4,575 research outputs found
High-resolution ab initio three-dimensional X-ray diffraction microscopy
Coherent X-ray diffraction microscopy is a method of imaging non-periodic
isolated objects at resolutions only limited, in principle, by the largest
scattering angles recorded. We demonstrate X-ray diffraction imaging with high
resolution in all three dimensions, as determined by a quantitative analysis of
the reconstructed volume images. These images are retrieved from the 3D
diffraction data using no a priori knowledge about the shape or composition of
the object, which has never before been demonstrated on a non-periodic object.
We also construct 2D images of thick objects with infinite depth of focus
(without loss of transverse spatial resolution). These methods can be used to
image biological and materials science samples at high resolution using X-ray
undulator radiation, and establishes the techniques to be used in
atomic-resolution ultrafast imaging at X-ray free-electron laser sources.Comment: 22 pages, 11 figures, submitte
A Multiobjective Approach Applied to the Protein Structure Prediction Problem
Interest in discovering a methodology for solving the Protein Structure Prediction problem extends into many fields of study including biochemistry, medicine, biology, and numerous engineering and science disciplines. Experimental approaches, such as, x-ray crystallographic studies or solution Nuclear Magnetic Resonance Spectroscopy, to mathematical modeling, such as minimum energy models are used to solve this problem. Recently, Evolutionary Algorithm studies at the Air Force Institute of Technology include the following: Simple Genetic Algorithm (GA), messy GA, fast messy GA, and Linkage Learning GA, as approaches for potential protein energy minimization. Prepackaged software like GENOCOP, GENESIS, and mGA are in use to facilitate experimentation of these techniques. In addition to this software, a parallelized version of the fmGA, the so-called parallel fast messy GA, is found to be good at finding semi-optimal answers in reasonable wall clock time. The aim of this work is to apply a Multiobjective approach to solving this problem using a modified fast messy GA. By dividing the CHARMm energy model into separate objectives, it should be possible to find structural configurations of a protein that yield lower energy values and ultimately more correct conformations
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
Now we’re cooking: new successes for shake-and-bake
AbstractShake-and-bake is an automatic procedure for phase determination developed for large molecules. The procedure is based on a minimal function which is optimized through alternate cycles of reciprocal space phase refinement and real-space filtering. The shake-and-bake technique has now been used to determine the structures of several small proteins
Impact of synchrotron radiation on macromolecular crystallography: a personal view
This article, largely based on personal experiences of the authors, reviews the early history of the application of synchrotron radiation to structural biology, and particularly protein crystallography, to show the tremendous impact that this experimental innovation has had on these disciplines
Multivariate Analysis Applications in X-ray Diffraction
: Multivariate analysis (MA) is becoming a fundamental tool for processing in an efficient
way the large amount of data collected in X-ray diffraction experiments. Multi-wedge data
collections can increase the data quality in case of tiny protein crystals; in situ or operando setups
allow investigating changes on powder samples occurring during repeated fast measurements;
pump and probe experiments at X-ray free-electron laser (XFEL) sources supply structural
characterization of fast photo-excitation processes. In all these cases, MA can facilitate the extraction
of relevant information hidden in data, disclosing the possibility of automatic data processing even
in absence of a priori structural knowledge. MA methods recently used in the field of X-ray
diffraction are here reviewed and described, giving hints about theoretical background and possible
applications. The use of MA in the framework of the modulated enhanced diffraction technique is
described in detail
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