Adair-based hemoglobin equilibrium with oxygen, carbon dioxide and hydrogen ion activity.

As has been known for over a century, oxygen binding onto hemoglobin is influenced by the activity of hydrogen ions (H⁺), as well as the concentration of carbon dioxide (CO2). As is also known, the binding of both CO2and H⁺ on terminal valine-1 residues is competitive. One-parametric situations of these hemoglobin equilibria at specific levels of H⁺, O2or CO2are also well described. However, we think interpolating or extrapolating this knowledge into an 'empirical' function of three independent variables has not yet been completely satisfactory. We present a model that integrates three orthogonal views of hemoglobin oxygenation, titration, and carbamination at different temperatures. The model is based only on chemical principles, Adair's oxygenation steps and Van't Hoff equation of temperature dependences. Our model fits the measurements of the Haldane coefficient and CO2hemoglobin saturation. It also fits the oxygen dissociation curve influenced by simultaneous changes in H⁺, CO2and O2, which makes it a strong candidate for integration into more complex models of blood acid-base with gas transport, where any combination of mentioned substances can appear.

Experience with Teaching Different Modeling Techniques on the example of Glucose Insulin Regulation Model.

In order to teach different modeling techniques we demonstrate equation-based, block-schema based, compartment and component-based modeling using acausal and object-oriented modeling language - Modelica. Hands-on implementation using all these techniques and comparing them towards same system (in our case glucose-insulin regulation) we teach pros and cons of each technique. Equation-based or block-schema based may be rapidly implemented from literature. However, compartment based or component-based models brings better understanding of modeled reality. When students have such experience, they tend to assess published papers more critically and do more complex system analysis.

West-Life: A Virtual Research Environment for structural biology.

The West-Life project (https://about.west-life.eu/) is a Horizon 2020 project funded by the European Commission to provide data processing and data management services for the international community of structural biologists, and in particular to support integrative experimental approaches within the field of structural biology. It has developed enhancements to existing web services for structure solution and analysis, created new pipelines to link these services into more complex higher-level workflows, and added new data management facilities. Through this work it has striven to make the benefits of European e-Infrastructures more accessible to life-science researchers in general and structural biologists in particular.

Experiences in teaching of modeling and simulation with emphasize on equation-based and acausal modeling techniques.

This work introduces experiences of teaching modeling and simulation for graduate students in the field of biomedical engineering. We emphasize the acausal and object-oriented modeling technique and we have moved from teaching block-oriented tool MATLAB Simulink to acausal and object oriented Modelica language, which can express the structure of the system rather than a process of computation. However, block-oriented approach is allowed in Modelica language too and students have tendency to express the process of computation. Usage of the exemplar acausal domains and approach allows students to understand the modeled problems much deeper. The causality of the computation is derived automatically by the simulation tool.

Surviving sepsis--a 3D integrative educational simulator.

Computer technology offers greater educational possibilities, notably simulation and virtual reality. This paper presents a technology which serves to integrate multiple modalities, namely 3D virtual reality, node-based simulator, Physiomodel explorer and explanatory physiological simulators employing Modelica language and Unity3D platform. This emerging tool chain should allow the authors to concentrate more on educational content instead of application development. The technology is demonstrated through Surviving sepsis educational scenario, targeted on Microsoft Windows Store platform.

Modeling of short-term mechanism of arterial pressure control in the cardiovascular system: object-oriented and acausal approach.

This letter introduces an alternative approach to modeling the cardiovascular system with a short-term control mechanism published in Computers in Biology and Medicine, Vol. 47 (2014), pp. 104-112. We recommend using abstract components on a distinct physical level, separating the model into hydraulic components, subsystems of the cardiovascular system and individual subsystems of the control mechanism and scenario. We recommend utilizing an acausal modeling feature of Modelica language, which allows model variables to be expressed declaratively. Furthermore, the Modelica tool identifies which are the dependent and independent variables upon compilation. An example of our approach is introduced on several elementary components representing the hydraulic resistance to fluid flow and the elastic response of the vessel, among others. The introduced model implementation can be more reusable and understandable for the general scientific community.