Past exam of the biological physics course of the University of Oxford / 2022 / 6

Position from many photons. An isolated fluorophore produces a diffraction-broadened point spread function, but its unknown center can be inferred much more precisely than the width of that function. Fit a calibrated two-dimensional Gaussian function plus background to the detected photon positions or pixel intensities. If the point spread function has width $s$ and $N_{\gamma }$ independent photons are detected, negligible background gives localization precision approximately $s/\sqrt{N_{\gamma }}$. Pixelation and background worsen it; a commonly useful approximate variance iswhere $a$ is pixel size in the specimen plane and ${\sigma }_{\mathrm{bg}}$ is background noise per pixel in photon units. Bright, isolated emitters can therefore have nanometre localization precision despite a spot hundreds of nanometres wide. Stage drift, finite exposure motion, incorrect fitting, label displacement and photobleaching can dominate the photon limit.^[ref]

Walking mechanism. Myosin V is a two-headed, processive molecular motor that advances along actin with center-of-mass steps of about $37\mathrm{nm}$. A simple inchworm model retains the identity of the leading head, so a label fixed to one head would move approximately $37\mathrm{nm}$ on every cycle. In a hand-over-hand model the heads exchange lead: a label close to one head alternates a displacement near $74\mathrm{nm}$ with a near-zero displacement while the other head passes. For a label at offset $x$ from the midpoint, the more general alternating pair is $37-2x$ and $37+2x$ nanometres. The pair sums to $74\mathrm{nm}$; individual steps need not always equal $74\mathrm{nm}$.

Single-label imaging records a moving spot on a camera while the motor travels along surface-associated actin. Fitting the spot in successive frames resolves plateaus and jumps much smaller than the diffraction width. The observed alternating displacements distinguish a passing-head mechanism from uniform inchworm steps. This experiment combines a specific geometric prediction with single-molecule fluorescence microscopy; the center-of-mass stride alone would not make that distinction.^[ref]

Resolving a labelled structure. Accurate localization of one emitter does not automatically resolve two simultaneously overlapping emitters. Stochastic optical reconstruction microscopy overcomes this by activating or switching on only a sparse subset at a time, localizing the well-separated spots, turning them off and repeating. The accumulated coordinates reconstruct a densely labelled structure at scales below the diffraction limit. The original demonstration used repeated photoswitching and localization of individual dyes to reconstruct subdiffraction features.^[ref]

The useful structural resolution depends on both localization precision and label sampling density, as well as drift, fluorophore blinking, optical aberrations and linkage error. Sparse activation separates emitters in time; it does not shrink the diffraction-limited point spread function. A reconstructed image must have enough independent labels to represent its finest claimed feature.

An ionic atmosphere. A negatively charged molecule attracts positive counterions and repels negative co-ions; signs reverse for a positive molecule. The resulting electric double layer partially screens the bare electric field. Far from an isolated molecule, the electrolyte recovers its neutral bulk composition. At thermodynamic equilibrium, spatial uniformity of each species' electrochemical potential requiresThe logarithm implicitly uses a common reference density. This result for Boltzmann ion densities in a symmetric electrolyte neglects ion correlations, finite size and nonideal activities, but shows immediately why equal concentrations of the two signs do not persist close to a charged surface.

Self-consistent screening. Insert these densities into Poisson's equation, with solvent permittivity $ϵ$ and fixed charge density ${\rho }_f$:This is the Poisson-Boltzmann equation. For a symmetric monovalent salt with bulk density $n_s$ of each sign, outside the fixed charge it becomesFor $|z_{i}e\psi |\ll k_{B}T$, linearizing and using bulk neutrality gives the Debye–Hückel approximationThus added salt shortens the Debye length: electrostatic screening becomes stronger over a shorter distance. The factor of two in a $1:1$ salt comes from two ionic species, not from double-counting the density of salt pairs.

For example, a charged sphere of radius $a$ and total charge $Q$ has the exterior linearized solutionassuming fixed uniform surface charge and no ions inside. It follows from the decaying spherical solution and $-ϵ{\psi }^{\prime }(a)=Q/(4\pi a^2)$. At zero salt it reduces to the Coulomb potential; at finite salt it decays exponentially as well as geometrically. The excess mobile charge integrates to $-Q$ in an infinite neutralizing reservoir, although a finite sphere surrounding the molecule generally contains only part of that ionic atmosphere.

Biophysical scales and limitations. In water at room temperature, the monovalent formula is approximately ${\lambda }_D=0.304\mathrm{nm}/\sqrt{I/(\mathrm{mol}{\mathrm{L}}^{-1})}$, with $I$ the ionic strength. It gives about $0.79\mathrm{nm}$ at $0.15\mathrm{mol}{\mathrm{L}}^{-1}$ and $9.6\mathrm{nm}$ at $1\mathrm{mmol}{\mathrm{L}}^{-1}$. Consequently the same charged protein can exert very different long-range interactions mediated by electrostatics at different salt concentrations. Close to strongly charged DNA, the linear approximation fails; nonlinear screening, counterion condensation, ion-specific adsorption and changes of surface ionization through charge regulation may matter. Mean-field theory also misses strong multivalent-ion correlations and finite-size saturation: the exponential law cannot be extrapolated to arbitrarily large near-surface concentrations.

An ion channel can disturb cellular electrical activity by changing unitary electrical conductance, open probability, gating kinetics or the number delivered to the cell membrane. A useful organizing relation isHere outward electric current is positive. Altering one channel's biophysical behavior changes the balance governing membrane potential and hence the timing or recurrence of action potentials.

Long QT syndrome, type 3. Certain disease-associated SCN5A variants impair fast ion-channel inactivation of the cardiac voltage-gated sodium channel NaV1.5. Instead of vanishing promptly after the upstroke, a small persistent inward sodium electric current remains during the plateau and repolarization. Because $V<E_{\mathrm{Na}}$ in this phase, the residual electric current is inward and opposes the outward electric currents that would terminate the cardiac action potential. The ventricular action potential lasts longer, extending the QT interval on the electrocardiogram. Excessively prolonged or uneven repolarization permits early afterdepolarizations and dangerous ventricular rhythm disturbances.

Genetic association identifies the channel, while voltage clamp distinguishes defective ion-channel inactivation from a mere increase in channel abundance. Recordings of disease-associated channels show persistent or bursting openings; coupling measured mutant sodium electric current into an otherwise modeled cardiac membrane through dynamic clamp tests whether that kinetic defect prolongs the action potential. The phenotype is variant-specific: not every SCN5A variant increases late electric current or causes long QT syndrome.^[ref][ref]

Myotonia congenita. CLCN1 encodes the skeletal-muscle ClC-1 chloride channel, which normally supplies a large resting stabilizing electrical conductance. Because the chloride reversal potential is near the resting membrane potential, that pathway resists small depolarizing disturbances. Loss of functional channels, reduced electrical conductance, or a shift in opening toward more positive membrane potential reduces the resting electrical shunt. Potassium accumulation in the transverse-tubule space during activity can then produce larger depolarizing afterpotentials and trigger further muscle action potentials after the intended stimulus has ceased. Continued electrical firing sustains contraction and delays relaxation: this is myotonia, rather than a primary inability of the contractile apparatus to relax.

Patient-family linkage and variant analysis connect the disease to ClC-1. Functional recordings of disease-associated channels demonstrate shifted voltage dependence and reduced availability near resting membrane potential; single-channel and noise measurements also resolve two conductive protopores and their gating behavior. Different variants can act through different mechanisms, so a gating shift is an example rather than an explanation of every case.^{[ref][ref][ref]}

These examples connect contrasting current defects to their consequences: persistent inward sodium electric current prolongs cardiac action potentials, whereas loss of stabilizing resting chloride electrical conductance permits repetitive skeletal-muscle action potentials. Both causal chains require functional channel measurements in addition to a disease-associated sequence change.