Abstract
We study a reduced Poisson–Nernst–Planck (PNP) system for a charged spherical solute immersed in a solvent with multiple ionic or molecular species that are electrostatically neutralized in the far field. Some of these species are assumed to be in equilibrium. The concentrations of such species are described by the Boltzmann distributions that are further linearized. Others are assumed to be reactive, meaning that their concentrations vanish when in contact with the charged solute. We present both semi-analytical solutions and numerical iterative solutions to the underlying reduced PNP system, and calculate the reaction rate for the reactive species. We give a rigorous analysis on the convergence of our simple iteration algorithm. Our numerical results show the strong dependence of the reaction rates of the reactive species on the magnitude of its far field concentration as well as on the ionic strength of all the chemical species. We also find non-monotonicity of electrostatic potential in certain parameter regimes. The results for the reactive system and those for the non-reactive system are compared to show the significant differences between the two cases. Our approach provides a means of solving a PNP system which in general does not have a closed-form solution even with a special geometrical symmetry. Our findings can also be used to test other numerical methods in large-scale computational modeling of electro-diffusion in biological systems.
Keywords: Electro-diffusion, Reaction rates, Ionic concentrations, Boltzmann distributions, The Debye–Hückel approximation, The Poisson–Nernst–Planck system, Semi-analytical solution, Iteration method
1. Introduction
Concentrations of ionic and molecular species are key quantities in the description of biomolecular processes at nanometer to submicron scales. For instance, the concentrations of ligands (substrates), receptors (enzymes), and ions regulate almost all biomolecular and cellular activities. Variations in such concentrations often result from molecular diffusion, reaction, and production or depletion. As the random motion arising from thermal fluctuations, molecular diffusion causes the spread of localized signals for intracellular and intercellular communications. Chemical reaction and enzymatic regulation are also associated with the diffusion, production, and depletion of molecular species. This way, molecular diffusion and enzyme reaction form a coupled system which is often associated with signal transduction, gene expression, and metabolism networking.
Biomolecular diffusion is often driven by an electric field. In such electro-diffusion, the electrostatics can strongly affect the diffusion which in turn affects the rate of association between molecules such as the binding of a ligand to a receptor; cf. e.g., Refs. [1,2]. The electric field in a charged biomolecular system is determined not only by target macromolecules but also by the concentrations of all the charged species, including diffusive ions and small charged molecules.
Mean-field approximations of diffusive molecules or ions are often given by the system of Poisson–Nernst–Planck (PNP) equations. Such a system describes properly the coupling of electrostatics and diffusion of charged chemical species. The PNP system is a combination of Nernst–Planck equations and Poisson equation. The Nernst–Planck equations describe the time evolution of concentrations of chemical species. They are of the form
where ci = ci(x, t) is the local concentration of the ith charged molecular or ionic species with charge qi at the spatial point x at time t, Di the diffusion constant, and β the inverse thermal energy. The Poisson equation, given by
relates the electrostatic potential ψ and the charge density ρ that consists of both fixed and mobile charges, the latter being a linear combination of all the concentrations ci. Here ε is the product of the dielectric coefficient and the vacuum permittivity ε0. (More details of these equations are given in the next section.)
In case of no chemical reaction, the steady-state Nernst–Planck equations lead to the Boltzmann distributions of concentrations in terms of the electrostatic potential [3]. The Poisson equation then becomes the Poisson–Boltzmann equation [4-10]. For reactive chemical species, the non-equilibrium charge distributions deviate from the Boltzmann distribution, and the Poisson equation is needed to determine the electrostatic field. In this case, the PNP system can then be used to calculate the reaction rate. Such calculations are important, as recent studies have shown that substrate concentrations affect the reaction rates, a fact that is ignored in the usual Debye–Hückel limiting law [3,11].
The PNP system can be hardly solved analytically, even for the steady-state system with a very simple geometry. The main difficulty arises from the nonlinear coupling of the electrostatic potential and concentrations of chemical species. Numerical methods for PNP systems have been developed for simple one-dimensional settings and complex three-dimensional models, and have been combined with the Brownian dynamics simulations; cf. Refs. [12-21].
In this work, we consider a reduced PNP system for diffusion of ionic or molecular species in a solution in an electric field induced by charged molecules. The modification from the full PNP system is made by assuming that the concentration of each non-reactive molecular species is given by the Boltzmann distribution. Such distributions are linearized, mimicking the Debye–Hückel approximation. The concentration fields to be determined are those of reactive species. We focus on a spherical, uniformly charged solute particle in a solvent with multiple molecular or ionic species, and only consider the steady-state of the system. We first derive semi-analytical solutions of the underlying, reduced PNP system. We then present a simple iteration method for numerically solving the system using our semi-analytical solution formula. The convergence of our numerical method is proved. We further calculate numerically the equilibrium concentrations, electrostatic potential, and the reaction rates of reactive species. We finally compare our result with that of the case of no reactive species. Our work provides a means of solving a PNP system which in general does not have a closed-form solution even with a special geometrical symmetry. Our findings can also be used to test other numerical methods in large-scale computational modeling of electro-diffusion in biological systems.
In Section 2, we describe our reduced PNP system. In Section 3, we derive the semi-analytical solution formula and present our numerical scheme for obtaining the solution. In Section 4, we use our formula and scheme to calculate the electrostatic potential, the molecular or ionic concentrations, and the reaction rates of reactive species. In Section 5, we compare our results with the case that all the chemical species are non-reactive. Finally, in Section 6, we draw conclusions. In Appendix A, we give details of our derivation of our semi-analytical solution formulas; in Appendix B, we prove the convergence of our numerical scheme.
2. Model description
We first describe our reduced Poisson–Nernst–Planck (PNP) system for a general case in which some charged solutes are immersed in a solvent. There are multiple, diffusive ionic or molecular species in the solvent. Some of them are reactive and some are not. We then describe our reduced PNP system for a uniformly charged spherical solute in a solvent with multiple ionic or molecular species.
2.1. The general case
Let Ω denote the entire region of an underlying solvation system. Let Ωm and Ωs denote the solute region and solvent region, respectively. Let also Γ denote the interface that separates Ωs and Ωm, cf. Fig. 2.1. We shall use the interface Γ as the dielectric boundary. Let εm and εs denote the dielectric constant of the solute region Ωm and that of the solvent region Ωs, respectively. We define
Fig. 2.1.

The entire region of a solvation system Ω is divided into the solute region Ωm and the solvent region Ωs by the dielectric boundary Γ.
We assume that the solutes are charged with a fixed charge density ρf = ρf(x) distributed over the solute region Ωm. We also assume that there are M ionic or molecular species in the solvent. We denote by ci(x) the local concentration of the ith such chemical species at a spatial point x in the solvent region Ωs. The mobile local charge density in the solvent region is given by
where qj = zje with zj the valence of jth species and e the elementary charge. We recall for any region D in the space that the characteristic function χD = χD(x) is defined by χD(x) = 1 if x ∈ D and χD(x) = 0 if x ∉ D. With the characteristic functions χΩm and χΩs, the total charge density ρ = ρ(x) of the entire system region is then given by
The full Poisson–Nernst–Planck (PNP) system that models the diffusive ionic or molecular species consists of the following equations:
| (2.1) |
| (2.2) |
together with some initial and boundary conditions. Here, ψ is the electrostatic potential. All the concentrations c1, … , cM and the potential ψ can depend on time t. The parameters D1, … , DM are diffusion constants. We shall only consider steady-state solutions to this PNP system. Therefore, we set the time-derivative terms to zero and assume that all the concentrations and the electrostatic potential are independent on time.
We assume that the boundary conditions for the entire system are given by
in the case that is the entire space, and by
in the case that Ω is not the entire space but rather has a nonempty boundary ∂Ω, where are given positive numbers that represent the bulk concentrations.
We assume that the first m species (1 ≤ m < M) are reactive and the others are non-reactive. These are defined through the boundary conditions for the concentrations on the interface Γ as follows:
| (2.3) |
| (2.4) |
where ∂/∂n denotes the normal derivative with the unit normal n pointing from the solute region Ωm to the solvent region Ωs, cf. Fig. 2.1. The condition (2.3) means that when an ion or molecule of the ith species hits the boundary Γ, it disappears due to chemical reaction. Notice that the flux of the ith species is defined by
Consequently, the diffusion equation and the no-flux boundary condition are given respectively by
which are exactly (2.1) and (2.4), respectively.
For the non-reactive species (m < i ≤ M), the steady-state diffusion equations, the boundary conditions, and the corresponding no-flux boundary conditions on Γ in fact lead to the Boltzmann distributions for any x ∈ Ωs and all i = m + 1, … ,M. This means that cm+1, … , cM are all in equilibrium. Therefore, the only concentrations that are unknown variables are those of reactive species c1, … , cm. Our steady-state PNP system becomes
| (2.5) |
We now assume the electrostatic neutrality in the far field of the solvent: . With this assumption, we obtain the small potential approximation
where
| (2.6) |
This can be viewed as a parameter of partial ionic strength. The Poisson equation (2.5) for the electrostatic potential ψ can now be approximated by
To summarize, our reduced PNP system is
| (2.7) |
| (2.8) |
| (2.9) |
| (2.10) |
| (2.11) |
2.2. The case of a spherical solute
We assume now that the solute region Ωm is a sphere centered at the origin with radius a, cf. Fig. 2.2, Thus, the solute region, the solvent region, and the solute–solvent interface are given respectively by
Fig. 2.2.

The geometry of a spherical solute.
We assume that the fixed charge density is a constant: ρf (x) = Q in Ωm. We also assume as before that only the first m species are reactive and the others are not. From (2.7)-(2.11), we have
| (2.12) |
| (2.13) |
| (2.14) |
| (2.15) |
| (2.16) |
We observe that Eq. (2.15) for the potential ψ is equivalent to the following equations and jump conditions [9]
| (2.17) |
| (2.18) |
| (2.19) |
where the jump [[u]] across Γ for any function u is defined by [[u]] = u∣Ωs – u∣Ωm on Γ.
3. Semi-analytical and numerical solutions
In this section, we solve semi-analytically and numerically the boundary-value problem (2.12)-(2.16).
3.1. Semi-analytical solutions
Our system (2.12)-(2.16) is radially symmetric. Hence all the concentrations c1, … , cM and the potential ψ are functions of r = ∣x∣. With a series of calculations presented in Appendix A, we obtain the following semi-analytical solution
| (3.1) |
| (3.2) |
where
| (3.3) |
and the integration constants are
| (3.4) |
| (3.5) |
| (3.6) |
Notice that all these integration constants depend on the function which in turn depends on all the unknown functions c1 = c1(r), … , cm = cm(r). In (3.1), ψ(r) is given as a functional of c1(r), … , cm(r) through that is defined in (3.3). In (3.2), c1(r), … , cm(r) are presented through the potential ψ(r).
3.2. Numerical solutions
We use the semi-analytical solution formulas (3.1)-(3.6) to find numerical solutions of c1, … , cm and ψ. To do so, we first construct initial concentrations (). We then use (3.1) with ci replaced by to compute ψ(1). Next, we use (3.2) with ψ replaced by ψ(1) to compute . We repeat this process until an error tolerance is reached. In practice, we choose a finite interval to replace [a, ∞).
Algorithm
- Step 1. Choose a number A ⪢ a and discretize the interval [a, A] with a uniform grid size Δr. Choose an error tolerance δ > 0. Construct an initial guess:
Set n = 0. Step 2. Calculate ψ(n) = ψ(n)(r) (a ≤ r ≤ A), using (3.1) (the part r > a) with replacing ci (1 ≤ i ≤ m) and A replacing ∞, respectively.
Step 3. Calculate for i = 1, … ,m using (3.2) with replacing ci (1 ≤ i ≤ m), ψ(n) replacing ψ, and A replacing ∞, respectively.
- Step 4. If
then stop. Otherwise set n := n + 1 and go to Step 2.
In all of our numerical calculations, we choose our parameters the same as or close to those in Ref. [3], mimicking some real systems. Our main parameters are:
| (3.7) |
where the temperature T = 300 K. Our tests indicate that the value A we choose is large enough so that the underlying problem on the infinite interval (a, ∞) is well approximated by that on the finite interval (a, A). Other parameters are Q, q1, , and κ. They will be specified later. As in Ref. [3], we introduce the parameter
Notice that the summation is taken over all the species, rather than those of non-reactive ones as in the definition of κ (cf. (2.6)). Clearly, when other parameters are given, the parameters I and κ determine each other. The units for the electrostatic potential ψ is kcal/mol e with e being the elementary charge.
We have performed a convergence test on our numerical algorithm. In this test, we choose our parameters as in (3.7) and
In Table 3.1, we show the L∞ error and order of convergence of our numerical scheme. The L∞ error is defined to be the ratio of the discrete maximum norm of the difference of our numerical solution and that of a reference solution which is obtained using the same numerical method but with a very fine mesh. The order of convergence is defined to be log2(eL∞(Δr)/eL∞(Δr/2)), where e(δr) and e(δr/2) are the L∞ error corresponding to the step size Δr and that to Δr/2, respectively. In Fig. 3.1, we show the log–log plot of the error for both the concentration c1 and the electrostatic potential ψ. From these, we find that our numerical algorithm converges with the order of convergence close to 1 for both the concentration c1 and the potential ψ.
Table 3.1.
The L∞ errors in the convergence test.
| Δr | L∞ error of c1 | Order | L∞error of ψ | Order |
|---|---|---|---|---|
| 1 | 28.3950 | - | 0.0070 | - |
| 1/2 | 20.9970 | 0.4355 | 0.0036 | 0.9768 |
| 1/4 | 11.9072 | 0.8183 | 0.0018 | 1.0011 |
| 1/8 | 6.0658 | 0.9731 | 0.0009 | 1.0251 |
| 1/16 | 2.9848 | 1.0231 | 0.0004 | 1.0513 |
| 1/32 | 1.4072 | 1.0848 | 0.0002 | 1.1024 |
| 1/64 | 0.6056 | 1.2164 | 0.0001 | 1.2241 |
| 1/128 | 0.2023 | 1.5820 | 0.0000 | 1.5859 |
Fig. 3.1.
The log–log plot of the error eL∞(c1) and eL∞(ψ) vs. 1/Δr. The slope of the solid line on left is 1.10 and that on right is 1.14.
We now give a convergence analysis for the general case. For convenience, let us denote c = (c1, … , cm) and write the solutions (3.1) and (3.2), in the interval (a, ∞), in the following operator forms, respectively:
| (3.8) |
| (3.9) |
This means that P[c] is the function of r > a given by (3.1) (the part for r > a), and Ti[ψ] is the function of r > a given by (3.2). With these notations, our algorithm is then as follows: Choose c(0) ∈ (L∞(a, ∞))m. Compute
| (3.10) |
The following lemma shows that P and T1, … , Tm define continuous operators from respective spaces; its proof is given in Appendix B.
Lemma 3.1
If c = (c1, … , cm) ∈ (L∞(a, ∞))m then P[c] ∈ L∞(a, ∞). Moreover, P : (L∞(a, ∞))m → L∞(a, ∞) is continuous.
If ψ ∈ L∞(a, ∞) then Ti[ψ] ∈ L∞(a, ∞) for all i = 1, … , m. Moreover, T[ψ] = (T1[ψ], … , Tm[ψ]) defines a continuous mapping T : L∞(a, ∞) → (L∞(a, ∞))m.
To state and prove our main convergence result, we need the following:
Lemma 3.2
Let and be such that . Let for .
(1) There exist exactly two distinct fixed points of f in , both being positive.
Let be the smaller fixed point of f. Then f (x) ≤ x* for any x ∈ [0, x*].
Proof
Let . Then and . Clearly, g’(x) has a unique zero , and g(x) attains its minimum at xm with the minimum value , since . Note that and g(x) → +∞ as x → +∞. Thus the continuous function g(x) has at least one zero in (0, xm) and another zero in (xm, +∞). These are in fact the only zeros, since g”(x) > 0 for all . These two zeros of g(x) are the two fixed points of f (x), both positive.
If 0 ≤ x ≤ x* then .
We define
| (3.11) |
| (3.12) |
| (3.13) |
| (3.14) |
Let be the smaller fixed point of as defined in Lemma 3.2.
Proposition 3.1
Assume that . Assume also that c(0) ∈ (L∞(a, ∞))m satisfies ∣∣c(0)∣∣∞ ≤ x*. Then the sequences and defined in (3.10) converge in L∞(a, ∞) and (L∞(a, ∞))m to the solution of (3.1) and (3.2), respectively.
The proof of this main convergence result is given in Appendix B. Here we make some remarks.
In our numerical calculations that are reported in the next section, we use parameters that are compatible with those used in Ref. [3]. For such parameters, the condition of convergence is much simplified.
Our convergence condition is only sufficient. Our extensive numerical tests suggest that our iteration algorithm converges if .
- If our condition of convergence is not satisfied, then our algorithm may not converge. For instance, using the parameters (3.7) and
we find that the sequence produced by our algorithm does not converge.
4. Numerical results of concentrations, potential, and reaction rates
We now report our results of numerical calculations. We use the parameters in (3.7) and
| (4.1) |
Several different values of the constant charge density Q are chosen for our calculations.
4.1. Concentrations and potential
Fig. 4.1 shows our numerical solution of the electrostatic potential ψ(r) and the concentration c1(r) with Q = 3/(4π) e Å−3 and Q = −3/(4π) e Å−3, respectively. The change of the sign of Q does not affect the concentration c1(r) but changes the sign of the electrostatic potential ψ(r). Notice that the potential is monotonic in these cases.
Fig. 4.1.
Numerical solution of the electrostatic potential and the concentration c1(r). Top: Q = 3/(4π) e Å−3. Bottom: Q = −3/(4π) e Å−3.
We now keep the same set of parameters except changing Q so that its magnitude is very small. Fig. 4.2 shows the numerical solution of the potential ψ(r) and concentration c1(r) with Q = 0.0025 e Å−3 and Q = −0.0025 e Å−3, respectively. We see clearly that the potential is no longer monotonic.
Fig. 4.2.
Numerical solution of the electrostatic potential and the concentration c1(r). The potential is non-monotone. Top: Q = 0.0025 e Å−3. Bottom: Q = −0.0025 e Å−3.
The non-monotonicity of potential can be seen from our semi-analytic solution formula (3.1) for the case of M = 3 (three ionic or molecular species) and m = 1 (one reactive species). If Q and q1 have the same sign, then there exists a range of Q values such that the potential is non-monotonic. In fact, let us assume for example that q1 < 0 and Q < 0. By (3.1) and (3.6) we have
| (4.2) |
Here for the case m = 1 we have . In general, we have for all r ≥ a. If this is so, then we have from (4.2) that ψ(a) > 0 if Q > 0 is small enough. On the other hand, we have from (3.1) and the continuity condition (2.19) that ψ’(a+) > 0. This means that the potential increases near a+. But ψ(+∞) = 0 by (2.16). Therefore, the potential is not monotonic.
4.2. Reaction rates
We define the reaction rate for the ith (1 ≤ i ≤ m) reactive species to be . By (3.2) and a straightforward calculation, we have .
We fix again the parameters as in (3.7) and (4.1), and set Q = 3/(4π) e Å−3. We plot in Fig. 4.3 the reaction rate vs. ionic strength for different values of the bulk concentration . We also plot the reaction rate R1 vs. the bulk concentration in Fig. 4.4 at different levels of ionic strength. It is clear from these plots that the reaction rate decreases as the ionic strength increases for each fixed bulk concentration . The rate also increases with increases for each fixed I.
Fig. 4.3.

Reaction rates R1 vs. the ionic strength I for different bulk concentrations .
Fig. 4.4.

Reaction rates R1 vs. bulk concentration for different values of ionic strength.
5. Comparison with the case of no reaction
We now consider the case that all the chemical species are non-reactive, and compare the related results with those presented in the previous section on reactive species. Non-reactive diffusive species are characterized by the non-reactive boundary condition. In this case, the concentration of each of the species satisfies the Boltzmann distribution. Therefore, the system reduces to partial differential equation for the electrostatic potential only, together with some side conditions. To make our comparison more reasonable, we linearize the concentrations for i = m + 1, … ,M, as before. The resulting equation and side conditions are
| (5.1) |
| (5.2) |
| (5.3) |
where κ is defined in (2.6). These should be compared with (2.17)-(2.19).
As before, we obtain exactly the same formula (3.1) with constants , , K2 given by (3.4)-(3.6) but the quantity should be replaced by
This and (3.1) can be used to numerically compute the potential.
We test the example in Section 4 with the parameters given in (3.7) and (4.1). Fig. 5.1 shows our numerical results for Q = −3/(4π) e Å−3. We find that for both of the reactive and non-reactive systems the potential ψ(r) is similar and also the concentration c1(r) is similar. Here for the non-reactive case the concentration c1(r) is defined by the Boltzmann distribution.
Fig. 5.1.
Comparison of the reactive and non-reactive systems with Q = −3/(4π) e Å−3.
If we change Q from −3/(4π) e Å−3 to 3/(4π) e Å−3, then the potential also changes sign, as seen in Figure Fig. 5.2. It is clear that the potential for the reactive case is different from that for the non-reactive case. Moreover, the concentration c1(r) is quite different for these two cases. For the non-reactive case the concentration is very large near the dielectric boundary r = a.
Fig. 5.2.
Comparison of the reactive and non-reactive systems with Q = 3/(4π) e Å−3.
Finally in Fig. 5.3 we plot our results for Q = 0.0025 e Å−3. We see the non-monotonic behavior of the potential for the reactive system, as predicted before, but the monotonic behavior of the non-reactive system.
Fig. 5.3.
Comparison of the reactive and non-reactive systems with Q = 0.0025 e Å−3.
6. Conclusions and discussions
We have studied a reduced PNP system for a spherical, uniformly charged solute immersed in a solvent. We have obtained a semi-analytical solution formula which is in the form of a system of integral equations. Our simple iteration scheme based on this formulation is shown to be convergent.
The widely used PNP system, even in its reduced form, is hard to solve analytically or numerically. Our work, though focused on the spherical geometry, has provided some solution method to such a system. Our analytical and numerical results can be used to test other methods for large-scale calculations. Our convergence analysis can also be possibly generalized to systems with a more complicated geometry.
We have numerically calculated equilibrium concentrations, electrostatic potential, and the reaction rate. Our numerical results agree with those reported in Ref. [3]. Moreover, we have discovered a new property: when the charge Q is very small in magnitude, the potential ψ can be non-monotonic. We have offered some explanation for this using our semi-analytical solution formula. We also confirmed numerically that such non-monotonicity does not exist in the case for non-reactive chemical species.
We emphasize that our detailed studies on a special case can be used to investigate other physical properties of charged solvation systems. These include the effect of substrate concentrations to reaction that is ignored in the usual Debye–Hückel limiting law [3,11], the effect of solvent excluded volume in a charged solvation system [8], and ionic distributions around charged solutes that has been studied by transformed Poisson–Boltzmann relations [22]. Our approach can be also used to study the dynamical PNP system [3].
Acknowledgements
B. Li was supported by the US National Science Foundation (NSF) through the grant DMS-0811259, by the NSF Center for Theoretical Biological Physics (CTBP) with the NSF grant PHY-0822283, and by the US Department of Energy through the grant DE-FG02-05ER25707. B. Lu was partially supported by the 100 Talents Program of the Chinese Academy of Sciences. Z. Wang and J.A. McCammaon were supported by NSF, NIH, HHMI, CTBP, NBCR, and Accelrys.
Appendix A
We present in this appendix details of the derivation of the semi-analytical solution formulas (3.1)-(3.6) to the system (2.12)-(2.16). We recall the following formulas for a smooth, radially symmetric function u = u(r) with r = ∣x∣ > 0 and
| (A.1) |
| (A.2) |
| (A.3) |
where denotes the position vector at a point with ∣x∣ = r.
Using (A.1), we obtain from (2.17) that
This leads to
where K1 and K2 are two constants. Since the spherical solute has a uniform (constant) charge density, the potential ψ should be continuous inside the spherical solute region. Thus ψ(0) < ∞ and hence K1 = 0. Therefore,
| (A.4) |
By our notation (cf. (3.3)) and (A.1), Eq. (2.18) becomes
| (A.5) |
It is easy to verify that the corresponding homogeneous equation (i.e., the equation with replaced by 0) has two linearly independent solutions eκr /r and e−κr /r. Therefore, using the method of variation of parameters, we obtain a particular solution to the inhomogeneous equation (A.5)
Hence the general solution to (A.5) is
| (A.6) |
where and are two integration constants. Notice that (3.1) is just the combination of (A.4) and (A.6).
By the boundary conditions (2.13) and (2.14), each concentration field ci = ci(r) (1 ≤ i ≤ m) is bounded on [a, ∞). Thus the function is also continuous and bounded on [a, ∞). Using (B.1), we find that the last term in (A.6) is bounded. Therefore, from the boundary condition ψ(∞) = 0 (cf. (2.16)) and the first and third terms in (A.6), we must have
This implies (3.4). By the solution formulas (A.4) and (A.6), and the jump conditions (2.19) and (A.2), we have
Solving these two equations for and K2, we obtain (3.5) and (3.6).
Now we solve the boundary-value problem of diffusion equation (2.12)-(2.14). Fix i with 1 ≤ i ≤ m. By (A.2), Eq. (2.12) becomes
| (A.7) |
Denoting
| (A.8) |
we have by (A.7) and (A.3) that . Solving this linear first-order ordinary differential equation, we obtain hi(r) = K3r−2, with K3 a constant. Therefore, this and (A.8) lead to
This is also a linear first-order ordinary differential equation for ci = ci(r), and can be solved. The result is
| (A.9) |
The boundary condition ci(a) = 0 implies K4 = 0. The boundary condition leads to . This and (A.9) lead to (3.2).
Appendix B
In this appendix, we prove Lemma 3.1 and Proposition 3.1. For convenience, we shall denote by the norm of L∞(a, ∞) or (L∞(a, ∞))m. We recall for any nonzero that
| (B.1) |
Proof of Lemma 3.1
-
Let c1, … , cm ∈ L∞(a, ∞). By our definition (3.8),
By (3.3), we have . It follows from (3.5) and (B.1), together with simple calculations, that(B.2)
For the last term in (B.2) we have
Now consider the sum of the first and third terms in (B.2). By (3.4) and (B.1), we have
Therefore, P[c1, … , cm] ∈ L∞(a, ∞).To prove the continuity of P : (L∞(a, ∞))m → L∞(a, ∞), we observe that P is in fact an affine operator. Therefore, similar calculations lead to
where μ > 0 is a constant independent of c and . Hence P is continuous. -
Let ψ ∈ L∞(a, ∞). Fix an index i with 1 ≤ i ≤ m. We have by our definition (3.9) and (3.2) that
Clearly,
Therefore Ti[ψ] ∈ L∞(a, ∞).To prove the continuity of Ti : L∞(a, ∞) → L∞(a, ∞), we need only to prove that each part of Ti is continuous. Let ϕ, ψ ∈ L∞(a, ∞). It follows from the mean-value theorem that
Similarly,
The upper limit r can be replaced by ∞ in these integrals. All these together imply that
where μ’ > 0 is a constant independent of ϕ and ψ. Therefore, each Ti : L∞(a, ∞) → L∞(a, ∞) is continuous.
Lemma B.1
If then for all k =1, 2, ….
Proof
By induction, it suffices to show that, for any c ∈ (L∞(a, ∞))m, ∥(T ○ P)[c]∥∞ ≤ x* if ∥c∥∞ ≤ x*. Let ψ = p[c]. The definition of P : (L∞(a, ∞))m → L∞(a, ∞) (cf. (3.8)) and the solution formula (3.1) imply that
where is defined in (3.3). By (B.1) we have
Similarly, we have
and
Combining all these and using (3.3), we obtain
| (B.4) |
Now the solution formula (3.2) and the definition of T : L∞(a, ∞) → (L∞(a, ∞))m (3.9) imply that
This and (B.4) lead to
The proof is complete.
Proof of Proposition 3.1
By (3.10) and Lemma 3.1, it suffices to prove that the sequence {c(k)} produced by (B.3) converges. For each j ≥ 1 we have by the mean-value theorem for operators that
where
| (B.5) |
with ξ(j) a convex combination of c(j) and c(j+1). Here and below D denotes the Fréchet derivative of the corresponding operators and denotes the space of all bounded linear operators from a Banach space X to another Banach space Y. The existence of the Fréchet derivative for the corresponding operator is shown automatically when estimates of the norm of such derivatives are given.
We shall prove below that the assumptions of the proposition imply that there exists a constant θ with 0 < θ < 1 such that θj ≤ θ for all j = 1, 2, …. Suppose so, we then have
Consequently,
Hence {c(k)} is a Cauchy sequence in (L∞(a, ∞))m and thus it converges in (L∞(a, ∞))m to some c(∞). By (3.10) and Lemma 3.1, {ψ(k)} then converges in L∞(a, ∞) to some ψ(∞). Now it follows from (3.10) that ψ(∞) = P[c(∞)] and c(∞) = T[ψ(∞)] as desired.
We now estimate the norm θj. Let c ∈ (L∞(a, ∞))m. By the Chain Rule for Fréchet derivatives, we have
| (B.6) |
Recall that
| (B.7) |
Let u = (u1, … , um) ∈ (L∞(a, ∞))m. Then . This is a function of r > a. Notice that P : (L∞(a, ∞))m → L∞(a, ∞) is an affine mapping. Denote by χE(r) the characteristic function of a set E, i.e., χE(r) = 1 if r ∈ E and χE(r) = 0 if r ∉ E. We then obtain from all (3.1), (3.3)-(3.5) and (B.1), and a series of calculations that
This and (B.7) lead to
| (B.8) |
Let now ψ = P[c] ∈ L∞(a, ∞). We estimate
| (B.9) |
Let f ∈ L∞(a, ∞). We have
Straight forward calculations using the definition of Ti : L∞(a, ∞) → L∞(a, ∞) for each i (cf. (3.9)) leads to
where in the last step we used the fact that for all r > a, which follows from the definition of Ti : L∞(a, ∞) → L∞(a, ∞) (cf. (3.9)) and (3.2). Consequently, we have by (B.9) that
This and (B.4), together with the fact that ψ = P[c], imply
| (B.10) |
Since ξj in (B.5) is a convex combination, we have by Lemma B.1 that
Therefore, combining (B.5), (B.6), (B.8) and (B.10), we conclude that
References
- [1].Radic Z, Quinn DM, McCammon JA, Taylor P. Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin. J. Biol. Chem. 1997;272:23265–23277. doi: 10.1074/jbc.272.37.23265. [DOI] [PubMed] [Google Scholar]
- [2].Sheinerman FB, Norel R, Honig B. Electrostatic aspects of protein–protein interactions. Curr. Opin. Struct. Biol. 2000;10:153–159. doi: 10.1016/s0959-440x(00)00065-8. [DOI] [PubMed] [Google Scholar]
- [3].Lu BZ, Zhou YC, Huber GA, Bond SD, Holst MJ, McCammon JA. Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J. Chem. Phys. 2007;127:135102. doi: 10.1063/1.2775933. [DOI] [PubMed] [Google Scholar]
- [4].Che J, Dzubiella J, Li B, McCammon JA. Electrostatic free energy and its variations in implicit solvent models. J. Phys. Chem. B. 2008;112:3058–3069. doi: 10.1021/jp7101012. [DOI] [PubMed] [Google Scholar]
- [5].Davis ME, McCammon JA. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 1990;90:509–521. [Google Scholar]
- [6].Fixman M. The Poisson–Boltzmann equation and its application to polyelecrolytes. J. Chem. Phys. 1979;70:4995–5005. [Google Scholar]
- [7].Grochowski P, Trylska J. Continuum molecular electrostatics, salt effects and counterion binding—A review of the Poisson–Boltzmann model and its modifications. Biopolymers. 2008;89:93–113. doi: 10.1002/bip.20877. [DOI] [PubMed] [Google Scholar]
- [8].Li B. Continuum electrostatics for ionic solutions with nonuniform ionic sizes. Nonlinearity. 2009;22:811–833. [Google Scholar]
- [9].Li B. Minimization of electrostatic free energy and the Poisson–Boltzmann equation for molecular solvation with implicit solvent. SIAM J. Math. Anal. 2009;40:2536–2566. [Google Scholar]
- [10].Sharp KA, Honig B. Calculating total electrostatic energies with the nonlinear Poisson–Boltzmann equation. J. Phys. Chem. 1990;94:7684–7692. [Google Scholar]
- [11].Lu BZ, McCammon JA. Kinetics of diffusion-controlled enzymatic reactions with charged substrates. 2009. preprint. [DOI] [PMC free article] [PubMed]
- [12].Eisenberg RS. Computing the field in proteins and channels. J. Membr. Biol. 1996;150:1–25. doi: 10.1007/s002329900026. [DOI] [PubMed] [Google Scholar]
- [13].Kurnikova MG, Coalson RD, Graf P, Nitzan A. A lattice relaxation algorithm for three-dimensional Poisson–Nernst–Planck theory with application to ion transport through the gramicidin A channel. Biophys. J. 1999;76:642–656. doi: 10.1016/S0006-3495(99)77232-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [14].Cardenas AE, Coalson RD, Kurnikova MG. Three-dimensional Poisson–Nernst–Planck theory studies: Influence of membrane electrostatics on gramicidin A channel conductance. Biophys. J. 2000;79:80–93. doi: 10.1016/S0006-3495(00)76275-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [15].Hollerbach U, Chen DP, Busath DD, Eisenberg R. Predicting function from structure using the Poisson–Nernst–Planck equations: Sodium current in the gramicidin A channel. Langmuir. 2000;16:5509–5514. [Google Scholar]
- [16].Furini S, Zerbetto F, Cavalcanti S. Application of the Poisson–Nernst–Planck theory with space-dependent diffusion coefficients to KcsA. Biophys. J. 2006;91:3162–3169. doi: 10.1529/biophysj.105.078741. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [17].Corry B, Kuyucak S, Chung SH. Tests of continuum theories as models of ion channels: II. Poisson–Nernst–Planck theory versus Brownian dynamics. Biophys. J. 2000;78:2364–2381. doi: 10.1016/S0006-3495(00)76781-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [18].Berneche S, Roux B. A microscopic view of ion conduction through the K+ channel. Proc. Natl. Acad. Sci. USA. 2003;100:8644–8648. doi: 10.1073/pnas.1431750100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [19].Noskov SY, Im W, Roux B. Ion permeation through the α-Hemolysin channel: Theoretical studies based on Brownian dynamics and Poisson–Nernst–Planck electrodiffusion theory. Biophys. J. 2004;87:2299–2309. doi: 10.1529/biophysj.104.044008. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [20].Roux B, Allen T, Berneche S, Im W. Theoretical and computational models of ion channels. Q. Rev. Biophys. 2004;37:15–103. doi: 10.1017/s0033583504003968. [DOI] [PubMed] [Google Scholar]
- [21].Lopreore CL, Bartol TM, Coggan JS, Keller DX, Sosinsky GE, Ellisman MH, Sejnowski TJ. Computational modeling of three-dimensional electrodiffusion in biological systems: Application to the node of ranvier. Biophys. J. 2008;95:2624–2635. doi: 10.1529/biophysj.108.132167. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [22].Qian H, Schellman JA. Transformed Poisson–Boltzmann relations and ionic distributions. J. Phys. Chem. B. 2000;104:11528–11540. [Google Scholar]






