Past exam of the soft condensed matter course of the University of Cambridge / 2022 / Section B / 5

The gap is not a fixed mechanical separation. Thermal fluctuations of the wall compete with drift towards the microtubule under the opposing force. A monomer can be incorporated only after the gap reaches its length. The Smoluchowski equation describes this overdamped drift and diffusion of gap probability density.

For gap potential energy $U(x)=Fx$, the equation and its probability current areThe drift mobility is $D\beta$, the overdamped consequence of the fluctuation-dissipation relation for a Langevin particle. Equivalently, this coefficient is fixed by requiring the zero-current solution to be the Boltzmann distribution $p\propto e^{-\beta U}$. Solve this equation with the appropriate exclusion, incorporation and probability-normalization conditions. The steady flux through the incorporation threshold gives the addition rate $j_0$; the elongation speed is $v=\delta j_0$.

There is a regime distinction in the printed problem. The absorbing boundary imposed in part (c) means instantaneous incorporation once a gap opens, and leads to the diffusion-limited Brownian ratchet with constant load. A genuinely reaction-limited polymerization Brownian ratchet instead assumes fast gap equilibration followed by a finite chemical addition rate, giving an exponential gating factor multiplying that chemical rate. The equations requested in the subsequent parts specify the former model, which is the one solved here.

In the steady state, conservation of probability requires $J_x=0$, so $J=j_0$ is constant. The sign is positive because increasing gap reaches the incorporation boundary, whereas the deterministic drift points towards smaller gap. ThusAn integrating factor $e^{\beta Fx}$ givesSubstitution makes the check particularly transparent:so ${\partial }_{t}p=-J_x=0$. The constant offset is necessary for nonzero transport; a pure Boltzmann distribution would have $J=0$ and could not describe a steady succession of addition events. The $F=0$ limit is taken after applying the boundary conditions, avoiding the apparent singularity of the displayed parametrization.

In this polymerization Brownian ratchet model, a gap of width $\delta$ immediately accommodates one monomer. That event advances the tip by $\delta$ and resets the gap to zero. The threshold is therefore an absorbing boundary condition for a diffusion,All waiting-time probability lies within $0\le x<\delta$, so the steady occupation probability density satisfiesThere is a reinjection flux $j_0$ at $x=0$ equal to the absorption flux at $x=\delta$. The nonpenetration constraint at zero is a reflecting boundary condition for a diffusion during each individual waiting episode. For the stationary reset process it must not be confused with setting the net current $J(0^{+})$ to zero: the source at reset supplies $J(0^{+})=j_0$. This is how a normalized steady density can coexist with a nonzero exit flux.

Put $k=\beta F$ and $q=k\delta$. The absorbing boundary condition for a diffusion gives $A=j_0{e}^q/(Dk)$, henceThis is nonnegative throughout the allowed interval. Normalizing the probability density givesThereforeEquivalently the normalized density isThe denominator is positive for $q>0$, since $e^q>1+q$. The dimensions are consistent: $j_0$ has units of inverse time, $A$ and $p$ of inverse length, and $q$ is dimensionless.

For a small opposing force, the relevant parameter is $q=\beta F\delta \ll 1$. A Taylor series givessoIn particular the zero-force rate is finite, despite the numerator and denominator of the original expression both vanishing.

For $q\gg 1$, the exponential dominates the denominator:Opening a monomer-sized gap is exponentially rare at high opposing force. The algebraic $F^2$ prefactor belongs to this first-passage model and must not be discarded when quoting the leading asymptotic rate.

Each addition starts a new statistically identical waiting episode at zero gap. Thus the addition rate is the reciprocal of a mean first-passage time, not the reciprocal of the mean gap:This can also be derived without the steady density. If $T(x)$ is the mean time to reach $\delta$ starting at gap $x$, its backward Smoluchowski equation isThe first boundary is reflecting and the second absorbing. An integrating factor gives $T^{\prime }(x)=[1-e^{\beta Fx}]/(D\beta F)$, whenceAt weak force, $\tau \simeq {\delta }^2/(2D)$ is the time for a freely diffusing wall to move a monomer length, with reflection at the tip. At strong force, opening the gap requires work $F\delta$, with Boltzmann distribution suppression $e^{-\beta F\delta }$. The drift establishes a near-tip thermal length ${\ell }_F=k_{B}T/F$ and a diffusion time ${\ell }_F^2/D$; consequentlyThe exponentially long wait explains why the growth slows. There is no additional chemical waiting time in the imposed absorbing-threshold model; such a time would be needed to describe the separate reaction-limited polymerization Brownian ratchet regime.