Past exam of the soft matter and biological physics course of the University of Cambridge / 2013 / Paper 1 / 3

In gel sieving of synthetic polymers, gel electrophoresis combines drift under an electric field with size- and conformation-dependent obstruction by a porous matrix. In weak-field free solution, force balance gives $v=\mu E$ and, in a simple effective-charge/effective-friction model, $\mu =q_{\mathrm{eff}}/\zeta$. The mobility is motion relative to the medium, so fluid motion from electro-osmosis must be accounted for separately. This is the operational mobility convention, not a claim that the bare structural charge is always the effective driving charge.^[ref]

For a chain with free-draining polymer friction with approximately constant effective electric charge per segment, both charge and friction scale with $N$. The free-solution mobility can therefore become nearly independent of length, making size separation poor. A gel adds steric constraints. Coils smaller than the mesh can pass relatively easily; larger coils require deformation and pore-to-pore rearrangement. A schematic weak-sieving law is $\mu (c_g)\simeq \mu (0)e^{-K_r{c}_g}$, where matrix concentration $c_g$ and retardation coefficient $K_r$ are defined by a calibration; it is not a universal size law.

When a long flexible charged polymer is confined to a tube of available paths, reptation supplies another regime. An additive-friction model gives contour diffusion $D_c\propto N^{-1}$ and renewal time $\tau \sim N^2/D_c\propto N^3$. For ideal large-scale chain statistics, $R^2\propto N$, so centre-of-mass diffusion scales as $N^{-2}$. With total effective driving charge proportional to $N$, weak-field mobility can then scale as $N^{-1}$. This assumes screened/ideal large-scale conformations and linear response; strong-field alignment, trapping and nonideal matrices can alter the scaling.

Operationally, load narrow zones of independently characterized synthetic standards and sample into a controlled gel, apply a known field and detect migration positions after a measured time. Compare with a free-solution measurement, vary matrix concentration and field, and control temperature, ionic strength, pH and matrix charge. Larger gel pores or lower matrix concentration usually reduce sieving within a given calibrated material system. Excessive field causes Joule heating and can change conformation and mobility. adsorption or electro-osmotic drift can mimic a size effect; standards should match charge chemistry and topology as well as nominal mass.

Band centres move as $\mu Et$ while ordinary diffusion gives ${\sigma }_x^2(t)={\sigma }_x^2(0)+2Dt$. Resolution depends on separation of centres relative to band widths, not travel distance alone. A neutral tracer helps identify bulk flow, and multiple concentrations test adsorption or overloading. A mobility or band position does not uniquely determine size without a regime-specific calibration. TODO: biomolecular examples, sample preparation and biological applications are user deferred; the account here concerns synthetic charged polymers only.

Use SI units, uniform absolute permittivity $\epsilon$ and a neutral bulk reservoir. Local equilibrium of ideal mobile ions gives $n_i=n_{i,\infty }{e}^{-z_{i}e\psi /(k_{B}T)}$. Combining their charge with the Poisson equation yieldsThe reference is $\psi =0$ in the bulk. Boundary data specify fixed charge, fixed potential or a surface reaction/charge regulation law. These are physically different problems. The mean-field theory assumes point ions, thermal equilibrium and a continuum solvent; ion-size packing, dielectric structure and strong electrostatic correlations can invalidate it.

For a symmetric monovalent electrolyte let $n_{\infty }$ count each sign and define $u=e\psi /(k_{B}T)$, ${\kappa }_D^2=2e^2{n}_{\infty }/(\epsilon k_{B}T)$. Outside fixed sources,For $|u|\ll 1$, the Debye-Hückel approximation is ${\nabla }^{2}u={\kappa }_D^{2}u$. A planar wall bounding electrolyte in $z>0$ has $\psi ={\psi }_0{e}^{-{\kappa }_{D}z}$; assuming zero field on the other side, its charge is $\sigma =\epsilon {\kappa }_D{\psi }_0$. A sphere of radius $a$ and total charge $Q$ instead givesThe factors arise from geometry and boundary conditions; planar screening cannot be substituted unchanged for a small sphere. The weak-potential condition must hold where the potential is largest, particularly at the surface.

The nonlinear planar Poisson-Boltzmann profile is also exactly integrable. Multiply $u^{\prime \prime }={\kappa }_D^2\sinh u$ by $u^{\prime }$ and use $u,u^{\prime }\to 0$ at infinity:The sign selects a profile decaying to the bulk for either sign of surface potential. Integration givesFor weak $u_0$ this reduces to the linear solution. Strong surface potentials have a bounded far-field amplitude $4\gamma$, while the near-wall ion density still grows strongly. There is no need to permit the negative ion densities produced by an invalid extrapolation of a linearized density formula.

The same first integral yields the Grahame equation and its diffuse-layer differential capacitance per unit area:These describe the diffuse layer. A compact interfacial layer adds a voltage drop and can place its capacitance in series with $C_D$; a measured electrode capacitance need not equal the ideal diffuse contribution.^[ref]

For comparison, a planar counterion-only double layer next to a negative plane has positive counterions and no salt reservoir. Its profile is algebraic:Integrating $en(z)$ over $z>0$ gives $|\sigma |$, checking charge neutrality. This problem cannot be obtained by putting a finite reservoir density into the symmetric-electrolyte answer without changing its boundary conditions.

Applications include screening around synthetic colloids, diffuse-layer electrode capacitance and forces between charged plates. In planar geometry, the bulk-subtracted normal stress is constant:At the midpoint of identical plates, symmetry sets $E=0$, so the remaining excess ionic osmotic pressure determines their repulsion. A comparison with force or capacitance measurements should vary salt and surface potential independently, test charge regulation and adsorption, and distinguish compact-layer effects from failures of diffuse screening. Nonlinear Poisson-Boltzmann theory retains finite-potential Boltzmann populations, but still omits correlations and finite-ion-volume saturation.

TODO: user-deferred organism-specific biology. The bacterial behaviour, mechanisms, experiments and biological applications are intentionally left unsolved.