Hemodynamics and Transport in Patient-specific Abdominal Aortic Aneurysms

163 Pages·2016·18.84 MB·English

by  Amirhossein Arzani

UC Berkeley
UC Berkeley Electronic Theses and Dissertations
Title
Hemodynamics and Transport in Patient-specific Abdominal Aortic Aneurysms
Permalink
https://escholarship.org/uc/item/3x35d1mx
Author
Arzani, Amirhossein
Publication Date
2016

Peer reviewed|Thesis/dissertation
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University of California
Hemodynamics and Transport in Patient-specific Abdominal Aortic Aneurysms
by
Amirhossein Arzani
A dissertation submitted in partial satisfaction of the
requirements for the degree of
Doctor of Philosophy
in
Engineering – Mechanical Engineering
in the
Graduate Division
of the
University of California, Berkeley
Committee in charge:
Professor Shawn C. Shadden, Chair
Professor Mohammad R. K. Mofrad
Professor Per-Olof Persson
Fall 2016
Hemodynamics and Transport in Patient-specific Abdominal Aortic Aneurysms
Copyright 2016
by
Amirhossein Arzani
1
Abstract
Hemodynamics and Transport in Patient-specific Abdominal Aortic Aneurysms
by
Amirhossein Arzani
Doctor of Philosophy in Engineering – Mechanical Engineering
University of California, Berkeley
Professor Shawn C. Shadden, Chair
Abdominalaorticaneurysm(AAA)isapermanentlocalenlargementoftheabdominalaorta.
Complexanatomies, presenceofsidebranches,andpulsatilityofbloodflowcreatesacomplex
chaotic flow field in AAAs. The progression of AAA can lead to rupture, which is one of
the leading causes of death in the elderly. In this study, the flow topology in AAAs, role
of hemodynamics in AAA progression, complex vectorial wall shear stress (WSS) patterns,
and near-wall transport in AAAs were investigated.
Patient-specific computational fluid dynamics (CFD) was used to obtain blood flow in-
formation. Lagrangian coherent structures (LCS) were computed to study the flow physics.
The utility of these structures in studying chaotic mixing and transport, flow separation, and
vortex wall interaction was demonstrated in different patients. The effect of exercise on flow
topology and quantitative mixing was evaluated. The evolution of a systolic vortex formed
in the proximal region, strongly influenced the flow topology in the aneurysms. Intraluminal
thrombus (ILT) deposition and lumen progression were quantified in several patients using
magneticresonanceimagingovera2–3yearfollowup. Point-wisespatialcorrelationofhemo-
dynamic parameters to ILT deposition, revealed a negative correlation between oscillatory
shear stress and ILT deposition. This was attributed to persistence recirculation, which can
lead to unidirectional backward WSS.
Complex vectorial variations in WSS was studied. Namely, variations in WSS magni-
tude, direction, and vector in space and time were quantified and compared. Several new
WSS measures were introduced to better quantify WSS vectorial variations. The concept
of Lagrangian wall shear stress structures (WSS LCS) was introduced. WSS was scaled to
obtain a first order representation of near-wall velocity. Tracers representing biochemicals
in thin concentration boundary layers were tracked on the aneurysm surface based on the
WSS vector field. Formation of coherent structures from WSS tracers were shown. The
WSS LCS organize near-wall transport in high Schmidt number flows and could be used to
predict regions of high near-wall stagnation and concentration. A wall shear stress exposure
time (WSSET) measure was introduced to quantify near-wall stagnation and concentration.
Excellent agreement between WSSET and surface concentration obtained from 3D contin-
2
uum mass transport was obtained. Finally, the important roles that WSS fixed points play
in cardiovascular flows was discussed.
i
To the best wife and parents in the world.
ii
Contents
Contents ii
1 Introduction 1
1.1 Patient-specific computational fluid dynamics (CFD) . . . . . . . . . . . . . 1
1.2 Abdominal aortic aneurysm (AAA) . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 Thesis outline and objective . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2 Patient-specific computational fluid dynamics (CFD) 7
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2 Patient-specific CFD simulation of abdominal aortic aneurysms . . . . . . . 7
3 Flow topology in patient-specific abdominal aortic aneurysms using La-
grangian coherent structures 11
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4 Effect of exercise on flow topology and mixing 28
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
4.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
4.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
5 Abdominal aortic aneurysm progression and intraluminal thrombus de-
position 45
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
5.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
5.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
5.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
6 Vectorial characterization of WSS patterns in aneurysms 64
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
iii
6.2 WSS characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
6.3 WSS gradient calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
6.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
6.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
7 Lagrangian wall shear stress structures and near-wall transport 80
7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
7.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
7.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
7.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
8 Near-wall stagnation in large arteries 94
8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
8.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
8.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
8.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
9 On the importance of wall shear stress fixed points in cardiovascular flow116
9.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
9.2 WSS fixed points and flow topology . . . . . . . . . . . . . . . . . . . . . . . 118
9.3 WSS fixed points and near-wall transport . . . . . . . . . . . . . . . . . . . . 119
9.4 WSS fixed points and endothelial cells . . . . . . . . . . . . . . . . . . . . . 121
9.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
10 Conclusion 123
10.1 Future directions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
10.2 Resultant journal publications . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Bibliography 127
iv
Acknowledgments
I have been blessed to have amazing people in my life. I owe much of my success to
them, and I certainly can not thank them enough. My journey into graduate school started
in Fall 2010 when I started my Masters degree at Illinois Institute of Technology (IIT). I
was lucky to have a young enthusiastic advisor, Shawn Shadden, who continued to be my
advisor at Berkeley. Shawn was everything a student could ask for. He contributed a lot to
my professional developments. I have learned a lot from him, which will be a treasure for
my future career. During the early years, with his remarkable patience, Shawn spent a lot
of time with me, helping me with my research. Whenever I had a question or a problem, I
knew I had Shawn next door who was always ready to help. I still remember how much time
he spent with me during the early years to improve my presentation skills. After my Masters
thesis won the Midwestern Association of Graduate Schools Distinguished Thesis Award, I
was invited to give a talk at the meeting. After my presentation, I was asked by a senior
faculty how I possessed such presentation skills. My answer was very clear, my advisor,
Shawn Shadden. I would also like to thank him for believing in me. When I first told him
about the ideas I had to study wall shear stress (WSS), which constitutes the second half of
my thesis, he was skeptical at first. However, his trust led to what I believe is the highlight
of my thesis.
I have also always treasured the excellent instructors I have had in my education. I am
grateful to Dr. Hasan Nagib and Dr. Kevin Cassel at IIT. Dr. Nagib taught me how to
think of fluid mechanics in terms of vorticity, and Dr. Cassel showed me how to deliver
crystal clear lectures. I would also like to thank Dr. Panos Papadopoulos at Berkeley, for
his inspirational style of teaching finite element methods. I would also like to thank my
qualifying exam committee, Dr. Mohammad Mofrad, Dr. Panos Papadopoulos, Dr. Tony
Keaveny, and Dr. Per-Olof Persson.
I am also very thankful to my very friendly lab-mates. Sahar Hendabadi at IIT who
helped me a lot during my first days, when I was not familiar with many things. Kirk
Hansen for his critical, thought provoking comments that led to some improvements in my
research. Adam Updegrove for helping us with the new features in SimVascular and also
for always answering my technical programming questions. I am also thankful to all the
other members of the Shadden lab who created a friendly environment that I will always
remember. I would like to particularly mention our lab soccer team (known as the Carotid
Kids) for the fun moments, and for winning the Etcheverry cup every single time! I would
also like to thank my very good friend Reza Kamyar, whom I learned a lot from. Reza
taught me a lot about what it means to be a graduate student.
This thesis could not have been done, without my collaborators. I am thankful to Dr.
Ronald Dalman and Dr. Ga-Young Suh from Stanford for providing the imaging data,
which was used to build the patient-specific models. Also, for providing the longitudinal
aneurysm progression data. I would like to thank Dr. Charles Taylor and Dr. Andrea Les
from Stanford for providing the velocity data for our first studies. I am also thankful to Dr.
Alberto Gambaruto from University of Bristol, whom I met in the 2014 World Congress of
v
Biomechanics. This led to a collaboration on the Lagrangian WSS study. I am extremely
thankful to Dr. Guoning Chen from University of Houston. Guoning provided me with his
code for surface vector field calculations, which I extended to use for the Lagrangian WSS
and WSS fixed points studies. I perhaps could not have successfully extended his code, if it
was not for his quick and thorough responses. Guoning was always responsive and helpful
with emails, and I am very thankful to him.
Finally, but most importantly, I would like to thank my lovely family. My beloved
beautiful wife, Samaneh, who I have always felt next to me in the passed years, even during
the hard times when we were thousands of miles apart. Her presence has changed my life in
so many beautiful ways, and she sometimes makes me wonder if there is anything else that I
want for myself in this life. My sister, Vida, who is currently a postgraduate student of oral
and maxillofacial radiology. I am also truly grateful to my parents, whom I have always felt
their support. There is no way that I can imagine myself in my current position, if it was not
for all the unconditional love and support that I have received from my mother and father
through all stages of my life. My father, Ahmad, who is a Professor at Isfahan University of
Technology, was my first role model. I was lucky to live in an academic environment from my
early childhood days, where my father’s success in his career was one of my biggest motives
to move in this path.
My research was supported by NIH Grant No. 5R21HL108272 and an NSF CAREER
AWARD, Grant No. 1354541.