Agustí Emperador

Longitudinal modes of quantum dots in magnetic fields

Abstract.The far infrared longitudinal spin and density responses of two-dimensional quantum dots are discussed within local spin-density functional theory. The influence of a partial spin polarization, induced by a perpendicular static magnetic field, is taken into account in the coupling of spin and density channels. As an illustrative application, the case of a dot made of 5 electrons in parabolic confinement is discussed.We show that in the presence of massive particles such as nucleons, the standard low energy expansion in powers of meson momenta and light quark masses in general only converges in part of the low energy region. The expansion of the scalar form factor

FlexServ: an integrated tool for the analysis of protein flexibility

\sigma(t)

Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.

, for instance, breaks down in the vicinity of

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations.

t=4M_\pi^2

Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins

. In the language of heavy baryon chiral perturbation theory, the proper behaviour in the threshold region only results if the multiple internal line insertions generated by relativistic kinematics are summed up to all orders. We propose a method that yields a coherent representation throughout the low energy region while keeping Lorentz and chiral invariance explicit at all stages. The method is illustrated with a calculation of the nucleon mass and of the scalar form factor to order

Density-functional calculations of magnetoplasmons in quantum rings

p^4

Protein flexibility from discrete molecular dynamics simulations using quasi‐physical potentials

.

Multipole modes and spin features in the Raman spectrum of nanoscopic quantum rings

SUMMARY FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols for the coarse-grained determination of protein dynamics using different versions of Normal Mode Analysis (NMA), Brownian dynamics (BD) and Discrete Dynamics (DMD). It can also analyze user provided trajectories. The server allows a complete analysis of flexibility using a large variety of metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness analysis, collectivity measures, Lindemanns indexes, residue correlation, chain-correlations, dynamic domain determination, hinge point detections, etc. Data is presented through a web interface as plain text, 2D and 3D graphics. AVAILABILITY http://mmb.pcb.ub.es/FlexServ; http://www.inab.org

Exploration of conformational transition pathways from coarse-grained simulations

A systematic study of two coarse-grained techniques for the description of protein dynamics is presented. The two techniques exploit either Brownian or discrete molecular dynamics algorithms applied in the context of simple C(alpha)-C(alpha) potentials, like those used in coarse-grained normal mode analysis. Coarse-grained simulations of the flexibility of protein metafolds are compared to those computed with fully atomistic molecular dynamics simulations using state-of-the-art physical potentials and explicit solvent. Both coarse-grained models efficiently capture critical features of the protein dynamics.

Coarse-grained Representation of Protein Flexibility. Foundations, Successes, and Shortcomings

We present a new method for estimating pathways for conformational transitions in macromolecules from the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell-Demon sampling techniques. The method can work with high efficiency at different levels of resolution, including the atomistic one, and can help to define initial pathways for further exploration by means of more accurate atomistic molecular dynamics simulations. The method is implemented in a freely available Web-based application accessible at http://mmb.irbbarcelona.org/MDdMD .