A method for estimating yield of maize inbred lines by assimilating WOFOST model with Sentinel-2 satellite data.

Maize is the most widely planted food crop in China, and maize inbred lines, as the basis of maize genetic breeding and seed breeding, have a significant impact on China's seed security and food safety. Satellite remote sensing technology has been widely used for growth monitoring and yield estimation of various crops, but it is still doubtful whether the existing remote sensing monitoring means can distinguish the growth difference between maize inbred lines and hybrids and accurately estimate the yield of maize inbred lines. This paper explores a method for estimating the yield of maize inbred lines based on the assimilation of crop models and remote sensing data, initially solves the problem. At first, this paper analyzed the WOFOST(World Food Studies)model parameter sensitivity and used the MCMC(Markov Chain Monte Carlo) method to calibrate the sensitive parameters to obtain the parameter set of maize inbred lines differing from common hybrid maize; then the vegetation indices were selected to establish an empirical model with the measured LAI(Leaf Area Index) at three key development stages to obtain the remotely sensed estimated LAI; finally, the yield of maize inbred lines in the study area was estimated and mapped pixel by pixel using the EnKF(Ensemble Kalman Filter) data assimilation algorithm. Also, this paper compares a method of assimilation by setting a single parameter. Instead of the WOFOST parameter optimization process, a parameter representing the growth weakness of the inbred lines was set in WOFOST to distinguish the inbred lines from the hybrids. The results showed that the yield estimated by the two methods compared with the field measured yield data had R2: 0.56 and 0.18, and RMSE: 684.90 Kg/Ha and 949.95 Kg/Ha, respectively, which proved that the crop growth model of maize inbred lines established in this study combined with the data assimilation method could initially achieve the growth monitoring and yield estimation of maize inbred lines.

Building a Better Forecast: Reformulating the Ensemble Kalman Filter for Improved Applications to Volcano Deformation.

As the volume of data collected at monitored volcanoes continues to expand, researchers will need quick, reliable, and automated methods of inverting those data into useful models of the underlying magma systems. Recently adapted from other fields for use in volcanology, the Ensemble Kalman Filter (EnKF) is one such inversion technique that has been used to produce several successful forecasts and hind-casts of volcanic unrest, correlating geodetic deformation with mechanical stresses around the magma reservoir. However, given the similarity in which changes to a reservoir's size and pressure are expressed at the surface, the filter can have trouble fully resolving magmatic conditions. In this study, we therefore test several different published variations of the EnKF workflow to produce an optimal configuration for use in future forecasting efforts. By generating synthetic observations of ground deformation under known conditions and then assimilating them through different implementations of the EnKF, we find that many variants favored in other fields underperform for this specific application. We conclude that correlations between model parameters that develop within the EnKF's Monte Carlo ensemble distort the filter's ability to correctly update the model state, causing the filter to systematically favor changes in some parameters over others and ultimately converge to a partially inaccurate solution. This effect can be somewhat mitigated by interrupting these parameter correlations, and the filter remains sensitive to many aspects of the magma system regardless. However, further research and novel approaches will be needed to truly optimize the EnKF for use in volcanology.

Release process identification of non-instantaneous point source pollution in rivers via reverse flow and pollution routing.

Source identification is fundamental for managing sudden river water pollution; however, it is a challenging task. Although numerous studies have investigated this issue, most involve optimization or statistical models for instantaneous pollution and do not consider the reverse propagation and release processes. Herein, we propose an approach for identifying the release process of non-instantaneous point source pollution in rivers, based on reverse flow and pollution routing. The identification approach can trace the historical trajectory of pollutants and their release processes, providing the necessary information for treating accidental pollution. The effectiveness and efficiency of the proposed approach were tested and demonstrated using hypothetical and real-world river cases. The results indicated that the approach identified the release process with high accuracy, and second-round identification using the ensemble Kalman filter could generally improve the identification results from the reverse routing model. This approach was feasible in different cases of observation error, although the error considerably reduced its accuracy. The identification results were also found to be substantially influenced by release duration, with a shorter release time corresponding to an inferior identification result. Nevertheless, the approach worked well in real-world river cases and was generally not affected by the release location, pollutant diffusion, or river geomorphology. In addition, the new approach has advantages in computational efficiency and applicability over traditional methods.

Fetal Electrocardiogram Extraction from the Mother's Abdominal Signal Using the Ensemble Kalman Filter.

Fetal electrocardiogram (fECG) assessment is essential throughout pregnancy to monitor the wellbeing and development of the fetus, and to possibly diagnose potential congenital heart defects. Due to the high noise incorporated in the abdominal ECG (aECG) signals, the extraction of fECG has been challenging. And it is even a lot more difficult for fECG extraction if only one channel of aECG is provided, i.e., in a compact patch device. In this paper, we propose a novel algorithm based on the Ensemble Kalman filter (EnKF) for non-invasive fECG extraction from a single-channel aECG signal. To assess the performance of the proposed algorithm, we used our own clinical data, obtained from a pilot study with 10 subjects each of 20 min recording, and data from the PhysioNet 2013 Challenge bank with labeled QRS complex annotations. The proposed methodology shows the average positive predictive value (PPV) of 97.59%, sensitivity (SE) of 96.91%, and F1-score of 97.25% from the PhysioNet 2013 Challenge bank. Our results also indicate that the proposed algorithm is reliable and effective, and it outperforms the recently proposed extended Kalman filter (EKF) based algorithm.

A Novel Data Sampling Driven Kalman Filter Is Designed by Combining the Characteristic Sampling of UKF and the Random Sampling of EnKF.

In order to improve the performance of the Kalman filter for nonlinear systems, this paper contains the advantages of UKF statistical sampling and EnKF random sampling, respectively, and establishes a new design method of sampling a driven Kalman filter in order to overcome the shortcomings of UKF and EnKF. Firstly, a new sampling mechanism is proposed. Based on sigma sampling with UKF statistical constraints, random sampling similar to EnKF is carried out around each sampling point, so as to obtain a large sample data ensemble that can better describe the characteristics of the system variables to be evaluated. Secondly, by analyzing the spatial distribution characteristics of the obtained large sample ensemble, a sample weight selection and assignment mechanism with the centroid of the data ensemble as the optimization goal are established. Thirdly, a new Kalman filter driven by large data sample ensemble is established. Finally, the effectiveness of the new filter is verified by computer numerical simulation experiments.

Mathematical modeling of COVID-19 pandemic in the context of sub-Saharan Africa: a short-term forecasting in Cameroon and Gabon.

In this paper, we propose and analyse a compartmental model of COVID-19 to predict and control the outbreak. We first formulate a comprehensive mathematical model for the dynamical transmission of COVID-19 in the context of sub-Saharan Africa. We provide the basic properties of the model and compute the basic reproduction number $\mathcal {R}_0$ when the parameter values are constant. After, assuming continuous measurement of the weekly number of newly COVID-19 detected cases, newly deceased individuals and newly recovered individuals, the Ensemble of Kalman filter (EnKf) approach is used to estimate the unmeasured variables and unknown parameters, which are assumed to be time-dependent using real data of COVID-19. We calibrated the proposed model to fit the weekly data in Cameroon and Gabon before, during and after the lockdown. We present the forecasts of the current pandemic in these countries using the estimated parameter values and the estimated variables as initial conditions. During the estimation period, our findings suggest that $\mathcal {R}_0 \approx 1.8377 $ in Cameroon, while $\mathcal {R}_0 \approx 1.0379$ in Gabon meaning that the disease will not die out without any control measures in theses countries. Also, the number of undetected cases remains high in both countries, which could be the source of the new wave of COVID-19 pandemic. Short-term predictions firstly show that one can use the EnKf to predict the COVID-19 in Sub-Saharan Africa and that the second vague of the COVID-19 pandemic will still increase in the future in Gabon and in Cameroon. A comparison between the basic reproduction number from human individuals $\mathcal {R}_{0h}$ and from the SARS-CoV-2 in the environment $\mathcal {R}_{0v}$ has been done in Cameroon and Gabon. A comparative study during the estimation period shows that the transmissions from the free SARS-CoV-2 in the environment is greater than that from the infected individuals in Cameroon with $\mathcal {R}_{0h}$ = 0.05721 and $\mathcal {R}_{0v}$ = 1.78051. This imply that Cameroonian apply distancing measures between individual more than with the free SARS-CoV-2 in the environment. But, the opposite is observed in Gabon with $\mathcal {R}_{0h}$ = 0.63899 and $\mathcal {R}_{0v}$ = 0.39894. So, it is important to increase the awareness campaigns to reduce contacts from individual to individual in Gabon. However, long-term predictions reveal that the COVID-19 detected cases will play an important role in the spread of the disease. Further, we found that there is a necessity to increase timely the surveillance by using an awareness program and a detection process, and the eradication of the pandemic is highly dependent on the control measures taken by each government.

Assimilation of Sentinel 1 and SMAP - based satellite soil moisture retrievals into SWAT hydrological model: the impact of satellite revisit time and product spatial resolution on flood simulations in small basins.

In runoff generation process, soil moisture plays an important role as it controls the magnitude of the flood events in response to the rainfall inputs. In this study, we investigated the ability of a new era of satellite soil moisture retrievals to improve the Soil & Water Assessment Tool (SWAT) daily discharge simulations via soil moisture data assimilation for two small (< 500 km2) and hydrologically different catchments located in Central Italy. We ingested 1) the Soil Moisture Active and Passive (SMAP) Enhanced L3 Radiometer Global Daily 9 km EASE-Grid soil moisture, 2) the Advanced SCATterometer (ASCAT) H113 soil moisture product released within the EUMETSAT Satellite Application Facility on Support to Operational Hydrology and Water Management (H-SAF) which has a nearly daily temporal resolution and sampling of 12.5 km, and 3) a fused ASCAT/Sentinel-1 (S1) satellite soil moisture product named SCATSAR-SWI with temporal and spatial sampling of 1 day and 1 km, respectively into SWAT hydrological model via the Ensemble Kalman Filter (EnKF). Different configurations were tested with the aim of exploring the effect of the hydrological regime, the land use conditions, the spatial sampling and the revisit time of the products (which controls the amount of available data to be potentially ingested). Results show a general improvement of SWAT discharge simulations for all products in terms of error and Nash Sutcliffe efficiency index. In particular, we found a relatively good behavior of both the active and the passive products in terms of low flows improvement especially for the catchment characterized by a higher baseflow component. The benefit of the higher spatial resolution of SCATSAR-SWI obtained via S1 over ASCAT was small, likely due to very challenging areas for the S1 retrieval. Eventually, better performances were obtained for the passive product in the more forested catchment. With the aim of exploring the benefit of having more frequent satellite soil moisture observations to be ingested, we tested the performance of the ASCAT product with a reduced temporal sampling obtained by temporally matching ASCAT observations to that of SMAP. The results show a significant reduction of the performance of ASCAT, suggesting that the correction frequency (due to the higher number of observations available) for small catchments is an important aspect for improving flood forecasting as it helps to adjust more frequently the pre-storm soil moisture conditions.

NO x Emission Changes Over China During the COVID-19 Epidemic Inferred From Surface NO2 Observations.

The COVID-19 epidemic has substantially limited human activities and affected anthropogenic emissions. In this work, daily NO x emissions are inferred using a regional data assimilation system and hourly surface NO2 measurement over China. The results show that because of the coronavirus outbreak, NO x emissions across the whole mainland China dropped sharply after 31 January, began to rise slightly in certain areas after 10 February, and gradually recover across the country after 20 February. Compared with the emissions before the outbreak, NO x emissions fell by more than 60% and ~30% in many large cities and most small to medium cities, respectively. Overall, NO x emissions were reduced by 36% over China, which were mainly contributed by transportation. Evaluations show that the inverted changes over eastern China are credible, whereas those in western China might be underestimated. These findings are of great significance for exploring the reduction potential of NO x emissions in China.

A Maximum Likelihood Ensemble Filter Via A Modified Cholesky Decomposition For Non-Gaussian Data Assimilation.

This paper proposes an efficient and practical implementation of the Maximum Likelihood Ensemble Filter via a Modified Cholesky decomposition (MLEF-MC). The method works as follows: via an ensemble of model realizations, a well-conditioned and full-rank square-root approximation of the background error covariance matrix is obtained. This square-root approximation serves as a control space onto which analysis increments can be computed. These are calculated via Line-Search (LS) optimization. We theoretically prove the convergence of the MLEF-MC. Experimental simulations were performed using an Atmospheric General Circulation Model (AT-GCM) and a highly nonlinear observation operator. The results reveal that the proposed method can obtain posterior error estimates within reasonable accuracies in terms of ℓ - 2 error norms. Furthermore, our analysis estimates are similar to those of the MLEF with large ensemble sizes and full observational networks.

Joint Assimilation of Leaf Area Index and Soil Moisture from Sentinel-1 and Sentinel-2 Data into the WOFOST Model for Winter Wheat Yield Estimation.

It is well known that timely crop growth monitoring and accurate crop yield estimation at a fine scale is of vital importance for agricultural monitoring and crop management. Crop growth models have been widely used for crop growth process description and yield prediction. In particular, the accurate simulation of important state variables, such as leaf area index (LAI) and root zone soil moisture (SM), is of great importance for yield estimation. Data assimilation is a useful tool that combines a crop model and external observations (often derived from remote sensing data) to improve the simulated crop state variables and consequently model outputs like crop total biomass, water use and grain yield. In spite of its effectiveness, applying data assimilation for monitoring crop growth at the regional scale in China remains challenging, due to the lack of high spatiotemporal resolution satellite data that can match the small field sizes which are typical for agriculture in China. With the accessibility of freely available images acquired by Sentinel satellites, it becomes possible to acquire data at high spatiotemporal resolution (10-30 m, 5-6 days), which offers attractive opportunities to characterize crop growth. In this study, we assimilated remotely sensed LAI and SM into the Word Food Studies (WOFOST) model to estimate winter wheat yield using an ensemble Kalman filter (EnKF) algorithm. The LAI was calculated from Sentinel-2 using a lookup table method, and the SM was calculated from Sentinel-1 and Sentinel-2 based on a change detection approach. Through validation with field data, the inverse error was 10% and 35% for LAI and SM, respectively. The open-loop wheat yield estimation, independent assimilations of LAI and SM, and a joint assimilation of LAI + SM were tested and validated using field measurement observation in the city of Hengshui, China, during the 2016-2017 winter wheat growing season. The results indicated that the accuracy of wheat yield simulated by WOFOST was significantly improved after joint assimilation at the field scale. Compared to the open-loop estimation, the yield root mean square error (RMSE) with field observations was decreased by 69 kg/ha for the LAI assimilation, 39 kg/ha for the SM assimilation and 167 kg/ha for the joint LAI + SM assimilation. Yield coefficients of determination (R2) of 0.41, 0.65, 0.50, and 0.76 and mean relative errors (MRE) of 4.87%, 4.32%, 4.45% and 3.17% were obtained for open-loop, LAI assimilation alone, SM assimilation alone and joint LAI + SM assimilation, respectively. The results suggest that LAI was the first-choice variable for crop data assimilation over SM, and when both LAI and SM satellite data are available, the joint data assimilation has a better performance because LAI and SM have interacting effects. Hence, joint assimilation of LAI and SM from Sentinel-1 and Sentinel-2 at a 20 m resolution into the WOFOST provides a robust method to improve crop yield estimations. However, there is still bias between the key soil moisture in the root zone and the Sentinel-1 C band retrieved SM, especially when the vegetation cover is high. By active and passive microwave data fusion, it may be possible to offer a higher accuracy SM for crop yield prediction.

MATLAB algorithm to implement soil water data assimilation with the Ensemble Kalman Filter using HYDRUS.

Data assimilation is becoming a promising technique in hydrologic modelling to update not only model states but also to infer model parameters, specifically to infer soil hydraulic properties in Richard-equation-based soil water models. The Ensemble Kalman Filter method is one of the most widely employed method among the different data assimilation alternatives. In this study the complete Matlab© code used to study soil data assimilation efficiency under different soil and climatic conditions is shown. The code shows the method how data assimilation through EnKF was implemented. Richards equation was solved by the used of Hydrus-1D software which was run from Matlab. •MATLAB routines are released to be used/modified without restrictions for other researchers•Data assimilation Ensemble Kalman Filter method code.•Soil water Richard equation flow solved by Hydrus-1D.

An Assessment of the Impact of Land Thermal Infrared Observation on Regional Weather Forecasts Using Two Different Data Assimilation Approaches.

Recent studies have shown the unique value of satellite-observed land surface thermal infrared (TIR) information (e.g., skin temperature) and the feasibility of assimilating land surface temperature (LST) into land surface models (LSMs) to improve the simulation of land-atmosphere water and energy exchanges. In this study, two different types of LST assimilation techniques are implemented and the benefits from the techniques are compared. One of the techniques is to directly assimilate LST using ensemble Kalman filter (EnKF) data assimilation (DA) utilities. The other is to use the Atmosphere-Land Exchange Inversion model (ALEXI) as an "observation operator" that converts LST retrievals into the soil moisture (SM) proxy based on the ratio of actual to potential evapotranspiration (fPET), which is then assimilated into an LSM. While most current studies have shown some success in both directly the assimilating LST and assimilating ALEXI SM proxy into offline LSMs, the potential impact of the assimilation of TIR information through coupled numerical weather prediction (NWP) models is unclear. In this study, a semi-coupled Land Information System (LIS) and Weather Research and Forecast (WRF) system is employed to assess the impact of the two different techniques for assimilating the TIR observations from NOAA GOES satellites on WRF model forecasts. The NASA LIS, equipped with a variety of LSMs and advanced data assimilation tools (e.g., the ensemble Kalman Filter (EnKF)), takes atmospheric forcing data from the WRF model run, generates updated initial land surface conditions with the assimilation of either LST- or TIR-based SM and returns them to WRF for initializing the forecasts. The WRF forecasts using the daily updated initializations with the TIR data assimilation are evaluated against ground weather observations and re-analysis products. It is found that WRF forecasts with the LST-based SM assimilation have better agreement with the ground weather observations than those with the direct LST assimilation or without the land TIR data assimilation.

Non Invasive Blood Flow Features Estimation in Cerebral Arteries from Uncertain Medical Data.

A methodology for non-invasive estimation of the pressure in internal carotid arteries is proposed. It uses data assimilation and Ensemble Kalman filters in order to identify unknown parameters in a mathematical description of the cerebral network. The approach uses patient specific blood flow rates extracted from Magnetic Resonance Angiography and Magnetic Resonance Imaging. This construction is necessary as the simulation of blood flows in complex arterial networks, such as the circle of Willis, is not straightforward because hemodynamic parameters are unknown as well as the boundary conditions necessary to close this complex system with many outlets. For instance, in clinical cases, the values of Windkessel model parameters or the Young's modulus and the thickness of the arteries are not available on per-patient cases. To make the approach computational efficient, a reduced order zero-dimensional compartment model is used for blood flow dynamics. Using this simplified model, the proof-of-concept study demonstrates how to use the EnKF as an optimization tool to find parameters and how to make the inverse hemodynamic problem tractable. The predicted blood flow rates in the internal carotid arteries and the predicted systolic and diastolic brachial blood pressures are found to be in good agreement with the clinical measurements.

Uncertainty Quantification in a Patient-Specific One-Dimensional Arterial Network Model: EnKF-Based Inflow Estimator.

Successful clinical use of patient-specific models for cardiovascular dynamics depends on the reliability of the model output in the presence of input uncertainties. For 1D fluid dynamics models of arterial networks, input uncertainties associated with the model output are related to the specification of vessel and network geometry, parameters within the fluid and wall equations, and parameters used to specify inlet and outlet boundary conditions. This study investigates how uncertainty in the flow profile applied at the inlet boundary of a 1D model affects area and pressure predictions at the center of a single vessel. More specifically, this study develops an iterative scheme based on the ensemble Kalman filter (EnKF) to estimate the temporal inflow profile from a prior distribution of curves. The EnKF-based inflow estimator provides a measure of uncertainty in the size and shape of the estimated inflow, which is propagated through the model to determine the corresponding uncertainty in model predictions of area and pressure. Model predictions are compared to ex vivo area and blood pressure measurements in the ascending aorta, the carotid artery, and the femoral artery of a healthy male Merino sheep. Results discuss dynamics obtained using a linear and a nonlinear viscoelastic wall model.

Validation and Parameter Sensitivity Tests for Reconstructing Swell Field Based on an Ensemble Kalman Filter.

The swell propagation model built on geometric optics is known to work well when simulating radiated swells from a far located storm. Based on this simple approximation, satellites have acquired plenty of large samples on basin-traversing swells induced by fierce storms situated in mid-latitudes. How to routinely reconstruct swell fields with these irregularly sampled observations from space via known swell propagation principle requires more examination. In this study, we apply 3-h interval pseudo SAR observations in the ensemble Kalman filter (EnKF) to reconstruct a swell field in ocean basin, and compare it with buoy swell partitions and polynomial regression results. As validated against in situ measurements, EnKF works well in terms of spatial-temporal consistency in far-field swell propagation scenarios. Using this framework, we further address the influence of EnKF parameters, and perform a sensitivity analysis to evaluate estimations made under different sets of parameters. Such analysis is of key interest with respect to future multiple-source routinely recorded swell field data. Satellite-derived swell data can serve as a valuable complementary dataset to in situ or wave re-analysis datasets.

[Simulating of carbon fluxes in bamboo forest ecosystem using BEPS model based on the LAI assimilated with Dual Ensemble Kalman Filter]. / 双集合卡尔曼滤波LAI同化结合BEPS模型的竹林生态系统碳通量模拟.

LAI is one of the most important observation data in the research of carbon cycle of forest ecosystem, and it is also an important parameter to drive process-based ecosystem model. The Moso bamboo forest (MBF) and Lei bamboo forest (LBF) were selected as the study targets. Firstly, the MODIS LAI time series data during 2014-2015 was assimilated with Dual Ensemble Kalman Filter method. Secondly, the high quality assimilated MBF LAI and LBF LAI were used as input dataset to drive BEPS model for simulating the gross primary productivity (GPP), net ecosystem exchange (NEE) and total ecosystem respiration (TER) of the two types of bamboo forest ecosystem, respectively. The modeled carbon fluxes were evaluated by the observed carbon fluxes data, and the effects of different quality LAI inputs on carbon cycle simulation were also studied. The LAI assimilated using Dual Ensemble Kalman Filter of MBF and LBF were significantly correlated with the observed LAI, with high R2 of 0.81 and 0.91 respectively, and lower RMSE and absolute bias, which represented the great improvement of the accuracy of MODIS LAI products. With the driving of assimilated LAI, the modeled GPP, NEE, and TER were also highly correlated with the flux observation data, with the R2 of 0.66, 0.47, and 0.64 for MBF, respectively, and 0.66, 0.45, and 0.73 for LBF, respectively. The accuracy of carbon fluxes modeled with assimilated LAI was higher than that acquired by the locally adjusted cubic-spline capping method, in which, the accuracy of mo-deled NEE for MBF and LBF increased by 11.2% and 11.8% at the most degrees, respectively.

Integrating remotely sensed surface water extent into continental scale hydrology.

In hydrological forecasting, data assimilation techniques are employed to improve estimates of initial conditions to update incorrect model states with observational data. However, the limited availability of continuous and up-to-date ground streamflow data is one of the main constraints for large-scale flood forecasting models. This is the first study that assess the impact of assimilating daily remotely sensed surface water extent at a 0.1° × 0.1° spatial resolution derived from the Global Flood Detection System (GFDS) into a global rainfall-runoff including large ungauged areas at the continental spatial scale in Africa and South America. Surface water extent is observed using a range of passive microwave remote sensors. The methodology uses the brightness temperature as water bodies have a lower emissivity. In a time series, the satellite signal is expected to vary with changes in water surface, and anomalies can be correlated with flood events. The Ensemble Kalman Filter (EnKF) is a Monte-Carlo implementation of data assimilation and used here by applying random sampling perturbations to the precipitation inputs to account for uncertainty obtaining ensemble streamflow simulations from the LISFLOOD model. Results of the updated streamflow simulation are compared to baseline simulations, without assimilation of the satellite-derived surface water extent. Validation is done in over 100 in situ river gauges using daily streamflow observations in the African and South American continent over a one year period. Some of the more commonly used metrics in hydrology were calculated: KGE', NSE, PBIAS%, R2, RMSE, and VE. Results show that, for example, NSE score improved on 61 out of 101 stations obtaining significant improvements in both the timing and volume of the flow peaks. Whereas the validation at gauges located in lowland jungle obtained poorest performance mainly due to the closed forest influence on the satellite signal retrieval. The conclusion is that remotely sensed surface water extent holds potential for improving rainfall-runoff streamflow simulations, potentially leading to a better forecast of the peak flow.

Impacts of using an ensemble Kalman filter on air quality simulations along the California-Mexico border region during Cal-Mex 2010 field campaign.

The purpose of this study is to investigate the impact of using an ensemble Kalman filter (EnKF) on air quality simulations in the California-Mexico border region on two days (May 30 and June 04, 2010) during Cal-Mex 2010. The uncertainties in ozone (O3) and aerosol simulations in the border area due to the meteorological initial uncertainties were examined through ensemble simulations. The ensemble spread of surface O3 averaged over the coastal region was less than 10ppb. The spreads in the nitrate and ammonium aerosols are substantial on both days, mostly caused by the large uncertainties in the surface temperature and humidity simulations. In general, the forecast initialized with the EnKF analysis (EnKF) improved the simulation of meteorological fields to some degree in the border region compared to the reference forecast initialized with NCEP analysis data (FCST) and the simulation with observation nudging (FDDA), which in turn leading to reasonable air quality simulations. The simulated surface O3 distributions by EnKF were consistently better than FCST and FDDA on both days. EnKF usually produced more reasonable simulations of nitrate and ammonium aerosols compared to the observations, but still have difficulties in improving the simulations of organic and sulfate aerosols. However, discrepancies between the EnKF simulations and the measurements were still considerably large, particularly for sulfate and organic aerosols, indicating that there are still ample rooms for improvement in the present data assimilation and/or the modeling systems.