Search results for "methods"
showing 10 items of 4526 documents
Illumina-based RiboMethSeq approach for mapping of 2'-O-Me residues in RNA
2016
International audience; RNA 2'-O-methylation is one of the ubiquitous nucleotide modifications found in many RNA types from Bacteria, Archaea and Eukarya. RNAs bearing 2'-O-methylations show increased resistance to degradation and enhanced stability in helices. While the exact role of each 2'-O-Me residue remained elusive, the catalytic protein Fibrillarin (Nop1 in yeast) responsible for 2'-O-methylation in eukaryotes, is associated with human pathologies. Therefore, there is an urgent need to precisely map and quantify hundreds of 2'-O-Me residues in RNA using high-throughput technologies. Here, we develop a reliable protocol using alkaline fragmentation of total RNA coupled to a commonly …
Acute Type Refinements of Tetrahedral Partitions of Polyhedral Domains
2001
We present a new technique to perform refinements on acute type tetrahedral partitions of a polyhedral domain, provided that the center of the circumscribed sphere around each tetrahedron belongs to the tetrahedron. The resulting family of partitions is of acute type; thus, all the tetrahedra satisfy the maximum angle condition. Both these properties are highly desirable in finite element analysis.
High-order Runge–Kutta–Nyström geometric methods with processing
2001
Abstract We present new families of sixth- and eighth-order Runge–Kutta–Nystrom geometric integrators with processing for ordinary differential equations. Both the processor and the kernel are composed of explicitly computable flows associated with non trivial elements belonging to the Lie algebra involved in the problem. Their efficiency is found to be superior to other previously known algorithms of equivalent order, in some case up to four orders of magnitude.
Order optimal preconditioners for fully implicit Runge-Kutta schemes applied to the bidomain equations
2010
The partial differential equation part of the bidomain equations is discretized in time with fully implicit Runge–Kutta methods, and the resulting block systems are preconditioned with a block diagonal preconditioner. By studying the time-stepping operator in the proper Sobolev spaces, we show that the preconditioned systems have bounded condition numbers given that the Runge–Kutta scheme is A-stable and irreducible with an invertible coefficient matrix. A new proof of order optimality of the preconditioners for the one-leg discretization in time of the bidomain equations is also presented. The theoretical results are verified by numerical experiments. Additionally, the concept of weakly po…
Fictitious Domain Methods for the Numerical Solution of Two-Dimensional Scattering Problems
1998
Fictitious domain methods for the numerical solution of two-dimensional scattering problems are considered. The original exterior boundary value problem is approximated by truncating the unbounded domain and by imposing a nonreflecting boundary condition on the artificial boundary. First-order, second-order, and exact nonreflecting boundary conditions are tested on rectangular and circular boundaries. The finite element discretizations of the corresponding approximate boundary value problems are performed using locally fitted meshes, and the discrete equations are solved with fictitious domain methods. A special finite element method using nonmatching meshes is considered. This method uses …
Numerical Investigations of an Implicit Leapfrog Time-Domain Meshless Method
2014
Numerical solution of partial differential equations governing time domain simulations in computational electromagnetics, is usually based on grid methods in space and on explicit schemes in time. A predefined grid in the problem domain and a stability step size restriction need. Recently, the authors have reformulated the meshless framework based on smoothed particle hydrodynamics, in order to be applied for time domain electromagnetic simulation. Despite the good spatial properties, the numerical explicit time integration introduces, also in a meshless context, a severe constraint. In this paper, at first, the stability condition is addressed in a general way by allowing the time step inc…
BEM-Based Magnetic Field Reconstruction by Ensemble Kálmán Filtering
2022
Abstract Magnetic fields generated by normal or superconducting electromagnets are used to guide and focus particle beams in storage rings, synchrotron light sources, mass spectrometers, and beamlines for radiotherapy. The accurate determination of the magnetic field by measurement is critical for the prediction of the particle beam trajectory and hence the design of the accelerator complex. In this context, state-of-the-art numerical field computation makes use of boundary-element methods (BEM) to express the magnetic field. This enables the accurate computation of higher-order partial derivatives and local expansions of magnetic potentials used in efficient numerical codes for particle tr…
A marching in space and time (MAST) solver of the shallow water equations. Part II: The 2D model
2007
Abstract A novel methodology for the solution of the 2D shallow water equations is proposed. The algorithm is based on a fractional step decomposition of the original system in (1) a convective prediction, (2) a convective correction, and (3) a diffusive correction step. The convective components are solved using a Marching in Space and Time (MAST) procedure, that solves a sequence of small ODEs systems, one for each computational cell, ordered according to the cell value of a scalar approximated potential. The scalar potential is sought after computing first the minimum of a functional via the solution of a large linear system and then refining locally the optimum search. Model results are…
A numerical meshless particle method in solving the magnetoencephalography forward problem
2012
In this paper, a numerical meshless particle method is presented in order to solve the magnetoencephalography forward problem for analyzing the complex activation patterns in the human brain. The forward problem is devoted to compute the scalp potential and magnetic field distribution generated by a set of current sources representing the neural activity, and in this paper, it has been approached by means of the smoothed particle hydrodynamics method suitably handled. The Poisson equation generated by the quasi-stationary Maxwell’s curl equations, by assuming Neumann boundary conditions has been considered, and the current sources have been simulated by current dipoles. The adopted meshless…
Tiger nut and its by-products valorization: From extraction of oil and valuable compounds to development of new healthy products
2018
Abstract Consumer's growing demand for consumption of “Horchata de chufa”, a Spanish beverage produced from tiger nut tubers, has led to large-scale production of tiger nuts, and its subsequent processing for the food industry. Recent investigations clearly show that tiger nut is a valuable source of stable vegetable oils, rich in monounsaturated fatty acids, and phytosterols as well as high-added value compounds (proteins, carbohydrates, vitamins, minerals and bioactive compounds). Several conventional (Soxhlet) and alternative innovative (SC-CO2, enzyme, high pressure, etc.) extraction methods have been developed for the efficient recovery of tiger nut oil and high-added value compounds. …