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The hydrodynamic radius is the radius of a hypothetical no-slip sphere with the same translational diffusion coefficient as the dissolved species. In the dilute continuum regime the Stokes–Einstein relation giveswhere $k_B$ is the Boltzmann constant, $T$ the absolute temperature, $\eta$ the dynamic viscosity of the solvent, and $D$ the translational diffusion coefficient. This effective radius need not equal the radius of gyration or a geometric molecular radius. It is a useful descriptor for SEC molar mass calibration, rather than a complete specification of how every shape enters every pore.

Polystyrene is a polymer used as a calibration-standard family in organic-solvent size-exclusion chromatography. Its hydrodynamic size in a specified solvent supplies a conditional SEC molar mass calibration for other dissolved chains.

SEC molar mass calibration measures standards under the same column, solvent, and temperature conditions as the unknown. Over a suitable fractionation interval, a common empirical approximation iswhere $M_{\mathrm{ref}}$ specifies the molar mass unit and $b$ has inverse-volume units. Interpolation is conditional on the standards' size–molar mass relationship. SEC measures access associated with hydrodynamic size, so a branched polymer, an extended chain, and a compact protein need not share that relationship.

In this model the $80,000$, $40,000$, and $20,000\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$ standards have hydrodynamic radii $2\sqrt{2}$, $2$, and $\sqrt{2}\mathrm{nm}$ and elute at $7$, $9$, and $11\mathrm{mL}$. An unknown at $8\mathrm{mL}$ would be assigned $M_{\mathrm{app}}=40,000\sqrt{2}\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$ by this calibration. But a $40,000\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$ species that expands from $2$ to $2\sqrt{2}\mathrm{nm}$ elutes at $7\mathrm{mL}$ and is assigned $80,000\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$ without gaining any mass. The numbers demonstrate ambiguity, rather than predict a real unfolding transition.

Changes in conformational isomerism, protein folding, protein denaturation, and protein aggregation can therefore shift peaks. Association usually increases size; compaction can reduce size at unchanged molar mass. Adsorption creates a different ambiguity: delayed elution need not indicate a smaller species. A different solvent can change both polymer coil dimensions and interactions with the packing. The SEC protein conformation experiment tests these alternatives with additional detectors.

Size-exclusion chromatography separates dissolved molecules by their hydrodynamic size in the chosen solvent. A larger species that cannot enter the packing's pores travels with the liquid between particles and elutes earlier. Smaller species explore more internal liquid and elute later. The column is not a sieve that permanently traps the large species: exclusion makes them leave first. “Gel filtration” is common for aqueous separations; “gel permeation chromatography” is common for organic-solvent analysis of polymers. SEC molar mass calibration translates size-dependent elution into a standard-relative estimate of molar mass, rather than a universal absolute measurement.

This makes SEC useful for separating proteins from small dissolved species, comparing protein aggregation, and characterizing dissolved polymer chains. The residual-group monitoring of polyurethane formation experiment already illustrates polymer calibration: its reported molar masses are relative to polystyrene standards. Size-exclusion characterization of chain polymers explains why an elution trace alone cannot count chains or establish their growth mechanism.

Suppose a synthetic polymer population contains three chains of molar mass $10000\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$ for every one chain of molar mass $40000\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$. Multiplying both chain counts by any common factor leaves the averages unchanged. Substitution into the existing number-average molar mass and weight-average molar mass definitions givesThe larger chains are only one quarter of the chain count but supply $40000/70000=4/7$ of the mass. Thus a weighted mean that emphasizes mass gives a larger result than one that weights each molecule equally. Total mass divided by total chain amount of substance gives $M_n$, while $M_w/N_{\mathrm{A}}$ is not the mean mass of a randomly chosen chain. Inferring chain counts from size-exclusion chromatography still requires the existing SEC detector response and SEC molar mass calibration assumptions.