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Chen, Yang

Publications and source records attributed to Chen, Yang.

At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Feature Design for Protein Interface Hotspots Using KFC2 and Rosetta

Protein–protein interactions regulate many essential biological processes and play an important role in health and disease. The process of experimentally characterizing protein residues that contribute the most to protein–protein interaction affinity and specificity is laborious. Thus, developing models that accurately characterize hotspots at protein–protein interfaces provides important information about how to inhibit therapeutically relevant protein–protein interactions. During the course of the ICERM WiSDM workshop 2017, we combined the KFC2a protein–protein interaction hotspot prediction features with Rosetta scoring function terms and interface filter metrics. A two-way and three-way forward selection strategy was employed to train support vector machine classifiers, as was a reverse feature elimination strategy. From these results, we identified subsets of KFC2a and Rosetta combined features that show improved performance over KFC2a features alone.

Seeger, Franziska↗
DOE OSTI2019

Constraining the thermally pulsing asymptotic giant branch phase with resolved stellar populations in the Small Magellanic Cloud

The thermally-pulsing asymptotic giant branch (TP-AGB) experienced by low- andintermediate-mass stars is one of the most uncertain phases of stellar evolution and themodels need to be calibrated with the aid of observations. To this purpose, we couplehigh-quality observations of resolved stars in the Small Magellanic Cloud (SMC) withdetailed stellar population synthesis simulations computed with theTRILEGALcode.The strength of our approach relies on the detailed spatially-resolved star formationhistory of the SMC, derived from the deep near-infrared photometry of the VISTAsurvey of the Magellanic Clouds, as well as on the capability to quickly and accuratelyexplore a wide variety of parameters and effects with theCOLIBRIcode for the TP-AGB evolution. Adopting a well-characterized set of observations – star counts andluminosity functions – we set up a calibration cycle along which we iteratively changea few key parameters of the TP-AGB models until we eventually reach a good fit tothe observations. Our work leads to identify two best-fitting models that mainly differin the efficiencies of the third dredge-up and mass loss in TP-AGB stars with initialmasses larger than about 3 M. On the basis of these calibrated models we providea full characterization of the TP-AGB stellar population in the SMC in terms of stel-lar parameters (initial masses, C/O ratios, carbon excess, mass-loss rates). Extensivetables of isochrones including these improved models are publicly available

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Molecular architecture of a cylindrical self-assembly at human centrosomes

The cell is constructed by higher-order structures and organelles through complex interactions among distinct structural constituents. The centrosome is a membraneless organelle composed of two microtubule-derived structures called centrioles and an amorphous mass of pericentriolar material. Super-resolution microscopic analyses in various organisms revealed that diverse pericentriolar material proteins are concentrically localized around a centriole in a highly organized manner. However, the molecular nature underlying these organizations remains unknown. Here we show that two human pericentriolar material scaffolds, Cep63 and Cep152, cooperatively generate a heterotetrameric α-helical bundle that functions in conjunction with its neighboring hydrophobic motifs to self-assemble into a higher-order cylindrical architecture capable of recruiting downstream components, including Plk4, a key regulator for centriole duplication. Mutations disrupting the self-assembly abrogate Plk4-mediated centriole duplication. Because pericentriolar material organization is evolutionarily conserved, this work may offer a paradigm for investigating the assembly and function of centrosomal scaffolds in various organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Soil Moisture Variability Intensifies and Prolongs Eastern Amazon Temperature and Carbon Cycle Response to El Niño–Southern Oscillation

El Niño–Southern Oscillation (ENSO) is an important driver of climate and carbon cycle variability in the Amazon. Sea surface temperature (SST) anomalies in the equatorial Pacific drive teleconnections with temperature directly through changes in atmospheric circulation. These circulation changes also impact precipitation and, consequently, soil moisture, enabling additional indirect effects on temperature through land–atmosphere coupling. To separate the direct influence of ENSO SST anomalies from the indirect effects of soil moisture, a mechanism-denial experiment was performed to decouple their variability in the Energy Exascale Earth System Model (E3SM) forced with observed SSTs from 1982 to 2016. Soil moisture variability was found to amplify and extend the effects of SST forcing on eastern Amazon temperature and carbon fluxes in E3SM. During the wet season, the direct, circulation-driven effect of ENSO SST anomalies dominated temperature and carbon cycle variability throughout the Amazon. During the following dry season, after ENSO SST anomalies had dissipated, soil moisture variability became the dominant driver in the east, explaining 67%–82% of the temperature difference between El Niño and La Niña years, and 85%–91% of the difference in carbon fluxes. These results highlight the need to consider the interdependence between temperature and hydrology when attributing the relative contributions of these factors to interannual variability in the terrestrial carbon cycle. Specifically, when offline models are forced with observations or reanalysis, the contribution of temperature may be overestimated when its own variability is modulated by hydrology via land–atmosphere coupling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Surrogate Modeling for Capacity Planning of Charging Station Equipped With Photovoltaic Panel and Hydropneumatic Energy Storage

Due to the promising potential for environmental sustainability, there has been a significant increase of electric vehicles (EVs) and plug-in hybrid electric vehicles (PHEV) in the market. To support this increasing demand for EVs and PHEVs, challenges related to capacity planning and investment costs of public charging infrastructure must be addressed. Hence, in this paper, a capacity planning problem for charging stations is developed and aims to balance the current capital investment costs and future operational revenue. The charging station is assumed to be equipped with the solar photovoltaic (PV) panel and an energy storage system, which could be electric battery or recently invented hydropneumatic energy storage (ground-level integrated diverse energy storage (GLIDES)) system. A co-optimization model that minimizes investment and operation cost is established to determine optimal solution while considering capacity planning and following operations. EV mobility is modeled as an Erlang-loss system. Meanwhile, stochastic programming is adopted to capture uncertainties from solar radiation and charging demand of EV fleet. To provide a more general and computationally efficient model, main configuration parameters are sampled in design space and then fixed in solving the co-optimization model. Sampled parameters include EV charging slots number, PV area, capacity of energy storage system, and daily mean EV arrival number. Based on the sampled parameter combinations and its responses, black-box mappings are then constructed using surrogate models, which could provide insights for charging station placement in different practical situations. The effectiveness of the proposed surrogate modeling approach is demonstrated in numerical experiments. Here, the results indicate better profit advantage of GLIDES over battery system with the increased power capacity

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2018

Forest response to rising CO 2 drives zonally asymmetric rainfall change over tropical land

Understanding how anthropogenic CO 2 emissions will influence future precipitation is critical for sustainably managing ecosystems, particularly for drought-sensitive tropical forests. Although tropical precipitation change remains uncertain, nearly all models from the Coupled Model Intercomparison Project Phase 5 predict a strengthening zonal precipitation asymmetry by 2100, with relative increases over Asian and African tropical forests and decreases over South American forests. Here we show that the plant physiological response to increasing CO 2 is a primary mechanism responsible for this pattern. Applying a simulation design in the Community Earth System Model in which CO 2 increases are isolated over individual continents, we demonstrate that different circulation, moisture and stability changes arise over each continent due to declines in stomatal conductance and transpiration. The sum of local atmospheric responses over individual continents explains the pan-tropical precipitation asymmetry. Our analysis suggests that South American forests may be more vulnerable to rising CO 2 than Asian or African forests.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Nonlinear saturation of the slab ITG instability and zonal flow generation with fully kinetic ions

Fully kinetic turbulence models are of interest for their potential to validate or replace gyrokinetic models in plasma regimes where the gyrokinetic expansion parameters are marginal. Here, we demonstrate fully kinetic ion capability by simulating the growth and nonlinear saturation of the ion-temperature-gradient instability in shearless slab geometry assuming adiabatic electrons and including zonal flow dynamics. The ion trajectories are integrated using the Lorentz force, and the cyclotron motion is fully resolved. Linear growth and nonlinear saturation characteristics show excellent agreement with analogous gyrokinetic simulations across a wide range of parameters. The fully kinetic simulation accurately reproduces the nonlinearly generated zonal flow. In conclusion, this work demonstrates nonlinear capability, resolution of weak gradient drive, and zonal flow physics, which are critical aspects of modeling plasma turbulence with full ion dynamics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS2017

A Pan-Tropical Cascade of Fire Driven by El Nino/Southern Oscillation

The El Nino/Southern Oscillation (ENSO) has a pronounced influence on year-to-year variations in climate. The response of fires to this forcing is complex and has not been evaluated systematically across different continents. Here we use satellite data to create a climatology of burned-area and fire emissions responses, drawing on six El Nino and six La Nina events during 1997-2016. On average, reductions in precipitation and terrestrial water storage increased fire emissions in pan-tropical forests by 133% during and following El Nino as compared with La Nina. Fires peaked in equatorial Asia early in the ENSO cycle when El Nino was strengthening (Aug-Oct), before moving to southeast Asia and northern South America (Jan-Apr), Central America (Mar-May) and the southern Amazon (Jul-Oct) during the following year. Large decreases in fire occurred across northern Australia during Sep-Oct of the second year from a reduced fuel availability. Satellite observations of aerosols and carbon monoxide provided independent confirmation of the spatiotemporal evolution of fire anomalies. The predictable cascade of fire across different tropical continents described here highlights an important time delay in the Earth system's response to precipitation redistribution. These observations help to explain why the growth rate of atmospheric CO2 increases during El Nino and may contribute to improved seasonal fire forecasts.

Chen, Yang↗
DOE OSTI2017

Final Technical Report on “Center for Nonlinear Simulation of Energetic Particles in Burning Plasmas (CSEP)”

The gyrokinetic turbulence code GEM is used to study reverse shear Alfven eigenmodes in the DIII-D tokamak, cylindrical tearing mode, the nonlinear saturation mechanism of Alfven eigenmodes, and verify other gyrokinetic codes. It is used to study the stability of Alfven waves in the presence of fusion product alpha particles in ITER. New algorithm features and physics capabilities are added to GEM, including a novel discretization method for the Poisson equation, a vorticity approach to the fluid electron model and a low-n solver in cylindrical geometry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Is HESS J1912+101 Associated with an Old Supernova Remnant?

HESS J1912+101 is a shell-like TeV source that has no clear counterpart in multiwavelength. Using CO and H i data, we reveal that V {sub LSR} ∼ +60 km s{sup −1} molecular clouds (MCs), together with shocked molecular gas and high-velocity neutral atomic shells, are concentrated toward HESS J1912+101. The prominent wing profiles up to V {sub LSR} ∼ +80 km s{sup −1} seen in {sup 12}CO ( J = 1–0 and J = 3–2) data, as well as the high-velocity expanding H i shells up to V {sub LSR} ∼ +100 km s{sup −1}, exhibit striking redshifted-broadening relative to the quiescent gas. These features provide compelling evidences for large-scale perturbation in the region. We argue that the shocked MCs and the high-velocity H i shells may originate from an old supernova remnant (SNR). The distance to the SNR is estimated to be ∼4.1 kpc based on the H i self-absorption method, which leads to a physical radius of 29.0 pc for the ∼(0.7–2.0) × 10{sup 5} years old remnant with an expansion velocity of ≳40 km s{sup −1}. The +60 km s{sup −1} MCs and the disturbed gas are indeed found to coincide with the bright TeV emission, supporting the physical association between them. Naturally, the shell-like TeV emission comes from the decay of neutral pions produced by interactions between the accelerated hadrons from the SNR and the surrounding high-density molecular gas.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Exploring the structural changes on excitation of a luminescent organic bromine-substituted complex by in-house time-resolved pump-probe diffraction

The structural changes accompanying the excitation of the luminescent dibromobenzene derivative, 1,4-dibromo-2,5-bis(octyloxy)benzene, have been measured by in-house monochromatic time-resolved (TR) diffraction at 90 K. Results show an increment of the very short intermolecular Br•••Br contact distance from 3.290 Å to 3.380 Å. These calculations show the Br…Br interaction to be strongly repulsive in both the Ground and Excited states but significantly relaxed by the lengthening of the contact distance on excitation. The stability of the crystals is attributed to the many weak C-H···Br and C-H···π intermolecular interactions. Our study described is the first practical application of In-House Time-Resolved diffraction, made possible by the continuing increase in the brightness of X-ray sources and the sensitivity of our detectors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Molecular Environments of Three Large Supernova Remnants in the Third Galactic Quadrant: G205.5+0.5, G206.9+2.3, and G213.0–0.6

We present CO observations toward three large supernova remnants (SNRs) in the third Galactic quadrant using the Purple Mountain Observatory Delingha 13.7 m millimeter-wavelength telescope. The observations are part of the high-resolution CO survey of the Galactic plane between Galactic longitudes l=−10{sup ∘} to 250{sup ∘} and latitudes b=−5{sup ∘} to 5{sup ∘}. CO emission was detected toward the three SNRs: G205.5+0.5 (Monoceros Nebula), G206.9+2.3 (PKS 0646+06), and G213.0–0.6. Both SNRs G205.5+0.5 and G213.0–0.6 exhibit the morphological agreement (or spatial correspondences) between the remnant and the surrounding molecular clouds (MCs), as well as kinematic signatures of shock perturbation in the molecular gas. We confirm that the two SNRs are physically associated with their ambient MCs and the shock of SNRs is interacting with the dense, clumpy molecular gas. SNR G206.9+2.3, which is close to the northeastern edge of the Monoceros Nebula, displays the spatial coincidence with molecular partial shell structures at V {sub LSR} ∼ 15 km s{sup −1}. While no significant line broadening has been detected within or near the remnant, the strong morphological correspondence between the SNR and the molecular cavity implies that SNR G206.9+2.3 is probably associated with the CO gas and is evolving in the low-density environment. The physical features of individual SNRs, together with the relationship between SNRs and their nearby objects, are also discussed.

79 ASTRONOMY AND ASTROPHYSICS↗