A variational approach to camera motion smoothing

[EN] In this paper we study a variational problem derived from a computer vision application: video camera calibration with smoothing constraint. By video camera calibration we meanto estimate the location, orientation and lens zoom-setting of the camera for each video frame taking into account image visible features. To simplify the problem we assume that the camera is mounted on a tripod, in such case, for each frame captured at time t , the calibration is provided by 3 parameters : (1) P(t) (PAN) which represents the tripod vertical axis rotation, (2) T(t) (TILT) which represents the tripod horizontal axis rotation and (3) Z(t) (CAMERA ZOOM) the camera lens zoom setting. The calibration function t -> u(t) = (P(t),T(t),Z(t)) is obtained as the minima of an energy function I[u] . In thIs paper we study the existence of minima of such energy function as well as the solutions of the associated Euler-Lagrange equations.

Multi-modal diffeomorphic demons registration based on point-wise mutual information

In this paper we propose a variational approach for multimodal image registration based on the diffeomorphic demons algorithm. Diffeomorphic demons has proven to be a robust and efficient way for intensity-based image registration. However, the main drawback is that it cannot deal with multiple modalities. We propose to replace the standard demons similarity metric (image intensity differences) by point-wise mutual information (PMI) in the energy function. By comparing the accuracy between our PMI based diffeomorphic demons and the B-Spline based free-form deformation approach (FFD) on simulated deformations, we show the proposed algorithm performs significantly better.

Numerical model of the human cornea based on stromal microstructure: identification of mechanical properties for two age groups

The optical quality of the human eye mainly depends on the refractive performance of the cornea. The shape of the cornea is a mechanical balance between intraocular pressure and tissue intrinsic stiffness. Several surgical procedures in ophthalmology alter the biomechanics of the cornea to provoke local or global curvature changes for vision correction. Legitimated by the large number of surgical interventions performed every day, the demand for a deeper understanding of corneal biomechanics is rising to improve the safety of procedures and medical devices. The aim of our work is to propose a numerical model of corneal biomechanics, based on the stromal microstructure. Our novel anisotropic constitutive material law features a probabilistic weighting approach to model collagen fiber distribution as observed on human cornea by Xray scattering analysis (Aghamohammadzadeh et. al., Structure, February 2004). Furthermore, collagen cross-linking was explicitly included in the strain energy function. Results showed that the proposed model is able to successfully reproduce both inflation and extensiometry experimental data (Elsheikh et. al., Curr Eye Res, 2007; Elsheikh et. al., Exp Eye Res, May 2008). In addition, the mechanical properties calculated for patients of different age groups (Group A: 65-79 years; Group B: 80-95 years) demonstrate an increased collagen cross-linking, and a decrease in collagen fiber elasticity from younger to older specimen. These findings correspond to what is known about maturing fibrous biological tissue. Since the presented model can handle different loading situations and includes the anisotropic distribution of collagen fibers, it has the potential to simulate clinical procedures involving nonsymmetrical tissue interventions. In the future, such mechanical model can be used to improve surgical planning and the design of next generation ophthalmic devices.

Discussion of "Simplified Model of Low Cycle Fatigue for RC Frames"

To model strength degradation due to low cycle fatigue, at least three different approaches can be considered. One possibility is based on the formulation of a new free energy function and damage energy release rate, as was proposed by Ju(1989). The second approach uses the notion of bounding surface introduced in cyclic plasticity by Dafalias and Popov (1975). From this concept, some models have been proposed to quantify damage in concrete or RC (Suaris et al. 1990). The model proposed by the author to include fatigue effects is based essentially in Marigo (1985) and can be included in this approach.

Finite elastic deformations of transversely isotropic circular cylindrical tubes

We consider the finite radially symmetric deformation of a circular cylindrical tube of a homogeneous transversely isotropic elastic material subject to axial stretch, radial deformation and torsion, supported by axial load, internal pressure and end moment. Two different directions of transverse isotropy are considered: the radial direction and an arbitrary direction in planes normal locally to the radial direction, the only directions for which the considered deformation is admissible in general. In the absence of body forces, formulas are obtained for the internal pressure, and the resultant axial load and torsional moment on the ends of the tube in respect of a general strain-energy function. For a specific material model of transversely isotropic elasticity, and material and geometrical parameters, numerical results are used to illustrate the dependence of the pressure, (reduced) axial load and moment on the radial stretch and a measure of the torsional deformation for a fixed value of the axial stretch.

Discontinuous solutions and boundary value problems for non-linearly elastic fibre-reinforced materials

En este trabajo se han analizado varios problemas en el contexto de la elasticidad no lineal basándose en modelos constitutivos representativos. En particular, se han analizado problemas relacionados con el fenómeno de perdida de estabilidad asociada con condiciones de contorno en el caso de material reforzados con fibras. Cada problema se ha formulado y se ha analizado por separado en diferentes capítulos. En primer lugar se ha mostrado el análisis del gradiente de deformación discontinuo para un material transversalmente isótropo, en particular, el modelo del material considerado consiste de una base neo-Hookeana isótropa incrustada con fibras de refuerzo direccional caracterizadas con un solo parámetro. La solución de este problema se vincula con instabilidades que dan lugar al mecanismo de fallo conocido como banda de cortante. La perdida de elipticidad de las ecuaciones diferenciales de equilibrio es una condición necesaria para que aparezca este tipo de soluciones y por tanto las inestabilidades asociadas. En segundo lugar se ha analizado una deformación combinada de extensión, inación y torsión de un tubo cilíndrico grueso donde se ha encontrado que la deformación citada anteriormente puede ser controlada solo para determinadas direcciones de las fibras refuerzo. Para entender el comportamiento elástico del tubo considerado se ha ilustrado numéricamente los resultados obtenidos para las direcciones admisibles de las fibras de refuerzo bajo la deformación considerada. En tercer lugar se ha estudiado el caso de un tubo cilíndrico grueso reforzado con dos familias de fibras sometido a cortante en la dirección azimutal para un modelo de refuerzo especial. En este problema se ha encontrado que las inestabilidades que aparecen en el material considerado están asociadas con lo que se llama soluciones múltiples de la ecuación diferencial de equilibrio. Se ha encontrado que el fenómeno de instabilidad ocurre en un estado de deformación previo al estado de deformación donde se pierde la elipticidad de la ecuación diferencial de equilibrio. También se ha demostrado que la condición de perdida de elipticidad y ^W=2 = 0 (la segunda derivada de la función de energía con respecto a la deformación) son dos condiciones necesarias para la existencia de soluciones múltiples. Finalmente, se ha analizado detalladamente en el contexto de elipticidad un problema de un tubo cilíndrico grueso sometido a una deformación combinada en las direcciones helicoidal, axial y radial para distintas geotermias de las fibras de refuerzo . In the present work four main problems have been addressed within the framework of non-linear elasticity based on representative constitutive models. Namely, problems related to the loss of stability phenomena associated with boundary value problems for fibre-reinforced materials. Each of the considered problems is formulated and analysed separately in different chapters. We first start with the analysis of discontinuous deformation gradients for a transversely isotropic material under plane deformation. In particular, the material model is an augmented neo-Hookean base with a simple unidirectional reinforcement characterised by a single parameter. The solution of this problem is related to material instabilities and it is associated with a shear band-type failure mode. The loss of ellipticity of the governing differential equations is a necessary condition for the existence of these material instabilities. The second problem involves a detailed analysis of the combined non-linear extension, inflation and torsion of a thick-walled circular cylindrical tube where it has been found that the aforementioned deformation is controllable only for certain preferred directions of transverse isotropy. Numerical results have been illustrated to understand the elastic behaviour of the tube for the admissible preferred directions under the considered deformation. The third problem deals with the analysis of a doubly fibre-reinforced thickwalled circular cylindrical tube undergoing pure azimuthal shear for a special class of the reinforcing model where multiple non-smooth solutions emerge. The associated instability phenomena are found to occur prior to the point where the nominal stress tensor changes monotonicity in a particular direction. It has been also shown that the loss of ellipticity condition that arises from the equilibrium equation and ^W=2 = 0 (the second derivative of the strain-energy function with respect to the deformation) are equivalent necessary conditions for the emergence of multiple solutions for the considered material. Finally, a detailed analysis in the basis of the loss of ellipticity of the governing differential equations for a combined helical, axial and radial elastic deformations of a fibre-reinforced circular cylindrical tube is carried out.

A new label fusion method using graph cuts: application to hippocampus segmentation

The aim of this paper is to develop a probabilistic modeling framework for the segmentation of structures of interest from a collection of atlases. Given a subset of registered atlases into the target image for a particular Region of Interest (ROI), a statistical model of appearance and shape is computed for fusing the labels. Segmentations are obtained by minimizing an energy function associated with the proposed model, using a graph-cut technique. We test different label fusion methods on publicly available MR images of human brains.

A gradient-enhanced large-deformation continuum damage model for fibre-reinforced materials

A non-local gradient-based damage formulation within a geometrically non-linear setting is presented. The hyperelastic constitutive response at local material point level is governed by a strain energy which is additively composed of an isotropic matrix and of an anisotropic fibre-reinforced material, respectively. The inelastic constitutive response is governed by a scalar [1–d]-type damage formulation, where only the anisotropic elastic part is assumed to be affected by the damage. Following the concept in Dimitrijević and Hackl [28], the local free energy function is enhanced by a gradient-term. This term essentially contains the gradient of the non-local damage variable which, itself, is introduced as an additional independent variable. In order to guarantee the equivalence between the local and non-local damage variable, a penalisation term is incorporated within the free energy function. Based on the principle of minimum total potential energy, a coupled system of Euler–Lagrange equations, i.e., the balance of linear momentum and the balance of the non-local damage field, is obtained and solved in weak form. The resulting coupled, highly non-linear system of equations is symmetric and can conveniently be solved by a standard incremental-iterative Newton–Raphson-type solution scheme. Several three-dimensional displacement- and force-driven boundary value problems—partially motivated by biomechanical application—highlight the mesh-objective characteristics and constitutive properties of the model and illustratively underline the capabilities of the formulation proposed

A gradient-enhanced continuum damage model with application to fibre-reinforced tissues at finite strains

A non-local gradient-based damage formulation within a geometrically non-linear set- ting is presented. The hyperelastic constitutive response at local material point level is governed by a strain energy function which is additively composed by an isotropic neo-Hookean matrix and by an anisotropic fibre-reinforced material based on the model proposed by T. Gasser, R. Ogden, and G. Holzapfel.

A study of the mechanical behaviour of the human aortic artery by means of non-linear finite element models

En la presente tesis desarrollamos una estrategia para la simulación numérica del comportamiento mecánico de la aorta humana usando modelos de elementos finitos no lineales. Prestamos especial atención a tres aspectos claves relacionados con la biomecánica de los tejidos blandos. Primero, el análisis del comportamiento anisótropo característico de los tejidos blandos debido a las familias de fibras de colágeno. Segundo, el análisis del ablandamiento presentado por los vasos sanguíneos cuando estos soportan cargas fuera del rango de funcionamiento fisiológico. Y finalmente, la inclusión de las tensiones residuales en las simulaciones en concordancia con el experimento de apertura de ángulo. El análisis del daño se aborda mediante dos aproximaciones diferentes. En la primera aproximación se presenta una formulación de daño local con regularización. Esta formulación tiene dos ingredientes principales. Por una parte, usa los principios de la teoría de la fisura difusa para garantizar la objetividad de los resultados con diferentes mallas. Por otra parte, usa el modelo bidimensional de Hodge-Petruska para describir el comportamiento mesoscópico de los fibriles. Partiendo de este modelo mesoscópico, las propiedades macroscópicas de las fibras de colágeno son obtenidas a través de un proceso de homogenización. En la segunda aproximación se presenta un modelo de daño no-local enriquecido con el gradiente de la variable de daño. El modelo se construye a partir del enriquecimiento de la función de energía con un término que contiene el gradiente material de la variable de daño no-local. La inclusión de este término asegura una regularización implícita de la implementación por elementos finitos, dando lugar a resultados de las simulaciones que no dependen de la malla. La aplicabilidad de este último modelo a problemas de biomecánica se estudia por medio de una simulación de un procedimiento quirúrgico típico conocido como angioplastia de balón. In the present thesis we develop a framework for the numerical simulation of the mechanical behaviour of the human aorta using non-linear finite element models. Special attention is paid to three key aspects related to the biomechanics of soft tissues. First, the modelling of the characteristic anisotropic behaviour of the softue due to the collagen fibre families. Secondly, the modelling of damage-related softening that blood vessels exhibit when subjected to loads beyond their physiological range. And finally, the inclusion of the residual stresses in the simulations in accordance with the opening-angle experiment The modelling of damage is addressed with two major and different approaches. In the first approach a continuum local damage formulation with regularisation is presented. This formulation has two principal ingredients. On the one hand, it makes use of the principles of the smeared crack theory to avoid the mesh size dependence of the structural response in softening. On the other hand, it uses a Hodge-Petruska bidimensional model to describe the fibrils as staggered arrays of tropocollagen molecules, and from this mesoscopic model the macroscopic material properties of the collagen fibres are obtained using an homogenisation process. In the second approach a non-local gradient-enhanced damage formulation is introduced. The model is built around the enhancement of the free energy function by means of a term that contains the referential gradient of the non-local damage variable. The inclusion of this term ensures an implicit regularisation of the finite element implementation, yielding mesh-objective results of the simulations. The applicability of the later model to biomechanically-related problems is studied by means of the simulation of a typical surgical procedure, namely, the balloon angioplasty.

Structure-based conformational preferences of amino acids

Proteins can be very tolerant to amino acid substitution, even within their core. Understanding the factors responsible for this behavior is of critical importance for protein engineering and design. Mutations in proteins have been quantified in terms of the changes in stability they induce. For example, guest residues in specific secondary structures have been used as probes of conformational preferences of amino acids, yielding propensity scales. Predicting these amino acid propensities would be a good test of any new potential energy functions used to mimic protein stability. We have recently developed a protein design procedure that optimizes whole sequences for a given target conformation based on the knowledge of the template backbone and on a semiempirical potential energy function. This energy function is purely physical, including steric interactions based on a Lennard-Jones potential, electrostatics based on a Coulomb potential, and hydrophobicity in the form of an environment free energy based on accessible surface area and interatomic contact areas. Sequences designed by this procedure for 10 different proteins were analyzed to extract conformational preferences for amino acids. The resulting structure-based propensity scales show significant agreements with experimental propensity scale values, both for α-helices and β-sheets. These results indicate that amino acid conformational preferences are a natural consequence of the potential energy we use. This confirms the accuracy of our potential and indicates that such preferences should not be added as a design criterion.

Pressure-induced protein-folding/unfolding kinetics

We use an off-lattice minimalist model to describe the effects of pressure in slowing down the folding/unfolding kinetics of proteins when subjected to increasingly larger pressures. The potential energy function used to describe the interactions between beads in the model includes the effects of pressure on the pairwise interaction of hydrophobic groups in water. We show that pressure affects the participation of contacts in the transition state. More significantly, pressure exponentially decreases the chain reconfigurational diffusion coefficient. These results are consistent with experimental results on the kinetics of pressure-denaturation of staphylococcal nuclease.

The degree of nonlinearity and anisotropy of blood vessel elasticity

Blood vessel elasticity is important to physiology and clinical problems involving surgery, angioplasty, tissue remodeling, and tissue engineering. Nonlinearity in blood vessel elasticity in vivo is important to the formation of solitons in arterial pulse waves. It is well known that the stress–strain relationship of the blood vessel is nonlinear in general, but a controversy exists on how nonlinear it is in the physiological range. Another controversy is whether the vessel wall is biaxially isotropic. New data on canine aorta were obtained from a biaxial testing machine over a large range of finite strains referred to the zero-stress state. A new pseudo strain energy function is used to examine these questions critically. The stress–strain relationship derived from this function represents the sum of a linear stress–strain relationship and a definitely nonlinear relationship. This relationship fits the experimental data very well. With this strain energy function, we can define a parameter called the degree of nonlinearity, which represents the fraction of the nonlinear strain energy in the total strain energy per unit volume. We found that for the canine aorta, the degree of nonlinearity varies from 5% to 30%, depending on the magnitude of the strains in the physiological range. In the case of canine pulmonary artery in the arch region, Debes and Fung [Debes, J. C. & Fung, Y. C.(1995) Am. J. Physiol. 269, H433–H442] have shown that the linear regime of the stress–strain relationship extends from the zero-stress state to the homeostatic state and beyond. Both vessels, however, are anisotropic in both the linear and nonlinear regimes.

Native protein sequences are close to optimal for their structures

How large is the volume of sequence space that is compatible with a given protein structure? Starting from random sequences, low free energy sequences were generated for 108 protein backbone structures by using a Monte Carlo optimization procedure and a free energy function based primarily on Lennard–Jones packing interactions and the Lazaridis–Karplus implicit solvation model. Remarkably, in the designed sequences 51% of the core residues and 27% of all residues were identical to the amino acids in the corresponding positions in the native sequences. The lowest free energy sequences obtained for ensembles of native-like backbone structures were also similar to the native sequence. Furthermore, both the individual residue frequencies and the covariances between pairs of positions observed in the very large SH3 domain family were recapitulated in core sequences designed for SH3 domain structures. Taken together, these results suggest that the volume of sequence space optimal for a protein structure is surprisingly restricted to a region around the native sequence.

Protein fluctuations are sensed by stimulated infrared echoes of the vibrations of carbon monoxide and azide probes

The correlation functions of the fluctuations of vibrational frequencies of azide ions and carbon monoxide in proteins are determined directly from stimulated photon echoes generated with femtosecond infrared pulses. The asymmetric stretching vibration of azide bound to carbonic anhydrase II exhibits a pronounced evolution of its vibrational frequency distribution on the time scale of a few picoseconds, which is attributed to modifications of the ligand structure through interactions with the nearby Thr-199. When azide is bound in hemoglobin, a more complex evolution of the protein structure is required to interchange the different ligand configurations, as evidenced by the much slower relaxation of the frequency distribution in this case. The time evolution of the distribution of frequencies of carbon monoxide bound in hemoglobin occurs on the ≈10-ps time scale and is very nonexponential. The correlation functions of the frequency fluctuations determine the evolution of the protein structure local to the probe and the extent to which the probe can navigate those parts of the energy landscape where the structural configurations are able to modify the local potential energy function of the probe.