Related papers: Comment on " A simple model for DNA denaturation"
We respond to the comment arXiv:1809.03931 put forward by Li-Han Chen, Zhen Liu, and Jian-Tin Zheng on our work Kiesel, Platt, and Thomale, Phys. Rev. Lett. 110, 126405 (2013). All misunderstandings and misconceptions communicated in the…
In previous work, I described several examples combining reduction and emergence: where reduction is understood a la Ernest Nagel, and emergence is understood as behaviour or properties that are novel (by some salient standard). Here, my…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
Arguments are provided which show that extension of renormalizability in quantum field theory is possible. A dressed scheme for the perturbation expansion is proposed. It is proven that in this scheme a nonrenormalizable interaction becomes…
We consider polymers in which M randomly selected pairs of monomers are restricted to be in contact. Analytical arguments and numerical simulations show that an ideal (Gaussian) chain of N monomers remains expanded as long as M<<N. This…
We study DNA adsorption and renaturation in a water-phenol two-phase system, with or without shaking. In very dilute solutions, single-stranded DNA is adsorbed at the interface in a salt-dependent manner. At high salt concentrations the…
In this paper, we show how the method of field theoretical renormalization group may be used to analyze universal shape properties of long polymer chains in porous environment. So far such analytical calculations were primarily focussed on…
We analyze the results obtained recently by Khazael and Sebastiani (J. Chem. Phys. \textbf{147}, 194303 (2017)) for two coupled methyl rotors. We show that one of the avoided crossings obtained by those authors is in fact a true crossing…
A dynamical model of the dielectric screening of conjugated polymers is introduced and solved using the density matrix renormalization group method. The model consists of a line of quantized dipoles interacting with a polymer chain. The…
Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…
This paper reports some experimental results validating in a broader context a variant of PCR, called XPCR, previously introduced and tested on relatively short synthetic DNA sequences. Basic XPCR technique confirmed to work as expected, to…
This paper has been withdrawn by the authors, due a oversimplified decoherence model. It will be substituted by a new work.
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
We extend the key idea behind the generalized Petviashvili method of Ref. \cite{gP} by proposing a novel technique based on a similar idea. This technique systematically eliminates from the iteratively obtained solution a mode that is…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
We have performed fully atomistic classical molecular dynamics (MD) simulations to calculate the effective interaction between two polyamidoamine (PAMAM) dendrimers. Using the umbrella sampling (US) technique, we have obtained the potential…
The subtracted kernel approach is shown to be a powerful method to be implemented recursively in scattering equations with regular plus point-like interactions. The advantages of the method allows one to recursively renormalize the…
We analyze variants of the contact process that are built by modifying the percolative structure given by the graphical construction and develop a robust renormalization argument for proving extinction in such models. With this method, we…
The renormalization group method developed by Ken Wilson more than four decades ago has revolutionized the way we think about problems involving a broad range of energy scales such as phase transitions, turbulence, continuum limits and…
The elasticity of DNA catenanes, i.e. multiply linked DNA rings, is investigated using the Gauss invariant as a minimal model for topology conservation. An effective elastic free energy as a function of the distance $R$ between segments…