bluuebunny/crossref_metadata_2025_split huggingface dataset:
Approximation of Spatio-Temporal Random Processes Using Tensor Decomposition
Authors: Ghosh Debraj , Suryawanshi Anup 
Published: July 2016

AbstractA new representation of spatio-temporal random processes is proposed in this work. In practical applications, such processes are used to model velocity fields, temperature distributions, response of vibrating systems, to name a few. Finding an efficient representation for any random process leads to encapsulation of information which makes it more convenient for a practical implementations, for instance, in a computational mechanics problem. For a single-parameter process such as spatial or temporal process, the eigenvalue decomposition of the covariance matrix leads to the well-known Karhunen-Loève (KL) decomposition. However, for multiparameter processes such as a spatio-temporal process, the covariance function itself can be defined in multiple ways. Here the process is assumed to be measured at a finite set of spatial locations and a finite number of time instants. Then the spatial covariance matrix at different time instants are considered to define the covariance of the process. This set of square, symmetric, positive semi-definite matrices is then represented as a third-order tensor. A suitable decomposition of this tensor can identify the dominant components of the process, and these components are then used to define a closed-form representation of the process. The procedure is analogous to the KL decomposition for a single-parameter process, however, the decompositions and interpretations vary significantly. The tensor decompositions are successfully applied on (i) a heat conduction problem, (ii) a vibration problem, and (iii) a covariance function taken from the literature that was fitted to model a measured wind velocity data. It is observed that the proposed representation provides an efficient approximation to some processes. Furthermore, a comparison with KL decomposition showed that the proposed method is computationally cheaper than the KL, both in terms of computer memory and execution time.
A Second Order Finite-Difference Ghost-Point Method for Elasticity Problems on Unbounded Domains with Applications to Volcanology
Authors: Coco Armando , Currenti Gilda , Negro Ciro Del , Russo Giovanni 
Published: July 2016

AbstractWe propose a finite-difference ghost-point approach for the numerical solution of Cauchy-Navier equations in linear elasticity problems on arbitrary unbounded domains. The technique is based on a smooth coordinate transformation, which maps an unbounded domain into a unit square. Arbitrary geometries are defined by suitable level-set functions. The equations are discretized by classical nine-point stencil on interior points, while boundary conditions and high order reconstructions are used to define the field variables at ghost-points, which are grid nodes external to the domain with a neighbor inside the domain. The linear system arising from such discretization is solved by a multigrid strategy. The approach is then applied to solve elasticity problems in volcanology for computing the displacement caused by pressure sources. The method is suitable to treat problems in which the geometry of the source often changes (explore the effects of different scenarios, or solve inverse problems in which the geometry itself is part of the unknown), since it does not require complex re-meshing when the geometry is modified. Several numerical tests are successfully performed, which asses the effectiveness of the present approach.
An Accurate Cartesian Method for Incompressible Flows with Moving Boundaries
Authors: Bergmann M. , Hovnanian J. , Iollo A. 
Published: July 2016

AbstractAn accurate cartesian method is devised to simulate incompressible viscous flows past an arbitrary moving body. The Navier-Stokes equations are spatially discretized onto a fixed Cartesian mesh. The body is taken into account via the ghost-cell method and the so-called penalty method, resulting in second-order accuracy in velocity. The accuracy and the efficiency of the solver are tested through two-dimensional reference simulations. To show the versatility of this scheme we simulate a three-dimensional self propelled jellyfish prototype.
Dimension-Reduced Hyperbolic Moment Method for the Boltzmann Equation with BGK-Type Collision
Authors: Cai Zhenning , Fan Yuwei , Li Ruo , Qiao Zhonghua 
Published: July 2016

AbstractWe develop the dimension-reduced hyperbolic moment method for the Boltzmann equation, to improve solution efficiency using a numerical regularized moment method for problems with low-dimensional macroscopic variables and high-dimensional microscopic variables. In the present work, we deduce the globally hyperbolic moment equations for the dimension-reduced Boltzmann equation based on the Hermite expansion and a globally hyperbolic regularization. The numbers of Maxwell boundary condition required for well-posedness are studied. The numerical scheme is then developed and an improved projection algorithm between two different Hermite expansion spaces is developed. By solving several benchmark problems, we validate the method developed and demonstrate the significant efficiency improvement by dimension-reduction.
A New Approach for Error Reduction in the Volume Penalization Method
Authors: Iwakami Wakana , Yatagai Yuzuru , Hatakeyama Nozomu , Hattori Yuji 
Published: July 2016

AbstractA new approach for reducing error of the volume penalization method is proposed. The mask function is modified by shifting the interface between solid and fluid by toward the fluid region, where v and η are the viscosity and the permeability, respectively. The shift length is derived from the analytical solution of the one-dimensional diffusion equation with a penalization term. The effect of the error reduction is verified numerically for the one-dimensional diffusion equation, Burgers’ equation, and the two-dimensional Navier-Stokes equations. The results show that the numerical error is reduced except in the vicinity of the interface showing overall second-order accuracy, while it converges to a non-zero constant value as the number of grid points increases for the original mask function. However, the new approach is effectivewhen the grid resolution is sufficiently high so that the boundary layer,whose width is proportional to , is resolved. Hence, the approach should be used when an appropriate combination of ν and η is chosen with a given numerical grid.
Remarkable Thermal Contraction in Small Size Single-Walled Boron Nanotubes
Authors: Zha Xianhu , Li Shuang , Zhang Ruiqin , Lin Zijing 
Published: July 2016

AbstractDensity functional theory combined with the Grüneisen approximation is used to calculate the thermal properties of single-walled boron nanotubes (BNTs). The specific heat and thermal expansion are investigated. The thermal expansion coefficient of the BNT is found to be significantly correlated with tube size and chirality. A remarkable thermal contraction is found at small tube diameters. These results indicate that BNTs would have potential applications in sensors, actuators, and memory materials.
An Efficient Calculation of Photonic Crystal Band Structures Using Taylor Expansions
Authors: Klindworth Dirk , Schmidt Kersten 
Published: July 2016

AbstractIn this paper we present an efficient algorithm for the calculation of photonic crystal band structures and band structures of photonic crystal waveguides. Our method relies on the fact that the dispersion curves of the band structure are smooth functions of the quasi-momentum in the one-dimensional Brillouin zone. We show the derivation and computation of the group velocity, the group velocity dispersion, and any higher derivative of the dispersion curves. These derivatives are then employed in a Taylor expansion of the dispersion curves. We control the error of the Taylor expansion with the help of a residual estimate and introduce an adaptive scheme for the selection of nodes in the one-dimensional Brillouin zone at which we solve the underlying eigenvalue problem and compute the derivatives of the dispersion curves. These derivatives are then employed in a Taylor expansion of the dispersion curves. We control the error of the Taylor expansion with the help of a residual estimate and introduce an adaptive scheme for the selection of nodes in the one-dimensional Brillouin zone at which we solve the underlying eigenvalue problem and compute the derivatives of the dispersion curves. The proposed algorithm is not only advantageous as it decreases the computational effort to compute the band structure but also because it allows for the identification of crossings and anti-crossings of dispersion curves, respectively. This identification is not possible with the standard approach of solving the underlying eigenvalue problem at a discrete set of values of the quasi-momentum without taking the mode parity into account.
A Unified Fractional-Step, Artificial Compressibility and Pressure-Projection Formulation for Solving the Incompressible Navier-Stokes Equations
Authors: Könözsy László , Drikakis Dimitris 
Published: July 2016

AbstractThis paper introduces a unified concept and algorithm for the fractional-step (FS), artificial compressibility (AC) and pressure-projection (PP) methods for solving the incompressible Navier-Stokes equations. The proposed FSAC-PP approach falls into the group of pseudo-time splitting high-resolution methods incorporating the characteristics-based (CB) Godunov-type treatment of convective terms with PP methods. Due to the fact that the CB Godunov-type methods are applicable directly to the hyperbolic AC formulation and not to the elliptical FS-PP (split) methods, thus the straightforward coupling of CB Godunov-type schemes with PP methods is not possible. Therefore, the proposed FSAC-PP approach unifies the fully-explicit AC and semi-implicit FS-PP methods of Chorin including a PP step in the dual-time stepping procedure to a) overcome the numerical stiffness of the classical AC approach at (very) low and moderate Reynolds numbers, b) incorporate the accuracy and convergence properties of CB Godunov-type schemes with PP methods, and c) further improve the stability and efficiency of the AC method for steady and unsteady flow problems. The FSAC-PPmethod has also been coupled with a non-linear, full-multigrid and fullapproximation storage (FMG-FAS) technique to further increase the efficiency of the solution. For validating the proposed FSAC-PP method, computational examples are presented for benchmark problems. The overall results show that the unified FSAC-PP approach is an efficient algorithm for solving incompressible flow problems.
Numerical Study of Stability and Accuracy of the Immersed Boundary Method Coupled to the Lattice Boltzmann BGK Model
Authors: Cheng Yongguang , Zhu Luoding , Zhang Chunze 
Published: July 2016

AbstractThis paper aims to study the numerical features of a coupling scheme between the immersed boundary (IB) method and the lattice Boltzmann BGK (LBGK) model by four typical test problems: the relaxation of a circular membrane, the shearing flow induced by a moving fiber in the middle of a channel, the shearing flow near a non-slip rigid wall, and the circular Couette flow between two inversely rotating cylinders. The accuracy and robustness of the IB-LBGK coupling scheme, the performances of different discrete Dirac delta functions, the effect of iteration on the coupling scheme, the importance of the external forcing term treatment, the sensitivity of the coupling scheme to flow and boundary parameters, the velocity slip near non-slip rigid wall, and the origination of numerical instabilities are investigated in detail via the four test cases. It is found that the iteration in the coupling cycle can effectively improve stability, the introduction of a second-order forcing term in LBGK model is crucial, the discrete fiber segment length and the orientation of the fiber boundary obviously affect accuracy and stability, and the emergence of both temporal and spatial fluctuations of boundary parameters seems to be the indication of numerical instability. These elaborate results shed light on the nature of the coupling scheme and may benefit those who wish to use or improve the method.
Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?
Authors: Pang Xiaodong , Zhou Huan-Xiang 
Published: July 2016

AbstractThe Poisson-Boltzmann equation is widely used for modeling the electro-statics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The default choice for the dielectric boundary has been the molecular surface, but the use of the van der Waals surface has also been advocated. Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations. The assignment of the solvent high dielectric constant to interstitial voids in the solute is often used as a criticism against the van der Waals surface. However, this assignment may not be as unrealistic as previously thought, since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent.
Modeling the Influence of Salt on the Hydrophobic Effect and Protein Fold Stability
Authors: Date Mihir S. , Dominy Brian N. 
Published: July 2016

AbstractSalt influences protein stability through electrostatic mechanisms as well as through nonpolar Hofmeister effects. In the present work, a continuum solvation based model is developed to explore the impact of salt on protein stability. This model relies on a traditional Poisson-Boltzmann (PB) term to describe the polar or electrostatic effects of salt, and a surface area dependent term containing a salt concentration dependent microscopic surface tension function to capture the non-polar Hofmeister effects. The model is first validated against a series of cold-shock protein variants whose salt-dependent protein fold stability profiles have been previously determined experimentally. The approach is then applied to HIV-1 protease in order to explain an experimentally observed enhancement in stability and activity at high (1M) NaCl concentration. The inclusion of the salt-dependent non-polar term brings the model into quantitative agreement with experiment, and provides the basis for further studies into the impact of ionic strength on protein structure, function, and evolution.
Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model
Authors: Song Wei , Lin Yuchun , Baumketner Andrij , Deng Shaozhong , Cai Wei , Jacobs Donald J. 
Published: July 2016

AbstractWe recently developed the Image-Charge Solvation Model (ICSM), which is an explicit/implicit hybrid model to accurately account for long-range electrostatic forces in molecular dynamics simulations [Lin et al., J. Chem. Phys., 131,154103,2009]. The ICSM has a productive spherical volume within the simulation cell for which key physical properties of bulk water are reproduced, such as density, radial distribution function, diffusion constants and dielectric properties. Although the reaction field (RF) is essential, it typically accounts for less than 2% of the total electrostatic force on a water molecule. This observation motivates investigating further the role of the RF within the ICSM. In this report we focus on distributions of forces and torques on water molecules as a function of distance from the origin and make extensive tests over a range of model parameters where Coulomb forces are decomposed into direct interactions from waters modeled explicitly and the RF. Molecular torques due to the RF typically account for 20% of the total torque, revealing why the RF plays an important role in the dielectric properties of simulated water. Moreover, it becomes clear that the buffer layer in the ICSM is essential to mitigate artifacts caused by the discontinuous change in dielectric constants at the explicit/implicit interface.
A Local Velocity Grid Approach for BGK Equation
Authors: Bernard Florian , Iollo Angelo , Puppo Gabriella 
Published: July 2016

AbstractThe solution of complex rarefied flows with the BGK equation and the Discrete Velocity Method (DVM) requires a large number of velocity grid points leading to significant computational costs. We propose an adaptive velocity grid approach exploiting the fact that locally in space, the distribution function is supported only by a sub-set of the global velocity grid. The velocity grid is adapted thanks to criteria based on local temperature, velocity and on the enforcement of mass conservation. Simulations in 1D and 2D are presented for different Knudsen numbers and compared to a global velocity grid BGK solution, showing the computational gain of the proposed approach.
Structural Determinants of a Typical Leucine-Rich Repeat Protein
Authors: Martins Joao M. , Ramos Rui M. , Moreira Irina S. 
Published: July 2016

AbstractThe structural and functional description of protein-protein complexes and their comprehension is a key concept, not only to increase the scientific knowledge in basic terms but also for the application to the biomedical and pharmaceutical industry. The binding association between proteins is nowadays attribute to a few key residues at the interface – the hot-spots. The complex between the RNase inhibitor (RI) and RNaseA protein provides an excellent system to study the role of the functional epitope as it is essential in various molecular recognition processes and constitute one of the tightest complexes known. An energetic pattern of the interface is accomplished by computational alanine scanning mutagenesis and a dynamical characterization is accomplished by a detailed study of the molecular dynamical simulations. A special emphasis is given to the role of solvation across the interface and the shielding of warm-and hot-spots from water.
A Parallel Computational Model for Three-Dimensional, Thermo-Mechanical Stokes Flow Simulations of Glaciers and Ice Sheets
Authors: Leng Wei , Ju Lili , Gunzburger Max , Price Stephen 
Published: July 2016

AbstractThis paper focuses on the development of an efficient, three-dimensional, thermo-mechanical, nonlinear-Stokes flow computational model for ice sheet simulation. The model is based on the parallel finite element model developed in [14] which features high-order accurate finite element discretizations on variable resolution grids. Here, we add an improved iterative solution method for treating the nonlinearity of the Stokes problem, a new high-order accurate finite element solver for the temperature equation, and a new conservative finite volume solver for handling mass conservation. The result is an accurate and efficient numerical model for thermo-mechanical glacier and ice-sheet simulations. We demonstrate the improved efficiency of the Stokes solver using the ISMIP-HOM Benchmark experiments and a realistic test case for the Greenland ice-sheet. We also apply our model to the EISMINT-II benchmark experiments and demonstrate stable thermo-mechanical ice sheet evolution on both structured and unstructured meshes. Notably, we find no evidence for the “cold spoke” instabilities observed for these same experiments when using finite difference, shallow-ice approximation models on structured grids.
El microrrelato como material didáctico en la adquisición de la gramática en ELE
Authors: Rodríguez Rodríguez María Nayra , García-Perera Dara 
Published: July 2016

<div data-canvas-width="692.285333333333">En el presente artículo, se pretende realizar una reflexión sobre la introducción de la literatura de la lengua metaen el aula de lenguas extranjeras. Analizaremos el uso del microrrelato en el aula de español como lengua extranjera (ELE) como material didáctico. Para ello, investigaremos las diferentes metodologías de enseñanza que se han puesto en práctica e indagaremos sobre la validez de este género como material idóneo para la enseñanza de la gramática. Realizaremos un acercamiento a la atención a la forma (AF) como un enfoque efectivo en el que se integre la enseñanza de la gramática dentro de un contexto comunicativo.</div><p> </p>
Holocene hydrological changes in the Rhône River (NW Mediterranean) as
recorded in the marine mud belt
Authors: Bassetti Maria-Angela , Berné Serge , Sicre Marie-Alexandrine , Dennielou Bernard , Alonso Yoann , Buscail Roselyne , Jalali Bassem , Hebert Bertil , Menniti Christophe 
Published: July 2016

Abstract. Expanded marine Holocene archives are relatively scarce in the Mediterranean Sea because most of the sediments were trapped in catchment areas during this period. Mud belts are the most suitable targets to access expanded Holocene records. These sedimentary bodies represent excellent archives for the study of sea–land interactions and notably the impact of the hydrological activity on sediment accumulation. We retrieved a 7.2 m long sediment core from the Rhône mud belt in the Gulf of Lions in an area where the average accumulation rate is ca. 0.70 m 1000 yr−1. This core thus provides a continuous and high-resolution record of the last 10 ka cal BP. A multiproxy dataset (XRF core scan, 14C dates, grain size and organic-matter analysis) combined with seismic stratigraphic analysis was used to document decadal to centennial changes in the Rhône hydrological activity. Our results show that (1) the early Holocene was characterized by high sediment delivery likely indicative of local intense (but short-duration) rainfall events, (2) important sediment delivery around 7 ka cal BP presumably related to increased river flux, (3) a progressive increase in continental/marine input during the mid-Holocene despite increased distance from river outlets due to sea-level rise possibly related to higher atmospheric humidity caused by the southward migration of the storm tracks in the North Atlantic, (4) multidecadal to centennial humid events took place in the late Holocene. Some of these events correspond to the cold periods identified in the North Atlantic (Little Ice Age, LIA; Dark Ages Cold Period) and also coincide with time intervals of major floods in the northern Alps. Other humid events are also observed during relatively warm periods (Roman Humid Period and Medieval Climate Anomaly).