Connection between type B (or C) and F factorizations and construction of algebras

In a recent paper (Del Sol Mesa A and Quesne C 2000 J. Phys. A: Math. Gen. 33 4059), we started a systematic study of the connections among different factorization types, suggested by Infeld and Hull, and of their consequences for the construction of algebras. We devised a general procedure for constructing satellite algebras for all the Hamiltonians admitting a type E factorization by using the relationship between type A and E factorizations. Here we complete our analysis by showing that for Hamiltonians admitting a type F factorization, a similar method, starting from either type B or type C ones, leads to other types of algebras. We therefore conclude that the existence of satellite algebras is a characteristic property of type E factorizable Hamiltonians. Our results are illustrated with the detailed discussion of the Coulomb problem.Comment: minor changes, 1 additional reference, final form to be published in JP

Satellite potentials for hypergeometric Natanzon potentials

As a result of the so(2,1) of the hypergeometric Natanzon potential a set of potentials related to the given one is determined. The set arises as a result of the action of the so(2,1) generators.Comment: 9 page

Intertwining symmetry algebras of quantum superintegrable systems on the hyperboloid

A class of quantum superintegrable Hamiltonians defined on a two-dimensional hyperboloid is considered together with a set of intertwining operators connecting them. It is shown that such intertwining operators close a su(2,1) Lie algebra and determine the Hamiltonians through the Casimir operators. By means of discrete symmetries a broader set of operators is obtained closing a so(4,2) algebra. The physical states corresponding to the discrete spectrum of bound states as well as the degeneration are characterized in terms of unitary representations of su(2,1) and so(4,2).Comment: 11 pages, 5 figure

Connection Between Type A and E Factorizations and Construction of Satellite Algebras

Recently, we introduced a new class of symmetry algebras, called satellite algebras, which connect with one another wavefunctions belonging to different potentials of a given family, and corresponding to different energy eigenvalues. Here the role of the factorization method in the construction of such algebras is investigated. A general procedure for determining an so(2,2) or so(2,1) satellite algebra for all the Hamiltonians that admit a type E factorization is proposed. Such a procedure is based on the known relationship between type A and E factorizations, combined with an algebraization similar to that used in the construction of potential algebras. It is illustrated with the examples of the generalized Morse potential, the Rosen-Morse potential, the Kepler problem in a space of constant negative curvature, and, in each case, the conserved quantity is identified. It should be stressed that the method proposed is fairly general since the other factorization types may be considered as limiting cases of type A or E factorizations.Comment: 20 pages, LaTeX, no figure, to be published in J. Phys.

Multi-Harmony: detecting functional specificity from sequence alignment

Many protein families contain sub-families with functional specialization, such as binding different ligands or being involved in different protein–protein interactions. A small number of amino acids generally determine functional specificity. The identification of these residues can aid the understanding of protein function and help finding targets for experimental analysis. Here, we present multi-Harmony, an interactive web sever for detecting sub-type-specific sites in proteins starting from a multiple sequence alignment. Combining our Sequence Harmony (SH) and multi-Relief (mR) methods in one web server allows simultaneous analysis and comparison of specificity residues; furthermore, both methods have been significantly improved and extended. SH has been extended to cope with more than two sub-groups. mR has been changed from a sampling implementation to a deterministic one, making it more consistent and user friendly. For both methods Z-scores are reported. The multi-Harmony web server produces a dynamic output page, which includes interactive connections to the Jalview and Jmol applets, thereby allowing interactive analysis of the results. Multi-Harmony is available at http://www.ibi.vu.nl/ programs/shmrwww

Deformations of the Boson sp(4,R)sp(4,R) Representation and its Subalgebras

The boson representation of the sp(4,R) algebra and two distinct deformations of it, are considered, as well as the compact and noncompact subalgebras of each. The initial as well as the deformed representations act in the same Fock space. One of the deformed representation is based on the standard q-deformation of the boson creation and annihilation operators. The subalgebras of sp(4,R) (compact u(2) and three representations of the noncompact u(1,1) are also deformed and are contained in this deformed algebra. They are reducible in the action spaces of sp(4,R) and decompose into irreducible representations. The other deformed representation, is realized by means of a transformation of the q-deformed bosons into q-tensors (spinor-like) with respect to the standard deformed su(2). All of its generators are deformed and have expressions in terms of tensor products of spinor-like operators. In this case, an other deformation of su(2) appears in a natural way as a subalgebra and can be interpreted as a deformation of the angular momentum algebra so(3). Its representation is reducible and decomposes into irreducible ones that yields a complete description of the same

Generalized Morse Potential: Symmetry and Satellite Potentials

We study in detail the bound state spectrum of the generalized Morse potential~(GMP), which was proposed by Deng and Fan as a potential function for diatomic molecules. By connecting the corresponding Schr\"odinger equation with the Laplace equation on the hyperboloid and the Schr\"odinger equation for the P\"oschl-Teller potential, we explain the exact solvability of the problem by an $so(2,2)$ symmetry algebra, and obtain an explicit realization of the latter as $su(1,1) \oplus su(1,1)$. We prove that some of the $so(2,2)$ generators connect among themselves wave functions belonging to different GMP's (called satellite potentials). The conserved quantity is some combination of the potential parameters instead of the level energy, as for potential algebras. Hence, $so(2,2)$ belongs to a new class of symmetry algebras. We also stress the usefulness of our algebraic results for simplifying the calculation of Frank-Condon factors for electromagnetic transitions between rovibrational levels based on different electronic states.Comment: 23 pages, LaTeX, 2 figures (on request). one LaTeX problem settle

Supersymmetry and superalgebra for the two-body system with a Dirac oscillator interaction

Some years ago, one of the authors~(MM) revived a concept to which he gave the name of single-particle Dirac oscillator, while another~(CQ) showed that it corresponds to a realization of supersymmetric quantum mechanics. The Dirac oscillator in its one- and many-body versions has had a great number of applications. Recently, it included the analytic expression for the eigenstates and eigenvalues of a two-particle system with a new type of Dirac oscillator interaction of frequency~$\omega$. By considering the latter together with its partner corresponding to the replacement of~$\omega$ by~$-\omega$, we are able to get a supersymmetric formulation of the problem and find the superalgebra that explains its degeneracy.Comment: 21 pages, LaTeX, 1 figure (can be obtained from the authors), to appear in J. Phys.

Short-range oscillators in power-series picture

A class of short-range potentials on the line is considered as an asymptotically vanishing phenomenological alternative to the popular confining polynomials. We propose a method which parallels the analytic Hill-Taylor description of anharmonic oscillators and represents all our Jost solutions non-numerically, in terms of certain infinite hypergeometric-like series. In this way the well known solvable Rosen-Morse and scarf models are generalized.Comment: 23 pages, latex, submitted to J. Phys. A: Math. Ge

Efficient Identification of Critical Residues Based Only on Protein Structure by Network Analysis

Despite the increasing number of published protein structures, and the fact that each protein's function relies on its three-dimensional structure, there is limited access to automatic programs used for the identification of critical residues from the protein structure, compared with those based on protein sequence. Here we present a new algorithm based on network analysis applied exclusively on protein structures to identify critical residues. Our results show that this method identifies critical residues for protein function with high reliability and improves automatic sequence-based approaches and previous network-based approaches. The reliability of the method depends on the conformational diversity screened for the protein of interest. We have designed a web site to give access to this software at http://bis.ifc.unam.mx/jamming/. In summary, a new method is presented that relates critical residues for protein function with the most traversed residues in networks derived from protein structures. A unique feature of the method is the inclusion of the conformational diversity of proteins in the prediction, thus reproducing a basic feature of the structure/function relationship of proteins