117,439 research outputs found
AURA: Atlas of UTR Regulatory Activity
No full textSUMMARY:
The Atlas of UTR Regulatory Activity (AURA) is a manually curated and comprehensive catalog of human mRNA untranslated regions (UTRs) and UTR regulatory annotations. Through its intuitive web interface, it provides full access to a wealth of information on UTRs that integrates phylogenetic conservation, RNA sequence and structure data, single nucleotide variation, gene expression and gene functional descriptions from literature and specialized databases.
AVAILABILITY:
http://aura.science.unitn.it
CONTACT:
[email protected]; [email protected]
SUPPLEMENTARY INFORMATION:
Supplementary data are available at Bioinformatics online
Vorticity-stabilized virtual elements for the Oseen equation
No full textIn this paper, we extend the divergence-free VEM of [L. Beiraõ da Veiga, C. Lovadina and G. Vacca, Virtual elements for the Navier-Stokes problem on polygonal meshes, SIAM J. Numer. Anal. 56 (2018) 1210-1242] to the Oseen problem, including a suitable stabilization procedure that guarantees robustness in the convection-dominated case without disrupting the divergence-free property. The stabilization is inspired from [N. Ahmed, G. R. Barrenechea, E. Burman, J. Guzman, A. Linke and C. Merdon, A pressure-robust discretization of Oseen's equation using stabilization in the vorticity equation, SIAM J. Numer. Anal. 59 (2021) 2746-2774] and includes local SUPG-like terms of the vorticity equation, internal jump terms for the velocity gradients, and an additional VEM stabilization. We derive theoretical convergence results that underline the robustness of the scheme in different regimes, including the convection-dominated case. Furthermore, as in the non-stabilized case, the influence of the pressure on the velocity error is moderate, as it appears only through higher-order terms
Curvilinear Virtual Elements for 2D solid mechanics applications
No full textIn the present work we generalize the curvilinear Virtual Element technology, introduced for a simple linear scalar problem in a previous work, to generic 2D solid mechanic problems in small deformations. Such generalization also includes the development of a novel Virtual Element space for displacements that contains rigid body motions. Our approach can accept a generic black-box (elastic or inelastic) constitutive algorithm and, in addition, can make use of curved edges thus leading to an exact approximation of the geometry. Rigorous theoretical interpolation properties for the new space on curvilinear elements are derived. We develop an extensive numerical test campaign, both on elastic and inelastic problems, to assess the behavior of the scheme. The results are very promising and underline the advantages of the curved VEM approach over the standard one in the presence of curved geometries
A denoising tool for the reconstruction of cortical geometries from MRI
No full textThe reconstruction of individual geometries from medical imaging is quite a standard in the framework of patient-specific medicine. A major drawback in such a context is represented by noise inherent to the data acquisition. Low signal-to-noise ratios can negatively impact extraction algorithms, and result in artefacts or poor quality of the reconstructed meshes. Direct application of numerical methods on such meshes can yield misleading results. Indeed, artefacts and badly shaped elements may corrupt numerical simulations or induce relevant errors in the computation of meaningful geometrical quantities, such as the curvature or the geodesic surface distance. In this paper, we propose a denoising procedure to remove artefacts from a triangular mesh of a three-dimensional closed surface which represents a brain cortex. For this purpose, we combine a smoothing technique (i.e., the Taubin or the HC-Laplacian smoothing) with an edge-flipping algorithm. To control the denoising procedure, we introduce a stopping criterion that takes into account both the improvement of the mesh quality and the loss of volume enclosed by the surface. On a brain cortical surface reconstructed from Magnetic Resonance Imaging (MRI) data, we first perform a tuning analysis of the parameters involved in the smoothing algorithm, then we investigate the effectiveness of the denoising procedure. Finally, as an example of relevant geometrical feature, we study the improvement generated by the proposed algorithm on the computation of the cortical curvature
SUPG-stabilized virtual elements for diffusion-convection problems: A robustness analysis
No full textThe objective of this contribution is to develop a convergence analysis for SUPG-stabilized Virtual Element Methods in diffusion-convection problems that is robust also in the convection dominated regime. For the original method introduced in [Benedetto et al., CMAME 2016] we are able to show an "almost uniform"error bound (in the sense that the unique term that depends in an unfavourable way on the parameters is damped by a higher order mesh-size multiplicative factor). We also introduce a novel discretization of the convection term that allows us to develop error estimates that are fully robust in the convection dominated cases. We finally present some numerical result
The Stokes complex for Virtual Elements in three dimensions
No full textThis paper has two objectives. On one side, we develop and test numerically divergence-free Virtual Elements in three dimensions, for variable "polynomial" order. These are the natural extension of the two-dimensional divergence-free VEM elements, with some modification that allows for a better computational efficiency. We test the element's performance both for the Stokes and (diffusion dominated) Navier-Stokes equation. The second, and perhaps main, motivation is to show that our scheme, also in three dimensions, enjoys an underlying discrete Stokes complex structure. We build a pair of virtual discrete spaces based on general polytopal partitions, the first one being scalar and the second one being vector valued, such that when coupled with our velocity and pressure spaces, yield a discrete Stokes complex
Robust Finite Elements for Linearized Magnetohydrodynamics
No full textWe introduce a pressure robust Finite Element Method for the linearized Magnetohydrodynamics equations in three space dimensions, which is provably quasi-robust also in the presence of high fluid and magnetic Reynolds numbers. The proposed scheme uses a non-conforming BDM approach with suitable DG terms for the fluid part, combined with an H1-conforming choice for the magnetic fluxes. The method introduces also a specific CIP-type stabilization associated to the coupling terms. Finally, the theoretical result are further validated by numerical experiments
Pressure robust SUPG-stabilized finite elements for the unsteady Navier–Stokes equation
No full textIn the present contribution, we propose a novel conforming finite element scheme for the time-dependent Navier–Stokes equation, which is proven to be both convection quasi-robust and pressure robust. The method is built combining a "divergence-free" velocity/pressure couple (such as the Scott-Vogelius element), a discontinuous Galerkin in time approximation and a suitable streamline upwind Petrov–Galerkin-curl stabilization. A set of numerical tests, in accordance with the theoretical results, is included
Gyroid Lattice Heat Exchangers: Comparative Analysis on Thermo-Fluid Dynamic Performances
No full textIn recent years, additive manufacturing has reached the required reliability to effectively compete with standard production techniques of mechanical components. In particular, the geometrical freedom enabled by innovative manufacturing techniques has revolutionized the design trends for compact heat exchangers. Bioinspired structures, such as the gyroid lattice, have relevant mechanical and heat exchange properties for their light weight and increased heat exchange area, which also promotes the turbulent regime of the coolant. This work focuses its attention on the effect of the relevant design parameters of the gyroid lattice on heat exchange performances. A numerical comparative analysis is carried out from the thermal and fluid dynamic points of view to give design guidelines. The results of numerical analyses, performed on cylindrical samples, are compared to the experimental results on the pressure drop. Lattices samples were successfully printed with material extrusion, which is a low-cost and easy-to-use metal AM technology. For each lattice sample, counter pressure, heat exchange, and turbulence intensity ratio are calculated from the numerical point of view and discussed. At the end, the gyroid lattice is proven to be very effective at enhancing the heat exchange in cylindrical pipes. Guidelines are given about the choice of the best lattice, depending on the considered applications
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