Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “affinity”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Development of Mixed Matrix Membranes by Using NH 2 ‐Functionalized UiO‐66 and [APTMS][AC] Ionic Liquid for the Separation of CO 2

The ever‐escalating CO 2 concentration in the atmosphere calls for accelerated development and deployment of carbon capture processes to reduce emissions. Mixed matrix membranes (MMMs), which are fabricated by incorporating the beneficial properties of highly selective inorganic fillers into a polymer matrix, have exhibited significant progress and the ability to enhance the performance of a membrane for gas separation. In this research, an amine‐based ionic liquid (IL) [APTMS][AC] was prepared, which has greater CO 2 affinity and greater solubility due to its amine moiety. The metal–organic framework (MOF) UiO‐66 with a multidimensional crystalline structure was used as a filler due to its appropriate porosity and tunable properties, and it was functionalized with NH 2 . MOFs were further modified with an IL to prepare UiO‐66@IL and UiO‐66‐NH 2 @IL, and MMMs incorporating each MOF were fabricated with the polymer Pebax‐1657. All the prepared membranes and MOFs were characterized to predict their separation efficiency. Several characterization techniques, namely, FTIR spectroscopy, XRD, and SEM, were used to successfully synthesize UiO‐66@IL and UiO‐66‐NH 2 @IL composites and confirmed proper dispersion and excellent polymer‒filler compatibility at filler loadings ranging from 0 to 30 wt.%. The separation performances were investigated, and the results showed that the incorporation of RTIL with the highly crystalline structure and large surface area of UiO‐66 enhanced the separation efficiency of the membrane. The permeability of CO 2 for all fabricated membranes continuously increased with increasing filler concentration, wherein the permeability was comparatively high for the UiO‐66‐NH 2 MMMs. The CO 2 /CH 4 selectivity improved by 35%, 54%, and 60%, respectively, for UiO‐66@IL, UiO‐66‐NH 2 , and UiO‐66‐NH 2 @IL MMMs compared to simple UiO‐66 for CO 2 /CH 4 and by 28%, 36%, and 63%, respectively, for CO 2 /N 2 , with an increase in filler loading in the MMMs.

Khalid, Hafiza Mamoona (ORCID:0009000135165855)↗
DOE OSTI2021

radkit v1.2

The radkit software suite (python) consists of three primary libraries: stark, trajan, and curie. The trajan library provides the tools to analyze and manipulate data from lidar and inertial measurement unit (IMU) devices as well as trajectories from algorithms such as simultaneous localization and mapping (SLAM). These components allow reading and writing standard data formats, performing rigid affine transformations, discretizing three-dimensional space, and visualizing data products. The curie library comprises a standard set of object-oriented tools for radiation data and analysis in the following modules: (1) listmode and binmode data classes with methods for manipulation, plotting, slicing and file IO; (2) radiological/nuclear source detection/identification analysis results; (3) source encounters of correlated analyses and (4) energy-dependent angular detector response functions. The stark package provides low-level tools that are leveraged by both curie and trajan. The tools are flexible for offline analysis as well as performant for real-time integrations. The radkit libraries have associated Robot Operating System packages for use in real-time and robotic systems.

Joshi, Tenzing↗
DOE OSTI2021

HSolo v.1.0

SAND2021-11023 O HSolo is a library for estimating similarity, affine, projective homographies from matches produced by image feature detectors such as SURF and SIFT. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Gonzales, Antonio↗
DOE OSTI2023

3D_MolGNN_RL

3D-MolGNNRL, couples reinforcement learning (RL) to a deep generative model based on 3D-Scaffold to generate target candidates specific to a protein pocket building up atom by atom from the core scaffold. 3D-MolGNNRL provides an efficient way to optimize key features within a protein pocket using a parallel graph neural network model. The agent learns to build molecules in 3D space while optimizing the binding affinity, potency, and synthetic accessibility of the candidates generated for the SARS-CoV-2 Main protease

Kumar, Neeraj↗
DOE OSTI2024

BIORAD

Machine learning prediction of protein-protein binding affinity

Gans, Jason [Los Alamos National Laboratory]↗
DOE OSTI2025

Maskman

SAND2025-04369O Maskman is a user-friendly tool designed to create hex masks, which are essential for optimizing application performance in high-performance computing environments. By converting a list of integers into binary and then hex masks, Maskman simplifies the process of setting application affinity. This ensures that software runs efficiently on specific nodes within a computing cluster. Ideal for researchers and developers, Maskman streamlines the preparation of inputs for HPC schedulers, enhancing resource management and improving overall system performance. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Pase, Douglas [Sandia National Lab. (SNL-CA), Live↗
DOE OSTI2025

fast3

Code to train neural network models for binding affinity prediction

Kim, Hyojin [Lawrence Livermore National Laborator↗
DOE OSTI2026

radkit base v1.6

The radkit (base) software suite (python) consists of three primary libraries: stark, trajan, and curie. The trajan library provides the tools to analyze and manipulate data from lidar and inertial measurement unit (IMU) devices, cameras, as well as trajectories from algorithms such as simultaneous localization and mapping (SLAM). These components allow reading and writing standard data formats, performing rigid affine transformations, discretizing three-dimensional space, and visualizing data products. The curie library comprises a standard set of object-oriented tools for radiation data and analysis in the following modules: (1) listmode and binmode data classes with methods for manipulation, plotting, slicing and file IO; (2) radiological/nuclear source detection/identification analysis results; (3) source encounters of correlated analyses and (4) energy-dependent angular detector response functions. The stark package provides low-level tools that are leveraged by both curie and trajan. The tools are flexible for offline analysis as well as performant for real-time integrations.

Salathe, Marco [Lawrence Berkeley National Laborat↗
DOE OSTI2022

Therapeutic Targeting of LIF Overcomes Macrophage-mediated Immunosuppression of the Local Tumor Microenvironment

Abstract Purpose: Leukemia inhibitory factor (LIF) is a multifunctional cytokine with numerous reported roles in cancer and is thought to drive tumor development and progression. Characterization of LIF and clinical-stage LIF inhibitors would increase our understanding of LIF as a therapeutic target. Experimental Design: We first tested the association of LIF expression with transcript signatures representing multiple processes regulating tumor development and progression. Next, we developed MSC-1, a high-affinity therapeutic antibody that potently inhibits LIF signaling and tested it in immune competent animal models of cancer. Results: LIF was associated with signatures of tumor-associated macrophages (TAM) across 7,769 tumor samples spanning 22 solid tumor indications. In human tumors, LIF receptor was highly expressed within the macrophage compartment and LIF treatment drove macrophages to acquire immunosuppressive capacity. MSC-1 potently inhibited LIF signaling by binding an epitope that overlaps with the gp130 receptor binding site on LIF. MSC-1 showed monotherapy efficacy in vivo and drove TAMs to acquire antitumor and proinflammatory function in syngeneic colon cancer mouse models. Combining MSC-1 with anti-PD1 leads to strong antitumor response and a long-term tumor-free survival in a significant proportion of treated mice. Conclusions: Overall, our findings highlight LIF as a therapeutic target for cancer immunotherapy.

Oncology↗
DOE OSTI2024

CD46-Targeted Theranostics for PET and 225 Ac-Radiopharmaceutical Therapy of Multiple Myeloma

Multiple myeloma is a plasma cell malignancy with an unmet clinical need for improved imaging methods and therapeutics. Recently, we identified CD46 as an overexpressed therapeutic target in multiple myeloma and developed the antibody YS5, which targets a cancer-specific epitope on this protein. We further developed the CD46-targeting PET probe [ 89 Zr]Zr-DFO-YS5 for imaging and [ 225 Ac]Ac-DOTA-YS5 for radiopharmaceutical therapy of prostate cancer. These prior studies suggested the feasibility of the CD46 antigen as a theranostic target in multiple myeloma. Herein, we validate [ 89 Zr]Zr-DFO-YS5 for immunoPET imaging and [ 225 Ac]Ac-DOTA-YS5 for radiopharmaceutical therapy of multiple myeloma in murine models. In vitro saturation binding was performed using the CD46 expressing MM.1S multiple myeloma cell line. ImmunoPET imaging using [ 89 Zr]Zr-DFO-YS5 was performed in immunodeficient (NSG) mice bearing subcutaneous and systemic multiple myeloma xenografts. For radioligand therapy, [ 225 Ac]Ac-DOTA-YS5 was prepared, and both dose escalation and fractionated dose treatment studies were performed in mice bearing MM1.S-Luc systemic xenografts. Tumor burden was analyzed using BLI, and body weight and overall survival were recorded to assess antitumor effect and toxicity. [ 89 Zr]Zr-DFO-YS5 demonstrated high affinity for CD46 expressing MM.1S multiple myeloma cells (K d = 16.3 nmol/L). In vitro assays in multiple myeloma cell lines demonstrated high binding, and bioinformatics analysis of human multiple myeloma samples revealed high CD46 expression. [ 89 Zr]Zr-DFO-YS5 PET/CT specifically detected multiple myeloma lesions in a variety of models, with low uptake in controls, including CD46 knockout (KO) mice or multiple myeloma mice using a nontargeted antibody. In the MM.1S systemic model, localization of uptake on PET imaging correlated well with the luciferase expression from tumor cells. A treatment study using [ 225 Ac]Ac-DOTA-YS5 in the MM.1S systemic model demonstrated a clear tumor volume and survival benefit in the treated groups. Our study showed that the CD46-targeted probe [ 89 Zr]Zr-DFO-YS5 can successfully image CD46-expressing multiple myeloma xenografts in murine models, and [ 225 Ac]Ac-DOTA-YS5 can effectively inhibit the growth of multiple myeloma. These results demonstrate that CD46 is a promising theranostic target for multiple myeloma, with the potential for clinical translation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Novel Anti-LY6G6D/CD3 T-Cell–Dependent Bispecific Antibody for the Treatment of Colorectal Cancer

Abstract New therapeutics and combination regimens have led to marked clinical improvements for the treatment of a subset of colorectal cancer. Immune checkpoint inhibitors have shown clinical efficacy in patients with mismatch-repair–deficient or microsatellite instability–high (MSI-H) metastatic colorectal cancer (mCRC). However, patients with microsatellite-stable (MSS) or low levels of microsatellite instable (MSI-L) colorectal cancer have not benefited from these immune modulators, and the survival outcome remains poor for the majority of patients diagnosed with mCRC. In this article, we describe the discovery of a novel T-cell–dependent bispecific antibody (TDB) targeting tumor-associated antigen LY6G6D, LY6G6D-TDB, for the treatment of colorectal cancer. RNAseq analysis showed that LY6G6D was differentially expressed in colorectal cancer with high prevalence in MSS and MSI-L subsets, whereas LY6G6D expression in normal tissues was limited. IHC confirmed the elevated expression of LY6G6D in primary and metastatic colorectal tumors, whereas minimal or no expression was observed in most normal tissue samples. The optimized LY6G6D-TDB, which targets a membrane-proximal epitope of LY6G6D and binds to CD3 with high affinity, exhibits potent antitumor activity both in vitro and in vivo. In vitro functional assays show that LY6G6D-TDB–mediated T-cell activation and cytotoxicity are conditional and target dependent. In mouse xenograft tumor models, LY6G6D-TDB demonstrates antitumor efficacy as a single agent against established colorectal tumors, and enhanced efficacy can be achieved when LY6G6D-TDB is combined with PD-1 blockade. Our studies provide evidence for the therapeutic potential of LY6G6D-TDB as an effective treatment option for patients with colorectal cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Discovery of BBO-11818, a Potent and Selective Noncovalent Inhibitor of (ON) and (OFF) KRAS with Activity against Multiple Oncogenic Mutants

Although KRAS G12C -specific inhibitors have been introduced, no approved targeted therapies exist for other clinically significant KRAS mutants, including KRAS G12D and KRAS G12V . We discovered BBO-11818, a potent, selective, orally bioavailable noncovalent pan-KRAS inhibitor capable of targeting multiple KRAS mutants in both the inactive GDP-bound (OFF) and active GTP-bound (ON) states. BBO-11818 binds in the Switch-II/Helix 3 pocket, inducing conformational changes incompatible with effector binding, and demonstrates high-affinity binding to mutant KRAS with strong selectivity over NRAS and HRAS. BBO-11818 potently inhibited MAPK signaling and cellular viability specifically in KRAS-driven lines and produced tumor regressions in KRAS-mutant xenograft models. Combination studies with anti–PD-1, anti-EGFR antibodies, and a RAS:PI3Kα breaker compound showed enhanced efficacy. BBO-11818 has entered phase I clinical trials for patients with various KRAS mutations in colorectal, pancreatic, and lung cancers (NCT06917079).

Stahlhut, Carlos [BridgeBio Oncology Therapeutics,↗
DOE OSTI2020

A new genus and species of xanthoid crab (Decapoda: Brachyura) from offshore hard bank habitats in the Gulf of Mexico

Speciose populations of small xanthoid crabs on offshore banks and reefs of the northern Gulf of Mexico include a new species that is not assignable to presently named genera. Morphological diagnoses of the new genus and species are underpinned by previously published gene sequence analyses, originally misattributed to another species but now known to apply to this taxon. Herein named Guinope tiara n. gen., n. sp., the species shows molecular phylogenetic affinities with the family Linnaeoxanthidae Stevcic, 2005, an ally of panopeid and pseudorhombilid crabs. Specimens from Occulina banks off the Florida Atlantic coast, previously regarded to represent Garthiope barbadensis (Rathbun, 1921), are not that species but instead morphologically assignable to Guinope n. gen. Whether they represent variants of Guinope tiara n. gen, n. sp. or a second species of the genus awaits the collection of fresh materials for DNA analyses.

Zoology↗
DOE OSTI2024

EMC3 regulates trafficking and pulmonary toxicity of the SFTPC I73T mutation associated with interstitial lung disease

The most common mutation in surfactant protein C gene (SFTPC), SFTPC I73T , causes interstitial lung disease with few therapeutic options. We previously demonstrated that EMC3, an important component of the multiprotein endoplasmic reticulum membrane complex (EMC), is required for surfactant homeostasis in alveolar type 2 epithelial (AT2) cells at birth. In the present study, we investigated the role of EMC3 in the control of SFTPC I73T metabolism and its associated alveolar dysfunction. Using a knock-in mouse model phenocopying the I73T mutation, we demonstrated that conditional deletion of Emc3 in AT2 cells rescued alveolar remodeling/simplification defects in neonatal and adult mice. Proteomic analysis revealed that Emc3 depletion reversed the disruption of vesicle trafficking pathways and rescued the mitochondrial dysfunction associated with I73T mutation. Affinity mass spectrometry analysis identified potential EMC3 interacting proteins in lung AT2 cells, including Valosin Containing Protein (VCP) and its interactors. Treatment of Sftpc I73T knock-in mice and SFTPC I73T expressing iAT2 cells derived from SFTPC I73T patient-specific iPSCs with the specific VCP inhibitor CB5083 restored alveolar structure and SFTPC I73T trafficking respectively. Taken together, the present work identifies the EMC complex and VCP in the metabolism of the disease-associated SFTPC I73T mutant, providing novel therapeutical targets for SFTPC I73T -associated interstitial lung disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Advancing South American Water and Climate Science Through Multi-Decadal Convection-Permitting Modeling

The South America Affinity Group (SAAG) was established in early 2019 by the National Center for Atmospheric Research (NCAR) Water Systems Program as a community effort focused on improving hydroclimate science over South America. SAAG supports large research efforts such as the ANDEX Regional Hydroclimate Program as well as individual research groups. The group started with a dozen members and quickly grew to over 100 participants from more than ten countries. For the past four years, the SAAG has been meeting online every two weeks and has organized sessions at international conferences such as the American Geophysical Union Fall Meeting and the Convection-Permitting Climate Workshop. At the core of the SAAG effort are two multi-decadal convection permitting (CP) model simulations with 4-km grid spacing for historical and future climates over the South American continent. Additionally, a major observational data collection effort has been undertaken, including in-situ station data from South American meteorological and water services, gridded products, satellite-based observations, and field campaign data. In conclusion, this article discusses the research needs and scientific goals that drive this community of scientists with diverse backgrounds and interests.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

SAXS analysis of the intrinsic tenase complex bound to a lipid nanodisc highlights intermolecular contacts between factors VIIIa/IXa

Abstract The intrinsic tenase (Xase) complex, formed by factors (f) VIIIa and fIXa, forms on activated platelet surfaces and catalyzes the activation of factor X to Xa, stimulating thrombin production in the blood coagulation cascade. The structural organization of the membrane-bound Xase complex remains largely unknown, hindering our understanding of the structural underpinnings that guide Xase complex assembly. Here, we aimed to characterize the Xase complex bound to a lipid nanodisc with biolayer interferometry (BLI), Michaelis–Menten kinetics, and small-angle X-ray scattering (SAXS). Using immobilized lipid nanodiscs, we measured binding rates and nanomolar affinities for fVIIIa, fIXa, and the Xase complex. Enzyme kinetic measurements demonstrated the assembly of an active enzyme complex in the presence of lipid nanodiscs. An ab initio molecular envelope of the nanodisc-bound Xase complex allowed us to computationally model fVIIIa and fIXa docked onto a flexible lipid membrane and identify protein–protein interactions. Our results highlight multiple points of contact between fVIIIa and fIXa, including a novel interaction with fIXa at the fVIIIa A1–A3 domain interface. Lastly, we identified hemophilia A/B-related mutations with varying severities at the fVIIIa/fIXa interface that may regulate Xase complex assembly. Together, our results support the use of SAXS as an emergent tool to investigate the membrane-bound Xase complex and illustrate how mutations at the fVIIIa/fIXa dimer interface may disrupt or stabilize the activated enzyme complex.

Hematology↗
DOE OSTI2020

iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots

The interaction between proteins and nucleic acids plays pivotal roles in various biological processes such as transcription, translation, and gene regulation. Hot spots are a small set of residues that contribute most to the binding affinity of a protein-nucleic acid interaction. Compared to the extensive studies of the hot spots on protein-protein interfaces, the hot spot residues within protein-nucleic acids interfaces remain less well-studied, in part because mutagenesis data for protein-nucleic acids interaction are not as abundant as that for protein-protein interactions. In this study, we built a new computational model, iPNHOT, to effectively predict hot spot residues on protein-nucleic acids interfaces. One training data set and an independent test set were collected from dbAMEPNI and some recent literature, respectively. To build our model, we generated 97 different sequential and structural features and used a two-step strategy to select the relevant features. The final model was built based only on 7 features using a support vector machine (SVM). The features include two unique features such as ΔSASsa 1/2 and esp3, which are newly proposed in this study. Based on the cross validation results, our model gave F1 score and AUROC as 0.725 and 0.807 on the subset collected from ProNIT, respectively, compared to 0.407 and 0.670 of mCSM-NA, a state-of-the art model to predict the thermodynamic effects of protein-nucleic acid interaction. The iPNHOT model was further tested on the independent test set, which showed that our model outperformed other methods. Here, by collecting data from a recently published database dbAMEPNI, we proposed a new model, iPNHOT, to predict hotspots on both protein-DNA and protein-RNA interfaces. The results show that our model outperforms the existing state-of-art models. Our model is available for users through a webserver: http://zhulab.ahu.edu.cn/iPNHOT/.

59 BASIC BIOLOGICAL SCIENCES↗