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Delft University of Technology

The divergence-conforming immersed boundary method

Application to vesicle and capsule dynamics

Casquero, Hugo ; Bona-Casas, Carles ; Toshniwal, Deepesh; Hughes, Thomas J.R. ; Gomez, Hector ;

Zhang, Yongjie Jessica

DOI

10.1016/j.jcp.2020.109872

Publication date

2021

Document Version

Final published version

Published in

Journal of Computational Physics

Citation (APA)

Casquero, H., Bona-Casas, C., Toshniwal, D., Hughes, T. J. R., Gomez, H., & Zhang, Y. J. (2021). The

divergence-conforming immersed boundary method: Application to vesicle and capsule dynamics. Journal

of Computational Physics, 425, 1-26. [109872]. https://doi.org/10.1016/j.jcp.2020.109872

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Contents lists available atScienceDirect

Journal

of

Computational

Physics

www.elsevier.com/locate/jcp

The

divergence-conforming

immersed

boundary

method:

Application

to

vesicle

and

capsule

dynamics

Hugo Casquero

a

,

,

Carles Bona-Casas

b

,

Deepesh Toshniwal

c

,

Thomas J.R. Hughes

d

,

Hector Gomez

e

,

Yongjie

Jessica Zhang

a

aDepartmentofMechanicalEngineering,CarnegieMellonUniversity,Pittsburgh,PA15213,UnitedStates bDepartamentdeFísica&IAC3,UniversitatdelesIllesBalears,PalmadeMallorca,07122,Spain

cDelftInstituteofAppliedMathematics,DelftUniversityofTechnology,VanMourikBroekmanweg6,XEDelft2628,theNetherlands dOdenInstituteforComputationalEngineeringandSciences,201East24thStreet,C0200,Austin,TX78712-1229,UnitedStates eSchoolofMechanicalEngineering,PurdueUniversity,WestLafayette,IN47907,UnitedStates

a

r

t

i

c

l

e

i

n

f

o

a

b

s

t

r

a

c

t

Articlehistory:

Received20December2019 Receivedinrevisedform19September 2020

Accepted23September2020 Availableonline6October2020

Keywords:

Fluid-structureinteraction Immersedboundarymethod Volumeconservation Isogeometricanalysis Vesicles

Capsules

We extend the recently introduced divergence-conforming immersed boundary (DCIB) method[1] tofluid-structureinteraction(FSI)problemsinvolvingclosedco-dimensionone solids.Wefocusoncapsulesandvesicles,whosediscretizationisparticularlychallenging duetothehigher-orderderivativesthatappearintheirformulations.Intwo-dimensional settings, weemploy cubic B-splineswith periodicknot vectorstoobtain discretizations of closed curves with C2 inter-element continuity. In three-dimensional settings, we use analysis-suitable bi-cubic T-splines toobtain discretizations ofclosed surfaces with at least C1 inter-element continuity. Largespurious changesof the fluidvolume inside closedco-dimensiononesolidsarea well-knownissueforIBmethods.TheDCIBmethod resultsinvolumechangesordersofmagnitudelowerthanconventionalIBmethods.This is a byproductof discretizingthe velocity-pressure pairwith divergence-conforming B-splines,whichleadtonegligibleincompressibilityerrorsattheEulerianlevel.Thehigher inter-element continuity ofdivergence-conformingB-splines isalso crucialto avoidthe quadrature/interpolationerrorsofIBmethodsbecomingthedominantdiscretizationerror. Benchmarkandapplicationproblemsofvesicleandcapsuledynamicsaresolved,including mesh-independencestudiesandcomparisonswithothernumericalmethods.

©2020TheAuthors.PublishedbyElsevierInc.ThisisanopenaccessarticleundertheCC BY-NC-NDlicense(http://creativecommons.org/licenses/by-nc-nd/4.0/).

1. Introduction

Immersedapproachesforfluid-structureinteraction(FSI)havebeenusedtotackleawiderangeofopenquestions involv-ingtheinteractionofincompressibleviscousfluidswithincompressibleelasticsolids.However, thereliabilityofimmersed approaches, such asthe immersedboundary (IB)method [2–9] andthe ficticious domain(FD) method[10–14], is often jeopardized bylarge errorsin imposingthe incompressibility constraintattheEulerianand/or Lagrangian levels[15–19]. Althoughthisissuewasfirstmentionedmorethantwodecadesago[15],solvingthisproblematitsrootandwithoutside effects thatlimit theapplicability oftheresultingimmersed methodhasprovento beextremelychallenging. Inthe case ofdiscretizations based onfinitedifferencesor finitevolumes, thedominanterror isdueto thefact that theLagrangian

*

Correspondingauthor.

E-mailaddress:hugocp@andrew.cmu.edu(H. Casquero).

https://doi.org/10.1016/j.jcp.2020.109872

0021-9991/©2020TheAuthors.PublishedbyElsevierInc.ThisisanopenaccessarticleundertheCCBY-NC-NDlicense (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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velocity obtained fromthe Eulerianvelocity using discretizeddelta functionsis farfrom beinga solenoidal field even if theEulerianvelocity isproperlyenforcedtobe divergence-freewithrespecttothefinite-difference/finite-volume approx-imation ofthedivergenceoperator [15,20,21]. Inthecaseofdiscretizations basedon finiteelements,the dominanterror is due tothe fact that the weakly divergence-freeEulerian velocity is far frombeing a solenoidal field [22,23,18]. Most ofthe proposed solutionsto reducethe incompressibility errorsdonot tackletheaforementioned rootcausesandtryto mitigatetheireffectsinstead.Tonameafew,penaltytermsareoftenaddedtotrytodecreasethespuriouschangeoffluid volumeinsideclosedco-dimensiononesolids[24–26],apost-processingcorrectionusingaLagrangemultiplierisusedafter each timestep toslightlychangethenodalcoordinatesofclosedco-dimensiononesolidstopreserve their innervolume [27,21,8],andextremelylargegrad-divstabilizationisaddednearthefluid-solidinterfacetoobtaina velocityfieldthatis closertoasolenoidalfieldinthisregion[22,18].Therearesomerecentsolutionsthateffectivelytackletheaforementioned rootcauses,butcompromise theapplicabilityofthe resultantnumericalmethod.In[20],afinite-difference discretization isproposedthatresultsinLagrangianvelocityfieldsthataresolenoidal,butthemethodislimitedtoperiodicdomains.In [28,18],an extendedfinite-elementdiscretizationisproposed thatleads toweaklydivergence-freeEulerianvelocitiesthat are goodapproximations ofa solenoidalfield by capturing thepressure discontinuityatthe fluid-solidinterface, butthe methodhasonlybeendevelopedfortwo-dimensionalsettingsthusfar.

Sincetheadventofisogeometricanalysis(IGA)[29,30],spline-baseddiscretizationsofimmersedapproachesforFSI prob-lemshaveproliferated[31–42].ThisincludesNURBS-basedandT-spline-basedgeneralizationsoftheIBmethod[32,34] and the FDmethod[33,35,38], whichare two ofthe mostwidespreadimmersed approachesforchallenging FSI applications. Unfortunately, the issuefound in classical finite-element discretizations ofweakly divergence-free Eulerianvelocities not beingagoodapproximationtoasolenoidalfieldpersistsinspline-baseddiscretizations[33,43].Adefinitivesolutiontothis problemistouseEuleriandiscretizationsthatresultinpointwisesatisfactionoftheincompressibility constraint.However, suchdiscretizations arescarceandapriceisoftenpaidinanotheraspectofthenumericalmethodincomparisonwitha standarddiscretization.Scott-Vogeliuselements[44] wereinitiallydevelopedfortwo-dimensionalsettings.Althoughthere havebeenattemptstogeneralizeScott-Vogeliuselements tothree-dimensionalsettings[45,46],afullgeneralization isstill out ofreach [46]. In addition, the proof of inf-sup stabilityof Scott-Vogelius elements is not trivial anddifferent proofs areavailableintheliteratureunderdifferentassumptions[44,47,48].Raviart-Thomaselements[49] arenot H1-conforming and therefore the Galerkinmethod cannot be used to discretize the Navier-Stokes equations in primal form. In[50,51], thehigherinter-elementcontinuityofsplineswasleveragedtodefineasmoothgeneralizationofRaviart-Thomaselements, theso-calleddivergence-conformingB-splines.Divergence-conformingB-splinesarepointwise divergence-free,inf-sup stable, H1-conforming,non-negative,andpressure-robust[52–54].Moreover,theirhigherinter-elementcontinuityishighly bene-ficialinIBandFDmethodsavoidingthenecessityofperformingnumericalintegrationofintegrandsthatincludeEulerian functionswith jumpsin the interiorofLagrangian elements [5,55,56,1].As a result, divergence-conforming B-splinesare an idealcandidateforthe EuleriandiscretizationofimmersedapproachesforFSI.1 Divergence-conformingB-splineshave

alreadybeenusedinageneralizationoftheFDmethodthatconsidersopenco-dimensiononesolids,theso-called immer-sogeometric method[58], andina generalizationofthe IBmethodthatconsiders co-dimensionzerosolids,the so-called divergence-conforming immersedboundary(DCIB)method[1]. In[58,1],negligibleincompressibilityerrorswere obtained atthe Eulerianlevel.In [1], itwas also shownthat thespurious changeof solidvolume was orders ofmagnitudelower thaninotherIBmethods.

The capabilityofdivergence-conformingB-splinestopreserve thefluid volumeinsidea closedco-dimensiononesolid has not beenstudied yet. Thisis neededin a variety ofFSI applications, such asstudying the behavior ofcapsules and vesicles underflow.Both capsulesandvesicles containaviscous fluidintheir interiors,buttheir wallsare verydifferent. A capsule wallis a thinpolymeric sheet,has shearresistance, andisextensible. Avesicle wallis a phospholipidbilayer, hasbendingresistance,andisinextensible.Bothcapsulesandvesiclescanbeengineeredinlaboratoriesandareoftenused in bioengineeringapplications,such asdrugdelivery [59], encapsulationofhemoglobinforartificial blood[60], and con-struction ofcell-like bioreactors [61]. Vesicles are also presentat the boundary ofbiological cells, playinga key role in intercellular communicationandin pathologicalprocesses suchas cancerandautoimmune diseases [62,63]. Capsuleand vesicleformulationsareoftencombinedtobeusedasnumericalproxiesforredbloodcells[64–66].Developing discretiza-tions of capsule and vesicle formulations as well as coupling theseformulations with a fluid solver are active fieldsof research[67,68].ThemainbenchmarkproblemconsistsinreplicatingthemotionsofvesiclesandcapsulesinCouetteflow. Thetwo principalmotionsaretanktreading(TT) andtumbling(TU).IntheTTmotion,thewallandtheinnerfluidrotate resemblingthetreadofatank.IntheTUmotion,thewallandtheinnerfluidundergoaflippingmotionresemblingarigid body.Asignificantchallengeofcapsuleandvesicleformulationsistoaccuratelycomputethehigh-orderderivativespresent intheirformulations.Insteadofusingdirectlytheformulaeofdifferentialgeometrytoevaluatethenormalvector,the cur-vature,orthesecondderivativesofthecurvature,variousworkaroundshavebeenusedsuchasspring-likediscretizations fortwo-dimensionalvesicles[69,70], C0-continuoustriangularmeshesusingtrigonometricformulaeforthree-dimensional vesicles [71,72],C0-continuous triangularmeshesusingquadraticinterpolationforthree-dimensionalvesicles [25,73],and

1 In[57],inf-sup stable,pointwisedivergence-free,H1-conforming,andpressure-robusttetrahedralelementsonsimplicialtriangulationsareconstructed. Thepressure spaceis simplythespace ofpiecewiseconstantsandthe velocityspace consistsofpiecewisecubic polynomialsenrichedwith rational functions.Althoughthesetetrahedralelementsdonothavethehigherinter-elementcontinuityofdivergence-conformingB-splines,theiruseinimmersed approachesforFSIisalsoworthconsideration.

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C0-continuoustriangularmeshesforthree-dimensionalcapsules[74–76].However, thehigherinter-element continuityof splinesopensthedoortodirectevaluationoftheaforementionedquantitiesusingtheformulaeofdifferentialgeometry.

Inthiswork,theDCIBmethodisappliedtoFSIproblemsinvolvingclosedco-dimensiononesolids.Theaccuracyofthe DCIBmethodpreservingthefluidvolumewithinclosedco-dimensiononesolidsiscomparedwithrespecttoconventional IB methods [77,16] and IB methods tailoredto haveimproved volumeconservation [15,20].In orderto discretize closed curveswithupto Cp−1 inter-element continuity,insteadofworkingwithopenknot vectorsasitisdone inconventional IGA, wework withB-splinesof degree p defined on periodic knotvectors. In orderto discretizeclosedsurfaces withat least C1 inter-element continuity,we use analysis-suitableT-splines [78–82]. Thesespline-baseddiscretizations of closed co-dimensiononesolidsinconjunctionwithperformingintegrationbypartsenablesthecomputationoftheforcesexerted by capsules andvesicles on the fluid by directly evaluating formulae of differential geometry. We consider a Heaviside function andits associatedequation iscoupledtotheNavier-Stokesequationsinorder toconsiderinnerandouter fluids withdifferentviscosities,whichisthemoststraightforwardmannertotriggerthetransitionfromTTmotiontoTUmotion inCouetteflow.Severalquantitativecomparisonsareincludedwithrespecttotheboundaryintegralmethod(BIM)[83],an IBmethodbasedonthelattice-Boltzmannmethod(LBM)[26],andIBmethodsbasedonfinitedifferences[84,20].

Thepaperisoutlinedasfollows.Section2definesthekinematicconceptsthatareneededtohandleclosedco-dimension one solidsinthe DCIBmethod.Section 3setsforththe governingequationsforclosedco-dimensiononesolidsthat have inner and outer fluids with different viscosities. Section 4 describes the variational form of the FSI problem, which is the startingpoint toperform thediscretizationprocess. Section 5.1presentsthespline-basedspatial discretizationof the DCIBmethodforclosed co-dimensiononesolids. Section 5.2describesthefully-implicit time discretizationbasedonthe generalized-αmethod.Section5.3describestheblock-iterativesolutionstrategyusedtosolvethefinalsystemofnonlinear algebraic equations.Section6includesfivenumericalexamples.Thefirstexampleisatwo-dimensionalprobleminvolving a closed curve with active behavior. This isa benchmark problem forstudying how accurately IBmethods preserve the areaoffluidinsidetheclosedcurve.TheperformanceoftheDCIBmethodiscomparedwithotherIBmethods.Thesecond andthird examples considercommonbenchmark problemsforformulations ofvesicles andcapsules underflow, respec-tively.Quantitiesofinterest,such astheTT inclinationangle,theTUperiod,theTaylordeformation parameter,andshear stresses,arecomparedwithothernumericalmethods.TakingadvantageofthegeometricalflexibilityoftheDCIBmethod, the fourthandfifth examples study vesicle dynamicsin Taylor-Couette flowand capsule segregationin Hagen-Poiseuille flow,respectively.ConclusionsaredrawninSection7.

2. Kinematics

TheIBmethodsolvesthe(Eulerian)Navier-Stokesequationsinboththefluidandsoliddomainswithadded(Lagrangian) source terms that depend onthe position ofthe solid. Inorder to havea closed systemof equations,the Navier-Stokes equationsarecoupledwiththekinematicequation thatrelatestheLagrangiandisplacementofthesolidwiththeEulerian velocityoftheNavier-Stokesequations.

Letd

= {

2

,

3

}

and

(

0

,

T

)

bethenumberofspatialdimensionsandthetimeintervalofinterest,respectively.Intherest of thissection, we define Lagrangian and Eulerianquantities that are neededto state the governingequations of theIB methodforclosedco-dimensiononesolids,withemphasisontwo-dimensionalvesiclesandthree-dimensionalcapsules.

2.1. Lagrangiandescription

We considersolidswhose kinematicsare described by closedcurvesandclosed surfacesind

=

2

,

3, respectively.The solid occupies,attime t, theregion



t

⊂ R

d,which can beobtained astheimage ofa referenceconfiguration



R

⊂ R

d

throughthemapping

ϕ

: 

R

× (

0

,

T

)

→ 

t.Let X

∈ 

R beamaterialparticle.TheLagrangianunknownofthemathematical

modelistheLagrangiandisplacementu

: 

R

× (

0

,

T

)

→ R

d,verifying

ϕ

=

X

+

u.Thedeformedconfiguration,thereference

configuration,andtheLagrangiandisplacementcanbeparametrizedinspaceusingd

1 parametriccoordinates.

2.1.1. Closedcurve

Let

ξ

L be theparametriccoordinate.Whenworkingwithtwo-dimensionalvesicles,itiscommontoreparametrizethe closedcurveintermsofitsarclength s,whichisdonetakingintoaccountthat

ds

=













d

ϕ

d

ξ

L













d

ξ

L, (1)

where

||

· ||

denotesthelengthofavector.Usingthearclengthastheparametriccoordinate,theunittangentvectortothe closedcurveisobtainedby

t

=

d

ϕ

ds. (2)

(5)

C =

det

d

ϕ

x ds d

ϕ

y ds d2

ϕ

x ds2 d2

ϕ

y ds2

. (3)

Thesignof

C

dependsontheorientationofthecurveprovidedbytheparametrization.Wealwaysuseclosedcurveswhose parametriccoordinatemovescounterclockwise.Asaresult,acirclehaspositivecurvature.Theunit outwardnormalvector totheclosedcurveisobtainedby

n

=

d

ϕ

y ds

,

d

ϕ

x ds

. (4) 2.1.2. Closedsurface

Let

ξ

L

= {ξ

1L

,

ξ

2L

}

be theparametric coordinates.Inthefollowing,indicesinGreek letterstakethevalues1

,

2 and sum-mationoverrepeatedGreekindicesisimplied.Non-unittangentvectorstotheclosedsurfaceareobtainedby

aα

=

ϕ

∂ξ

L

α

. (5)

Theunitoutwardnormalvectortotheclosedsurfaceisobtainedby

n

=

a1

×

a2

||

a1

×

a2

||

, (6)

wheretheparametriccoordinates

ξ

L

1 and

ξ

2L havebeenchoseninsuchawaythata1

×

a2 pointsintheoutwarddirection. Thecovariantmetriccoefficientsoftheclosedsurfacearedefinedas

aαβ

=

aα

·

aβ. (7)

The contravariant metric coefficients can be computed as the inverse matrix of the covariant coefficients, i.e.,

aαβ

=

aαβ

1

. The contravariantmetric coefficientsare used to obtain the contravariantbase vectorsfrom the covariant base vectors,namely,

=

aαβa

β.Thecovariantcurvaturecoefficientsoftheclosedsurfacearedefinedas

bαβ

=

aα

∂ξ

βL

·

n. (8)

TheChristoffelsymbolsaredefinedas



γαβ

=

aα

∂ξ

βL

·

a

γ. (9)

ThequantitiesinEqs.(5)-(9) aredefinedwithrespecttothedeformedconfiguration,butanalogousquantitiesaredefined withrespecttothereferenceconfigurationanddenotedby ˚aα, ˚n, ˚aαβ, ˚aαβ, ˚aα , ˚bαβ,and



˚γαβ.

2.2. Euleriandescription

Let

⊂ R

d bethetime-independentregioncontainingboththefluidandthesolidandletx

bea spatialposition. Forthesakeofbrevityandsinceitholdstrueinalltheexamplesofthispaper,weassumethatthesolidisfullyimmersed in the fluid, i.e.,



t

∩ ∂

= ∅

t

∈ (

0

,

T

)

. The Eulerianvariables of the mathematical modelare the Eulerian velocity v

:

× (

0

,

T

)

→ R

d,thepressurep

:

× (

0

,

T

)

→ R

,andtheHeavisidefunctionH

:

× (

0

,

T

)

→ R

(theHeavisidefunctionis onlyneededwhenfluidswithdifferentinnerandouterviscositiesareconsidered).Thephysicaldomain

andtheEulerian variablescanbeparametrizedinspaceusingd parametriccoordinates.

3. Governingequations

Atthecontinuous level,themathematicalmodeloftheIBmethodisequivalenttotheboundary-fittedFSIformulation [5,55]. The strong form of the IB method forclosed co-dimension one solids with different inner and outer viscosities is stated as follows: Given

ρ

∈ R

+,

μ

o

∈ R

+,

μ

i

∈ R

+, g

V

× (

0

,

T

)

→ R

d, v0

:

→ R

d, u0

: 

R

→ R

d, and vB

:

× (

0

,

T

)

→ R

d,findv

:

× (

0

,

T

)

→ R

d, p

:

× (

0

,

T

)

→ R

, H

:

× (

0

,

T

)

→ R

,andu

: 

R

× (

0

,

T

)

→ R

d,suchthat,

ρ

v

t





x

+ ∇

x

· (

v

v

)



= ∇

x

· (

2

μ

xsymv

)

− ∇

xp

+

gV

+



t f

δ(

x

ϕ

(

X

,

t

))

d



t in

× (

0

,

T

)

, (10)

x

·

v

=

0 in

× (

0

,

T

)

, (11)

(6)

u

t





X

=



v

δ(

x

ϕ

(

X

,

t

))

d

in



t

× (

0

,

T

)

, (12)

xH

= −∇

x

·



t n

δ(

x

ϕ

(

X

,

t

))

d



t in

× (

0

,

T

)

, (13)

μ

=

μ

iH

+

μ

o

(

1

H

)

in

× (

0

,

T

)

, (14) v

=

v0 on

× {

0

}

, (15) u

=

u0 on



0

× {

0

}

, (16) v

=

vB on

× (

0

,

T

)

, (17) H

=

0 on

× (

0

,

T

)

, (18)

where

ρ

isthedensity,

μ

i and

μ

o are theinner andouter fluidviscosities, respectively, gV isanexternal force perunit

of volumeacting onthe system,

symx

(

·)

is thesymmetric gradient operatordefined by

sym

x v

= (∇x

v

+ ∇x

vT

)/

2, v0 is theinitialvelocity, u0 istheinitialdisplacement, vB istheboundaryvelocity,

δ(x

ϕ

(X,

t

))

=



di=1

δ(

xi

ϕ

i

(X,

t

))

isthe

d-dimensionalDiracdeltafunction, and f

: 

R

× (

0

,

T

)

→ R

d is theforce exerted bythe solidon thefluid. Thenotation

v

t





x and

∂u

t





X

indicatesthatthetimederivativeistakenholdingx andX fixed,respectively.

Eqs. (10)-(12) represent the linear momentum balanceequation, the mass conservation equation, andthe kinematic equation that relatestheLagrangiandisplacement withthe Eulerianvelocity,respectively. Eqs.(13)-(14) areaddedto the standard IB formulation when

μ

i

=

μ

o. The derivation of Eqs. (13)-(14) can be found in [85]. For brevity and since it

holdstrueinall theexamplesofthispaper,weassume thatthe innerfluid,theouter fluid,andthesolid havethe same density

ρ

.InnerandouterfluidswithdifferentdensitiescanbeconsideredusingtheHeavisidefunction H akintothecase

μ

i

=

μ

o.Aclosedco-dimensiononesolidwithdifferentdensitythanthefluid canbeconsideredinananalogousmanner

aswe considered co-dimension zerosolidswithdifferent densitythan thefluid in [1] provided that a solid formulation with a consistent time evolution ofits thicknessis used. Eqs. (15)-(16) define the initial condition for the velocity and the displacement, respectively. Eqs. (17)-(18) definethe boundary condition for the velocity andthe Heaviside function, respectively.ForbrevityDirichletboundaryconditionsforthevelocityareappliedonthewholeboundaryinSections3,4, and5,butNeumannandperiodicboundaryconditionscanbeappliedintheDCIBmethodfollowingthestandardprocedures ofvariationalmethodsasdoneinSection6.

Theexpressionsof f fortwo-dimensionalvesiclesandthree-dimensionalcapsulesaredetailedbelow.

3.1. Two-dimensionalvesicles

Asderivedin[86],theLagrangianforceperunitlengthexertedbythevesicleonthefluidis

f

=

κ

d 2

C

ds2

+

κ

C

3 2

− Cζ



n

+

d

ζ

dst

,

(19)

where

κ

isthebendingrigidityofthevesicle,

ζ

isaLagrangemultiplierthatenforcesthevesicledeformationstobelocally inextensible,andanullspontaneouscurvatureisconsidered.NotethatEq.(19) dependsonthedeformedconfiguration,but notthereferenceconfiguration.Inordertocircumventnumericalinstabilities,wereplace

ζ

bythefollowingexpression

ζ

=

4CI

λ



λ

2

1



, (20)

whereCI isthedilatationmodulusand

λ

= ||

d

ϕ

L

,

t

)/

d

ξ

L

||/||

d

ϕ

L

,

0

)/

d

ξ

L

||

isthestretchratio.Eq.(20) isequivalent to

consideringacapsulewithperimeterstrain-energyfunctionorHelmholtzfreeenergygivenby

WI

=

CI



λ

2

1



2

. (21)

Eq.(21) isatwo-dimensionalanalogtothedilatationalcomponentofthesurfacestrain-energyfunctionproposedin[87].

3.2. Three-dimensionalcapsules

Asderivedin[88],theLagrangianforceperunitareaexertedbythecapsuleonthefluidis

f

=

Tαβ

∂ξ

L α

+ 

α αλTλβ

+ 

β αλTαλ



aβ

+

Tαβbαβn, (22) with

(7)

Tαβ

=

2 Js

Ws

I1 ˚aαβ

+

2 J s

Ws

I2 aαβ, (23) I1

=

˚aαβaαβ

2, (24)

I2

=

det

(

˚aαβ

)

det

(

aαβ

)

1, (25)

Js

=



I2

+

1, (26)

where T αβ are the contravariant coefficientsof the membrane forces in the deformed configuration, W

s is the surface

strain-energyfunction,I1 andI2 aretheinvariantsofthedeformation,and Jsistheratioofdeformedlocalsurfaceareato

referencelocalsurfacearea.Notethat Eq.(22) dependsonboth thedeformedandreferenceconfigurations.Eqs.(22)-(26) define a membrane formulation, i.e., transverse shear andbending are neglected. This membraneformulation takesinto account bothgeometric andmaterialnonlinearities. Examplesofconstitutiveequationsare theneo-Hookeanlawandthe Skalaklaw[87] definedas

Ws

=

Gs 2

I1

1

+

1 I2

+

1



, (27) Ws

=

Gs 4

(

I 2 1

+

2I1

2I2

)

+

CI 4

(

J 2 s

1

)

2, (28)

respectively, where Gs is the surface shear modulus. When CI

Gs,the Skalak law leads to locally inextensible

mem-branes, butitcanbeusedtomodelother typesofmembraneswhenCI



Gs.The neo-HookeanandSkalaklawsresultin

significantly differentmaterialresponsesunderlarge deformations,e.g., underuniaxialextension,the neo-Hookeanlawis strain-softeningwhereastheSkalaklawisstrain-hardening[89].

4. Variationalformulation

Givensuitable trial solutionspaces (

S

v,

S

p,

S

u,and

S

H) andweighting function spaces(

V

v,

V

p,

V

u,and

V

H), the

variationalformoftheIBmethodisstatedasfollows:Findv

∈ S

v,p

∈ S

p,u

∈ S

u,andH

∈ S

H,suchthat,

B

((

w

,

q

,

s

,

M

), (

v

,

p

,

u

,

H

))

L

(

w

)

=

0

∀(w

,

q

,

s

,

M

)

∈ V

v

× V

p

× V

u

× V

H, (29) with B

((

w

,

q

,

s

,

M

), (

v

,

p

,

u

,

H

))

=

w

,

ρ

v

t





x



− (∇

xw

,

ρ

v

v

)

− (∇

x

·

w

,

p

)

+



xw

,

2

μ

o

xsymv



+



xw

,

2H

(

μ

i

μ

o

)

xsymv



+ (

q

,

x

·

v

)

− (

w

ϕ

,

f

)

t

+

s

,

u

t





X

v

ϕ



t

+ (∇

xM

,

xH

)

+ (∇

xM

ϕ

,

n

)

t, (30) L

(

w

)

=



w

,

gV



, (31)

where

(

·,

·)

and

(

·,

·)

t denotetheL

2 innerproductoverthedomains

and



t,respectively.Asmathematicallyshownin

[5,6],thevariationalformulationoftheIBmethodenablestheeliminationoftheDiracdeltafunctions.NotethatEq.(13) is notconsideredin[5,6],butitsDiracdeltafunctioniseliminatedinthesameway.

4.1. Two-dimensionalvesicles

In this case, f contains a term involvingone factorwith fourth-order derivatives (d2

C/

ds2) and anotherfactor with second-order derivatives (n). Therefore, integration by parts in the variational form can be applied once to remove the fourth-orderderivativesfromthevariationalform,namely,



t

κ

d 2

C

ds2n

· (

w

ϕ

)

ds

= −



t

κ

d

C

ds dn ds

· (

w

ϕ

)

ds



t

κ

d

C

dsn

·

d

(

w

ϕ

)

ds ds, (32)

wherewehaveassumedthat

κ

isaconstant.Asaresult,adiscretizationoftheclosedcurvewithC2 inter-element conti-nuityisneededtodirectlycomputetheterm

(w

ϕ

,

f

)

t.

(8)

4.2. Three-dimensionalcapsules

Inthiscase, f containsa terminvolving onefactorwithsecond-order derivatives(bαβ) andanotherfactorwith first-order derivatives (T αβ). Therefore, integration by parts cannot be usedto decrease the order of thesederivatives anda discretizationoftheclosedsurfacewithC1 inter-elementcontinuityisneededtodirectlycomputetheterm

(w

ϕ

,

f

)

t.

5. Discretization

ThissectiondescribestheDCIBmethodforclosedco-dimensiononesolids.TheDCIBmethoddiscretizesthevariational formulationdefinedinEqs.(29)-(31).Thus,devisingsmeareddeltafunctionsisnotneededintheDCIBmethod.Bycontrast, IBmethodsthatdiscretizethestrongformdefinedinEqs.(10)-(18) requiresmeareddeltafunctions.

5.1. Spatialdiscretization

InadditiontothedifficultyofaccuratelyimposingtheincompressibilityconstraintinIBmethods,anadditionalchallenge istoaccurately computeintegralsinwhichbothEulerianandLagrangianfunctionsareinvolved.Thespatial discretization oftheDCIBmethodhasbeenpurposefullydesignedtotacklethesetwochallenges.

5.1.1. Closedcurves

We discretizeclosedcurvesusing B-splinesofdegree p with periodic knotvectorsandglobalCp−1 continuity.Letus startdefiningthemapping FL

: [

0

,

1

]

→ 

R usingB-splinesasfollows

FL



ξ

L



=

nL



C=1 PLC



NCL



ξ

L



,

ξ

L

∈ [

0

,

1

]

, (33)

wherethesuperscript L standsfor“Lagrangian”,

{

PL C

}

n

L

C=1 are thecontrolpoints thatdefinethereferenceconfigurationof thesolid,and

{

NCL

}

CnL=1 areuni-variateB-splinebasisfunctions.

Uni-variateB-splinebasisfunctionsarecomputedfromaknotvector



usingtheCox-deBoorrecursionformula[90,29]. Aknotvector isafinitenon-decreasingsequenceofrealnumbers



= {ξ

1

,

ξ

2

,

...,

ξ

nL+p+1

}

,where

ξ

i isthe i-thknot, p is

thepolynomial degree,andnL is thenumberofuni-variateB-splinebasis functions.The parametricdomain ofthecurve is definedby the interval

p+1

,

ξ

nL+1

]

(we impose

ξ

p+1

=

0 and

ξ

nL+1

=

1). A knotspan isthe difference betweentwo

consecutiveknots(

ξ

i

= ξ

i+1

− ξ

i).Insidenonzeroknotspans,B-splinebasisfunctionsarepolynomialsofdegree p.Since

theknotscan berepeated,wedefine asequenceofknotswithoutrepetitions(calledbreakpoints)

η

= {

η

1

,

η

2

,

...,

η

m

}

and

anothersequencewiththeknotmultiplicitiesr

= {

r1

,

r2

,

...,

rm

}

.Knotmultiplicity controlsthecontinuityofB-splinebasis

functionsatbreakpoints,namely,B-splinebasisfunctionshave

α

i

=

p

ricontinuousderivativesat

η

i.

Anopen (orclamped)knotvectorisobtainedwhenr1

=

rm

=

p

+

1.Openknotvectorsfacilitatethestrongimposition

ofDirichletboundaryconditions,whichhasmadeopenknotvectorsthestandardchoiceinIGA.However,whenusingopen knotvectors, imposingperiodicboundaryconditionsrequiresbuildingasystemofconstraints.Theseconstraintsgetmore complicatedasthecontinuityattheperiodicboundaryisincreased(see[91] foradescriptionofhowtoimposeC1 period-icitywithopenknotvectors).AnalternativeistobuildtheperiodicityintotheB-splinespace.Thisisaccomplishedusing periodic(oruniform)knotvectorsinsteadofopenknotvectors.Periodicknotvectorshavenorepeatedknotsandtheknots are evenly distributed. Reference[92] buildsthe geometry usingopen knotvectors. After that, the knot vectorsare un-clamped,i.e.,transformedintoperiodicknotvectors,whichrequiresmodifyingthecontrolpointstopreservethegeometry. ThisstrategyisappropriatetoimposeCp−1 periodicityingeometriesthatarenotclosed,e.g.,imposingCp−1periodicityto thevelocity andthepressureina straight channel.However, whenthegeometryisclosedand Cp−1 periodicitymustbe imposedtoboththegeometryandtheunknownsoftheproblem, periodicknotvectorsmustbe usedfromthebeginning. This isthe strategy thatwe follow hereforthe closedcurve andthe Lagrangian displacement.Toobtain Cp−1 periodic-ity, thelast p control points mustbe wrappedwiththe first p controlpoints, namely, PLnLp+1

=

P

L 1, P L nLp+2

=

P L 2,..., PnLL

=

P L

p.AnexampleofaB-splineclosedcurveisshowninFigs.1and2.

Invokingtheisoparametricconcept,theLagrangiandisplacementisparameterizedasfollows



uhL



ξ

L

,

t



=

nL



C=1 uC

(

t

)

NLC



ξ

L



,

ξ

L

∈ [

0

,

1

]

, (34)

whereuC

(

t

)

arethecontrolvariablesoftheLagrangiandisplacement.Asaresult,thedeformedconfigurationis

parameter-izedasfollows



ϕ

hL



ξ

L

,

t



=

nL



C=1 PCL



NCL



ξ

L



+

nL



C=1 uC

(

t

)

NCL



ξ

L



,

ξ

L

∈ [

0

,

1

]

. (35)

(9)

Fig. 1. Giventheperiodicknotvector= {−0.6,−0.4,−0.2,0.0,0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6}andp=3,theB-splinebasisfunctions{NL C}8C=1 are plotted.

Fig. 2. TwoB-splinecurvesareplottedusing= {−0.6,−0.4,−0.2,0.0,0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6}andp=3.(a)Anopencurveinwhichallthe controlpointshavedifferentcoordinates.(b)AC2-continuousclosedcurveobtainedbywrappingthelast3controlpointswiththefirst3controlpoints, i.e.,PL

6=PL1,PL7=PL2,andPL8=P3L.ThecontrolpointsaredenotedbyredsquaresandtheB-splinecurvesarecoloredinblue.(Forinterpretationofthe colorsinthefigure(s),thereaderisreferredtothewebversionofthisarticle.)

Thenonzeroknotspansdefinetheelementsofamesh

M

L in

[

0

,

1

]

,thismeshiscalledtheLagrangianmeshfromnowon.

TheLagrangianmeshcanbepushed forwardtothereferenceconfigurationandthedeformedconfigurationusingEq.(33) andEq.(35),respectively.Alltheintegralsposedonthedomain



htL

= 

ϕ

hL

(

[

0

,

1

],

t

)

arecomputedusingGaussquadrature

intheelementsoftheLagrangianmesh,namely,p

+

1 quadraturepointsareusedperelement.UsingtheBubnov-Galerkin method,thediscretetrialandweightingfunctionspacesfortheLagrangiandisplacementaredefinedasfollows

S

hL u

=



uhL

|

uhL

FL

=

uhL

,



uhL

(

·,

t

)

span

{

NLC

L

)

}

nCL=1



, (36)

V

hL u

=



shL

|

shL

FL

=

shL

,



shL

(

·,

t

)

span

{

NCL

L

)

}

nCL=1



. (37) 5.1.2. Closedsurfaces

Wediscretizeclosedsurfacesusingbi-cubicanalysis-suitableT-splines(AST-splines)withatleastC1 inter-element con-tinuity. AST-splinesareunstructuredandeightextraordinary pointswithvalence threeareenough tobuildsimpleclosed surfacessuchasasphereinthe“soccerball” parameterization.AdetailedexplanationofhowtoconstructtheAST-spline surfacesthatweuseinthisworkcanbefoundin[81].

5.1.3. Navier-Stokesequations

The spatial discretization of the Eulerian velocity, the pressure, and their weighting functions is performed using divergence-conformingB-splines,whicharesmoothgeneralizationsofRaviart-Thomasmixedfiniteelements.

(10)

Letusstartbydefiningthemapping FE

: 

→

hE usingnon-uniformrationalB-splines(NURBS)asfollows FE



ξ

E



=

nE



i=1 PiE wi



NiE



ξ

E





nE j=1wj



NEj



ξ

E



,

ξ

E

∈ 

, (38)

where the superscript E stands for “Eulerian”,



= [

0

,

1

]

d,

{

PE i

}

n

E

i=1 are the control points that define the geometry of the physicaldomain,

{

wi

}

n

E

i=1 arethe weightsassociated withthecontrol points,and

{

NiE

}

n

E

i=1 area setofd-variatebasis functions. Thed-variateB-splinebasisfunctionsareobtainedasthetensorproductofuni-variateB-splinebasis functions [90,29].NURBSbasisfunctionsreducetoB-splinebasisfunctionswhenwi

=

1

i

1

,

2

,

...,

nE sinceB-splinebasisfunctions

formapartitionofunity.Themainreasontoconsiderweights wi

=

1 istoexactlyrepresentcertaingeometriessuchasa

circularcylinder.

Thenonzeroknotspansofthed knotvectorsusedtoobtainthebasisfunctions

{

NiE

}

ni=E1 definetheelementsofamesh

M

E in



; thismeshiscalledtheEulerianmeshfromnowon.TheEulerianmeshcan bepushed forwardto thephysical

domain

hE usingEq.(38).Alltheintegralsposedonthedomain

hE arecomputedusingGaussquadratureintheelements

oftheEulerianmesh.

ThediscretetrialandweightingfunctionspacesforthevelocityandthepressurearedefinedusingthePiolaand integral-preservingtransformations,respectively,asfollows

S

hE v

=



vhE

|

vhE

FE

=

D F E



vhE det

(

D FE

)

,



v hE

(

·,

t

)

∈ 

V E LhE

,



vhE

·

nhE

= 

v B

·

nh E on

∂ 

× (

0

,

T

)



, (39)

S

hE p

=

p hE

|

phE

FE

=



ph E det

(

D FE

)

,



p hE

(

·,

t

)

∈ 

P R EhE

,







phEd



=

0

, (40)

V

hE v

=



whE

|

whE

FE

=

D F E



whE det

(

D FE

)

,



w hE

(

·) ∈ 

V E Lh E

,



whE

·

nhE

=

0 on

∂ 

× (

0

,

T

)



, (41)

V

hE p

=



qhE

|

qhE

FE

=



q hE det

(

D FE

)

,



q hE

(

·) ∈ 

P R Eh E



, (42) with



V E Lh E

=



S

k+1,k k,k−1

(

M

E

)

× S

k,k+1 k−1,k

(

M

E

)

if d

=

2,

S

k+1,k,k k,k−1,k−1

(

M

E

)

× S

k,k+1,k k−1,k,k−1

(

M

E

)

× S

k,k,k+1 k−1,k−1,k

(

M

E

)

if d

=

3, (43)



P R Eh E

=



S

k,k k−1,k−1

(

M

E

)

if d

=

2,

S

k,k,k k−1,k−1,k−1

(

M

E

)

if d

=

3, (44)

where D FE isthegradientofthemapping FE,



nhE istheunitoutwardnormalto



,and

S

p1,p2,...,pd

α12,...,αd

(

M

E

)

isthed-variate

B-splinespaceofbasisfunctionsdefinedon

M

E that,indirectioni,havedegreep

i andC αi continuityatallinteriorknots.

InEqs. (39)-(44), wedefineddivergence-conforming B-splinespaces ofmaximalcontinuitysince thesewill bethespaces usedthroughouttheexamplesofthispaper.NotethatonlythenormalDirichletboundaryconditionhasbeenimposedon the velocity discrete space, the tangential Dirichlet boundaryconditions will be imposed weakly usingNitsche’s method inthe semi-discrete form.Letusdefine thebasis functions

{

NvE

l,Al

}

nvl Al=1 and

{

N E p,B

}

n p

B=1 such thatspan

{

NvE1,A1

E

)

}

nv1 A1=1

×

...

×

span

{

NE vd,Ad

E

)

}

nAvdd=1

= 

V E Lh E andspan

{

NE p,B

E

)

}

nBp=1

= 

P R Eh E

,wherenvl andnp arethetotalnumberofdegreesof

freedomthatthel-thcomponentofthevelocityandthepressurehave,respectively.

The above choicesof spaces areinf-sup stableandthe discrete function spacesfor thevelocity and thepressure are

H1-conformingandL2-conforming,respectively,fork

1.Inaddition,imposingthediscreteEulerianvelocitytobeweakly divergence-freeresultsinasolenoidalfield,i.e.,



qhE

,

x

·

vh E



hE

=

0

q hE

∈ V

hE p

=⇒ ∇

x

·

vh E

=

0

x

hE

,

t

∈ [

0

,

T

]

, (45) as mathematically shownin [52,54]. Thatis, weak incompressibility impliesstrong (i.e.,pointwise) incompressibility for divergence-conformingB-splines.

(11)

5.1.4. Heavisidefunction

ThespatialdiscretizationoftheHeavisidefunctionanditsweightingfunctionisperformedusingB-splines.Thediscrete trialandweightingfunctionspacesfortheHeavisidefunctionaredefinedas

S

hE H

=

HhE

|

HhE

FE

= 

HhE

,



HhE

(

·,

t

)

∈ 

H E Ah E

, 

HhE

=

0 on

∂ 

× (

0

,

T

)

, (46)

V

hE H

=

MhE

|

MhE

FE

= 

MhE

,



MhE

(

·,

t

)

∈ 

H E Ah E

, 

MhE

=

0 on

∂ 

× (

0

,

T

)

, (47) with



H E Ah E

=



S

k,k k−1,k−1

(

M

E

)

if d

=

2,

S

k,k,k k−1,k−1,k−1

(

M

E

)

if d

=

3. (48)

Letusdefine thebasis functions

{

NHE,D

}

nDH=1 such that span

{

NEH,D

E

)

}

nDH=1

= 

H E Ah

E

,wherenH isthe numberofdegrees

of freedom that the discrete Heaviside function has.As mentioned in [85], some overshootsand undershoots may take placeneartheinterface. Whenthevalue of HhE

ata quadraturepointisgreater thanoneorlessthanzero,thisvalueis substitutedbyoneandzero,respectively.

5.1.5. Semi-discreteform

The semi-discrete form ofthe DCIB method for closedco-dimension one solids is stated asfollows: Find vhE

∈ S

hvE,

phE

∈ S

hE p ,uh L

∈ S

hL u ,andHh E

∈ S

hE

H,suchthatforall wh

E

∈ V

hE v ,qh E

∈ V

hE p ,sh L

∈ V

hL u ,andMh E

∈ V

hE H B



(

whE

,

qhE

,

shL

,

MhE

), (

vhE

,

phE

,

uhL

,

HhE

)



b



whE

,

vhE



L



whE



+

l



whE



=

0, (49) with b



whE

,

vhE



=



F∈∂ hE



F 2

μ

o

(

wh E

)

||

· (∇

xsymvh E nhE

)

d



F∈∂ hE



F

ρ

(

whE

)

||

·

vhE

(

vB

·

nh E

)

+d

+



F∈∂ hE



F 2

μ

o

(

xsymwh E nhE

)

· (v

hE

)

||d



F∈∂ hE



F 2

μ

o Cpen hF

(

whE

)

||

· (v

hE

)

||d

, (50) l



whE



=



F∈∂ hE



F

ρ

(

whE

)

||

·

vB

(

vB

·

nh E

)

d

+



F∈∂ hE



F 2

μ

o

(

xsymwh E nhE

)

· (

vB

)

||d



F∈∂ hE



F 2

μ

o Cpen hF

(

whE

)

||

· (v

B

)

||d

, (51)

where theterms b



whE

,

vhE



andl



whE



havebeenadded to thesemi-discrete formto weakly imposethe tangential DirichletboundaryconditionsusingNitsche’smethod,nhE istheoutwardunitnormalvectorto

hE,

(

·)||

= (·)

−((·)

·

nhE

)n

hE isthevectortangentialcomponent,

(v

B

·

nh

E

)

+

=

vB

·

nh E ifvB

·

nh E

>

0 and0 otherwise,

(v

B

·

nh E

)

=

vB

·

nh E ifvB

·

nh E

0 and0 otherwise,hF isthemeshsizeinthedirectionnormaltothefaceF ,andCpenistheNitsche’spenalizationparameter.

AllthenumericalresultsofthispaperusethevalueCpen

=

5

(

k

+

1

)

asproposedin[52].

Note that the integrals ofIB methods posed on thesolid domain includeEulerian functionssuch as vhE

, whE

, MhE,

andtheirfirstderivatives.InordertoevaluatetheseEulerianfunctionsataquadraturepointwithgivenparametric coordi-nates

ξ

GL intheLagrangianmesh,wefollowtwosteps.First,wecomputethephysicalcoordinatesxG

h

E

associatedwith theparametric coordinates

ξ

LG asxG

= 

ϕ

h

L

LG

,

t

)

.Then, wecompute theparametric coordinates

ξ

EG inthe Eulerianmesh

associated withxG as

ξ

EG

= (

FE

)

−1

(x

G

)

. The NURBS mapping FE can be invertedanalytically in manycases ofpractical

interest andwhen that isnot thecase, the mappingis invertedsolving a d

×

d system ofnonlinear algebraic equations. Once

ξ

EG isknown,Eulerianfunctionscanbeevaluatedusingstandardprocedures.Thus,nointerpolationorapproximation hasbeenusedtoevaluatetheEulerianfunctionsatthequadraturepointsoftheLagrangianmesh.However,thequadrature errors oftheintegralsposedon



htL are largerthan instandardvariational methodssince theelementboundariesofthe

Eulerianmesh(wheretheEulerianfunctionshavereducedregularity)oftenintersecttheinterioroftheintegrationregions beingused(the elementsofthe Lagrangianmesh).As opposedtostandardfiniteelements, wheretheinter-element con-tinuity of vhE

, whE

, MhE

is C0 (andits firstderivativeshavejumps),2 divergence-conforming B-splinesenableustoraise

2 In[56],toavoidperformingnumericalintegrationofintegralsthatincludeEulerianfunctionswithjumpsinsidetheintegrationregions,vhE andwhE areprojectedintotheLagrangianmeshbyevaluatingtheEulerianfunctionsatthenodesoftheLagrangianmeshtousethosevaluesasnodalvaluesof

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