an open-source procedure for the simulation of nasal aerodynamics

137 Pages·2013·17.82 MB·English

Politecnico di Milano

Facoltà di Ingegneria Industriale

Corso di Laurea Magistrale in Ingegneria
Aeronautica

OpenNOSE: an open-source
procedure for the simulation of nasal
aerodynamics

Relatore: Tesi di Laurea di:
Prof. Maurizio Quadrio Chiara Pesci
Matricola 755599

Anno Accademico 2012 - 2013

“Fu così che a sei anni io rinunziai a quella che avrebbe potuto essere la mia gloriosa
carriera da pittore. Il fallimento del mio disegno numero uno e del mio disegno
numero due mi aveva disanimato. I grandi non capiscono mai niente da soli e i
bambini si stancano di spiegargli tutto ogni volta. Allora scelsi un’altra professione e
imparai a pilotare gli aeroplani”.
da Il Piccolo Principe
– Antoine De Saint-Exupéry [1943]

Contents
Contents v
List of Figures vii
List of Tables xi
1 Introduction 1
1.1 The project . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Thesis structure . . . . . . . . . . . . . . . . . . . . . . . . 3
2 Nasal Cavity Flow 5
2.1 The Upper Human Respiratory Tract . . . . . . . . . . . . 5
2.1.1 Physiology . . . . . . . . . . . . . . . . . . . . . . . 5
2.1.2 Anatomy . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2 Experiments and numerical simulation . . . . . . . . . . . 9
2.2.1 Experimental results . . . . . . . . . . . . . . . . . 9
2.2.2 CFD results . . . . . . . . . . . . . . . . . . . . . . 10
3 Numerical simulation of the nasal cavity flow 21
3.1 Navier-Stokes Equations . . . . . . . . . . . . . . . . . . . 21
3.1.1 Reynolds averaged Navier-Stokes equations . . . . . 22
3.2 Turbulence models . . . . . . . . . . . . . . . . . . . . . . 24
3.2.1 k −ω −SST Model . . . . . . . . . . . . . . . . . 25
3.2.2 k −k −ω Model . . . . . . . . . . . . . . . . . . 27
T L
4 Simulation setup 35
4.1 Creation of the geometry . . . . . . . . . . . . . . . . . . . 35
4.1.1 3D-Slicer . . . . . . . . . . . . . . . . . . . . . . . . 35
4.1.2 FreeCAD . . . . . . . . . . . . . . . . . . . . . . . 36
4.1.3 Blender . . . . . . . . . . . . . . . . . . . . . . . . 36
4.2 OpenFOAM . . . . . . . . . . . . . . . . . . . . . . . . . . 37
v
Contents
4.2.1 Mesh generation . . . . . . . . . . . . . . . . . . . 38
4.2.2 Initial and boundary condition . . . . . . . . . . . . 41
5 Results 47
5.1 Laminar and turbulence models . . . . . . . . . . . . . . . 47
5.1.1 Velocity and Pressure Fields . . . . . . . . . . . . . 47
5.1.2 Wall Shear Stress . . . . . . . . . . . . . . . . . . . 54
5.1.3 Turbulent Kinetic Energy . . . . . . . . . . . . . . 56
5.1.4 Turbulence Frequency ω . . . . . . . . . . . . . . . 60
5.2 Pre- and Post-Virtual Surgery . . . . . . . . . . . . . . . . 61
5.2.1 Global Quantities . . . . . . . . . . . . . . . . . . . 61
5.2.2 Local Quantities . . . . . . . . . . . . . . . . . . . 64
6 Conclusions 75
6.1 Achievements . . . . . . . . . . . . . . . . . . . . . . . . . 75
6.2 Future development . . . . . . . . . . . . . . . . . . . . . . 76
A 3D-Slicer 77
A.1 Introduction to CT . . . . . . . . . . . . . . . . . . . . . . 78
A.2 Slicer Procedure . . . . . . . . . . . . . . . . . . . . . . . . 79
B FreeCAD Geometry Decomposition 83
C Geometry Morphing: Blender 87
C.1 Introduction to Blender . . . . . . . . . . . . . . . . . . . . 88
C.2 Sculpt Mode . . . . . . . . . . . . . . . . . . . . . . . . . . 90
C.3 Edit Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
D Generation of the Mesh 97
D.1 blockMesh Utility . . . . . . . . . . . . . . . . . . . . . . . 97
D.2 snappyHexMesh Utility . . . . . . . . . . . . . . . . . . . . 100
D.2.1 Castellated Mesh . . . . . . . . . . . . . . . . . . . 101
D.2.2 Snap Phase . . . . . . . . . . . . . . . . . . . . . . 105
D.2.3 Adding layers . . . . . . . . . . . . . . . . . . . . . 107
Bibliography 113
vi
List of Figures
2.1 Anatomical features of the nose . . . . . . . . . . . . . . . 6
2.2 Views of nasal cavity . . . . . . . . . . . . . . . . . . . . . 7
2.3 Sagittal view of nasal cavity: cells and sinuses highlighted . 8
2.4 (a). Silicone nasal cavity flow phantom viewed sagittally
from the left and (b) axially from the bottom. Figure from
Spence et al. [33] . . . . . . . . . . . . . . . . . . . . . . . 10
2.5 Geometry and the post-surgery models, figures from [22] . . 16
2.6 Virtualsurgerymodelsandrealpre-andpost-surgery, figure
from [29] . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.1 Illustrationofwall-limitingconceptfork production, figure
L
from [39] . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.1 Three surfaces divided, back view . . . . . . . . . . . . . . 36
4.2 Pre-surgery mesh . . . . . . . . . . . . . . . . . . . . . . . 41
5.1 Coronal section highlighted in the nasal cavity. . . . . . . . 48
5.2 Velocity magnitude [m/s], coronal section. . . . . . . . . . 49
5.3 ν [m2/s], coronal section. . . . . . . . . . . . . . . . . . . 49
T
5.4 U velocity component [m/s], sagittal section. . . . . . . . 50
Y
5.5 Sagittal section highlighted in the nasal cavity. . . . . . . . 51
5.6 U velocity component [m/s], sagittal section. . . . . . . . 52
Y
5.7 Pressure field [m2/s2], sagittal section. . . . . . . . . . . . . 53
5.8 Wall Shear Stresses, particular of the pharynx. . . . . . . . 54
5.9 Wall Shear Stresses, particular of the nasal valve. . . . . . . 55
5.10 Turbulent and laminar fluctuations [m2/s2] with k −k −ω
T L
model. Sagittal section, refer to figure 5.5 for the position
in the nasal cavity. . . . . . . . . . . . . . . . . . . . . . . . 56
5.11 Turbulent fluctuations with turbulence models, throat section 57
5.12 Turbulent kinetic energy [m2/s2]. . . . . . . . . . . . . . . . 58
5.13 Turbulent kinetic energy [m2/s2]. . . . . . . . . . . . . . . . 59
5.14 Turbulence frequency ω [s−1], section from figure 5.13(f). . 60
vii
List of Figures
5.15 Pre-surgery. U for flow rates computation. . . . . . . . . . 62
y
5.16 Post-surgery. U for flow rates computation. . . . . . . . . 62
y
5.17 Pressure [m2/s2], sagittal view. . . . . . . . . . . . . . . . . 64
5.18 Velocity streamlines. . . . . . . . . . . . . . . . . . . . . . . 65
5.19 Exampleofvelocitymagnitude[m/s], sagittalview, location
in the nasal cavity highlighted in figure 5.13(e). . . . . . . . 65
5.20 U at the septal deviation [m/s], coronal section. . . . . . . 66
y
5.21 U after the septal deviation [m/s], coronal section. . . . . 67
y
5.22 U streamlines in the obstruction region. . . . . . . . . . . . 67
y
5.23 Highest turbulent kinetic energy regions [m2/s2]. . . . . . . 68
5.24 Turbulent kinetic energy [m2/s2]; sagittal section, refer to
figure 5.13(e). . . . . . . . . . . . . . . . . . . . . . . . . . 69
5.25 Turbulent kinetic energy [m2/s2]; sagittal section, 5.13(f). . 69
5.26 Turbulent kinetic energy [m2/s2]; coronal section. . . . . . . 70
5.27 Turbulencefrequencyω [s−1]; coronalsection, refertofigure
5.12(f). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
5.28 Vorticity component ω [s−1]; sagittal section. . . . . . . . 71
X
5.29 Vorticity component ω [s−1]; sagittal section, deviated side. 72
X
5.30 Wall shear stresses. . . . . . . . . . . . . . . . . . . . . . . 73
A.1 Sagittal view in gray scale from a CT . . . . . . . . . . . . 77
A.2 Slicer start-up module . . . . . . . . . . . . . . . . . . . . . 78
A.3 Interface of Slicer after applying the Editor module . . . . . 80
A.4 Slicer frame meanwhile the user is setting the HU threshold 81
A.5 Slicer frame meanwhile the user is excluding ears . . . . . . 81
A.6 Slicer frame with 3D reconstruction . . . . . . . . . . . . . 82
B.1 Back view of entire surface in transparency . . . . . . . . . 83
B.2 FreeCAD frames . . . . . . . . . . . . . . . . . . . . . . . . 84
B.3 Side view of nasal cavity in transparency . . . . . . . . . . 84
B.4 Three surfaces divided, back view . . . . . . . . . . . . . . 85
C.1 Opening scene of Blender with default objects . . . . . . . 88
C.2 Blender scene with more views, icon highlighted . . . . . . 89
C.3 Sculpt mode: brush types . . . . . . . . . . . . . . . . . . . 91
C.4 Stl geometry imported in Blender . . . . . . . . . . . . . . 93
C.5 Particular of the geometry . . . . . . . . . . . . . . . . . . 93
C.6 Particular of the region to modify . . . . . . . . . . . . . . 94
C.7 Particular of the geometry modified . . . . . . . . . . . . . 95
C.8 Particular of the geometry modified . . . . . . . . . . . . . 96
D.1 Resultant block mesh for this work . . . . . . . . . . . . . . 99
viii
List of Figures
D.2 ParaView frames . . . . . . . . . . . . . . . . . . . . . . . . 99
D.3 Different values for nCellsBetweenLevels . . . . . . . . . . . 101
D.4 Examples of level entries producing different refinement . . 102
D.5 Refinement levels . . . . . . . . . . . . . . . . . . . . . . . 103
D.6 Resultant castellated mesh, sagittal view of the nasal cavity 104
D.7 ParaView frames, castellated mesh . . . . . . . . . . . . . . 105
D.8 Comparison between different nSmoothPatch . . . . . . . . 106
D.9 ParaView frames, snapped mesh . . . . . . . . . . . . . . . 106
D.10 Layers distrubution scheme . . . . . . . . . . . . . . . . . . 107
D.11 Comparison between differen featureAngle . . . . . . . . . . 109
D.12 Throat, mesh with layers . . . . . . . . . . . . . . . . . . . 111
D.13 Mesh with layers, axial view . . . . . . . . . . . . . . . . . 111
ix