Past exam of the soft condensed matter course of the University of Cambridge / 2021 / Section A

In the weak-field reptation regime of agarose gel electrophoresis, the electrophoretic mobility of a long linear DNA chain scales as $\mu \propto M^{-1}$, where $M$ is its number of base pairs. One way to see the scaling is that the constrained-chain diffusion coefficient scales as $D\propto M^{-2}$, whereas its effective electric charge scales as $M$; the drift response is proportional to $DM$. With the same electric field and running time, the migration distance is therefore $x=\mu Et\propto M^{-1}$. The time cancels from the ratio, givingHere “kbp” means a thousand base pairs, not a rate. The second gel band has traveled farther and corresponds to the shorter chain under this migration model. The inverse-length law applies only over an appropriate migration regime.^[ref].

At very low agarose concentration the mesh becomes too open to sieve these chains effectively. In the free-solution limit the chain's electric charge and friction are both approximately proportional to its length, so both chains have nearly the same electrophoretic mobility and their gel bands cease to separate well. At very high agarose concentration the pores become small and transport is strongly hindered; over a fixed experimental time both chains migrate very little, so their absolute spatial separation again becomes small. Increasing gel concentration can improve resolution over an intermediate range, but not indefinitely.

The numerical result is conditional on the inverse-length reptation law. Actual gel electrophoresis size calibration often uses an empirical approximately linear relation between distance and $\log M$ over a specified range. One known band alone cannot fix that relation's slope. The PDF supplies neither gel concentration nor a calibration curve, so $8.9\mathrm{kbp}$ is the standard model estimate rather than a uniquely calibrated experimental size.

Choose a coordinate $z$ measured from the sphere centre towards increasing distance from the block, so an atom in the sphere is at height $L+z$. Summing the atom–block potential energy with the sphere's number density givesFor $R/L\ll 1$, a uniformly valid Taylor series over the sphere isThe odd moments vanish by reflection symmetry. The sphere volume is $V_s=4\pi R^3/3$, and its second moment isConsequentlyThe first finite-radius correction is therefore $-4{\pi }^{2}B{n}^2{R}^5/(15L^5)$. There is no relative $R/L$ correction because the first moment about the centre is zero. The leading term is just the number of sphere atoms times the potential at its centre; the correction increases the attraction because the nearer atoms contribute more strongly than the farther atoms lose.

This is the far-field sphere-plane dispersion energy, with Hamaker constant $A_H={\pi }^{2}B{n}^2$. It must be distinguished from the near-contact sphere-plane dispersion force, whose small parameter is the surface gap divided by the radius. Here $L$ is explicitly the centre-to-plane distance.

Let $z$ increase down the pipe, $a=0.015\mathrm{m}$ be its radius and $r$ the distance from its axis. For steady, fully developed laminar flow of a Newtonian fluid, the axial Navier-Stokes equations reduce toWrite $K=-dp/dz+\rho g\sin 20^{\circ }$. Integrating twice, regularity at $r=0$ excludes a logarithmic term, and the no-slip boundary condition $u(a)=0$ gives the Hagen-Poiseuille flow profileThe volumetric flow rate follows by integrating over the circular cross-section:For the intended gravity-driven case with no imposed axial pressure gradient, $dp/dz=0$. Substitution givesandThe corresponding mean speed is about $0.1047\mathrm{m}{\mathrm{s}}^{-1}$ and the diameter-based Reynolds number is $\rho \overline{u}(2a)/\eta \simeq 3.49$, consistent with laminar flow. The original PDF does not specify inlet and outlet pressures. If they impose an additional pressure gradient, the general result with $K$ above applies; gravity alone does not determine that extra contribution.