25,725 research outputs found
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
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
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
Energy resolved STM mapping of C 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 between electrons on
neighbor and non neighbor sites 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
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