Vertically coupled quantum dots in the local spin-density functional theory

We have investigated the structure of double quantum dots vertically coupled at zero magnetic field within local spin-density functional theory. The dots are identical and have a finite width, and the whole system is axially symmetric. We first discuss the effect of thickness on the addition spectrum of one single dot. Next, we describe the structure of coupled dots as a function of the interdot distance for different electron numbers. Addition spectra, Hund's rule and molecular-type configurations are discussed. It is shown that self-interaction corrections to the density functional results do not play a very important role in the calculated addition spectra.Comment: Typeset using Revtex, 14 pages and 12 Postscript figures, to be published in Phys. Rev.

Far-infrared spectroscopy of nanoscopic InAs rings

We have employed time-dependent local-spin density theory to analyze the far-infrared transmission spectrum of InAs self-assembled nano-rings recently reported [A. Lorke et al, cond-mat/9908263 (1999)]. The overall agreement between theory and experiment is good, which on the one hand confirms that the experimental peaks indeed reflect the ring-like structure of the sample, and on the other hand, asseses the suitability of the theoretical method to describe such small nanostructures. The addition energies of one- and two-electron rings are also reported and compared with the corresponding capacitance spectra.Comment: Typeset using Revtex, 7 pages and 8 Postscript figure

Optimizing a coarse-grained model for the recognition of protein-protein binding

We are optimizing a force-field to be used with our coarsegrained protein model for the recognition of protein -protein binding. We have found that, apart from ranking correctly the ligand-receptor conformations generated in a protein-protein docking algorithm, our model is able to distinguish binding (experimental structure) from nonbinding (false positive) conformations for many complexes. This suggests us that the model could have a good performance in complete cross-docking, a method aimed to recognize the possible binding between any two proteins that are unknown to interact.Peer Reviewe

Spin and density longitudinal response of quantum dots in time-dependent local-spin-density approximation

The longitudinal dipole response of a quantum dot has been calculated in the far-infrared regime using local spin density functional theory. We have studied the coupling between the collective spin and density modes as a function of the magnetic field. We have found that the spin dipole mode and single particle excitations have a sizeable overlap, and that the magnetoplasmon modes can be excited by the dipole spin operator if the dot is spin polarized. The frequency of the dipole spin edge mode presents an oscillation which is clearly filling factor ($\nu$) related. We have found that the spin dipole mode is especially soft for even $\nu$ values, becoming unstable for magnetic fields in the region $1 < \nu \leq 2$. Results for selected number of electrons and confining potentials are discussed. An analytical model which reproduces the main features of the microscopic spectra has been developed.Comment: We have added some new references and minor changes on the mnuscript have been mad

Wave-vector dependence of spin and density multipole excitations in quantum dots

We have employed time-dependent local-spin density functional theory to analyze the multipole spin and charge density excitations in GaAs-AlGaAs quantum dots. The on-plane transferred momentum degree of freedom has been taken into account, and the wave-vector dependence of the excitations is discussed. In agreement with previous experiments, we have found that the energies of these modes do not depend on the transferred wave-vector, although their intensities do. Comparison with a recent resonant Raman scattering experiment [C. Sch\"uller et al, Phys. Rev. Lett {\bf 80}, 2673 (1998)] is made. This allows to identify the angular momentum of several of the observed modes as well as to reproduce their energies.Comment: 14 pages in REVTEX and 14 postscript figure

Wave-vector dependence of spin and density multipole excitations in quantum dots

We have employed time-dependent local-spin density functional theory to analyze the multipole spin and charge density excitations in GaAs-AlGaAs quantum dots. The on-plane transferred momentum degree of freedom has been taken into account, and the wave-vector dependence of the excitations is discussed. In agreement with previous experiments, we have found that the energies of these modes do not depend on the transferred wave-vector, although their intensities do. Comparison with a recent resonant Raman scattering experiment [C. Sch\"uller et al, Phys. Rev. Lett {\bf 80}, 2673 (1998)] is made. This allows to identify the angular momentum of several of the observed modes as well as to reproduce their energies.Comment: 14 pages in REVTEX and 14 postscript figure

Optimizing a coarse-grained model for the recognition of protein-protein binding

We are optimizing a force-field to be used with our coarsegrained protein model for the recognition of protein -protein binding. We have found that, apart from ranking correctly the ligand-receptor conformations generated in a protein-protein docking algorithm, our model is able to distinguish binding (experimental structure) from nonbinding (false positive) conformations for many complexes. This suggests us that the model could have a good performance in complete cross-docking, a method aimed to recognize the possible binding between any two proteins that are unknown to interact.Peer Reviewe