113 research outputs found
Conformational analysis of nucleic acids revisited: Curves+
We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamic
Characterizing Distances of Networks on the Tensor Manifold
At the core of understanding dynamical systems is the ability to maintain and
control the systems behavior that includes notions of robustness,
heterogeneity, or regime-shift detection. Recently, to explore such functional
properties, a convenient representation has been to model such dynamical
systems as a weighted graph consisting of a finite, but very large number of
interacting agents. This said, there exists very limited relevant statistical
theory that is able cope with real-life data, i.e., how does perform analysis
and/or statistics over a family of networks as opposed to a specific network or
network-to-network variation. Here, we are interested in the analysis of
network families whereby each network represents a point on an underlying
statistical manifold. To do so, we explore the Riemannian structure of the
tensor manifold developed by Pennec previously applied to Diffusion Tensor
Imaging (DTI) towards the problem of network analysis. In particular, while
this note focuses on Pennec definition of geodesics amongst a family of
networks, we show how it lays the foundation for future work for developing
measures of network robustness for regime-shift detection. We conclude with
experiments highlighting the proposed distance on synthetic networks and an
application towards biological (stem-cell) systems.Comment: This paper is accepted at 8th International Conference on Complex
Networks 201
Méthode de Galerkin Discontinue : Cas de l'analyse isogéométrique
International audienceThe objective of Isogeometric Analysis is to address the design and analysis with exactlythe same geometric patterns. For this, the Lagrange polynomials usually used in interpolation arereplaced by B-Splines functions. In this context, we present in this work a new Discontinuous Galerkin(DG) method applied to the numerical solution of hyperbolic equations. The method is based on thechoice of a local Bernstein basis and Gauss-Legendre formulas to approximate the different integrals.We use a Lax-Friedrichs scheme to calculate the numerical flux.L'objectif de l'Analyse IsoGéométrique est de traiter la conception et l'analyse avec exactement les mêmes modèles géométriques. Pour cela, les polynômes de Lagrange classiquement utilisés pour l'interpolation sont remplacés par des fonctions B-Splines. Dans ce cadre, nous présentons dans ce travail une nouvelle méthode de type Galerkin Discontinue (GD), appliquée à la résolution numérique des équations hyperboliques. La méthode est basée sur le choix d'une base locale de Bernstein et des formules de Gauss-Legendre pour approcher les différentes intégrales. Nous utilisons un schéma de Lax-Friedrichs pour calculer les flux numériques
The closest elastic tensor of arbitrary symmetry to an elasticity tensor of lower symmetry
The closest tensors of higher symmetry classes are derived in explicit form
for a given elasticity tensor of arbitrary symmetry. The mathematical problem
is to minimize the elastic length or distance between the given tensor and the
closest elasticity tensor of the specified symmetry. Solutions are presented
for three distance functions, with particular attention to the Riemannian and
log-Euclidean distances. These yield solutions that are invariant under
inversion, i.e., the same whether elastic stiffness or compliance are
considered. The Frobenius distance function, which corresponds to common
notions of Euclidean length, is not invariant although it is simple to apply
using projection operators. A complete description of the Euclidean projection
method is presented. The three metrics are considered at a level of detail far
greater than heretofore, as we develop the general framework to best fit a
given set of moduli onto higher elastic symmetries. The procedures for finding
the closest elasticity tensor are illustrated by application to a set of 21
moduli with no underlying symmetry.Comment: 48 pages, 1 figur
Conformational analysis of nucleic acids revisited: Curves
We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics
Towards Reliable Automatic Protein Structure Alignment
A variety of methods have been proposed for structure similarity calculation,
which are called structure alignment or superposition. One major shortcoming in
current structure alignment algorithms is in their inherent design, which is
based on local structure similarity. In this work, we propose a method to
incorporate global information in obtaining optimal alignments and
superpositions. Our method, when applied to optimizing the TM-score and the GDT
score, produces significantly better results than current state-of-the-art
protein structure alignment tools. Specifically, if the highest TM-score found
by TMalign is lower than (0.6) and the highest TM-score found by one of the
tested methods is higher than (0.5), there is a probability of (42%) that
TMalign failed to find TM-scores higher than (0.5), while the same probability
is reduced to (2%) if our method is used. This could significantly improve the
accuracy of fold detection if the cutoff TM-score of (0.5) is used.
In addition, existing structure alignment algorithms focus on structure
similarity alone and simply ignore other important similarities, such as
sequence similarity. Our approach has the capacity to incorporate multiple
similarities into the scoring function. Results show that sequence similarity
aids in finding high quality protein structure alignments that are more
consistent with eye-examined alignments in HOMSTRAD. Even when structure
similarity itself fails to find alignments with any consistency with
eye-examined alignments, our method remains capable of finding alignments
highly similar to, or even identical to, eye-examined alignments.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Hyperbolic planforms in relation to visual edges and textures perception
We propose to use bifurcation theory and pattern formation as theoretical
probes for various hypotheses about the neural organization of the brain. This
allows us to make predictions about the kinds of patterns that should be
observed in the activity of real brains through, e.g. optical imaging, and
opens the door to the design of experiments to test these hypotheses. We study
the specific problem of visual edges and textures perception and suggest that
these features may be represented at the population level in the visual cortex
as a specific second-order tensor, the structure tensor, perhaps within a
hypercolumn. We then extend the classical ring model to this case and show that
its natural framework is the non-Euclidean hyperbolic geometry. This brings in
the beautiful structure of its group of isometries and certain of its subgroups
which have a direct interpretation in terms of the organization of the neural
populations that are assumed to encode the structure tensor. By studying the
bifurcations of the solutions of the structure tensor equations, the analog of
the classical Wilson and Cowan equations, under the assumption of invariance
with respect to the action of these subgroups, we predict the appearance of
characteristic patterns. These patterns can be described by what we call
hyperbolic or H-planforms that are reminiscent of Euclidean planar waves and of
the planforms that were used in [1, 2] to account for some visual
hallucinations. If these patterns could be observed through brain imaging
techniques they would reveal the built-in or acquired invariance of the neural
organization to the action of the corresponding subgroups.Comment: 34 pages, 11 figures, 2 table
A measure of bending in nucleic acids structures applied to A-tract DNA
A method is proposed to measure global bending in DNA and RNA structures. It relies on a properly defined averaging of base-fixed coordinate frames, computes mean frames of suitably chosen groups of bases and uses these mean frames to evaluate bending. The method is applied to DNA A-tracts, known to induce considerable bend to the double helix. We performed atomistic molecular dynamics simulations of sequences containing the A4T4 and T4A4 tracts, in a single copy and in two copies phased with the helical repeat. Various temperature and salt conditions were investigated. Our simulations indicate bending by roughly 10° per A4T4 tract into the minor groove, and an essentially straight structure containing T4A4, in agreement with electrophoretic mobility data. In contrast, we show that the published NMR structures of analogous sequences containing A4T4 and T4A4 tracts are significantly bent into the minor groove for both sequences, although bending is less pronounced for the T4A4 containing sequence. The bending magnitudes obtained by frame averaging are confirmed by the analysis of superhelices composed of repeated tract monomers
Statistical Computing on Non-Linear Spaces for Computational Anatomy
International audienceComputational anatomy is an emerging discipline that aims at analyzing and modeling the individual anatomy of organs and their biological variability across a population. However, understanding and modeling the shape of organs is made difficult by the absence of physical models for comparing different subjects, the complexity of shapes, and the high number of degrees of freedom implied. Moreover, the geometric nature of the anatomical features usually extracted raises the need for statistics on objects like curves, surfaces and deformations that do not belong to standard Euclidean spaces. We explain in this chapter how the Riemannian structure can provide a powerful framework to build generic statistical computing tools. We show that few computational tools derive for each Riemannian metric can be used in practice as the basic atoms to build more complex generic algorithms such as interpolation, filtering and anisotropic diffusion on fields of geometric features. This computational framework is illustrated with the analysis of the shape of the scoliotic spine and the modeling of the brain variability from sulcal lines where the results suggest new anatomical findings
A Fresh Variational-Analysis Look at the Positive Semidefinite Matrices World
International audienceEngineering sciences and applications of mathematics show unambiguously that positive semidefiniteness of matrices is the most important generalization of non-negative real num- bers. This notion of non-negativity for matrices has been well-studied in the literature; it has been the subject of review papers and entire chapters of books. This paper reviews some of the nice, useful properties of positive (semi)definite matrices, and insists in particular on (i) characterizations of positive (semi)definiteness and (ii) the geometrical properties of the set of positive semidefinite matrices. Some properties that turn out to be less well-known have here a special treatment. The use of these properties in optimization, as well as various references to applications, are spread all the way through. The "raison d'être" of this paper is essentially pedagogical; it adopts the viewpoint of variational analysis, shedding new light on the topic. Important, fruitful, and subtle, the positive semidefinite world is a good place to start with this domain of applied mathematics
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