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A biopolymer is a polymer produced by a living system, including proteins, nucleic acids and polysaccharides. Local chemical structure, sequence and interactions can give it stiffness or preferred conformations beyond those of an ideal chain. Biopolymer mechanics uses models such as the worm-like chain and the helix-coil transition model to represent those features.

Ideal and self-avoiding walks. An ideal chain has independent isotropic coarse-grained steps and permits self-intersections in its mathematical model. For $N$ steps of length $b$, the cross terms average to zero, so its root-mean-square end-to-end distance of a polymer chain obeysA self-avoiding walk excludes repeated occupancy or intersection at the segment scale. This represents positive excluded volume in a dilute good solvent. The nonlocal constraint correlates otherwise distant portions of the chain and swells it:The Flory approximation replaces this exponent by $3/5$, by balancing stretching free energy $R^2/(N{b}^2)$ with an interaction contribution $v{N}^2/R^3$. The result is a more extended and less internally dense coil than the ideal walk; self-avoidance changes the statistics, not merely the local step length.

Two ideal-chain regimes. At the theta temperature for a dilute polymer–solvent pair, leading effective segment attractions and repulsions cancel. Large-scale chain statistics are approximately ideal, even though microscopic atoms still have finite size. In a homogeneous polymer melt, surrounding chains screen long-range excluded volume interactions of a chosen chain, again making its equilibrium large-scale size approximately ideal. Local bond-angle correlations must be included in an effective statistical length such as the Kuhn length. Polymer entanglements can slow the dynamics without invalidating this leading equilibrium size law.

Semiflexible DNA. The nucleic acid double helix gives double-stranded DNA a bending stiffness and substantial local orientational persistence. Independent step orientations are therefore a poor description on short scales, while self-avoidance alone does not specify the energy cost of bending. The worm-like chain describes the molecule as a continuously bendable, locally inextensible curve $\mathbf{r}(s)$ parameterized by arc length $s$, with unit tangent $\mathbf{t}(s)=d\mathbf{r}/ds$. Its bending energy iswhere $A$ is bending stiffness. In the free three-dimensional model, the persistence length is ${\ell }_p=A/(k_{B}T)$ andThus ${\ell }_p$ is the contour separation over which tangent alignment falls by the factor $e^{-1}$; it quantifies stiffness relative to thermal bending. The model bridges locally rod-like and globally coil-like conformations. It omits long-range self-avoidance in its simplest form, so sufficiently long dilute DNA can require excluded-volume corrections.

Flexible and rigid limits. Integrating the tangent correlation over the two contour positions gives the end-to-end distance of a worm-like chain:For a very flexible chain on the scale of its total length, $L/{\ell }_p\gg 1$, the exponential is negligible andThis is the ideal chain result with Kuhn length $b_K=2{\ell }_p$ and effective step count $N_K=L/(2{\ell }_p)$. Many persistent sections have decorrelated orientations. The flexible limit means a large ratio $L/{\ell }_p$ within the continuum model's range, not an extrapolation of the persistence length below all molecular length scales.

For a nearly rigid chain, $L/{\ell }_p\ll 1$, the constant and linear terms in the exponential cancel those outside it. The Taylor series givessoThis is the expected rod limit: all tangents are nearly aligned, and the end-to-end distance approaches the arc length.

Helix–coil curves. A helix-coil transition model allows ordered helical runs and disordered coil regions. Use $s$ and $\sigma$ with exactly the free-energy conventions defined in the paper. A negative $\Delta F_{\mathrm{hc}}$ gives $s>1$ and favors the helical state; a positive junction cost gives $0<\sigma <1$ and penalizes starting new domains. The supplied helical fraction is the long-chain form associated with the Zimm-Bragg model.

Its main features follow directly without assuming a sharp transition. Put $Q=(s-1{)}^2+4s\sigma$. For every $\sigma >0$,and differentiating givesThus all curves rise monotonically and cross at $(1,1/2)$. Increasing the boundary free-energy cost reduces $\sigma$, suppresses frequent coil–helix boundaries and makes longer runs favorable. The transition region becomes narrower and steeper: balancing $(s-1{)}^2$ against $4s\sigma$ gives a width of order $\sqrt{\sigma }$ near $s=1$.

For $\sigma =1$, the fraction simplifies to $\boxed{f_h=s/(1+s)}$, the noncooperative two-state result. For $0<\sigma \ll 1$, the steep curve describes cooperative helix formation. In the singular limit $\sigma \downarrow 0$, it approaches zero for $s<1$ and one for $s>1$; its midpoint remains $1/2$ when approached through positive $\sigma$. Setting $\sigma =0$ directly makes the formula indeterminate at $s=1$. For any fixed positive $\sigma$, the given long-chain curve is smooth: it is a cooperative crossover, not a true discontinuity. The plot varies $s$ at fixed $\sigma$; in an actual temperature scan both parameters may change, and a finite chain can further round the crossover.