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 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.

scholarly journals Two-Dimensional Numerical Modeling of Flow in Physical Models of Rock Vane and Bendway Weir Configurations

Water ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 458
Author(s):  
Drew C. Baird ◽  
Benjamin Abban ◽  
S. Michael Scurlock ◽  
Steven B. Abt ◽  
Christopher I. Thornton
Keyword(s):  
Numerical Modeling ◽  
Physical Model ◽  
Numerical Models ◽  
Hydraulic Performance ◽  
Physical Models ◽  
Protection Measures ◽  
Design Engineers ◽  
Model Study ◽  
Study Results ◽  
Wide Range

While there are a wide range of design recommendations for using rock vanes and bendway weirs as streambank protection measures, no comprehensive, standard approach is currently available for design engineers to evaluate their hydraulic performance before construction. This study investigates using 2D numerical modeling as an option for predicting the hydraulic performance of rock vane and bendway weir structure designs for streambank protection. We used the Sedimentation and River Hydraulics (SRH)-2D depth-averaged numerical model to simulate flows around rock vane and bendway weir installations that were previously examined as part of a physical model study and that had water surface elevation and velocity observations. Overall, SRH-2D predicted the same general flow patterns as the physical model, but over- and underpredicted the flow velocity in some areas. These over- and underpredictions could be primarily attributed to the assumption of negligible vertical velocities. Nonetheless, the point differences between the predicted and observed velocities generally ranged from 15 to 25%, with some exceptions. The results showed that 2D numerical models could provide adequate insight into the hydraulic performance of rock vanes and bendway weirs. Accordingly, design guidance and implications of the study results are presented for design engineers.

scholarly journals Design of 3D Additively Manufactured Hybrid Structures for Cranioplasty

Materials ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 181
Author(s):  
Roberto De Santis ◽  
Teresa Russo ◽  
Julietta V. Rau ◽  
Ida Papallo ◽  
Massimo Martorelli ◽  
...  
Keyword(s):  
Physical Models ◽  
Cranial Bone ◽  
Head Model ◽  
Rigid Sphere ◽  
Element Analysis ◽  
Aliphatic Polyesters ◽  
Hybrid Device ◽  
Wide Range ◽  
Hybrid Devices ◽  
Technical Solutions

A wide range of materials has been considered to repair cranial defects. In the field of cranioplasty, poly(methyl methacrylate) (PMMA)-based bone cements and modifications through the inclusion of copper doped tricalcium phosphate (Cu-TCP) particles have been already investigated. On the other hand, aliphatic polyesters such as poly(ε-caprolactone) (PCL) and polylactic acid (PLA) have been frequently investigated to make scaffolds for cranial bone regeneration. Accordingly, the aim of the current research was to design and fabricate customized hybrid devices for the repair of large cranial defects integrating the reverse engineering approach with additive manufacturing, The hybrid device consisted of a 3D additive manufactured polyester porous structures infiltrated with PMMA/Cu-TCP (97.5/2.5 w/w) bone cement. Temperature profiles were first evaluated for 3D hybrid devices (PCL/PMMA, PLA/PMMA, PCL/PMMA/Cu-TCP and PLA/PMMA/Cu-TCP). Peak temperatures recorded for hybrid PCL/PMMA and PCL/PMMA/Cu-TCP were significantly lower than those found for the PLA-based ones. Virtual and physical models of customized devices for large cranial defect were developed to assess the feasibility of the proposed technical solutions. A theoretical analysis was preliminarily performed on the entire head model trying to simulate severe impact conditions for people with the customized hybrid device (PCL/PMMA/Cu-TCP) (i.e., a rigid sphere impacting the implant region of the head). Results from finite element analysis (FEA) provided information on the different components of the model.

High-frequency ventilation

1984 ◽  
Vol 64 (2) ◽  
pp. 505-543 ◽  
Author(s):  
J. M. Drazen ◽  
R. D. Kamm ◽  
A. S. Slutsky
Keyword(s):  
Experimental Data ◽  
Gas Exchange ◽  
Dead Space ◽  
Gas Transport ◽  
Physical Models ◽  
High Frequency Ventilation ◽  
General Description ◽  
Wide Range ◽  
Dead Space Volume ◽  
Space Volume

Complete physiological understanding of HFV requires knowledge of four general classes of information: 1) the distribution of airflow within the lung over a wide range of frequencies and VT (sect. IVA), 2) an understanding of the basic mechanisms whereby the local airflows lead to gas transport (sect. IVB), 3) a computational or theoretical model in which transport mechanisms are cast in such a form that they can be used to predict overall gas transport rates (sect. IVC), and 4) an experimental data base (sect. VI) that can be compared to model predictions. When compared with available experimental data, it becomes clear that none of the proposed models adequately describes all the experimental findings. Although the model of Kamm et al. is the only one capable of simulating the transition from small to large VT (as compared to dead-space volume), it fails to predict the gas transport observed experimentally with VT less than equipment dead space. The Fredberg model is not capable of predicting the observed tendency for VT to be a more important determinant of gas exchange than is frequency. The remaining models predict a greater influence of VT than frequency on gas transport (consistent with experimental observations) but in their current form cannot simulate the additional gas exchange associated with VT in excess of the dead-space volume nor the decreased efficacy of HFV above certain critical frequencies observed in both animals and humans. Thus all of these models are probably inadequate in detail. One important aspect of these various models is that some are based on transport experiments done in appropriately scaled physical models, whereas others are entirely theoretical. The experimental models are probably most useful in the prediction of pulmonary gas transport rates, whereas the physical models are of greater value in identifying the specific transport mechanism(s) responsible for gas exchange. However, both classes require a knowledge of the factors governing the distribution of airflow under the circumstances of study as well as requiring detail about lung anatomy and airway physical properties. Only when such factors are fully understood and incorporated into a general description of gas exchange by HFV will it be possible to predict or explain all experimental or clinical findings.

Numerical Jet Atomization: Part II — Modeling Information and Comparison With DNS Results

2006 ◽  
Author(s):  
P. A. Beau ◽  
T. Me´nard ◽  
R. Lebas ◽  
A. Berlemont ◽  
S. Tanguy ◽  
...  
Keyword(s):  
Level Set ◽  
Volume Fraction ◽  
Computing Time ◽  
Mass Conservation ◽  
Liquid Volume ◽  
Liquid Density ◽  
Wide Range ◽  
The Mean ◽  
Break Up ◽  
Primary Break

The main objective of our work is to develop direct numerical simulation tools for the primary break up of a jet. Results can help to determine closure relation in the ELSA model [1] which is based on a single-phase Eulerian model and on the transport equation for the mean liquid/gas interface density in turbulent flows. DNS simulations are carried out to obtain statistical information in the dense zone of the spray where nearly no experimental data are available. The numerical method should describe the interface motion precisely, handle jump conditions at the interface without artificial smoothing, and respect mass conservation. We develop a 3D code [2], where interface tracking is ensured by Level Set method, Ghost Fluid Method [3] is used to capture accurately sharp discontinuities, and coupling between Level Set and VOF methods is used for mass conservation [4]. Turbulent inflow boundary conditions are generated through correlated random velocities with a prescribed length scale. Specific care has been devoted to improve computing time with MPI parallelization. The numerical methods have been applied to investigate physical processes that are involved in the primary break up of an atomizing jet. The chosen configuration is close as possible of Diesel injection (Diameter D = 0.1 mm, Velocity = 100m/s, Liquid density = 696kg/m3, Gas density = 25kg/m3). Typical results will be presented. From the injector nozzle, the turbulence initiates some perturbations on the liquid surface, that are enhanced by the mean shear between the liquid jet and the surrounding air. The interface becomes very wrinkled and some break-up is initiated. The induced liquid parcels show a wide range of shapes. Statistics are carried out and results will be provided for liquid volume fraction, liquid/gas interface density, and turbulent correlations.

scholarly journals An introduction to learning algorithms and potential applications in geomorphometry and earth surface dynamics

2016 ◽  
Author(s):  
Andrew Valentine ◽  
Lara Kalnins
Keyword(s):  
Learning Algorithm ◽  
Learning Algorithms ◽  
Earth Surface ◽  
Surface Dynamics ◽  
Wide Range ◽  
Computational Implementation ◽  
Potential Applications ◽  
Abstract Learning ◽  
The Relationship

Abstract. "Learning algorithms" are a class of computational tool designed to infer information from a dataset, and then apply that information predictively. They are particularly well-suited to complex pattern recognition, or to situations where a mathematical relationship needs to be modelled, but where the underlying processes are not well-understood, are too expensive to compute, or where signals are over-printed by other effects. If a representative set of examples of the relationship can be constructed, a learning algorithm can assimilate its behaviour, and may then serve as an efficient, approximate computational implementation thereof. A wide range of applications in geomorphometry and earth surface dynamics may be envisaged, ranging from classification of landforms through to prediction of erosion characteristics given input forces. Here, we provide a practical overview of the various approaches that lie within this general framework, review existing uses in geomorphology and related applications, and discuss some of the factors that determine whether a learning algorithm approach is suited to any given problem.

scholarly journals Bridging the gap between science communication practice and theory: Reflecting on a decade of practitioner experience using polar outreach case studies to develop a new framework for public engagement design

Polar Record ◽  
2019 ◽  
Vol 55 (4) ◽  
pp. 297-310 ◽  
Author(s):  
Rhian A. Salmon ◽  
Heidi A. Roop
Keyword(s):  
Case Studies ◽  
Public Engagement ◽  
Science Communication ◽  
Practical Training ◽  
Power Structures ◽  
International Polar Year ◽  
Communication Practice ◽  
Wide Range ◽  
Training Resources ◽  
New Framework

AbstractThe International Polar Year 2007–2008 stimulated a wide range of education, outreach and communication (EOC) related to polar research, and catalysed enthusiasm and networks that persist ten years on. Using a multi-method approach that incorporates case studies, auto-ethnographic interviews, and survey data, we interrogate the opportunities and limitations of polar EOC activities and propose a new framework for practical, reflexive, engagement design. Our research suggests that EOC activities are under-valued and often designed based on personal instinct rather than strategic planning, but that there is also a lack of accessible tools that support a more strategic design process. We propose three foci for increasing the professionalisation of practitioner approaches to EOC: (1) improved articulation of goals and objectives; (2) acknowledgement of different drivers, voices and power structures; and (3) increased practical training, resources and reporting structures. We respond to this by proposing a framework for planning and design of public engagement that provides an opportunity to become more transparent and explicit about the real goals of an activity and what “success” looks like. This is critical to effectively evaluate, learn from our experiences, share them with peers, and ultimately deliver more thoughtfully designed, effective engagement.

NUMERICAL SIMULATION OF RAYLEIGH–TAYLOR INSTABILITY BASED ON AN IMPROVED PARTICLE LEVEL SET METHOD

2014 ◽  
Vol 11 (04) ◽  
pp. 1350094 ◽  
Author(s):  
HUI TIAN ◽  
GUOJUN LI ◽  
XIONGWEN ZHANG
Keyword(s):  
Level Set Method ◽  
Level Set ◽  
Stokes Equations ◽  
Density Ratio ◽  
Immiscible Fluids ◽  
Taylor Instability ◽  
Wide Range ◽  
Particle Level ◽  
Rayleigh Taylor Instability ◽  
Particle Level Set Method

An improved particle correction procedure for particle level set method is proposed and applied to the simulation of Rayleigh–Taylor instability (RTI) of the incompressible two-phase immiscible fluids. In the proposed method, an improved particle correction method is developed to deal with all the relative positions between escaped particles and cell corners, which can reduce the disturbance arising in the distance function correction process due to the non-normal direction movement of escaped particles. The improved method is validated through accurately capturing the moving interface of the Zalesak's disk. Furthermore, coupled with the projection method for solving the Navier–Stokes equations, the time-dependent evolution of the RTI interface over a wide range of Reynolds numbers, Atwood numbers and Weber numbers are numerically investigated. A good agreement between the present results and the existing analytical solutions is obtained and the accuracy of the proposed method is further verified. Moreover, the effects of control parameters including viscosity, density ratio, and surface tension coefficient on the evolution of RTI are analyzed in detail, and a critical Weber number for the development of RTI is found.

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