable tools to solve such tasks. Bayesian optimization, a sequential global optimization approach, is a popular active-learning framework. Past studies have demonstrated its efficiency in solving chemistry and engineering problems. Here we introduce NEXTorch, a library in Python/PyTorch, to facilitate laboratory or computational design using Bayesian optimization. NEXTorch offers fast predictive modeling, flexible optimization loops, visualization capabilities, easy interfacing with legacy software, and multiple types of parameters and data type conversions. It provides GPU acceleration, parallelization, and state-of-the-art Bayesian optimization algorithms and supports both automated an d human-in-the-loop optimization. The comprehensive online documentation introduces Bayesian optimization theory and several examples from catalyst synthesis, reaction condition optimization, parameter estimation, and reactor geometry optimization. NEXTorch is open-source and available on GitHub

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design of Novel Hot Gas Component for Gas Turbine Engines Enabled by Materials and Additive Manufacturing Process Development

This CRADA project was the result of a project award under FOA-DOE-0001980. The overarching FOA project team consisted of researchers from Carpenter Technology Corporation (CTC), Solar Turbines Incorporated (Solar), Pennsylvania State University (PSU), University of California-Santa Barbara (UCSB), and Oak Ridge National Laboratory (ORNL). Evaluations were conducted on two high-γ’ superalloys that were designed by CTC and the UCSB. One alloy named GammaPrint-700 (GP-700) is a cobalt-base superalloy. The other alloy named GammaPrint-1100 (GP-1100) is a nickel-base (Ni-base) superalloy. PSU provided expertise and experimental testing of the thermal performance of AM micro-cooling architectures. ORNL provided expertise with the AM superalloy materials characterization and AM processing science. Solar provided turbine component design expertise. The focus of this CRADA report is to document the efforts between ORNL and CTC towards the development of superalloys designed for AM. The project goal was to use an AM processable high-temperature superalloy and design for Additive Manufacturing (DfAM) techniques to design an efficient turbine component (i.e. a turbine tip shoe) with enhanced cooling features that can only be fabricated through additive manufacturing (AM). The efficiencies of existing combined heat and power (CHP) engines are capped by both component design and materials limitations. However, AM of a tip shoe component from a γ’strengthened superalloy offers the design flexibility to increase the efficiency and power of an industrial gas turbine. This project brought about advancements in the DfAM tip shoe design space and in the area of high temperature superalloys processable through laser powder bed fusion (LPBF) AM. State of art computation design tools were utilized to optimize unique cooling features into a tip shoe component design. A two-prong materials development approach was taken to support development of the AM tip shoe geometry. The first approach centered on investigating the processability and the appropriate process science for the industry standard high-γ’ nickel-base (Ni-base) superalloy Mar-M247. This superalloy is typically cast and considered non-weldable by traditional welding standards. In the course of this work, the alloy was not deemed feasible for process scale-up due to significant cracking issues during printing. The second approach focused on the development and evaluation of a novel cobalt-base superalloy, GammaPrint™-700 (GP-700 and a Ni-base superalloy, GammaPrint™-1100 (GP-1100) designed to mitigate the significant AM processing issues with Mar-M247. The processability of these two alloys were investigated through electron beam melting (EBM) binder-jet AM (BJAM), and LPBF as a risk mitigation for manufacturability. To be considered a candidate material for down-selection to proceed to full-scale AM tip shoe engine testing trials, the high temperature creep rupture strength was required to achieve at a minimum, a Larsen Miller Parameter (LMP) increase of 10.9% over the baseline material LPBF AM Hastelloy X.

99 GENERAL AND MISCELLANEOUS↗

Design of Novel Hot Gas Component for Gas Turbine Engines Enabled by Materials and Additive Manufacturing Process Development

This CRADA project was the result of a project award under FOA-DOE-0001980. The overarching FOA project team consisted of researchers from Carpenter Technology Corporation (CTC), Solar Turbines Incorporated (Solar), Pennsylvania State University (PSU), University of California-Santa Barbara (UCSB), and Oak Ridge National Laboratory (ORNL). Evaluations were conducted on two high-γ’ superalloys that were designed by CTC and the UCSB. One alloy named GammaPrint-700 (GP-700) is a cobalt-base superalloy. The other alloy named GammaPrint-1100 (GP-1100) is a nickel-base (Ni-base) superalloy. PSU provided expertise and experimental testing of the thermal performance of AM micro-cooling architectures. ORNL provided expertise with the AM superalloy materials characterization and AM processing science. Solar provided turbine component design expertise. The focus of this CRADA report is to document the efforts between ORNL and CTC towards the development of superalloys designed for AM. The project goal was to use an AM processable high-temperature superalloy and design for Additive Manufacturing (DfAM) techniques to design an efficient turbine component (i.e. a turbine tip shoe) with enhanced cooling features that can only be fabricated through additive manufacturing (AM). The efficiencies of existing combined heat and power (CHP) engines are capped by both component design and materials limitations. However, AM of a tip shoe component from a γ’strengthened superalloy offers the design flexibility to increase the efficiency and power of an industrial gas turbine. This project brought about advancements in the DfAM tip shoe design space and in the area of high temperature superalloys processable through laser powder bed fusion (LPBF) AM. State of art computation design tools were utilized to optimize unique cooling features into a tip shoe component design. A two-prong materials development approach was taken to support development of the AM tip shoe geometry. The first approach centered on investigating the processability and the appropriate process science for the industry standard high-γ’ nickel-base (Ni-base) superalloy Mar-M247. This superalloy is typically cast and considered non-weldable by traditional welding standards. In the course of this work, the alloy was not deemed feasible for process scale-up due to significant cracking issues during printing. The second approach focused on the development and evaluation of a novel cobalt-base superalloy, GammaPrint™-700 (GP-700 and a Ni-base superalloy, GammaPrint™-1100 (GP-1100) designed to mitigate the significant AM processing issues with Mar-M247. The processability of these two alloys were investigated through electron beam melting (EBM) binder-jet AM (BJAM), and LPBF as a risk mitigation for manufacturability. To be considered a candidate material for down-selection to proceed to fullscale AM tip shoe engine testing trials, the high temperature creep rupture strength was required to achieve at a minimum, a Larsen Miller Parameter (LMP) increase of 10.9% over the baseline material LPBF AM Hastelloy X.

36 MATERIALS SCIENCE↗

Finite elements for Matérn-type random fields: Uncertainty in computational mechanics and design optimization

This work highlights an approach for incorporating realistic uncertainties into scientific computing workflows based on finite elements, focusing on prevalent applications in computational mechanics and design optimization. We leverage Matérn-type Gaussian random fields (GRFs) generated using the SPDE method to model aleatoric uncertainties, including environmental influences, variating material properties, and geometric ambiguities. Our focus lies on delivering practical GRF realizations that accurately capture imperfections and variations and understanding how they impact the predictions of computational models as well as the shape and topology of optimized designs. Here we describe a numerical algorithm based on solving a generalized SPDE to sample GRFs on arbitrary meshed domains. The algorithm leverages established techniques and integrates seamlessly with the open-source finite element library MFEM and associated scientific computing workflows, like those found in industrial and national laboratory settings. Our solver scales efficiently for large-scale problems and supports various domain types, including surfaces and embedded manifolds. We showcase its versatility through biomechanics and topology optimization applications, emphasizing the potential to influence these domains. The flexibility and efficiency of SPDE-based GRF generation empowers us to run large-scale optimization problems on 2D and 3D domains, including finding optimized designs on embedded surfaces, and to generate design features and topologies beyond the reach of conventional techniques. Moreover, these capabilities allow us to model and quantify geometric uncertainties on reconstructed submanifolds, such as the interpolated surfaces of cerebral aneurysms provided by postprocessing CT scans. In addition to offering benefits in these specific domains, the proposed techniques transcend specific applications and generalize to arbitrary forward and backward problems in uncertainty quantification involving finite elements.

97 MATHEMATICS AND COMPUTING↗

Computational Modeling To Adapt Neutralizing Antibody

Monoclonal antibodies (mAbs) is the leading therapy for viral infections because it provides immediate protection and can be administered at higher levels than in a natural immune response. Finding mAbs that neutralize a broad spectrum of viral targets has proven difficult because many species and strains exist and blanket targeting is a slow and laborious process to experimentally screen 108 variants. A new method is needed to rapidly redesign mAbs for homologous targets. This project speeds up redesign using structure-based computational design to reduce the mAbs search space to a manageable level and screen mutants at a much higher rate than in experiments. Computation will also provide critical knowledge about the fundamental interactions. The project will adapt S230, a human antibody that neutralizes SARS-CoV, to neutralize SARS-COV-2.

60 APPLIED LIFE SCIENCES↗

Metamaterials as a Platform for the Development of Novel Materials for Energy Applications

To explore the fundamental properties of metamaterials (MMs) / metasurfaces and their potential for control of energy at the sub‐wavelength scale in support of the mission of the Department of Energy and the office of Basic Energy Sciences. Electromagnetic metamaterials provide a platform for the discovery and design of new materials with novel structures, functions, and properties. The PI proposes to advance the knowledge base of these materials through fundamental investigations of the experimental and theoretical properties of metamaterials for the discovery, prediction and design of new materials with novel structures, functions, and properties. The proposed research activities emphasize a complete basic research program including the conceptual / computational design, fabrication / synthesis of the materials, and the characterization and analysis of their electromagnetic properties. The proposed project explores the fundamental properties of metamaterials / metasurfaces and their potential for energy applications. There are three main topics which will be investigated: 1) Dispersion engineering with metamaterials and metasurfaces, 2) Epsilon near zero metamaterial absorbers and emitters, and 3) All dielectric metamaterials. The program implements a complete basic research program consisting of theory / design, modeling, characterization, and analysis, in order to fully characterize metamaterials and metasurfaces, while at the same time minimizing iterations necessary to achieve the proposal goals.

36 MATERIALS SCIENCE↗