Related papers: Pseudo-RNA with parallel aligned single-strands an…
This work examines a field theory for RNA-like molecules in a good solvent. The field theory is based on a lattice model for single- and double-strand RNA with a periodic base sequence, and otherwise contains all known relevant details…
We examine the statistics of conformations of a linear polymer in a solvent. The polymer is allowed to form double polymers. We closely follow a classical technique to derive a field theory for the problem from an $O\left(n\right)$…
This work examines field theories for RNA-like polymers with single strand and double strand polymers and a periodic base sequence. These field theories originate from lattice models, describe polymers in a good solvent, and in principle…
A universality class describing the statistics of the merging of two single polymer strands to a double polymer strand and the reverse process is examined. The polymers can have an intrinsic direction, and the simpler case, where only…
Following Poland and Scheraga, we consider a simplified model for the denaturation transition of DNA. The two strands are modeled as interacting polymer chains. The attractive interactions, which mimic the pairing between the four bases,…
We present a mean-field dynamical theory for single semiflexible polymers which can precisely capture, without fitting parameters, recent fluorescence correlation spectroscopy results on single monomer kinetics of DNA strands in solution.…
We prove that the Laessig-Wiese (LW) field theory for the freezing transition of the secondary structure of random RNA is renormalizable to all orders in perturbation theory. The proof relies on a formulation of the model in terms of random…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
We formulate semi-classical field theory as an approximate decoherence-free-subspace of a finite-dimensional quantum-gravity hilbert space. A complementarity construction can be realized as a unitary transformation which changes the…
Using renormalized field theory, we examine the dynamics of a growing surface, driven by an obliquely incident particle beam. Its projection on the reference (substrate) plane selects a ``parallel'' direction, so that the evolution equation…
We construct the lattice gauge theory of the group G_N, the semidirect product of the permutation group S_N with U(1)^N, on an arbitrary Riemann surface. This theory describes the branched coverings of a two-dimensional target surface by…
Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…
Formation of RNA secondary structures is an example of the sequence-structure problem omnipresent in biopolymers. A theoretical question of recent interest is whether a random RNA sequence undergoes a finite temperature glass transition. We…
We find the gravity dual of a marginal deformation of ${\cal N}=4$ super Yang Mills, and discuss some of its properties. This deformation is intimately connected with an $SL(2,R)$ symmetry of the gravity theory. The $SL(2,R)$ transformation…
Based on a semi-empirical generalized Anderson-Newns model we construct a pseudo-particle description for electron emission due to de-excitation of metastable molecules at surfaces. The pseudo-particle approach allows us to treat resonant…
The classification of one parameter local Coulomb branch solution of theories with eight supercharges is given by assuming that it is given by a genus $g$ fiberation of Riemann surfaces. The crucial point is the fact that certain conjugacy…
It is explained how field-theoretic methods and the dynamic renormalisation group (RG) can be applied to study the universal scaling properties of systems that either undergo a continuous phase transition or display generic scale…
We develop a renormalized continuum field theory for a directed polymer interacting with a random medium and a single extended defect. The renormalization group is based on the operator algebra of the pinning potential; it has novel…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
We study secondary structures of random RNA molecules by means of a renormalized field theory based on an expansion in the sequence disorder. We show that there is a continuous phase transition from a molten phase at higher temperatures to…