scholarly journals Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus

2021 ◽  
Author(s):  
Kerstin Schmid ◽  
Andreas Knote ◽  
Alexander Mueck ◽  
Keram Pfeiffer ◽  
Sebastian von Mammen ◽  
...  
Keyword(s):  
Experimental Data ◽  
Gas Exchange ◽  
Three Dimensional ◽  
Theoretical Models ◽  
Simulation Software ◽  
Visual Simulation ◽  
Model Parameters ◽  
Interactive Simulation ◽  
Temporal Model ◽  
Spatio Temporal

In interdisciplinary fields such as systems biology, close collaboration between experimentalists and theorists is crucial for the success of a project. Theoretical modeling in physiology usually describes complex systems with many interdependencies. On one hand, these models have to be grounded on experimental data. On the other hand, experimenters must be able to penetrate the model in its dependencies in order to correctly interpret the results in the physiological context. When theorists and experimenters collaborate, communicating results and ideas is sometimes challenging. We promote interactive, visual simulations as an engaging way to communicate theoretical models in physiology and to thereby advance our understanding of the process of interest. We defined a new spatio-temporal model for gas exchange in the human alveolus and implemented it in an interactive simulation software named Alvin. In Alvin, the course of the simulation can be traced in a three-dimensional rendering of an alveolus and dynamic plots. The user can interact by configuring essential model parameters. Alvin allows to run and compare multiple simulation instances simultaneously. The mathematical model was developed with the aim of visualization and the simulation software was engineered based on a requirements analysis. Our work resulted in an integrative gas exchange model and an interactive application that exceed the current standards. We exemplified the use of Alvin for research by identifying unknown dependencies in published experimental data. Employing a detailed questionnaire, we showed the benefits of Alvin for education. We postulate that interactive, visual simulation of theoretical models, as we have implemented with Alvin on respiratory processes in the alveolus, can be of great help for communication between specialists and thereby advancing research.

scholarly journals Three-dimensional data-tracking simulations of sprinting using a direct collocation optimal control approach

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10975
Author(s):  
Nicos Haralabidis ◽  
Gil Serrancolí ◽  
Steffi Colyer ◽  
Ian Bezodis ◽  
Aki Salo ◽  
...  
Keyword(s):  
Experimental Data ◽  
Reaction Force ◽  
Three Dimensional ◽  
Contact Model ◽  
Model Parameters ◽  
Ground Contact ◽  
Control Approach ◽  
Average Percentage ◽  
Data Tracking ◽  
The Individual

Biomechanical simulation and modelling approaches have the possibility to make a meaningful impact within applied sports settings, such as sprinting. However, for this to be realised, such approaches must first undergo a thorough quantitative evaluation against experimental data. We developed a musculoskeletal modelling and simulation framework for sprinting, with the objective to evaluate its ability to reproduce experimental kinematics and kinetics data for different sprinting phases. This was achieved by performing a series of data-tracking calibration (individual and simultaneous) and validation simulations, that also featured the generation of dynamically consistent simulated outputs and the determination of foot-ground contact model parameters. The simulated values from the calibration simulations were found to be in close agreement with the corresponding experimental data, particularly for the kinematics (average root mean squared differences (RMSDs) less than 1.0° and 0.2 cm for the rotational and translational kinematics, respectively) and ground reaction force (highest average percentage RMSD of 8.1%). Minimal differences in tracking performance were observed when concurrently determining the foot-ground contact model parameters from each of the individual or simultaneous calibration simulations. The validation simulation yielded results that were comparable (RMSDs less than 1.0° and 0.3 cm for the rotational and translational kinematics, respectively) to those obtained from the calibration simulations. This study demonstrated the suitability of the proposed framework for performing future predictive simulations of sprinting, and gives confidence in its use to assess the cause-effect relationships of technique modification in relation to performance. Furthermore, this is the first study to provide dynamically consistent three-dimensional muscle-driven simulations of sprinting across different phases.

THEORETICAL MODELS FOR MAGNETIC PROPERTIES OF IRON PNICTIDES

2013 ◽  
Vol 27 (16) ◽  
pp. 1350071 ◽  
Author(s):  
M. VUJINOVIĆ ◽  
M. PANTIĆ ◽  
D. KAPOR ◽  
P. MALI
Keyword(s):  
Magnetic Properties ◽  
Heisenberg Model ◽  
Degrees Of Freedom ◽  
Random Phase ◽  
Three Dimensional ◽  
Theoretical Models ◽  
Wave Dispersion ◽  
Model Parameters ◽  
Neel Temperature ◽  
Néel Temperature

We attempt to describe the magnetic properties of parent pnictide compounds by using both the J1–J2 Heisenberg model and its three-dimensional generalization, the J1–J2–Jc model. We also include spin anisotropy in the XY plane. In order to obtain the average magnetization and spin wave dispersion, we use the Green's functions method for spin operators in the random phase approximation. We obtain estimates for the model parameters by considering the low temperature experimental dispersion for the compounds CaFe 2 As 2 and BaFe 2 As 2 and conclude that theoretical dispersion can fit the experimental one if spatially anisotropic Hamiltonian is used. A good agreement between theory and experiment indicates that the Heisenberg model is applicable to parent pnictides at low temperatures. The applicability of the model for higher temperatures is checked by calculating the Néel temperature for both compounds. It turns out that the model overestimates the measured critical temperature. The Heisenberg model is not applicable to parent pnictides, for temperature comparable to Néel temperature. Our results thus confirm that all the magnetic properties of parent pnictides cannot be described with purely localized degrees of freedom, and that the itinerant magnetism should have an important role in these compounds. All results given in Sec. 3 are general and could be used in description of classes of compounds with spin stripe structure.

Off-Road Vehicle Dynamics Mobility Simulation With a Compaction Based Deformable Terrain Model

2013 ◽  
Author(s):  
Justin Madsen ◽  
Andrew Seidl ◽  
Dan Negrut
Keyword(s):  
Vehicle Dynamics ◽  
Transfer Functions ◽  
Soil Mechanics ◽  
Three Dimensional ◽  
Interaction Model ◽  
Simulation Software ◽  
Repeated Loading ◽  
Model Parameters ◽  
Vehicle Simulation ◽  
Terrain Model

This paper discusses the terramechanics models developed to incorporate a physics-based, three dimensional deformable terrain database model with vehicle dynamics mobility simulation software. The vehicle model is contained in Chrono, a research-grade C++ based Application Programming Interface (API) that enables accurate multibody simulations. The terrain database is also contained in a C++ based API, and includes a general tire-terrain interaction model which is modular to allow for any tire model that supports the Standard Tire Interface (STI) to operate on the terrain. Furthermore, the ability to handle arbitrary, three dimensional traction element geometry allows for tracked vehicles (or vehicle hulls) to also interact with the deformable terrain. The governing equations of the terrain are based on a soil compaction model that includes both the propagation of subsoil stresses due to vehicular loads, and the resulting visco-elastic-plastic stress/strain on the affected soil volume. Non-flat, non-homogenous and non-uniform soil densities, rutting, repeated loading and strain hardening effects are all captured in the vehicle mobility response as a result of the general 3-D tire/terrain model developed. Pedo-transfer functions allow for the calculation of the soil mechanics model parameters from existing soil measurements. This terrain model runs at near real-time speed, due to parallel CPU and GPU implementation. Results that exercise the force models developed with the 3-D tire geometry are presented and discussed for a kinematically driven tire and a full vehicle simulation.

CHARMONIUM SPECTRA AND DECAYS IN A SEMIRELATIVISTIC MODEL

2012 ◽  
Vol 27 (22) ◽  
pp. 1250127 ◽  
Author(s):  
BHAGHYESH ◽  
K. B. VIJAYA KUMAR
Keyword(s):  
Wave Function ◽  
Wave Equation ◽  
Mass Spectra ◽  
Three Dimensional ◽  
Theoretical Models ◽  
Model Parameters ◽  
Decay Properties ◽  
Oscillator Wave Function ◽  
Harmonic Oscillator Wave Function ◽  
Relativistic Kinetic Energy

We investigate the spectra and decays of charmonium [Formula: see text] system in a semirelativistic potential model. The Hamiltonian of our model consists of a relativistic kinetic energy term, a vector Coulomb-like potential and a scalar confining potential. From this Hamiltonian a spinless wave equation is obtained. The wave equation is then reduced to the form of a single particle Schrödinger equation. The spin dependent potentials are introduced as a perturbation. The three-dimensional harmonic oscillator wave function is employed as a trial wave function and the [Formula: see text] mass spectra is obtained by the variational method. The model parameters and the wave function that reproduce the mass spectra of the [Formula: see text] mesons are then used to investigate some of the decay properties. The results obtained are then compared with the experimental data and with the predictions of other theoretical models. We also propose possible [Formula: see text] assignments for the recently observed charmonium or charmonium-like states.

scholarly journals Sensitivity of a data-assimilation system for reconstructing three-dimensional cardiac electrical dynamics

2020 ◽  
Vol 378 (2173) ◽  
pp. 20190388 ◽  
Author(s):  
Matthew J. Hoffman ◽  
Elizabeth M. Cherry
Keyword(s):  
Data Assimilation ◽  
Temporal Dynamics ◽  
Complex Dynamics ◽  
Three Dimensional ◽  
Model Error ◽  
Model Parameters ◽  
Ensemble Spread ◽  
Spatio Temporal ◽  
System States ◽  
Parameter Values

Modelling of cardiac electrical behaviour has led to important mechanistic insights, but important challenges, including uncertainty in model formulations and parameter values, make it difficult to obtain quantitatively accurate results. An alternative approach is combining models with observations from experiments to produce a data-informed reconstruction of system states over time. Here, we extend our earlier data-assimilation studies using an ensemble Kalman filter to reconstruct a three-dimensional time series of states with complex spatio-temporal dynamics using only surface observations of voltage. We consider the effects of several algorithmic and model parameters on the accuracy of reconstructions of known scroll-wave truth states using synthetic observations. In particular, we study the algorithm’s sensitivity to parameters governing different parts of the process and its robustness to several model-error conditions. We find that the algorithm can achieve an acceptable level of error in many cases, with the weakest performance occurring for model-error cases and more extreme parameter regimes with more complex dynamics. Analysis of the poorest-performing cases indicates an initial decrease in error followed by an increase when the ensemble spread is reduced. Our results suggest avenues for further improvement through increasing ensemble spread by incorporating additive inflation or using a parameter or multi-model ensemble. This article is part of the theme issue ‘Uncertainty quantification in cardiac and cardiovascular modelling and simulation’.

scholarly journals A three-dimensional stochastic spatio-temporal model of cell spreading

2007 ◽  
Author(s):  
Yuguang Xiong ◽  
Padmini Rangamani ◽  
Benjamin Dubin-Thaler ◽  
Michael Sheetz ◽  
Ravi Iyengar
Keyword(s):  
Three Dimensional ◽  
Cell Spreading ◽  
Temporal Model ◽  
Spatio Temporal

It Blinks, It Thinks?

Nuncius ◽  
2017 ◽  
Vol 32 (2) ◽  
pp. 412-439
Author(s):  
Flora Lysen
Keyword(s):  
Brain Activity ◽  
Three Dimensional ◽  
Visual Language ◽  
Active Living ◽  
Brain Images ◽  
Material Surfaces ◽  
Temporal Model ◽  
Education Model ◽  
Spatio Temporal ◽  
The Brain

This article traces attempts in the 1930s to create a spatio-temporal model of the active, living brain. Images and models of electric, illuminated displays – derived from electro-technology and engineering – allowed for a changing imaginary of a brain that was immediately accessible. The example of the Luminous Brain Model, a three-dimensional science education model, demonstrates how the visual language of illumination could serve as a flexible rhetorical tool that offered sensations of liveliness to modern viewers and promised to show a transparent view of a dynamic brain. Alternatively, various scientists in the 1930s used the analogy of the brain as an illuminated electric news ticker to conceptualize temporal patterns of changing brain activity, thus drawing the brain into a new metropolitan sphere of material surfaces with real-time mediation. These two historical imaginaries of blinking brains reveal new trajectories of the ‘metaphorical circuits’ through which technology and cerebral biology are mutually articulated.

3D Visual Simulation on Nanchang Hangkong University

2013 ◽  
Vol 756-759 ◽  
pp. 1040-1044
Author(s):  
Xiao Ning Cheng ◽  
Ka Sun ◽  
Xiao Feng Zhang
Keyword(s):  
Spatial Information ◽  
Three Dimensional ◽  
School Enrollment ◽  
Simulation Software ◽  
Visual Simulation ◽  
University Campus ◽  
Alumni Relations ◽  
Three Dimensional Modeling ◽  
Dimensional Modeling ◽  
Employment Education

This paper combined with computer graphics and related spatial information sciences technologies, made use of the software Vega Prime, On the basis of three-dimensional modeling of Nanchang HangKong University campus, built a campus three-dimensional visual simulation software, which can achieve the campus landscape, zoom, rotation, scaling, flight roaming and static and dynamic simulation capabilities, such as the fountain, lake, pedestrians, vehicles, etc. The use of this technology has great importance on school enrollment, employment, education, alumni relations, showing the school strength and other aspects.

scholarly journals Dynamic 3D Simulation of Flood Risk Based on the Integration of Spatio-Temporal GIS and Hydrodynamic Models

2019 ◽  
Vol 8 (11) ◽  
pp. 520 ◽  
Author(s):  
Yongxing Wu ◽  
Fei Peng ◽  
Yang Peng ◽  
Xiaoyang Kong ◽  
Heming Liang ◽  
...  
Keyword(s):  
Decision Support ◽  
Flood Risk ◽  
Three Dimensional ◽  
Visual Simulation ◽  
Hydrodynamic Models ◽  
Seamless Integration ◽  
Modeling Technology ◽  
Risk Simulation ◽  
Spatio Temporal ◽  
Flood Simulations

Dynamic visual simulation of flood risk is crucial for scientific and intelligent emergency management of flood disasters, in which data quality, availability, visualization, and interoperability are important. Here, a seamless integration of a spatio-temporal Geographic Information System (GIS) with one-dimensional (1D) and two-dimensional (2D) hydrodynamic models is achieved for data flow, calculation processes, operation flow, and system functions. Oblique photography-based three-dimensional (3D) modeling technology is used to quickly build a 3D model of the study area (including the hydraulic engineering facilities). A multisource spatio-temporal data platform for dynamically simulating flood risk was built based on the digital earth platform. Using the spatio-temporal computation framework, a dynamic visual simulation and decision support system for flood risk management was developed for the Xiashan Reservoir. The integration method proposed here was verified using flood simulation calculations, dynamic visual simulations, and downstream river channel and dam-break flood simulations. The results show that the proposed methods greatly improve the efficiency of flood risk simulation and decision support. The methods and system put forward in this study can be applied to flood risk simulations and practical management.

scholarly journals An Overland Flood Model for Geographical Information Systems

Water ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2397
Author(s):  
Ceyhun Ozcelik ◽  
Yuri Gorokhovich
Keyword(s):  
Surface Roughness ◽  
Information Systems ◽  
Boundary Conditions ◽  
Geographical Information Systems ◽  
Simulation Software ◽  
Geographical Information ◽  
Model Parameters ◽  
Gis Model ◽  
Flood Model ◽  
Spatio Temporal

A variety of flood models and commercial flood simulation software are provided in the literature, with different accuracies and precisions changing from coarse to fine, depending on model structure and detailed descriptions of basin and hydrologic properties. These models generally focus on river processes, taking overland processes as inputs of 1D or 2D hydrodynamic or hydrologic river flow models. Due to the discrete structure of overland flow and unknown-dynamic boundary conditions, such classical approaches are not cable of fast and reliable spatio–temporal estimations for overland flows, and require detailed and well-organized spatial data that cannot be immediately obtained during an emergency. A spatially-distributed Geographical Information Systems (GIS) based flood model is developed in this study to simulate overland floods, using cellular automata principles. GIS raster cells are considered hydrologic homogeneous areas throughout which hydrologic properties remain constant. Hydrodynamic flow principles, conservations of mass, momentum and energy are applied at pixel level to simulate floodwaters. The proposed GIS model is capable of directly manipulating spatio–temporal pixel level data (e.g., topography, precipitation, infiltration, surface roughness etc.) for modeling of rainfall-induced overland floods; therefore, it can provide fast, temporal and spatial flood depth estimations as well as maximum flood depths and times of concentration for all pixels throughout a study area. The model is quite simple and easy to apply via easily creatable GIS input layers, and is thus very convenient for preliminary engineering applications that need quick and fast response. Its main advantage is that it does not need a predefined flood boundary and boundary conditions. This advantage is especially valuable for coastal plains where delineation of a basin is generally too difficult. Floodwaters of Cyclone Nargis/Myanmar were simulated to test the model. Sensitivity analyses were applied to evaluate the effects of the model parameters (i.e., surface roughness and infiltration rates) on simulation results. The study shows that the proposed GIS model can be readily applied for the fast and inexpensive modeling of rainfall caused floods in areas where flood boundaries and boundary conditions cannot be clearly identified.

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