Multisite Model Research Articles

Absolutely robust controllers for chemical reaction networks.

In this work, we design a type of controller that consists of adding a specific set of reactions to an existing mass-action chemical reaction network in order to control a target species. This set of reactions is effective for both deterministic and stochastic networks, in the latter case controlling the mean as well as the variance of the target species. We employ a type of network property called absolute concentration robustness (ACR). We provide applications to the control of a multisite phosphorylation model as well as a receptor-ligand signalling system. For this framework, we use the so-called deficiency zero theorem from chemical reaction network theory as well as multiscaling model reduction methods. We show that the target species has approximately Poisson distribution with the desired mean. We further show that ACR controllers can bring robust perfect adaptation to a target species and are complementary to a recently introduced antithetic feedback controller used for stochastic chemical reactions.

An Aging Model of NH3 Storage Sites for Predicting Kinetics of NH3 Adsorption, Desorption and Oxidation over Hydrothermally Aged Cu-Chabazite

A unified transient kinetic model which can predict the adsorption, desorption and oxidation kinetics of NH3 over hydrothermally aged Cu-chabazite was developed. The model takes into account the variation of fractional coverages of NH3 storage sites due to hydrothermal aging. In order to determine the fractional coverage of these sites, the catalyst was aged for various times at a certain temperature followed by NH3 adsorption, desorption and temperature-programmed desorption (TPD) experiments. TPD profiles were deconvoluted mainly into three peaks with centres at 317, 456 and 526 °C, respectively. Hydrothermal aging resulted in the progressive increase in the intensity of the peak at 317 °C and decrease in the intensity of the peaks at 456 and 526 °C, along with decreased NH3 oxidation at high temperatures. A model for hydrothermal aging kinetics of the fractional coverage of storage sites was developed using three reactions with appropriate rate expressions with parameters regressed from experimental data. The model was then incorporated into a multi-site kinetic model for the degreened Cu-Chabazite by the addition of aging reactions on each storage site. The effects of both aging time and temperature on the kinetics NH3 adsorption, desorption and oxidation were successfully predicted in the 155-540 °C range. This study is the first step towards the development of a hydrothermal aging-unified kinetic model of NH3-Selective Catalytic Reduction over Cu-chabazite.

The Ca2+ permeation mechanism of the ryanodine receptor revealed by a multi-site ion model

Ryanodine receptors (RyR) are ion channels responsible for the release of Ca2+ from the sarco/endoplasmic reticulum and play a crucial role in the precise control of Ca2+ concentration in the cytosol. The detailed permeation mechanism of Ca2+ through RyR is still elusive. By using molecular dynamics simulations with a specially designed Ca2+ model, we show that multiple Ca2+ ions accumulate in the upper selectivity filter of RyR1, but only one Ca2+ can occupy and translocate in the narrow pore at a time, assisted by electrostatic repulsion from the Ca2+ within the upper selectivity filter. The Ca2+ is nearly fully hydrated with the first solvation shell intact during the whole permeation process. These results suggest a remote knock-on permeation mechanism and one-at-a-time occupation pattern for the hydrated Ca2+ within the narrow pore, uncovering the basis underlying the high permeability and low selectivity of the RyR channels.

Comparing Nonbonded Metal Ion Models in the Divalent Cation Binding Protein PsaA.

Divalent metal cations are essential for many biological processes; however, accurately modeling divalent metal ions has proved a significant challenge for molecular dynamics force fields. Here we show that the choice of ion model influences the observed dynamics in PsaA, a metal binding protein from Streptococcus pneumoniae. We conduct extensive unbiased simulations and free energy calculations of PsaA bound to its cognate ligand Mn2+ and inhibitory ligand Zn2+ using three nonbonded ion models: a 12-6 model, a 12-6-4 model, and a multisite model. The observed coordination geometries and metal binding dynamics are sensitive to the choice of ion model, with the most dramatic differences observed in free energy calculations of ion release. We show that the conformational ensemble of Mn-bound PsaA is more similar to the crystallographic metal bound open state. This work extends the current model of PsaA metal binding and provides a framework for the rationalization of experimentally determined metal binding behavior. Our findings support the use of the 12-6-4 ion model for further simulations of divalent cation binding proteins.

Ammonia dynamic modelling over Cu-SSZ-13 catalyst for NOx emission control in diesel vehicles

Based on the ammonia storage mechanism over Cu-SSZ-13 catalyst, a temperature-dependent heterogeneity constant was introduced in the dual-site model, and was compared with traditional dual-site and multi-site model based on a series NH3-TPD tests in this work.

Predictive two-phase modeling and improvement for industrial UnipolⓇ polypropylene process – Development and a case study

This work presents a two-phase model describing propylene catalytic polymerization for UnipolⓇ technology with a fluidized bed reactor (FBR) using Aspen PlusⓇ software and the sequential modular simulation approach. The hydrodynamic aspects of the FBR were incorporated to provide better realism in describing the performance of the FBR. A detailed kinetic multi-site model for polymerization reactions occurring inside the FBR was proposed. Industrial data from a UnipolⓇ plant during normal operation were used to calibrate the model parameters. Obtained data sets were tested and screened to confirm data validity for establishing the model and averting incorrect outcomes. The model was validated against different industrial data and then was used to investigate the influences of different process variables on the plant's performance. Finally, the model was used to improve the process illustrating a prospective for remarkable savings in energy consumption in the process while enhancing the plant throughput.

Sorption of americium / europium onto magnetite under saline conditions: Batch experiments, surface complexation modelling and X-ray absorption spectroscopy study

HypothesisThis study investigates the adsorption of americium and its chemical analogue europium on magnetite, which is expected to form as a major long-term steel canister corrosion product under anoxic and highly saline conditions. ExperimentsThe sorption of europium on magnetite (solid/liquid ratio = 0.5 g/L) was investigated batch wise in NaCl brines with ionic strength I = 1 m, 3.5 m, and 6.67 m, as a function of pHm for two europium concentrations (6 × 10−10m, 1.2 × 10−5m). Information on the chemical nature of the surface species was obtained by X-ray absorption spectroscopy (XAS) at the americium L3-edge. FindingsRetention of europium by magnetite of >99.5% was found above pHm 6.4 for all ionic strengths for europium concentration of 6 × 10−10m. No ionic strength effect was observed in this pHm range. At 1.2 × 10−5m europium concentration, 95 ± 4% sorption was found above pHm 7.5 for I = 1 m and above pHm 8.0 for I = 3.5 m and 6.67 m. A small ionic strength effect was observed in this case. X-ray absorption spectroscopy (XAS) results are consistent with the batch sorption experiment outcomes, showing an insignificant effect of ionic strength on the pHm dependent sorption. Results from potentiometric titrations of the solid phase, batch sorption experiments and spectroscopy were interpreted consistently with a charge distribution multi-site (CD-MUSIC) triple layer surface complexation model assuming surface coordination of the metal ion via a tridentate binding mode.

A case report of triple neural tube defect: revisiting the multisite closure theory

BackgroundTriple neural tube defects are rare. To the author’s knowledge, there are only four reported cases available in the literature up to date. Controversies exist with regards to the development of neural tube defects. We revisit the multisite closure theory and try to explain the mechanism of neural tube defects in our case.Case presentationWe report a case of one-month-old baby boy who presented to us with three distinct neural tube defects. He had occipital and cervical encephaloceles along with thoracolumbar myelomeningocele accompanied by syrinx and mild hydrocephalus. All the three defects were surgically corrected with good neurological outcome.ConclusionIn the multisite model of human neural tube closure, there are only two fusion sites and two neuropores unlike in mouse. This can explain the origin of open neural tube defects including anencephaly and myelomeningocele (as in our case) but cannot account for the development of encephalocele, which appears to be a post neurulation defect.

Multi-site watershed model calibration for evaluating best management practice effectiveness in reducing fecal pollution

In this study, the Soil and Water Assessment Tool (SWAT) is coupled with the Bacteria Source Load Calculator (BSLC) to develop alternative scenarios of agricultural best management practice (BMP) implementation and septic system repair to achieve total maximum daily load (TMDL) targets for Escherichia coli (E. coli) in a small agricultural watershed located in Michigan, USA. Due to the uncertainty involved in bacterial source estimation from wildlife and failing septic systems in agricultural watersheds, we propose a method for estimating their respective bacteria loading during SWAT calibration, which was performed at eight sampling locations and validated at a ninth. BMP implementation scenarios were prioritized based on their ability to meet TMDL targets at the lowest cost using a spatially targeted subwatershed ranking identifying the greatest E. coli source contribution. BMP effectiveness is driven by E. coli source locations defined in the BSLC-SWAT linkage. The framework developed here, from linking BSLC to SWAT to ranking subwatersheds, was effective in meeting the TMDL targets and is readily transferable to other watersheds. Agricultural BMPs were unsuccessful in meeting TMDL targets, but the target can be met by repairing about 60 of 110 estimated failing septic tanks.

Time to branch out? Application of hierarchical survival models in plant phenology

The sensitivity of phenology to environmental drivers can vary across geography and species. As such, models developed to predict phenology are typically site- or taxon-specific. Generation of site- and taxon-specific models is limited by the intensive in-situ phenological monitoring effort required to generate sufficient data to parameterize each model. Where in-situ phenological observations exist, the data are often subject to analytical issues due to the limited duration of any individual monitoring program, spotty site- and species- level coverage, lack of standardized methodology, and infrequent or variable census intervals. Together, these characteristics constrain our ability to make phenological inferences outside of select sites and taxa where long-duration, intensive monitoring has occurred. In this study, we leveraged two national, standardized phenology datasets to develop a multi-species and multi-site state-space survival model of the onset of deciduous tree and shrub spring (leaf out) and fall (leaf-color) events across temperate ecoregions of the United States. We used data from two national-scale phenological databases, a 9-year, broadly distributed dataset from the USA National Phenology Network and a 4-year dataset from the National Ecological Observatory Network, to quantify regional and interspecific variation in sensitivity to environmental drivers for both spring and fall leaf phenophases. Spring leaf out was generally promoted by longer days, spring growing degree day accumulation, overwinter chilling, and was suppressed by frost events, whereas fall leaf color was promoted by shorter days and cold accumulation. The sensitivity to most environmental drivers tended to be more variable among species than among the regions as defined here (EPA ecoregions of North America, excluding desert and tropical areas). The results of this study lay the groundwork for incorporating the growing collection of phenological observations into a generalized framework for predicting the transition states for any species, in any location.

MUSIC Speciation of γ-Al2O3 at the Solid Liquid Interface: How DFT Calculations Can Help with Amorphous and Poorly Crystalline Materials.

Transition aluminum oxides, such as γ-Al2O3 or alumina, are widely used in many different technical applications that rely on the surface reactivity of this material at the solid liquid interface. The speciation of surface sites of this material confronts several obstacles. On the one hand, alumina is a poorly crystalline oxide, thus allowing for a limited amount of empirical structural information for an important number of surface sites with different trends in reactivity and, on the other hand, it is a metastable material. In this work, we show several ways in which the multisite complexation model, combined with atomistic information from density functional theory and ab initio molecular dynamics (AIMD), can manage to perform speciation calculations of γ-Al2O3 surface sites at the solid liquid interface. Although the results are in good qualitative agreement with experimental titration curves, and they can serve as a guide for the interpretation of the reactivity of this material at the initial stages of an impregnation experiment and chemical weathering phenomena, this work highlights the need of more complex AIMD simulations to accurately model these phenomena in γ-Al2O3 surface/liquid interfaces.

Multi-site and multi-period optimization model for strategic planning of a renewable hydrogen energy network from biomass waste and energy crops

This study proposes an optimization-based approach for strategically planning a biomass-based hydrogen energy network. In achieving this goal, the superstructure of a biomass-based hydrogen energy system is proposed, which includes different biomass resources (biomass waste and energy crops) and various technologies (production, storage and terminal, refueling station, and transportation). A multi-site and multi-period optimization model is then developed using a mixed integer linear programming to determine the optimal investment timing and regional allocation alongside the selection of proper biomass types and technology combinations. The capability of the proposed approach is validated through a case study of Jeju Island, Korea. As a result, it was identified that the optimal network configuration as well as the investment and operation strategies are determined by the biomass type and regional biomass availability. In addition, the sustainability of the proposed energy system was analyzed using the criteria such as energy security and environmental protection, as well as economics.

Simultaneous arsenic and fluoride removal using {201}TiO2-ZrO2: Fabrication, characterization, and mechanism.

The coexistence of arsenic (As) and fluoride (F) in drinking water is an urgent environmental issue that causes increasing public concerns. The need for effective simultaneous removal of As and F has motived great research efforts. Herein, a novel {201}TiO2-ZrO2 composite was synthesized and its application mechanism was explored. Batch adsorption experiments show that the As(III), As(V), and F adsorption followed the pseudo-second-order kinetics with the Langmuir adsorption capacity at 58.5, 21.6, and 13.1 mg/g, respectively. EXAFS and in situ ATR-FTIR results suggested that TiO2 surface sites were occupied by As(III) and As(V) in bidentate binuclear structures, and ZrO2 sites preferentially adsorbed As(III) and F in monodentate mononuclear configurations. This molecular structure obtained in the mono-adsorption system was integrated with the charge distribution multisite surface complexation model to accurately predict the As and F co-existing adsorption behaviors. The results in competitive adsorption, regeneration, and application evidenced that the {201}TiO2-ZrO2 composite is a promising adsorbent for simultaneous As and F removal.

Effects of energetic heterogeneity on gas adsorption and gas storage in geologic shale systems

Capturing heterogeneity in an adsorbate-adsorbent interaction is important to understand the underlying mechanisms controlling adsorption behavior; especially, for natural shale characterized by various mineral compositions and multi-scale pore sizes, its energetic heterogeneity is extremely complex. In this work, experimental investigations of methane adsorption on natural shale were conducted over a range of pressures (0.5–20 MPa) and temperatures (333–393 K), and a multi-site model was introduced to describe the measured adsorption isotherms. Specially, the adsorption energy distribution in our model is related to a pore-size and surface-property dependent function, rather than any traditionally assumed ones, such as Gaussian or exponential distributions. Besides, as an apparent indicator of adsorbent heterogeneity, isosteric heat was analyzed for our studied shales. Results showed that isosteric heat for an energetically homogeneous adsorbent is a constant, while the observed heat for our studied shales gradually decreases with an increase in surface coverage. This coverage-dependent heat is mainly controlled by the ordered occupation of gas molecules on heterogeneous adoption sites; in this respect, the most favorable sites with the highest energy are occupied first followed by secondary sites with lower energy. Furthermore, in application fields, our proposed model can be used to estimate total gas in place for a whole shale gas reservoir and gas resources contributed by individual pores. This work presents comprehensive knowledge about the effect of surface heterogeneity on methane adsorption on shale, and can thus be used as a solid foundation for accurately estimating gas storage and production in geologic systems.

The Ruthenium-106 plume over Europe in 2017: a source-receptor model to estimate the source region

Between the end of September and the beginning of October 2017, low but detectable air concentrations of Ruthenium-106 (R106u) were measured throughout the European atmosphere. To date, the source has not been clearly identified. This study aims at constraining the location of the most likely emission source, by combining HYSPLIT back trajectories and a multi-site source-receptor model. The model follows a concentration weighted trajectory (CWT) approach, based on a R106u measurement dataset gathered by the International Atomic Energy Agency (IAEA) shortly after the event and shared by the French Institut de Radioprotection et de Sûreté Nucléaire (IRSN). The back trajectories are computed using Global Data Assimilation System (GDAS) and ERA-Interim meteorological data, with horizontal resolution from 1.5° to 0.5°. The effect of the starting altitude was also investigated. The source-receptor model results show that the most likely emission source region extends from Ukraine to the West to the Russian Volga and Ural regions to the East, in accordance with two previous studies. The analyses also show that the identified source region is relatively insensitive to the type of meteorological data, their horizontal resolution and values of starting altitude. The model precision is found to increase with increasing number of receptors. The method is fully open-source, requires low computational resources and is therefore suited to estimate the source origin of radioactive pollutants on a real time basis, providing an additional tool to more sophisticated atmospheric models.

Oxalic Acid Adsorption on Rutile: Molecular Dynamics and ab Initio Calculations.

Detailed analysis of the adsorption of oxalic acid ions, that is, oxalate and hydrogenoxalate, on the rutile (110) surface was carried out using molecular dynamics augmented by free energy calculations and supported by ab initio calculations. The predicted adsorption on perfect nonhydroxylated and hydroxylated surfaces with surface charge density from neutral to +0.208 C/m2 corresponding to pH values of about 6 and 3.7, respectively, agrees with experimental adsorption data and charge-distribution multisite ion complexation model predictions obtained using the most favorable surface complexes identified in our simulations. We found that outer-sphere complexes are the most favorable, owing to strong hydrogen binding of oxalic acid ions with surface hydroxyls and physisorbed water. The monodentate complex, the most stable among inner-sphere complexes, was about 15 kJ/mol higher in energy, but separated by a large energy barrier. Other inner-sphere complexes, including some previously suggested in the literature as likely adsorption structures such as bidentate and chelate complexes, were found to be unstable both by classical and by ab initio modeling. Both the surfaces and (hydrogen)oxalate ions were modeled using charges scaled to 75% of the nominal values in accord with the electronic continuum theory and our earlier parameterization of (hydrogen)oxalate ions, which showed that nominal charges exaggerate ion-water interactions.

Synchronized generation of high-resolution gridded precipitation and temperature fields

In this study, synchronized gridded precipitation and temperature generators were developed and evaluated in terms of their ability to reconstruct the spatial structure and other statistical properties of high-resolution CaPA (Canadian Precipitation Analysis) precipitation and GEM (Global Environmental Multiscale Model) temperature products. The precipitation generator is an extension to the gridded multi-site occurrence-amount model. While the multi-site framework is not efficiently applicable to regions with limited precipitation information and sparse observation network, this paper provides the full mathematical description of estimating the model based on high-resolution gridded products. The temperature model, on the other hand, introduces the first gridded hourly generator in the literature in which cyclic temperature components are conditioned using wet and dry day status information. This was achieved using harmonic functions establishing the connection between the simulated daily precipitation occurrence time-series and the moments of the generated temperature data. One of the key features of the proposed gridded generators is the capacity to produce temporally coherent fields of precipitation and temperature; an essential prerequisite for hydrologic modeling applications. The generators were evaluated in terms of their ability to reproduce the standard, interannual, and extreme-value characteristics of observed gridded products. The gridded precipitation model can preserve key statistical and spatial properties of the gridded CaPA observations to an acceptable level, while similar to the original multi-site framework, it falls short to capture long dry spells and the interannual variability of monthly total precipitation. The temperature model, on the other hand, preserves the majority of key features of the gridded GEM temperature observations, including the first two moments of the hourly data and the cumulative frequency of maximum and minimum temperature thresholds. The only notable defect identified is the departure of the interannual variability of the generated maximum and minimum temperatures from those observed.

Discrete <i>k</i>-nearest neighbor resampling for simulating multisite precipitation occurrence and model adaption to climate change

Abstract. Stochastic weather simulation models are commonly employed in water resources management, agricultural applications, forest management, transportation management, and recreational activities. Stochastic simulation of multisite precipitation occurrence is a challenge because of its intermittent characteristics as well as spatial and temporal cross-correlation. This study proposes a novel simulation method for multisite precipitation occurrence employing a nonparametric technique, the discrete version of the k-nearest neighbor resampling (KNNR), and couples it with a genetic algorithm (GA). Its modification for the study of climatic change adaptation is also tested. The datasets simulated from both the discrete KNNR (DKNNR) model and an existing traditional model were evaluated using a number of statistics, such as occurrence and transition probabilities, as well as temporal and spatial cross-correlations. Results showed that the proposed DKNNR model with GA-simulated multisite precipitation occurrence preserved the lagged cross-correlation between sites, while the existing conventional model was not able to reproduce lagged cross-correlation between stations, so long stochastic simulation was required. Also, the GA mixing process provided a number of new patterns that were different from observations, which was not feasible with the sole DKNNR model. When climate change was considered, the model performed satisfactorily, but further improvement is required to more accurately simulate specific variations of the occurrence probability.

Evaluation of a multisite telehealth group model for persistent pain management for rural/remote participants.

Individuals living in rural/remote areas have recognised barriers to specialist services for persistent pain management. Although there is current evidence to support the use of telehealth to deliver individual pain management support, there is minimal evidence to support the use of pain management programs delivered within a group model, using telehealth. The aim of the present research was to perform a formative evaluation of a persistent pain management program implemented using a multisite telehealth group model, and to examine consumer perceptions. The Manage Your Pain multisite telehealth group program was developed as a modified hub-and-spoke model. The model allowed participants from multiple rural/remote 'spoke' sites in Queensland, Australia to access four 2-hour specialist persistent pain management sessions from a metropolitan interdisciplinary persistent pain management centre ('hub' site, 491-1009 km from spoke sites), and simultaneously enable real-time access/interactions between participants at each of the spoke sites. Twenty-one individuals living with persistent pain participated in one of five multisite telehealth groups over the 10-month period. All participants completed standard pain scales before and after the pain management program, including Chronic Pain Acceptance Questionnaire 20 (CPAQ20), Brief Pain Inventory (BPI), Depression Anxiety Stress Scale (DASS 21), Pain Self Efficacy Questionnaire (PSEQ) and the Participant Reported Outcomes Measurement Information System &#40;PROMIS&#41;. The Patient Impression of Change Scale (PICS), a telehealth perceptions survey, and a semi-structured telephone interview were completed post-program. Results revealed significant (p<0.05) improvements in the activity subscale and total score of the CPAQ, with 6 (30%) showing reliable improvement (90% confidence interval), indicating higher levels of activity engagement and pain acceptance after the program. Four (19%) participants made reliable improvement on the BPI interference. Post-program, the PICS revealed 65% of participants reported improvements in overall function, 61% indicated improved mood, 57% reported improved physical activity and 50% had some improvement in pain. Post-program, less than 10% of participants reported having technical (audio, visual) issues that had impacted on their sessions, and more than 90% found telehealth to be comfortable, convenient and would consider using it for their healthcare in the future. Post-program, most participants felt they had connected and were in a shared health experience with other group members through the multisite telehealth model. The interviews revealed three main themes: 'group experiences', which involved comments relating to the dynamics of the group and the shared experience; 'telehealth accessibility', which pertained to perceptions of the telehealth model for accessing specialist services; and 'limitations and concerns', where participants spoke of possible improvements to the program delivery model. Results confirmed that participants received benefit from the pain management program and that they had positive perceptions of receiving the service using a telehealth model. The present findings provide positive data to support using telehealth to deliver specialist persistent pain management for individuals who face accessibility issues in rural and remote communities. The model also demonstrated that positive elements of group treatment can be achieved through telehealth group models.

Sorption of nickel ontogoethite (α-FeOOH) and desorption kinetics of aged synthetic Ni-goethite: Implication for Ni laterite ore

We have measured the sorption of Ni as a function of surface loading and pH with a series of laboratory experiments. We fit the data using a multisite surface complexation model incorporating the basic Stern model to describe the surface electrostatics. At 0.75 wt% Ni and above, however, we cannot model the sorption data in terms of simple surface complexation but must invoke polynuclear complexes (or surface precipitates) to fit the sorption edges. In addition to surface complexation and surface precipitates, Ni is associated with goethite via structural incorporation. After 21 days of sorption, about 90% of the sample with the highest Ni concentration is reversible while 60% of the sample with the lowest concentration (0.03 wt% Ni) is irreversible. In contrast, after 365 days of sorption about 50–60% of the sorbed Ni is irreversible in all the grades (0.003–2.56 wt% Ni) suggesting almost uniform structural incorporation in the lattice of goethite.