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DOE OSTI2023

Deploying synthetic coevolution and machine learning to engineer protein-protein interactions

Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain–affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. Further, the integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Synthetic overlapping genes stabilize genetic systems

Overlapping genes—wherein two different proteins are translated from alternative reading frames of the same DNA sequence—provide a means to stabilize an engineered gene by directly linking its evolutionary fate with that of an overlapping gene. However, creating overlapping gene pairs is challenging, as it requires redesigning both protein products to accommodate overlap constraints. Here, we present a new “overlapping, alternate-frame insertion” (OAFI) method for creating synthetic overlapping genes by inserting an “inner” gene, encoded in an alternate frame, into a flexible region of an “outer” gene. Using OAFI, we create new overlapping gene pairs of genetic reporters and bacterial toxins within an antibiotic resistance gene. We show that both the inner and outer genes retain function despite redesign, with translation of the inner gene influenced by its overlap position in the outer gene. Importantly, we show that, despite these inner gene sequences not contributing to outer gene function, selection for the outer gene alters the permitted inactivating mutations in the inner gene, and that overlapping toxins can restrict horizontal gene transfer of the antibiotic resistance gene. Overall, OAFI offers a versatile tool for synthetic biology, expanding the applications of overlapping genes in gene stabilization and biocontainment.

Biological and medical sciences↗

DOE OSTI2025

Revisiting synthetic lethality of Gcn5-related N-acetyltransferase (GNAT) family mutations in Haloferax volcanii

ABSTRACT Lysine acetylation is a post-translational modification that occurs in all domains of life, highlighting its evolutionary significance. Previous genome comparison identified three Gcn5-related N-acetyltransferase (GNAT) family members as lysine acetyltransferase homologs (Pat1, Pat2, and Elp3) and two deacetylase homologs (Sir2 and HdaI) in the halophilic archaeonHaloferax volcanii, withelp3andpat2proposed as a synthetic lethal gene pair. Here, we advance these findings by performing single and double mutagenesis ofelp3with thepat1andpat2lysine acetyltransferase gene homologs. Genome sequencing and PCR screens of these strains reveal successful generation of Δelp3,Δpat1Δelp3, and Δpat2Δelp3mutant strains. Although these mutant strains exhibited a reduced growth rate compared to the parent, they remained viable. Overall, this study provides genetic evidence thatelp3andpat2, while impacting cell growth, are not a synthetic lethal gene pair as previously reported. IMPORTANCE Here, we reveal by whole-genome sequencing that the GNAT family gene homologselp3andpat2can be deleted in the sameHaloferax volcaniistrain. Beyond the targeted deletions, minimal differences between the parent and Δelp3Δpat2mutant were observed, suggesting that suppressor mutations are not responsible for our ability to generate this double mutant strain. Elp3 and Pat2, thus, may not share as close a functional relationship as implied by earlier study. Our finding is significant as Elp3 is thought to function in acetylation in tRNA modification, while Pat2 likely functions in the lysine acetylation of proteins.

Microbiology↗

DOE OSTI2025

Structural features of 11 synthetic bacteriochlorins — comparisons with chlorins and porphyrins

As part of a program to develop the fundamental science of synthetic bacteriochlorins — analogues of Nature’s light-harvesting pigments in anoxygenic photosynthesis — 11 synthetic free base bacteriochlorins have been examined by single-crystal X-ray diffraction analysis. In each bacteriochlorin, each pyrroline ring contains a gem-dimethyl group to block adventitious (aerobic) dehydrogenation. The structural features of the bacteriochlorins (tetrahydroporphyrins) are compared with the less saturated counterparts, chlorins (dihydroporphyrins) and porphyrins. Only slight structural perturbation accrues due to the presence of the gem-dimethyl groups. Furthermore, the results presented herein may aid in understanding metal chelation processes and underpin the development of functional solid-state molecular assemblies.

X-ray diffraction↗

DOE OSTI2021

Models for synthetic data generation

The software includes a suite of probabilistic statistical/machine learning models that can generate discrete synthetic data. Each model is trained on a set of real (private) data and then it can be used to generate synthetic but statistically similar data. Once ready, the model can generate as many samples as we want. Finally, in addition to the actual models, the software includes code to process data, evaluate results (based on cross validation), and produce reports.

De Oliveira Sales, Ana Paula↗

DOE OSTI2024

Synthetic β-sheets mimicking fibrillar and oligomeric structures for evaluation of spectral X-ray scattering technique for biomarker quantification

Archetypical cross-β spines sharpen the boundary between functional and pathological proteins including β-amyloid, tau, α-synuclein and transthyretin are linked to many debilitating human neurodegenerative and non-neurodegenerative amyloidoses. An increased focus on development of pathogenic β-sheet specific fluid and imaging structural biomarkers and conformation-specific monoclonal antibodies in targeted therapies has been recently observed. Identification and quantification of pathogenic oligomers remain challenging for existing neuroimaging modalities. We propose two artificial β-sheets which can mimic the nanoscopic structural characteristics of pathogenic oligomers and fibrils for evaluating the performance of a label free, X-ray based biomarker detection and quantification technique. Highly similar structure with elliptical cross-section and parallel cross-β motif is observed among recombinant α-synuclein fibril, Aβ-42 fibril and artificial β-sheet fibrils. We then use these β-sheet models to assess the performance of spectral small angle X-ray scattering (sSAXS) technique for detecting β-sheet structures. sSAXS showed quantitatively accurate detection of antiparallel, cross-β artificial oligomers from a tissue mimicking environment and significant distinction between different oligomer packing densities such as diffuse and dense packings. The proposed synthetic β-sheet models mimicked the nanoscopic structural characteristics of β-sheets of fibrillar and oligomeric states of Aβ and α-synuclein based on the ATR-FTIR and SAXS data. The tunability of β-sheet proportions and shapes of structural motifs, and the low-cost of these β-sheet models can become useful test materials for evaluating β-sheet or amyloid specific biomarkers in a wide range of neurological diseases. By using the proposed synthetic β-sheet models, our study indicates that the sSAXS has potential to evaluate different stages of β-sheet-enriched structures including oligomers of pathogenic proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Spectroscopy of GR1 centers in synthetic diamonds

We report on the spectroscopic characterization, absorption saturation, and excited-state dynamics of GR1 centers in synthetic diamonds. The non-linear optical measurements reveal an efficient bleaching of the GR1 center’s ground level under ns-pulsed 633 nm excitation. The maxima of absorption and emission cross sections were estimated to be 4.5 × 10 −17 cm 2 and 9 × 10 −17 cm 2 at 630 nm and 780 nm, respectively. The radiative lifetime of the excited level was estimated to be 8.5 ns. The 658 nm probe kinetics uncovered relaxation of 1 T 2 excited level going predominantly to a metastable state with a lifetime of 220 μs. An induced absorption detected with the use of a highly concentrated diamond sample could be due to up-conversion and photoionization processes in additional impurity-vacancy center with absorption at the short-wavelength tail of GR1. The results presented here indicate that synthetic diamonds with GR1 centers could serve as near infrared gain media or passive Q-switchers for laser cavities over the 633–750 nm spectral range. Optimization of the center concentration and the crystal parameters are required to minimize the induced absorption at the lasing wavelengths.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Enabling AI in synthetic biology through Construction File specification

The Construction File (CF) specification establishes a standardized interface for molecular biology operations, laying a foundation for automation and enhanced efficiency in experiment design. It is implemented across three distinct software projects: PyDNA_CF_Simulator, a Python project featuring a ChatGPT plugin for interactive parsing and simulating experiments; ConstructionFileSimulator, a field-tested Java project that showcases 'Experiment' objects expressed as flat files; and C6-Tools, a JavaScript project integrated with Google Sheets via Apps Script, providing a user-friendly interface for authoring and simulation of CF. The CF specification not only standardizes and modularizes molecular biology operations but also promotes collaboration, automation, and reuse, significantly reducing potential errors. The potential integration of CF with artificial intelligence, particularly GPT-4, suggests innovative automation strategies for synthetic biology. While challenges such as token limits, data storage, and biosecurity remain, proposed solutions promise a way forward in harnessing AI for experiment design. This shift from human-driven design to AI-assisted workflows, steered by high-level objectives, charts a potential future path in synthetic biology, envisioning an environment where complexities are managed more effectively.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A Comparative Study of Deep Learning Models for Fracture and Pore Space Segmentation in Synthetic Fractured Digital Rocks

This study focuses on the comparative study of deep learning (DL) models for pore space and discrete fracture networks (DFNs) segmentation in synthetic fractured digital rocks, specifically targeting low-permeability rock formations, such as shale and tight sandstones. Accurate characterization of pore space and DFNs is critical for subsequent property analysis and fluid flow modeling. Four DL models, SegNet, U-Net, U-Net-wide, and nested U-Net (i.e., U-Net++), were trained, validated, and tested using synthetic datasets, including input and label image pairs with varying properties. The model performance was assessed regarding pixel-wise metrics, including the F1 score and pixel-wise difference maps. In addition, the physics-based metrics were considered for further analysis, including sample porosity and absolute permeability. Particularly, We first simulated the permeability of porous media containing only pore space and then simulated the permeability of porous media with DFNs added. The difference between these two values is used to quantify the connectivity of segmented DFNs, which is an important parameter for low-permeability rocks. The pixel-wise metrics showed that the nested U-Net model outperformed the rest of the DL models in pore space and DFNs segmentation, with the SegNet model exhibiting the second-best performance. Particularly, nested U-Net enhanced segmentation accuracy for challenging boundary pixels affected by partial volume effects. The U-Net-wide model achieved improved accuracy compared to the U-Net model, which indicated the influence of parameter numbers. Similarly, nested U-Net has the closest match to the ground truth of physics-based metrics, including the porosity of pore space and DFNs, and the permeability difference quantifying the connectivity of DFNs. The findings highlight the effectiveness of DL models, especially the U-Net++ model with nested architecture and redesigned skip connections, in accurately segmenting pore spaces and DFNs, which are crucial for pore-scale fluid flow and transport simulation in low-permeability rocks.

Wang, Hongsheng↗

DOE OSTI2020

Bistatic Synthetic Aperture Radar - Issues Analysis and Design

The physical separation of the transmitter from the receiver into perhaps separate flight vehicles (with separate flight paths) in a bistatic Synthetic Aperture radar system adds considerable complexity to an already complex system. Synchronization of waveform parameters and timing attributes become problematic, and notions of even the synthetic aperture itself take on a new level of abstractness. Consequently, a high-performance, fine-resolution, and reliable bistatic SAR system really needs to be engineered from the ground up, with tighter specifications on a number of parameters, and entirely new functionality in other areas. Nevertheless, such a bistatic SAR system appears viable.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Synthetic Aperture Radar Height of Focus

Synthetic Aperture Radar (SAR) projects a 3-D scene’s reflectivity into a 2-D image. In doing so, it generally focusses the image to a surface, usually a ground plane. Consequently, scatterers above or below the focal/ground plane typically exhibit some degree of distortion manifesting as a geometric distortion and misfocusing or smearing. Limits to acceptable misfocusing define a Height of Focus (HOF), analogous to Depth of Field in optical systems. This may be exacerbated by the radar’s flightpath during the synthetic aperture data collection. It might also be exploited for target height estimation and offer insight to other height estimation techniques.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Source Physics Experiment: Rock Valley Interferometric Synthetic Aperture RADAR Earthquake Detection Study

Seismic signals from 1993 show a series of magnitude (Mw) 3.7 or less seismic events in Rock Valley on the Nevada National Security Site (NNSS). Historic synthetic aperture radar images of that location were found that could provide interferometric synthetic aperture radar (InSAR) measures of the ground height during 1993. Given this historic SAR imagery, we explore answering the question if ground movement from the 1993 Rock Valley earthquake activity could be sensed by remote sensing means. Finding earthquake surface movement would assist in locating the Rock Valley fault and the 1993 earthquake hypocenter where the Source Physics Experiment Phase III series of experiments will be conducted. In this report, we show that InSAR can sense very small height differences, and for the European Radar Satellite-1 InSAR collections during 1992 and 1993 over Rock Valley earth surface movements were measured with 8 mm uplift and 12.5 mm subsidence over isolated areas. One of these earth movement areas coincides with an InSAR image pair coherence drop between March 5, 1993 and June 18, 1993. The coherence drop is over an approximately 13 square km area south southeast of Skull Mountain centered at 36° 43' 30" N latitude and 116° 05' 00" W longitude. Measured small surface movement and a loss of InSAR coherence may be caused by the series of earthquakes. The location of these InSAR detections may also coincide with water drainage or erosion displacement. There are no records to disambiguate the earthquake and erosion earth surface motion possibilities. Therefore, the InSAR findings of earth surface movement by InSAR are inconclusive.

58 GEOSCIENCES↗

DOE OSTI2022

Extension of Interferometric Synthetic Aperture Radar to Multiple Phase-Centers (Midyear LDRD Final Report – second edition)

This document contains the final report for the midyear LDRD titled "Extension of Interferometric Synthetic Aperture Radar to Multiple Phase-Centers." This report presents an overview of several methods for approaching the two-target in layover problem that exists in interferometric synthetic aperture radar systems. Simulation results for one of the methods are presented. In addition, a new direct approach is introduced.

42 ENGINEERING↗

DOE OSTI2023

Creation of Synthetic Electric Grids (SPP/MISO) Supporting PERFORM (Final Report)

Over the course of the project, two “realistic but not real” synthetic transmission-level grid models over the SPP-MISO and ERCOT footprints were created to provide more realistic data and increase the reliability and resiliency of the grids under a variety of scenarios. The synthetic ERCOT transmission grid is compatible with the distribution grid developed in collaboration with NREL. All generators are based on the EIA 860 data and a column with EIA plant code and Gen ID is added to generators of both grids so that they can be easily mapped. The improvements are also made to electric grids including N-1 contingencies with some remedial actions, improving the transmission lines to avoid lines in lakes, including an HVDC line to the SPP-MISO case, providing several generator parameters and their temporal constraints that were not included in EIA 860 form, generators’ cost curves, load offer curves, adding phase shifters and tap changers with impedance correction tables, adding reactive power control and partitioning the grids into active and reactive reserve zones and determine different types of the required reserve for each zone. Hourly load time series at the bus level were generated to create scenarios for solving power flow in different loading conditions. Weather measurement information and the models of renewable generators are used to directly include the impact of weather on the grids. Based on a variety of load and weather conditions the grids are improved to accommodate different conditions. The ERCOT 7k-bus grids were also modeled for the year 2030 with predicted improvements in renewable resources. The renewable generation model was also improved with historic weather data included. The impact of electric vehicles on the ERCOT grid is also modeled.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Quantifying the effect of 3D models on moment tensor results using synthetic data

Moment tensors provide vital information on seismic source properties for seismic events. Moment tensors require seismic wavespeed models to compute Green’s functions, which measure the impulse response between a given source and receiver. Traditionally, researchers have used one-dimensional velocity models to calculate Green’s functions since 1D Green’s functions are computationally cheap to compute. Local 1D velocity models can also accurately model waveforms at short distances (< 500 km). However, 1D velocity models do not account for lateral heterogeneity, which can cause significant misfit in tectonically complex regions such as the Middle East (Covellone and Savage, 2012). Green’s functions calculated using 3D seismic wavespeed models have been shown to perform better in tectonically complex regions (Covellone and Savage, 2012; Kintner and Modrak, 2022), so we are interested in quantifying the effect of considering 3D structure on moment tensor inversion results. The Middle East is an ideal study area for a synthetic moment tensor test for two reasons. Firstly, the Middle East is a tectonically complex region that has been heavily studied. Secondly, the Middle East has significant seismic activity throughout the region, but imperfect station coverage due to limited open data through large swaths of the domain. The tectonic complexity and uneven station coverage will test real-world performance even in a synthetic experiment.

58 GEOSCIENCES↗

DOE OSTI2025

Synthetic Pathways to gamma-Graphyne and Related Allotropes of Carbon

Graphynes, two-dimensional carbon lattices combining sp 1 and sp 2 hybridized atoms, were predicted theoretically more than three decades ago, but few structures have been realized to date. These carbons are believed to possess remarkable mechanical and electronic properties, including high charge carrier mobilities comparable to those in graphene (10 4 to 10 5 cm 2 V -1 s -1 ). Unlike graphene, certain graphynes are predicted to be intrinsic semiconductors. Among these intriguing structures, γ-graphyne stands out as the structurally simplest and most symmetric sp 1 /sp 2 lattice. γ-Graphyne was first theorized in 1987. In contrast with graphene, γ-graphyne will be a semiconductor with a small band gap suitable for fabrication of electronic devices. This solves one of the fundamental problems of carbon-based electronics, the necessity for inducing a band gap in graphene. γ-Graphyne has the potential to form the basis for the next generation of carbon-based electronics operating at speeds unattainable by traditional silicon chips. Unlike silicon, γ-graphyne is a direct band gap semiconductor, and it will feature exceptional strength comparable to that of other 2D carbon allotropes. Such combination of properties may enable a new generation of highly efficient, ultra-light and flexible solar cells. Despite being a potentially “magical” material, γ-graphyne remained synthetically elusive for over three decades. The primary goals of this project were: (1) Synthesis of bulk γ-graphyne phases through solution-phase 2D polymerizations; (2) Experimental exploration of the physical and chemical properties of γ-graphyne; and (3) Mechanistic and theoretical studies of the novel chemical transformations developed in Goal 1. Common pyrolytic and vapor-deposition methodologies used for the synthesis of graphitic allotropes are unsuitable for graphyne and other sp 1 -contaning structures, as acetylenes readily convert to graphene and amorphous carbon at high temperatures. In contrast, this proposal is based on solution-based 2D polymerization. The major advantages of this approach over the traditional high temperature techniques are the potential to adjust the structure of the material with atomic precision, and the possibility of using structurally complex and relatively fragile repeat units. The outcomes of this research can revolutionize carbon nanotechnology, expanding the field’s structural toolbox beyond primarily graphitic and benzenoid structures. Understanding the chemistry of sp 1 carbon allotropes can lead to entirely new classes of structures with unique properties, including graphyne ribbons, nanotubes, quantum dots, and heterostructures with other 2D materials. Furthermore, the development of reliable and robust synthetic pathways towards periodic covalent molecular sheets with atomically precise structures shall have a profound impact on chemistry and materials science.

2D polymerization↗

DOE OSTI2025

Propulsion of synthetic protocells and coacervates driven by biochemical catalysis

An important area in the design of biomolecular materials is the mimicry of cellular function through the assembly of molecular components into synthetic cells, or protocells. Through compartmentalization and subsequent evolution, biological cells have achieved the goals of specificity, amplification, and response. By assembling cell-like structures that mimic the organization and size of a natural cell but that incorporate novel components and respond to synthetic triggers, we can extend their capabilities beyond what is currently achievable in biology. For applications in energy, these include the ability to convert chemical to mechanical energy, and to enable the response of sensors and responders once a threshold has been reached. This technical report summarizes progress made on this project as of Dec 31, 2023.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Synthetic Infrasound Data for Machine Learning Detectors

Synthetic data is a powerful tool to generate large amounts of training data for machine learning models. The methods outlined in this report will be used to retrain the deep learning classifier for increased accuracy. Synthetic data will be useful to address the natural class imbalance between the different categories in the original ML work. Additionally, these tools will be applied for a variety of signal analysis methods that would use signals with a known signal-to-noise ratio for validation and testing.

58 GEOSCIENCES↗