Engineering Papers⌕ Search

Engineering topics

Gao, Yi

Publications and source records attributed to Gao, Yi.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A VR-based volumetric medical image segmentation and visualization system with natural human interaction

Volume rendering produces informative two-dimensional (2D) images from a 3-dimensional (3D) volume. It highlights the region of interest and facilitates a good comprehension of the entire data set. However, volume rendering faces a few challenges. First, a high-dimensional transfer function is usually required to differentiate the target from its neighboring objects with subtle variance. Unfortunately, designing such a transfer function is a strenuously trial-and-error process. Second, manipulating/visualizing a 3D volume with a traditional 2D input/output device suffers dimensional limitations. To address all the challenges, we design NUI-VR 2 , a natural user interface-enabled volume rendering system in the virtual reality space. NUI-VR 2 marries volume rendering and interactive image segmentation. It transforms the original volume into a probability map with image segmentation. A simple linear transfer function will highlight the target well in the probability map. More importantly, we set the entire image segmentation and volume rendering pipeline in an immersive virtual reality environment with a natural user interface. NUI-VR 2 eliminates the dimensional limitations in manipulating and perceiving 3D volumes and dramatically improves the user experience.

42 ENGINEERING↗
DOE OSTI2021

Chemical insights into the multi-regime low-temperature oxidation of di-n-propyl ether: Jet-stirred reactor experiments and kinetic modeling

To further understand the combustion characteristics and the reaction pathways of acyclic ethers, in this work the oxidation of di-n-propyl ether (DPE) was investigated in a jet-stirred reactor (JSR) combined with a photoionization molecular-beam mass spectrometer. The experiments were carried out at near-atmospheric pressure (700 Torr) and over a temperature range of 425–850 K. Based on the experimental data and previous studies on ether oxidation, a new kinetic model was constructed and used to interpret the oxidation chemistry of DPE. In DPE oxidation, a high reactivity at low temperatures and two negative temperature coefficient (NTC) zones were observed. These behaviors are explained in this work by taking advantage of the obtained species information and the modeling analyses: the two NTC zones are caused by the competition of chain branching and termination reactions of the fuel itself and specific oxidation intermediates, respectively. Furthermore, the general requirements to have double-NTC behavior are discussed. A variety of crucial fuel-specific C 6 species, such as ketohydroperoxides and diones, were detected in the species pool of DPE oxidation. Their formation pathways are illuminated based on rate-of-production (ROP) analyses. Propanal was identified as the most abundant small molecule intermediate, and its related reactions have an important impact on the oxidation process of DPE. Both acetic acid and propionic acid were detected in high concentrations. A new formation pathway of propionic acid is proposed and incorporated into the kinetic model to achieve a more accurate prediction for propionic acid mole fractions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Discovery of AG-270, a First-in-Class Oral MAT2A Inhibitor for the Treatment of Tumors with Homozygous MTAP Deletion

The metabolic enzyme methionine adenosyltransferase 2A (MAT2A) was recently implicated as a synthetic lethal target in cancers with deletion of the methylthioadenosine phosphorylase (MTAP) gene, which is adjacent to the CDKN2A tumor suppressor and codeleted with CDKN2A in approximately 15% of all cancers. Previous attempts to target MAT2A with small-molecule inhibitors identified cellular adaptations that blunted their efficacy. Here, we report the discovery of highly potent, selective, orally bioavailable MAT2A inhibitors that overcome these challenges. Fragment screening followed by iterative structure-guided design enabled >10 000-fold improvement in potency of a family of allosteric MAT2A inhibitors that are substrate noncompetitive and inhibit release of the product, S-adenosyl methionine (SAM), from the enzyme’s active site. We demonstrate that potent MAT2A inhibitors substantially reduce SAM levels in cancer cells and selectively block proliferation of MTAP-null cells both in tissue culture and xenograft tumors. These data supported progressing AG-270 into current clinical studies (ClinicalTrials.gov NCT03435250).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Quantum Phase Transition of Correlated Iron-Based Superconductivity in LiFe 1 - x Co x As

The interplay between unconventional Cooper pairing and quantum states associated with atomic scale defects is a frontier of research with many open questions. So far, only a few of the high-temperature superconductors allow this intricate physics to be studied in a widely tunable way. We use scanning tunneling microscopy to image the electronic impact of Co atoms on the ground state of the LiFe$_{1-x}Co_{x}$ As system. We observe that impurities progressively suppress the global superconducting gap and introduce low energy states near the gap edge, with the superconductivity remaining in the strong-coupling limit. Unexpectedly, the fully opened gap evolves into a nodal state before the Cooper pair coherence is fully destroyed. Here, our systematic theoretical analysis shows that these new observations can be quantitatively understood by the nonmagnetic Born-limit scattering effect in an s±-wave superconductor, unveiling the driving force of the superconductor to metal quantum phase transition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Effects of farnesoid-X-receptor SUMOylation mutation on myocardial ischemia/reperfusion injury in mice

Highlights: • Effect of FXR SUMOylation on myocardial apoptosis during MI/R injury was studied. • Cardiac-specific overexpression of wild-type and SUMOylation-resistant FXR in mice. • FXR was SUMOylated in the heart tissue and SUMOylation levels decreased after MI/R. • SUMOylation plays essential roles in regulating FXR function in MI/R injury. Myocardial ischemia/reperfusion (MI/R) injury induces excessive cellular apoptosis and contributes significantly to final infarct size. We previously demonstrated that a nuclear receptor, Farnesoid X receptor (FXR), plays a crucial role in mediating myocardial apoptosis. The FXR functions are regulated by post translational modifications (PTM). However, whether the proapoptotic effect of FXR in MI/R injury is regulated by PTM remains unclear. Here, we aimed to study the effect of SUMOylation, a PTM involved in the pathogenesis of MI/R injury per se, on the proapoptotic effect of FXR in MI/R injury. We observed that FXR could be SUMOylated in heart tissues, and FXR SUMOylation levels were downregulated in ischemia reperfused myocardium. By overexpression of SUMOylation-defective FXR mutant, it was demonstrated that decreased SUMOylation augmented the detrimental effect of FXR, via activation of mitochondrial apoptosis pathway and autophagy dysfunction in MI/R injury. Further mechanistic studies suggested that decreased SUMOylation levels increased the transcription activity of FXR, and the subsequently upregulated FXR target gene SHP mediated the proapoptotic effects of FXR. Taken together, we provided the first evidence that the cardiac effects of FXR could be regulated by SUMOylation, and that manipulating FXR SUMOylation levels may hold therapeutic promise for constraining MI/R injury.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Facet-specific interaction between methanol and TiO 2 probed by sum-frequency vibrational spectroscopy

Significance Facet engineering has become a major strategy for designing crystalline catalysts, yet many fundamental issues, including facet-specific interaction with adsorbates, remain unsolved due to lack of experimental investigation. Using surface-specific sum-frequency vibrational spectroscopy, we have conducted an in-depth study of methanol adsorption on four different facets of TiO 2 under ambient conditions. The spectra revealed that for the four facets investigated, dissociation of adsorbed methanol occurs only when surface defects are present. Adsorption kinetics and energetics appeared nearly the same on different facets, but the Fermi resonance coupling strength for CH 3 of adsorbed methanol was found to depend sensitively on facets and methanol coverage, and could serve as a gauge for studying facet effects on molecular adsorption and surface reactions.

Yang, Deheng↗
DOE OSTI2018

MiR-181a contributes gefitinib resistance in non-small cell lung cancer cells by targeting GAS7

Tyrosine kinase inhibitors (TKIs) exert potent therapeutic efficacy in non-small cell lung cancers (NSCLC) harboring epidermal growth factor receptor (EGFR) activating mutations. However, a major impediment for the effective treatment is the development of drug resistance. Some evidence supports a role for miRNAs in modulating NSCLC TKIs resistance. Here we show that miR-181a is significantly up-regulated in gefitinib-resistant cells compared with gefitinib-sensitive cells. Upregulation of miR-181a caused resistance of gefitinib, whereas downregulation of miR-181a sensitized NSCLC cells to gefitinib. Furthermore, the miR-181a plasma levels were significantly increased in acquired gefitinib resistant NSCLC patients compared with the plasma levels prior to gefitinib treatment in each patient. Bioinformatics analysis and luciferase reporter assay showed that growth arrest-specific 7 (GAS7) was a direct target gene of miR-181a. A significant inverse correlation between the expression of miR-181a and GAS7 was identified in NSCLC tissues. Downregulation of GAS7 expression could antagonize gefitinib re-sensitivity in PC9GR mediated by knockdown of miR-181a via AKT/ERK pathways and epithelial-to-mesenchymal transition markers. Additionally, GAS7 expression was downregulated in a large cohort of NSCLC patients, and a high mRNA level of GAS7 was associated with improved overall survival. Collectively, our findings provide a novel basis for using miR-181a/GAS7-based therapeutic strategies to reverse gefitinib resistance in NSCLC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

AAV-mediated conversion of human pluripotent stem cell-derived pacemaker

Malfunction of nodal pacemaker (Pm) cardiomyocytes (CMs) due to diseases or aging leads to rhythm generation disorders, necessitating electronic Pm implantation. We functionally reprogrammed human pluripotent stem cell (hPSC) derived-ventricular (V) CMs into -PmCMs via recombinant adeno-associated virus serotype 9 (rAAV9)-mediated overexpression of engineered HCN1 channel (HCN1ΔΔΔ) whose S3-S4 linker has been strategically deleted by design to promote cardiac pacemaking. rAAV9-HCN1ΔΔΔ-reprogrammed hPSC-PmCMs converted from -VCMs showed automaticity and action potential parameters typical of native nodal PmCMs. Implantation of rAAV9-HCN1ΔΔΔ-based BPm in a preclinical porcine model of complete heart block significantly reduced the dependence on device-supported pacing and generated spontaneous heart rhythms from the BPm. Collectively, these results have further laid the groundwork on BPm for future translation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines

Motivation: Sensitivity analysis and parameter tuning are important processes in large-scale image analysis. They are very costly because the image analysis workflows are required to be executed several times to systematically correlate output variations with parameter changes or to tune parameters. An integrated solution with minimum user interaction that uses effective methodologies and high performance computing is required to scale these studies to large imaging datasets and expensive analysis workflows. Results: The experiments with two segmentation workflows show that the proposed approach can (i) quickly identify and prune parameters that are non-influential; (ii) search a small fraction (about 100 points) of the parameter search space with billions to trillions of points and improve the quality of segmentation results (Dice and Jaccard metrics) by as much as 1.42 x compared to the results from the default parameters; (iii) attain good scalability on a high performance cluster with several effective optimizations. Conclusions: Our work demonstrates the feasibility of performing sensitivity analyses, parameter studies and auto-tuning with large datasets. The proposed framework can enable the quantification of error estimations and output variations in image segmentation pipelines.

Biochemistry & Molecular Biology↗
DOE OSTI2016

Evolution of anatase surface active sites probed by in situ sum-frequency phonon spectroscopy

Surface active sites of crystals often govern their relevant surface chemistry, yet to monitor them in situ in real atmosphere remains a challenge. Using surface-specific sum-frequency spectroscopy, we identified the surface phonon mode associated with the active sites of undercoordinated titanium ions and conjoint oxygen vacancies, and used it to monitor them on anatase (TiO 2 ) (101) under ambient conditions. In conjunction with theory, we determined related surface structure around the active sites and tracked the evolution of oxygen vacancies under ultraviolet irradiation. We further found that unlike in vacuum, the surface oxygen vacancies, which dominate the surface reactivity, are strongly regulated by ambient gas molecules, including methanol and water, as well as weakly associated species, such as nitrogen and hydrogen. The result revealed a rich interplay between prevailing ambient species and surface reactivity, which can be omnipresent in environmental and catalytic applications of titanium dioxides.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Simulation of optical response functions in molecular junctions

Here, we discuss theoretical approaches to nonlinear optical spectroscopy of molecular junctions. Optical response functions are derived in a form convenient for the implementation of Green function techniques, and their expressions in terms of pseudoparticle nonequilibrium Green functions are proposed. The formulation allows to account for both intramolecular interactions and hybridization of molecular states with those of contacts. Within a generic model and utilizing two-dimensional optical spectroscopy as an example, the methodology is compared with exact simulations and is shown to work where the traditional Liouville space approach fails.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Optical spectroscopy of molecular junctions: Nonequilibrium Green’s functions perspective

We consider optical spectroscopy of molecular junctions from the quantum transport perspective when radiation field is quantized and optical response of the system is simulated as photon flux. Using exact expressions for photon and electronic fluxes derived within the nonequilibrium Green function (NEGF) methodology and utilizing fourth order diagrammatic perturbation theory (PT) in molecular coupling to radiation field, we perform simulations employing realistic parameters. Results of the simulations are compared to the bare PT which is usually employed in studies on nonlinear optical spectroscopy to classify optical processes. We show that the bare PT violates conservation laws, while flux conserving NEGF formulation mixes optical processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

“Nodal Gap” induced by the incommensurate diagonal spin density modulation in underdoped high- T c superconductors

Recently it was revealed that the whole Fermi surface is fully gapped for several families of underdoped cuprates. The existence of the finite energy gap along the d -wave nodal lines (nodal gap) contrasts the common understanding of the d -wave pairing symmetry, which challenges the present theories for the high- T c superconductors. Here we propose that the incommensurate diagonal spin-density-wave order can account for the above experimental observation. The Fermi surface and the local density of states are also studied. Our results are in good agreement with many important experiments in high- T c superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Sublinear scaling for time-dependent stochastic density functional theory

A stochastic approach to time-dependent density functional theory is developed for computing the absorption cross section and the random phase approximation (RPA) correlation energy. The core idea of the approach involves time-propagation of a small set of stochastic orbitals which are first projected on the occupied space and then propagated in time according to the time-dependent Kohn-Sham equations. The evolving electron density is exactly represented when the number of random orbitals is infinite, but even a small number (≈16) of such orbitals is enough to obtain meaningful results for absorption spectrum and the RPA correlation energy per electron. We implement the approach for silicon nanocrystals using real-space grids and find that the overall scaling of the algorithm is sublinear with computational time and memory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗