bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical Analysis of an Adaptive FEM for Distributed Flux Reconstruction
Authors: Li Mingxia , Li Jingzhi , Mao Shipeng
Published: July 2016

This paper studies convergence analysis of an adaptive finite element algorithm for numerical estimation of some unknown distributed flux in a stationary heat conduction system, namely recovering the unknown Neumann data on interior inaccessible boundary using Dirichlet measurement data on outer accessible boundary. Besides global upper and lower bounds established in [23], a posteriori local upper bounds and quasi-orthogonality results concerning the discretization errors of the state and adjoint variables are derived. Convergence and quasi-optimality of the proposed adaptive algorithm are rigorously proved. Numerical results are presented to illustrate the quasi-optimality of the proposed adaptive method.
Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation
Authors: Chen Duan , Wei Guo-Wei
Published: July 2016

Proton transport is one of the most important and interesting phenomena in living cells. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins. We describe proton dynamics quantum mechanically via a density functional approach while implicitly model other solvent ions as a dielectric continuum to reduce the number of degrees of freedom. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic level. We formulate a total free energy functional to put proton kinetic and potential energies as well as electrostatic energy of all ions on an equal footing. The variational principle is employed to derive nonlinear governing equations for the proton transport system. Generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained from the variational framework. Theoretical formulations for the proton density and proton conductance are constructed based on fundamental principles. The molecular surface of the channel protein is utilized to split the discrete protein domain and the continuum solvent domain, and facilitate the multiscale discrete/continuum/quantum descriptions. A number of mathematical algorithms, including the Dirichlet to Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to demonstrate the performance of the proposed proton transport model and validate the efficiency of proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. The proton conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and validates the proposed model.
Implicit-Explicit Runge-Kutta Schemes for the Boltzmann-Poisson System for Semiconductors
Authors: Dimarco Giacomo , Pareschi Lorenzo , Rispoli Vittorio
Published: July 2016

In this paper we develop a class of Implicit-Explicit Runge-Kutta schemes for solving the multi-scale semiconductor Boltzmann equation. The relevant scale which characterizes this kind of problems is the diffusive scaling. This means that, in the limit of zero mean free path, the system is governed by a drift-diffusion equation. Our aim is to develop a method which accurately works for the different regimes encountered in general semiconductor simulations: the kinetic, the intermediate and the diffusive one. Moreover, we want to overcome the restrictive time step conditions of standard time integration techniques when applied to the solution of this kind of phenomena without any deterioration in the accuracy. As a result, we obtain high order time and space discretization schemes which do not suffer from the usual parabolic stiffness in the diffusive limit. We show different numerical results which permit to appreciate the performances of the proposed schemes.
Dirichlet-to-Neumann Mapping for the Characteristic Elliptic Equations with Symmetric Periodic Coefficients
Authors: Kang Jingsu , Zhang Meirong , Zheng Chunxiong
Published: July 2016

Based on the numerical evidences, an analytical expression of the Dirichlet-to-Neumann mapping in the form of infinite product was first conjectured for the one-dimensional characteristic Schrödinger equation with a sinusoidal potential in [Commun. Comput. Phys., 3(3): 641-658, 2008]. It was later extended for the general second-order characteristic elliptic equations with symmetric periodic coefficients in [J. Comp. Phys., 227: 6877-6894, 2008]. In this paper, we present a proof for this Dirichlet-to-Neumann mapping.
Local Discontinuous Galerkin Methods for the 2D Simulation of Quantum Transport Phenomena on Quantum Directional Coupler
Authors: Guo Li , Xu Yan
Published: July 2016

In this paper, we present local discontinuous Galerkin methods (LDG) to simulate an important application of the 2D stationary Schrödinger equation called quantum transport phenomena on a typical quantum directional coupler, which frequency change mainly reflects in y-direction. We present the minimal dissipation LDG (MD-LDG) method with polynomial basis functions for the 2D stationary Schrödinger equation which can describe quantum transport phenomena. We also give the MD-LDG method with polynomial basis functions in x-direction and exponential basis functions in y-direction for the 2D stationary Schrödinger equation to reduce the computational cost. The numerical results are shown to demonstrate the accuracy and capability of these methods.
Fourth Order Difference Approximations for Space Riemann-Liouville Derivatives Based on Weighted and Shifted Lubich Difference Operators
Authors: Chen Minghua , Deng Weihua
Published: July 2016

High order discretization schemes play more important role in fractional operators than classical ones. This is because usually for classical derivatives the stencil for high order discretization schemes is wider than low order ones; but for fractional operators the stencils for high order schemes and low order ones are the same. Then using high order schemes to solve fractional equations leads to almost the same computational cost with first order schemes but the accuracy is greatly improved. Using the fractional linear multistep methods, Lubich obtains thev-th order (v <6) approximations of theα-th derivative (α >0) or integral (α <0) [Lubich, SIAM J. Math. Anal., 17, 704-719, 1986], because of the stability issue the obtained scheme can not be directly applied to the space fractional operator withαЄ (1,2) for time dependent problem. By weighting and shifting Lubich’s 2nd order discretization scheme, in [Chen & Deng, SINUM, arXiv:1304.7425] we derive a series of effective high order discretizations for space fractional derivative, called WSLD operators there. As the sequel of the previous work, we further provide new high order schemes for space fractional derivatives by weighting and shifting Lubich’s 3rd and 4th order discretizations. In particular, we prove that the obtained 4th order approximations are effective for space fractional derivatives. And the corresponding schemes are used to solve the space fractional diffusion equation with variable coefficients.
The Modern Information Technologies and Visualization Methods for Analysis of Computer Simulation Results for Complex Plasma
Authors: Ramazanov T. S. , Kodanova S. K. , Issanova M. K. , Bastykova N. Kh. , Moldabekov Zh. A.
Published: July 2016

In this paper we present a software package based on modern information technologies that allows rapid analysis and visualization of the properties of complex plasmas. The properties of plasma are simulated by two means. First of all, we have applied the molecular dynamics simulation method which numerically solves the equations of motions for plasma particles. Secondly, we calculate microscopic properties of plasma by using the Boltzmann equation with additional relations, initial and boundary conditions.
A Conservative Local Discontinuous Galerkin Method for the Schrödinger-KdV System
Authors: Xia Yinhua , Xu Yan
Published: July 2016

In this paper we develop a conservative local discontinuous Galerkin (LDG) method for the Schrödinger-Korteweg-de Vries (Sch-KdV) system, which arises in various physical contexts as a model for the interaction of long and short nonlinear waves. Conservative quantities in the discrete version of the number of plasmons, energy of the oscillations and the number of particles are proved for the LDG scheme of the Sch-KdV system. Semi-implicit time discretization is adopted to relax the time step constraint from the high order spatial derivatives. Numerical results for accuracy tests of stationary traveling soliton, and the collision of solitons are shown. Numerical experiments illustrate the accuracy and capability of the method.
A Nonlinear PIC Algorithm for High Frequency Waves in Magnetized Plasmas Based on Gyrocenter Gauge Kinetic Theory
Authors: Liu Jian , Yu Zhi , Qin Hong
Published: July 2016

Numerical methods based on gyrocenter gauge kinetic theory are suitable for first principle simulations of high frequency waves in magnetized plasmas. The δf gyrocenter gauge PIC simulation for linear rf wave has been previously realized. In this paper we further develop a full-f nonlinear PIC algorithm appropriate for the nonlinear physics of high frequency waves in magnetized plasmas. Numerical cases of linear rf waves are calculated as a benchmark for the nonlinear GyroGauge code, meanwhile nonlinear rf-wave phenomena are studied. The technique and advantage of the reduction of the numerical noise in this full-f gyrocenter gauge PIC algorithm are also discussed.
A Scalable Numerical Method for Simulating Flows Around High-Speed Train Under Crosswind Conditions
Authors: Yan Zhengzheng , Chen Rongliang , Zhao Yubo , Cai Xiao-Chuan
Published: July 2016

This paper presents a parallel Newton-Krylov-Schwarz method for the numerical simulation of unsteady flows at high Reynolds number around a high-speed train under crosswind. With a realistic train geometry, a realistic Reynolds number, and a realistic wind speed, this is a very challenging computational problem. Because of the limited parallel scalability, commercial CFD software is not suitable for supercomputers with a large number of processors. We develop a Newton-Krylov-Schwarz based fully implicit method, and the corresponding parallel software, for the 3D unsteady incompressible Navier-Stokes equations discretized with a stabilized finite element method on very fine unstructured meshes. We test the algorithm and software for flows passing a train modeled after China’s high-speed train CRH380B, and we also compare our results with results obtained from commercial CFD software. Our algorithm shows very good parallel scalability on a supercomputer with over one thousand processors.
DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi
Authors: Votapka Lane W. , Czapla Luke , Zhenirovskyy Maxim , Amaro Rommie E.
Published: July 2016

A new VMD plugin that interfaces with DelPhi to provide ensemble-averaged electrostatic calculations using the Poisson-Boltzmann equation is presented. The general theory and context of this approach are discussed, and examples of the plugin interface and calculations are presented. This new tool is applied to systems of current biological interest, obtaining the ensemble-averaged electrostatic properties of the two major influenza virus glycoproteins, hemagglutinin and neuraminidase, from explicitly solvated all-atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems.
Solving Two-Mode Shallow Water Equations Using Finite Volume Methods
Authors: Castro Diaz Manuel Jesús , Cheng Yuanzhen , Chertock Alina , Kurganov Alexander
Published: July 2016

In this paper, we develop and study numerical methods for the two-mode shallow water equations recently proposed in [S. STECHMANN, A. MAJDA, and B. KHOUIDER, Theor. Comput. Fluid Dynamics, 22 (2008), pp. 407-432]. Designing a reliable numerical method for this system is a challenging task due to its conditional hyperbolicity and the presence of nonconservative terms. We present several numerical approaches—two operator splitting methods (based on either Roe-type upwind or central-upwind scheme), a central-upwind scheme and a path-conservative central-upwind scheme—and test their performance in a number of numerical experiments. The obtained results demonstrate that a careful numerical treatment of nonconservative terms is crucial for designing a robust and highly accurate numerical method.
The Lognormal Distribution and Quantum Monte Carlo Data
Authors: Moodley Mervlyn
Published: July 2016

Quantum Monte Carlo data are often afflicted with distributions that resemble lognormal probability distributions and consequently their statistical analysis cannot be based on simple Gaussian assumptions. To this extent a method is introduced to estimate these distributions and thus give better estimates to errors associated with them. This method entails reconstructing the probability distribution of a set of data, with given mean and variance, that has been assumed to be lognormal prior to undergoing a blocking or renormalization transformation. In doing so, we perform a numerical evaluation of the renormalized sum of lognormal random variables. This technique is applied to a simple quantum model utilizing the single-thread Monte Carlo algorithm to estimate the ground state energy or dominant eigenvalue of a Hamiltonian matrix.
Approximation of Spatio-Temporal Random Processes Using Tensor Decomposition
Authors: Ghosh Debraj , Suryawanshi Anup
Published: July 2016

A 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

We 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

An 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

We 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

A 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

Density 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

In 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

This 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

This 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

The 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

Salt 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

We 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

The 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

The 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

This 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

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.

 
La ansiedad ante las destrezas orales en la clase de español lengua extranjera: una propuesta blended-learning con sinohablantes
Authors: Falero Parra Francisco Javier
Published: July 2016

Numerosos estudios han destacado el impacto negativo que conlleva padecer ansiedad en el proceso de adquisición de una lengua extranjera, y cómo este fenómeno afecta a las destrezas orales. En este artículo se presentan los resultados de una investigación realizada en el Instituto Cervantes de Pekín entre estudiantes de nivel A2 y que persigue un doble objetivo: determinar qué destrezas lingüísticas son una fuente real de estrés para los aprendientes; y por otra parte, analizar el impacto de una propuesta metodológica blended learning para desarrollar las destrezas orales. Los resultados confirman que la expresión oral y la comprensión auditiva aumentan la ansiedad del alumnado, mientras que el análisis de las producciones realizadas en el experimento señalan una mejora cuantitativa de las mismas junto con la reducción del factor ansiógeno. El componente motivador aportado por el uso de dispositivos móviles en clase invita a ampliar la experiencia a otros cursos y niveles.
Cytotoxicity Evaluation of Amoxicillin and Potassium Clavulanate in Perna perna Mussels
Authors: Souza Amanda de , Moreno Beatriz Barbosa , De Almeida João Emanoel , Rogero Sizue Ota , Pereira Camilo Dias Seabra , Rogero José Roberto
Published: July 2016

Pharmaceutical compounds are identified in environmental matrices in the order of magnitude of ng L-1 to Î¼g L-1. Among the drugs, antibiotics have been receiving special attention due to the problems caused to aquatic biota. The aim of this study was to evaluate the cytotoxicity of Amoxicillin and Potassium Clavulanate, in isolated and associated forms, to marine mussels Perna perna through neutral red retention time assay (NRRT), which assesses the stability of lisossomal membrane of test-organisms hemocytes. Amoxicillin caused cytotoxicity to the mussels in concentrations of OEC= 1 ng L-1, IC25-24h= 0.44 ng L-1, IC25-48h= 1.19 ng L-1 and IC25-72h= 0.85 ng L-1, Potassium Clavulanate was cytotoxic at concentrations of OEC= 10 ngL-1 in 24h; 50 ng L-1 and 100 ng L-1 at 48h and 72h. The inhibitory concentration values (IC25) were: 3.11 ng L-1, 3.45 ng L-1 and 3.43 ng L-1 at 24h, 48h and 72h respectively. In the test conducted with the combination of drugs, all concentrations were cytotoxic to mussels in 48h. In 72h only 40 ng L-1 Amoxicillin + 10 ng L-1 Potassium Clavulanate and 200 ng L-1 Amoxicillin + 50 ng L-1 Potassium Clavulanate were cytotoxic. The IC25 for Amoxicillin was 1.67 ng L-1 in 48h and 1.36 ng L-1 in 72h. For Potassium Clavulanate was 0.42 ng L-1 in 48h and in 72h was 0.34 ng L-1.
How does the OH reactivity affect the ozone production efficiency: case studies in Beijing and Heshan
Authors: Yang Yudong , Shao Min , Keβel Stephan , Li Yue , Lu Keding , Lu Sihua , Williams Jonathan , Zhang Yuanhang , Zeng Liming , Nölscher Anke C. , Wu Yusheng , Wang Xuemei , Zheng Junyu
Published: July 2016

Abstract. Total OH reactivity measurements have been conducted in August 2013 on the Peking University campus, Beijing and from October to November 2014 in Heshan, Guangdong Province. The daily median result for OH reactivity was 19.98 ± 11.03 s−1 in Beijing and 30.62 ± 19.76 s−1 in Heshan. Beijing presented a significant diurnal variation with maxima over 27 s−1 in the early morning and minima below 16 s−1 in the afternoon. Measurements in Heshan gave a much flatter diurnal pattern. Missing reactivity was observed at both sites, with 21 % missing in Beijing and 32 % missing in Heshan. Unmeasured primary species, such as branched-alkenes could contribute to missing reactivity in Beijing, especially in morning rush hour. An observation-based model with the Regional Atmospheric Chemical Mechanism 2 was used to understand the daytime missing reactivity in Beijing by adding unmeasured oxygenated volatile organic compounds and simulated intermediates of primary VOCs degradation. However, the model failed to explain the missing reactivity in Heshan, where the ambient air was found to be more aged, and the missing reactivity was presumably to attribute to oxidized species, such as aldehydes, acids and di-carbonyls. The ozone production efficiency was 27 % higher in Beijing and 35 % higher in Heshan when constrained by the measured reactivity, compared to the calculation with measured and modeled species included, indicating the importance of quantifying the OH reactivity for better understanding ozone chemistry.
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).
Domestic drones: the politics of verticality and the surveillance industrial
complex
Authors: Bracken-Roche Ciara
Published: July 2016

Abstract. Drones are being introduced as innovative and cost-effective technologies for civil, commercial, and recreational purposes in the domestic realm. While the presence of these technologies is increasing, regulations are being introduced in order to ensure their safe and responsible use. As drones are adopted for a number of purposes, the “de facto practices settle around it, rendering change much more difficult” (Gersher, 2014), and so the policy debates must consider all contingencies and unintended consequences of their use. This paper discusses the background of unmanned aerial vehicles (UAVs), their role as surveillance technologies, and how they reinforce asymmetries in power and visibility that contribute to a politics of verticality, ultimately arguing that surveillance concerns must become part of the discussion at the policy and regulatory level in order to mitigate any harms. Where drones are already used for care and control as technologies of surveillance, privileged use of drones by public and police agencies could further reinforce a politics of verticality (Weizman, 2002), resulting in specific types of space, risk, and population management.
Coastal flooding: impact of waves on storm surge during
extremes. A case study for the German Bight
Authors: Staneva Joanna , Wahle Kathrin , Koch Wolfgang , Behrens Arno , Fenoglio-Marc Luciana , Stanev Emil V.
Published: July 2016

Abstract. This study addresses impact of wind, waves, tidal forcing and baroclinicity on the sea level of the German Bight during extremes. The role of waves-induced processes, tides and baroclinicity is quantified and the results are compared with observational data that include various in-situ measurements as well as satellite data. A coupled, high-resolution, model system is used to simulate the wind waves, water level and three-dimensional hydrodynamics. The effects of the wind waves on sea level variability are studied accounting for wave-dependent stress, wave-breaking parameterization and wave-induced effects on vertical mixing. The analyses of the coupled model results reveal a closer match with observations than for the stand-alone circulation model, especially during the extreme storm Xaver in December 2013. The predicted surge of the coupled model enhances significantly during extremes when considering wave-current interaction processes. The wave-dependent approach yields to a contribution of more than 30 % in some coastal area during extremes. The improved skill resulting from the new developments justifies further use of coupled wave and three dimensional circulation models for improvement of coastal flooding predictions.
Internal Control and Revenue Fund Management among County Governments in Kenya
Authors: Oyaro Cleophas Omariba , Angwenyi Orina Ronald
Published: July 2016

Informed by the auditor general’s report of 2014 in which massive frauds and misuse of the revenue fund across counties in Kenya were reported, the study sought to establish the link between internal control and revenue fund management. The study adopted components of the Committee of Sponsoring Organizations of the Treadway Commission 2013 framework in its conceptualization. The study arrived at mixed results in terms of the relationship and nature of association between the components and revenue fund management. In addition, the study did not provide enough evidence to believe whether or not there existed significant differences in internal control among county governments in Kenya. This alluded to inconsistencies in implementation of internal control among the devolved units. Lastly, the study indicated that even if the framework has been successful used in implementation of internal control among listed companies in the United States, the same framework cannot be effectively used in implementation of internal control in the context of a devolved system of government such as is in Kenya.
Amniotic Membrane Transplantation with Narrow-Strip Conjunctival Autograft vs Conjunctival Autograft for Recurrent Pterygia
Authors: Barbosa José B. , De Farias Charles Costa , Hirai Flávio E. , Pereira Gomes José Á.
Published: July 2016

Purpose

To compare amniotic membrane transplantation (AMT) associated with narrow-strip conjunctival autograft vs conjunctival autograft alone for the treatment of recurrent pterygium.

Methods

In this prospective consecutive interventional study, patients with recurrent pterygium were randomly divided into one of 2 groups; group 1: patients undergoing AMT associated with autologous conjunctival graft; and group 2: patients undergoing conjunctival autograft alone.

Results

Of the 80 operated eyes included in this study, 39 (group 1, mean patient age 52.1 ± 11.7 SD years) underwent AMT associated with narrow-strip conjunctival autograft and 41 (group 2, mean patient age 45.8 ± 12.9 SD years) underwent conjunctival autograft alone. In group 1, 6 eyes (15.4%) had grade 1 pterygium, 19 eyes (48.7%) had grade 2 pterygium, and 14 eyes (35.9%) had grade 3 pterygium. In the second group, 5 eyes (12.2%) had grade 1 pterygium, 18 eyes (43.9%) had grade 2 pterygium, and 14 eyes (35.9%) had grade 3 pterygium. No statistically significant difference was found between the 2 groups (p = 0.752). Of the 39 eyes in group 1, recurrent pterygium was observed in 7 cases (17.9%). However, of the 41 eyes in group 2, recurrent pterygium was observed in only 4 cases (9.75%). No statistically significant difference was found between the 2 groups (p = 0.2684).

Conclusions

The results of this study indicate that conjunctival autograft alone might be a better surgical choice for the treatment of recurrent pterygia than combining it with AMT; however, this second option provides a good surgical alternative in cases where little conjunctival donor tissue is available.
Miscibility Evaluation of Poly(L-Lactic Acid)/Poly(Lactic Acid-co-lysine) Blends
Authors: Yao Junyan , Zhang Shijie , Li Wudan , Li Yujie
Published: July 2016

Background

The amorphous poly(lactic acid- co-lysine) (PLL) with hydrophilic reactive groups was synthesized by the condensing copolymerization and the blending miscibility of poly(L-lactic acid) (PLLA) and PLL was investigated.

Methods

The miscibility of PLLA and PLL was evaluated by analyzing the thermal properties, crystallization behaviors, crystal morphologies and mechanical properties of the PLLA/PLL blends.

Results

The results indicated that amorphous PLL changed the crystallization behaviors and thermal properties of PLLA, decreasing the crystallinity of PLLA in the blends. The amorphous PLL molecule chains in PLLA/PLL blends were able to enter into the lamellars of PLLA spherulites and affect the crystallization behaviors of PLLA, resulting in imperfect, spherulite structures of PLLA. The formation of hydrogen bonds between PLLA molecular chains and PLL molecular chains enabled partial compatibility in this blend system.

Conclusions

The existence of PLL improved the hydrophility of PLLA/PLL blends, led to a higher content of PLL in the PLLA/PLL blend system, and better hydrophilic properties of the blend system. The PLL was partially miscible with the PLLA, and the PLLA/PLL blend with 10 wt% PLL had improved tensile properties.