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DOE OSTI2023

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform ( RPX ) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Massively parallel, computationally guided design of a proenzyme

Proteins have shown promise as therapeutics and diagnostics, but their effectiveness is limited by our inability to spatially target their activity. To overcome this limitation, we developed a computationally guided method to design inactive proenzymes or zymogens, which are activated through cleavage by a protease. Since proteases are differentially expressed in various tissues and disease states, including cancer, these proenzymes could be targeted to the desired microenvironment. We tested our method on the therapeutically relevant protein carboxypeptidase G2 (CPG2). We designed Pro-CPG2s that are inhibited by 80 to 98% and are partially to fully reactivatable following protease treatment. The developed methodology, with further refinements, could pave the way for routinely designing protease-activated protein-based therapeutics and diagnostics that act in a spatially controlled manner. Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to redesign any chosen enzyme to be similarly stimulus responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for proenzyme design. For a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effectively designed variants shows that they are inhibited by ∼80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98% but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing proenzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the prodomain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of proproteins with precise spatial regulation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Computer-aided design file format for additive manufacturing and methods of file generation

A tessellated output file format describing a computer-aided design (CAD) model including a plurality of vertices, a plurality of curves, a plurality of surfaces, and at least one volume, the tessellated output file format comprising base polygon data, a vertex metadata container, a curve metadata container, and a surface metadata container. The base polygon data defines the CAD model for additive manufacturing and includes a plurality of connected polygons, each polygon including a plurality of nodes, a plurality of edges, and a face. The vertex metadata container includes a listing of CAD model vertices and one polygon node associated with each CAD model vertex. The curve metadata container includes a listing of CAD model curves and at least one polygon edge associated with each CAD model curve. The surface metadata container includes a listing of CAD model surfaces and at least one polygon face associated with each CAD model surface.

Vernon, Gregory John↗

DOE OSTI2022

Computer-aided design file format for additive manufacturing and methods of file generation

A method of generating a tessellated output file comprising receiving a computer-aided design (CAD) model file defining a CAD model including a plurality of vertices, a plurality of curves, a plurality of surfaces, and at least one volume; generating base polygon data defining the CAD model for additive manufacturing, the base polygon data including a plurality of connected polygons, each polygon including a plurality of nodes, a plurality of edges, and a face; generating data for a vertex metadata container including a listing of CAD model vertices and one polygon node associated with each CAD model vertex; generating data for a curve metadata container including a listing of CAD model curves and at least one polygon edge associated with each CAD model curve; and generating data for a surface metadata container including a listing of CAD model surfaces and at least one polygon face associated with each CAD model surface.

Vernon, Gregory John↗

DOE OSTI2021

Thermal-striping analysis methodology for sodium-cooled reactor design

Computational fluid dynamics simulations have been performed to study the applicability of engineering CFD methods for thermals striping analysis. Thermal striping is the fluctuating temperature profile in a solid caused by fluctuating fluid temperature, and the resulting fluctuating thermal stresses cause high cycle fatigue and eventual material failure. Here this study presents the methodology for thermal striping analysis that including a transient conjugate heat transfer RANS model and benchmark the results against a sodium triple jet experiment. The multiphysics calculations are implemented to analyze the thermal stresses in the solid domain caused by the coupled heat transfer between the fluid and solid domains. Validation data from a liquid sodium triple jet experiment include time-averaged temperature measurements and power spectra of the temperature signal. The numerical results agree well with these experimental measures, demonstrating key features such as the dominant frequency of temperature fluctuations. The applicability of a low-cost wall treatment method is demonstrated, enabling key computational savings. Finally, the performance of two finite element stress analysis software packages is compared, and the validity of the lower-cost method is confirmed. These results demonstrate the applicability of engineering methods for computational thermal striping calculations, enabling thermal striping estimations in large fluid systems such as the core of a Sodium-cooled nuclear reactor.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

A Computational Framework for Control Co-Design of Resilient Cyber–Physical Systems With Applications to Microgrids

Critical infrastructure networks, such as power and transportation networks, can be modelled as cyber-physical systems. As the complexity of such systems grow, there is need for developing metrics and design tools that will co-optimize the physical components of the system and the control policies to guarantee resilience against cyber and natural threats. To that end, we develop a simulation-based control co-design computational framework that will concurrently determine the system and control parameters of a cyber-physical system to meet pre-specified resilience, operational and economic objectives. Here, the capabilities of the developed co-design engine is demonstrated by designing the physical components and control parameters of a microgrid system that will meet its resiliency objectives when subjected to various cyber and physical threats.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Multi-scale computer-aided design and photo-controlled macromolecular synthesis boosting uranium harvesting from seawater

By integrating multi-scale computational simulation with photo-regulated macromolecular synthesis, this study presents a new paradigm for smart design while customizing polymeric adsorbents for uranium harvesting from seawater. A dissipative particle dynamics (DPD) approach, combined with a molecular dynamics (MD) study, is performed to simulate the conformational dynamics and adsorption process of a model uranium grabber, i.e., PAO m -b-PPEGMA n , suggesting that the maximum adsorption capacity with atomic economy can be achieved with a preferred block ratio of 0.18. The designed polymers are synthesized using the PET-RAFT polymerization in a microfluidic platform, exhibiting a record high adsorption capacity of uranium (11.4 ± 1.2 mg/g) in real seawater within 28 days. This study offers an integrated perspective to quantitatively assess adsorption phenomena of polymers, bridging metal-ligand interactions at the molecular level with their spatial conformations at the mesoscopic level. The established protocol is generally adaptable for target-oriented development of more advanced polymers for broadened applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Enhancing the Functionality of a Hollow Scaffold Solid State Bioreactor via Computer Aided Design Optimization

The concern over greenhouse gases, methane (CH 4 ) and carbon dioxide (CO 2 ), is increasing rapidly. There have been strides to find solutions to this global issue but there is not a clear path to a successful end goal. The concentration of CH 4 and CO 2 in the atmosphere has increased significantly over the last 60 years, methane is a great source of concern due to its ability to trap a high amount of heat in the atmosphere. These greenhouse gases contribute to global warming which has caused changes in the environment, including the melting of ice caps, and altered weather patterns. Solutions for these pressing challenges have led to different avenues of methane mitigation one of which is the development of solid-state bioreactors. These reactors harness the power of biological species that have evolved to use methane as an energy source. The development and optimization of Hollow Scaffold Solid State Bioreactors (HS-SSBR) has become readily available due to the advancements in additive manufacturing technology and accessibility of computer aided design (CAD) software. With laboratory scale experiments, time and effort are of great importance. Enhancing the design of the HS-SSBR to create a more user-friendly interface, but also increase the functionality of the reactor. The reactor's design improvements focus on better dispersion of methane and circulation of media.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Quantum Computer-Aided Design: Digital Quantum Simulation of Quantum Processors

With the increasing size of quantum processors, submodules that constitute the processor hardware will become too large to accurately simulate on a classical computer. Therefore, one would soon have to fabricate and test each new design primitive and parameter choice in time-consuming coordination between design, fabrication, and experimental validation. Here we show how one can design and test the performance of next-generation quantum hardware—by using existing quantum computers. Focusing on superconducting transmon processors as a prominent hardware platform, we compute the static and dynamic properties of individual and coupled transmons. We show how the energy spectra of transmons can be obtained by variational hybrid quantum-classical algorithms that are well suited for near-term noisy quantum computers. In addition, single- and two-qubit gate simulations are demonstrated via Suzuki-Trotter decomposition. Our methods pave a promising way towards designing candidate quantum processors when the demands of calculating submodule properties exceed the capabilities of classical computing resources.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains

Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2023

Computationally Guided Design of Multiple Impurities Tolerant Electrode (Final Report)

The current project was based on a combined experimental and computational approach, which can help recommend better cathode materials under multiple impurities conditions. The PI will mainly take in charge of experimental and computational thermodynamics of the selected cathode materials for the SOFC applications under multiple impurities. While the co-PI will run the electrochemical tests of the cathodes recommended and eventually the long-term degradation tests. At the end of the project, a multiple tolerant cathode material based on the combined experimental and computational approach will be recommended and the reliability of the commonly used accelerated testing will be evaluated. It will address multiple impurities poisoning effect of SO2, CO2, Cr and H2O on the LSM, LSCF and LNO cathodes by identifying the formation of the detrimental secondary phases by XRD, SEM and TEM techniques. And further recommended cathode material will be subjected to electrochemical testing and the most promising ones will be applied to long-term tests. The hybrid approach the PI proposed will not only be applied to the design of multiple impurities tolerant cathodes but will also be considered in the future oxygen electrode applications in SOECs or reversible SOCs. This hybrid computational and experimental approach includes four sections: 1) Investigation of single impurity poisoning on LSM, LSCF and LNO cathodes in the presence of SO2, CO2, Cr. In this section, LSM, LSCF cathodes from FuelCellMaterials and LNO cathodes from Sol-Gel synthesis will be heat-treated in the above single impurity. And the formation of the secondary phases as well as the corresponding simulations will be cross compared, which shows good agreement between each other. Meanwhile, the accelerated testing approach will be evaluated in these systems compared with the previous published work to understand the reliability of the approach. 2) Investigation of multiple impurities poisoning on LSM, LSCF and LNO cathodes in the presence of Cr+H2O, SO2+Cr and SO2+Cr+H2O conditions. We have also applied these 3 candidate cathodes under these multiple impurities’ conditions and the long-term degradation mechanism of the multiple impurities will be understood with the help of the combined experimental and computational approach. Meanwhile, the synergistic effect of those impurities will be compared with the individual ones in the same cathode system to further reveal the actual operating conditions. 3) Electrochemical testing and polarization of the recommended cathode. We have demonstrated very low polarization resistance in LSCF (core)-LSM (shell) electrodes using MSD process and analyzed impedance spectra using DRT analysis and confirming that the low polarization resistance in LSM infiltrated MSD cells is due to reduction in polarization resistance associated with O2-adsorption process. 4). Long-term degradation testing. We have developed a versatile MSD-based process to deposit various continuous coatings onto porous scaffolds and established baseline for longer term Cr-impurity testing in future projects.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Computationally-Aided Design of a Small-Scale Radioactive Waste Glass Melter

To provide mission support to the Hanford Waste Immobilization and Treatment Plant for the vitrification of legacy nuclear tank waste, a reduced-scale vitrification pilot system is being designed to process simulated and actual radioactive tank wastes. The tank waste will be separated into high-level waste (HLW) and low-activity waste (LAW) fractions, where the majority by mass (~90%) is LAW and by activity (>95%) is HLW. The first tank waste to be processed at the WTP will be LAW. Since Hanford tank waste and the resultant melter feed compositions are known to vary widely, pilot-scale operations are essential to identify potential problems, provide needed data, confirm assumptions, and determine impacts to full-scale melters and off-gas systems from these different feeds. In addition, the reduced-scale melter system must be capable of quickly providing results to operations without the typically high costs of radioactive operations and provide an engineering platform in close proximity to local operations staff. The objective is to produce similar process conditions to those encountered in the full-scale LAW melters and minimize the volume of radioactive waste necessary for the evaluations. To this end, melter design features are being explored to increase production without significantly increasing surface area, melter glass volumes or compromising data quality. In support of these objectives, a set of computational fluid dynamic models have been developed to provide insight into the flow patterns within these small melters and evaluate design features to increase production without significantly increasing glass inventory. Computed velocities were evaluated at the interface between the cold cap and the molten glass pool and within the bulk glass pool. A method was developed to correlate results to an estimated melt rate and down-select design features that produce the highest gains.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Computationally-Aided Design of a Small-Scale Radioactive Waste Glass Melter

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in viscoelastic biomaterials exhibiting fluid-like properties under rest and low shear, but solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly in a manner similar to formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.

36 MATERIALS SCIENCE↗

DOE OSTI2024

De novo design of pH-responsive self-assembling helical protein filaments

Abstract Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2022

Design of protein-binding proteins from the target structure alone

The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder–target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein–protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Computationally Aided Design of a Small-Scale Waste-Glass Melter - 20452

To provide mission support to the WTP for the vitrification of legacy nuclear tank waste at the Hanford site, a reduced-scale vitrification pilot system is being designed to process simulated and actual radioactive tank wastes. The waste stored in underground tanks will be separated into HLW and LAW fractions, where the majority is LAW by mass (approximately 90%) and HLW by activity (greater than 95%). The first tank waste to be processed at the WTP will be LAW. Because Hanford tank waste and the resultant melter feed compositions are known to vary widely, pilot-scale operations are essential to identify potential problems, provide needed data, confirm assumptions, and determine impacts to full-scale melters and off-gas systems from these different feeds. In addition, the reduced-scale melter system must be capable of quickly providing results to operations without the typically high cost of full-scale radioactive operations and to provide an engineering platform in close proximity to local operations staff. The objectives of this computational modeling effort are to produce process conditions like those encountered in the WTP LAW melters and to minimize the volume of radioactive waste necessary for the evaluations. To this end, melter design features are being explored to increase production without significantly increasing surface area or melter-glass volumes or compromising data quality. In support of these objectives, a set of computational fluid dynamic models was developed to provide insight into the flow patterns within these small melters and evaluate design features to increase production without significantly increasing glass inventory. Computed velocities were evaluated at the interface between the cold cap and the molten-glass pool and within the bulk-glass pool. Since melt rate correlates with the velocity underneath the cold cap, this information can be used to select design features that produce the highest gains. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Final Report

This final progress report describes the development of the CANDO Software package at ThirdLaw Technologies LLC (TLT) towards a software platform that will be used by its subsidiary company ThirdLaw Molecular LLC (TLM) for the development of therapeutic Spiroligomer™ molecules. ThirdLaw Molecular LLC is 95% owned by ThirdLaw Technologies LLC. TLM is developing a new therapeutics platform based on Spiroligomer™ molecules and is currently funded by the Department of Defense, Defense Threat Reduction Agency (DOD/DTRA W15QKN209C004). Spiroligomer™ molecules are complex, highly-preorganized macromolecules with programmable three-dimensional shapes. Spiroligomer™ molecules are currently synthesized by TLM in the form of large (>880,000 member) DNA-encoded libraries and screened against dangerous bacteria and viruses as part of the DOD/DTRA project. The CANDO software package is being developed to enable the computational design of Spiroligomer™ molecules for the development of therapeutic and diagnostic molecules. Towards this end, over the period of the grant we implemented software algorithms and a user interface within CANDO to enable the computational design of Spiroligomer™ molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗