Simulation Dotaz Zobrazit nápovědu
The European Stroke Organisation (ESO) Simulation Committee was established in 2017 with the intent to promote simulation education and training in the stroke field. The application of simulation methodology in education and training improves healthcare professional performances in real clinical practice and patient outcomes. We evaluated the implementation of simulation training in stroke medicine, how it can significantly affect stroke pathways and quality of care. We herewith describe simulation techniques in the acute stroke setting. Simulation programs place the trainees in a safe environment, allowing both role-playings for decision making training and procedural simulation for technical skills improvement. This paper includes the position of the Committee on the key points, principles, and steps in order to set up and promote simulation programs in European stroke centers. Stroke is an emergency, and hyperacute phase management requires knowledge, expertise, optimal multidisciplinary team working, and timely actions in a very narrow time window. The ESO Simulation Committee promotes the implementation of simulation training in stroke care according to a specific and validated methodology.
- Klíčová slova
- Stroke medicine training, stroke management, stroke simulation,
- Publikační typ
- časopisecké články MeSH
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
We present a new simple extension of multiple walker metadynamics which makes it possible to simulate simultaneously multiple different molecular systems and to predict their free energy surfaces, named Altruistic metadynamics. Similarly to basic metadynamics, it uses a bias potential in the form of hills summed over the simulation. Each system adds a big hill to its "own" bias potential and smaller hills to bias potentials of other systems, hence, each system enhances sampling of other systems. This makes it possible to achieve either faster reaching of the stationary point or higher accuracy of the calculated free energy surfaces. This should be efficient in modeling of series of chemically similar systems, for example, in computational drug screening by metadynamics. The method was tested on model energy surfaces, alanine dipeptide modeled in different force fields and monosaccharides of D-hexopyranose series.
- MeSH
- simulace molekulární dynamiky * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem 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
Large biomolecular systems are at the heart of many essential cellular processes. The dynamics and energetics of an increasing number of these systems are being studied by computer simulations. Pushing the limits of length- and timescales that can be accessed by current hard- and software has expanded the ability to describe biomolecules at different levels of detail. We focus in this review on the ribosome, which exemplifies the close interplay between experiment and various simulation approaches, as a particularly challenging and prototypic nanomachine that is pivotal to cellular biology due to its central role in translation. We sketch widely used simulation methods and demonstrate how the combination of simulations and experiments advances our understanding of the function of the translation apparatus based on fundamental physics.
- Klíčová slova
- antibiotics, computer simulations, cryo-EM, cryogenic electron microscopy, molecular dynamics, ribosome, translation,
- MeSH
- počítačová simulace MeSH
- ribozomy * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.
- Klíčová slova
- adaptive biasing force simulations, biasing potential replica-exchange simulation, conformational sampling, molecular dynamics simulation, saccharides,
- MeSH
- antigeny krevních skupin chemie genetika MeSH
- disacharidy chemie genetika MeSH
- konformace sacharidů MeSH
- lidé MeSH
- sekvenční analýza * MeSH
- simulace molekulární dynamiky * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- antigeny krevních skupin MeSH
- disacharidy 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
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
ADAS and autonomous technologies in vehicles become more and more complex, which increases development time and expenses. This paper presents a new real-time ADAS multisensory validation system, which can speed up the development and implementation processes while lowering its cost. The proposed test system integrates a high-quality 3D CARLA simulator with a real-time-based automation platform. We present system experimental verifications on several types of sensors and testing system architectures. The first, open-loop experiment explains the real-time capabilities of the system based on the Mobileye 6 camera sensor detections. The second experiment runs a real-time closed-loop test of a lane-keeping algorithm (LKA) based on the Mobileye 6 line detection. The last experiment presents a simulation of Velodyne VLP-16 lidar, which runs a free space detection algorithm. Simulated lidar output is compared with the real lidar performance. We show that the platform generates reproducible results and allows closed-loop operation which, combined with a real-time collection of event information, promises good scalability toward complex ADAS or autonomous functionalities testing.
UNLABELLED: An environment for simulation of dynamics of genetic regulatory networks is presented. The model is based on the recurrent neural network principle and allows to interactively simulate various genetic regulatory interactions under different features of the system. The results are displayed graphically. AVAILABILITY: http://proteom.biomed.cas.cz/genexp
- MeSH
- genetické inženýrství metody MeSH
- genom MeSH
- genomika metody MeSH
- geny fyziologie MeSH
- modely genetické * MeSH
- počítačová simulace MeSH
- regulace genové exprese fyziologie MeSH
- software * MeSH
- stanovení celkové genové exprese MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
