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Review Topical Sections

Molecular mechanisms of neurodegenerative disease (NDD)

  • Degenerative nerve diseases affect body's balance, movement, speech, breathing and heart function. Classification of neurodegenerative disorders can be done on the basis of their molecular cause, like abnormal protein aggregation, involved cell death or loss of function of involved cell. Parkinson's disease (PD) is associated with aggregation of α-synuclein, while Alzheimer disease (AD) is associated with tau, amyloid-β42 protein aggregation. TDP-43 aggregation was found in Amyloidosis. Besides, Argyrophilic grain disease (AGD); Amyotrophic lateral sclerosis (ALS); Astrocyte plaque (AP); ALS and Parkinsonism-Dementia Complex (APDC); Aging-related tau astrogliopathy (ARTAG); Ballooned neuron (BN); Cerebral age-related TDP-43 with sclerosis (CARTS); Corticobasal degeneration (CBD); Chronic traumatic encephalopathy (CTE); Dementia with Lewy bodies (DLB); Dystrophic neuritis (DN); Facial onset sensory and motor neuronopathy (FOSMN); Glial cytoplasmic inclusions (GCI); globular glial tauopathy (GGT); Guadeloupean Parkinsonism (GP); idiopathic REM sleep behavior disorder (iRBD); Limbic-predominant age-related TDP-43 encephalopathy (LATE); Lewy bodies (LB); Lewy body diseases (LBD); Lewy neuritis (LN); muscle cells (MC); multiple system atrophy (MSA); multisystem proteinopathy (MSP); Neuronal cytoplasmic inclusions (NCI); neurofibrillary tangles (NFT); neuronal intranuclear inclusions (NII); neuropil threads (NPT); Nodding Syndrome (NS); oligodendroglial coiled bodies (OCB); oligodendroglial Pick's body-like inclusions (OPiBLI); pure autonomic failure (PAF); primary age-related tauopathy (PART); Pick's bodies (PiB); Pick's disease (PiD); Primary lateral sclerosis (PLS); Progressive muscular atrophy (PMA); progressive supranuclear palsy (PSP); pretangles (PT); tufted astrocyte (TA), are several neurodegenerative diseases name according to their involved protein factor(s).

    The cause may be genetic, may also be sporadic. Alcoholism, pesticides, a tumor, or a stroke are sometimes noticed in the disease background. Sometimes the cause remains totally unknown. Neurodegeneration, till date, cannot be cured. Only some palliative treatments may relieve some of the symptoms but temporarily. Further, some types of NDD could also be fatal.

    Our focus, in this review, is mainly on AD and PD since they vastly affect millions of people in the world, and occurs when nerve cells lose functional ability and/or die over time. AD and PD, the likelihood of developing the issues rise dramatically with age. Unfortunately, there is no cure at present for them except some palliative measure to give some comfort to the victims. Improvement of our understanding about the cause(s) of neurodegenerative diseases may help to design the new approaches for treatment and prevention of the ailments. In recent days, high-throughput technologies like RNA sequencing, network biology, and Omics data provide insights of all neurodegenerative disease.

    Graphical abstract 

    Citation: Ashok Chakraborty, Anil Diwan. Molecular mechanisms of neurodegenerative disease (NDD)[J]. AIMS Molecular Science, 2023, 10(3): 171-185. doi: 10.3934/molsci.2023012

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  • Degenerative nerve diseases affect body's balance, movement, speech, breathing and heart function. Classification of neurodegenerative disorders can be done on the basis of their molecular cause, like abnormal protein aggregation, involved cell death or loss of function of involved cell. Parkinson's disease (PD) is associated with aggregation of α-synuclein, while Alzheimer disease (AD) is associated with tau, amyloid-β42 protein aggregation. TDP-43 aggregation was found in Amyloidosis. Besides, Argyrophilic grain disease (AGD); Amyotrophic lateral sclerosis (ALS); Astrocyte plaque (AP); ALS and Parkinsonism-Dementia Complex (APDC); Aging-related tau astrogliopathy (ARTAG); Ballooned neuron (BN); Cerebral age-related TDP-43 with sclerosis (CARTS); Corticobasal degeneration (CBD); Chronic traumatic encephalopathy (CTE); Dementia with Lewy bodies (DLB); Dystrophic neuritis (DN); Facial onset sensory and motor neuronopathy (FOSMN); Glial cytoplasmic inclusions (GCI); globular glial tauopathy (GGT); Guadeloupean Parkinsonism (GP); idiopathic REM sleep behavior disorder (iRBD); Limbic-predominant age-related TDP-43 encephalopathy (LATE); Lewy bodies (LB); Lewy body diseases (LBD); Lewy neuritis (LN); muscle cells (MC); multiple system atrophy (MSA); multisystem proteinopathy (MSP); Neuronal cytoplasmic inclusions (NCI); neurofibrillary tangles (NFT); neuronal intranuclear inclusions (NII); neuropil threads (NPT); Nodding Syndrome (NS); oligodendroglial coiled bodies (OCB); oligodendroglial Pick's body-like inclusions (OPiBLI); pure autonomic failure (PAF); primary age-related tauopathy (PART); Pick's bodies (PiB); Pick's disease (PiD); Primary lateral sclerosis (PLS); Progressive muscular atrophy (PMA); progressive supranuclear palsy (PSP); pretangles (PT); tufted astrocyte (TA), are several neurodegenerative diseases name according to their involved protein factor(s).

    The cause may be genetic, may also be sporadic. Alcoholism, pesticides, a tumor, or a stroke are sometimes noticed in the disease background. Sometimes the cause remains totally unknown. Neurodegeneration, till date, cannot be cured. Only some palliative treatments may relieve some of the symptoms but temporarily. Further, some types of NDD could also be fatal.

    Our focus, in this review, is mainly on AD and PD since they vastly affect millions of people in the world, and occurs when nerve cells lose functional ability and/or die over time. AD and PD, the likelihood of developing the issues rise dramatically with age. Unfortunately, there is no cure at present for them except some palliative measure to give some comfort to the victims. Improvement of our understanding about the cause(s) of neurodegenerative diseases may help to design the new approaches for treatment and prevention of the ailments. In recent days, high-throughput technologies like RNA sequencing, network biology, and Omics data provide insights of all neurodegenerative disease.

    Graphical abstract 



    The viscous Stokes problem seeks unknown functions u and p that fulfill the following equations,

    νΔu+p=finΩ, (1.1)
    u=0inΩ, (1.2)
    u=gonΩ, (1.3)

    where Ω is a polygonal domain in R2. For the nonhomogeneous boundary condition u=gonΩ, one can use the standard procedure by letting u=u0+ug. ug is a known function satisfying ug=g on Ω and u0 is zero at Ω and satisfies (1.1) and (1.2) with different righthand sides. For the sake of simplicity, we only consider the homogeneous boundary condition, i.e., g=0. The scheme can be extended to the nonhomogeneous boundary condition. Using the standard notation for the Sobolev spaces, the weak formulation for the Stokes problems (1.1)–(1.3), in the primary velocity-pressure form, we seek u[H10(Ω)]2 and pL20(Ω) such that,

    {(νu,v)(v,p)=(f,v), v[H10(Ω)]2,(u,q)=0,   qL20(Ω).

    In the standard finite element discretization schemes, pressure and velocity unknowns are approximated simultaneously via a saddle-point system. To avoid solving such an indefinite system, the divergence-free finite element methods have been proposed to compute the numerical velocity by solving a symmetric positive-definite system in a divergence-free subspace. Due to the discrete or exact divergence-free property, such a method eliminates the pressure from the coupled systems, resulting in a symmetric positive definite system with a smaller size. Previously, a divergence-free basis was constructed for different finite element methods, e.g., [1,2,3,4]. The original divergence-free weak Galerkin (WG) method was proposed in [3].

    Unlike most existing divergence-free finite element methods, the discrete divergence-free WG method considered in this paper allows the meshes to consist of a mix of general polygons and hanging nodes. However, although the basis functions are discrete divergence-free, they may not guarantee good velocity approximation since the velocity error may depend on viscosity and pressure. This is because the div-free scheme is non-pressure-robust; thus, the velocity error bound depends on viscosity and pressure. Small viscosity values or inaccurate pressure approximations may produce an incorrect velocity solution to ruin the simulation.

    This paper shows that the numerical pollution mentioned above, caused by small viscosities or large pressure errors, also appears for the previous discrete divergence-free WG method. In this paper, we contribute to modify the original scheme and investigate the technique to remove viscosity and pressure effects in the velocity approximations with minimal effort. The technique follows the previous work of the authors and employs the velocity-reconstruction operator to modify the load term. This reconstruction technique was first proposed by Linke [5,6] and was then widely used to modify the existing finite element scheme for Stokes problems [7,8,9,10,11,12,13,14,15,16] and other incompressible fluid problems due to the minimal efforts required to achieve the desired good quality in numerical solutions [17,18,19,20,21,22]. Unlike using the H(div) basis functions in H(div) finite element methods, the velocity reconstruction operator is designed to map the original velocity basis functions to a suitable subspace of the H(div) space. Then, this modification only changes the load term assembly, but the stiffness matrix remains the same. In addition to the velocity reconstruction operator, we also mention that there are other advanced approaches to achieve the desired pressure-robustness [17,23,24]. Due to the page limitation, we only cite an incomplete list of the previous schemes featuring pressure-robustness. For example, Zhang [25,26] constructed divergence-free pairs of finite element spaces and used it to solve incompressible fluid problems [27,28]. Another successful strategy is to employ the Stokes complex of the lowest regularity [29] and the approximate velocity in the H(div) space [30]. A similar approach has been used in hybrid discontinuous Galerkin methods (HDG) to achieve the desired pressure-robustness [31,32,33]. More details on divergence-free and pressure-robust schemes can be found in the review paper [34]. Recently, there is another approach to achieve the desired robustness by enriching the Raviart-Thomas (RT) basis functions into the H1 -finite element spaces [35,36]. In this paper, we focus on designing the proper velocity-reconstruction operator and modifying the source term assembly to achieve robustness. The advantages of this modification lie in the potential to recycle the researchers' previous codes and enhance the former work with minimal changes to the reliable numerical approximation. We also demonstrate the pressure recovery procedure for the case that requires a pressure approximation.

    The rest of this paper is organized as follows. In Section 2, we first introduce the notation and two existing numerical algorithms and then propose the robust pressure algorithm and the pressure recovery scheme. In Section 3, we demonstrate the main error estimates for the Stokes problem. Several numerical experiments are presented in Section 4. We conclude this paper in Section 5.

    This section recalls the standard WG method and proposes our new divergence-free and pressure-robust WG methods. Let Th be a partition of the domain Ω consisting of a mix of polygons satisfying the set of conditions specified in [37]. Let Eh denote the set of all edges in Th and E0h=EhΩ be the set of all interior edges. Based on the partition Th, we introduce the following finite element spaces Wh and Vh for the pressure and velocity variables, respectively,

    Wh={q: qL20(Ω), q|TP0(T)},Vh={v={v0,vb}: {v0,vb}|T[P1(T)]2×[P0(e)]2, eT, vb=0 on Ω},

    where Pk(ω) denotes the space of polynomials of degree at most k restricted to ω=e or T.

    The discrete weak gradient and divergence operators are defined locally on each TTh as follows.

    Definition 2.1. The discrete weak gradient w:Vh[P0(T)]2×2 and weak divergence operator w:VhP0(T) are defined as follows,

    (wv,q)T=vb,qnT,q[P0(T)]2×2,(wv,φ)T=vbn,φT,φP0(T).

    For each edge eEh, let Qb be the L2 projection from [L2(e)]2 onto [P0(e)]2. Then, we define

    a(v,w):=TTh(νwv, ww)T+TThνhTQbv0vb,Qbw0wbT,b(v,q):=TTh(wv, q)T.

    Here, hT denotes the mesh size for the element T. Then, a standard WG algorithm (see [38]) is as follows.

    Algorithm 2.1. Standard weak Galerkin algorithm (SWG) A numerical approximation for (1.1)–(1.3) is to seek uh={u0,ub}Vh and phWh such that

    a(uh,v)b(v,ph)=(f,v0), v={v0,vb}Vh,b(uh,q)=0,    qWh.

    Algorithm 2.1 produces a saddle system, which can be challenging due to its indefiniteness, strong coupling between velocity and pressure, and large size. In some cases, linear solvers for this large system involving both velocity and pressure may not be effective. Instead, we use the divergence-free basis to decouple the velocity and pressure and solve a smaller system, which is symmetric positive definite.

    In this section, we introduce the divergence-free basis. First, we define the discrete divergence-free subspace Dh of Vh in the usual way (see [1,2,3]) as follows,

    Dh={vVh;b(v,q)=0,qWh}. (2.1)

    Following the techniques introduced in [3] and using the definition (2.1), we explicitly construct the basis functions as the following three types.

    Dh=span{Φ1,,Φ6NKΨ0,Υ1,,ΥNEΨt,Λ1,,ΛNVΨV}. (2.2)

    1) Type 1 (Ψ0): For each TiTh, i=1,,NK with NK being the number of elements, all the six linearly independent linear functions Φ6(i1)+1,Φ6(i1)+2,,Φ6(i1)+6 in Vh are discrete divergence-free since they are nonzero only in the interior of element Ti.

    2) Type 2 (Ψt): For each eiE0h, i=1,,NE with NE being the number of interior edges, let tei be its tangential vector and Ψei,1 and Ψei,2 be the two basis functions of Vh that are nonzero only on ei. Define Υi:=C1Ψei,1+C2Ψei,2 such that Υi|ei=tei. It is easy to verify that Υi is discrete divergence-free using the divergence theorem. Note that Υi is nonzero only on ei.

    3) Type 3 (ΨV): For each interior vertex PiVh, i=1,,NV with NV being the number of interior vertices, there are r elements sharing Pi which form a hull HPi as shown in Figure 1. Consequently, there are r interior edges ej (j=1,,r) incident with Pi. Let nej be a normal vector on ej, and we assume that the normal vectors nej j=1,,r are counterclockwise around the vertex Pi as shown in Figure 1. For each ej, let Ψej,1 and Ψej,2 be the two basis functions of Vh, which are nonzero only on ej. Define Θj=C1Ψej,1+C2Ψej,2Vh such that Θj|ej=nej and then define Λi=rj=11|ej|Θj, which is discrete divergence-free by the divergence theorem. The construction can be applied to triangular and polygonal grids, as shown in Figure 1.

    Figure 1.  Hull HPi for triangular grids and polygonal grids.

    The dimension of Vh is 6NK+2NE. Since we use a piecewise constant space Wh for the pressure, there are NK1 divergence-free constraints. Subtracting the number of divergence-free constraints from the total degrees of freedom (DoFs), (6NK+2NE)(NK1)=6NK+NE+NV (where we use the Euler's formula in 2D), we get the dimension of the discrete divergence-free subspace Dh. Note that the total number of the three types of divergence-free basis functions is exactly 6NK+NE+NV, indicating that we found all the basis functions that are supported locally. Specifically, the above basis functions correspond to the components of u0 and ub={ut,uV}. The basis functions for u0, i.e., {Ψ0}, are defined only on the interior of each element T, which is the same as the previous SWG element. The basis functions for ut, that is, {Ψt}, are defined only on each edge eE0h along the tangential direction, and the basis functions for uV, i.e., {ΨV}, are defined only on the edges incident with the vertex V.

    Using the divergence-free basis (2.2), the decoupled algorithm can be proposed to solely solve the velocity uh as follows; see [3] for more details.

    Algorithm 2.2. Divergence-free WG algorithm A discrete divergence free approximation for (1.1)–(1.3) is to find uh={u0,ub}Dh such that

    a(uh, v)=(f,v0),v={v0,vb}Dh.

    Although this algorithm decouples the unknown variables in u and p, it is essentially equivalent to the SWG Algorithm 2.1. Thus, the velocity error still depends on the pressure error (see Theorem 1 and Table 2). This may cause inaccuracy and instability when problems occur with a low viscosity and a pressure singularity. This computational challenge can be resolved using the pressure-robust enhancement, which will be discussed in the next section.

    We shall employ the velocity reconstruction operator to enhance Algorithm 2.2. The reconstruction operator Πhv:Dh˜DhH(div;Ω) is defined as

    eΠhvnds=evnds. (2.3)

    Let ˜Dh|T=RT0(T)H(div;Ω). As the fact that Ψt is aligning the tangential direction on each edge, we only need to compute the reconstruction operator corresponding to ΨV={Λ1ΛNV}. It gives

    Πhv={0, if v=v0Ψ0,0, if v=vbΨt,ΠhΛj, if v=vbΨV=span{Λi,i=1,,NV}.

    Here, it is easy to verify that in (2.3): ΠhΛi=rj=1signejϕRT0ej, where ϕRT0ej is the corresponding RT0 basis on the edge e. We associate a unit normal vector ne with eE0h, which is assumed to be oriented from T+ to T. If e is a boundary edge/face, then ne is the unit outward normal vector to Ω. For the outer normal n, if [n|T]ej=nej, we assign signej=1; if [n|T]ej=nej, we assign signej=1. Thus, by employing Πh, we propose the following pressure-robust scheme.

    Algorithm 2.3. Pressure-robust divergence-free WG algorithm A pressure-robust divergence-free approximation for (1.1)–(1.3) is to find uh={u0,ub}Dh satisfying

    a(uh,v)=(f,Πhv),v={v0,vb}Dh.

    As we can see from the discretization, the stiffness matrix is the same as Algorithm 2.2, but only the load vector changes. By this minor modification, the desired pressure-robustness can be achieved. The results will be demonstrated in Theorem 2 and validated in numerical experiments.

    Remark 2.1. For triangular, rectangular, tetrahedral, and cubic meshes, we can directly employ the associated RT0 or RT[0] basis functions to perform the velocity reconstruction. For polygonal / polyhedral meshes, the techniques in [7,8] can be used to build the operator Πhv.

    In Algorithms 2.2 and 2.3, we decouple the unknowns and only compute the velocity solution uh. In some cases, the pressure variable is also needed. In this section, we propose the following procedure that computes the pressure after obtaining the velocity uh.

    Algorithm 2.4. Pressure recovering algorithm The pressure can be obtained by solving the following equation: find phWh such that

    b(v,ph)=(v)a(uh,v), vVhDh.

    Here, (v)=(f,v0) for Algorithm 2.2 and (v)=(f,Πhv) for Algorithm 2.3. As vVhDh, let us assume ph=ph|T is already known, and we can choose v={v0=0,vb=ne} with eT and the value of p+h=ph on the adjacent element sharing the edge e is not computed. Then, the definition of b(,) implies b(v,ph)=(wv,ph)=Tvbne,phT=vbne,[[ph]]e=|e|(p+hph). Here, ne denotes the normal direction from the current element T to its adjacent element that shares the edge e. In the implementation, we can assume ph|T1=0 to start and compute all the values in ph|T as above sequentially and locally. There is no need to form the global matrix explicitly.

    In the above proposed algorithms, we can do further DoFs enhancement by eliminating the unknowns corresponding to u0 to obtain a smaller system. This elimination can be done locally when the global matrix is assembled via static condensation. To state the local elimination procedure, denote by Dh(T) the restriction of Dh on T, i.e.,

    Dh(T)={v={v0,vb}Dh,v(x)=0, for xT}.

    Algorithm 2.5. An approximation to the problem (1.1)–(1.3) is given by seeking uh={u0,ut,ub}Dh satisfying a global equation

    a(uh,v)=0, v={0,Ψt,Ψb}Dh,

    and a local system on each element TTh,

    a(uh,v)=(f,v0), v={Ψ0,0,0}Dh(T).

    Remark 2.2. The above algorithm consists of a local system solved on each element TTh to eliminate u0 and a global system for ub, and a global system has ub as its only unknowns that will reduce the number of unknowns of the WG system. The comparison of DoFs is shown in Figure 2.

    Figure 2.  Sparsity pattern for Algorithm 2.2/2.3 (left) and Algorithm 2.5 (right) for uniform mesh with h=1/16.

    In this section, we present the error analysis of Algorithm 2.3 to demonstrate its advantages. Denote by Q0 the L2 projection operator from [L2(T)]2 onto [P1(T)]2. Define Qhu={Q0u,Qbu}Vh and let Qhp be the local L2 projections onto P0(T). Furthermore, we define the following norm corresponding to {the} WG finite element methods:

    |||v|||:=(TTh(wv2T+h1TQbv0vb2T))1/2.

    The following optimal error estimates have been derived in [3,38].

    Theorem 3.1. (Non-pressure robust scheme) Let (u;p)[H10(Ω)H2(Ω)]2×(L20(Ω)H1(Ω)) be the solution of (1.1)–(1.3) and (uh;ph)Vh×Wh be the solutions of (1.1)–(1.3) and Algorithm 2.1 or Algorithms 2.2–2.4, respectively. Then, the following error estimate holds true,

    |||Qhuuh|||Ch(u2+1νp1),QhpphCh(νu2+p1). (3.1)

    Proof. The proofs can be found in [3].

    Theorem 3.2. (Pressure-robust scheme) Let (u;p)[H10(Ω)H2(Ω)]2×(L20(Ω)H1(Ω)) be the solution of (1.1)–(1.3) and (uh;ph)Vh×Wh be the solution of (1.1)–(1.3) and Algorithms 2.3 and 2.4, respectively. Then, the following error estimate holds true,

    |||Qhuuh|||Chu2,QhpphChνu2. (3.2)

    Proof. By estimating the inconsistent errors caused by changing the righthand load vector and following the techniques in [3], the theorem can be proved.

    Remark 3.1. Although the divergence-free scheme only needs to solve the velocity component, the velocity error may still depend on the pressure, which is a non-pressure-robust scheme as shown in Theorem 1. By modifying the load vector, we completely remove the pressure dependence in the error estimate to achieve the desired pressure robustness. Besides, the pressure-robust error analysis can be obtained similarly to the rigorous analysis in [7].

    In this section, we test several benchmark problems to report numerical performance and validate the convergence results shown in Theorems 1 and 2. In all numerical tests, triangular meshes have been used.

    Let Ω=(0,1)×(0,1) and the exact solution u and p be,

    u=(10x2y(x1)2(2y1)(y1)10xy2(2x1)(x1)(y1)2) and p=10(2x1)(2y1).

    Denote the errors e={(Q0uu0,Qbuub)} and ϵ=Qhpph. We first compare the computational cost corresponding to Algorithm 2.1, Algorithm 2.2/2.3, and Algorithm 2.5. Since the stiffness matrix corresponding to Algorithms 2.2 and 2.3 is identical, we only compute the DoFs for Algorithm 2.2. The profiles for DoFs are reported in Table 1. Here, we exclude the unknowns for ub for the Dirichlet boundary as computing the required DoFs.

    Table 1.  Example 4.1: Comparison of DoFs for different algorithms. Here, "DoFs" denotes the degrees of freedom and "nnz" denotes the number of nonzeros of the stiffness matrix.
    Algorithm 2.1 Algorithm 2.2/2.3 Algorithm 2.5
    N DoFsu DoFsp DoFs DoFs nnz DoFs nnz
    4 272 32 304 241 1861 49 360
    8 1120 128 1248 993 8805 225 1984
    16 4544 512 5056 4033 38, 245 961 9168
    32 18, 304 2048 20, 352 16, 257 159, 333 3969 39, 280
    64 73, 472 8192 81, 664 65, 281 650, 341 16, 129 162, 480
    128 294, 400 32, 768 327, 168 261, 633 2, 627, 685 65, 025 660, 784
    256 1, 178, 624 131, 072 1, 309, 696 1, 047, 553 10, 563, 685 261, 121 2, 665, 008

     | Show Table
    DownLoad: CSV

    In this table, we first observe that the required DoFs can be significantly reduced by employing the divergence-free basis. Since we only modify the assembly of the source term in Algorithm 2.3, the required DoFs in Algorithms 2.2 and 2.3 remain the same. As static condensation is employed (Algorithm 2.5), the DoFs of the global system can be further reduced. For example, when N=256, the size of the global system is reduced from 1 M to 0.2 M, while the density of the matrix increased from 1E-5 to 4E-5.

    Next, we will test the performance corresponding to non-pressure-robust scheme, Algorithm 2.2/Algorithm 2.4, and pressure-robust scheme, Algorithm 2.3/Algorithm 2.4, for a sequence of meshes and varying values in ν. In Table 2, we report the error profiles and the convergence results. We observed that:

    Table 2.  Example 4.1: Error profiles and convergence results.
    1/h e0 order e0 order ϵ order e0 order e0 order ϵ order
    Algorithm 2.2/Algorithm 2.4 Algorithm 2.3/Algorithm 2.4
    ν=1
    8 6.30E-2 5.23E-1 1.29E+0 8.27E-3 1.70E-1 2.71E-2
    16 1.72E-2 1.9 2.84E-1 0.9 6.31E-1 1.0 2.17E-3 1.9 8.74E-2 1.0 1.17E-2 1.2
    32 4.47E-3 1.9 1.47E-1 0.9 3.00E-1 1.1 5.50E-4 2.0 4.41E-2 1.0 5.32E-3 1.1
    64 1.13E-3 2.0 7.44E-2 1.0 1.44E-1 1.1 1.38E-4 2.0 2.21E-2 1.0 2.57E-3 1.0
    128 2.84E-4 2.0 3.74E-2 1.0 6.98E-2 1.0 3.46E-5 2.0 1.10E-2 1.0 1.27E-3 1.0
    ν=1E-2
    8 6.21E+0 5.10E+1 1.29E+0 8.27E-3 1.70E-1 2.71E-4
    16 1.70E+0 1.9 2.79E+1 0.9 6.31E-1 1.0 2.17E-3 1.9 8.74E-2 1.0 1.17E-4 1.2
    32 4.41E-1 1.9 1.45E+1 0.9 3.00E-1 1.1 5.50E-4 2.0 4.41E-2 1.0 5.32E-5 1.1
    64 1.12E-1 2.0 7.32E+0 1.0 1.44E-1 1.1 1.38E-4 2.0 2.21E-2 1.0 2.57E-5 1.0
    128 2.80E-2 2.0 3.68E+0 1.0 6.98E-2 1.0 3.46E-5 2.0 1.10E-2 1.0 1.27E-5 1.0
    ν=1E-4
    8 6.21E+2 5.10E+3 1.29E+0 8.27E-3 1.70E-1 2.71E-6
    16 1.70E+2 1.9 2.79E+3 0.9 6.31E-1 1.0 2.17E-3 1.9 8.74E-2 1.0 1.17E-6 1.2
    32 4.41E+1 1.9 1.45E+3 0.9 3.00E-1 1.1 5.50E-4 2.0 4.41E-2 1.0 5.32E-7 1.1
    64 1.12E+1 2.0 7.32E+2 1.0 1.44E-1 1.1 1.38E-4 2.0 2.21E-2 1.0 2.57E-7 1.0
    128 2.80E+0 2.0 3.68E+2 1.0 6.98E-2 1.0 3.46E-5 2.0 1.10E-2 1.0 1.27E-7 1.0
    ν=1E-6
    8 6.21E+4 5.10E+5 1.29E+0 8.27E-3 1.70E-1 2.71E-8
    16 1.70E+4 1.9 2.79E+5 0.9 6.31E-1 1.0 2.17E-3 1.9 8.74E-2 1.0 1.17E-8 1.2
    32 4.41E+3 1.9 1.45E+5 0.9 3.00E-1 1.1 5.50E-4 2.0 4.41E-2 1.0 5.32E-9 1.1
    64 1.12E+3 2.0 7.32E+4 1.0 1.44E-1 1.1 1.38E-4 2.0 2.21E-2 1.0 2.57E-9 1.0
    128 2.80E+2 2.0 3.68E+4 1.0 6.98E-2 1.0 3.46E-5 2.0 1.10E-2 1.0 1.27E-9 1.0
    ν=1E-8
    8 6.21E+6 5.10E+7 1.29E+0 8.27E-3 1.70E-1 2.71E-10
    16 1.70E+6 1.9 2.79E+7 0.9 6.31E-1 1.0 2.17E-3 1.9 8.74E-2 1.0 1.17E-10 1.2
    32 4.41E+5 1.9 1.45E+7 0.9 3.00E-1 1.1 5.50E-4 2.0 4.41E-2 1.0 5.32E-11 1.1
    64 1.12E+5 2.0 7.32E+6 1.0 1.44E-1 1.1 1.38E-4 2.0 2.21E-2 1.0 2.57E-11 1.0
    128 2.80E+4 2.0 3.68E+6 1.0 6.98E-2 1.0 3.46E-5 2.0 1.10E-2 1.0 1.27E-11 1.0

     | Show Table
    DownLoad: CSV

    ● All the error profiles produced by Algorithm 2.2/Algorithm 2.4 and Algorithm 2.3/Algorithm 2.4 result in the optimal convergence rate: the velocity error measured in H1-norm and pressure error measured in L2-norm are of order O(h); the velocity error measured in L2-norm is of order O(h2). The convergence rates stay the same for different viscosity values ν.

    ● The velocity errors produced by the non-pressure-robust scheme Algorithms 2.2–2.4 depend on the viscosity ν. When ν decreases, the velocity error measured in the norms H1- and L2- increases on the order of 1ν. In contrast, the pressure errors measured in L2-norm stay the same as ν varies. These observations agree with (3.1).

    ● The velocity errors produced by pressure-robust scheme Algorithms 2.3 and 2.4 do not depend on the viscosity ν. When ν decreases, the velocity error measured in the norms H1- and L2- remains the same. In contrast, the pressure error measured in L2-norm decreases at the order ν. These observations agree with (3.2).

    ● The above observations validate that, although the scheme can decouple the unknowns in velocity and pressure and solve them independently, the div-free finite element space is sometimes insufficient to ensure the accuracy of numerical solutions with satisfaction.

    In this test, we shall consider the nonhomogeneous Dirichlet boundary conditions. Let Ω=(0,1)×(0,1) and the exact solution is taken as

    u=(sin(πx)sin(πy)cos(πx)cos(πy)), and p=sinx.

    It is easy to see that u|Ω0. Thus, one needs to modify the method in order to deal with nonhomogeneous Dirichlet boundary conditions.

    Table 3 reports the error profiles and convergence results. We compare the performance of Algorithm 2.2/2.4 and Algorithm 2.3/2.4 on a sequence of meshes with different values of ν. To start, non-pressure-robust scheme Algorithm 2.2 and pressure-robust scheme Algorithm 2.3 have been employed to simulate the numerical velocity component. Then, when the velocity approximation is available, Algorithm 2.4 is used to recover the unknown pressure. As in the above test, though Algorithm 2.2 can decouple velocity/pressure and solely solve the unknown velocity, Algorithm 2.2 fails to produce reliable numerical solutions when the viscosity values are small. In contrast, the pressure-robust scheme Algorithm 2.3 is able to produce a viscosity-independent simulation for the velocity. As viscosity values vary, velocity errors (measured in the L2-norm and the H1-norm) remain the same. Furthermore, reducing viscosity values ν produces a more accurate numerical pressure, which gives a convergence rate for the pressure measured in the L2-norm as O(h). These numerical results confirm the theoretical conclusions in the above section.

    Table 3.  Example 4.2: Error profiles and convergence results.
    1/h e0 order e0 order ϵ order e0 order e0 order ϵ order
    Algorithm 2.2/Algorithm 2.4 Algorithm 2.3/Algorithm 2.4
    ν=1
    8 5.12E-2 5.83E-1 4.57E-1 2.81E-2 8.76E-1 7.62E-1
    16 1.28E-2 2.0 2.91E-1 1.0 2.36E-1 1.0 7.69E-3 1.9 4.54E-1 0.9 4.41E-1 0.8
    32 3.18E-3 2.0 1.46E-1 1.0 1.19E-1 1.0 2.00E-3 1.9 2.30E-1 1.0 2.37E-1 0.9
    64 7.95E-4 2.0 7.29E-2 1.0 5.95E-2 1.0 5.06E-4 2.0 1.15E-1 1.0 1.23E-1 0.9
    128 1.99E-4 2.0 3.65E-2 1.0 2.98E-2 1.0 1.27E-4 2.0 5.78E-2 1.0 6.29E-2 1.0
    ν=1E-2
    8 3.80E-1 2.87 1.99E-2 2.81E-2 8.76E-1 7.43E-3
    16 9.79E-2 2.0 1.47 1.0 1.01E-2 1.0 7.69E-3 1.9 4.54E-1 0.9 4.36E-3 0.8
    32 2.47E-2 2.0 7.44E-1 1.0 5.16E-3 1.0 2.00E-3 1.9 2.30E-1 1.0 2.36E-3 0.9
    64 6.20E-3 2.0 3.73E-1 1.0 2.63E-3 1.0 5.06E-4 2.0 1.15E-1 1.0 1.23E-3 0.9
    128 1.55E-3 2.0 1.87E-1 1.0 1.33E-3 1.0 1.27E-4 2.0 5.78E-2 1.0 6.28E-4 1.0
    ν=1E-4
    8 3.51E+1 2.91E+2 2.41E-2 2.81E-2 8.76E-1 1.43E-4
    16 9.06 2.0 1.51E+2 0.9 1.24E-2 1.0 7.69E-3 1.9 4.54E-1 0.9 2.40E-5 2.6
    32 2.29 2.0 7.65E+1 1.0 6.36E-3 1.0 2.00E-3 1.9 2.30E-1 1.0 1.29E-5 0.9
    64 5.74E-1 2.0 3.84E+1 1.0 3.24E-3 1.0 5.06E-4 2.0 1.15E-1 1.0 9.36E-6 0.5
    128 1.44E-1 2.0 1.92E+1 1.0 1.64E-3 1.0 1.27E-4 2.0 5.78E-2 1.0 5.53E-6 0.8
    ν=1E-6
    8 3.50E+3 2.92E+4 2.41E-2 2.81E-2 8.76E-1 2.08E-4
    16 9.05E+2 2.0 1.51E+4 0.9 1.24E-2 1.0 7.69E-3 1.9 4.54E-1 0.9 5.40E-5 1.9
    32 2.29E+2 2.0 7.65E+3 1.0 6.37E-3 1.0 2.00E-3 1.9 2.30E-1 1.0 1.37E-5 2.0
    64 5.74E+1 2.0 3.84E+3 1.0 3.25E-3 1.0 5.06E-4 2.0 1.15E-1 1.0 3.40E-6 2.0
    128 1.44E+1 2.0 1.92E+3 1.0 1.64E-3 1.0 1.27E-4 2.0 5.78E-2 1.0 8.26E-7 2.0
    ν=1E-8
    8 3.50E+5 2.92E+6 2.41E-2 2.81E-2 8.76E-1 2.09E-4
    16 9.05E+4 2.0 1.51E+6 0.9 1.24E-2 1.0 7.69E-3 1.9 4.54E-1 0.9 5.44E-5 1.9
    32 2.29E+4 2.0 7.65E+5 1.0 6.37E-3 1.0 2.00E-3 1.9 2.30E-1 1.0 1.39E-5 2.0
    64 5.74E+3 2.0 3.84E+5 1.0 3.25E-3 1.0 5.06E-4 2.0 1.15E-1 1.0 3.50E-6 2.0
    128 1.44E+3 2.0 1.92E+5 1.0 1.64E-3 1.0 1.27E-4 2.0 5.78E-2 1.0 8.80E-7 2.0

     | Show Table
    DownLoad: CSV

    In this test, let Ω=(0,1)×(0,1) and the exact solution u and p be,

    u=(3πsin(πx)3sin(πy)2cos(πy)3πsin(πx)2sin(πy)3cos(πx)) and p=sin(πx).

    In this test, the top (y=1), left (x=0), and bottom (y=0) boundaries are assumed to be the Dirichlet boundary conditions. The right boundary (x=1) employs the Neumann boundary condition.

    We perform convergence tests on a sequence of meshes with varying viscosity values ν. The error profiles for the velocity and pressure solutions are plotted in Figures 35, in which we vary the mesh size h. The numerical results are similar to the two examples above. Figure 3 demonstrates the velocity errors measured in the L2-norm. When we use the non-pressure-robust scheme Algorithm 2.2/2.4, the errors converge at the second order for different values of ν. However, the velocity error depends on ν and the pressure. As the pressure error does not dominate the velocity errors, the error increases as a factor 1ν. This means that Algorithm 2.2/2.4 fails to produce reliable numerical solutions for the velocity. In contrast, Algorithm 2.3/2.4 outperforms Algorithm 2.2/2.4 and produces a robust numerical simulation. The velocity errors show an invariant behavior for varying viscosity values ν.

    Figure 3.  Example 4.3: Convergence results for Algorithm 2.2/2.4 (Left) and Algorithm 2.3/2.4 (Right) for velocity errors measured in L2-norm.
    Figure 4.  Example 4.3: Convergence results for Algorithm 2.2/2.4 (Left) and Algorithm 2.3/2.4 (Right) for velocity errors measured in H1-norm.
    Figure 5.  Example 4.3: Convergence results for Algorithm 2.2/2.4 (Left) and Algorithm 2.3/2.4 (Right) for pressure errors measured in L2-norm.

    The H1-error of the velocity is plotted in Figure 4. We observe the same behavior and can draw the same conclusion as above.

    Lastly, the L2-error of the pressure is plotted in Figure 5. Algorithm 2.2/2.4 first produces a better pressure approximation before the dominance of pressure error hp1. However, as the viscosity variable ν decreases, the pressure term will dominate the error, i.e., hp1hνu2. Thus, pressure errors show a constant behavior on the same mesh with decreasing values of ν. On the other hand, Algorithm 2.3/2.4 outperforms Algorithm 2.2/2.4. For small ν, Algorithm 2.3/2.4 produces much better pressure solutions. All of the above tests validate our theoretical conclusions.

    In this paper, we enhanced the divergence-free WG finite element method proposed in [3] by modifying the load function via the velocity reconstruction operator. Our proposed algorithm results in a symmetric positive definite matrix, and the velocity error is pressure-robust. Moreover, we illustrated the procedure for recovering the pressure variables. Numerical experiments are presented to validate the theoretical results. As a future work plan, we will consider the development of an effective preconditioner, which may improve the efficiency further. In addition, the construction of a high-order (k>2) divergence-free basis will be given and analyzed in our future work.

    The authors declare they have not used Artificial Intelligence (AI) tools in the creation of this article.

    Jay Chu is partially supported by the Ministry of Science and Technology of Taiwan under the research grant MOST 111-2115-M-007-012. Xiaozhe Hu is partially supported by the National Science Foundation under the grant DMS-2208267. Lin Mu is partially supported by the National Science Foundation under the grant DMS-2309557.

    The authors declare there are no conflicts of interest.


    Acknowledgments



    We acknowledge colleagues, secretaries, and Ms. Bethany Pond for helpful manuscript preparation and editing.

    Conflict of interest



    Both of the authors declare that the research was conducted without any potential conflict of interest from any commercial or financial institution.

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