Abstract
The muscle contraction, operation of ATP synthase, maintaining the shape of a cell are believed to be secured by motor proteins, which can be modelled using the Brownian ratchet mechanism. We consider the randomly flashing ratchet model of a Brownian motor, where the particles can be in two states, only one of which is sensitive the applied spatially periodic potential (the mathematical setting is a pair of weakly coupled reaction-diffusion and Fokker–Planck equations). We prove that this mechanism indeed generates unidirectional transport by showing that the amount of mass in the wells of the potential decreases/increases from left to right. The direction of transport is unambiguously determined by the location of each minimum of the potential with respect to the so-called diffusive mean of its adjacent maxima. The transport can be generated not only by an asymmetric potential, but also by a symmetric potential and asymmetric transition rates, and as a consequence of the general result we derive explicit conditions when the latter happens. When the transitions are localized on narrow active sites in the protein conformation space, we find a more explicit characterization of the bulk transport direction, and infer that some common preconditions of the motor effect are redundant.
Similar content being viewed by others
References
Ait-Haddou R, Herzog W (2003) Brownian ratchet models of molecular motors. Cell Biochem Biophys 38:191–214
Amengual P, Allison A, Toral R, Abbott D (2004) Discrete-time ratchets, the Fokker-Planck equation and Parrondo’s paradox. Proc R Soc Lond Ser A Math Phys Eng Sci 460:2269–2284
Astumian RD (1997) Thermodynamics and kinetics of a Brownian motor. Science 276:917–922
Chipot M, Hastings S, Kinderlehrer D (2004) Transport in a molecular motor system. M2AN Math Model Numer Anal 38:1011–1034
Chipot M, Kinderlehrer D, Kowalczyk M (2003) A variational principle for molecular motors. Meccanica 38:505–518
Diestel J (1991) Uniform integrability: an introduction. School on measure theory and real analysis (Grado, 1991). Rend Istit Mat Univ Trieste 23:41–80
Friedman A, Hu B (2007) Uniform convergence for approximate traveling waves in linear reaction-hyperbolic systems. Indiana Univ Math J 56:2133–2158
Harmer G, Abbott D, Taylor P (2000) The paradox of Parrondo’s games. Proc R Soc Lond Ser A Math Phys Eng Sci 456:247–259
Hastings S, Kinderlehrer D, McLeod JB (2007/2008) Transport in multiple state systems. SIAM J Math Anal 39:1208–1230
Jordan R, Kinderlehrer D, Otto F (1998) The variational formation of the Fokker-Planck equation. SIAM J Math Anal 29:1–17
Jülicher F (1999) Force and motion generation of molecular motors: a generic description. In: Müller SC, Parisi J, Zimmermann W (eds) Transport and structure, their competitive roles in biophysics and chemistry, Lecture Notes in Physics, vol 532. Springer, New York, pp 46–74
Jülicher F, Ajdari A, Prost J (1997) Modeling molecular motors. Rev Modern Phys 69:1269–1281
Kinderlehrer D, Kowalczyk M (2002) Diffusion-mediated transport and the flashing ratchet. Arch Rat Mech Anal 161:149–179
Littman W (1963) Generalized subharmonic functions: Monotonic approximations and an improved maximum principle. Ann Scuola Norm Sup Pisa 17(3):207–222
Mennerat-Robilliard C (1999) Atomes froids dans des réseaux optiques - Quelques facettes surprenantes d’un système modèle. Thèse de Doctorat de l’Université Paris-VI, LKB/ENS - Université Paris-VI
Mirrahimi S, Souganidis PE (2013) A homogenization approach for the motion of motor proteins. Nonlinear Differ Equ Appl 20:129–147
Parrondo JMR, Blanco JM, Cao FJ, Brito R (1998) Efficiency of Brownian motors. Europhys Lett 43:248–254
Parrondo JMR, de Cisneros BJ (2002) Energetics of Brownian motors: a review. Appl Phys A 75:179–191
Paxton WF, Sundararajan S, Mallouk TE, Sen A (2006) Chemical locomotion. Angew Chem Int Ed 45:5420–5429
Perthame B, Souganidis PE (2009a) Asymmetric potentials and motor effect: a homogenization approach. Ann Inst Henri Poincaré Anal Non Linéaire 26:2055–2071
Perthame B, Souganidis PE (2009b) Asymmetric potentials and motor effect: a large deviation approach. Arch Rat Mech Anal 193:153–169
Perthame B, Souganidis PE (2011) A homogenization approach to flashing ratchets. Nonlinear Differ Equ Appl 18:45–58
Peskin CS, Ermentrout B, Oster G et al (1994) The correlation ratchet: a novel mechanism for generating directed motion by ATP hydrolysis. In: Mow VC (ed) Cell mechanics and cellular engineering. Springer, New York, pp 479–489
Prost J, Chauwin JF, Peliti L, Ajdari A (1994) Asymmetric pumping of particles. Phys Rev Lett 72:2652–2655
Reimann P, Hänggi P (2002) Introduction to the physics of Brownian motors. Appl Phys A 75:169–178
Spirin AS (2009) The ribosome as a conveying thermal ratchet machine. J Biol Chem 284(32):21103–21119
Vorotnikov D (2011) The flashing ratchet and unidirectional transport of matter. Discrete Contin Dyn Syst Ser B 16:963–971
Acknowledgments
The research was partially supported by CMUC and FCT (Portugal), through European program COMPETE/FEDER under the project PEst-C/MAT/UI0324/2011. The author thanks David Kinderlehrer who introduced him to ratchets, and Philippe Verkerk for a discussion on the topic. He also thanks the unknown referees for detailed comments which helped to significantly improve this article
Author information
Authors and Affiliations
Corresponding author
Appendices
Appendix A: Proof of Propositions 2.1 and 3.1
Let \(G(x,y)\) be Green’s function of the Sturm–Liouville operator
on \((A,B)\) with homogeneous Neumann boundary condition. Then \(U(x)=G(x,s)\) is a solution to (9) if an only if \(G(A,s)=G(B,s)\).
By the distributional maximum principle (Littman 1963, Theorem B), \(G(x,y)>0\). Observe that
Hence, the function \(G(x,A)\) is decreasing in \(x\), and \(G(x,B)\) is increasing. Thus, the function
is also (strictly) decreasing. At the ends of the segment, we have \(g(A)=G(A,A)-G(B,A)> 0\) and \(g(B)=G(A,B)-G(B,B) < 0\). Since \(g\) is a continuous function, there is unique \(s\in (A,B)\) such that \(G(A,s)=G(B,s)\). The first proposition is proven.
Now, let
We claim that
Since \(G\) is Green’s function,
and
and the inequality is strict at least at one point. In particular, \(g_1\) cannot be identically zero.
Assume that \(g_1(A)\le 0\). By the maximum principle, \(g_1\) cannot have non-positive minima within \((A,\frac{A+B}{2})\). But
so \(A\) must be a minimum point. Let \(g_2(x)=g_1(x)-g_1(A)\). Then \(g_2\) is non-negative, and
Thus,
Since \(g_2(A)=0\), by the mean value theorem,
for some \(c, A<c<x\le \frac{A+B}{2}\). The Gronwall lemma implies \(g_2\equiv 0\), so, by (42), \(g_1\equiv 0\), and we get a contradiction.
Hence,
We have observed above that \(g(B)<0\), so there is \(s\in (\frac{A+B}{2},B)\) such that \(g(s)=0\), and this number \(s\) is the \(\phi \)-diffusive mean.
Appendix B: Proof of Proposition 3.2
Without loss of generality, \([A,B]=[0,1]\). Denoting the solutions of (9) corresponding to \(\phi _n\) and \(s_n\) by \(U_n\), we infer that
The function \(U_n\) is positive and thus convex on \((0,s_n)\) and \((s_n,1)\). Hence, due to the boundary conditions, the derivative \((U_n)_x(x)\) is positive/negative when \(x< s_n\) / \(x >s_n\), and tends toward its supremum/infimum as \(x\) approaches \(s_n\) from the left/right, resp. Moreover, the maximum of \(U_n\) is achieved at \(s_n\), and the minima are reached at \(0\) and \(1\).
It is easy to see that
for large \(n\), and
Hence, (46) implies
whence
Without loss of generality, there exists a limit \(s^*\in [0,1]\) of the sequence \(\{s_n\}\). Assume that \(s^*\ne s_*\), or, more particularly, \(s_*>s^*\) (the opposite case may be examined in a similar way). This yields that the value of the integral \(\int _0^{s_n} \phi _n(x) \) tends to zero as \(n\rightarrow + \infty \). But integration of (9) implies that the left derivative \((U_n)^\prime _- (s_n)\) is equal to \(\int _0^{s_n} \phi _n(x) U_n(x)\,dx\). Due to (50), this integral goes to zero as \(n\rightarrow + \infty \). Using the information on the behaviour of \(U_n\) summarized after equality (46), we conclude that \(\Vert (U_n)_x\Vert _{C[0,s_n]}\rightarrow 0\). Due to (50), without loss of generality there exists a constant \(U_*\) such that
But
Hence,
uniformly on \([0,1]\).
Let us now test (9) with a smooth function \(h\) such that \(h(s_*)=0, h(s^*)=1, h_x(0)=0, h_x(1)=0\), obtaining
Passing to the limit, we find that the left-hand side goes to zero and the right-hand side goes to one, arriving at a contradiction.
Appendix C: Proof of Theorem 4.1
Consider the set of functions
Inverse induction shows that for any \(i=1,\dots , k\) and \(y\in B\) one has
Let us define a mapping \(\mathcal A \) on \(B\). For each \(y\in B\), we let \(\mathcal A (y)=Y\), where \(Y\) is the solution of the problem
To put it differently,
Then, the set \(B\) is invariant for the map \(\mathcal A \). In fact, let \(y\in B\). Then (56) implies
Further,
Finally, fix \(x_*\in [0,1-1/k]\). Then there is a number \(n\) such that \(x_*\in [x_n,x_{n+1})\). Set
We claim that
Indeed, integration of (22) gives
Thus, the function \(q_i\) is increasing on the segment \([0,a_i]\) and decreasing on \([a_i,1]\). Assume first \(x_*\le a_n\). Then, if \(i<n\), we have \(q_i(x_*)>q_i(x_*+1/k)\). Since \(y\in B\), we also have \(\widehat{(\nu y)}_i >\widehat{(\nu y)}_n= N_*\), and (59) holds true. If \(i>n\), we have \(q_i(x_*)<q_i(x_*+1/k)\) and \(\widehat{(\nu y)}_i < N_*\), and (59) again holds. If \(i=n\), (59) is trivial. Now, let \(x_*> a_n\). In this case, if \(i<n+1\), \(q_i(x_*)>q_i(x_*+1/k)\) and \(\widehat{(\nu y)}_i >\widehat{(\nu y)}_{n+1}= N_*\); if \(i>n+1, q_i(x_*)<q_i(x_*+1/k)\) and \(\widehat{(\nu y)}_i < N_*\); and if \(i=n+1\), (59) is again trivial.
Formulas (57), (59), (26) and (55) yield
so the invariance of \(B\) is confirmed.
Observe that \(\mathcal A \) is a compact linear operator in \(L_1(0,1)\). Indeed, let \(\mathbb B \) be the unit ball of the space \(L_1(0,1)\). Due to (57), its image \(\mathcal A (\mathbb B )\) is a bounded subset of the linear span of \(\{q_1,\dots ,q_k \}\), thus being a relatively compact subset of a finite-dimensional subspace of \(L_1(0,1)\).
Let us show that (25) may have at most one solution, so \(\mathcal A \) can have at most one fixed point in \(B\). If not, let \({\tilde{Q}}\) be the difference of two distinct solutions. Then
Moreover,
whence
From (22) we deduce
Therefore, the matrix \([\mathcal P _{ij}]=[\widehat{(\nu q_i)}_j ]\) is ergodic, i.e. it has positive entries, and the sum of the elements in every row is equal to one. By the Perron–Frobenius theorem, it has an eigenvector \([\xi _i]\) corresponding to the simple eigenvalue \(1\), so that \(\xi _j=\sum _{i=1}^k \xi _i \mathcal P _{ij}\), and all the components \(\xi _i\) are positive. On the other hand, by (64), \([\Xi _i]=[\widehat{(\nu \tilde{Q})}_i ] \) is another eigenvector of \([\mathcal P _{ij}]\) corresponding to the same eigenvalue. The sum of its components is zero due to (62), so it cannot be collinear with \([\xi _i]\) unless it is a zero vector. Since \(1\) is a simple eigenvalue, all \(\widehat{(\nu \tilde{Q})}_i\) are zeros, so \(\tilde{Q}\equiv 0\) by virtue of (63).
The set \(B\) is closed, convex and bounded in \(L_1(0,1)\). By Schauder’s fixed point principle, \(\mathcal A \) has a fixed point \(Q\) in \(B\), which is automatically a solution to (25). It remains to notice that \(Q\) is continuous as a linear combination of \(q_i\), so (27) holds for all \(0\le x\le 1-1/k\).
Appendix D: Proof of Lemma 4.1
Let us notice that
where \(u\) and \(v\) are the (unique) solutions to the following problems
and
Since \(S\) is the \(\nu /\varsigma \)-diffusive mean of \(0\) and \(1/k\), there exists a solution \(U_1\) to the problem
The solution \(u\) to (67) can be constructed in the following way:
Thus, \(u\) is \(1/k\)-periodic, i.e.
Set
Then it suffices to show that
Note that
By the maximum principle, if the minimum of \(d\) is non-positive, it is attained at \(0\) or \(x_k\). To ascertain that this cannot happen, we are going to prove that
Set
and let \(\theta \) be the solution of the Cauchy problem
Note that \(\theta \) is non-negative and \(1/k\)-periodic.
Integration of (68) gives
Therefore
From (79) we deduce
and
Using the distributional maximum principle (Littman 1963, Theorem B), we conclude that
so
Appendix E: Proof of Lemma 5.1
It suffices to prove that the set
is dense in \(C[0,1]\).
Let \(h\in C^2[0,1]\) be an arbitrary function which is locally constant near the zeros of \(b\). These functions constitute a dense subset \(O_1\) of \(C[0,1]\). Let
Clearly, \(\varphi \) is equal to a constant \(c^-_i\) (resp. \(c^+_i\)) in a left (resp. right) neighbourhood of the point \(x_i\). But
so \(c^-_i=c^+_i=h(x_i)\). Thus, \(\varphi \) is \(C^2\)-smooth and \(\varphi _x(0)=\varphi _x(1)=0\). By virtue of (86), \(O_1\) is contained in \(O\).
Appendix F: Proof of Lemma 5.2
The solution \(r\) to (30) can be written explicitly:
Note that it is unique in \(L_1(0,1)\). Indeed, if \(r_1\) is another solution, then \(\omega =r-r_1\) satisfies the conditions of Lemma 5.1.
We need to show that \(r\rightarrow \sum \limits _{i=1}^k\widehat{R}_i\delta _{a_i}\) weakly-\(*\), uniformly with respect to \(R\in \mathcal R \). It suffices to prove that, for each \(i, r\rightarrow \widehat{R}_i\delta _{a_i}\) weakly-\(*\) on the interval \((x_i,x_{i+1})\), uniformly in \(R\in \mathcal R \). We restrict ourselves to the case \(i=1\), and the others are analogous.
We calculate, integrating by parts,
Let us show that for every \(x_*\in (0,a)\)
uniformly in \(R\in \mathcal R \). Indeed, let \(s_\kappa <x_*\) be such that
Observe that \(s_\kappa \rightarrow 0\) as \(\kappa \rightarrow +\infty \). We have
as \(\kappa \rightarrow +\infty \).
Due to (90), for any \(f_0\in C[0,1/k]\),
uniformly in \(R\in \mathcal R \).
Similarly, for all \(x^*\in (a,1/k)\) and \(f_0\in C[0,1/k]\),
uniformly in \(R\in \mathcal R \).
Fix \(\varepsilon >0\) and \(f\in C[0,1/k]\). Let \(x_*\) and \(x^*\) be so close to \(a\) that \(|f(x)-f(a)|\le \varepsilon /2\) provided \(x_*\le x \le x^*\). Then
Due to (93) and (94) with \(f_0=f-f(a)\),
for sufficiently large \(\kappa \). Thus,
Appendix G: Proof of Lemma 5.3
Let \(r_{\sigma ,\kappa }\) be the solution of the system
Then, by Lemma 5.2,
uniformly in \(\sigma \). Thus, it suffices to prove that for every \(\kappa \) there is \(\epsilon _\kappa >0\) such that
This would follow from the claim that for every \(\kappa \) there is \(\epsilon _\kappa >0\) so that for \(\sigma \le \epsilon _\kappa \) we have \(d(w_{\sigma ,\kappa }, r_{\sigma ,\kappa }) < 1/\kappa \). If it is not true, then for some \(\kappa \) there exists a sequence \(\sigma _n\rightarrow 0\) such that
Since \(w_{\sigma _n,\kappa }\) and \(r_{\sigma _n,\kappa }\) are solutions of the problems (32) and (98), we have
for any \(\varphi \in C^2[0,1], \varphi _x(0)=\varphi _x(1)=0\). Since the sequences \(w_{\sigma _n,\kappa }\) and \(r_{\sigma _n,\kappa }\) lie in the space of probability measures, which is weakly-* compact, without loss of generality there exist their weak-* limits \(w_\kappa \) and \(r_\kappa \). Clearly,
On the other hand, taking the difference of (100) and (101), and passing to the limit, we find \(\langle w_{\kappa }-r_{\kappa },\varphi +\kappa b\varphi _x\rangle =0,\) so \(w_{\kappa }=r_{\kappa }\) by Lemma 5.1, and we arrive at a contradiction.
Appendix H: Proof of Lemma 5.4
Multiplying the second equation in (16) by \(P\) and integrating, we find
whence
Hence,
The pair \((w_{\sigma ,\kappa }, R_{\sigma ,\kappa })=(\eta p,\nu P)\) satisfies (32). Due to (105), the set \(\mathcal R =\{\nu P\,|\, \sigma >0,\kappa >0\}\) is uniformly bounded and thus uniformly integrable. By Lemma 5.3, for every \(\kappa \) there exists \(\epsilon _\kappa >0\) such that
Assume that (34) is not true, i.e. there exist \(\delta >0\) and sequences \(\kappa _n\rightarrow \infty \) and \(\sigma _n\le \epsilon _{\kappa _n}\) such that for the corresponding solutions \((p_n, P_n)=(p_{\sigma _n,\kappa _n},P_{\sigma _n,\kappa _n})\) to (16) we have \(\Vert P_{n}-Q\Vert _{C[0,1]}>\delta \). Since the embedding \(W_2^1(0,1)\subset C[0,1]\) is compact, without loss of generality we may assume that \(P_n\) converges to some limit \(P_0\) in \(C[0,1]\). Obviously,
Passing to the limit in the second, forth and the last equations in (16)—the combination of the first two is understood in the weak sense (8)—and remembering (106), we find
By Theorem 4.1, \(P_0\) coincides with \(Q\), which contradicts (107).
From (106) we deduce
Due to (34) and \(1/k\)-periodicity of \(\eta \), (108) implies that
weakly-* as \(\kappa \rightarrow +\infty ,\ \sigma \le \epsilon _\kappa \). Taking test functions which are equal to \(1\) in one of the wells and are zero at the minima of the potential located outside of that well, we derive (35) from (109).
Rights and permissions
About this article
Cite this article
Vorotnikov, D. Analytical aspects of the Brownian motor effect in randomly flashing ratchets. J. Math. Biol. 68, 1677–1705 (2014). https://doi.org/10.1007/s00285-013-0684-4
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00285-013-0684-4
Keywords
- Flashing ratchet
- Motor protein
- Fokker–Planck equation
- Stationary solution
- Diffusive mean
- Transport
- Conformation
- Active site