arXiv subjects

Elena Rivas

Publications and source records attributed to Elena Rivas.

4 recordsLinked to original sources

arXiv1998

A dynamic programming algorithm for RNA structure prediction including pseudoknots

We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the algorithm is complex, which led us to adopt a useful graphical representation (Feynman diagrams) borrowed from quantum field theory. We present an implementation of the algorithm that generates the optimal minimum energy structure for a single RNA sequence, using standard RNA folding thermodynamic parameters augmented by a few parameters describing the thermodynamic stability of pseudoknots. We demonstrate the properties of the algorithm by using it to predict structures for several small pseudoknotted and non-pseudoknotted RNAs. Although the time and memory demands of the algorithm are steep, we believe this is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model.

physics.bio-ph↗

arXiv1996

Extended Dualization: a method for the Bosonization of Anomalous Fermion Systems in Arbitrary Dimension

The technique of extended dualization developed in this paper is used to bosonize quantized fermion systems in arbitrary dimension $D$ in the low energy regime. In its original (minimal) form, dualization is restricted to models wherein it is possible to define a dynamical quantized conserved charge. We generalize the usual dualization prescription to include systems with dynamical non--conserved quantum currents. Bosonization based on this extended dualization requires the introduction of an additional rank $0$ (scalar) field together with the usual antisymmetric tensor field of rank $(D-2)$. Our generalized dualization prescription permits one to clearly distinguish the arbitrariness in the bosonization from the arbitrariness in the quantization of the system. We study the bosonization of four--fermion interactions with large mass in arbitrary dimension. First, we observe that dualization permits one to formally bosonize these models by invoking the bosonization of the free massive Dirac fermion and adding some extra model--dependent bosonic terms. Secondly, we explore the potential of extended dualization by considering the particular case of \underbar{chiral} four--fermion interactions. Here minimal dualization is inadequate for calculating the extra bosonic terms. We demonstrate the utility of extended dualization by successfully completing the bosonization of this chiral model. Finally, we consider two examples in two dimensions which illuminate the utility of using extended dualization by showing how quantization ambiguities in a fermionic theory propagate into the bosonized version. An explicit parametrization of the quantization ambiguities of the chiral current in the Chiral Schwinger model is obtained. Similarly, for the sine--Gordon interaction in the massive Thirring model the quantization

hep-th↗

arXiv1992

The S, U and Δρparameters in the Zaragoza proposal for lattice chiral gauge fermions

Using the Zaragoza proposal for lattice chiral gauge fermions, the S, U and Δρparameters have been calculated at one loop. It is shown that the continuum values for these quantities can be reproduced without requiring explicit fine tuning of counterterms. Furthermore, fermion fields doubling is not necessary. To the best of our knowledge, the Zaragoza proposal is the only scheme which has these properties. A necessary (although not sufficient) symmetry is found to support the calculations. Previous results for some of these parameters in other lattice chiral regularizations are revisited in the light of this symmetry.

hep-lat↗

arXiv1992

Absence of Chiral Fermions in the Eichten--Preskill Model

The model proposed by Eichten and Preskill for obtaining theories with chiral fermions from the lattice is shown to undergo spontaneous symmetry breaking. In addition, the fermions appear to be Dirac-like everywhere in the phase diagram with no room for undoubled Weyl fermions. The phase diagram of a closely related Higgs-Yukawa model is similar to that of the Smit--Swift model, which also does not give rise to chiral fermions. These results cast serious doubts on the original scenario for the emergence of chiral fermions.

hep-lat↗