Selecting fast folding proteins by their rate of convergence

We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using only the very initial parts of the dynamical trajectories. It does not require any preliminary knowledge of the native state and can be applied to different kinds of models, including atomistic descriptions. We tested the method within both the lattice and off-lattice model frameworks and obtained several so far unknown good folders. The unbiased algorithm also allows to determine the optimal folding temperature and takes at least 3--4 orders of magnitude less time steps than those needed to compute folding times

Exact and approximate symmetries for light propagation equations with higher order nonlinearity

For the first time exact analytical solutions to the eikonal equations in (1+1) dimensions with a refractive index being a saturated function of intensity are constructed. It is demonstrated that the solutions exhibit collapse; an explicit analytical expression for the self-focusing position, where the intensity tends to infinity, is found. Based on an approximated Lie symmetry group, solutions to the eikonal equations with arbitrary nonlinear refractive index are constructed. Comparison between exact and approximate solutions is presented. Approximate solutions to the nonlinear Schrodinger equation in (1+2) dimensions with arbitrary refractive index and initial intensity distribution are obtained. A particular case of refractive index consisting of Kerr refraction and multiphoton ionization is considered. It is demonstrated that the beam collapse can take place not only at the beam axis but also in an off-axis ring region around it. An analytical condition distinguishing these two cases is obtained and explicit formula for the self-focusing position is presented.Comment: 25 pages, 5 figure

Extraordinary transverse magneto-optical Kerr effect in a superlens

It has been shown that a slab of a negative index material can behave as a superlens enhancing the imaging resolution beyond the wavelength limit. We show here that if such a slab possesses in addition some magneto-optical activity, it could act as an ideal optical filter and exhibit an extraordinary transverse magneto-optical Kerr effect. Moreover, we show that losses, which spoil the imaging resolution of these lenses, are a necessary ingredient to observe this effect.Comment: 5 pages, 6 figure

Energy resolved STM mapping of C60_{60} on metal surfaces: A theoretical study

We present a detailed theoretical study of scanning tunneling imaging and spectroscopy of \Csixty on silver and gold surfaces, motivated by the recent experiments and discussion by X. Lu et al. [PRL \textbf{90}, 096802 (2003) and PRB \textbf{70}, 115418 (2004)]. The surface/sample/tip system is described within a self--consistent DFT based tight--binding model. The topographic and conductance images are computed at constant current from a full self--consistent transport theory based on nonequilibrium Green's functions and compared with those simulated from the local density of states. The molecular orbitals of \Csixty are clearly identified in the energy resolved maps, in close correspondence with the experimental results. We show how the tip structure and orientation can affect the images. In particular, we consider the effects of truncated tips on the energy resolved maps.Comment: 9 pages, 8 figure

Enhancement of entanglement in one-dimensional disordered systems

The pairwise quantum entanglement of sites in disordered electronic one-dimensional systems (rings) is studied. We focus on the effect of diagonal and off diagonal disorder on the concurrence $C_{ij}$ between electrons on neighbor and non neighbor sites $i,j$ as a function of band filling. In the case of diagonal disorder, increasing the degree of disorder leads to a decrease of the concurrence with respect to the ordered case. However, off-diagonal disorder produces a surprisingly strong enhancement of entanglement. This remarkable effect occurs near half filling, where the concurrence becomes up to 15% larger than in the ordered system.Comment: 21 pages, 9 figure

All-electron theory of the coupling between laser-induced coherent phonons in bismuth

Using first principles, all-electron calculations and dynamical simulations we study the behavior of the A_1g and E_g coherent phonons induced in Bi by intense laser pulses. We determine the potential landscapes in the laser heated material and show that they exhibit phonon-softening, phonon-phonon coupling, and anharmonicities. As a consequence the E_g mode modulates the A_1g oscillations and higher harmonics of both modes appear, which explains recent isotropic reflectivity measurements. Our results offer a unified description of the different experimental observations performed so far on bismuth.Comment: 3 figure

Theory for the optimal control of time-averaged quantities in open quantum systems

We present variational theory for optimal control over a finite time interval in quantum systems with relaxation. The corresponding Euler-Lagrange equations determining the optimal control field are derived. In our theory the optimal control field fulfills a high order differential equation, which we solve analytically for some limiting cases. We determine quantitatively how relaxation effects limit the control of the system. The theory is applied to open two level quantum systems. An approximate analytical solution for the level occupations in terms of the applied fields is presented. Different other applications are discussed