14,271 research outputs found
Introduction to protein folding for physicists
The prediction of the three-dimensional native structure of proteins from the
knowledge of their amino acid sequence, known as the protein folding problem,
is one of the most important yet unsolved issues of modern science. Since the
conformational behaviour of flexible molecules is nothing more than a complex
physical problem, increasingly more physicists are moving into the study of
protein systems, bringing with them powerful mathematical and computational
tools, as well as the sharp intuition and deep images inherent to the physics
discipline. This work attempts to facilitate the first steps of such a
transition. In order to achieve this goal, we provide an exhaustive account of
the reasons underlying the protein folding problem enormous relevance and
summarize the present-day status of the methods aimed to solving it. We also
provide an introduction to the particular structure of these biological
heteropolymers, and we physically define the problem stating the assumptions
behind this (commonly implicit) definition. Finally, we review the 'special
flavor' of statistical mechanics that is typically used to study the
astronomically large phase spaces of macromolecules. Throughout the whole work,
much material that is found scattered in the literature has been put together
here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to
arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co
Principled Design and Implementation of Steerable Detectors
We provide a complete pipeline for the detection of patterns of interest in
an image. In our approach, the patterns are assumed to be adequately modeled by
a known template, and are located at unknown position and orientation. We
propose a continuous-domain additive image model, where the analyzed image is
the sum of the template and an isotropic background signal with self-similar
isotropic power-spectrum. The method is able to learn an optimal steerable
filter fulfilling the SNR criterion based on one single template and background
pair, that therefore strongly responds to the template, while optimally
decoupling from the background model. The proposed filter then allows for a
fast detection process, with the unknown orientation estimation through the use
of steerability properties. In practice, the implementation requires to
discretize the continuous-domain formulation on polar grids, which is performed
using radial B-splines. We demonstrate the practical usefulness of our method
on a variety of template approximation and pattern detection experiments
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