Abstract
We consider a system of coupled reaction-diffusion equations that models the interaction between multiple types of chemical species, particularly the interaction between one messenger RNA and different types of non-coding microRNAs in biological cells. We construct various modeling systems with different levels of complexity for the reaction, nonlinear diffusion, and coupled reaction and diffusion of the RNA interactions, respectively, with the most complex one being the full coupled reaction-diffusion equations. The simplest system consists of ordinary differential equations (ODE) modeling the chemical reaction. We present a derivation of this system using the chemical master equation and the mean-field approximation, and prove the existence, uniqueness, and linear stability of equilibrium solution of the ODE system. Next, we consider a single, nonlinear diffusion equation for one species that results from the slow diffusion of the others. Using variational techniques, we prove the existence and uniqueness of solution to a boundary-value problem of this nonlinear diffusion equation. Finally, we consider the full system of reaction-diffusion equations, both steady-state and time-dependent. We use the monotone method to construct iteratively upper and lower solutions and show that their respective limits are solutions to the reaction-diffusion system. For the time-dependent system of reaction-diffusion equations, we obtain the existence and uniqueness of global solutions. We also obtain some asymptotic properties of such solutions.
Keywords: RNA, gene expression, reaction-diffusion systems, well-posedness, variational methods, monotone methods, maximum principle
1 Introduction
Let Ω be a bounded domain in ℝ3 with a smooth boundary ∂Ω. Let N ≥ 1 be an integer. Let Di (i = 1, …, N), D, βi (i = 1, …, N), β, and ki (i = 1, …, N) be positive numbers. Let αi (i = 1, …, N) and α be nonnegative functions on Ω × (0, ∞). We consider the following system of coupled reaction-diffusion equations:
| (1.1) |
| (1.2) |
together with the boundary and initial conditions
| (1.3) |
| (1.4) |
where ∂/∂n denotes the normal derivative along the exterior unit normal n at the boundary ∂Ω, and all ui0 (i = 1, …, N) and υ0 are nonnegative functions on Ω.
The reaction-diffusion system (1.1)–(1.4) is a biophysical model of the interaction between different types of Ribonucleic acid (RNA) molecules, a class of biological molecules that are crucial in the coding and decoding, regulation, and expression of genes [23]. Small, non-coding RNAs (sRNA) regulate developmental events such as cell growth and tissue differentiation through binding and reacting with messenger RNA (mRNA) in a cell. Different sRNA species may competitively bind to different mRNA targets to regulate genes [4, 6, 12, 13, 16, 21]. Recent experiments suggest that the concentration of mRNA and different sRNA in cells and across tissue is linked to the expression of a gene [22]. One of the main and long-term goals of our study of the reaction-diffusion system (1.1)–(1.4) is therefore to possibly provide some insight into how different RNA concentrations can contribute to turning genes “on” or “off” across various length scales, and eventually to the gene expression.
In Eqs. (1.1) and (1.2), the function ui = ui(x, t) for each i (1 ≤ i ≤ N) represents the local concentration of the ith sRNA species at x ∈ Ω and time t. We assume a total of N sRNA species. The function υ = υ(x, t) represents the local concentration of the mRNA species at x ∈ Ω and time t. For each i (1 ≤ i ≤ N), Di is the diffusion coefficient and βi is the self-degradation rate of the ith sRNA species. Similarly, D is the diffusion coefficient and β is the self-degradation rate of mRNA. For each i (1 ≤ i ≤ N), ki is the rate of reaction between the ith sRNA and mRNA. We neglect the interactions among different sRNA species as they can be effectively described through their diffusion and self-degradation coefficients. The reaction terms uiυ (i = 1, …, N) result from the mean-field approximation. The nonnegative functions αi = αi(x, t) (i = 1, …, N) and α = α(x, t) (x ∈ Ω, t > 0) are the production rates of the corresponding RNA species, and are termed transcription profiles. Notice that we set the linear size of the region Ω to be of tissue length to account for the RNA interaction across different cells [22].
The reaction-diffusion system model (1.1)–(1.4) was first proposed for the special case N = 1 and one space dimension in [14]; cf. also [12, 15, 19]. The full model with N(≥ 2) sRNA species was proposed in [7].
An interesting feature of the reaction-diffusion system (1.1)–(1.4), first discovered in [14], is that the increase in the diffusivity (within certain range) of an sRNA species sharpens the concentration profile of mRNA. Figure 1 depicts numerically computed steady-state solutions to the system (1.1)–(1.3) in one space dimension with N = 1, Ω = (0, 1), D = 0, a few selected values of D1, β1 = β = 0.01, k1 = 1, and
| (1.5) |
| (1.6) |
One can see that as the diffusion constant D1 of the sRNA increases, the profile of the steady-state concentration υ = υ(x) of the mRNA sharpens.
Figure 1.
Numerical solutions to the steady-state equations with the boundary conditions (1.1)–(1.3) in one space dimension with N = 1, Ω = (0, 1), D = 0, β1 = β = 0.01, k1 = 1, and α1 and α given in (1.5) and (1.6), respectively. The numerically computed, steady-state concentration of mRNA υ = υ(x) (0 < x < 1) sharpens as the the diffusion constant D1 of the sRNA increases from 0.00001 to 0.0005, 0.0001, and 0.001.
As one of a series of studies on the reaction-diffusion system modeling, analysis, and computation of the the RNA interactions, the present work focuses on: (1) the construction of various modeling systems with different levels of complexity for the reaction, nonlinear diffusion, and coupled reaction and diffusion, respectively, with the most complex one being the full reaction-diffusion system (1.1)–(1.4); and (2) the mathematical justification for each of the models, proving the well-posedness of the corresponding differential equations. To understand how the reaction terms (i.e., the product terms uiυ in (1.1) and (1.2)) come from, we shall first, however, present a brief derivation of the corresponding reaction system (i.e., no diffusion) for the case N = 1 using a chemical master equation and the mean-field approximation [19].
We shall consider our different modeling systems in four cases.
Case 1. We consider the following system of ordinary different equations (ODE) for the concentrations ui = ui(t) ≥ 0 (i = 1, …, N) and υ = υ(t) ≥ 0:
| (1.7) |
| (1.8) |
where all αi (i = 1, …, N) and α are nonnegative numbers. We shall prove the existence, uniqueness, and linear stability of the steady-state solution to this ODE system; cf. Theorem 3.1.
Case 2. We consider the situation where all the diffusion coefficients Di (i = 1, …, N) are much smaller than the diffusion coefficient D. That is, we consider the approximation Di = 0 (i = 1, …, N). Assume all α and αi (i = 1, …, N) are independent of time t. The steady-state solution of ui in Eq. (1.1) with Di = 0 leads to ui = αi/(βi+kiυ) (i = 1, …, N). These expressions, coupled with the υ-equation (1.2), imply that the steady-state solution υ ≥ 0 should satisfy the following nonlinear diffusion equation and boundary condition:
| (1.9) |
| (1.10) |
The single, nonlinear equation (1.9) is the Euler–Lagrange equation of some energy functional. We shall use the direct method in the calculus of variations to prove the existence and uniqueness of the nonnegative solution to the boundary-value problem (1.9) and (1.10); cf. Theorem 4.1.
Case 3. We consider the following steady-state system corresponding to (1.1)–(1.4) for the concentrations ui ≥ 0 (i = 1, …, N) and υ ≥ 0:
| (1.11) |
| (1.12) |
| (1.13) |
Here again we assume that α and αi (i = 1, …, N) are independent of time t. We shall use the monotone method [20] to prove the existence of a solution to this system of reaction-diffusion equations; cf. Theorem 5.1. The monotone method amounts to constructing sequences of upper and lower solutions, extracting convergent subsequences, and proving that the limits are desired solutions.
Case 4. This is the full reaction-diffusion system (1.1)–(1.4). We shall prove the existence and uniqueness of global solution to this system; cf. Theorem 6.1. To do so, we first consider local solutions, i.e., solutions defined on a finite time interval. Again, we use the monotone method to construct iteratively upper and lower solutions and show their limits are the desired solutions. Unlike in the case of steady-state solutions, we are not able to use high solution regularity, as that would require compatibility conditions. Rather, we use an integral representation of solution to our initial-boundary-value problem. We then use the Maximum Principle for systems of linear parabolic equations to obtain the existence and uniqueness of global solution. We also study some additional properties such as the asymptotic behavior of solutions to the full system.
While our underlying reaction-diffusion system has been proposed to model RNA interactions in molecular biology, its basic mathematical properties are similar to some of those reaction-diffusion systems modeling other physical and biological processes. Our preliminary analysis presented here therefore shares some common features in the study of reaction-diffusion systems; cf. e.g., [10, 17] and the references therein. Our continuing mathematical effort in understanding the reaction and diffusion of RNA is to analyze the qualitative properties of solutions to the corresponding equations, in particular, the asymptotic behavior of such solutions as certain parameters become very small or large.
The rest of this paper is organized as follows: In Section 2, we present a brief derivation of the reaction system (1.7) and (1.8) for the case N = 1 using a chemical master equation and the mean-field approximation. In Section 3, we consider the system of ODE (1.7) and (1.8) and prove the existence, uniqueness, and linear stability of steady-state solution. In Section 4, we prove the existence and uniqueness of the boundary-value problem of the single nonlinear diffusion equation (1.9) and (1.10) for the concentration υ of mRNA. In Section 5 we prove the existence of a steady-state solution to the system of reaction-diffusion equations (1.11)–(1.13). In Section 6, we prove the existence and uniqueness of global solution to the full system of time-dependent, reaction-diffusion equations (1.1)–(1.4). Finally, in Section 7, we prove some asymptotic properties of solutions to the full system of time-dependent reacation-diffusion equations.
2 Derivation of the Reaction System
We give a brief derivation of the reaction system (1.7) and (1.8), and make a remark on how the full reaction-diffusion system (1.1)–(1.4) is formulated.
For simplicity, we shall consider two chemical species: mRNA and one sRNA. Figure 2 describes sRNA-mediated gene silencing within the cell and depicts the different rates in which mRNA and sRNA populations may change at time t. In the figure, αs and αm describe the sRNA and mRNA production rates, βs and βm describe the sRNA and mRNA independent degradation rates, and γ describes the coupled degradation rate at time t. Notice in the rate diagram that the mRNA and sRNA binding process is irreversible. The numerical value of each of these rates can be determined via experimental data [15].
Figure 2.
Kinetic scheme of the interaction of sRNA and mRNA in a cell. Here, αs and αm represent the production rates of sRNA and mRNA, respectively; βs and βm represent the independent degradation rates of sRNA and mRNA, respectively; and γ represents the coupled degradation rate of sRNA and mRNA.
We denote by Mt and St the numbers of mRNA and sRNA, respectively, in a given cell at time t, and consider the two continuous-time processes (Mt)t≥0 and (St)t≥0. We assume that (Mt, St)t≥0 is a stationary continuous-time Markov chain with state space S with the following ordering:
We assume that the total numbers of mRNA and sRNA are finite, and hence the state space is finite. For any given state (m, s) ∈ S, we denote by Pm,s(t) the probability that the system is in this state, i.e., Pm,s(t) = P(Mt = m, St = s). For convenience, we extend S to include integer pairs (m, s) for m < 0 or s < 0 and set Pm,s(t) = 0 if m < 0 or s < 0. Note that
| (2.1) |
for any t ≥ 0. Note also that the averages 〈Mt〉, 〈St〉, and 〈MtSt〉 are defined by
| (2.2) |
The following master equation describes the reactions defined in Figure 2:
where a dot denotes the time derivative. Using this and (2.2), we obtain by a series of calculations that
| (2.3) |
where
By our convention that Pm,s(t) = 0 if m < 0 or s < 0, we have by the change of index m − 1 → m and (2.1) that
Similarly, by changing the index s − 1 → s, we have
Changing m + 1 → m, we obtain by (2.2) that
Changing s + 1 → s and noting ms = 0 when s = 0, we have
Finally, changing m + 1 → m and s + 1 → s, we obtain by (2.2) that
Inserting all Am, As, Bm, Bs and C into (2.3), we obtain
| (2.4) |
Similarly, we have
| (2.5) |
We now make the mean-field assumption: 〈MtSt〉 = 〈Mt〉 〈St〉. If we denote by υ(t) = 〈Mt〉 and u1(t) = 〈St〉, the spatially homogeneous concentrations of mRNA and sRNA, respectively, then we obtain (1.7) (N = 1) from (2.4) and (1.8) from (2.5) (N = 1), respectively, with α1 = αm, β1 = βm, k1 = γ, α = αs, and β = βs.
We remark that based on Fick’s law the spatial diffution of the underlying sRNA and mRNA molecules can be described by DiΔui (i = 1, …, N) and DΔu with all Di and D the diffusion constants, respectively [1, 11, 17]. Here we have neglected any possible and more complicated processes such as cross diffusion and anomalous diffusion. Combining these terms with the reaction system (1.7) and (1.8), we obtain the full reaction-diffusion system (1.1)–(1.4) as our mathematical model for the RNA interaction.
3 Reaction System: Steady-State Solution and Its Linear Stability
Theorem 3.1
Assume all βi, ki, and αi (i = 1, …, N), and β, k, and α are positive numbers. The system of ODE
| (3.1) |
| (3.2) |
has a unique equilibrium solution (u10, …, uN0, υ0) ∈ ℝN+1 with all ui0 > 0 (i = 1, …, N) and υ0 > 0. Moreover, it is linearly stable.
Proof
If (u1, …, uN, υ) ∈ ℝN+1 is an equilibrium solution to (3.1) and (3.2) with all ui > 0 (i = 1, …, N) and υ > 0, then should satisfy
| (3.3) |
and the solution should be given by
| (3.4) |
Thus the key here is to prove that there is a unique solution S > 0 to (3.3).
Define g : [0, ∞) → ℝ by
| (3.5) |
Clearly, g is smooth in [0, ∞), g(0) < 0, and g(+∞) = +∞. Thus F := {s ≥ 0 : g(s) ≥ 0} is nonempty, closed, and bounded below. Let s0 = min F. Then s0 > 0 and g(s0) = 0. Moreover, g′(s0) ≥ 0. By direct calculations, we have
Thus g′(s) > g′(s0) = 0 for s > s0. Hence g(s) > g(s0) = 0 for s > s0. Therefore s0 is the unique solution to g = 0 on [0, ∞).
Set now
| (3.6) |
| (3.7) |
Clearly, all ui0 > 0 (i = 1, …, N) and υi0 > 0. Note that , since g(s0) = 0. Thus (3.7) implies which together with (3.6) further imply βiui0 + kiui0υ0 = αi (i = 1, …, N). Therefore (u10, …, uN0, υ0) is an equilibrium solution to (3.1) and (3.2).
Assume both (u10, …, uN0, υ0) and (ū10, …, ūN0, ῡ0) are equilibrium solutions to (3.1) and (3.2) with all ui0 > 0 and ūi0 > 0 (i = 1, …, N), υ0 > 0 and ῡ0 > 0. Then, by (3.3) and (3.5), and satisfy g(S0) = 0 and g(S̅0) = 0, respectively. By the uniqueness of solution s0 of g = 0, we then have S̅0 = S0 = s0. It then follows from (3.6) and (3.7) that ui0 = ūi0 (i = 1, …, N) and υ0 = ῡ0. Therefore the equilibrium solution is unique.
The linearized system for (U1, …, UN, V) around the equilibrium solution (u10, …, uN0, υ0) is given by
Let w = (U1, …, UN, V)T, where the superscript T denotes the transpose. This system is then dw/dt = Mw, where
It is easy to see that M is strictly column diagonally dominant with negative diagonal entries. Gers̆gorin’s Theorem (with columns replacing rows) [8] then implies that the real part of any eigenvalue of M is negative. This leads to the desired linear stability.
4 A Single Nonlinear Diffusion Equation: Existence and Uniqueness of Solution
Theorem 4.1
Assume Ω is a bounded domain in ℝ3 with a Lipschitz-continuous boundary ∂Ω. Assume D, β, and all βi and ki (i = 1, …, N) are positive numbers. Assume αi ∈ L2(Ω) with αi ≥ 0 a.e. in Ω (i = 1, …, N) and α ∈ L2(Ω) with α ≥ 0 a.e. in Ω. Then there exists a unique weak solution υ ∈ H1(Ω) with υ ≥ 0 a.e. in Ω to the boundary-value problem
| (4.1) |
| (4.2) |
The same statement is true if the Neumann boundary condition (4.2) is replaced by the Dirichlet boundary condition υ = υ0 on ∂Ω for some υ0 ∈ H1(Ω) with υ0 ≥ 0 on ∂Ω.
Proof
We prove the case with the Neumann boundary condition (4.2) as the Dirichlet boundary condition can be treated similarly. We define J : H1(Ω) → ℝ ∪ {±∞} by
where ln s = −∞ for s ≤ 0. Define g(s) = s − ln(1 + s) for s ∈ ℝ. It is easy to see that g = +∞ on (−∞,−1], and g is strictly convex and attains its unique minimum at 0 with g(0) = 0 on (−1,∞). Thus, since the term in the summation in J is (αiβi/ki)g(kiu/βi) ≥ 0, there exist constants C1, C2 ∈ ℝ with C1 > 0 such that
| (4.3) |
Denote θ = infu∈H1(Ω) J[u]. Clearly, θ is finite. Standard arguments [2, 5, 9] with an energy-minimizing sequence, using Fatou’s lemma to treat the lower-order terms in J, lead to the existence of u ∈ H1(Ω) such that J[u] = θ.
Now, we prove that |u| is also a minimizer of J on H1(Ω). In fact, we prove more generally that if w ∈ H1(Ω) then J[|w|] ≤ J[w]. (If u = υ0 on ∂Ω, then |u| = |υ0| = υ0 on ∂Ω, since υ0 ≥ 0 on ∂Ω.) First, |w|2 = w2 and |∇|w|| = |∇w| a.e. in Ω. Since α is nonnegative in Ω, we also have −α|w| ≤ −αw a.e. in Ω. Consider h(s) = g(|s|) − g(s) with again g(s) = s − ln(1 + s). If s ≤ −1 then h(s) = −∞. For s ∈ (−1, 0), we have h(s) = −2s + ln(1 + s) − ln(1 − s) and h′(s) = 2s2/(1 − s2) > 0. Thus h(s) < h(0) = 0. If s ≥ 0 then h(s) = 0. Hence h(s) ≤ 0 for all s ∈ ℝ. Consequently, by the definition of J and the fact that all α ≥ 0 and αi ≥ 0 (i = 1, …, N) a.e. in Ω, we have J[|w|] ≤ J[w].
Denote now υ = |u|. Then υ is also a minimizer of J on H1(Ω) and υ ≥ 0 in Ω. Let η ∈ H1(Ω) ∩ L∞(Ω) and fix i (1 ≤ i ≤ N). It follows from the Mean-Value Theorem and Lebesgue Dominated Convergence Theorem that
Since υ minimizes J over H1(Ω), we have (d/dt)|t=0J[υ+tη] = 0 for all η ∈ H1(Ω)∩L∞(Ω). Standard calculations then imply that
Notice that 0 ≤ αiβi/(βi + kiυ) ≤ αi a.e. in Ω for all i = 1, …, N. Therefore, since H1(Ω) ∩ L∞(Ω) is dense in H1(Ω), we can replace η ∈ H1(Ω) ∩ L∞(Ω) by η ∈ H1(Ω). Consequently, the minimizer υ ∈ H1(Ω) is a weak solution to (4.1) and (4.2).
If υ̂ ∈ H1(Ω) is also a nonnegative weak solution to (4.1) and (4.2), then w = υ − υ̂ is a weak solution to DΔw−bw = 0 in Ω and ∂nw = 0 on ∂Ω, where is in H1(Ω) and b ≥ β > 0 in Ω. Therefore w = 0 a.e. in Ω. Hence the solution is unique.
We remark that the regularity of the solution υ to the boundary-value problem (4.1) and (4.2) depends on the smoothness of the domain Ω and that of the variable coefficients αi (i = 1, …, N) and the source function α. Since the solution υ is nonnegative and the nonlinear term of υ is bounded, the regularity of υ is in fact similar to that of the solution to a linear elliptic problem. For instance, if ∂Ω is of the class Ck and all α, αi ∈ Wk,p(Ω) (i = 1, …, N) for some nonnegative integer k and p ∈ [2, ∞), then υ ∈ Wk+2,p(Ω). If ∂Ω is of the class C2,γ and all α, αi ∈ C0,γ(Ω̅) (i = 1, …, N) for some γ ∈ (0, 1), then υ ∈ C2,γ (Ω̅).
5 Reaction-Diffusion System: Existence of Steady-State Solution
Theorem 5.1
Let Ω be a bounded domain in ℝ3. Assume all Di, D, βi, β, and ki (i = 1, …, N) are positive constants. Assume all αi and α (i = 1, …, N) are nonnegative functions on Ω.
- Assume the boundary ∂Ω of Ω is in the class C2,μ for some μ ∈ (0, 1). Assume also αi, α ∈ C0,μ (Ω̅) (i = 1, …, N). There exist u1, …, uN, υ ∈ C2,μ (Ω̅) with ui ≥ 0 (i = 1, …, N) and u ≥ 0 in Ω such that (u1, …, uN, υ) is a solution to the boundary-value problem
(5.1) (5.2) (5.3) Assume the boundary ∂Ω of Ω is in the class C2 and all αi, α ∈ L2(Ω) (i = 1, …, N). There exist u1, …, uN, υ ∈ H2(Ω) with ui ≥ 0 (i = 1, …, N) and u ≥ 0 in Ω such that (u1, …, uN, υ) is a solution to the system of boundary-value problems (5.1)–(5.3).
We remark that we do not know if the solution is unique. Our numerical calculations indicate that the solution may not be unique. If αi (i = 1, …, N) satisfy some additional assumptions, then we may have the solution uniqueness; see [18] (Theorem 6.2, Chapter 8).
Proof
(1) We divide our proof in five steps.
Step 1. Construction of upper solutions and lower solutions. We define , ῡ(0), , υ̲(0) (i = 1, …, N) to be constant functions such that:
| (5.4) |
It is clear that
| (5.5) |
| (5.6) |
| (5.7) |
| (5.8) |
| (5.9) |
| (5.10) |
Step 2. Iteration. Let
| (5.11) |
Define iteratively the functions , υ̲(k), , ῡ(k) (i = 1, …, N) for k = 1, 2, … by
| (5.12) |
| (5.13) |
| (5.14) |
| (5.15) |
| (5.16) |
| (5.17) |
We recall that, for any constants D̂ > 0 and ĉ > 0, and any q ∈ C0,μ(Ω̅), the standard theory of elliptic boundary-value problems guarantees the existence and uniqueness of solution w ∈ C2,μ(Ω̅) to the boundary-value problem [5]
Moreover, there exists a constant C > 0, independent of q, such that
| (5.18) |
It therefore follows from (5.4) and a simple induction argument that there are unique solutions to the above boundary-values problems (5.12)–(5.17), defining our functions , υ̲(k), , ῡ(k), i = 1, …, N and k = 1, 2, …, all in C2,μ(Ω̅).
Step 3. Comparison. We now prove for any k ≥ 1 that
| (5.19) |
| (5.20) |
It follows from (5.4), (5.5), (5.12) with k = 1, (5.11), (5.7), and (5.14) with k = 1 that
The Maximum Principle [5] implies then in Ω̅ (i = 1, …, N). Similarly, we have , ῡ(0) ≥ ῡ(1), and υ̲(0) ≤ υ̲(1) in Ω̅ for all i = 1, …, N.
By (5.4), (i = 1, …, N) and υ̲(0) ≥ 0. Next, by (5.12) with k = 1, (5.15) with k = 1, (5.11), and (5.4), we obtain
We also have by (5.14) and (5.17) with k = 1 that on ∂Ω (i = 1, …, N). The Maximum Principle then implies in Ω̅ for all i = 1, …, N. Similarly, we have ῡ(1) ≥ υ̲(1) in Ω̅. We thus have proved
Assume now k ≥ 2 and
| (5.21) |
| (5.22) |
We prove
| (5.23) |
| (5.24) |
By (5.12) with k − 1 replacing k, (5.12), (5.21), (5.22), and (5.11), we obtain
We also have by the boundary conditions (5.14) that on ∂Ω (i = 1, …, N). The Maximum Principle now implies in Ω̅ for all i = 1, …, N. Similarly, we have in Ω̅ (i = 1, …, N). By (5.16), (5.21), (5.22), and (5.11), we have
Since ∂nῡ(k−1) = ∂nῡ(k) on ∂Ω, we thus have ῡ(k−1) ≥ ῡ(k) in Ω̅. Similarly, υ̲(k−1) ≤ υ̲(k) in Ω̅.
By (5.12), (5.15), (5.21), (5.22), and (5.11), we have
These and the corresponding boundary conditions for and lead to in Ω̅ for all i = 1, …, N. By (5.13), (5.16), (5.21), (5.22), and (5.11), we have
This together with the fact that ∂nῡ(k−1) = ∂nυ̲(k−1) imply υ̲(k) ≤ ῡ(k) in Ω̅. We have proved (5.23) and (5.24). By induction, we have proved (5.19) and (5.20).
Step 4. Regularity and boundedness. From the above iteration (5.5)–(5.10), we obtain by (5.19) and (5.20) uniformly bounded sequences of nonnegative C2,μ(Ω̅)-functions , {ῡ(k)}, and {υ̲(k)}. By standard Hölder estimates for elliptic problems, we conclude that all the sequences (1 ≤ i ≤ N), (1 ≤ i ≤ N), {‖ῡ(k)‖C2,μ(Ω̅)}, and {‖υ̲(k)‖C2,μ(Ω̅)} are bounded.
Step 5. Convergence to solution. From Step 4, the sequences and (1 ≤ i ≤ N), {ῡ(k)}, and {υ̲(k)} are bounded in C2(Ω̅) and pointwise monotonic on Ω̅. Therefore, they converge pointwise to some functions ūi and u̲i (1 ≤ i ≤ N), ῡ, and υ̲ on Ω̅, respectively. By the Arzela–Ascoli Theorem, there exist C2(Ω̅)-convergent subsequences and (1 ≤ i ≤ N), , and , of and (1 ≤ i ≤ N), {υ̲(k)}, and {ῡ(k)}, respectively. Clearly, these subsequences converge in C2(Ω̅) to ūi (1 ≤ i ≤ N), u̲i (1 ≤ i ≤ N), ῡ, and υ̲, respectively. Note that each of the subsequences and (1 ≤ i ≤ N), {ῡ(kj−1)}, and {υ̲(kj−1)} also converges pointwise to its respective limit. Now replace k in (5.12)–(5.17) by kj and sending j → ∞, we conclude that (ū1, ⋯, ūN, υ̲) and (u̲1, ⋯, u̲N, ῡ) are C2(Ω̅)-solutions of the system (5.1)–(5.3).
(2) This part can be proved similarly. The sequences of functions and (1 ≤ i ≤ N), {ῡ(k)}, and {υ̲(k)} can be defined as weak solutions of the corresponding boundary-value problems. Moreover, By using the estimate ‖w‖H2(Ω) ≤ C‖q‖L2(Ω), replacing (5.18), we have that all the sequences are bounded in H2(Ω). The monotonicity and pointwise boundedness imply that these sequences converge, respectively, to some functions ūi and u̲i (1 ≤ i ≤ N), ῡ, and υ̲ on Ω̅, all being nonnegative. Instead of using the Arzela–Ascoli Theorem, we use the fact that H2(Ω) is a Hilbert space and use also Sobolev compact embedding theorem to extract the subsequences and (1 ≤ i ≤ N), , and that converge weakly in H2(Ω) and strongly in H1(Ω) to the pointwise limiting functions ūi and u̲i (1 ≤ i ≤ N), ῡ, and υ̲, respectively. Finally, we use the weak forms of the equations to pass to the limit. For instance, we have for any ϕ ∈ H1(Ω) and all j = 1, 2, … that
Sending j → ∞, we have by the H1(Ω)-convergence of and the pointwise convergence of and that
Therefore, (ū1, …, ūN, υ̲) and (u̲1, ⋯, u̲N, ῡ) are the weak (and nonnegative) solutions in H2(Ω) of the system (5.1)–(5.3).
6 Reaction-Diffusion System: Existence and Uniqueness of Global Solution to Time-Dependent Problem
Our goal in this section is to prove the existence and uniqueness of global solution for the reaction-diffusion system (1.1)–(1.4). We shall first prove the existence and uniqueness of local solution to this system. Our proof of the existence of a lcoal solution is similar to that of Theorem 5.1 on the existence of steady-state solution but involves the representation formula and regularity of solutions to linear parabolic equations. The uniqueness of a local solution is obtained by the Maximum Principle for systems of linear parabolic equations.
For any set Ω ⊆ ℝ3 and any T > 0, we denote ΩT = Ω × (0, T]. If Ω ⊆ ℝ3 is open, we also denote by the class of functions u : ΩT → ℝ of (x, t) that are continuously differentiable in t and twice continuously differentiable in x = (x1, x2, x3) on Ω.
Theorem 6.1
(Existence and uniqueness of local solution). Let Ω be a bounded domain in ℝ3 with a C2-boundary ∂Ω. Let Di, βi, and ki (i = 1, …, N), D and β, and T be all positive numbers. Let (i = 1, …, N) and be all nonnegative functions on . Assume ui0 ∈ C1(Ω̅) (i = 1, …, N) and υ0 ∈ C1(Ω̅) are all nonnegative functions on Ω̅. Then there exist unique (i = 1, …, N) and such that all ui ≥ 0 (i = 1, …, N) and υ ≥ 0 in and
| (6.1) |
| (6.2) |
| (6.3) |
| (6.4) |
Proof
We first prove the existence of solution in four steps.
Step 1. Construction of upper solutions and lower solutions. We choose the constant functions , ῡ(0), , and υ̲(0) (i = 1, …, N) on by
It is clear that
Step 2. Iteration. Let
| (6.5) |
Define iteratively the functions , υ̲(k), , and ῡ(k) (i = 1, …, N) on ΩT for k = 1, 2, … by
| (6.6) |
| (6.7) |
| (6.8) |
| (6.9) |
| (6.10) |
| (6.11) |
| (6.12) |
| (6.13) |
The theory for initial-boundary-value problems of linear parabolic equations (cf. Theorem 2 in Chapter 5 of [3], or Theorem 1.2 in Chapter 2 of [18]) guarantees the existence of solutions , υ̲(1), , and ῡ(1) (i = 1, …, N) for k = 1 that are all in and are all Hölder continuous in x uniformly in . Suppose , υ̲(k), , and ῡ(k) (i = 1, …, N) for k ≥ 1 exist, and are all in and Hölder continuous in x uniformly in . Then the theory for initial-boundary-value problems of linear parabolic equations then implies that the solutions , υ̲(k+1), , and ῡ(k+1) (i = 1, …, N) all exist, are in , and are Hölder continuous in x uniformly in . By induction, we have for all k = 1, 2, … the existence of the solutions , υ̲(k), , and ῡ(k) (i = 1, …, N) in that are Hölder continuous in x uniformly in .
In fact, there is a representation formula for our solutions. Suppose is Hölder continuous in x uniformly on and suppose g ∈ C1(Ω̅). Let satisfy
| (6.14) |
| (6.15) |
| (6.16) |
Then we can extend g to a C1-function on a neighborhood of Ω̅ as the boundary ∂Ω is of the class C2. Hence we have the following representation of the solution to the initial-boundary-value problem (6.14)–(6.16) (cf. Section 3 of Chapter 5 of [3] and Theorem 8.3.2 of [18]):
| (6.17) |
where
| (6.18) |
| (6.19) |
Here the infinite series converges and the function F(x, t) is bounded.
Step 3. Comparison. Notice by (6.5) that
By the Maximum Principle for parabolic equations [2, 3, 9, 18] and using arguments similar to those for the steady-state solutions (cf. Step 3 in the proof of Theorem 5.1 in Section 5), we then have from the iteration (6.6)–(6.13) in Step 2 that
| (6.20) |
| (6.21) |
Step 4. Convergence to solution. By the monotonicity (6.20) and (6.21), we have the pointwise limits
These limits are nonnegative bounded measurable functions. In particular,
Let us now fix i (1 ≤ i ≤ N) and set for each integer k ≥ 1
| (6.22) |
Note that each is Hölder continuous in x uniformly in . Moreover,
| (6.23) |
It follows from (6.6), (6.8), and (6.9) that
| (6.24) |
| (6.25) |
| (6.26) |
Therefore, by the representation (6.17) and (6.19) for the solution to (6.14)–(6.16) that are now replaced by (6.24)–(6.26), we have
where Γ is given in (6.18) with D replaced by Di.
Since the sequence is uniformly bounded in and converges (cf. (6.23)), the sequence is uniformly bounded in ∂Ω × (0, T] and converges. Further, the series in the expression of converges absolutely. Therefore, the sequence is also uniformly bounded on ∂Ω × (0, T] and converges. Let the limit be Ψi = Ψi(x, t). Taking the limit as k → ∞ and using the Lebesgue Dominated Convergence Theorem, we obtain by (6.23) that
| (6.27) |
| (6.28) |
where Γ is given in (6.18) with D replaced by Di.
Since ui0 ∈ C1(Ω̅), the first term in (6.27) is a function of (x. t) in C2(ΩT). Since qi is bounded, the second term in (6.27) is also a continuous function of (x, t) on . By (6.28), the function Ψi(x, t) is continuous on ∂Ω × [0, T]. Thus the third term in (6.27) and hence ūi = ūi(x, t) is a continuous function in . Similarly, υ̲ = υ̲(x, t) is a continuous function in . Therefore, qi = qi(x, t) as defined in (6.22) is continuous in . Repeat the same argument using (6.27) and (6.28), we have that ūi is in fact Hölder continuous in x uniformly in . Similarly, υ̲ is Hölder continuous in x uniformly in . Finally, qi is Hölder continuous in x uniformly in . Therefore, we have the interior regularity of all ūi (i = 1, …, N) and υ̲; cf. [3] (Theorem 2 in Section 5.3). Now (6.22), (6.27), and (6.28) imply that ūi, and υ̲, solve (6.1) with u and υ replaced by ūi and υ̲, respectively. The existence of solutions to other equations can be obtained similarly.
We now prove the uniqueness in three steps.
Step 1. We prove that solutions (ū1, …, ūN, υ̲) and (u̲1, …, u̲N, ῡ) obtained above satisfy u̲i = ūi (i = 1, …, N) and υ̲ = ῡ in .
In fact, setting wi = ūi − u̲i (i = 1, …, N) and w = ῡ − υ̲, we have
The uniqueness of solution to linear systems of parabolic equations then lead to wi = 0 (i = 1, …, N) and w = 0.
Step 2. We prove the following: If is any other solution to (6.1)–(6.4) such that (i = 1, …, N) and υ̲(0) ≤ υ* ≤ ῡ(0) in , then (i = 1, …, N) and υ̲ = υ* = ῡ in .
In fact, let us replace by and keep unchanged in the iteration in Step 2. Then, (k = 0, 1, …), and the sequence (k = 0, 1, …) remains unchanged and it converges to the solution (u̲1, …, u̲N, ῡ). Therefore, by the iteration we get (i = 1, …, N) and υ* ≤ ῡ in . A similar argument leads to (i = 1, …, N) and υ̲ ≤ υ* in . These, together with the result proved in Step 1, imply (i = 1, …, N) and υ̲ = υ* = ῡ in .
Step 3. If we have two nonnegative solutions defined on , then we can choose all (i = 1, …, N) and ῡ(0) (in the iteration in Step 2 of proving existence) large enough to bound from above these solutions in . Then, both of these solutions must be the same as those constructed by iterative upper and lower solutions. The uniqueness is therefore proved.
Theorem 6.2
(Existence and uniqueness of global solution). Let Ω be a bounded domain in ℝ3 with a C2-boundary ∂Ω. Let Di (i = 1, …, N), D, βi (i = 1, …, N), β, and ki (i = 1, …, N) be all positive numbers. Let αi ∈ C1(Ω̅ × [0, ∞)) (i = 1, …, N) and α ∈ C1(Ω̅ × [0, ∞)) be all nonnegative functions on Ω̅ × [0, ∞). Assume ui0 ∈ C1(Ω̅) (i = 1, …, N) and υ0 ∈ C1(Ω̅) are all nonnegative functions on Ω̅. Then there exists a unique nonnegative solution (u1, …, uN, υ) to the system (1.1)–(1.4) with all ui (i = 1, …, N) and υ being continuous on Ω̅ × [0, ∞) and continuously differentiable in t ∈ (0, ∞) and twice continuously differentiable in x ∈ Ω.
Proof
Let Tm = m (m = 1, 2, …). Then for each Tm, the system has a unique solution defined on . By the uniqueness of local solution, the solution corresponding to Tm and that to Tn are identical on [0, Tm] if m ≤ n. Therefore, on each finite interval of time, all the solutions are the same as long as they are defined on that interval. Hence we have the existence of a global solution. It is unique since the local solution is unique.
7 Reaction-Diffusion System: Asymptotic Behavior
We now assume that all αi (i = 1, …, N) and α are independent of time t and consider the initial-boundary-value problem of the full, time-dependent system of reaction-diffusion equations (1.1)–(1.4). Given the initial data ui0 (i = 1, …, N) and υ0, the system has a unique global solution ui = ui (x, t) (i = 1, …, N) and υ = υ(x, t) by Theorem 6.2. We ask if the limit of the solution as t → ∞ exists, and if so, if the limit is a steady-state solution.
We first state the following result and omit its proof as it is similar to that for the special case for two equations; cf. Corollary 8.3.1 in [18]:
Proposition 7.1
Let Ω, T, and Di (i = 1, …, N) be all the same as in Theorem 6.1. Let (i, j = 1, …, N) be such that ai,j ≥ 0 in ΩT if i ≠ j. Suppose (i = 1, …, N) satisfy
Then wi ≥ 0 in (i = 1, …, N).
The following theorem states indicates particularly that if the initial values are large constant functions then the global solutions to the time-dependent problem are monotonic in time t and the limits as t → ∞ are steady-state solutions.
Theorem 7.1
Let Ω be a bounded domain in ℝ3 with its boundary ∂Ω in the class C2,μ for some μ ∈ (0, 1). Let Di, βi, and ki (i = 1, …, N), and D and β be all the same as in Theorem 6.1. Let αi ∈ C1(Ω̅) (i = 1, …, N) and α ∈ C1(Ω̅) be all nonnegative on Ω̅. Let (Ū1, …, ŪN, V̲) be the nonnegative solution to the system (1.1)–(1.4) with the initial values (i = 1, …, N) and V̲ (·, 0) = υ̲(0) all being constant functions. Let (U̲1, …, U̲N, V̅) be the nonnegative solution to the system (1.1)–(1.4) with the initial values (i = 1, …, N) and V̅ (·, 0) = ῡ(0) all being constant functions. Assume , ῡ(0) ≥ ‖α‖L∞(Ω)/β, and (i = 1, …, N). Then the following hold true:
Ūi ≥ U̲i (i = 1, …, N) and V̅ ≥ V̲ in Ω̅ × [0, ∞).
Ūi (i = 1, …, N) and V̅ are monotonically nonincreasing in t and U̲i (i = 1, …, N) and V̲ are monotonically nondecreasing in t.
If is any solution to (5.1)–(5.3) such that (i = 1, …, N) and on Ω̅, then (i = 1, …, N) and on Ω̅.
Proof
(1) Let T > 0. Let Wi = Ūi − U̲i (i = 1, …, N) and W = V̅ − V̲. We then have
Therefore, we get by Proposition 7.1 that Wi ≥ 0 (i = 1, …, N) and W ≥ 0 in . Since T > 0 is arbitrary, we obtain the desired inequality on Ω × [0, ∞).
(2) Let T > 0 and δ > 0. Set W̅i(x, t) = Ūi(x, t) − Ūi(x, t + δ) (i = 1, …, N) and W̲(x, t) = V̲ (x, t + δ) − V̲ (x, t). Then
Again by Proposition 7.1 we get W̅i ≥ 0 (i = 1, …, N) and W̲ ≥ 0. Hence Ūi (i = 1, …, N) are monotonically nonincreasing in t and V̲ is monotonically nondecreasing in t. Similarly, U̲i (i = 1, …, N) are monotonically nondecreasing in t and V̅ is monotonically nonincreasing in t.
(3) By Part (1) we have Ūi,s ≥ U̲i,s (i = 1, …, N) and V̅s ≥ V̲s on Ω̅. The claim that (Ū1,s, …, ŪN,s, V̲s) and (U̲1,s, …, U̲N,s, V̅s) are solutions of the time-independent system (5.1)–(5.3) can be proved similarly as the proof of Theorem 10.4.3 in [18] and that of Theorem 3.6 in [20].
(4) This part can proved by the same argument in Step 2 in the proof of uniqueness of solution of Theorem 6.1.
Theorem 7.2
Let Ω, Di, D, βi, β, ki, αi, α, , ῡ(0), υ̲(0), Ūi, U̲i, V̅, and V̲ (i = 1, …, N) be all the same as in Theorem 7.1. Let ui0 ∈ C1(Ω̅) (i = 1, …, N) and υ0 ∈ C1(Ω̅) be such that and υ̲(0) ≤ υ0 ≤ ῡ(0) (i = 1, …, N) in Ω̅. Let (u1, …, uN, υ) be the unique nonnegative global solution to the time-dependent problem (1.1)–(1.4) with the initial data (u10, …, uN0, υ0). Then Ūi ≥ ui ≥ U̲i (i = 1, …, N) and V̅ ≥ υ ≥ V̲ in Ω̅ × [0, ∞).
Proof
This is similar to the proof of Part (1) of Theorem 7.1.
The following two corollaries relate the uniqueness of steady-state solution to the asymptotic behavior of solution to the time-dependent problem.
Corollary 7.1
With the assumption of Theorem 7.2, the following hold true:
That Ūi,s = U̲i,s (i = 1, …, N) and V̅s = V̲s in Ω̅ if and only if the steady-state solution (u1,s, …, uN,s) ∈ (C2(Ω̅))N+1 satisfying (i = 1, …, N) and υ̲(0) ≤ υs ≤ ῡ(0) in Ω̅ is unique.
If the steady-state solution (u1,s, …, uN,s) ∈ (C2(Ω̅))N+1 that satisfies (i = 1, …, N) and υ̲(0) ≤ υs ≤ ῡ(0) in Ω̅ is unique, then for any initial data (u10, …, uN0, υ0) ∈ (C1(Ω̅))N+1 with (i = 1, …, N) and υ̲(0) ≤ υ0 ≤ ῡ(0) in Ω̅, the corresponding nonnegative solution (u1, …, uN, υ) of the time-dependent problem (1.1)–(1.4) converges to (u1,s, …, uN,s, υs) as t → ∞.
If the nonnegative steady-state solution in (C2(Ω̅))N+1 is unique, then the nonnegative global solution to the time-dependent problem with any nonnegative initial data in (C1(Ω̅))N+1 converges to this steady-state solution as t → ∞.
Proof
(1) This follows immediately from Theorem 7.2.
(2) This follows from Theorem 7.1 and Theorem 7.2.
(3) Choose (i = 1, …, N) and ῡ(0) all large enough and apply Part (2).
Corollary 7.2
With the same assumption as in Corollary 7.1, if Ūi,s ≠ U̲i,s for some i with 1 ≤ i ≤ N or V̅s ≠ V̲s, then: (1) For any initial data (u10, …, uN0, υ0) ∈ (C1(Ω̅))N+1 with (i = 1, …, N) and V̅s ≤ υ0 ≤ ῡ(0) in Ω̅, the corresponding nonnegative global solution (u1, …, uN, υ) of the time-dependent problem (1.1)–(1.4) converges to (U̲1,s, …, U̲N,s, V̅s) as t → ∞; and (2) For any initial data (u10, …, uN0, υ0) ∈ (C1(Ω̅))N+1 with (i = 1, …, N) and υ̲(0) ≤ υ0 ≤ V̲s in Ω̅, the corresponding nonnegative global solution (u1, …, uN, υ) of the time-dependent problem (1.1)–(1.4) converges to (Ū1,s, …, ŪN,s, V̲s) as t → ∞.
Proof
This is similar to the proof of Theorem 7.1.
Acknowledgment
This work was supported by the San Diego Fellowship (M.E.H.) the US National Science Foundation (NSF) through grant DMS-0811259 (B.L.) and DMS-1319731 (B.L.), Center for Theoretical Biological Physics through NSF grant PHY-0822283 (B.L.), the National Institutes of Health (NIH) through grant R01GM096188 (B.L.), and Beijing Teachers Training Center for Higher Education (W.Y.). The authors thank Professor Herbert Levine for introducing to them the mean-field model for RNA interactions, and Professor Daomin Cao and Professor Yuan Lou for helpful discussions. They also thank the anonymous referee for many helpful suggestions.
Footnotes
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Contributor Information
Maryann E. Hohn, Email: maryann.hohn@uconn.edu.
Bo Li, Email: bli@math.ucsd.edu.
Weihua Yang, Email: whyang@bjut.edu.cn.
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