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Applications of the Surface Finite Element
                  Method

                Tom Ranner

             Mathematics Department




             September 2011
          ENUMATH 2011, Leicester
The Problem
  Many processes in biology and fluid mechanics are governed by
  diffusion on a membrane or interface coupled to diffusion in an
  enclosed bulk region. Other approaches to this problem include a
  boundary integral formulation1 and a finite volume approach2 . We
  wish to using the surface finite element method3 along with
  standard finite element techniques4 for the bulk region.




    1
        Booty and Siegel 2010
    2
        Novak, Gao, Choi, Resasco, Schaff, and Slepchenko 2007
    3
        Dziuk 1988; Dziuk and Elliott 2007
    4
        Lenoir 1986
Example 1: Turing Instabilities
          GTP-binding proteins (GTPase) molecules are important
          regulators in cells that continuously run through an
          activation/deactivation and
          membrane-attachment/membrane-detachment cycle.
          Activated GTPase is able to localise in parts of the
          membranes and to induce cell polarity5 .
          This can be modelled by Turing instabilities in a
          reaction-diffusion system with attachment and detachment.




                               Figure 5
                               Rho GT Pases and cell migration. Cell migration requires actin-dependent protrusions at the front (re  d)
                               and contractile actin:myosin filaments (re at the rear. In addition, microtubules (gre n) originating from
                                                                        d)                                          e
                               thecentrosome(purple arepreferentially stabilized in thedirection of migration allowing targeted vesicle
                                                      )
                               trafficking from the Golgi (b wn) to the leading edge.
                                                           ro




                         Figure: Example of cell polarisation from6
     5
         R¨tz and R¨ger 2011
          a        o
     6
         Jaffe and Hall 2005
Example 2: Surfactant problem
   Surfactants, or surface contaminants, significantly alter the
   interfacial properties of a fluid by changing the surface tension.
   An example is the tip-streaming of thin threads or small droplets
   from a drop or bubble this is stretched in an imposed extensional
   flow7 .




                        FIG. 2. Microfluidic flow focusing geometry. ͑ a͒ Schematic diagram of the
                        design denoting flow of both the inner and outer liquids from left to right.
                        ͑ b͒ Image of the orifice region of an actual microchannel ͓ outlined with the
                         dashed line in ͑ a͒ ͔ , including a typical image of the water-oil interface
                         extending toward the orifice from the upstream channel during a flow ex-
                         periment. Dimensions shown are Wup = 280 m, a = 90 m, ⌬Z = 180 m,
                        and Wor = 34 m.


                                                                              8
                                           Figure: Taken from
     7
         Booty and Siegel 2010
     8
         Anna and Mayer 2006
A Model Problem

  As a model problem we will look to solve the following elliptic
  problem:
  We assume we have a bounded domain Ω ⊆ Rn with Lipschitz
  boundary Γ. We wish to find u : Ω → R and v : Γ → R solution of
  the system

                      −∆u + u = f in Ω        (1a)
                                                      Γ
                            ∂u                              Ω
               (αu − βv ) +     = 0 on Γ      (1b)
                            ∂ν
         −∆Γ v + v − (αu − βv ) = g on Γ.     (1c)

  Here we assume α, β > 0 are given constants and f and g are
  known functions on Ω and Γ respectively. We denote by ∆Γ the
  Laplace-Beltrami operator on Γ.
A Model Problem: Weak form


  We can convert this to a weak form using integration by parts over
  Ω and Γ then using the boundary condition and taking an
  appropriate linear combination of the two resulting forms leads to
  the problem:
      Find u : Ω → R and v : Γ → R such that

         α       u·       η + uη + β        Γv   ·   Γξ   + vξ
             Ω                          Γ

                 +       (αu − βv )(αη − βξ) = α              fη+β       gξ
                     Γ                                    Ω          Γ
                             for all (η, ξ) ∈ H 1 (Ω) × H 1 (Γ).          (2)
A Model Problem: Existence, uniqueness and regularity

   Theorem (Existence and uniqueness)
   If α, β > 0 and (f , g ) ∈ L2 (Ω) × L2 (Γ), there exists a unique pair
   (u, v ) ∈ H 1 (Ω) × H 1 (Γ) which satisfies the weak form (2).

   Proof.
   Apply the Lax-Milgram theorem in the Hilbert space

         H 1 (Ω) × H 1 (Γ) := {(η, ξ) : η ∈ H 1 (Ω) and ξ ∈ H 1 (Γ)},

   with the norm
                                                                            1
                                                  2               2         2
              (η, ξ)   H 1 (Ω)×H 1 (Γ)   :=   η   H 1 (Ω)   + ξ   H 1 (Γ)
A Model Problem: Existence, uniqueness and regularity


   Theorem (Regularity)
   Under the extra assumption that Γ ∈ C 2 then
   (u, v ) ∈ H 2 (Ω) × H 2 (Γ) and

                        (u, v )    H 2 (Ω)×H 2 (Γ)   ≤ c (f , g )   L2 (Ω)×L2 (Γ) .



   Proof.
   Apply standard regularity results for bulk domains9 and surface
   domains10 to the weak form (2) with ξ = 0 and η = 0
   respectively.



     9
          Gilbarg and Trudinger 1983
     10
          Aubin 1982
A Model Problem: Domain Discretisation


 We define Ωh to be a polyhedral
 approximation of Ω, with boundary
 ∂Ωh = Γh , such that nodes of Γh lie on Γ.
 We take a quasi-uniform triangulation Th of
                                                   Γ
 Ωh with simplices and define
 h = max{diamT : T ∈ Th }.
                                                    h
                                                        Ωh
 With this construction Th |Γh , the restriction
 of Th to Γh is a quasi-uniform triangulation
 of Γh . We assume that T ∩ Γh has at most
 one face of T .
A Model Problem: Finite Element Approximation
   We define the following finite element spaces:

         Vh = {ηh : Ωh → R : ηh |T is linear, for each T ∈ Th }
           Sh = {ξh : Γh → R : ξh |e is linear, for each e ∈ Th |Γh }.

   The discrete problem is:
       Find (uh , vh ) ∈ Vh × Sh such that

       α          uh ·    ηh + uh ηh + β         Γh v h   ·   Γh ξh   + v h ξh
            Ωh                              Γh

              +         (αuh − βvh )(αηh − βξh ) = α               fh ηh + β          gh ξh
                   Γh                                         Ωh                 Γh
                           for all (ηh , ξh ) ∈ Vh × Sh .                        (3)

   fh and gh are some approximation of the data and will be specified
   later.
A Model Problem: Numerical example
   This method was implemented in the ALBERTA finite element
   toolbox11 , with Ω = {(x, y , z) : x 2 + y 2 /2 + z 2 /3 < 1} with
   α = β = 1, f (x, y , z) = 0 and g (x, y , z) = xy . fh and gh are taken
   as the interpolants of f and g .




     11
          Schmidt, Siebert, K¨ster, and Heine 2005
                             o
A Model Problem: Numerical example
   This method was implemented in the ALBERTA finite element
   toolbox11 , with Ω = {(x, y , z) : x 2 + y 2 /2 + z 2 /3 < 1} with
   α = β = 1, f (x, y , z) = 0 and g (x, y , z) = xy . fh and gh are taken
   as the interpolants of f and g .




     11
          Schmidt, Siebert, K¨ster, and Heine 2005
                             o
A Model Problem: Abstract form
   In order to perform error analysis, we introduce the following
   abstract forms:

                       a(Ω) (w , η) = α           w·       η + wη
                                              Ω

                        a(Γ) (y , ξ) = β          Γy   ·   Γξ   + yξ
                                              Γ

             a(×) (w , y ), (η, ξ) =          (αw − βy )(αη − βξ)
                                          Γ

   and
                 l (Ω) (η) = α       fη       l (Γ) (ξ) = β         gξ
                                 Ω                              Γ
   finally,
               a (w , y ), (η, ξ) = a(Ω) (w , η) + a(Γ) (y , ξ)
                                          + a(×) (w , y ), (η, ξ)
                       l (η, ξ) = l (Ω) (η) + l (Γ) (ξ).
A Model Problem: Abstract form
   and the following approximate forms:
                            (Ω)
                           ah (wh , ηh ) = α                  wh ·        ηh + wh ηh
                                                       Ωh
                              (Γ)
                            ah (yh , ξh ) = β                 Γh yh   ·    Γ h ξh   + yh ξh
                                                       Γh
              (×)
             ah      (wh , yh ), (ηh , ξh ) =          (αwh − βyh )(αηh − βξh )
                                                  Γh

   and
                    (Ω)                                 (Γ)
                  lh (ηh ) = α           fh ηh         lh (ξh ) = β                 gh ξh .
                                    Ωh                                       Γh
   finally,
                                                 (Ω)                       (Γh )
              ah (wh , yh ), (ηh , ξh ) = ah (wh , ηh ) + ah                       (yh , ξh )
                                                            (×)
                                                  + ah            (wh , yh ), (ηh , ξh )
                                                 (Ω)                (Γ)
                           lh (ηh , ξh ) = lh (ηh ) + lh (ξh ).
A Model Problem: Surface Lift



   Since the exact problem and the discrete problem are posed on
   different domains, we must relate the two domains. We start with
   the surface.
                                      We use normal projection of the
   p(x)     Γ d(x) ν(p(x))            domain. For h small enough, for
                                      each point x ∈ Γh there exists a
                         x
      x Γ
                                      unique p(x) ∈ Γ. Given by
            h
                         p(x)             p(x) = x − d(x)ν(p(x)).
A Model Problem: Surface Geometric Estimates
   These assumptions give us the following result12 .
   Lemma
   Let d denote a signed distance function for Γ, then

                                                d   L∞ (Γh )   ≤ ch2 .

   If we denote by µh the quotient of the measures on the surface and
   approximate surface, so that do = µh doh , we have that

                                          sup |1 − µh | ≤ ch2 .
                                               Γh

   Let P denote projection onto the tangent space of Γ and Ph
   projection onto the tangent space of Γh . We introduce the notation
          1
   Qh = µh (I − dH)PPh P(I − dH) then we have the estimate

                                           |I − µh Qh | ≤ ch2 .
     12
          Dziuk 1988; Dziuk and Elliott 2007
A Model Problem: Bulk domain perturbation I
   In order to relate the bulk domains, we introduce an exact
   triangulation13 of Ω.


                          T

                              F
                              T
                                  ^
                                  T



     13
          Bernardi 1989
     14
          Dubois 1987
A Model Problem: Bulk domain perturbation I
   In order to relate the bulk domains, we introduce an exact
   triangulation13 of Ω.
                                                    ~
                          h
                              T                    T
                                            ~
                                  F
                                  T
                                      ^     F
                                      T       T




           Dubois gives a construction of such maps FT to triangulate
           smooth domains Ω14 , details of which will not be given here.




     13
          Bernardi 1989
     14
          Dubois 1987
A Model Problem: Bulk domain perturbation I
   In order to relate the bulk domains, we introduce an exact
   triangulation13 of Ω.
                                                    ~
                          T         G|   hT        T
                                              ~
                              F
                              T
                                     ^        F
                                    T         T




           Dubois gives a construction of such maps FT to triangulate
           smooth domains Ω14 , details of which will not be given here.
                                                           −1
           We define Gh : Ωh → Ω locally by Gh |T : FT ◦ FT .



     13
          Bernardi 1989
     14
          Dubois 1987
A Model Problem: Bulk domain perturbation I
   In order to relate the bulk domains, we introduce an exact
   triangulation13 of Ω.
                                                   ~
               B   h      T       B
                                  h   G|  hT       T
                                               ~
                              F
                              T
                                      ^        F
                                      T        T




           Dubois gives a construction of such maps FT to triangulate
           smooth domains Ω14 , details of which will not be given here.
                                                           −1
           We define Gh : Ωh → Ω locally by Gh |T : FT ◦ FT .
           This is a diffeomorphism and is the identity when restricted to
           interior simplices, those with at most one boundary vertex.
           We call the domain where Gh is different from the identity Bh .
     13
          Bernardi 1989
     14
          Dubois 1987
A Model Problem: Bulk domain perturbation II

   Lemma (15 )
   Let T ∈ Th be a boundary simplex and T the associated exact
   triangle. We denote by Jh |T the absolute value of the determinant
   of DGh |T . Under the assumption that Th is quasi-uniform and
   Γ ∈ C 2 , then for sufficiently small h, we have that

                         DGh |T − I     L∞ (T )   ≤ ch
                        D 2 Gh |T − I   L∞ (T )
                                                  ≤c
                           J h |T − I   L∞ (T )   ≤ ch,

   for some constant independent of T and h. Furthermore,

                              |Bh | ≤ ch2 ,

   for some constant independent of h.
     15
          Lenoir 1986
A Model Problem: Lifted functions


      For ηh ∈ Vh we define its lift ηh : Ω → R by

                           ηh (Gh (x)) := ηh (x).

      For ξh ∈ Sh we define its lift ξh : Γ → R by

                           ξh (p(x)) := ξh (x).

      We also define the lifted finite element functions

              Vh = {ηh : ηh ∈ Vh }      Sh = {ξh : ξh ∈ Sh }.

      In the analysis, we will assume fh = f − and gh = g − to
      avoid smoothness requirements.
A Model Problem: Error Bounds


   Theorem
   Let (u, v ) ∈ H 2 (Ω) × H 2 (Γ) be the solution of the variational
   problem (2) and let (uh , vh ) ∈ Vh × Sh be the solution of the finite
   element scheme given by (3). Denote by uh and vh the lifts of uh
   and vh respectively. Then we have the following error bound:

                    (u − uh , v − vh )                        ≤ C1 h
                                           H 1 (Ω)×H 1 (Γ)

   where

           C1 = c    (u, v )   H 2 (Ω)×H 2 (Γ)   + (f , g )   L2 (Ω)×L2 (Γ)   .
A Model Problem: Error Bounds (cont.)



   Theorem (cont.)
   Furthermore, if f ∈ L∞ (Ω) and u ∈ W 1,∞ (Ω) then

                    (u − uh , v − vh )                        ≤ C2 h 2
                                              L2 (Ω)×L2 (Γ)

   where

   C2 = c   f   L∞ (Ω) +   g   L2 (Γ) +   u    W 1,∞ (Ω) +     u   H 2 (Ω) +   v   H 2 (Γ)   .
A Model Problem: Proof of error bounds I

   Lemma (Approximation property16 )
   For the lifted finite element spaces Vh and Sh , there exists an
   interpolation operator Ih : H 2 (Ω) × H 2 (Γ) → Vh × Sh such that

    w − Ih w        L2 (Ω)×L2 (Γ) +h   w − Ih w   H 1 (Ω)×H 1 (Γ)   ≤ ch2 w   H 2 (Ω)×H 2 (Γ)

   for all w ∈ H 2 (Ω) × H 2 (Γ).




     16
          Dziuk 1988; Lenoir 1986
A Model Problem: Proof of error bounds I

   Lemma (Approximation property16 )
   For the lifted finite element spaces Vh and Sh , there exists an
   interpolation operator Ih : H 2 (Ω) × H 2 (Γ) → Vh × Sh such that

    w − Ih w        L2 (Ω)×L2 (Γ) +h      w − Ih w   H 1 (Ω)×H 1 (Γ)   ≤ ch2 w       H 2 (Ω)×H 2 (Γ)

   for all w ∈ H 2 (Ω) × H 2 (Γ).

   Lemma (Bulk domain errors)
   Let wh , ηh ∈ Vh and denote their lifts by wh , ηh then

                                    (Ω)
             a(Ω) (wh , ηh ) − ah (wh , ηh ) ≤ ch wh                          ηh
                                                                  H 1 (Ω)          H 1 (Ω)
                                          (Ω)
                           l (Ω) (ηh ) − lh (ηh ) ≤ ch f        L2 (Ω)   ηh             .
                                                                               L2 (Ω)



     16
          Dziuk 1988; Lenoir 1986
A Model Problem: Proof of error bounds II
   Lemma (Surface domain errors)
   Let (wh , yh ), (ηh , ξh ) ∈ Vh × Sh and let yh , ξh denote the lifts of
   yh , ξh respectively and wh , ηh denote the lifts of the traces of
   wh , ηh . Then
                                (Γ)
            a(Γ) (yh , ξh ) − ah (yh , ξh )

                 ≤ ch2 yh                  ξh   H 1 (Γ)
                                H 1 (Γ)
                                                   (×)
            a(×) (wh , yh ), (ηh , ξh ) − ah                (wh , yh ), (ηh , ξh )

                 ≤ ch2 (wh , yh )                             (ηh , ξh )
                                          L2 (Γ)×L2 (Γ)                    L2 (Γ)×L2 (Γ)
                         (Γ)
            l (Γ) (ξh ) − lh (ξh )

                 ≤ ch2 f       L2 (Γ)     ξh            .
                                               L2 (Γ)
A Model Problem: Domain approximation errors III


   Lemma
   Under the extra assumptions that f ∈ L∞ (Ω) and w ∈ W 1,∞ (Ω)
   with w − the inverse lift of w onto Ωh . Let ηh ∈ Vh and denote its
   lifts by ηh then

                                       (Ω)
                    a(Ω) (w , ηh ) − ah (w − , ηh )
                         ≤ ch2 w       W 1,∞ (Ω)   ηh   H 1 (Ω)
                                 (Ω)
                    l (Ω) (ηh ) − lh (ηh )

                         ≤ ch2 f    L∞ (Ω)    ηh            .
                                                   L2 (Ω)
A Model Problem: Proof H 1 error bound I


   Notice for (ηh , ξh ) ∈ Vh × Sh , with lifts (ηh , ξh )

      Fh (ηh , ξh ) := a (u − uh , v − vh ), (ηh , ξh )
                    = l (ηh , ξh ) − a (uh , vh ), (ηh , ξh )
                    = l (ηh , ξh ) − lh (ηh , ξh )
                          + ah (uh , vh ), (ηh , ξh ) − a (uh , vh ), (ηh , ξh ).

   Hence

                   Fh ηh , ξh ) ≤ C1 h ηh , ξh                       .
                                                   H 1 (Ω)×H 1 (Γ)
A Model Problem: Proof of H 1 error bound II


   To prove the H 1 error bound, we rewrite the error as

             a (u − uh , v − vh ), (u − uh , v − vh )
                   = a (u − uh , v − vh ), (u, v ) − Ih (u, v )
                        + a (uh , v − vh ), Ih (u, v ) − (uh , vh )
                   = a (u − uh , v − vh ), (u, v ) − Ih (u, v )
                        + Fh Ih (u, v ) − (uh , vh ) .

   The result follows from the approximation property and the
   domain error results.
A Model Problem: Proof L2 error bound I



   To show the L2 bound we start by setting up a dual problem for
   ζ ∈ L2 (Ω) × L2 (Γ):
       Find wζ ∈ H 1 (Ω) × H 1 (Γ) such that

                  a (η, ξ), wζ ) = ζ, (η, ξ)   L2 (Ω)×L2 (Γ) .


   We assume this has a unique solution with the following regularity
   result
                  wζ H 2 (Ω)×H 2 (Γ) ≤ c ζ L2 (Ω)×L2 (Γ) .
A Model Problem: Proof L2 error bound II




   If we further assume that f ∈ L∞ (Ω) and u ∈ W 1,∞ (Ω), then we
   achieve the improved bound

              Fh (ηh , ξh )   ≤ C2 h2 (ηh , ξh )                     .
                                                   H 1 (Ω)×H 1 (Γ)

   This follows from applying the improved domain error results with
   the bound |Bh | ≤ ch2 .
A Model Problem: Proof L2 error bound III



   We start by writing the error

                            e = (u − uh , v − vh )

   as the data for the dual problem and test with e so that
                            2
                        e   L2 (Ω)×L2 (Γ)   = a(e, we ).

   Applying the interpolation theory, the H 1 bound, and the improved
   bound on Fh leads to the L2 bound.
A Model Problem: Numerical Results I



   To test the convergence rate, we applied this method with
   α = β = 1 on the unit ball using the ALBERTA finite element
   toolbox17 and the PARDISO numerical solver18 .
   The data was chosen so that the exact solution was

            u(x, y , z) = βxyz                   and          v (x, y , z) = (3 + α)xyz.

   We calculate the right hand side by setting fh and gh to be the
   interpolants of f and g in Vh and Sh .




     17
          Schmidt, Siebert, K¨ster, and Heine 2005
                             o
     18
          Schenk, Waechter, and Hagemann 2007; Schenk, Bollhofer, and Roemer 2006
A Model Problem: Errors

         h            L2 error        eoc            H 1 error      eoc
    8.201523e-01   2.817753e-02        -          2.586266e-01       -
    4.799888e-01   8.965317e-03    2.137583       1.517243e-01   0.995507
    2.555341e-01   2.362206e-03    2.115725       7.961819e-02   1.022867
    1.321787e-01   5.989949e-04    2.081457       4.024398e-02   1.035014
    6.736035e-02   1.502987e-04    2.051078       2.016042e-02   1.025427

                     Table: Bulk errors:     u − uh

         h            L2 error        eoc            H 1 error      eoc
    8.201523e-01   2.218139e-01        -          1.762399e+00
    4.799888e-01   6.606584e-02    2.260828       9.810869e-01   1.093411
    2.555341e-01   1.720835e-02    2.133950       5.028356e-01   1.060264
    1.321787e-01   4.346577e-03    2.087386       2.529537e-01   1.042257
    6.736035e-02   1.089298e-03    2.052899       1.266557e-01   1.026162

                    Table: Surface errors:    v − vh
More realistic coupling – Langmuir Kinetics I
   In many of the problems we consider, Langmuir kinetics govern the
   coupling between bulk and surface concentrations. We consider a
   bulk concentration u and a surface concentration v .
           We assume the following simple boundary condition19
                   “The net flux across the interface is the net
                   absorbtion minus desorption rates.”

           This is often interpreted by the adsorption-desroption flux on
           the surface given by

                                            κoff v − κon u(v − v ),

           where κoff is a rate of desorption, κon is a rate of adsorption,
           and v is a maximum desired surface concentration20 .

     19
          Kwon and Derby 2001
     20
          Georgievskii, Medvedev, and Stuchebrukhov 2002
More realistic coupling – Langmuir Kinetics II


       Sometimes we wish to impose v as a maximum more strongly
       by replacing the flux by

                           κoff v − κon u(v − v )+ ,

       where ()+ denotes the positive part.
       We can also consider the case where the surface concentration
       is far from saturation

                               κoff v − κon u,

       which is the linear case we have previously analysed.
More Realistic Coupling – Numerical Experiments


   To test the different coupling models, we have implement the
   following parabolic system. We wish to find u : Ω × [0, T ] → R
   and v : Γ × [0, T ] → R such that
                                     with q given by,
              ∂t u − ∆u = 0                 q = 0,
                     ∂u                     q = αu − βv ,
              −q +      =0
                     ∂ν                     q = αu(1 − v ) − βv ,
        ∂t v − ∆Γ v + q = 0.                q = αu(1 − v )+ − βv
   We implemented this method using the above method to descritse
   in space and semi-implicit time steping.
More Realistic Coupling – Numerical Experiments




   Figure: From left to right: q = 0, q = αu − βv , q = αu(1 − v ) − βv ,
   q = αu(1 − v )+ − βv
Turing Instabilities: Modelling

           We look to model the concentrations of active and inactive
           concentrations of GTPase on a cell membrane and in the
           cystosol contained within21 .
           We denote by Ω the cytosolic volume of the cell and Γ = ∂Ω
           the cell membrane. We look for a bulk concentration
           u : Ω → R of inactive GTPase, and surface concentrations,
           v1 , v2 : Γ → R, of active and inactive GTPase, respectively.
           We model the system using a
           reaction-diffusion-attachment/detachment system.
           For the reaction kinetics we assume simplified
           Michaelis–Menten type law for catalysed reactions and a
           Langmuir rate law for the attachment/detachment.


     21
          R¨tz and R¨ger 2011
           a        o
Turing Instabilities: Equations
   Nondimensionalisation leads to the following system.


           ∂t u = D∆u                                                  in Ω
           ∂t v1 = d1 ∆Γ v1 + γf (v1 , v2 )                            on Γ
           ∂t v2 = d2 ∆Γ v1 − γf (v1 , v2 ) + q(u, v1 , v2 )           on Γ


   where
                                                  v1                  v1
           f (v1 , v2 ) =    a1 + (a3 − a1 )             v2 − a4           ,
                                               a2 + v1             a5 + v1
   with the flux condition

                            −D u · ν = q(u, v1 , v2 ) on Γ

   with
                  q(u, v1 , v2 ) = αu(1 − (v1 + v2 ))+ − βv2 .
Turing Instabilities: Weak Form
   Using the same techniques as for the elliptic equation this leads to
   the weak form:
        Find (u, v1 , v2 ) ∈ H 1 (Ω) × H 1 (Γ) × H 1 (Γ) such that

       α           ∂t u η + D u ·            η +β           ∂t v2 ξ + d2   Γ v2   ·   Γξ
               Ω                                        Γ

               +         (αu(1 − (v1 + v2 ))+ − βv2 )(αη − βξ)
                     Γ

                         = −βγ          f (v1 , v2 )ξ
                                    Γ

               ∂t v1 ξ + d1       Γ v1   ·   Γ v2
           Γ

                         =γ       f (v1 , v2 )ξ,
                              Γ

       for all (η, ξ) ∈ H 1 (Ω) × H 1 (Γ).
Turing Instabilities: Discretisation


       We use a the above coupled bulk-surface finite element
       method to discretize in space.
       We discretise in time by treating the linear diffusion terms
       implicitly and the nonlinear reaction and
       attachment/detachment terms explicitly.
       Parameter choices:
           Diffusion Coefficients: D = 1000.0, d1 = 1.0, d2 = 1000.0
           Reaction Coefficients: a1 = 0.0, a2 = 20.0, a3 = 160.0,
           a4 = 1.0, a5 = 0.5
           Nondimensionalised constant: γ = 400.0
           Attachment/Detachment Coefficients: α = 0.1, β = 1.0
           Discretisation: τ = 1.0e − 3, h = 0.137025.
Turing Instabilities: Numerical Results




                Figure: Left: u, middle: v1 , right: v2
Turing Instabilities: Numerical Results




                Figure: Left: u, middle: v1 , right: v2
Turing Instabilities: Numerical Results – Final Frame




     Figure: Left: u (colour rescaled), middle: v1 , right: v2 , at final time
Conclusion


      We have developed a computational method for solving
      coupled bulk-surface partial differential equation.
      We have analysed a model problem and derived optimal order
      error estimates.
      We have applied the method to a
      reaction-diffusion-attachment/detachment problem from cell
      biology.
      In the future, we hope to perform analysis on the
      reaction-diffusion-attachment/detachment problem and look
      to derive error estimates.
      We also hope to look at time dependent domains.
References I

   Shelley L. Anna and Hans C. Mayer. Microscale tipstreaming in a
     microfluidic flow focusing device. Physics of Fluids, 18(12):
     121512, 2006.
   Thierry Aubin. Nonlinear analysis on manifolds, Monge-Ampere
     equations. Springer, 1982.
   Christine Bernardi. Optimal Finite-Element Interpolation on
     Curved Domains. SIAM J. Numer. Anal., 26(5):1212–1240,
     October 1989.
   Michael R. Booty and Mchael Siegel. A hybrid numerical method
     for interfacial fluid flow with soluble surfactant. J. Comput.
     Phys., 229(10):3864–3883, May 2010.
   Francois Dubois. Discrete vector potential representation of a
     divergence-free vector field in three-dimensional domains :
     numerical analysis of a model problem. SIAM J. Numer. Anal.,
     27(5):1103–1141, 1987.
References II
   Gerhard Dziuk. Finite elements for the Beltrami operator on
     arbitrary surfaces. In S Hildebrandt and R Leis, editors, Partial
     Differential Equations and Calculus of Variations, volume 1357
     of Lecture Notes in Mathematics 1357, pages 142–155. Springer,
     1988.
   Gerhard Dziuk and Charles M. Elliott. Surface finite elements for
     parabolic equations. J. Comput. Math., 25(4):385–407, 2007.
   Yuri Georgievskii, Emile S. Medvedev, and Alexei a.
     Stuchebrukhov. Proton transport via coupled surface and bulk
     diffusion. The Journal of Chemical Physics, 116(4):1692, 2002.
   David Gilbarg and Neil S. Trudinger. Elliptic partial differential
     equations of second order. Springer-Verlag, 1983.
   Aron B Jaffe and Alan Hall. Rho GTPases: biochemistry and
     biology. Annual review of cell and developmental biology, 21:
     247–69, January 2005.
References III
   Yong-Il Kwon and Jeffrey J. Derby. Modeling the coupled effects of
     interfacial and bulk phenomena during solution crystal growth.
     Journal of Crystal Growth, 230:328–335, 2001.
   Michel Lenoir. Optimal Isoparametric Finite Elements and Error
     Estimates for Domains Involving Curved Boundaries. SIAM J.
     Numer. Anal., 23(3):562–580, October 1986.
   Igor L. Novak, Fei Gao, Yung-Sze Choi, Diana Resasco, James C
     Schaff, and Boris M Slepchenko. Diffusion on a Curved Surface
     Coupled to Diffusion in the Volume: Application to Cell Biology.
     J. Comput. Phys., 226(2):1271–1290, October 2007.
   Andreas R¨tz and Matthias R¨ger. Turing instabilities in a
             a                 o
     mathematical model for signaling networks. Arxiv preprint
     arXiv:1107.1594, pages 1–21, 2011.
   Olaf Schenk, Matthias Bollhofer, and Rudolf A. Roemer. On
     large-scale diagonalization techniques for the Anderson model of
     localization. SIAM Rev., 28(3):963–983, 2006.
References IV



   Olaf Schenk, Andreas Waechter, and Michael Hagemann.
     Matching-based preprocessing algorithms to the solution of
     saddle-point problems in large-scale nonconvex interior-point
     optimization. Computat. Optim. Appl., 36(2–3):321–341, 2007.
   Alfred Schmidt, Kunibert G. Siebert, Daniel K¨ster, and
                                                o
     Claus-Justus Heine. Design of adaptive finite element software:
     the finite element toolbox ALBERTA. Springer-Verlag,
     Berlin-Heidelberg, 2005.

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Applications of the surface finite element method

  • 1. Applications of the Surface Finite Element Method Tom Ranner Mathematics Department September 2011 ENUMATH 2011, Leicester
  • 2. The Problem Many processes in biology and fluid mechanics are governed by diffusion on a membrane or interface coupled to diffusion in an enclosed bulk region. Other approaches to this problem include a boundary integral formulation1 and a finite volume approach2 . We wish to using the surface finite element method3 along with standard finite element techniques4 for the bulk region. 1 Booty and Siegel 2010 2 Novak, Gao, Choi, Resasco, Schaff, and Slepchenko 2007 3 Dziuk 1988; Dziuk and Elliott 2007 4 Lenoir 1986
  • 3. Example 1: Turing Instabilities GTP-binding proteins (GTPase) molecules are important regulators in cells that continuously run through an activation/deactivation and membrane-attachment/membrane-detachment cycle. Activated GTPase is able to localise in parts of the membranes and to induce cell polarity5 . This can be modelled by Turing instabilities in a reaction-diffusion system with attachment and detachment. Figure 5 Rho GT Pases and cell migration. Cell migration requires actin-dependent protrusions at the front (re d) and contractile actin:myosin filaments (re at the rear. In addition, microtubules (gre n) originating from d) e thecentrosome(purple arepreferentially stabilized in thedirection of migration allowing targeted vesicle ) trafficking from the Golgi (b wn) to the leading edge. ro Figure: Example of cell polarisation from6 5 R¨tz and R¨ger 2011 a o 6 Jaffe and Hall 2005
  • 4. Example 2: Surfactant problem Surfactants, or surface contaminants, significantly alter the interfacial properties of a fluid by changing the surface tension. An example is the tip-streaming of thin threads or small droplets from a drop or bubble this is stretched in an imposed extensional flow7 . FIG. 2. Microfluidic flow focusing geometry. ͑ a͒ Schematic diagram of the design denoting flow of both the inner and outer liquids from left to right. ͑ b͒ Image of the orifice region of an actual microchannel ͓ outlined with the dashed line in ͑ a͒ ͔ , including a typical image of the water-oil interface extending toward the orifice from the upstream channel during a flow ex- periment. Dimensions shown are Wup = 280 m, a = 90 m, ⌬Z = 180 m, and Wor = 34 m. 8 Figure: Taken from 7 Booty and Siegel 2010 8 Anna and Mayer 2006
  • 5. A Model Problem As a model problem we will look to solve the following elliptic problem: We assume we have a bounded domain Ω ⊆ Rn with Lipschitz boundary Γ. We wish to find u : Ω → R and v : Γ → R solution of the system −∆u + u = f in Ω (1a) Γ ∂u Ω (αu − βv ) + = 0 on Γ (1b) ∂ν −∆Γ v + v − (αu − βv ) = g on Γ. (1c) Here we assume α, β > 0 are given constants and f and g are known functions on Ω and Γ respectively. We denote by ∆Γ the Laplace-Beltrami operator on Γ.
  • 6. A Model Problem: Weak form We can convert this to a weak form using integration by parts over Ω and Γ then using the boundary condition and taking an appropriate linear combination of the two resulting forms leads to the problem: Find u : Ω → R and v : Γ → R such that α u· η + uη + β Γv · Γξ + vξ Ω Γ + (αu − βv )(αη − βξ) = α fη+β gξ Γ Ω Γ for all (η, ξ) ∈ H 1 (Ω) × H 1 (Γ). (2)
  • 7. A Model Problem: Existence, uniqueness and regularity Theorem (Existence and uniqueness) If α, β > 0 and (f , g ) ∈ L2 (Ω) × L2 (Γ), there exists a unique pair (u, v ) ∈ H 1 (Ω) × H 1 (Γ) which satisfies the weak form (2). Proof. Apply the Lax-Milgram theorem in the Hilbert space H 1 (Ω) × H 1 (Γ) := {(η, ξ) : η ∈ H 1 (Ω) and ξ ∈ H 1 (Γ)}, with the norm 1 2 2 2 (η, ξ) H 1 (Ω)×H 1 (Γ) := η H 1 (Ω) + ξ H 1 (Γ)
  • 8. A Model Problem: Existence, uniqueness and regularity Theorem (Regularity) Under the extra assumption that Γ ∈ C 2 then (u, v ) ∈ H 2 (Ω) × H 2 (Γ) and (u, v ) H 2 (Ω)×H 2 (Γ) ≤ c (f , g ) L2 (Ω)×L2 (Γ) . Proof. Apply standard regularity results for bulk domains9 and surface domains10 to the weak form (2) with ξ = 0 and η = 0 respectively. 9 Gilbarg and Trudinger 1983 10 Aubin 1982
  • 9. A Model Problem: Domain Discretisation We define Ωh to be a polyhedral approximation of Ω, with boundary ∂Ωh = Γh , such that nodes of Γh lie on Γ. We take a quasi-uniform triangulation Th of Γ Ωh with simplices and define h = max{diamT : T ∈ Th }. h Ωh With this construction Th |Γh , the restriction of Th to Γh is a quasi-uniform triangulation of Γh . We assume that T ∩ Γh has at most one face of T .
  • 10. A Model Problem: Finite Element Approximation We define the following finite element spaces: Vh = {ηh : Ωh → R : ηh |T is linear, for each T ∈ Th } Sh = {ξh : Γh → R : ξh |e is linear, for each e ∈ Th |Γh }. The discrete problem is: Find (uh , vh ) ∈ Vh × Sh such that α uh · ηh + uh ηh + β Γh v h · Γh ξh + v h ξh Ωh Γh + (αuh − βvh )(αηh − βξh ) = α fh ηh + β gh ξh Γh Ωh Γh for all (ηh , ξh ) ∈ Vh × Sh . (3) fh and gh are some approximation of the data and will be specified later.
  • 11. A Model Problem: Numerical example This method was implemented in the ALBERTA finite element toolbox11 , with Ω = {(x, y , z) : x 2 + y 2 /2 + z 2 /3 < 1} with α = β = 1, f (x, y , z) = 0 and g (x, y , z) = xy . fh and gh are taken as the interpolants of f and g . 11 Schmidt, Siebert, K¨ster, and Heine 2005 o
  • 12. A Model Problem: Numerical example This method was implemented in the ALBERTA finite element toolbox11 , with Ω = {(x, y , z) : x 2 + y 2 /2 + z 2 /3 < 1} with α = β = 1, f (x, y , z) = 0 and g (x, y , z) = xy . fh and gh are taken as the interpolants of f and g . 11 Schmidt, Siebert, K¨ster, and Heine 2005 o
  • 13. A Model Problem: Abstract form In order to perform error analysis, we introduce the following abstract forms: a(Ω) (w , η) = α w· η + wη Ω a(Γ) (y , ξ) = β Γy · Γξ + yξ Γ a(×) (w , y ), (η, ξ) = (αw − βy )(αη − βξ) Γ and l (Ω) (η) = α fη l (Γ) (ξ) = β gξ Ω Γ finally, a (w , y ), (η, ξ) = a(Ω) (w , η) + a(Γ) (y , ξ) + a(×) (w , y ), (η, ξ) l (η, ξ) = l (Ω) (η) + l (Γ) (ξ).
  • 14. A Model Problem: Abstract form and the following approximate forms: (Ω) ah (wh , ηh ) = α wh · ηh + wh ηh Ωh (Γ) ah (yh , ξh ) = β Γh yh · Γ h ξh + yh ξh Γh (×) ah (wh , yh ), (ηh , ξh ) = (αwh − βyh )(αηh − βξh ) Γh and (Ω) (Γ) lh (ηh ) = α fh ηh lh (ξh ) = β gh ξh . Ωh Γh finally, (Ω) (Γh ) ah (wh , yh ), (ηh , ξh ) = ah (wh , ηh ) + ah (yh , ξh ) (×) + ah (wh , yh ), (ηh , ξh ) (Ω) (Γ) lh (ηh , ξh ) = lh (ηh ) + lh (ξh ).
  • 15. A Model Problem: Surface Lift Since the exact problem and the discrete problem are posed on different domains, we must relate the two domains. We start with the surface. We use normal projection of the p(x) Γ d(x) ν(p(x)) domain. For h small enough, for each point x ∈ Γh there exists a x x Γ unique p(x) ∈ Γ. Given by h p(x) p(x) = x − d(x)ν(p(x)).
  • 16. A Model Problem: Surface Geometric Estimates These assumptions give us the following result12 . Lemma Let d denote a signed distance function for Γ, then d L∞ (Γh ) ≤ ch2 . If we denote by µh the quotient of the measures on the surface and approximate surface, so that do = µh doh , we have that sup |1 − µh | ≤ ch2 . Γh Let P denote projection onto the tangent space of Γ and Ph projection onto the tangent space of Γh . We introduce the notation 1 Qh = µh (I − dH)PPh P(I − dH) then we have the estimate |I − µh Qh | ≤ ch2 . 12 Dziuk 1988; Dziuk and Elliott 2007
  • 17. A Model Problem: Bulk domain perturbation I In order to relate the bulk domains, we introduce an exact triangulation13 of Ω. T F T ^ T 13 Bernardi 1989 14 Dubois 1987
  • 18. A Model Problem: Bulk domain perturbation I In order to relate the bulk domains, we introduce an exact triangulation13 of Ω. ~ h T T ~ F T ^ F T T Dubois gives a construction of such maps FT to triangulate smooth domains Ω14 , details of which will not be given here. 13 Bernardi 1989 14 Dubois 1987
  • 19. A Model Problem: Bulk domain perturbation I In order to relate the bulk domains, we introduce an exact triangulation13 of Ω. ~ T G| hT T ~ F T ^ F T T Dubois gives a construction of such maps FT to triangulate smooth domains Ω14 , details of which will not be given here. −1 We define Gh : Ωh → Ω locally by Gh |T : FT ◦ FT . 13 Bernardi 1989 14 Dubois 1987
  • 20. A Model Problem: Bulk domain perturbation I In order to relate the bulk domains, we introduce an exact triangulation13 of Ω. ~ B h T B h G| hT T ~ F T ^ F T T Dubois gives a construction of such maps FT to triangulate smooth domains Ω14 , details of which will not be given here. −1 We define Gh : Ωh → Ω locally by Gh |T : FT ◦ FT . This is a diffeomorphism and is the identity when restricted to interior simplices, those with at most one boundary vertex. We call the domain where Gh is different from the identity Bh . 13 Bernardi 1989 14 Dubois 1987
  • 21. A Model Problem: Bulk domain perturbation II Lemma (15 ) Let T ∈ Th be a boundary simplex and T the associated exact triangle. We denote by Jh |T the absolute value of the determinant of DGh |T . Under the assumption that Th is quasi-uniform and Γ ∈ C 2 , then for sufficiently small h, we have that DGh |T − I L∞ (T ) ≤ ch D 2 Gh |T − I L∞ (T ) ≤c J h |T − I L∞ (T ) ≤ ch, for some constant independent of T and h. Furthermore, |Bh | ≤ ch2 , for some constant independent of h. 15 Lenoir 1986
  • 22. A Model Problem: Lifted functions For ηh ∈ Vh we define its lift ηh : Ω → R by ηh (Gh (x)) := ηh (x). For ξh ∈ Sh we define its lift ξh : Γ → R by ξh (p(x)) := ξh (x). We also define the lifted finite element functions Vh = {ηh : ηh ∈ Vh } Sh = {ξh : ξh ∈ Sh }. In the analysis, we will assume fh = f − and gh = g − to avoid smoothness requirements.
  • 23. A Model Problem: Error Bounds Theorem Let (u, v ) ∈ H 2 (Ω) × H 2 (Γ) be the solution of the variational problem (2) and let (uh , vh ) ∈ Vh × Sh be the solution of the finite element scheme given by (3). Denote by uh and vh the lifts of uh and vh respectively. Then we have the following error bound: (u − uh , v − vh ) ≤ C1 h H 1 (Ω)×H 1 (Γ) where C1 = c (u, v ) H 2 (Ω)×H 2 (Γ) + (f , g ) L2 (Ω)×L2 (Γ) .
  • 24. A Model Problem: Error Bounds (cont.) Theorem (cont.) Furthermore, if f ∈ L∞ (Ω) and u ∈ W 1,∞ (Ω) then (u − uh , v − vh ) ≤ C2 h 2 L2 (Ω)×L2 (Γ) where C2 = c f L∞ (Ω) + g L2 (Γ) + u W 1,∞ (Ω) + u H 2 (Ω) + v H 2 (Γ) .
  • 25. A Model Problem: Proof of error bounds I Lemma (Approximation property16 ) For the lifted finite element spaces Vh and Sh , there exists an interpolation operator Ih : H 2 (Ω) × H 2 (Γ) → Vh × Sh such that w − Ih w L2 (Ω)×L2 (Γ) +h w − Ih w H 1 (Ω)×H 1 (Γ) ≤ ch2 w H 2 (Ω)×H 2 (Γ) for all w ∈ H 2 (Ω) × H 2 (Γ). 16 Dziuk 1988; Lenoir 1986
  • 26. A Model Problem: Proof of error bounds I Lemma (Approximation property16 ) For the lifted finite element spaces Vh and Sh , there exists an interpolation operator Ih : H 2 (Ω) × H 2 (Γ) → Vh × Sh such that w − Ih w L2 (Ω)×L2 (Γ) +h w − Ih w H 1 (Ω)×H 1 (Γ) ≤ ch2 w H 2 (Ω)×H 2 (Γ) for all w ∈ H 2 (Ω) × H 2 (Γ). Lemma (Bulk domain errors) Let wh , ηh ∈ Vh and denote their lifts by wh , ηh then (Ω) a(Ω) (wh , ηh ) − ah (wh , ηh ) ≤ ch wh ηh H 1 (Ω) H 1 (Ω) (Ω) l (Ω) (ηh ) − lh (ηh ) ≤ ch f L2 (Ω) ηh . L2 (Ω) 16 Dziuk 1988; Lenoir 1986
  • 27. A Model Problem: Proof of error bounds II Lemma (Surface domain errors) Let (wh , yh ), (ηh , ξh ) ∈ Vh × Sh and let yh , ξh denote the lifts of yh , ξh respectively and wh , ηh denote the lifts of the traces of wh , ηh . Then (Γ) a(Γ) (yh , ξh ) − ah (yh , ξh ) ≤ ch2 yh ξh H 1 (Γ) H 1 (Γ) (×) a(×) (wh , yh ), (ηh , ξh ) − ah (wh , yh ), (ηh , ξh ) ≤ ch2 (wh , yh ) (ηh , ξh ) L2 (Γ)×L2 (Γ) L2 (Γ)×L2 (Γ) (Γ) l (Γ) (ξh ) − lh (ξh ) ≤ ch2 f L2 (Γ) ξh . L2 (Γ)
  • 28. A Model Problem: Domain approximation errors III Lemma Under the extra assumptions that f ∈ L∞ (Ω) and w ∈ W 1,∞ (Ω) with w − the inverse lift of w onto Ωh . Let ηh ∈ Vh and denote its lifts by ηh then (Ω) a(Ω) (w , ηh ) − ah (w − , ηh ) ≤ ch2 w W 1,∞ (Ω) ηh H 1 (Ω) (Ω) l (Ω) (ηh ) − lh (ηh ) ≤ ch2 f L∞ (Ω) ηh . L2 (Ω)
  • 29. A Model Problem: Proof H 1 error bound I Notice for (ηh , ξh ) ∈ Vh × Sh , with lifts (ηh , ξh ) Fh (ηh , ξh ) := a (u − uh , v − vh ), (ηh , ξh ) = l (ηh , ξh ) − a (uh , vh ), (ηh , ξh ) = l (ηh , ξh ) − lh (ηh , ξh ) + ah (uh , vh ), (ηh , ξh ) − a (uh , vh ), (ηh , ξh ). Hence Fh ηh , ξh ) ≤ C1 h ηh , ξh . H 1 (Ω)×H 1 (Γ)
  • 30. A Model Problem: Proof of H 1 error bound II To prove the H 1 error bound, we rewrite the error as a (u − uh , v − vh ), (u − uh , v − vh ) = a (u − uh , v − vh ), (u, v ) − Ih (u, v ) + a (uh , v − vh ), Ih (u, v ) − (uh , vh ) = a (u − uh , v − vh ), (u, v ) − Ih (u, v ) + Fh Ih (u, v ) − (uh , vh ) . The result follows from the approximation property and the domain error results.
  • 31. A Model Problem: Proof L2 error bound I To show the L2 bound we start by setting up a dual problem for ζ ∈ L2 (Ω) × L2 (Γ): Find wζ ∈ H 1 (Ω) × H 1 (Γ) such that a (η, ξ), wζ ) = ζ, (η, ξ) L2 (Ω)×L2 (Γ) . We assume this has a unique solution with the following regularity result wζ H 2 (Ω)×H 2 (Γ) ≤ c ζ L2 (Ω)×L2 (Γ) .
  • 32. A Model Problem: Proof L2 error bound II If we further assume that f ∈ L∞ (Ω) and u ∈ W 1,∞ (Ω), then we achieve the improved bound Fh (ηh , ξh ) ≤ C2 h2 (ηh , ξh ) . H 1 (Ω)×H 1 (Γ) This follows from applying the improved domain error results with the bound |Bh | ≤ ch2 .
  • 33. A Model Problem: Proof L2 error bound III We start by writing the error e = (u − uh , v − vh ) as the data for the dual problem and test with e so that 2 e L2 (Ω)×L2 (Γ) = a(e, we ). Applying the interpolation theory, the H 1 bound, and the improved bound on Fh leads to the L2 bound.
  • 34. A Model Problem: Numerical Results I To test the convergence rate, we applied this method with α = β = 1 on the unit ball using the ALBERTA finite element toolbox17 and the PARDISO numerical solver18 . The data was chosen so that the exact solution was u(x, y , z) = βxyz and v (x, y , z) = (3 + α)xyz. We calculate the right hand side by setting fh and gh to be the interpolants of f and g in Vh and Sh . 17 Schmidt, Siebert, K¨ster, and Heine 2005 o 18 Schenk, Waechter, and Hagemann 2007; Schenk, Bollhofer, and Roemer 2006
  • 35. A Model Problem: Errors h L2 error eoc H 1 error eoc 8.201523e-01 2.817753e-02 - 2.586266e-01 - 4.799888e-01 8.965317e-03 2.137583 1.517243e-01 0.995507 2.555341e-01 2.362206e-03 2.115725 7.961819e-02 1.022867 1.321787e-01 5.989949e-04 2.081457 4.024398e-02 1.035014 6.736035e-02 1.502987e-04 2.051078 2.016042e-02 1.025427 Table: Bulk errors: u − uh h L2 error eoc H 1 error eoc 8.201523e-01 2.218139e-01 - 1.762399e+00 4.799888e-01 6.606584e-02 2.260828 9.810869e-01 1.093411 2.555341e-01 1.720835e-02 2.133950 5.028356e-01 1.060264 1.321787e-01 4.346577e-03 2.087386 2.529537e-01 1.042257 6.736035e-02 1.089298e-03 2.052899 1.266557e-01 1.026162 Table: Surface errors: v − vh
  • 36. More realistic coupling – Langmuir Kinetics I In many of the problems we consider, Langmuir kinetics govern the coupling between bulk and surface concentrations. We consider a bulk concentration u and a surface concentration v . We assume the following simple boundary condition19 “The net flux across the interface is the net absorbtion minus desorption rates.” This is often interpreted by the adsorption-desroption flux on the surface given by κoff v − κon u(v − v ), where κoff is a rate of desorption, κon is a rate of adsorption, and v is a maximum desired surface concentration20 . 19 Kwon and Derby 2001 20 Georgievskii, Medvedev, and Stuchebrukhov 2002
  • 37. More realistic coupling – Langmuir Kinetics II Sometimes we wish to impose v as a maximum more strongly by replacing the flux by κoff v − κon u(v − v )+ , where ()+ denotes the positive part. We can also consider the case where the surface concentration is far from saturation κoff v − κon u, which is the linear case we have previously analysed.
  • 38. More Realistic Coupling – Numerical Experiments To test the different coupling models, we have implement the following parabolic system. We wish to find u : Ω × [0, T ] → R and v : Γ × [0, T ] → R such that with q given by, ∂t u − ∆u = 0 q = 0, ∂u q = αu − βv , −q + =0 ∂ν q = αu(1 − v ) − βv , ∂t v − ∆Γ v + q = 0. q = αu(1 − v )+ − βv We implemented this method using the above method to descritse in space and semi-implicit time steping.
  • 39. More Realistic Coupling – Numerical Experiments Figure: From left to right: q = 0, q = αu − βv , q = αu(1 − v ) − βv , q = αu(1 − v )+ − βv
  • 40. Turing Instabilities: Modelling We look to model the concentrations of active and inactive concentrations of GTPase on a cell membrane and in the cystosol contained within21 . We denote by Ω the cytosolic volume of the cell and Γ = ∂Ω the cell membrane. We look for a bulk concentration u : Ω → R of inactive GTPase, and surface concentrations, v1 , v2 : Γ → R, of active and inactive GTPase, respectively. We model the system using a reaction-diffusion-attachment/detachment system. For the reaction kinetics we assume simplified Michaelis–Menten type law for catalysed reactions and a Langmuir rate law for the attachment/detachment. 21 R¨tz and R¨ger 2011 a o
  • 41. Turing Instabilities: Equations Nondimensionalisation leads to the following system. ∂t u = D∆u in Ω ∂t v1 = d1 ∆Γ v1 + γf (v1 , v2 ) on Γ ∂t v2 = d2 ∆Γ v1 − γf (v1 , v2 ) + q(u, v1 , v2 ) on Γ where v1 v1 f (v1 , v2 ) = a1 + (a3 − a1 ) v2 − a4 , a2 + v1 a5 + v1 with the flux condition −D u · ν = q(u, v1 , v2 ) on Γ with q(u, v1 , v2 ) = αu(1 − (v1 + v2 ))+ − βv2 .
  • 42. Turing Instabilities: Weak Form Using the same techniques as for the elliptic equation this leads to the weak form: Find (u, v1 , v2 ) ∈ H 1 (Ω) × H 1 (Γ) × H 1 (Γ) such that α ∂t u η + D u · η +β ∂t v2 ξ + d2 Γ v2 · Γξ Ω Γ + (αu(1 − (v1 + v2 ))+ − βv2 )(αη − βξ) Γ = −βγ f (v1 , v2 )ξ Γ ∂t v1 ξ + d1 Γ v1 · Γ v2 Γ =γ f (v1 , v2 )ξ, Γ for all (η, ξ) ∈ H 1 (Ω) × H 1 (Γ).
  • 43. Turing Instabilities: Discretisation We use a the above coupled bulk-surface finite element method to discretize in space. We discretise in time by treating the linear diffusion terms implicitly and the nonlinear reaction and attachment/detachment terms explicitly. Parameter choices: Diffusion Coefficients: D = 1000.0, d1 = 1.0, d2 = 1000.0 Reaction Coefficients: a1 = 0.0, a2 = 20.0, a3 = 160.0, a4 = 1.0, a5 = 0.5 Nondimensionalised constant: γ = 400.0 Attachment/Detachment Coefficients: α = 0.1, β = 1.0 Discretisation: τ = 1.0e − 3, h = 0.137025.
  • 44. Turing Instabilities: Numerical Results Figure: Left: u, middle: v1 , right: v2
  • 45. Turing Instabilities: Numerical Results Figure: Left: u, middle: v1 , right: v2
  • 46. Turing Instabilities: Numerical Results – Final Frame Figure: Left: u (colour rescaled), middle: v1 , right: v2 , at final time
  • 47. Conclusion We have developed a computational method for solving coupled bulk-surface partial differential equation. We have analysed a model problem and derived optimal order error estimates. We have applied the method to a reaction-diffusion-attachment/detachment problem from cell biology. In the future, we hope to perform analysis on the reaction-diffusion-attachment/detachment problem and look to derive error estimates. We also hope to look at time dependent domains.
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  • 50. References III Yong-Il Kwon and Jeffrey J. Derby. Modeling the coupled effects of interfacial and bulk phenomena during solution crystal growth. Journal of Crystal Growth, 230:328–335, 2001. Michel Lenoir. Optimal Isoparametric Finite Elements and Error Estimates for Domains Involving Curved Boundaries. SIAM J. Numer. Anal., 23(3):562–580, October 1986. Igor L. Novak, Fei Gao, Yung-Sze Choi, Diana Resasco, James C Schaff, and Boris M Slepchenko. Diffusion on a Curved Surface Coupled to Diffusion in the Volume: Application to Cell Biology. J. Comput. Phys., 226(2):1271–1290, October 2007. Andreas R¨tz and Matthias R¨ger. Turing instabilities in a a o mathematical model for signaling networks. Arxiv preprint arXiv:1107.1594, pages 1–21, 2011. Olaf Schenk, Matthias Bollhofer, and Rudolf A. Roemer. On large-scale diagonalization techniques for the Anderson model of localization. SIAM Rev., 28(3):963–983, 2006.
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