Positive discrete series representations of the Lie algebra su(1, 1) and the quantum algebra U q (su(1, 1)) are considered. The diagonalization of a self-adjoint operator (the Hamiltonian) in these representations and in tensor products of such representations is determined , and the generalized eigenvectors are constructed in terms of orthogonal polynomials. Using simple realizations of su(1, ...

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecu...

Electrostatic potentials around DNA are obtained by solving the nonlinear Poisson-Boltzmann (PB) equation. The detailed charge distribution of the DNA and the different polarizabilities of the macromolecule and solvent are included explicitly in the calculations. The PB equation is solved using extensions of a finite difference approach applied previously to proteins. Electrical potentials and ...

We have performed molecular dynamics (MD) simulations, with particle-mesh Ewald, explicit waters, and counterions, and binding specificity analyses using combined molecular mechanics and continuum solvent (MM-PBSA) on the bovine immunodeficiency virus (BIV) Tat peptide-TAR RNA complex. The solution structure for the complex was solved independently by Patel and co-workers and Puglisi and co-wor...

Fragment density functional theory (DFT) calculation of NMR chemical shifts for several proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and human ubiquitin) has been carried out. The present study is based on a recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach but the solvent effects are included by using the...

the combination of quantum mechanics (qm) and molecular mechanics (mm) methods hasbecome alternative tool for many applications that pure qm and mm could not be suitable.the qm/mm method has been used for different type of problems, for example: structuralbiology, surface phenomena, and liquid phase. in this paper we have performed these methods forsome antibiotics and vitamins and then we comp...

We solve the linearized Poisson-Boltzmann equation analytically, subject to justifiable approximations, for a suspension containing a large number of identical spherical macroions under conditions of constant surface charge and zero added salt, in order to investigate the phase behavior of charge-stabilized colloidal suspensions. Our results for the electrostatic part of the Helmholtz free ener...

The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods hasbecome alternative tool for many applications that pure QM and MM could not be suitable.The QM/MM method has been used for different type of problems, for example: structuralbiology, surface phenomena, and liquid phase. In this paper we have performed these methods forsome antibiotics and vitamins and then we comp...

We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson-Boltzmann equation. The method employs a wellconditioned boundary integral formulation for the electrostatic potential and its normal derivative on the molecular surface. The surface is triangulated and the integral equations are discretized by centroid c...