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DOE OSTI2020

Technology Transfer Excellence Award NTXBio

While a scientist at Los Alamos National Laboratory, Dr. Alex Koglin developed two compounds to create a better vaccine for Tuberculosis (TB). In 2015, Dr. Koglin took an entrepreneurial leave of absence from the Laboratory to start NTXBio, LLC. His objective was to develop and commercialize a TB vaccine based on two compounds he created while a scientist at the Los Alamos. In 2018, a total of 1.5 million people died from TB. According to the World Health Organization TB is the leading infectious disease resulting in death worldwide. Approximately one-quarter of the world’s population is infected with mycobacterium tuberculosis, the bacteria that causes TB. Dr. Koglin non-exclusively licensed the two compounds from Los Alamos and began further development of the technology in collaboration with the Government of South Africa and universities to address the need for a vaccine to prevent TB. In their research and development of the compounds there was no evidence of cross resistance between other bacteria and the bacteria that causes TB. The compounds were tested in mouse models and demonstrated they can treat TB. Also, the tests have not shown any of the massive side effects that the current treatments for TB are showing. The company started production of the compounds using current manufacturing processes. Using these processes NTXBio could not produce the compounds at a reasonable price to be available for patients in third world countries. The company shifted to developing a new methodology “invitro synthetic biology” that can increase the production of these compounds and other vaccine molecules in a more affordable way. Dr. Koglin’s startup NTXBio is working to positively influence and secure the world vaccine supply by developing rapid on-demand production of the full spectrum of protein vaccines. Starting with the TB vaccine and advancing to common childhood vaccines, emergency and experimental vaccines such as those needed for COVID-19. NTXBio is capable of accelerated prototyping and manufacturing with increased purity and greater stability while reducing both cost and production time. The newly developed production methodology can be applied to not only the TB compounds licensed from Los Alamos, but also to their compounds that advance vaccine production for other diseases. Their technology produces vaccines fast enough to be fully deployable in areas without the need of specialized storage conditions and response times.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2018

Evaluation of Modeling NO2 Concentrations Driven by Satellite-Derived and Bottom-Up Emission Inventories Using In-Situ Measurements Over China

Chemical transport models together with emission inventories are widely used to simulate NO2 concentrations over China, but validation of the simulations with in situ measurements has been extremely limited. Here we use ground measurements obtained from the air quality monitoring network recently developed by the Ministry of Environmental Protection of China to validate modeling surface NO2 concentrations from the CHIMERE regional chemical transport model driven by the satellite-derived DECSO and the bottom-up MIX emission inventories. We applied a correction factor to the observations to account for the interferences of other oxidized nitrogen compounds (NOz), based on the modeled ratio of NO2 to NOz. The model accurately reproduces the spatial variability in NO2 from in situ measurements, with a spatial correlation coefficient of over 0.7 for simulations based on both inventories. A negative and positive bias is found for the simulation with the DECSO (slopeD0.74 and 0.64 for the daily mean and daytime only) and the MIX (slopeD1.3 and 1.1) inventories, respectively, suggesting an underestimation and overestimation of NOx emissions from corresponding inventories. The bias between observed and modeled concentrations is reduced, with the slope dropping from 1.3 to 1.0 when the spatial distribution of NOx emissions in the DECSO inventory is applied as the spatial proxy for the MIX inventory, which suggests an improvement of the distribution of emissions between urban and suburban or rural areas in the DECSO inventory compared to that used in the bottom-up inventory. A rough estimate indicates that the observed concentrations, from sites predominantly placed in the populated urban areas, may be 10-40% higher than the corresponding model grid cell mean. This reduces the estimate of the negative bias of the DECSO-based simulation to the range of -30 to 0% on average and more firmly establishes that the MIX inventory is biased high over major cities. The performance of the model is comparable over seasons, with a slightly worse spatial correlation in summer due to the difficulties in resolving the more active NOx photochemistry and larger concentration gradients in summer by the model. In addition, the model well captures the daytime diurnal cycle but shows more significant disagreement between simulations and measurements during nighttime, which likely produces a positive model bias of about 15% in the daily mean concentrations. This is most likely related to the uncertainty in vertical mixing in the model at night.

NO2 modelling↗

DOE OSTI2020

Whose Gas is it anyway? Differentiating the Source of a Large Soil Vapor Plume beneath Two Adjacent Waste Sites - 20487

DOE contractor CH2M Hill Plateau Remediation Company is currently responsible for conducting groundwater contamination monitoring at several RCRA treatment, storage, and disposal units located on the Hanford Site in Richland, Washington State. The Nonradioactive Dangerous Waste Landfill treatment, storage, and disposal unit presents a distinct groundwater monitoring problem because of a large multi-contaminant soil vapor plume beneath it that is a likely source of low-level volatile organic compound groundwater contamination. Adjacent to Nonradioactive Dangerous Waste Landfill is the Solid Waste Landfill. Volatile organic compounds are inventory components of both the Nonradioactive Dangerous Waste Landfill and the Solid Waste Landfill. Therefore, it is possible that both sites could be contributing to the soil vapor plume. For regulatory purposes, it is important to differentiate which site is the primary contributor of volatile organic compounds to the plume. An approach was developed to identify the primary volatile organic compound source of the soil vapor plume beneath Nonradioactive Dangerous Waste Landfill and Solid Waste Landfill. The site conceptual model hypothesis of vapor-phase volatile organic compound transport to the dissolved phase in groundwater was tested by a simple mathematical model of vapor/liquid equilibrium concentrations at the groundwater/air interface. Once it was shown that vapor-phase volatile organic compound transport to groundwater was a valid conceptual model for Nonradioactive Dangerous Waste Landfill and Solid Waste Landfill, spatial and statistical methods were used to determine the primary site contributing to the majority of volatile organic compounds to the soil vapor plume. Average groundwater chloroform, tetrachloroethene, and trichloroethene concentrations from Nonradioactive Dangerous Waste Landfill and Solid Waste Landfill monitoring network wells were plotted on maps of the facilities and immediate vicinities and compared to soil vapor sampling probe locations. Principal component analysis and mixing ratios were used to identify source contributions of each treatment, storage, and disposal unit to the plume. Results of the vapor/liquid equilibrium concentrations mathematical model showed that transport phenomena outweigh steady-state equilibria. Estimated vapor/liquid equilibrium concentrations were considerably lower than soil vapor measurements. The results indicate that dynamic vadose zone and groundwater factors such as decreased vapor concentrations with depth, vapor dilution from dispersion in the vadose zone, and advective and diffusional volatile organic compound dilution in groundwater result in groundwater volatile organic compound concentrations much less than would be measured under steady-state equilibrium conditions. Site source contribution differentiation by principal component analysis and mixing ratios was inconclusive using actual soil gas data because of the similarity in concentration values in both datasets for Nonradioactive Dangerous Waste Landfill and Solid Waste Landfill. Similar data populations suggest mixing of the vapor contributions from both sites by dispersion through the soil matrix pore spaces. However, when groundwater volatile organic compound data were compared between the Nonradioactive Dangerous Waste Landfill and Solid Waste Landfill monitoring networks, Solid Waste Landfill mean concentrations were higher, suggesting more vapor-phase volatile organic compound transport to groundwater at those locations. Simulated volatile organic compound soil vapor and groundwater datasets created to test the methods developed for this study show that the method can be successful in source differentiation when significantly different datasets are compared. This paper will describe a method of testing a conceptual model for vapor-phase contaminant transport to groundwater and for differentiating site sources of contaminants comprising a mixed-constituent soil vapor plume. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

NASA NTRS1989

Numerical simulations of the seasonal/latitudinal variations of atomic oxygen and nitric oxide in the lower thermosphere and mesosphere

A 2-Dimensional zonally-averaged thermospheric model and the global University College London (UCL) thermospheric model have been used to investigate the seasonal, solar activity and geomagnetic variation of atomic oxygen and nitric oxide. The 2-dimensional model includes detailed oxygen and nitrogen chemistry, with appropriate completion of the energy equation, by adding the thermal infrared cooling by O and NO. This solution includes solar and auroral production of odd nitrogen compounds and metastable species. This model has been used for three investigations; firstly, to study the interactions between atmospheric dynamics and minor species transport and density; secondly, to examine the seasonal variations of atomic oxygen and nitric oxide within the upper mesosphere and thermosphere and their response to solar and geomagnetic activity variations; thirdly, to study the factor of 7 to 8 peak nitric oxide density increase as solar F sub 10.7 cm flux increases from 70 to 240 reported from the Solar Mesospheric Explorer. Auroral production of NO is shown to be the dominant source at high latitudes, generating peak NO densities a factor of 10 greater than typical number densities at low latitudes. At low latitudes, the predicted variation of the peak NO density, near 110 km, with the solar F sub 10.7 cm flux is rather smaller than is observed. This is most likely due to an overestimate of the soft X-ray flux at low solar activity, for times of extremely low support number, as occurred in June 1986. As observed on pressure levels, the variation of O density is small. The global circulation during solstice and periods of elevated geomagnetic activity causes depletion of O in regions of upwelling, and enhancements in regions of downwelling.

Rees, D.↗

DOE OSTI2023

Consideration of memory of spin and parity in the fissioning compound nucleus by applying the Hauser-Feshbach fission fragment decay model to photonuclear reactions

Prompt and β-delayed fission observables, such as the average number of prompt and delayed neutrons, the independent and cumulative fission product yields, and the prompt γ-ray energy spectra for the photonuclear reactions on 235,238 U and 239 Pu, are calculated with the Hauser-Feshbach fission fragment decay (HF 3 ⁢D) model and compared with available experimental data. Further, in the analysis of neutron-induced fission reactions to the case of photo-induced fission, an excellent reproduction of the delayed neutron yields supports a traditional assumption that the photo fission might be similar to the neutron-induced fission at the same excitation energies regardless of the spin and parity of the fissioning systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Linking Internal Dosimetries of the Propyl Metabolic Series in Rats and Humans Using Physiologically Based Pharmacokinetic (PBPK) Modeling

The metabolic series approach has successfully linked internal dosimetries of metabolically related compounds reducing cost and time for chemical risk assessments. Here, we developed a physiologically based pharmacokinetic (PBPK) model in rats and humans for the propyl metabolic series including propyl acetate, 1-propanol, propionaldehyde, and propionic acid. Manufacturers use these compounds as organic solvents and intermediates during chemical synthesis. Public exposures can occur through using consumer products containing propyl compounds like cosmetics, aerosol sprays, or foods. To develop the PBPK model, we measured in vitro metabolism of propyl acetate in blood and liver S9 fractions. We measured concentrations of propyl compounds in blood following intravenous (iv) infusion of 13C-propanol or 13C-propionic acid and closed chamber inhalation exposures to propyl acetate or propanol in rats. Using these studies and other published data, we modified an existing PBPK model for the butyl metabolic series to simulate time course concentrations of propyl compounds in rats and humans. Consistent with measured in vitro and in vivo data, the optimized propyl series model predicts rapid clearance of propyl acetate, higher concentrations of propanol in blood from propyl acetate inhalation compared to propanol inhalation, and low concentrations of propionic acid in blood from exposures to propyl acetate or propanol. Regulators can use this model as a tool for propyl compound risk assessment by linking internal dosimetries under various exposure scenarios.

Smith, Jordan N.↗

DOE OSTI2025

LinkML: an open data modeling framework

Background Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, nonstandardized spreadsheets, or data repositories. This lack of structure challenges interoperability, making data integration, validation, and reuse difficult. Findings LinkML (Linked Data Modeling Language) is an open framework that simplifies the process of authoring, validating, and sharing data. LinkML can describe a range of data structures, from flat, list-based models to complex, interrelated, and normalized models that utilize polymorphism and compound inheritance. It offers an approachable syntax that is not tied to any one technical architecture and can be integrated seamlessly with many existing frameworks. The LinkML syntax provides a standard way to describe schemas, classes, and relationships, allowing modelers to build well-defined, stable, and optionally ontology-aligned data structures. Once defined, LinkML schemas may be imported into other LinkML schemas. These key features make LinkML an accessible platform for interdisciplinary collaboration and a reliable way to define and share data semantics. Conclusions LinkML helps reduce heterogeneity, complexity, and the proliferation of single-use data models while simultaneously enabling compliance with FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. LinkML has seen increasing adoption in various fields, including biology, chemistry, biomedicine, microbiome research, finance, electrical engineering, transportation, and commercial software development. In short, LinkML makes implicit models explicitly computable and allows data to be standardized at their origin. LinkML documentation and code are available at https://linkml.io/.

AI-ready data↗

DOE OSTI2023

Machine learning predictions of high-Curie-temperature materials

Technologies that function at room temperature often require magnets with a high Curie temperature, $T$ C , and can be improved with better materials. Discovering magnetic materials with a substantial $T$ C is challenging because of the large number of candidates and the cost of fabricating and testing them. Using the two largest known datasets of experimental Curie temperatures, we develop machine-learning models to make rapid $T$ C predictions solely based on the chemical composition of a material. We train a random-forest model and a k -NN one and predict on an initial dataset of over 2500 materials and then validate the model on a new dataset containing over 3000 entries. The accuracy is compared for multiple compounds' representations (“descriptors”) and regression approaches. A random-forest model provides the most accurate predictions and is not improved by dimensionality reduction or by using more complex descriptors based on atomic properties. Further, a random-forest model trained on a combination of both datasets shows that cobalt-rich and iron-rich materials have the highest Curie temperatures for all binary and ternary compounds. An analysis of the model reveals systematic error that causes the model to over-predict low-$T$ C materials and under-predict high-$T$ C materials. For exhaustive searches to find new high-$T$ C materials, analysis of the learning rate suggests either that much more data is needed or that more efficient descriptors are necessary.

36 MATERIALS SCIENCE↗

NASA NTRS2000

Astrophysical Constraints on Chondrule Formation Models

Three petrologic constraints, heating and cooling timescales and the frequency of compound chondrules, are applied to the shock wave and lightning models of chondrule formation. Shocks fit the constraints well; lightning requires high gas densities.

Desch, S. J.↗

DOE OSTI2022

In Silico Prediction of the Toxicity of Nitroaromatic Compounds: Application of Ensemble Learning QSAR Approach

In this work, a dataset of more than 200 nitroaromatic compounds is used to develop Quantitative Structure–Activity Relationship (QSAR) models for the estimation of in vivo toxicity based on 50% lethal dose to rats (LD 50 ). An initial set of 4885 molecular descriptors was generated and applied to build Support Vector Regression (SVR) models. The best two SVR models, SVR_A and SVR_B, were selected to build an Ensemble Model by means of Multiple Linear Regression (MLR). The obtained Ensemble Model showed improved performance over the base SVR models in the training set (R 2 = 0.88), validation set (R 2 = 0.95), and true external test set (R 2 = 0.92). The models were also internally validated by 5-fold cross-validation and Y-scrambling experiments, showing that the models have high levels of goodness-of-fit, robustness and predictivity. The contribution of descriptors to the toxicity in the models was assessed using the Accumulated Local Effect (ALE) technique. The proposed approach provides an important tool to assess toxicity of nitroaromatic compounds, based on the ensemble QSAR model and the structural relationship to toxicity by analyzed contribution of the involved descriptors.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Uncertainty characterization in a coupled human-natural system: Modeling agricultural adaptation in the Great Lakes Region

The Great Lakes Region's water quality and ecological health are threatened by the export of nutrients from agricultural lands, which causes eutrophication, hypoxia, and destructive algal blooms. The intensification of hydrologic cycles brought about by climate change is expected to exacerbate nutrient loading in the region, and, at the same time, agricultural adaptation to changing conditions is also expected to affect loading through shifting amounts and timing of fertilization. Quantifying these future effects and their interactions necessitates modeling both the human and natural processes as a coupled system, by pairing land use and agricultural management with hydrologic modeling. At the same time, compounding uncertainties arising from the complex interactions in both systems significantly limit our predictive understanding of the region's impacts. This study utilizes the Soil and Water Assessment Tool (SWAT), developed for simulating the impact of various farmer decisions on watershed functions in Western Lake Erie watersheds, and an under-development agent-based model (ABM) for agricultural management decisions. The aim of this study is to use global sensitivity analysis on the coupled ABM and SWAT models to quantify how uncertainty in both models interactively affects nutrient loading. To do so, we will conduct Sobol sensitivity analysis experiments at different levels of coupling assumptions to quantify how various uncertain factors (e.g., soil moisture and crop choice) and their interactions affect our estimates of nutrient loading. The results of this analysis will allow us to quantify how complex interactions and dependencies between both systems amplify the effect of uncertainties. Insights gained from this study will have broader implications for modeling the adaptive co-evolution of human and natural systems under climate change and can inform effective management of nutrient loading in the Great Lakes Region.

Climate Change↗

NASA NTRS1999

Prebiotic Evolution of Nitrogen Compounds

Support from this four year grant has funded our research on two general problems. One involves attempts to model the abiotic formation of simple source compounds for functional biomolecules, their concentration from dilute state in the hydrosphere and, in several cases, surface induced reactions to form precursor monomers for bioactive end products (refs. 1-5). Because of the pervasiveness and antiquity of phosphate based biochemistry and the catalytic activity of RNA we have exploring the hypothesis of an RNA World as an early stage in the emergence of life. This concept is now rather generally considered, but has been questioned due to the earlier lack of an experimentally demonstrated successful scheme for the spontaneous formation of ribose phosphate, the key backbone molecule in RNA. That impediment has now been removed. This has been achieved by demonstrating probable sources of activated (condensed) highly soluble and strongly sorbed phosphates in nature (Refs. 1,2) and effective condensation of aldehyde phosphates to form ribose phosphate in high yield (ref.6), thereby placing the RNA World concept on a somewhat safer experimental footing. Like all work in this field these experiments are oversimplifications that largely ignore competing side reactions with other compounds expected to be present. None the less our choice of experimental conditions aim at selective processes that eliminate interfering reactions. We have also sought to narrow the credibility gap by simulating geophysically and geochemically plausible conditions surrounding the putative prebiotic reactions.

Arrhenius, G.↗

DOE OSTI2021

Kinetic modeling of anaerobic degradation of plant-derived aromatic mixtures by Rhodopseudomonas palustris

Abstract Rhodopseudomonas palustris is a model microorganism for studying the anaerobic metabolism of aromatic compounds. While it is well documented which aromatics can serve as sole organic carbon sources, co-metabolism of other aromatics is poorly understood. This study used kinetic modeling to analyze the simultaneous degradation of aromatic compounds present in corn stover hydrolysates and model the co-metabolism of aromatics not known to support growth of R. palustris as sole organic substrates. The simulation predicted that p -coumaroyl amide and feruloyl amide were hydrolyzed to p -coumaric acid and ferulic acid, respectively, and further transformed via p -coumaroyl-CoA and feruloyl-CoA. The modeling also suggested that metabolism of p -hydroxyphenyl aromatics was slowed by substrate inhibition, whereas the transformation of guaiacyl aromatics was inhibited by their p -hydroxyphenyl counterparts. It also predicted that substrate channeling may occur during degradation of p -coumaroyl-CoA and feruloyl-CoA, resulting in no detectable accumulation of p -hydroxybenzaldehyde and vanillin, during the transformation of these CoA ligated compounds to p- hydroxybenzoic acid and vanillic acid, respectively. While the simulation correctly represented the known transformation of p -hydroxybenzoic acid via the benzoyl-CoA pathway, it also suggested co-metabolism of vanillic acid and syringic acid, which are known not to serve as photoheterotrophic growth substrate for R. palustris .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Rethinking 𝛼−RuCl 3 : Parameters, models, and phase diagram

RuCl 3 was likely the first ever deliberately synthesized ruthenium compound, following the discovery of the 44 Ru element in 1844. For a long time it was known as an oxidation catalyst, with its physical properties being discrepant and confusing, until a decade ago when its allotropic form 𝛼−RuCl 3 rose to exceptional prominence. This “rediscovery” of 𝛼−RuCl 3 has not only reshaped the hunt for a material manifestation of the Kitaev spin liquid, but it has opened the floodgates of theoretical and experimental research in the many unusual phases and excitations that the anisotropic-exchange magnets as a class of compounds have to offer. Given its importance for the field of Kitaev materials, it is astonishing that the low-energy spin model that describes this compound and its possible proximity to the much-desired spin-liquid state is still a subject of significant debate ten years later. In the present study, we argue that the existing key phenomenological observations put strong natural constraints on the effective microscopic spin model of 𝛼−RuCl 3 , and specifically on its spin-orbit-induced anisotropic-exchange parameters that are responsible for the nontrivial physical properties of this material. These constraints allow one to focus on the relevant region of the multidimensional phase diagram of the 𝛼−RuCl 3 model, suggest an intuitive description of it via a different parametrization of the exchange matrix, offer a unifying view on the earlier assessments of its parameters, and bring closer together several approaches to the derivation of anisotropic-exchange models. We explore extended phase diagrams relevant to the 𝛼−RuCl 3 parameter space using quasiclassical, Luttinger-Tisza, exact diagonalization, and density-matrix renormalization-group methods, demonstrating a remarkably close quantitative accord between them on the general structure and hierarchy of the phases, with the zigzag, ferromagnetic, and incommensurate phases that are proximate to each other. As a result, one of the highlights is the detailed agreement on the nature of the incommensurate phases that realize two distinct counterrotating helical states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Roadmap for the future of extreme wildfire events

Background Extreme wildfire events (EWEs) represent a growing threat globally, posing substantial risks to ecosystems, human communities, and infrastructure. Despite increased recognition of their ecological, social, and economic significance, current definitions of EWEs vary widely, reflecting disciplinary biases and regional contexts. This article emerges from an interdisciplinary workshop convened to reassess and refine the definition of EWEs, examine their impacts across ecological and social dimensions, and identify critical knowledge gaps impeding our understanding of these infrequent but important events. Results Our synthesis highlights significant limitations with existing definitions, particularly their reliance on subjective thresholds and their emphasis on extreme fire behavior alone. EWEs encompass a spectrum of complex, multi-dimensional phenomena that extend beyond immediate biophysical characteristics to include cumulative social, economic, and ecological impacts. These impacts often manifest over extended timeframes and include hazardous environmental contamination, severe geomorphic disturbances, ecosystem transformations, and unintended consequences of post-fire management actions. Current wildfire modeling frameworks inadequately capture these compounding factors, particularly the interactions among social systems, ecological conditions, and extreme fire behavior. To overcome these issues, we advocate for an interdisciplinary and context-sensitive approach to defining and studying EWEs. This revised definition emphasizes wildfires exhibiting anomalies in fire behavior, ecological outcomes, or social impacts relative to historically observed baselines, accommodating variability across different geographic regions and ecological settings. Conclusions Adopting an interdisciplinary framework that integrates biophysical and social sciences will enhance the predictive capability of wildfire models and improve resilience planning and response strategies. Filling identified knowledge gaps—such as limited high-quality empirical fire behavior data and insufficient integration of social dynamics into modeling—will better prepare communities and ecosystems to cope with and adapt to EWEs. This inclusive approach underscores the necessity for collaboration across disciplines and sectors, essential to managing extreme wildfires in an era of increasing climatic and ecological uncertainty.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1994

Contrast Gain Control Model Fits Masking Data

We studied the fit of a contrast gain control model to data of Foley (JOSA 1994), consisting of thresholds for a Gabor patch masked by gratings of various orientations, or by compounds of two orientations. Our general model includes models of Foley and Teo & Heeger (IEEE 1994). Our specific model used a bank of Gabor filters with octave bandwidths at 8 orientations. Excitatory and inhibitory nonlinearities were power functions with exponents of 2.4 and 2. Inhibitory pooling was broad in orientation, but narrow in spatial frequency and space. Minkowski pooling used an exponent of 4. All of the data for observer KMF were well fit by the model. We have developed a contrast gain control model that fits masking data. Unlike Foley's, our model accepts images as inputs. Unlike Teo & Heeger's, our model did not require multiple channels for different dynamic ranges.

Watson, Andrew B.↗

NASA NTRS1990

Energetics of molecular-beam epitaxy models

The removal energies of constituent atoms from various unreconstructed semiconductor surfaces are calculated using a Green function method. An efficient difference-equation approach within the second-neighbor tight-binding model is employed. For a compound AB, binding energies for the A and B atoms on the (111), (-1 -1 -1), (100), and (110) surfaces are calculated. Analyses are made of the energy to remove an atom from the nearly full surface and from the nearly empty surface. Results are presented for Si, GaAs, CdTe, and HgTe; and the surface sublimation energies are found to depend on surface coverage and do not display a simple linear relationship to the number of bonds broken, as is often assumed in modeling growth by MBE.

Krishnamurthy, Srinivasan↗

DOE OSTI2025

SLAB: simultaneous labeling and binding affinity prediction for protein–ligand structures

Machine learning models are often used as scoring functions to predict the binding affinity of a protein–ligand complex. These models are trained with limited amounts of data with experimentally measured binding affinity values. A large number of compounds are labeled inactive through single-concentration screens without measuring binding affinities. These inactive compounds, along with the active ones, can be used to train binary classification models, while regression models are trained using compounds with binding affinities only. However, the classification and regression tasks are often handled separately, without sharing the learned feature representations. In this paper, we propose a novel model architecture that jointly performs regression and classification objectives, aiming to maximize data utilization and improve predictive performance by leveraging two complementary tasks. In our setup, the regression yields the binding affinity, whereas the classification task yields the label as active or inactive. We demonstrate our method using PDBbind, the standard 3D structure database, as well as a dataset of flavivirus protease compounds with binding affinity data. Our experiments show that the new joint training strategy improves the accuracy of the model, increasing applicability in various practical drug screening scenarios.

Biological and medical sciences↗