Phase transitions in heteropolymers with "secondary structure"

Semianalytical solutions of Ising-like and Potts-like magnetic polymers on the Bethe lattice

We study magnetic polymers, defined as self-avoiding walks where each monomer i carries a "spin" s_{i} and interacts with its first neighbor monomers, let us say j, via a coupling constant J(s_{i},s_{j}). Ising-like [s_{i}=±1, with J(s_{i},s_{j})=ɛs_{i}s_{j}] and Potts-like [s_{i}=1,...,q, with J(s_{i},s_{j})=ɛ(s_{i})δ(s_{i},s_{j})] models are investigated. Some particular cases of these systems have recently been studied in the continuum and on regular lattices and are related to interesting applications. Here, we solve these models on Bethe lattices of branching number σ, focusing on the ferromagnetic case in zero external magnetic field. In most cases, the phase diagrams present a nonpolymerized (NP) and two polymerized phases: a paramagnetic (PP) and a ferromagnetic (FP) one. However, quite different thermodynamic properties are found depending on q in the Potts-like polymers and on whether one uses the Ising or Potts coupling in the two-state systems. For instance, for the standard Potts model [where ɛ(1)=⋯=ɛ(q)] with q=2, beyond the θ-point (where the critical and discontinuous NP-PP transition lines meet), a second tricritical point connecting a critical and a discontinuous transition line between the PP-FP phases is found in the system. A triple point where the NP-PP, NP-FP, and PP-FP first-order transition lines meet is also present in the phase diagram. For q≥3 the PP-FP transition is always discontinuous, and the scenario with the triple and θ points appears for q≤6. Interestingly, for q≥7, as well as for the Ising-like model the θ point becomes metastable and the critical NP-PP transition line ends at a critical end point (CEP), where it meets the NP-FP and PP-FP coexistence lines. Importantly, these results indicate that when q≤6 the spin ordering transition is preceded by the polymer collapse transition, whereas for q≥7 and in the Ising case these transitions happen together at the CEPs. Some interesting nonstandard Potts models are also studied, such as the lattice version of the model for epigenetic marks in the chromatin introduced by Michieletto et al. [Phys. Rev. X 6, 041047 (2016)2160-330810.1103/PhysRevX.6.041047]. In addition, the solution of the dilute Ising and dilute Potts models on the Bethe lattice are also presented here, since they are important to understand the PP-FP transitions.

Critical and geometric properties of magnetic polymers across the globule-coil transition

We study a lattice model of a single magnetic polymer chain, where Ising spins are located on the sites of a lattice self-avoiding walk in d=2. We consider the regime where both conformations and magnetic degrees of freedom are dynamic, thus the Ising model is defined on a dynamic lattice and conformations generate an annealed disorder. Using Monte Carlo simulations, we characterize the globule-coil and ferromaget-to-paramagnet transitions, which occur simultaneously at a critical value of the spin-spin coupling. We argue that the transition is continuous-in contrast to d=3 where it is first order. Our results suggest that at the transition the metric exponent takes the θ-polymer value ν=4/7 but the crossover exponent ϕ≈0.7, which differs from the expected value for a θ polymer.

Critical behavior of magnetic polymers in two and three dimensions

We explore the critical behavior of two- and three-dimensional lattice models of polymers in dilute solution where the monomers carry a magnetic moment which interacts ferromagnetically with near-neighbor monomers. Specifically, the model explored consists of a self-avoiding walk on a square or cubic lattice with Ising spins on the visited sites. In three dimensions we confirm and extend previous numerical work, showing clearly the first-order character of both the magnetic transition and the polymer collapse, which happen together. We present results in two dimensions, where the transition is seen to be continuous. Finite-size scaling is used to extract estimates for the critical exponents and the transition temperature in the absence of an external magnetic field.

RNA folding in the presence of counterions

We present a general thermodynamic picture of the folding of RNA-like heteropolymer based on the basic physical principles. The Hamiltonian of the model includes all characteristic interactions explicitly. A particular attention is paid to the electrostatic interactions whose role in the RNA folding is known to be crucial. In this paper we study RNA folding with the full Hamiltonian and describe the spin-glass behavior on the level of tertiary structure. We show that formation of the stable tertiary structure is possible in the random RNA-like molecule. By including into the model the nonspecific interactions of the RNA molecule with counterions, we derive the logarithmic dependencies of the melting and freezing temperatures on the ion concentration, which is consistent with experimental data [R. Shiman and D. E. Draper, J. Mol. Biol. 302, 79 (2000)]. We also infer that the large RNA folds slower than the hierarchical model predicts, which was observed in the experiments.