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arXiv:2106.01690 · The Journal of Chemical Physics

Efimov-DNA phase diagram: Three stranded DNA on a cubic lattice

Somendra M. Bhattacharjee, Damien Paul Foster

Published Aug 12, 2021• 0 citations
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Abstract

We define a generalized model for three-stranded DNA consisting of two chains of one type and a third chain of a different type. The DNA strands are modeled by random walks on the three-dimensional cubic lattice with different interactions between two chains of the same type and two chains of different types. This model may be thought of as a classical analog of the quantum three-body problem. In the quantum situation, it is known that three identical quantum particles will form a triplet with an infinite tower of bound states at the point where any pair of particles would have zero binding energy. The phase diagram is mapped out, and the different phase transitions are examined using finite-size scaling. We look particularly at the scaling of the DNA model at the equivalent Efimov point for chains up to 10 000 steps in length. We find clear evidence of several bound states in the finite-size scaling. We compare these states with the expected Efimov behavior.

DOI
10.1063/5.0059153

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We define a generalized model for three-stranded DNA consisting of two chains of one type and a third chain of a different type. The DNA strands are modeled by random walks on the three-dimensional cubic lattice with different interactions between two chains of the same type and two chains of different types. This model may be thought of as a classical analog of the quantum three-body problem. In the quantum situation, it is known that three identical quantum particles will form a triplet with an infinite tower of bound states at the point where any pair of particles would have zero binding energy. The phase diagram is mapped out, and the different phase transitions are examined using finite-size scaling. We look particularly at the scaling of the DNA model at the equivalent Efimov point for chains up to 10 000 steps in length. We find clear evidence of several bound states in the finite-size scaling. We compare these states with the expected Efimov behavior.
A three-stranded DNA with short range base pairings only is known to exhibit a classical analog of the quantum Efimov effect, viz., a three-chain bound state at the two-chain melting point where no two are bound. By using a nonperturbative renormalization-group method for a rigid duplex DNA and a flexible third strand, with base pairings and strand exchange, we show that the Efimov-DNA is associated with a limit cycle type behavior of the flow of an effective three-chain interaction. The analysis also shows that thermally generated bubbles play an essential role in producing the effect. A toy model for the flow equations shows the limit cycle in an extended three-dimensional parameter space of the two-chain coupling and a complex three-chain interaction.
We study the melting of three-stranded DNA by using the real-space renormalization group and exact recursion relations. The prediction of an unusual Efimov-analog three-chain bound state, that appears at the critical melting of two-chain DNA, is corroborated by the zeros of the partition function. The distribution of the zeros has been studied in detail for various situations. We show that the Efimov DNA can occur even if the three-chain (i.e., three-monomer) interaction is repulsive in nature. In higher dimensions, a striking result that emerged in this repulsive zone is a continuous transition from the critical state to the Efimov DNA.
The aim of this thesis is to investigate, using simplified lattice models, whether the Efimov effect, well known in quantum mechanics, can arise in polymer physics too, particularly in a triple stranded DNA system. Such effect consists in the formation of stable trimer bound states when dimer bound states are not stable. We base strand interaction rules on a Poland-Scheraga model for a directed DNA-like polymer, double-stranded first and triple-stranded later. Within the Poland-Scheraga scheme, only interactions between base pairs with the same monomer indexes along the strands are permitted. Thus, the identification of the monomer index with imaginary time allows the formal mapping to the quantum problem in which particles interact at the same time. According to the transfer matrix method, we are able to extract information about the free-energy of the system from matrix eigenvalues. Studying them at the critical point of the unzipped-zipped phase transition we look for the similarities between the bound states in the polymer model and those predicted by Efimov theory for a three particle quantum system. In particular, in Efimov theory, an infinite series of trimer energy levels, with a constant ratio between consecutive levels, is found at the critical point of the 2-body problem.
The Efimov phenomenon manifests itself as an emergent discrete scaling symmetry in the quantum three-body problem. In the unitarity limit, it leads to an infinite tower of three-body bound states with energies forming a geometric sequence. In this work, we study the evolution of these so-called Efimov states using relativistic scattering theory. We identify them as poles of the three-particle SSS matrix in the complex energy plane, and we study how they transform from virtual states through bound states to resonances when we change the interaction strength. We dial the scattering parameters toward the unitarity limit and observe the emergence of the universal scaling of energies and couplings---a behavior known from the nonrelativistic case. We additionally find that Efimov resonances follow unusual, cyclic trajectories accumulating at the three-body threshold and then disappear at some values of the two-body scattering length. We propose a partial resolution to this ``missing states'' problem.
Universal behavior has been found inside the window of Efimov physics for systems with N=4,5,6N=4,5,6N=4,5,6 particles. Efimov physics refers to the emergence of a number of three-body states in systems of identical bosons interacting via a short-range interaction becoming infinite at the verge of binding two particles. These Efimov states display a discrete scale invariance symmetry, with the scaling factor independent of the microscopic interaction. Their energies in the limit of zero-range interaction can be parametrized, as a function of the scattering length, by a universal function. We have found, using the form of finite-range scaling introduced by A. Kievsky and M. Gattobigio [Phys. Rev A 87, 052719 (2013)], that the same universal function can be used to parametrize the ground and excited energy of $N\ensuremath{\le}6$ systems inside the Efimov-physics window. Moreover, we show that the same finite-scale analysis reconciles experimental measurements of three-body binding energies with the universal theory.