The conserved bridging domain on HCV E1E2 glycoprotein complex is targeted by neutralizing antibodies from diverse lineages
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Chen, Fang (ORCID:0000000234813363)↗
Engineering topics
Zhu, Jiang
Publications and source records attributed to Zhu, Jiang.
Larger Cloud Liquid Water Enhances Both Aerosol Indirect Forcing and Cloud Radiative Feedback in Two Earth System Models
Previous studies have noticed that the Coupled Model Intercomparison Project Phase 6 (CMIP6) models with a stronger cooling from aerosol-cloud interactions (ACI) also have an enhanced warming from positive cloud feedback, and these two opposing effects are counter-balanced in simulations of the historical period. However, reasons for this anti-correlation are less explored. In this study, we perturb the cloud ice microphysical processes to obtain cloud liquid of varying amounts in two Earth System Models (ESMs). We find that the model simulations with a larger liquid water path (LWP) tend to have a stronger cooling from ACI and a stronger positive cloud feedback. More liquid clouds in the mean-state present more opportunities for anthropogenic aerosol perturbations and also weaken the negative cloud feedback at middle to high latitudes. This work, from a cloud state perspective, emphasizes the influence of the mean-state LWP on effective radiative forcing due to ACI (ERF ACI ).
54 ENVIRONMENTAL SCIENCES↗
New Record Ocean Temperatures and Related Climate Indicators in 2023
The global physical and biogeochemical environment has been substantially altered in response to increased atmospheric greenhouse gases from human activities. In 2023, the sea surface temperature (SST) and upper 2000 m ocean heat content (OHC) reached record highs. The 0–2000 m OHC in 2023 exceeded that of 2022 by 15 ± 10 ZJ (1 Zetta Joules = 10 21 Joules) (updated IAP/CAS data); 9 ± 5 ZJ (NCEI/NOAA data). The Tropical Atlantic Ocean, the Mediterranean Sea, and southern oceans recorded their highest OHC observed since the 1950s. Associated with the onset of a strong El Niño, the global SST reached its record high in 2023 with an annual mean of ~0.23°C higher than 2022 and an astounding > 0.3°C above 2022 values for the second half of 2023. The density stratification and spatial temperature inhomogeneity indexes reached their highest values in 2023.
54 ENVIRONMENTAL SCIENCES↗
HIV-1 GP140 immunogens comprising modified NHR1 regions that stabilize pre-fusion envelope conformations
The present invention provides HIV-1 vaccine immunogens. Some of the immunogens contain a soluble gp140-derived protein that harbors a modified N-terminus of the HR1 region in gp41. Some of the immunogens contain an HIV-1 Env-derived trimer protein that is presented on a nanoparticle platform. The invention also provides methods of using the HIV-1 vaccine immunogens for eliciting an immune response or treating HIV infections.
Kong, Leopold↗
The Impacts of a Weakened Atlantic Meridional Overturning Circulation on ENSO in a Warmer Climate
This study quantifies the impacts of the Atlantic Meridional Overturning Circulation (AMOC) on the El Niño–Southern Oscillation (ENSO) under anthropogenic warming by comparing climate change model simulations with declining and fixed strengths of the overturning. After the 1980s, a weakened AMOC is shown to reduce the strength of the annual cycle of sea surface temperature (SST) in the eastern equatorial Pacific and induce anomalous cross-equatorial northerly winds there, which strengthens ENSO variability by about 11%. An analysis of the Bjerknes stability index reveals that this intensification of ENSO results mainly from enhanced Ekman upwelling feedback due to amplified atmospheric wind response to SST anomalies and oceanic upwelling response to equatorial wind stress anomalies. The weakened AMOC also promotes the occurrence of Central Pacific El Niño events and reduces ENSO skewness. These AMOC impacts on ENSO magnitude and complexity throughout the twenty-first century are however smaller than ENSO variations expected from internal climate variability.
54 ENVIRONMENTAL SCIENCES↗
Cryo-EM structure of the human Sirtuin 6–nucleosome complex
Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo–electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56.
59 BASIC BIOLOGICAL SCIENCES↗
Importance of ice nucleation and precipitation on climate with the Parameterization of Unified Microphysics Across Scales version 1 (PUMASv1)
Cloud microphysics is critical for weather and climate prediction. In this work, we document updates and corrections to the cloud microphysical scheme used in the Community Earth System Model (CESM) and other models. These updates include a new nomenclature for the scheme, now called Parameterization of Unified Microphysics Across Scales (PUMAS), and the ability to run the scheme on graphics processing units (GPUs). The main science changes include refactoring an ice number limiter and associated changes to ice nucleation, adding vapor deposition onto snow, and introducing an implicit numerical treatment for sedimentation. We also detail the improvements in computational performance that can be achieved with GPU acceleration. We then show the impact of these scheme changes on the (a) mean state climate, (b) cloud feedback response to warming, and (c) aerosol forcing. We find that corrections are needed to the immersion freezing parameterization and that ice nucleation has important impacts on climate. We also find that the revised scheme produces less cloud liquid and ice but that this can be adjusted by changing the loss process for cloud liquid (autoconversion). Furthermore, there are few discernible effects of the PUMAS changes on cloud feedbacks but some reductions in the magnitude of aerosol–cloud interactions (ACIs). Small cloud feedback changes appear to be related to the implicit sedimentation scheme, with a number of factors affecting ACIs.
54 ENVIRONMENTAL SCIENCES↗
Another Year of Record Heat for the Oceans
Abstract Changes in ocean heat content (OHC), salinity, and stratification provide critical indicators for changes in Earth’s energy and water cycles. These cycles have been profoundly altered due to the emission of greenhouse gasses and other anthropogenic substances by human activities, driving pervasive changes in Earth’s climate system. In 2022, the world’s oceans, as given by OHC, were again the hottest in the historical record and exceeded the previous 2021 record maximum. According to IAP/CAS data, the 0–2000 m OHC in 2022 exceeded that of 2021 by 10.9 ± 8.3 ZJ (1 Zetta Joules = 10 21 Joules); and according to NCEI/NOAA data, by 9.1 ± 8.7 ZJ. Among seven regions, four basins (the North Pacific, North Atlantic, the Mediterranean Sea, and southern oceans) recorded their highest OHC since the 1950s. The salinity-contrast index, a quantification of the “salty gets saltier—fresh gets fresher” pattern, also reached its highest level on record in 2022, implying continued amplification of the global hydrological cycle. Regional OHC and salinity changes in 2022 were dominated by a strong La Niña event. Global upper-ocean stratification continued its increasing trend and was among the top seven in 2022.
Meteorology & Atmospheric Sciences↗
Past and future ocean warming
Changes in ocean heat content (OHC) provide a measure of ocean warming, with impacts on the Earth system. This Review synthesizes estimates of past and future OHC changes using observations and models. The top 2,000 m of the global ocean has significantly warmed since the 1950s, gaining 351 ± 59.8 ZJ (1 ZJ = 10 21 J) from 1958 to 2019. The rate of warming increased from <5 to ~10 ZJ yr –1 from the 1960s to the 2010s. Observed area-averaged warming is largest in the Atlantic Ocean and southern oceans at 1.42 ± 0.09 and 1.40 ± 0.09 × 109 J m –2 , respectively, for the upper 2,000 m over 1958–2019. These observed patterns of heat gains are dominated by heat redistribution. Observationally constrained projections suggest that historic ocean warming is irreversible this century, with net warming dependent on the emission scenario. By 2100, projected warming in the top 2,000 m is 2–6 times that observed so far, ranging from 1,030 [839–1,228] ZJ for a low-emission scenario to 1,874 [1,637–2,109] ZJ for a high-emission scenario. The Pacific is projected to be the largest heat reservoir owing to its size, but area-averaged warming remains strongest in the Atlantic and southern oceans. Ocean warming has extensive impacts that pose risks to marine ecosystems and society. Here, the projected changes necessitate a continuation and improvement of observations and models, along with better uncertainty estimation.
54 ENVIRONMENTAL SCIENCES↗
Interpreting Precession-Driven δ O-18 Variability in the South Asian Monsoon Region
Speleothem records from the South Asian summer monsoon (SASM) region display variability in the ratio of O-18 and O-16 (δ O-18) in calcium carbonate at orbital frequencies. The dominant mode of variability in many of these records reflects cycles of precession. There are several potential explanations for why SASM speleothem records show a strong precession signal, including changes in temperature, precipitation, and circulation. Here we use an Earth system model with water isotope tracers and water-tagging capability to deconstruct the precession signal found in SASM speleothem records. Our results show that cycles of precession-eccentricity produce changes in SASM intensity that correlate with local temperature, precipitation, and δ O-18. However, neither the amount effect nor temperature differences are responsible for the majority of the SASM δ O-18 variability. Instead, changes in the relative moisture contributions from different source regions drive much of the SASM δ O-18 signal, with more nearby moisture sources during Northern Hemisphere summer at aphelion and more distant moisture sources during Northern Hemisphere summer at perihelion. Further, we find that evaporation amplifies the δ O-18 signal of soil water relative to that of precipitation, providing a better match with the SASM speleothem records. This work helps explain a significant portion of the long-term variability found in SASM speleothem records.
paleoclimate↗
Reduced ENSO Variability at the LGM Revealed by an Isotope-Enabled Earth System Model
Studying the El Nino Southern Oscillation (ENSO) in the past can help us better understand its dynamics and improve its future projections. However, both paleoclimate reconstructions and model simulations of ENSO strength at the Last Glacial Maximum (LGM; 21 ka B.P.) have led to contradicting results. Here we perform model simulations using the recently developed water isotope-enabled Community Earth System Model (iCESM). For the first time, model-simulated oxygen isotopes are directly compared with those from ENSO reconstructions using the individual foraminifera analysis (IFA). We find that the LGM ENSO is most likely weaker comparing with the preindustrial. The iCESM suggests that total variance of the IFA records may only reflect changes in the annual cycle instead of ENSO variability as previously assumed. Furthermore, the interpretation of subsurface IFA records can be substantially complicated by the habitat depth of thermocline-dwelling foraminifera and their vertical migration with a temporally varying thermocline.
El Niño–Southern Oscillation;isotope-enabled si↗
Improving Alaska Region Short-term Weather Forecast with Data Assimilation
No abstract available
Remote Sensing↗
Satellite Sounder Data Assimilation for Improving Alaska Region Weather Forecast
A case study and monthly statistical analysis using sounder data assimilation to improve the Alaska regional weather forecast model are presented. Weather forecast in Alaska faces challenges as well as opportunities. Alaska has a large land with multiple types of topography and coastal area. Weather forecast models must be finely tuned in order to accurately predict weather in Alaska. Being in the high-latitudes provides Alaska greater coverage of polar orbiting satellites for integration into forecasting models than the lower 48. Forecasting marine low stratus clouds is critical to the Alaska aviation and oil industry and is the current focus of the case study. NASA AIRS/CrIS sounder profiles data are used to do data assimilation for the Alaska regional weather forecast model to improve Arctic marine stratus clouds forecast. Choosing physical options for the WRF model is discussed. Preprocess of AIRS/CrIS sounder data for data assimilation is described. Local observation data, satellite data, and global data assimilation data are used to verify and/or evaluate the forecast results by the MET tools Model Evaluation Tools (MET).
Zhu, Jiang↗
Satellite Sounder Data Assimilation for Improving Alaska Region Weather Forecast
Data assimilation has been demonstrated very useful in improving both global and regional numerical weather prediction. Alaska has very coarser surface observation sites. On the other hand, it gets much more satellite overpass than lower 48 states. How to utilize satellite data to improve numerical prediction is one of hot topics among weather forecast community in Alaska. The Geographic Information Network of Alaska (GINA) at University of Alaska is conducting study on satellite data assimilation for WRF model. AIRS/CRIS sounder profile data are used to assimilate the initial condition for the customized regional WRF model (GINA-WRF model). Normalized standard deviation, RMSE, and correlation statistic analysis methods are applied to analyze one case of 48 hours forecasts and one month of 24-hour forecasts in order to evaluate the improvement of regional numerical model from Data assimilation. The final goal of the research is to provide improved real-time short-time forecast for Alaska regions.
Zhu, Jiang↗
Modeling of Turbulent Swirling Flows
Aircraft engine combustors generally involve turbulent swirling flows in order to enhance fuel-air mixing and flame stabilization. It has long been recognized that eddy viscosity turbulence models are unable to appropriately model swirling flows. Therefore, it has been suggested that, for the modeling of these flows, a second order closure scheme should be considered because of its ability in the modeling of rotational and curvature effects. However, this scheme will require solution of many complicated second moment transport equations (six Reynolds stresses plus other scalar fluxes and variances), which is a difficult task for any CFD implementations. Also, this scheme will require a large amount of computer resources for a general combustor swirling flow. This report is devoted to the development of a cubic Reynolds stress-strain model for turbulent swirling flows, and was inspired by the work of Launder's group at UMIST. Using this type of model, one only needs to solve two turbulence equations, one for the turbulent kinetic energy k and the other for the dissipation rate epsilon. The cubic model developed in this report is based on a general Reynolds stress-strain relationship. Two flows have been chosen for model evaluation. One is a fully developed rotating pipe flow, and the other is a more complex flow with swirl and recirculation.
Shih, Tsan-Hsing↗
Modification of the Two-equation Turbulence Model in NPARC to a Chien Low Reynolds Number K-epsilon Formulation
This report documents the changes that were made to the two-equation k-epsilon turbulence model in the NPARC (National-PARC) code. The previous model based on the low Reynolds number model of Speziale, was replaced with the low Reynolds number k-epsilon model of Chien. The most significant difference was in the turbulent Prandtl numbers appearing in the diffusion terms of the k and epsilon transport equations. A new inflow boundary condition and stability enhancements were also implemented into the turbulence model within NPARC. The report provides the rationale for making the change to the Chien model, code modifications required, and comparisons of the performances of the new model with the previous k-epsilon model and algebraic models used most often in PARC/NPARC. The comparisons show that the Chien k-epsilon model installed here improves the capability of NPARC to calculate turbulent flows.
Georgiadis, Nicholas J.↗
A New Reynolds Stress Algebraic Equation Model
A general turbulent constitutive relation is directly applied to propose a new Reynolds stress algebraic equation model. In the development of this model, the constraints based on rapid distortion theory and realizability (i.e. the positivity of the normal Reynolds stresses and the Schwarz' inequality between turbulent velocity correlations) are imposed. Model coefficients are calibrated using well-studied basic flows such as homogeneous shear flow and the surface flow in the inertial sublayer. The performance of this model is then tested in complex turbulent flows including the separated flow over a backward-facing step and the flow in a confined jet. The calculation results are encouraging and point to the success of the present model in modeling turbulent flows with complex geometries.
Shih, Tsan-Hsing↗
Modeling of Wall-Bounded Complex Flows and Free Shear Flows
Various wall-bounded flows with complex geometries and free shear flows have been studied with a newly developed realizable Reynolds stress algebraic equation model. The model development is based on the invariant theory in continuum mechanics. This theory enables us to formulate a general constitutive relation for the Reynolds stresses. Pope was the first to introduce this kind of constitutive relation to turbulence modeling. In our study, realizability is imposed on the truncated constitutive relation to determine the coefficients so that, unlike the standard k-E eddy viscosity model, the present model will not produce negative normal stresses in any situations of rapid distortion. The calculations based on the present model have shown an encouraging success in modeling complex turbulent flows.
Shih, Tsan-Hsing↗