scholarly journals High-Resolution Ecosystem Model of the Puck Bay (Southern Baltic Sea)—Hydrodynamic Component Evaluation

Water ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 2057 ◽  
Author(s):  
Dawid Dybowski ◽  
Jaromir Jakacki ◽  
Maciej Janecki ◽  
Artur Nowicki ◽  
Daniel Rak ◽  
...  
Keyword(s):  
Cross Sections ◽  
Ecosystem Model ◽  
Model System ◽  
Computational Power ◽  
Model Simulations ◽  
Hydrodynamic Parameters ◽  
Raster Maps ◽  
Dedicated Service ◽  
Scientific Fields ◽  
Puck Bay

In recent years, thanks to the enormous computational power of modern supercomputers, modeling has become one of the most highly evolving scientific fields. It is now possible to describe relatively large physical bodies and to study the changes occurring in these bodies with resolution never attainable before. The paper describes the initial implementation of the EcoPuckBay model system and presents the results of the model simulations compared to observations from monitoring stations and other model reanalyses. High correlation between model results and observations has been confirmed both in terms of spatial and temporal approach. Data acquired via simulations of the EcoPuckBay model was deployed in the project archive database. The dedicated service was created, allowing the user to visualize all produced hydrodynamic parameters as raster maps, time series, and/or cross-sections. This functionality is available online via the official WaterPUCK project website in the services web section. In the next stage of the project, this service will be upgraded to an operational state and forecasts will be added.

Shaping Organs: Shared Structural Principles Across Kingdoms

2020 ◽  
Vol 36 (1) ◽  
pp. 385-410
Author(s):  
O. Hamant ◽  
T.E. Saunders
Keyword(s):  
Model System ◽  
Model Systems ◽  
Structural Constraints ◽  
Molecular Control ◽  
Plant Model ◽  
Critical Part ◽  
Integrative View ◽  
Structural Principles ◽  
Cross Fertilization ◽  
Scientific Fields

Development encapsulates the morphogenesis of an organism from a single fertilized cell to a functional adult. A critical part of development is the specification of organ forms. Beyond the molecular control of morphogenesis, shape in essence entails structural constraints and thus mechanics. Revisiting recent results in biophysics and development, and comparing animal and plant model systems, we derive key overarching principles behind the formation of organs across kingdoms. In particular, we highlight how growing organs are active rather than passive systems and how such behavior plays a role in shaping the organ. We discuss the importance of considering different scales in understanding how organs form. Such an integrative view of organ development generates new questions while calling for more cross-fertilization between scientific fields and model system communities.

scholarly journals QSPcc reduces bottlenecks in computational model simulations

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Danilo Tomasoni ◽  
Alessio Paris ◽  
Stefano Giampiccolo ◽  
Federico Reali ◽  
Giulia Simoni ◽  
...  
Keyword(s):  
Programming Languages ◽  
Life Sciences ◽  
Arithmetic Mean ◽  
Natural Sciences ◽  
Systems Pharmacology ◽  
Lysosomal Storage ◽  
Quantitative Systems Pharmacology ◽  
Model Simulations ◽  
Scientific Fields ◽  
Storage Disorders

AbstractMathematical models have grown in size and complexity becoming often computationally intractable. In sensitivity analysis and optimization phases, critical for tuning, validation and qualification, these models may be run thousands of times. Scientific programming languages popular for prototyping, such as MATLAB and R, can be a bottleneck in terms of performance. Here we show a compiler-based approach, designed to be universal at handling engineering and life sciences modeling styles, that automatically translates models into fast C code. At first QSPcc is demonstrated to be crucial in enabling the research on otherwise intractable Quantitative Systems Pharmacology models, such as in rare Lysosomal Storage Disorders. To demonstrate the full value in seamlessly accelerating, or enabling, the R&D efforts in natural sciences, we then benchmark QSPcc against 8 solutions on 24 real-world projects from different scientific fields. With speed-ups of 22000x peak, and 1605x arithmetic mean, our results show consistent superior performances.

Mathematical Modeling of Cell Distribution in Alginate Microbeads

2005 ◽  
Vol 494 ◽  
pp. 531-536
Author(s):  
B. Obradović ◽  
B. Bugarski ◽  
Z. Todosijević ◽  
V. Nedović ◽  
D. Bugarski ◽  
...  
Keyword(s):  
Cross Sections ◽  
Food Industry ◽  
Three Dimensional ◽  
Model System ◽  
Cell Distribution ◽  
Brewing Yeast ◽  
Fermentation Time ◽  
Local Environments ◽  
Colony Forming Cell ◽  
Three Dimensional Simulations

Alginate is one of the mostly used hydrogels for cell entrapment aimed for applications in food industry, environmental engineering, pharmacy and biomedicine. One of the major parameters affecting cell viability and activity is cell distribution inside the immobilization matrix. In addition, changes in cell distribution over the cultivation time could indicate mass transfer limitations, favorable local environments or cell differentiation. In this study, immobilization and distribution of brewing yeast in alginate microbeads were investigated as a model system of colony forming cell growth. Cell distributions were attained by image analysis of histological cross sections of microbeads used in beer fermentation. A mathematical model based on cellular automata approach was developed for three-dimensional simulations of cell arrangement over the fermentation time.

scholarly journals Assessing the response of forest productivity to climate extremes in Switzerland using model-data fusion

2020 ◽  
Author(s):  
Volodymyr Trotsiuk ◽  
Keyword(s):  
Data Assimilation ◽  
Forest Ecosystem ◽  
Climate Extremes ◽  
Ecosystem Model ◽  
Elevational Gradient ◽  
Forest Productivity ◽  
Carbon Stocks ◽  
Forest Monitoring ◽  
Model Simulations ◽  
Using Data

<p>Under unprecedent climate change and increased frequency of extreme events, e.g. drought, it is important to assess and forecast forest ecosystem vulnerability and stability. Large volumes of data from observational and experimental networks, increases in computational power, advances in ecological models, and optimization methodologies are the main measures to improve quantitative forecasting in ecology. Data assimilation is a key tool to improve ecosystem state prediction and forecasting by combining model simulations and observations. We assimilated observations of carbon stocks and fluxes from 271 permanent long-term forest monitoring plots across Switzerland into the 3-PG forest ecosystem model using Bayesian inference, reducing the bias of model predictions from 14% to 5% for forest stem carbon stocks and from 45% to 9% for stem carbon stock changes, respectively. We then estimated the productivity of forests dominated by <em>Picea abies</em> and <em>Fagus sylvatica</em> for the period of 1960-2018 and tested for climate-induced shifts in productivity along elevational gradient and in extreme years. Overall, we demonstrated a high potential of using data assimilation to improve predictions of forest ecosystem productivity. Furthermore, our calibrated model simulations suggest that climate extremes affect forest productivity in more complex ways than by simply shifting the response upwards in elevation.</p>

scholarly journals Assessing the Impact of Chemical Loads from Agriculture Holdings on the Puck Bay Environment with the High-Resolution Ecosystem Model of the Puck Bay, Southern Baltic Sea

Water ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 2068
Author(s):  
Dawid Dybowski ◽  
Maciej Janecki ◽  
Artur Nowicki ◽  
Lidia Anita Dzierzbicka-Glowacka
Keyword(s):  
Assessment Tool ◽  
Pearson Correlation ◽  
Ecosystem Model ◽  
Agricultural Activity ◽  
Operational Mode ◽  
Flow Models ◽  
Statistical Measures ◽  
The Impact ◽  
Puck Bay

This paper describes the ecohydrodynamic predictive model EcoPuckBay—the ecosystem part—for assessing the state of the Puck Bay coastal environment and its ecosystem. We coupled the EcoPuckBay model with the land water flow models (Soil and Water Assessment Tool (SWAT) for surface water and Modflow for groundwater). To evaluate the quality of the results obtained from the EcoPuckBay model, a set of basic statistical measures for dissolved oxygen, chlorophyll-a, nitrates, and phosphates were calculated, such as mean, Pearson correlation coefficient (r), root-mean-square-error (RMSE), and standard deviation (STD). The analysis presented in this paper shows that the EcoPuckBay model produces reliable results. In addition, we developed a nutrient spread module to show the impact of agricultural activity on the waters of the Puck Bay. The EcoPuckBay model is also available in operational mode where users can access 60-h forecasts via the website of the WaterPUCK Project through the “Products” tab.

scholarly journals Laminar fluid flow in concentric annular ducts of non-conventional cross-section applying GBI method

2021 ◽  
Vol 10 (1) ◽  
pp. e10710111547
Author(s):  
Valdecir Alves dos Santos Júnior ◽  
Antonio Gilson Barbosa de Lima ◽  
Severino Rodrigues de Farias Neto ◽  
Igor Fernandes Gomes ◽  
Jonathan da Cunha Teixeira
Keyword(s):  
Fluid Flow ◽  
Cross Section ◽  
Cross Sections ◽  
Entrance Length ◽  
Medical Sciences ◽  
Hydrodynamic Parameters ◽  
Large Application ◽  
Elliptical Core ◽  
Good Concordance ◽  
Poiseuille Number

Fluid flow in concentric or eccentric annular ducts have been studied for decades due to large application in medical sciences and engineering areas. This paper aims to study fully developed fluid flow in straight ducts of concentric annular geometries (circular with circular core, elliptical with circular core, elliptical with elliptical core, and circular with elliptical core) using the Galerkin-based Integral method (GBI method). The choice of method was due to the fact that in the literature it is not applied in ducts of cross-sections of the annular shape with variations between circular and elliptical. Results of different hydrodynamics parameters such as velocity distribution, Hagenbach factor, Poiseuille number, and hydrodynamic entrance length, are presented and analyzed. In different cases, the predicted hydrodynamic parameters are compared with results reported in the literature and a good concordance was obtained.

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