YALES2BIO: a general multiscale solver for blood flowsnicoud/Cours/EMALCA - BIO.pdf · Institut de...
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Institut de Mathématiques et de
Modélisation de Montpellier
UMR 5149 – I3M
1
YALES2BIO: a general multiscale solver for
blood flows
Franck Nicoud* Simon Mendez Professor at Polytech’Montpellier Researcher at CNRS/I3M
Mechanical Engineering Dpt Chief architect
* and the other people from the YALES2BIO team
November, 2014 EMALCA, Puerto Madryn
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2 November, 2014 EMALCA, Puerto Madryn
WHERE I COME FROM
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3 November, 2014 EMALCA, Puerto Madryn
MY TWO SCIENTIFIC LIFES
Laboratory of Mathematics and
Modelling of Montpellier
University
CARDIO-VASCULAR BIOMECHANICS -
1ST TALK
European Center for Research and Advanced Training
in Scientific Computing
COMBUSTION INSTABILITIES - 2ND TALK
FRANCE
PARIS
TOULOUSE MONTPELLIER
IN TOULOUSE
IN MONTPELLIER
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4 November, 2014 EMALCA, Puerto Madryn
ABOUT BLOOD
Composition
• Plasma (55%)
• Red Blood Cells (≈44%)
• White Cells
• Platelets
• 4-5 millions of Cells per mm3 …
• Not a simple fluid: shear-thinning for viscosity …
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5 November, 2014 EMALCA, Puerto Madryn
ABOUT BLOOD
Blood
Newtonian Fluid (water, plasma…)
Shear rate (s-1)
Vis
co
sit
y (
10
3P
a.s
-1)
Red Blood cells in a
Blood sample
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ABOUT RED BLOOD CELLS
6
Cytoplasm
(Newtonian fluid)
Thin membrane
Mohandas, Blood, 2008.
6 November, 2014 EMALCA, Puerto Madryn
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SIMPLE CELLS, COMPLEX MEMBRANE
Lipid
bilayer
Cyto-
skeleton
Mechanics : resistance to - Area change
- Bending
- Shear
7 November, 2014 EMALCA, Puerto Madryn
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• Fluid mechanics point of view
Blood flow characteristics: how do pressure and velocity components evolve over space and time ?
Motion of solid materials (arteries, valves, stent, …) interacting with blood
Associated constraints (pressure, viscous)
• Medical point of view
Aneurysm rupture risk (leads to (lethal) hemorrhage) ,
Vascularization of the different parts of the arterial tree
Thrombus formation (leads to (lethal) emboli)
Hemolysis rate (destruction of red blood cells, leads to anemia)
November, 2014 EMALCA, Puerto Madryn
BLOOD FLOWS RELATED QUESTIONS
Cerebral Aneurysm
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The study of blood flows using numerical simulations, with the application to the optimization of biomedical devices
Can we optimize the hydrodynamic and thrombogenic performances while minimizing hemolysis ?
Extracorporeal circulation
Ventricular Assist Devices
Artificial hearts
Abiocor
Flow diverters
November, 2014 EMALCA, Puerto Madryn
OUR LONG-TERM OBJECTIVE AT I3M
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• Generally speaking :
multi-scale flows (10 mm – 10 cm)
fluid-structure interactions [Blood/arteries/valves OR Plasma/cell membranes]
• Macroscopic scale :
3D complex geometries ; complex rheology (shear thinning, thixotropic)
Pulsated BCs and transitional (neither laminar nor turbulent) flow regimes
• Microscopic scale :
Huge number of cells interacting
Highly deformable cells
• Others : Biochemistry, electric coupling, …
10
SOME BLOOD FLOWS-RELATED CHALLENGES
November, 2014 EMALCA, Puerto Madryn
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EXAMPLE OF COMPLEX MOVING GEOMETRIES
November, 2014 EMALCA, Puerto Madryn
Heart and Aorta arch over time
Sagittal cut
(CT scan - Moreno – CHU Toulouse)
Heart and Aorta at fixed time
3D view
(CT scan - Moreno – CHU Toulouse)
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• In-house solver www.math.univ-montp2.fr/~yales2bio
• Data structure inherited from the HPC YALES2 solver (CNRS GIS SUCCESS)
dedicated to the computation of turbulent reacting flows
www.coria-cfd.fr/index.php/YALES2
• Main features :
Methodologies adapted to micro and macro scale applications
fluid-structure interactions (moving meshes; Immersed boundaries)
Unstructured meshes (complex geometries)
High order, low dissipative schemes (transitional flows)
Massively parallel (good scaling up to 10000 cores)
November, 2014 EMALCA, Puerto Madryn
THE YALES2BIO PROJECT
12
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OUTLINE
13 13 November, 2014 EMALCA, Puerto Madryn
• Transitional hemodynamics in a realistic heart
• Fluid-structure interaction for Micro-scale computations
• Fluid-structure interaction for Macro-scale computations
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14 November, 2014 EMALCA, Puerto Madryn
NAVIER-STOKES EQUATIONS
• The 3D PDE’s governing the flow of a constant density (𝜌) fluid are:
Mass conservation (continuity): 𝜕𝑢𝑖𝜕𝑥𝑖= 0
Momentum: 𝜕𝑢𝑖𝜕𝑡+ 𝑢𝑗𝜕𝑢𝑖𝜕𝑥𝑗= −1
𝜌
𝜕𝑝
𝜕𝑥𝑖+𝜕
𝜕𝑥𝑗𝜈𝜕𝑢𝑖𝜕𝑥𝑗+𝜕𝑢𝑗𝜕𝑥𝑖 , with 𝑖 = 1,2,3
• Remarks: 𝑝 is pressure and 𝜈 is the kinematic viscosity (constant if Newtonian fluid)
The non-linear term 𝑢𝑗𝜕𝑢𝑖
𝜕𝑥𝑗 arises from the inertia effects ; if large enough, it is
responsible for turbulence generation
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15
REALISTIC FLOW IN A HUMAN LEFT HEART
• Flow characteristics:
• Length scale = 1 – 10 cm
• Reynolds number = 1000 – 5000 𝑹𝒆 =𝐕𝐞𝐥𝐨𝐜𝐢𝐭𝐲 × 𝐋𝐞𝐧𝐠𝐭𝐡
𝐕𝐢𝐬𝐜𝐨𝐬𝐢𝐭𝐲
• Flow most probably transitional: neither laminar nor turbulent
November, 2014 EMALCA, Puerto Madryn
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• Only the intra-cardiac blood flow is computed; the motion of the cardiac muscle is deduced from medical imaging.
• Rely on the OCFIA chain developed within a former ANR research project (http://www.ocfia.org/) with University Hospital of Toulouse
• Combining OCFIA and the flow solver YALES2BIO :
Chnafa et al., Comp. & Fluids, 2014
ECG-gated 3D medical images at a few instants over the cardiac
cycle (CT scan or MRI)
Deformable 3D mesh
representative of the patient
specific heart deformations
Transitional blood flow
compatible with the observed deformations
OCFIA YALES2BIO
November, 2014 EMALCA, Puerto Madryn
FUNCTIONAL IMAGING OF THE HEART
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17 November, 2014 EMALCA, Puerto Madryn
4D MESH FROM MEDICAL IMAGING
Aorta from CT scan
(Moreno – CHU Toulouse) Left heart from CT scan
(Chnafa – I3M Montpellier)
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November, 2014 18
EMALCA, Puerto Madryn
ABOUT TURBULENCE
• Turbulence is present in most of the flows met in the everyday life (clouds, shore breaks, wind, airplane wakes, …)
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November, 2014 19
EMALCA, Puerto Madryn
ABOUT TURBULENCE
• Turbulence is present in most of the flows met in the everyday life (clouds, shore breaks, wind, …)
• It results from the non-linearity of the Navier-Stokes equations
• Modeling it is extremely challenging, if even possible …
IS TURBULENCE PRESENT IN
CARDIAC HEMODYNAMICS ??
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November, 2014 20
EMALCA, Puerto Madryn
MODELING TURBULENCE
Wave number
Kinetic
energy
spectrum
• Direct Numerical Simulation
Solve all the scales - No model required
complexity increases like (Reynolds number)9/2
• Reynolds-Averaged Navier-Stokes
Model all the scales (e.g.: k-e model)
Hardly predictive; no suitable for transitional flows
• Large-Eddy Simulation offers an alternative view
• Direct Numerical Simulation
Solve all the scales - No model required
complexity increases like (Reynolds number)9/2
• Reynolds-Averaged Navier-Stokes
Model all the scales (e.g.: k-e model)
Hardly predictive; no suitable for transitional flows
• Large-Eddy Simulation offers an alternative view
• Direct Numerical Simulation
Solve all the scales - No model required
complexity increases like (Reynolds number)9/2
• Reynolds-Averaged Navier-Stokes
Model all the scales (e.g.: k-e model)
Hardly predictive; no suitable for transitional flows
• Large-Eddy Simulation offers an alternative view
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November, 2014 21
EMALCA, Puerto Madryn
ck
Modeled scales Resolved scales
LARGE-EDDY SIMULATION
Wave number
Kinetic
Energy
spectrum
• The filtered Navier-Stokes equations are solved
The largest scales are computed directly
The smallest scales (subgrid scales) are modeled so that their effect on the largest scales dynamics is accounted for
• Requires an efficient, HPC compatible and low dissipative flow solver.
• YALES2BIO (www.math.univ-montp2.fr/~yales2bio) gathers these properties
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Sigma model (Nicoud et al., 2011)
Systole Diastole
𝜇𝑡/𝜇
November, 2014 EMALCA, Puerto Madryn
SUBGRID SCALE VISCOSITY
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In-plane and vertical velocity
Vorticity modulus
Chnafa et al., Comp. & Fluids, 2014; Chnafa et al., Ed. A. Quarteroni, 2014
November, 2014 EMALCA, Puerto Madryn
FLOW VISUALIZATION
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The Q-criterion allows
visualizing vortices in the blood
flow. The point of view is also
rotation around the heart in the
movie.
𝑄 =1
2Ω2 − 𝑆2
(Jeong & Hussain 1995)
November, 2014 EMALCA, Puerto Madryn
FLOW VISUALIZATION
Chnafa et al., TSFP, 2013
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• Approx. 50 cycles were computed
• Vertical velocity at four probes over 6 cardiac cycles
Time (s)
Vert
ical
velo
cit
y (
m/s
)
November, 2014 EMALCA, Puerto Madryn
CYCLE TO CYCLE VARIATIONS
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• Approx. 50 cycles were computed
• Velocity vectors at the same instant at 3 different cycles
November, 2014 EMALCA, Puerto Madryn
CYCLE TO CYCLE VARIATIONS
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• Turbulence is not only randomness
• Phase-averaging the numerical results allows retrieving a large recirculation zone within the left ventricle
What about the large
scales ?
November, 2014 EMALCA, Puerto Madryn
PHASE-AVERAGED FLOW
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• Phase-averaging the numerical results allows retrieving a large recirculation zone within the left ventricle
• Coherent with observations from medical images
MRI
Eriksson et al.
Eu. Heart J. (2012)
Echocardiography
Hong et al.
Cardio. Imag. (2008)
November, 2014 EMALCA, Puerto Madryn
PHASE-AVERAGED FLOW
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• The KE of the mean flow large at early systole and diastole
• The KE of the
fluctuations large at late diastole
• Intensity of the fluctuations of order 30 % at late diastole 0 0.2 0.4 0.6 0.8 1.0
t/T
0
November, 2014 EMALCA, Puerto Madryn
KINETIC ENERGY IN THE VENTRICLE
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Frequency (Hz)
• The spectra show activity over a much wider frequency range at late diastole
• Looks pretty much like intermittent turbulence
• Only LES (or DNS but not RANS) can be predictive in this situation
November, 2014 EMALCA, Puerto Madryn
TIME-FREQUENCY ANALYSIS
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OUTLINE
• Transitional hemodynamics in a realistic heart
• Fluid-structure interaction for Micro-scale computations
• Fluid-structure interaction for Macro-scale computations
31 November, 2014 EMALCA, Puerto Madryn
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• Objective: Red blood cells under flows
- in complex domains
- and at « high » Reynolds number
Abkarian et al. BM 2008 Isèbe & Nérin IJNMBE 2013
November, 2014 EMALCA, Puerto Madryn
MICRO-SCALE COMPUTATIONS
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t t + Δt Conforming mesh method
November, 2014 EMALCA, Puerto Madryn
WHICH METHOD ?
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t t + Δt Conforming mesh method
Non-conforming mesh method
November, 2014 EMALCA, Puerto Madryn
WHICH METHOD ?
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• Membrane discretized by Lagrangian markers
massless membrane
convected by the fluid velocity
• From the membrane position: forces applied on the fluid
Peskin 1972, 2002, Unverdi & Tryggvason 1992, Bagchi et al.
dxm
dt u f
November, 2014 EMALCA, Puerto Madryn
FRONT-TRACKING – IMMERSED BOUNDARIES
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• Navier-Stokes forced by the membrane forces
• To each marker on the membrane corresponds a Dirac force which must be properly accounted for when solving for the fluid
Navier-Stokes
November, 2014 EMALCA, Puerto Madryn
FRONT-TRACKING – IMMERSED BOUNDARIES
𝜕𝑢𝑖𝜕𝑡+ 𝑢𝑗𝜕𝑢𝑖𝜕𝑥𝑗= −1
𝜌
𝜕𝑝
𝜕𝑥𝑖+𝜕
𝜕𝑥𝑗𝜈𝜕𝑢𝑖𝜕𝑥𝑗+𝜕𝑢𝑗
𝜕𝑥𝑖 + 𝑓𝑖
𝑚
𝑚
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REGULARIZATION
For the fluid:
FORCE PER UNIT VOLUME f(x)
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IMMERSED BOUNDARY METHOD
Peskin, AM 2002, Charrier et al. JSA 1993, Eggleton & Poppel PF 1998, Pinelli et al. JCP 2011, Yazdani & Bagchi JFM 2013
Eulerian
fluid grid Lagrangian
membrane grid
REGULARIZATION Navier-Stokes eqs
+
Membrane forces
Fluid velocity
Finite
volumes
Mechanical laws
+
Membrane
displacements
Membrane forces
Finite
elements
INTERPOLATION
Membrane
displacements
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Capsules in
simple
shear flow
Equilibrium
shapes of
vesicles
Vesicles in
simple shear
flow
Damped
oscillations
of capsules
Red cells
stretched by
optical
tweezers
Capsules in
simple shear
flow
Breyiannis et
al., TCFD
2000,
Woolfenden
2010
Veerapaneni et
al, JCP 2009,
Laadhari 2011
Veerapaneni et
al, JCP 2009,
Beaucourt et
al, PRE 2004
…
Martins
Afonso et al,
2014
Dao et al,
JMPS 2003
Mills et al
MCB 2004
Lac et al JFM
2004, Walter
et al IJNME
2010…
2D 3D
Mendez, Gibaud & Nicoud, J. Comp. Physics, 2014, ; Martins Afonso, Mendez & Nicoud, J. Fluid Mech., 2014
November, 2014 EMALCA, Puerto Madryn
VALIDATIONS
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Measurement apparatus for cell mechanics
Laser beam
Mills et al MCB (2004)
Experimental image
November, 2014 EMALCA, Puerto Madryn
OPTICAL TWEEZERS: PRINCIPLE
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• Biconcave red blood cell
• Mechanical properties modeled with a Skalak law (Es = 3.7 μN/m)
OPTICAL TWEEZERS: SIMULATION
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OPTICAL TWEEZERS: RESULTS
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Region of interest
Re ~ 300
in a 50μm aperture
November, 2014 EMALCA, Puerto Madryn
APPLICATION TO SIZING IN A CYTOMETER
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Electrical pulse
Counting: 1 pulse = 1 red blood cell
Sizing: Pulse size ~ Cell volume
time
November, 2014 EMALCA, Puerto Madryn
APPLICATION TO SIZING IN A CYTOMETER
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INFLUENCE OF THE CELL TRAJECTORY
Pulse characteristics are not related only to Cell volume
2 identical cells at 2 different initial locations
Movie by E. Gibaud (PhD student at I3M)
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OUTLINE
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• Transitional hemodynamics in a realistic heart
• Fluid-structure interaction for Micro-scale computations
• Fluid-structure interaction for Macro-scale computations
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• To be able to represent complex thin membranes (viscoelasticity, contact), a dedicated solid mechanics solver should be used
• Keeping the same numerical strategy (FT-IBM), the YALES2BIO fluid solver was coupled to the LMGC90 solver for complex rheology and contact (work with the LMGC lab in Montpellier)
+
Displacements
Forces
November, 2014 EMALCA, Puerto Madryn
ABOUT ARTIFICIAL ORGANS
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Movie by J. Sigüenza (PhD student at I3M)
November, 2014 EMALCA, Puerto Madryn
EXAMPLE WITH AORTIC VALVE
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Syncardia heart (Slepian et al., J. Biomech. 2013)
Abiocor, Carmat hearts,…
Abiocor
Carmat
How to compute the flow in these systems?
November, 2014 EMALCA, Puerto Madryn
AN ARTIFICIAL HEART
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Syncardia heart (Slepian et al., J. Biomech. 2013)
Carmat heart
Schematic from the French newspaper ‘Le Monde’
Left ventricle
Right ventricle
Secondary
fluid
Pump
November, 2014 EMALCA, Puerto Madryn
AN ARTIFICIAL HEART
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A first attempt in half the system: unstructured LES + flexible membrane
November, 2014 EMALCA, Puerto Madryn
HALF AN ARTIFICIAL HEART
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• A domain mimicking the left heart flow (only half of the heart is considered).
membrane
Top view
Side view
Secondary fluid
Blood
To aorta From pulm. veins
November, 2014 EMALCA, Puerto Madryn
SIMPLIFYING THE GEOMETRY
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MOVIE PRESENTATION
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MOVIE SHOWING 5 CYCLES FROM THE START
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TIME OF RESIDENCE (8 CYCLES)
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Probability
Density Function
Residence time of particles leaving the domain (in s)
• In this design, 67% of the red blood cells leave the domain after staying less than 1.5 s.
• 5% of the RBCs stay 3.5 seconds and more
November, 2014 EMALCA, Puerto Madryn
RESIDENCE TIME – STATISTICS
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• http://www.math.univ-montp2.fr/~yales2bio/
Publications
People involved
Other applications and movies
• Licensing:
YALES2BIO may be made freely available to any research team upon simple request [INSERM & CHU Toulouse, Univ. Avignon]
Industrial licenses can be setup on a case-by-case basis [Horiba Medical]
November, 2014 EMALCA, Puerto Madryn
MORE INFORMATION …
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Thank you for your attention
http://www.math.univ-montp2.fr/~yales2bio
We thank for financial support:
November, 2014 EMALCA, Puerto Madryn