Environment for Modeling and Simulation of Biosystems, Biosensors, and Lab-on-Chips

Compact Modeling of Reaction-Diffusion-Advection Mechanisms for the Virtual Prototyping of Lab-on-Chip

“…It takes the concentration as an input to calculate the reaction rate and produces molecular flux at the appropriate rate and in the appropriate direction. The way such biochemical reactions are connected to the lattice is described in [14].…”

SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems

“…For example, the interconnection of quantitative models of the human physiology (e.g., Physiomodel, Mateják and Kofránek, 2015), drugs pharmacokinetics/pharmacodynamics (e.g., Open Systems Pharmacology Suite, Eissing et al, 2011), (possibly semi-autonomous) biomedical devices, pharmacological protocol guidelines or treatment schemes, enables the set-up of in silico clinical trials for the (model-based) safety and efficacy pre-clinical assessment of such drugs, protocols, treatments, devices, using standard system engineering approaches to perform their simulation-based analysis at system level (see, e.g., Kanade et al, 2009;Mancini et al, 2013Mancini et al, , 2014Zuliani et al, 2013;Zuliani, 2015;Mancini et al, 2016aMancini et al, , 2017. Works in this direction include, e.g., (Schaller et al, 2016;Messori et al, 2018), where a model-based verification activity of a sensor-augmented insulin pump is conducted against a model of the human glucose metabolism in patients with diabetes mellitus, (Madec et al, 2019), where a model of a penicillin bio-sensor (integrating biochemistry, electrochemistry, and electronics models) is simulated to compute a first dimensioning of the sensor, and (Tronci et al, 2014;Mancini et al, 2015), where representative populations of virtual patients are generated from parametric models of the human physiology, a key step to enable in silico clinical trials (see, e.g., Mancini et al, 2018).…”

“…Attempts in this directions include, e.g., (Madec et al, 2017), where biochemical models are converted into Spice, a standard integrated electronic circuit simulator, for the model-based design of bio-sensors and labs-on-chip. Model conversion is performed exploiting clever analogies between the behaviour of biochemical systems and electronic circuits and between molecular diffusion and heat diffusion (Gendrault et al, 2014;Madec et al, 2019). SBML2Modelica acts at a higher level, by translating SBML models into a genuinely general-purpose cross-domain open system modelling language (Modelica), hence enabling seamless integration and co-simulation of SBML models with models of virtually all application domains, without the need to exploit cross-domain analogies, hence fully preserving model readability and extensibility.…”