simulation and modeling
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For the modeling of systems, the computers are more and more used while the other "media" (including the human intellect) carrying the models are abandoned. For the modeling of knowledges, i.e. of more or less general concepts (possibly used to model systems composed of instances of such concepts), the object-oriented programming is nowadays widely used. For the modeling of processes existing and developing in the time, computer simulation is used, the results of which are often presented by means of animation (graphical pictures moving and changing in time). Unfortunately, the object-oriented programming tools are commonly not designed to be of a great use for simulation while the programming tools for simulation do not enable their users to apply the advantages of the object-oriented programming. Nevertheless, there are exclusions enabling to use general concepts represented at a computer, for constructing simulation models and for their easy modification. They are described in the present paper, together with true definitions of modeling, simulation and object-oriented programming (including cases that do not satisfy the definitions but are dangerous to introduce misunderstanding), an outline of their applications and of their further development. In relation to the fact that computing systems are being introduced to be control components into a large spectrum of (technological, social and biological) systems, the attention is oriented to models of systems containing modeling components.
- MeSH
- počítačová simulace * MeSH
- programovací jazyk MeSH
- teoretické modely * MeSH
- Publikační typ
- časopisecké články MeSH
This study investigates the influence of varying degrees of stenosis on blood flow within elliptic arteries, emphasizing the critical role of artery shape in clinical evaluations as opposed to the commonly studied circular arteries. Unlike prior work, this research offers a precise definition of stenosis by incorporating the measured length, height, and position of the narrowing. Employing the non-Newtonian Williamson fluid model, we conducted comprehensive numerical simulations to examine blood flow through four distinct stenosis formations. The novelty of this work lies in its accurate modeling of stenosis and use of advanced mesh generation, combined with commercial software and the finite volume method, to capture detailed hemodynamic behavior. Visualized results, including pressure profiles, velocity line graphs, and streamlines, further underscore the distinctive flow dynamics shaped by the elliptic geometry. Key findings of the obtained results reveal that blood velocity peaks near the stenosis and drops significantly post-stenosis, with notable variations in flow patterns, energy loss, and pressure distribution across different stenosis types. Further, higher velocity of blood flow is observed in elliptic arteries in comparison with circular ones. In the area of the high corners of stenotic segments, the pressure profile reaches high values. As a result of the narrowing of the arterial cross-section, the varied time shows that the post-stenotic segment of the artery has a higher pressure than the pre-stenotic section. The varied time suggests that an axially symmetric profile will eventually be the norm for the flow within the arterial portion. These insights have profound implications for improving clinical diagnosis and treatment strategies for conditions related to stenosed elliptic arteries.
Purpose: Thermal dose-effect relations have demonstrated that clinical effectiveness of hyperthermia would benefit from more controlled heating of the tumor. Hyperthermia treatment planning (HTP) is a potent tool to study strategies enabling target conformal heating, but its accuracy is affected by patient modeling approximations. Homogeneous phantoms models are being used that do not match the body shape of patients in treatment position and often have unrealistic target volumes. As a consequence, simulation accuracy is affected, and performance comparisons are difficult. The aim of this study is to provide the first step toward standardization of HTP simulation studies in terms of patient modeling by introducing the Erasmus Virtual Patient Repository (EVPR): a virtual patient model database.Methods: Four patients with a tumor in the head and neck or the pelvis region were selected, and corresponding models were created using a clinical segmentation procedure. Using the Erasmus University Medical Center standard procedure, HTP was applied to these models and compared to HTP for commonly used surrogate models.Results: Although this study was aimed at presenting the EVPR database, our study illustrates that there is a non-negligible difference in the predicted SAR patterns between patient models and homogeneous phantom-based surrogate models. We further demonstrate the difference between actual and simplified target volumes being used today.Conclusion: Our study describes the EVPR for the research community as a first step toward standardization of hyperthermia simulation studies.
- Klíčová slova
- Hyperthermia, open research, patient models, standardization, treatment planning,
- MeSH
- hlava MeSH
- hypertermie * MeSH
- indukovaná hypertermie * MeSH
- lidé MeSH
- počítačová simulace MeSH
- referenční standardy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
This paper describes simulation of the cardiovascular system using a complex electronic circuit. In this study we have taken a slightly different approach to the modeling of the system and tried to advance existing electrical models by increasing more segments and parameters. The model consists of 42 segments representing the arterial system. Anatomical and physiological data for circuit parameters have been extracted from medical articles and textbooks. The frequency of heart is 1 Hz and the system operates in steady state condition. Each artery is modeled by one capacitor, resistor and inductor. The left and right ventricles are modeled using AC power suppliers and diodes. The results of the simulation including pressure and volume graphs exhibit operation of the cardiovascular system under normal condition. The results of the simulation have been compared with the relevant experimental observation and are in good agreement with them.
- MeSH
- lidé MeSH
- modely kardiovaskulární * MeSH
- počítačová simulace * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Stochastic models are commonly employed in the system and synthetic biology to study the effects of stochastic fluctuations emanating from reactions involving species with low copy-numbers. Many important models feature complex dynamics, involving a state-space explosion, stiffness, and multimodality, that complicate the quantitative analysis needed to understand their stochastic behavior. Direct numerical analysis of such models is typically not feasible and generating many simulation runs that adequately approximate the model's dynamics may take a prohibitively long time. RESULTS: We propose a new memoization technique that leverages a population-based abstraction and combines previously generated parts of simulations, called segments, to generate new simulations more efficiently while preserving the original system's dynamics and its diversity. Our algorithm adapts online to identify the most important abstract states and thus utilizes the available memory efficiently. CONCLUSION: We demonstrate that in combination with a novel fully automatic and adaptive hybrid simulation scheme, we can speed up the generation of trajectories significantly and correctly predict the transient behavior of complex stochastic systems.
- Klíčová slova
- Memoization, Population abstraction, Reaction networks, Stochastic simulation,
- MeSH
- algoritmy * MeSH
- biologické modely MeSH
- počítačová simulace * MeSH
- stochastické procesy * MeSH
- syntetická biologie metody MeSH
- Publikační typ
- časopisecké články MeSH
Capillary electrophoresis hyphenated with electrospray mass spectrometry (CE-ESI-MS) has emerged in the past decade as one of the most powerful bioanalytical techniques. As the sensitivity and efficiency of new CE-ESI-MS interface designs are continuously improving, numerical modeling can play important role during their development. In this review, different aspects of computer modeling and simulation of CE-ESI-MS interfaces are comprehensively discussed. Relevant essentials of hydrodynamics as well as state-of-the-art modeling techniques are critically evaluated. Sheath liquid-, sheathless-, and liquid-junction interfaces are reviewed from the viewpoint of multidisciplinary numerical modeling along with details of single and multiphase models together with electric field mediated flows, electrohydrodynamics, and free fluid-surface methods. Practical examples are given to help non-specialists to understand the basic principles and applications. Finally, alternative approaches like air amplifiers are also included. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 558-569, 2015.
- Klíčová slova
- CE-ESI-MS, CFD, interface design, modeling, simulation,
- MeSH
- algoritmy MeSH
- chemické modely MeSH
- elektroforéza kapilární přístrojové vybavení metody MeSH
- elektromagnetická pole MeSH
- hmotnostní spektrometrie s elektrosprejovou ionizací přístrojové vybavení metody MeSH
- hydrodynamika MeSH
- lidé MeSH
- počítačová simulace MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
BACKGROUND: Alzheimer's disease is one of the most common mental illnesses. It is posited that more than 25% of the population is affected by some mental disease during their lifetime. Treatment of each patient draws resources from the economy concerned. Therefore, it is important to quantify the potential economic impact. METHODS: Agent-based, system dynamics and numerical approaches to dynamic modeling of the population of the European Union and its patients with Alzheimer's disease are presented in this article. Simulations, their characteristics, and the results from different modeling tools are compared. RESULTS: The results of these approaches are compared with EU population growth predictions from the statistical office of the EU by Eurostat. The methodology of a creation of the models is described and all three modeling approaches are compared. The suitability of each modeling approach for the population modeling is discussed. CONCLUSION: In this case study, all three approaches gave us the results corresponding with the EU population prediction. Moreover, we were able to predict the number of patients with AD and, based on the modeling method, we were also able to monitor different characteristics of the population.
- Klíčová slova
- Alzheimer’s disease, agent-based model, numerical model, population modeling, population prediction, system dynamics.,
- MeSH
- Alzheimerova nemoc diagnóza epidemiologie MeSH
- biologické modely MeSH
- lidé MeSH
- systémová analýza * MeSH
- teoretické modely * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Simul 5 Complex is a one-dimensional dynamic simulation software designed for electrophoresis, and it is based on a numerical solution of the governing equations, which include electromigration, diffusion and acid-base equilibria. A new mathematical model has been derived and implemented that extends the simulation capabilities of the program by complexation equilibria. The simulation can be set up with any number of constituents (analytes), which are complexed by one complex-forming agent (ligand). The complexation stoichiometry is 1:1, which is typical for systems containing cyclodextrins as the ligand. Both the analytes and the ligand can have multiple dissociation states. Simul 5 Complex with the complexation mode runs under Windows and can be freely downloaded from our web page http://natur.cuni.cz/gas. The article has two separate parts. Here, the mathematical model is derived and tested by simulating the published results obtained by several methods used for the determination of complexation equilibrium constants: affinity capillary electrophoresis, vacancy affinity capillary electrophoresis, Hummel-Dreyer method, vacancy peak method, frontal analysis, and frontal analysis continuous capillary electrophoresis. In the second part of the paper, the agreement of the simulated and the experimental data is shown and discussed.
- MeSH
- cyklodextriny MeSH
- elektroforéza kapilární * MeSH
- počítačová simulace MeSH
- stereoizomerie MeSH
- teoretické modely * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- cyklodextriny MeSH
The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch-Torrey partial differential equation. Under the assumption of negligible water exchange between compartments, the time-dependent apparent diffusion coefficient can be directly computed from the solution of a diffusion equation subject to a time-dependent Neumann boundary condition. This paper describes a publicly available MATLAB toolbox called SpinDoctor that can be used 1) to solve the Bloch-Torrey partial differential equation in order to simulate the diffusion magnetic resonance imaging signal; 2) to solve a diffusion partial differential equation to obtain directly the apparent diffusion coefficient; 3) to compare the simulated apparent diffusion coefficient with a short-time approximation formula. The partial differential equations are solved by P1 finite elements combined with built-in MATLAB routines for solving ordinary differential equations. The finite element mesh generation is performed using an external package called Tetgen. SpinDoctor provides built-in options of including 1) spherical cells with a nucleus; 2) cylindrical cells with a myelin layer; 3) an extra-cellular space enclosed either a) in a box or b) in a tight wrapping around the cells; 4) deformation of canonical cells by bending and twisting; 5) permeable membranes; Built-in diffusion-encoding pulse sequences include the Pulsed Gradient Spin Echo and the Oscillating Gradient Spin Echo. We describe in detail how to use the SpinDoctor toolbox. We validate SpinDoctor simulations using reference signals computed by the Matrix Formalism method. We compare the accuracy and computational time of SpinDoctor simulations with Monte-Carlo simulations and show significant speed-up of SpinDoctor over Monte-Carlo simulations in complex geometries. We also illustrate several extensions of SpinDoctor functionalities, including the incorporation of T2 relaxation, the simulation of non-standard diffusion-encoding sequences, as well as the use of externally generated geometrical meshes.
- Klíčová slova
- Apparent diffusion coefficient, Bloch-torrey equation, Diffusion magnetic resonance imaging, Finite elements, Simulation,
- MeSH
- difuzní magnetická rezonance metody MeSH
- lidé MeSH
- mozek * MeSH
- neurozobrazování metody MeSH
- počítačová simulace MeSH
- software * MeSH
- teoretické modely * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreement with ab initio calculations obtained in the Gaussian03 program. Dihedral torsions of active groups of betulin were determined for both procedures, and related calculated structures were compared successfully. The selected force field was used for subsequent optimization of betulin in a water environment, and a conformational search was performed using quench molecular dynamics. The total energies of betulin and its interactions in water bulk were calculated, and the influence of water on betulin structure was investigated.
- MeSH
- molekulární konformace MeSH
- molekulární modely MeSH
- počítačová simulace MeSH
- simulace molekulární dynamiky * MeSH
- triterpeny chemická syntéza chemie MeSH
- voda chemie MeSH
- vodíková vazba MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- betulin MeSH Prohlížeč
- triterpeny MeSH
- voda MeSH
