Model Simulations Research Articles

Protein SUMOylation promotes cAMP-independent EPAC1 activation

Protein SUMOylation is a prevalent stress-response posttranslational modification crucial for maintaining cellular homeostasis. Herein, we report that protein SUMOylation modulates cellular signaling mediated by cAMP, an ancient and universal stress-response second messenger. We identify K561 as a primary SUMOylation site in exchange protein directly activated by cAMP (EPAC1) via site-specific mapping of SUMOylation using mass spectrometry. Sequence and site-directed mutagenesis analyses reveal that a functional SUMO-interacting motif in EPAC1 is required for the binding of SUMO-conjugating enzyme UBC9, formation of EPAC1 nuclear condensate, and EPAC1 cellular SUMOylation. Heat shock-induced SUMO modification of EPAC1 promotes Rap1/2 activation in a cAMP-independent manner. Structural modeling and molecular dynamics simulation studies demonstrate that SUMO substituent on K561 of EPAC1 promotes Rap1 interaction by increasing the buried surface area between the SUMOylated receptor and its effector. Our studies identify a functional SUMOylation site in EPAC1 and unveil a novel mechanism in which SUMOylation of EPAC1 leads to its autonomous activation. The findings of SUMOylation-mediated activation of EPAC1 not only provide new insights into our understanding of cellular regulation of EPAC1 but also will open up a new field of experimentation concerning the cross-talk between cAMP/EPAC1 signaling and protein SUMOylation, two major cellular stress response pathways, during cellular homeostasis.

Dose optimization of cefazolin in South African children undergoing cardiac surgery with cardiopulmonary bypass.

Cefazolin is an antibiotic used to prevent surgical site infections. During cardiac surgery with cardiopulmonary bypass (CPB), its efficacy target could be underachieved. We aimed to develop a population pharmacokinetic model for cefazolin in children and optimize the prophylactic dosing regimen. Children under 25 kg undergoing cardiac surgery with CPB and receiving cefazolin at standard doses (50 mg/kg IV every 4-6 h) were included in this analysis. A population pharmacokinetic model and Monte Carlo simulations were used to evaluate the probability of target attainment (PTA) for efficacy and toxicity with the standard regimen and an alternative regimen of continuous infusion, where loading and maintenance doses were calculated from model-derived individual parameters. Twenty-two patients were included, with median (range) age, body weight, and eGFR of 19.5 (1-94) months, 8.7 (2-21) kg, and 116 (48-159) mL/min, respectively. Six patients received an additional dose in the CPB circuit. A two-compartment disposition model with an additional compartment for the CPB was developed, including weight-based allometric scaling and eGFR. For a 10 kg patient with eGFR of 120 mL/min/1.73 m2, clearance was estimated as 0.856 L/h. Simulations indicated that the standard dosing regimen fell short of achieving the efficacy target >40% of the time within a dosing duration and in patients with good renal function, PTA ranged from <20% to 70% for the smallest to the largest patients, respectively, at high MICs. In contrast, the alternative regimen consistently maintained target concentrations throughout the procedure for all patients while using a lower overall dose.

Nitrate pollution deterioration in winter driven by surface ozone increase

Recently, nitrate (NO3–) levels in winter pollution in eastern China have been increasing yearly and have become the main component of PM2.5. The factors contributing to this rise in surface NO3– concentrations remain unclear, complicating the development of targeted pollution control measures. This study utilizes observational data from Shanghai during the winter 2019, alongside box model simulations, to recreate the NO3− pollution event and identify the key factors in the growth process. The analysis demonstrated that a rise in winter ozone levels significantly promotes NO3– production by facilitating NOx conversion via gas-phase and heterogeneous reactions. These findings could explain the correlation between the synchronous increase of surface ozone and NO3− in recent years. Furthermore, simulation of control strategies for NOx and volatile organic compounds (VOCs) identified an approach centered on ozone reduction as notably effective in mitigating winter NO3– pollution in the Yangtze River Delta.

Industrial robot arm dynamic modeling simulation and variable-gain iterative learning control strategy design

Industrial robot arm dynamic modeling simulation and variable-gain iterative learning control strategy design

Historical and future extreme climate events in highly vulnerable small Caribbean Islands

AbstractSmall Caribbean islands are on the frontline of climate change because of sea level rise, extreme rainfall and temperature events, and heavy hurricanes. The Archipelago of San Andrés, Providencia, and Santa Catalina (SAI), are Caribbean islands belonging to Colombia and declared a Biosphere Reserve by UNESCO. SAI is highly vulnerable to climate change impacts but no hydroclimatological study quantified the extreme climatic changes yet. This study analyzes historical (1960s-2020, 7 stations) and future (2071–2100, CMIP6 multi-model ensemble, for four scenarios: SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5) trends in mean and extreme precipitation and temperature duration, frequency, and intensity. We find that heatwaves have more than tripled in frequency and doubled their maximum duration since the end of the ‘80 s. Precipitation is historically reduced by 5%, with a reduction recorded in 5 stations and an increase in 2, while extreme rainfall events significantly increased in frequency and intensity in most stations. The hotter-and-drier climate is amplified in the future for all scenarios, with much drier extremes (e.g., -0.5─-17% wet days, +8%─30% consecutive dry days, and +60%─89% in hot days). Although we show that hurricanes Categories IV and V near SAI (&lt; 600 km) more than doubled since the’60 s, only a small fraction of extreme rainfall in the archipelago is associated with hurricanes or tropical storms. La Niña events also have no substantial influence on extreme precipitation. Interestingly, opposite and heterogeneous historical extreme rainfall trends are found across such small territory (&lt; 30 km2). Thus, downscaled hydrometeorological data and model simulations are essential to investigate future extreme climatic events and strengthen small Caribbean islands' climate change adaptation efforts.

Dark fluxes from electromagnetic cascades

We study dark sector production in electromagnetic (EM) cascades. This problem requires accurate simulations of Standard Model (SM) and dark sector processes, both of which impact angular and energy distributions of emitted particles that ultimately determine flux predictions in a downstream detector. We describe the minimal set of QED processes which must be included to faithfully reproduce a SM cascade, and identify a universal algorithm to generate a dark sector flux given a Monte-Carlo simulation of a SM shower. We provide a new tool, , which simulates EM cascades with associated dark vector production, and compare it against existing literature and “off the shelf” tools. The signal predictions at downstream detectors can strongly depend on the nontrivial interplay (and modelling) of SM and dark sector processes, in particular multiple Coulomb scattering and positron annihilation. We comment on potential impacts of these effects for realistic experimental setups.

Variational Monte Carlo study of stripes as a function of doping in the t−t′ Hubbard model

We perform variational Monte Carlo simulations of the single-band Hubbard model on the square lattice with both nearest (t) and next-nearest (t′) neighbor hoppings. Our work investigates the consequences of increasing hole doping on the instauration of stripes and the behavior of the superconducting order parameter, with a discussion on how the two phenomena affect each other. We consider two different values of the next-nearest neighbor hopping parameter, that are appropriate for describing cuprate superconductors. We observe that stripes are the optimal state in a wide doping range; the stripe wavelength reduces at increasing doping, until stripes melt into a uniform state for large values of doping. Superconducting pair–pair correlations, indicating the presence of superconductivity, are always suppressed in the presence of stripes. Our results suggest that the phase diagram for the single-band Hubbard model is dominated by stripes, with superconductivity being possible only in a narrow doping range between striped states and a nonsuperconducting metal.

Intermediate E-F layer dynamics study in the Brazilian low-latitude sector: observational data and simulations

This study investigates the downward motion of Intermediate E-F Layers (ILs) in the Brazilian low latitude sector through observation and modeling. Ionosonde data from São José dos Campos (SJC) and Palmas (PAL) were analyzed to investigate the seasonal variation of the IL parameters, including the virtual height (h'IL) and the top frequency (ftIL). The ILs primarily originated from F layer detachment followed by downward motion, peaking before 11 LT and disappearing well before sunset. Daily height variability ranged between 130 and 190 km, with peak frequencies around 4–5 MHz. Using meteor radar data as input, the Ionospheric E-region Model (MIRE) simulated diurnal and semidiurnal tides to analyze neutral wind effects on ILs descent. Model simulations for SJC (October 2008) and PAL (April and June 2009) revealed distinct wind oscillations influencing IL dynamics at heights below 140 km. In SJC, meridional wind shears controlled IL descent, with possible zonal wind interactions weakening ILs. Conversely, in PAL during April 2009, both zonal and meridional winds contributed to IL formation and altitude descent. However, discrepancies between observed and modeled descent rates suggest the need for considering additional atmospheric wave interactions in future modeling studies. June 2009 over PAL presented unique IL behavior, exhibiting a lower observed decay rate and daily height oscillations potentially linked to local modulations. Meanwhile, MIRE indicated that meridional wind shearing predominantly controlled IL descent in the morning, with zonal wind becoming relevant post-midday. These findings enhance our understanding of IL dynamics and their atmospheric drivers.

Does the Asian summer monsoon play a role in the stratospheric aerosol budget of the Arctic?

Abstract. The Asian summer monsoon has a strong convectional component with which aerosols are able to be lifted up into the lower stratosphere. Due to usually long lifetimes and long-range transport aerosols remain there much longer than in the troposphere and are also able to be advected around the globe. Our aim of this study is a synergy between simulations by Chemical Lagrangian Model of the Stratosphere (CLaMS) and KARL (Koldewey Aerosol Raman Lidar) at AWIPEV, Ny-Ålesund in the Arctic, by comparing CLaMS results with exemplary days of lidar measurements as well as analyzing the stratospheric aerosol background. We use global three-dimensional Lagrangian transport simulations including surface origin tracers as well as back trajectories to identify source regions of the aerosol particles measured over Ny-Ålesund. We analyzed lidar data for the year 2021 and found the stratosphere generally clear, without obvious aerosol layers from volcanic eruptions or biomass burnings. Still an obvious annual cycle of the backscatter coefficient with higher values in late summer to autumn and lower values in late winter has been found. Results from CLaMS model simulations indicate that from late summer to early autumn filaments with high fractions of air which originate in South Asia – one of the most polluted regions in the world – reach the Arctic at altitudes between 360 and 380 K potential temperature. We found a coinciding measurement between the overpass of such a filament and lidar observations, and we estimated that backscatter and depolarization increased by roughly 15 % during this event compared to the background aerosol concentration. Hence we demonstrate that the Asian summer monsoon is a weak but measurable source for Arctic stratospheric aerosol in late summer to early autumn.

Pacific Decadal Oscillation Modulates the Impacts of Bering Sea Ice Loss on North American Temperature

AbstractThe cold surges have frequently attacked North America (NA) in recent decades, which has been tied to the diminished sea‐ice over the Bering Sea. However, we find that the contribution of sea‐ice loss to NA winter coldness is state‐dependent on the Pacific Decadal Oscillation (PDO) phase. Using observations and CAM6 model simulations, we find that the phase regulates the atmospheric response to Bering ice loss. During the negative PDO phase (PDO−), there is an apparent eastward‐propagating wave train, accompanied by a strengthened Alaskan ridge and NA cold high, resulting in a robust cold over Central NA. Meanwhile, enhanced upward‐propagating planetary waves weaken the stratospheric polar vortex over the Pacific‐NA regions. During the positive phase (PDO+), the NA temperature response to Bering ice loss is quite weak or even warm. We speculate that more NA cold extremes will appear as the PDO− continues and less as the PDO− shifts to PDO+.

Deciphering the variations and mechanisms of global land monsoons during Marine Isotope Stage 3

Abstract Marine Isotope Stage 3 (MIS 3) is characterized by significant millennial-scale climatic oscillations between cold stadials and mild interstadials, which presents a valuable case for understanding hydrological response to abrupt climate change. Through a set of coupled model simulations, our results broadly show an anti-phased interhemispheric change in land monsoonal precipitation during the present-day relative to MIS 3 interstadial and the stadial-interstadial transition, with a general decrease in the Northern Hemisphere but an increase in the Southern Hemisphere. The anti-phased pattern is largely caused by the change in orbital insolation during the present-day relative to MIS 3 interstadial whereas by the weakened Atlantic Meridional Overturning Circulation during the interstadial-stadial transition. However, there are obvious discrepancies in precipitation response and underlying mechanisms among individual monsoon domains and across different periods. Based on the moisture budget analysis, we indicate that the dynamic factor mainly explains the decreased monsoonal rainfall in the Northern Hemisphere during the present-day relative to the MIS 3 interstadial, whereas the thermodynamic term is largely responsible for the increased precipitation in the Southern Hemisphere. In contrast, the dynamic factor plays an important role in the variation of precipitation over all the monsoon zones from the MIS 3 interstadial to stadial states, with the thermodynamic term mainly contributing to the decreased tropical monsoonal precipitation in the colder Northern Hemisphere. Our results help improve the understanding of global monsoon variations under intermediate glacial climate conditions and shed light on their behaviors under potentially rapid climate change in the future.

Depth localization of subsurface defects by optical dark-field confocal microscopy

Abstract Subsurface defects (SSD) in optical components pose a significant challenge for enhancing the power density of high-energy laser devices. This study investigated the issue of systematic deviation between the measured and actual depths of subsurface defects when employing optical dark-field confocal microscopy for three-dimensional measurements, which is attributed to refractive index disparities between the sample and the observation environment. This paper introduces geometric and diffraction optical models for correcting errors in the subsurface defect depth, along with a calculation method for determining the correction coefficient. By comparing the experimental data and model simulations, a linear relationship between the measured and actual depths was identified with linearity errors below 2.5% and a minimum of 0.67%. The correction coefficients derived from the optical diffraction model are in good agreement with those obtained experimentally. These findings offer valuable insights for calculating subsurface defect depth correction coefficients across various scenarios and requirements to ensure precise measurements.

Synoptic Analysis and WRF‐Chem Model Simulation of Dust Events in the Southwestern United States

AbstractDust transported from rangelands of the Southwestern United States (US) to mountain snowpack in the Upper Colorado River Basin during spring (March‐May) forces earlier and faster snowmelt, which creates problems for water resources and agriculture. To better understand the drivers of dust events, we investigated large‐scale meteorology responsible for organizing two Southwest US dust events from two different dominant geographic locations: (a) the Colorado Plateau and (b) the northern Chihuahuan Desert. High‐resolution Weather Research and Forecasting coupled with Chemistry model (WRF‐Chem) simulations with the Air Force Weather Agency dust emission scheme incorporating a MODIS albedo‐based drag‐partition was used to explore land surface‐atmosphere interactions driving two dust events. We identified commonalities in their meteorological setups. The meteorological analyses revealed that Polar and Sub‐tropical jet stream interaction was a common upper‐level meteorological feature before each of the two dust events. When the two jet streams merged, a strong northeast‐directed pressure gradient upstream and over the source areas resulted in strong near‐surface winds, which lifted available dust into the atmosphere. Concurrently, a strong mid‐tropospheric flow developed over the dust source areas, which transported dust to the San Juan Mountains and southern Colorado snowpack. The WRF‐Chem simulations reproduced both dust events, indicating that the simulations represented the dust sources that contributed to dust‐on‐snow events reasonably well. The representativeness of the simulated dust emission and transport in different geographic and meteorological conditions with our use of albedo‐based drag partition provides a basis for additional dust‐on‐snow simulations to assess the hydrologic impact in the Southwest US.

Developing a tile drainage module for the Cold Regions Hydrological Model: lessons from a farm in southern Ontario, Canada

Abstract. Systematic tile drainage is used extensively in poorly drained agricultural lands to remove excess water and improve crop growth; however, tiles can also transfer nutrients from farmlands to downstream surface water bodies, leading to water quality problems. Thus, there is a need to simulate the hydrological behaviour of tile drains to understand the impacts of climate or land management change on agricultural surface and subsurface runoff. The Cold Regions Hydrological Model (CRHM) is a physically based, modular modelling system developed for cold regions. Here, a tile drainage module is developed for CRHM. A multi-variable, multi-criteria model performance evaluation strategy was deployed to examine the ability of the module to capture tile discharge under both winter and summer conditions (NSE &gt; 0.29, RSR &lt; 0.84 and PBias &lt; 20 for tile flow and saturated storage simulations). Initial model simulations run at a 15 min interval did not satisfactorily represent tile discharge; however, model simulations improved when the time step was lengthened to hourly but also with the explicit representation of capillary rise for moisture interactions between the rooting zone and groundwater, demonstrating the significance of capillary rise above the saturated storage layer in the hydrology of tile drains in loam soils. Novel aspects of this module include the sub-daily time step, which is shorter than most existing models, and the use of field capacity and its corresponding pressure head to provide estimates of drainable water and the thickness of the capillary fringe, rather than using detailed soil retention curves that may not always be available. An additional novel aspect is the demonstration that flows in some tile drain systems can be better represented and simulated when related to shallow saturated storage dynamics.

Impact of Molecular Chlorine Production from Aerosol Iron Photochemistry on Atmospheric Oxidative Capacity in North China.

Elevated levels of atmospheric molecular chlorine (Cl2) have been observed during the daytime in recent field studies in China but could not be explained by the current chlorine chemistry mechanisms in models. Here, we propose a Cl2 formation mechanism initiated by aerosol iron photochemistry to explain daytime Cl2 formation. We implement this mechanism into the GEOS-Chem chemical transport model and investigate its impacts on the atmospheric composition in wintertime North China where high levels of Cl2 as well as aerosol chloride and iron were observed. The new mechanism accounts for more than 90% of surface air Cl2 production in North China and consequently increases the surface air Cl2 abundances by an order of magnitude, improving the model's agreement with observed Cl2. The presence of high Cl2 significantly alters the oxidative capacity of the atmosphere, with a factor of 20-40 increase in the chlorine radical concentration and a 20-40% increase in the hydroxyl radical concentration in regions with high aerosol chloride and iron loadings. This results in an increase in surface air ozone by about 10%. This new Cl2 formation mechanism will improve the model simulation capability for reactive chlorine abundances in the regions with high emissions of chlorine and iron.

Inversion of Left Ventricular Axial Shortening: In Silico Proof of Concept for Treatment of HFpEF

Left ventricular (LV) longitudinal function is mechanically coupled to the elasticity of the ascending aorta (AA). The pathophysiologic link between a stiff AA and reduced longitudinal strain and the subsequent deterioration in longitudinal LV systolic function is likely relevant in heart failure with preserved ejection fraction (HFpEF). The proposed therapeutic effect of freeing the LV apex and allowing for LV inverse longitudinal shortening was studied in silico utilizing the Living Left Heart Human Model (Dassault Systémes Simulia Corporation). LV function was evaluated in a model with (A) an elastic AA, (B) a stiff AA, and (C) a stiff AA with a free LV apex. The cardiac model simulation demonstrated that freeing the apex caused inverse LV longitudinal shortening that could abolish the deleterious mechanical effect of a stiff AA on LV function. A stiff AA and impairment of the LV longitudinal strain are common in patients with HFpEF. The hypothesis-generating model strongly suggests that freeing the apex and inverse longitudinal shortening may improve LV function in HFpEF patients with a stiff AA.

Experimental analysis and modeling of gas turbine engine performance: Design point and off-design insights through system of equations solutions

In this article, a systematic approach is presented for simulating turbojet engine performance at both design and off-design points. The construction of gas turbine engines involves a core, with additional components added based on the proposed methodology. Accurate formulation of component characteristics and their matching forms the basis for the system of equations needed for solving off-design engine performance. The developed algorithm's initial step involves comparing results with experimental data obtained from 230 N engines. Experimental testing utilizes a 780 N engine under diverse operating conditions, allowing determination of thrust values, fuel consumption, and outlet gas temperatures. An engine characteristic curve is derived under static conditions at ground level and validated against ground test results in Tehran. Unknown parameters are calibrated using a dedicated model, enabling the extraction of engine performance parameters across different corrected speeds. These results are then compared with GasTurb outputs. Comparative analysis between the proposed model's simulation and experimental data demonstrates high accuracy, affirming the reliability of the presented model.

Comparison of bulk snow density measurements using different methods

Snow density is one of the basic properties used to describe snow cover characteristics, and it is critical for remote sensing retrieval, water resources assessment and modeling inputs. There are many instruments available to measure snow density in situ. However, there are measurement errors of snow density for bulk and layers or gravimetric and electronic instruments, which may affect the accuracy of remote sensing retrieval and model simulation. Especially in China, due to the noticeable heterogeneity of snowpacks, it is necessary to evaluate in detail the performance and applicability of snow density instruments in different snowpack conditions. This study evaluated the performance of different snow density instruments: the Federal Sampler, the model VS–43 snow density cylinder (VS–43), the wedge snow density cutter (WC1000 and WC250), and the Snow Fork. The average bulk snow density of all instrument measurements was set as the reference value for evaluation. The results showed that as compared with the reference, the VS–43 cylinder presented the best performance for bulk snow density measurement in the measured range with the lowest RMSE (11 kg m−3), BIAS (3 kg m−3), and MRE (1.6%). For layer observation, bulk snow density was overestimated by 8.1% with WC1000 and underestimated by 11.4% with Snow Fork which was the worst performance compared with the reference value, and there were greater measurement errors of snow density in the depth hoar than other snow layers. Compared with grassland, the uncertainty of snow density measurements was slightly lower in forests. Overall, the Federal Sampler and VS–43 cylinder are more suitable for bulk snow density measurement in deep snowpack regions across China, and it is recommended to use WC1000, WC250 and Snow Fork to measure the snow density of snow layers in the snow stratigraphy.

Pathways of ice multiplication in nimbostratus clouds during the Indian summer monsoon

The present study illustrates the microphysical parameters of nimbostratus clouds during the Indian summer monsoon using airborne and radar observations conducted as part of the Cloud Aerosol Interaction and Precipitation Enhancement Experiment (CAIPEEX), and simulations with the Weather Research and Forecasting (WRF) model. The study also analyzes the impact of secondary ice production (emphasizing the microphysical pathways of Hallett-Mossop (HM) as represented in the models) on cloud processes using model sensitivity simulations. The effect of possible pathways of riming during the HM process is the focus of the sensitivity simulations. Aircraft observations showed higher ice particle concentrations in the Hallett–Mossop zone (−3 °C to - 8 °C) along with the existence of smaller and larger cloud droplets, rimed needles, columns, and snow particles. Observations strongly suggested the active presence of the HM process in this cloud. The observed mean values of microphysical parameters including liquid water content, ice number concentrations, and maximum vertical velocity, agreed well with model simulations. The number concentration and water content of ice crystals and snow decreased in the HM zone during the HM inactive case. A reduction in rainfall is also observed in the absence of HM. HM increases convection as it causes a sudden increase in the number concentration of small ice particles, which causes rainwater to freeze quickly and water vapour to be consumed by diffusional growth. Latent heating is produced by both effects, which energizes the convection.

Harvesting vibration energy by quad-stable piezoelectric cantilever beam: Modeling, fabrication and testing

The combination of beams with piezoelectric patches has become a prevalent energy harvesting tool due to its ease of use. Typical energy harvesting systems are usually linear, and their efficiency is not satisfying due to low-frequency bandwidth. In this paper, a quad-stable piezoelectric vibration energy harvester is analyzed both numerically and experimentally. The primary purpose of this investigation is to analyze the static and dynamic characteristics of a proposed quad-stable system to consider its potential for application in broadband energy harvesting comprehensively. The harvester system consists of a slotted cantilever beam, a piezoelectric patch, a pair of tip-mass blocks, and a double-sided clip. The cantilever beam is subjected to pre-displacement constraints made by a mutual self-constraint at the free end of it. The nonlinear behaviors of the harvester system, including snap-through and softening phenomena, are analyzed using the assumed modes and finite element method (FEM). The harvester’s vibration equation is solved numerically and through an FE model which is made by an in-house finite element software. A prototype is designed and fabricated to validate the mathematical model and FE simulation. The experimental force-displacement diagram of the harvester displays distinct discontinuities, reflecting abrupt transitions occurring while switching its stable states. The prototype dynamics are analyzed by harmonic base excitation with different amplitude levels in two conditions, including the presence and absence of the piezoelectric patch. The results obtained from the mathematical and FEM model demonstrate a satisfactory correlation with the experimental data. Furthermore, the experimental data reveal the occurrence of the snap-through phenomenon, accompanied by a significant widening of the frequency bandwidth at relatively high amplitude levels. The system has the ability to provide an average output electrical power of 0.288 mW for an electrical resistance of 3.262 kΩ at the excitation frequency of 12.695 Hz and base acceleration amplitude of 3g.