scholarly journals A level set-based approach for modeling cellular rearrangements in tissue morphogenesis

2020 ◽  
Author(s):  
Rhudaina Z. Mohammad ◽  
Hideki Murakawa ◽  
Karel Svadlenka ◽  
Hideru Togashi
Keyword(s):  
Level Set ◽  
Gradient Flow ◽  
Physical Parameters ◽  
Tissue Morphogenesis ◽  
Minimization Principle ◽  
Cell Contractility ◽  
Sensory Epithelia ◽  
Wide Range ◽  
Simulation Results ◽  
Cell Cell

Abstract Mathematical models and numerical simulations can provide an essential insight into the mechanisms through which local cell-cell interactions affect tissue-level cell morphology. Among such morphological phenomena, cellular patterns observed in developing sensory epithelia have gained keen attention of researchers in recent years, because they are thought to be of utmost importance for accurate sensory functions. However, most of current computational approaches to cellular rearrangements lack solid mathematical background and involve experimentally unreachable parameters, whereby only weak and ambiguous conclusions can be made based on simulation results. Here we present a simple mathematical model for tissue morphogenesis together with a level set-based numerical scheme for its solution as a tool to rigorously investigate evolving cellular patterns. This combined framework of a model and a numerical method features minimum possible number of physical parameters and guarantees reliability of simulation results, including correct handling of topology changes, such as cell intercalations. In this framework, we adopt the viewpoint of free energy minimization principle, and take cellular rearrangement as a gradient flow of a weighted surface energy associated with cell membrane, where the weights are related to physical parameters of the cells, for example, cell-cell adhesion and cell contractility. We present the applicability of this model to a wide range of tissue morphological phenomena, such as cell sorting, engulfment or internalization. In particular, we stress that this method is the first one to be successful in computationally reproducing the experimentally observed development of cellular mosaic patterns in sensory epithelia. Thanks to its simplicity and reliability, the model is able to capture the essence of biological phenomena, and may give a strong helping hand in deciphering unsolved questions of morphology.

scholarly journals A level set-based approach for modeling cellular rearrangements in tissue morphogenesis

2020 ◽  
Author(s):  
Rhudaina Z. Mohammad ◽  
Hideki Murakawa ◽  
Karel Svadlenka ◽  
Hideru Togashi
Keyword(s):  
Level Set ◽  
Gradient Flow ◽  
Physical Parameters ◽  
Tissue Morphogenesis ◽  
Minimization Principle ◽  
Cell Contractility ◽  
Sensory Epithelia ◽  
Wide Range ◽  
Simulation Results ◽  
Cell Cell

Abstract Mathematical models and numerical simulations can provide an essential insight into the mechanisms through which local cell-cell interactions affect tissue-level cell morphology. Among such morphological phenomena, cellular patterns observed in developing sensory epithelia have gained keen attention of researchers in recent years, because they are thought to be of utmost importance for accurate sensory functions. However, most of current computational approaches to cellular rearrangements lack solid mathematical background and involve experimentally unreachable parameters, whereby only weak and ambiguous conclusions can be made based on simulation results. Here we present a simple mathematical model for tissue morphogenesis together with a level set-based numerical scheme for its solution as a tool to rigorously investigate evolving cellular patterns. This combined framework of a model and a numerical method features minimum possible number of physical parameters and guarantees reliability of simulation results, including correct handling of topology changes, such as cell intercalations. In this framework, we adopt the viewpoint of free energy minimization principle, and take cellular rearrangement as a gradient flow of a weighted surface energy associated with cell membrane, where the weights are related to physical parameters of the cells, for example, cell-cell adhesion and cell contractility. We present the applicability of this model to a wide range of tissue morphological phenomena, such as cell sorting, engulfment or internalization. In particular, we stress that this method is the first one to be successful in computationally reproducing the experimentally observed development of cellular mosaic patterns in sensory epithelia. Thanks to its simplicity and reliability, the model is able to capture the essence of biological phenomena, and may give a strong helping hand in deciphering unsolved questions of morphology.

An Experimental Study of a Single-Degree-of-Freedom Impact Oscillator

2021 ◽  
Author(s):  
Shun Zhong ◽  
Jingyuan Tan ◽  
Zhicheng Cui ◽  
Tanghong Xu ◽  
Liqing Li
Keyword(s):  
Dynamical Behavior ◽  
Degree Of Freedom ◽  
Experimental Results ◽  
Physical Parameters ◽  
Impact Oscillator ◽  
Single Degree Of Freedom ◽  
Single Degree ◽  
Design Choice ◽  
Wide Range ◽  
Simulation Results

Purpose. Impacts appear in a wide range of mechanical systems. To study the dynamical behavior introduced by impact in practical way, a single-degree-of-freedom impact oscillator rig is designed. Originality. A simple piece-wise linear system with symmetrical flexible constraints is designed and manufactured to carry out a wide range of experimental dynamic analysis and ultimately to validate piece-wise models. The new design choice is based on the following criteria: accuracy in representing the mathematical model, manufacturing simplicity, flexibility in terms of parameter changes and cost effectiveness as well avoidance of the delay introduced by the structure. Meanwhile, the new design provides the possibility of the applications of the complex control algorithms. Design/methodology/approach. The design process is described in detail. The initial experimental results of the rig as well as numerical simulation results are given. In this rig, the mass driven force is generated by electromagnet, which can be adjusted and control easily. Also, most of the physical parameters can be varied in a certain range to enhance flexibility of the system allowing to observe subtle phenomena. Findings. Compared with the simulation results, the designed rig is proved to be validated. Then, the initial experimental results demonstrate potentials of this rig to study fundamental impact phenomena, which have been observed in various engineering systems. They also indicate that this rig can be a good platform for investigating nonlinear control methods.

scholarly journals A level set-based approach for modeling cellular rearrangements in tissue morphogenesis

2021 ◽  
Author(s):  
Rhudaina Mohammad ◽  
Hideki Murakawa ◽  
Karel Svadlenka ◽  
Hideru Togashi
Keyword(s):  
Level Set ◽  
Physical Models ◽  
Significant Feature ◽  
Mathematical Treatment ◽  
Computational Framework ◽  
Sensory Epithelia ◽  
Large Bulk ◽  
Wide Range ◽  
Computational Implementation ◽  
New Framework

Abstract Among morphological phenomena, cellular patterns in developing sensory epithelia have gained attention in recent years. Although physical models for cellular rearrangements are well-established thanks to a large bulk of experimental work, their computational implementation lacks solid mathematical background and involves experimentally unreachable parameters. Here we introduce a level set-based computational framework as a tool to rigorously investigate evolving cellular patterns, and study its mathematical and computational properties. We illustrate that a significant feature of the method is its ability to correctly handle complex topology changes, including frequent cell intercalations. Combining this accurate numerical scheme with an established mathematical model, we show that the new framework features minimum possible number of parameters and is capable of reproducing a wide range of tissue morphological phenomena, such as cell sorting, engulfment or internalization. In particular, thanks to precise mathematical treatment of cellular intercalations, this method is the first to successfully simulate experimentally observed development of cellular mosaic patterns in sensory epithelia.

scholarly journals A level set-based approach for modeling cellular rearrangements in tissue morphogenesis

2021 ◽  
Author(s):  
Rhudaina Z. Mohammad ◽  
Hideki Murakawa ◽  
Karel Svadlenka ◽  
Hideru Togashi
Keyword(s):  
Level Set ◽  
Physical Models ◽  
Mathematical Treatment ◽  
Computational Framework ◽  
Sensory Epithelia ◽  
Large Bulk ◽  
Wide Range ◽  
Computational Implementation ◽  
Topology Changes ◽  
New Framework

Abstract Among morphological phenomena, cellular patterns in developing sensory epithelia have gained attention in recent years. Although physical models for cellular rearrangements are well-established thanks to a large bulk of experimental work, their computational implementation lacks solid mathematical background and involves experimentally unreachable parameters. Here we introduce a level set-based computational framework as a tool to rigorously investigate evolving cellular patterns. We investigate its mathematical and computational properties, showing that it significantly surpasses existing schemes in its ability to correctly handle complex topology changes, including frequent cell intercalations. Combining this accurate numerical scheme with an established mathematical model, we show that the new framework features minimum possible number of parameters and is capable of reproducing a wide range of tissue morphological phenomena, such as cell sorting, engulfment or internalization. In particular, thanks to precise mathematical treatment of cellular intercalations, this method is the first to successfully simulate experimentally observed development of cellular mosaic patterns in sensory epithelia.

scholarly journals A Computational Study on the Role of Parameters for Identification of Thyroid Nodules by Infrared Images (and Comparison with Real Data)

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4459
Author(s):  
José R. González ◽  
Charbel Damião ◽  
Maira Moran ◽  
Cristina A. Pantaleão ◽  
Rubens A. Cruz ◽  
...  
Keyword(s):  
Heat Transfer ◽  
Thyroid Nodules ◽  
Numerical Study ◽  
Computational Study ◽  
Internal Heat ◽  
Heat Transfer Process ◽  
The Body ◽  
Physical Parameters ◽  
Infrared Sensors ◽  
Wide Range

According to experts and medical literature, healthy thyroids and thyroids containing benign nodules tend to be less inflamed and less active than those with malignant nodules. It seems to be a consensus that malignant nodules have more blood veins and more blood circulation. This may be related to the maintenance of the nodule’s heat at a higher level compared with neighboring tissues. If the internal heat modifies the skin radiation, then it could be detected by infrared sensors. The goal of this work is the investigation of the factors that allow this detection, and the possible relation with any pattern referent to nodule malignancy. We aim to consider a wide range of factors, so a great number of numerical simulations of the heat transfer in the region under analysis, based on the Finite Element method, are performed to study the influence of each nodule and patient characteristics on the infrared sensor acquisition. To do so, the protocol for infrared thyroid examination used in our university’s hospital is simulated in the numerical study. This protocol presents two phases. In the first one, the body under observation is in steady state. In the second one, it is submitted to thermal stress (transient state). Both are simulated in order to verify if it is possible (by infrared sensors) to identify different behavior referent to malignant nodules. Moreover, when the simulation indicates possible important aspects, patients with and without similar characteristics are examined to confirm such influences. The results show that the tissues between skin and thyroid, as well as the nodule size, have an influence on superficial temperatures. Other thermal parameters of thyroid nodules show little influence on surface infrared emissions, for instance, those related to the vascularization of the nodule. All details of the physical parameters used in the simulations, characteristics of the real nodules and thermal examinations are publicly available, allowing these simulations to be compared with other types of heat transfer solutions and infrared examination protocols. Among the main contributions of this work, we highlight the simulation of the possible range of parameters, and definition of the simulation approach for mapping the used infrared protocol, promoting the investigation of a possible relation between the heat transfer process and the data obtained by infrared acquisitions.

scholarly journals Design and Evaluation of Large-Scale IoT-Enabled Healthcare Architecture

2021 ◽  
Vol 11 (8) ◽  
pp. 3623
Author(s):  
Omar Said ◽  
Amr Tolba
Keyword(s):  
Packet Loss ◽  
Large Scale ◽  
Performance Metrics ◽  
Medical System ◽  
Healthcare Data ◽  
High Altitude Platforms ◽  
Wide Range ◽  
Simulation Results ◽  
Healthcare Architecture ◽  
The Internet Of Things

Employment of the Internet of Things (IoT) technology in the healthcare field can contribute to recruiting heterogeneous medical devices and creating smart cooperation between them. This cooperation leads to an increase in the efficiency of the entire medical system, thus accelerating the diagnosis and curing of patients, in general, and rescuing critical cases in particular. In this paper, a large-scale IoT-enabled healthcare architecture is proposed. To achieve a wide range of communication between healthcare devices, not only are Internet coverage tools utilized but also satellites and high-altitude platforms (HAPs). In addition, the clustering idea is applied in the proposed architecture to facilitate its management. Moreover, healthcare data are prioritized into several levels of importance. Finally, NS3 is used to measure the performance of the proposed IoT-enabled healthcare architecture. The performance metrics are delay, energy consumption, packet loss, coverage tool usage, throughput, percentage of served users, and percentage of each exchanged data type. The simulation results demonstrate that the proposed IoT-enabled healthcare architecture outperforms the traditional healthcare architecture.

scholarly journals Modelling H2 and its effects on star formation using a joint implementation of gadget-3 and KROME

2021 ◽  
Vol 504 (2) ◽  
pp. 2325-2345
Author(s):  
Emanuel Sillero ◽  
Patricia B Tissera ◽  
Diego G Lambas ◽  
Stefano Bovino ◽  
Dominik R Schleicher ◽  
...  
Keyword(s):  
Star Formation ◽  
Formation Rate ◽  
Physical Parameters ◽  
Density Profiles ◽  
Star Forming ◽  
Chemical Enrichment ◽  
Numerical Resolution ◽  
Stellar Radiation ◽  
Wide Range ◽  
The Impact

ABSTRACT We present p-gadget3-k, an updated version of gadget-3, that incorporates the chemistry package krome. p-gadget3-k follows the hydrodynamical and chemical evolution of cosmic structures, incorporating the chemistry and cooling of H2 and metal cooling in non-equilibrium. We performed different runs of the same ICs to assess the impact of various physical parameters and prescriptions, namely gas metallicity, molecular hydrogen formation on dust, star formation recipes including or not H2 dependence, and the effects of numerical resolution. We find that the characteristics of the simulated systems, both globally and at kpc-scales, are in good agreement with several observable properties of molecular gas in star-forming galaxies. The surface density profiles of star formation rate (SFR) and H2 are found to vary with the clumping factor and resolution. In agreement with previous results, the chemical enrichment of the gas component is found to be a key ingredient to model the formation and distribution of H2 as a function of gas density and temperature. A star formation algorithm that takes into account the H2 fraction together with a treatment for the local stellar radiation field improves the agreement with observed H2 abundances over a wide range of gas densities and with the molecular Kennicutt–Schmidt law, implying a more realistic modelling of the star formation process.

Data-Driven Analysis of Engine Mission Severity Using Non-Dimensional Groups

2021 ◽  
Author(s):  
Tim Brandes ◽  
Stefano Scarso ◽  
Christian Koch ◽  
Stephan Staudacher
Keyword(s):  
Support Vector Machine ◽  
Computation Time ◽  
Principal Component ◽  
General Term ◽  
Support Vector ◽  
Physical Parameters ◽  
Machine Model ◽  
Precision Error ◽  
Operational Conditions ◽  
Wide Range

Abstract A numerical experiment of intentionally reduced complexity is used to demonstrate a method to classify flight missions in terms of the operational severity experienced by the engines. In this proof of concept, the general term of severity is limited to the erosion of the core flow compressor blade and vane leading edges. A Monte Carlo simulation of varying operational conditions generates a required database of 10000 flight missions. Each flight is sampled at a rate of 1 Hz. Eleven measurable or synthesizable physical parameters are deemed to be relevant for the problem. They are reduced to seven universal non-dimensional groups which are averaged for each flight. The application of principal component analysis allows a further reduction to three principal components. They are used to run a support-vector machine model in order to classify the flights. A linear kernel function is chosen for the support-vector machine due to its low computation time compared to other functions. The robustness of the classification approach against measurement precision error is evaluated. In addition, a minimum number of flights required for training and a sensible number of severity classes are documented. Furthermore, the importance to train the algorithms on a sufficiently wide range of operations is presented.

Aerodynamic Similarity Principles and Scaling Laws for Windmilling Fans

2018 ◽  
Author(s):  
Dilip Prasad
Keyword(s):  
Rotational Speed ◽  
Pressure Loss ◽  
Scaling Laws ◽  
Dynamic Pressure ◽  
Stagnation Pressure ◽  
Design Parameters ◽  
Similarity Parameter ◽  
Wide Range ◽  
Simulation Results ◽  
Good Agreement

Windmilling requirements for aircraft engines often define propulsion and airframe design parameters. The present study is focused is on two key quantities of interest during windmill operation: fan rotational speed and stage losses. A model for the rotor exit flow is developed, that serves to bring out a similarity parameter for the fan rotational speed. Furthermore, the model shows that the spanwise flow profiles are independent of the throughflow, being determined solely by the configuration geometry. Interrogation of previous numerical simulations verifies the self-similar nature of the flow. The analysis also demonstrates that the vane inlet dynamic pressure is the appropriate scale for the stagnation pressure loss across the rotor and splitter. Examination of the simulation results for the stator reveals that the flow blockage resulting from the severely negative incidence that occurs at windmill remains constant across a wide range of mass flow rates. For a given throughflow rate, the velocity scale is then shown to be that associated with the unblocked vane exit area, leading naturally to the definition of a dynamic pressure scale for the stator stagnation pressure loss. The proposed scaling procedures for the component losses are applied to the flow configuration of Prasad and Lord (2010). Comparison of simulation results for the rotor-splitter and stator losses determined using these procedures indicates very good agreement. Analogous to the loss scaling, a procedure based on the fan speed similarity parameter is developed to determine the windmill rotational speed and is also found to be in good agreement with engine data. Thus, despite their simplicity, the methods developed here possess sufficient fidelity to be employed in design prediction models for aircraft propulsion systems.

scholarly journals Optical tools for ocean monitoring and research

Ocean Science ◽  
2009 ◽  
Vol 5 (4) ◽  
pp. 661-684 ◽  
Author(s):  
C. Moore ◽  
A. Barnard ◽  
P. Fietzek ◽  
M. R. Lewis ◽  
H. M. Sosik ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Ocean Color ◽  
Analytical Techniques ◽  
Optical Measurements ◽  
Physical Parameters ◽  
Optical Tools ◽  
Wide Range ◽  
Radiance Distribution ◽  
Ocean Monitoring ◽  
Methane Carbon

Abstract. Requirements for understanding the relationships between ocean color and suspended and dissolved materials within the water column, and a rapidly emerging photonics and materials technology base for performing optical based analytical techniques have generated a diverse offering of commercial sensors and research prototypes that perform optical measurements in water. Through inversion, these tools are now being used to determine a diverse set of related biogeochemical and physical parameters. Techniques engaged include measurement of the solar radiance distribution, absorption, scattering, stimulated fluorescence, flow cytometry, and various spectroscopy methods. Selective membranes and other techniques for material isolation further enhance specificity, leading to sensors for measurement of dissolved oxygen, methane, carbon dioxide, common nutrients and a variety of other parameters. Scientists are using these measurements to infer information related to an increasing set of parameters and wide range of applications over relevant scales in space and time.

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