A new enrichment space for the treatment of discontinuous pressures in multi-fluid flows

In this work, a new enrichment space to accommodate jumps in the pressure field at immersed interfaces in finite element formulations, is proposed. The new enrichment adds two degrees of freedom per element that can be eliminated by means of static condensation. The new space is tested and compared with the classical P1 space and to the space proposed by Ausas et al (Comp. Meth. Appl. Mech. Eng., Vol. 199, 10191031, 2010) in several problems involving jumps in the viscosity and/or the presence of singular forces at interfaces not conforming with the element edges. The combination of this enrichment space with another enrichment that accommodates discontinuities in the pressure gradient has also been explored, exhibiting excellent results in problems involving jumps in the density or the volume forces. Copyright (c) 2011 John Wiley & Sons, Ltd.

Unique Alterations of an Ultraconserved Non-Coding Element in the 3 ' UTR of ZIC2 in Holoprosencephaly

Coding region alterations of ZIC2 are the second most common type of mutation in holoprosencephaly (HPE). Here we use several complementary bioinformatic approaches to identify ultraconserved cis-regulatory sequences potentially driving the expression of human ZIC2. We demonstrate that an 804 bp element in the 3' untranslated region (3'UTR) is highly conserved across the evolutionary history of vertebrates from fish to humans. Furthermore, we show that while genetic variation of this element is unexpectedly common among holoprosencephaly subjects (6/528 or >1%), it is not present in control individuals. Two of six proband-unique variants are de novo, supporting their pathogenic involvement in HPE outcomes. These findings support a general recommendation that the identification and analysis of key ultraconserved elements should be incorporated into the genetic risk assessment of holoprosencephaly cases.

Remarks on Parametric Surface Waves in a Nonlinear and Non-Ideally Excited Tank

We studied free surface oscillations of a fluid in a cylinder tank excited by an electric motor with limited power supply. We investigated the possibility of parametric resonance in this system, showing that the excitation mechanism can generate chaotic response. Numerical experiments are carried out to present the existence of several types of regular and chaotic attractors. For the first time powers (power of the motor, power consumed by the damping force under fluid free surface oscillations, and a total power) are calculated, investigated, and shown for different regimes, regular and chaotic ones for parametric resonance interactions. [DOI: 10.1115/1.4005844]

Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region

Abstract Background The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification. Results We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2. Conclusion The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.

Strong Coupling Isotropization of Non-Abelian Plasmas Simplified

We study the isotropization of a homogeneous, strongly coupled, non-Abelian plasma by means of its gravity dual. We compare the time evolution of a large number of initially anisotropic states as determined, on the one hand, by the full nonlinear Einstein's equations and, on the other, by the Einstein's equations linearized around the final equilibrium state. The linear approximation works remarkably well even for states that exhibit large anisotropies. For example, it predicts with a 20% accuracy the isotropization time, which is of the order of t(iso) less than or similar to 1/T, with T the final equilibrium temperature. We comment on possible extensions to less symmetric situations.

Non-linear magnetohydrodynamic simulations of density evolution in Tore Supra sawtoothing plasmas

The plasma density evolution in sawtooth regime on the Tore Supra tokamak is analyzed. The density is measured using fast-sweeping X-mode reflectometry which allows tomographic reconstructions. There is evidence that density is governed by the perpendicular electric flows, while temperature evolution is dominated by parallel diffusion. Postcursor oscillations sometimes lead to the formation of a density plateau, which is explained in terms of convection cells associated with the kink mode. A crescent-shaped density structure located inside q = 1 is often visible just after the crash and indicates that some part of the density withstands the crash. 3D full MHD nonlinear simulations with the code XTOR-2F recover this structure and show that it arises from the perpendicular flows emerging from the reconnection layer. The proportion of density reinjected inside the q = 1 surface is determined, and the implications in terms of helium ash transport are discussed. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4766893]

Analysis of elastic functionally graded materials under large displacements via high-order tetrahedral elements

The purpose of this study is to present a position based tetrahedral finite element method of any order to accurately predict the mechanical behavior of solids constituted by functionally graded elastic materials and subjected to large displacements. The application of high-order elements makes it possible to overcome the volumetric and shear locking that appears in usual homogeneous isotropic situations or even in non-homogeneous cases developing small or large displacements. The use of parallel processing to improve the computational efficiency, allows employing high-order elements instead of low-order ones with reduced integration techniques or strain enhancements. The Green-Lagrange strain is adopted and the constitutive relation is the functionally graded Saint Venant-Kirchhoff law. The equilibrium is achieved by the minimum total potential energy principle. Examples of large displacement problems are presented and results confirm the locking free behavior of high-order elements for non-homogeneous materials. (C) 2011 Elsevier B.V. All rights reserved.

Chaos-based communication systems in non-ideal channels

Recently, many chaos-based communication systems have been proposed. They can present the many interesting properties of spread spectrum modulations. Besides, they can represent a low-cost increase in security. However, their major drawback is to have a Bit Error Rate (BER) general performance worse than their conventional counterparts. In this paper, we review some innovative techniques that can be used to make chaos-based communication systems attain lower levels of BER in non-ideal environments. In particular, we succinctly describe techniques to counter the effects of finite bandwidth, additive noise and delay in the communication channel. Although much research is necessary for chaos-based communication competing with conventional techniques, the presented results are auspicious. (C) 2011 Elsevier B. V. All rights reserved.

Assessment of variance components in nonlinear mixed-effects elliptical models

The issue of assessing variance components is essential in deciding on the inclusion of random effects in the context of mixed models. In this work we discuss this problem by supposing nonlinear elliptical models for correlated data by using the score-type test proposed in Silvapulle and Silvapulle (1995). Being asymptotically equivalent to the likelihood ratio test and only requiring the estimation under the null hypothesis, this test provides a fairly easy computable alternative for assessing one-sided hypotheses in the context of the marginal model. Taking into account the possible non-normal distribution, we assume that the joint distribution of the response variable and the random effects lies in the elliptical class, which includes light-tailed and heavy-tailed distributions such as Student-t, power exponential, logistic, generalized Student-t, generalized logistic, contaminated normal, and the normal itself, among others. We compare the sensitivity of the score-type test under normal, Student-t and power exponential models for the kinetics data set discussed in Vonesh and Carter (1992) and fitted using the model presented in Russo et al. (2009). Also, a simulation study is performed to analyze the consequences of the kurtosis misspecification.

Phase-Locked loops lock-in range in Frequency Modulated-Atomic Force Microscope nonlinear control system

Since the mid 1980s the Atomic Force Microscope is one the most powerful tools to perform surface investigation, and since 1995 Non-Contact AFM achieved true atomic resolution. The Frequency-Modulated Atomic Force Microscope (FM-AFM) operates in the dynamic mode, which means that the control system of the FM-AFM must force the micro-cantilever to oscillate with constant amplitude and frequency. However, tip-sample interaction forces cause modulations in the microcantilever motion. A Phase-Locked loop (PLL) is used to demodulate the tip-sample interaction forces from the microcantilever motion. The demodulated signal is used as the feedback signal to the control system, and to generate both topographic and dissipation images. As a consequence, a proper design of the PLL is vital to the FM-AFM performance. In this work, using bifurcation analysis, the lock-in range of the PLL is determined as a function of the frequency shift (Q) of the microcantilever and of the other design parameters, providing a technique to properly design the PLL in the FM-AFM system. (C) 2011 Elsevier B.V. All rights reserved.

Modeling of continuous thermal processing of a non-Newtonian liquid food under diffusive laminar flow in a tubular system

The classic conservative approach for thermal process design can lead to over-processing, especially for laminar flow, when a significant distribution of temperature and of residence time occurs. In order to optimize quality retention, a more comprehensive model is required. A model comprising differential equations for mass and heat transfer is proposed for the simulation of the continuous thermal processing of a non-Newtonian food in a tubular system. The model takes into account the contribution from heating and cooling sections, the heat exchange with the ambient air and effective diffusion associated with non-ideal laminar flow. The study case of soursop juice processing was used to test the model. Various simulations were performed to evaluate the effect of the model assumptions. An expressive difference in the predicted lethality was observed between the classic approach and the proposed model. The main advantage of the model is its flexibility to represent different aspects with a small computational time, making it suitable for process evaluation and design. (C) 2012 Elsevier Ltd. All rights reserved.

MULTIPLICITY OF NONRADIAL SOLUTIONS FOR A CLASS OF QUASILINEAR EQUATIONS ON ANNULUS WITH EXPONENTIAL CRITICAL GROWTH

In this paper, we establish the existence of many rotationally non-equivalent and nonradial solutions for the following class of quasilinear problems (p) {-Delta(N)u = lambda f(vertical bar x vertical bar, u) x is an element of Omega(r), u > 0 x is an element of Omega(r), u = 0 x is an element of Omega(r), where Omega(r) = {x is an element of R-N : r < vertical bar x vertical bar < r + 1}, N >= 2, N not equal 3, r >0, lambda > 0, Delta(N)u = div(vertical bar del u vertical bar(N-2)del u) is the N-Laplacian operator and f is a continuous function with exponential critical growth.

A generalized finite element method with global-local enrichment functions for confined plasticity problems

The main feature of partition of unity methods such as the generalized or extended finite element method is their ability of utilizing a priori knowledge about the solution of a problem in the form of enrichment functions. However, analytical derivation of enrichment functions with good approximation properties is mostly limited to two-dimensional linear problems. This paper presents a procedure to numerically generate proper enrichment functions for three-dimensional problems with confined plasticity where plastic evolution is gradual. This procedure involves the solution of boundary value problems around local regions exhibiting nonlinear behavior and the enrichment of the global solution space with the local solutions through the partition of unity method framework. This approach can produce accurate nonlinear solutions with a reduced computational cost compared to standard finite element methods since computationally intensive nonlinear iterations can be performed on coarse global meshes after the creation of enrichment functions properly describing localized nonlinear behavior. Several three-dimensional nonlinear problems based on the rate-independent J (2) plasticity theory with isotropic hardening are solved using the proposed procedure to demonstrate its robustness, accuracy and computational efficiency.

A nonlinear elasticity phantom containing spherical inclusions

The strain image contrast of some in vivo breast lesions changes with increasing applied load. This change is attributed to differences in the nonlinear elastic properties of the constituent tissues suggesting some potential to help classify breast diseases by their nonlinear elastic properties. A phantom with inclusions and long-term stability is desired to serve as a test bed for nonlinear elasticity imaging method development, testing, etc. This study reports a phantom designed to investigate nonlinear elastic properties with ultrasound elastographic techniques. The phantom contains four spherical inclusions and was manufactured from a mixture of gelatin, agar and oil. The phantom background and each of the inclusions have distinct Young's modulus and nonlinear mechanical behavior. This phantom was subjected to large deformations (up to 20%) while scanning with ultrasound, and changes in strain image contrast and contrast-to-noise ratio between inclusion and background, as a function of applied deformation, were investigated. The changes in contrast over a large deformation range predicted by the finite element analysis (FEA) were consistent with those experimentally observed. Therefore, the paper reports a procedure for making phantoms with predictable nonlinear behavior, based on independent measurements of the constituent materials, and shows that the resulting strain images (e. g., strain contrast) agree with that predicted with nonlinear FEA.