A finite element computer program for the calculation of the resonant frequencies of anisotropic materials

International Nuclear Information System (INIS)

Fleury, W.H.; Rosinger, H.E.; Ritchie, I.G.

1975-09-01

A set of computer programs for the calculation of the flexural and torsional resonant frequencies of rectangular section bars of materials of orthotropic or higher symmetry are described. The calculations are used in the experimental determination and verification of the elastic constants of anisotropic materials. The simple finite element technique employed separates the inertial and elastic properties of the beam element into station and field transfer matrices respectively. It includes the Timoshenko beam corrections for flexure and Lekhnitskii's theory for torsion-flexure coupling. The programs also calculate the vibration shapes and surface nodal contours or Chladni figures of the vibration modes. (author)

Plane-wave diffraction by periodic structures with artificial anisotropic dielectrics

International Nuclear Information System (INIS)

Kazerooni, Azadeh Semsar; Shahabadi, Mahmoud

2010-01-01

Periodic structures with artificial anisotropic dielectrics are studied. The artificial anisotropic dielectric material in this work is made of two alternating isotropic dielectric layers. By a proper choice of the dielectric constant of the layers, we can realize a uniaxial anisotropic medium with controllable anisotropy. The artificial anisotropic dielectric is then used in periodic structures. For these structures, the optical axis of the artificial dielectric is assumed to be parallel or perpendicular to the period of the structure. Diffraction of plane waves by these structures is analyzed by a fully vectorial rigorous matrix method based on a generalized transmission line (TL) formulation. The propagation constants and field distributions are computed and diffraction properties of such structures are studied to show that, by a proper choice of structural parameters, these periodic structures with artificial anisotropic dielectrics can be used as polarizers or polarizing mirrors

Generalization of Asaoka method to linearly anisotropic scattering: benchmark data in cylindrical geometry

International Nuclear Information System (INIS)

Sanchez, Richard.

1975-11-01

The Integral Transform Method for the neutron transport equation has been developed in last years by Asaoka and others. The method uses Fourier transform techniques in solving isotropic one-dimensional transport problems in homogeneous media. The method has been extended to linearly anisotropic transport in one-dimensional homogeneous media. Series expansions were also obtained using Hembd techniques for the new anisotropic matrix elements in cylindrical geometry. Carlvik spatial-spherical harmonics method was generalized to solve the same problem. By applying a relation between the isotropic and anisotropic one-dimensional kernels, it was demonstrated that anisotropic matrix elements can be calculated by a linear combination of a few isotropic matrix elements. This means in practice that the anisotropic problem of order N with the N+2 isotropic matrix for the plane and spherical geometries, and N+1 isotropic matrix for cylindrical geometries can be solved. A method of solving linearly anisotropic one-dimensional transport problems in homogeneous media was defined by applying Mika and Stankiewicz observations: isotropic matrix elements were computed by Hembd series and anisotropic matrix elements then calculated from recursive relations. The method has been applied to albedo and critical problems in cylindrical geometries. Finally, a number of results were computed with 12-digit accuracy for use as benchmarks [fr

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

Science.gov (United States)

Ramakrishnan, N.; Sunil Kumar, P. B.; Radhakrishnan, Ravi

2014-01-01

description, the protein is expressed in the form of a spontaneous curvature field. The approaches include field theoretical methods limited to the small deformation regime, triangulated surfaces and particle-based computational models to investigate the large-deformation regimes observed in the natural state of many biological membranes. Applications of these methods to understand the properties of biological membranes in homogeneous and inhomogeneous environments of proteins, whose underlying curvature fields are either isotropic or anisotropic, are discussed. The diversity in the curvature fields elicits a rich variety of morphological states, including tubes, discs, branched tubes, and caveola. Mapping the thermodynamic stability of these states as a function of tuning parameters such as concentration and strength of curvature induction of the proteins is discussed. The relative stabilities of these self-organized shapes are examined through free-energy calculations. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies. PMID:25484487

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins.

Science.gov (United States)

Ramakrishnan, N; Sunil Kumar, P B; Radhakrishnan, Ravi

2014-10-01

description, the protein is expressed in the form of a spontaneous curvature field. The approaches include field theoretical methods limited to the small deformation regime, triangulated surfaces and particle-based computational models to investigate the large-deformation regimes observed in the natural state of many biological membranes. Applications of these methods to understand the properties of biological membranes in homogeneous and inhomogeneous environments of proteins, whose underlying curvature fields are either isotropic or anisotropic, are discussed. The diversity in the curvature fields elicits a rich variety of morphological states, including tubes, discs, branched tubes, and caveola. Mapping the thermodynamic stability of these states as a function of tuning parameters such as concentration and strength of curvature induction of the proteins is discussed. The relative stabilities of these self-organized shapes are examined through free-energy calculations. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies.

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

Energy Technology Data Exchange (ETDEWEB)

Ramakrishnan, N., E-mail: ramn@seas.upenn.edu [Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA-19104 (United States); Department of Bioengineering, University of Pennsylvania, Philadelphia, PA-19104 (United States); Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104 (United States); Sunil Kumar, P.B., E-mail: sunil@physics.iitm.ac.in [Department of Physics, Indian Institute of Technology Madras, Chennai, 600036 (India); Radhakrishnan, Ravi, E-mail: rradhak@seas.upenn.edu [Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA-19104 (United States); Department of Bioengineering, University of Pennsylvania, Philadelphia, PA-19104 (United States); Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104 (United States)

2014-10-01

, the protein is expressed in the form of a spontaneous curvature field. The approaches include field theoretical methods limited to the small deformation regime, triangulated surfaces and particle-based computational models to investigate the large-deformation regimes observed in the natural state of many biological membranes. Applications of these methods to understand the properties of biological membranes in homogeneous and inhomogeneous environments of proteins, whose underlying curvature fields are either isotropic or anisotropic, are discussed. The diversity in the curvature fields elicits a rich variety of morphological states, including tubes, discs, branched tubes, and caveola. Mapping the thermodynamic stability of these states as a function of tuning parameters such as concentration and strength of curvature induction of the proteins is discussed. The relative stabilities of these self-organized shapes are examined through free-energy calculations. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies.

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

International Nuclear Information System (INIS)

Ramakrishnan, N.; Sunil Kumar, P.B.; Radhakrishnan, Ravi

2014-01-01

, the protein is expressed in the form of a spontaneous curvature field. The approaches include field theoretical methods limited to the small deformation regime, triangulated surfaces and particle-based computational models to investigate the large-deformation regimes observed in the natural state of many biological membranes. Applications of these methods to understand the properties of biological membranes in homogeneous and inhomogeneous environments of proteins, whose underlying curvature fields are either isotropic or anisotropic, are discussed. The diversity in the curvature fields elicits a rich variety of morphological states, including tubes, discs, branched tubes, and caveola. Mapping the thermodynamic stability of these states as a function of tuning parameters such as concentration and strength of curvature induction of the proteins is discussed. The relative stabilities of these self-organized shapes are examined through free-energy calculations. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies

Anisotropic ray trace

Science.gov (United States)

Lam, Wai Sze Tiffany

Optical components made of anisotropic materials, such as crystal polarizers and crystal waveplates, are widely used in many complex optical system, such as display systems, microlithography, biomedical imaging and many other optical systems, and induce more complex aberrations than optical components made of isotropic materials. The goal of this dissertation is to accurately simulate the performance of optical systems with anisotropic materials using polarization ray trace. This work extends the polarization ray tracing calculus to incorporate ray tracing through anisotropic materials, including uniaxial, biaxial and optically active materials. The 3D polarization ray tracing calculus is an invaluable tool for analyzing polarization properties of an optical system. The 3x3 polarization ray tracing P matrix developed for anisotropic ray trace assists tracking the 3D polarization transformations along a ray path with series of surfaces in an optical system. To better represent the anisotropic light-matter interactions, the definition of the P matrix is generalized to incorporate not only the polarization change at a refraction/reflection interface, but also the induced optical phase accumulation as light propagates through the anisotropic medium. This enables realistic modeling of crystalline polarization elements, such as crystal waveplates and crystal polarizers. The wavefront and polarization aberrations of these anisotropic components are more complex than those of isotropic optical components and can be evaluated from the resultant P matrix for each eigen-wavefront as well as for the overall image. One incident ray refracting or reflecting into an anisotropic medium produces two eigenpolarizations or eigenmodes propagating in different directions. The associated ray parameters of these modes necessary for the anisotropic ray trace are described in Chapter 2. The algorithms to calculate the P matrix from these ray parameters are described in Chapter 3 for

Chiral magnetic effect in the anisotropic quark-gluon plasma

International Nuclear Information System (INIS)

Ali-Akbari, Mohammad; Taghavi, Seyed Farid

2015-01-01

An anisotropic thermal plasma phase of a strongly coupled gauge theory can be holographically modelled by an anisotropic AdS black hole. The temperature and anisotropy parameter of the AdS black hole background of interest http://dx.doi.org/10.1007/JHEP07(2011)054 is specified by the location of the horizon and the value of the Dilaton field at the horizon. Interestingly, for the first time, we obtain two functions for the values of the horizon and Dilaton field in terms of the temperature and anisotropy parameter. Then by introducing a number of spinning probe D7-branes in the anisotropic background, we compute the value of the chiral magnetic effect (CME). We observe that in the isotropic and anisotropic plasma the value of the CME is equal for the massless quarks. However, at fixed temperature, raising the anisotropy in the system will increase the value of the CME for the massive quarks.

Delay-active damage versus non-local enhancement for anisotropic damage dynamics computations with alternated loading

International Nuclear Information System (INIS)

Desmorat, R.; Chambart, M.; Gatuingt, F.; Guilbaud, D.

2010-01-01

Anisotropic damage thermodynamics framework allows to model the concrete-like materials behavior and in particular their dissymmetric tension/compression response. To deal with dynamics applications such as impact, it is furthermore necessary to take into account the strain rate effect observed experimentally. This is done in the present work by means of anisotropic visco-damage, by introducing a material strain rate effect in the cases of positive hydrostatic stresses only. The proposed delay-damage law assumes no viscous effect in compression as the consideration of inertia effects proves sufficient to model the apparent material strength increase. High-rate dynamics applications imply to deal with wave propagation and reflection which can generate alternated loading in the impacted structure. In order to do so, the key concept of active damage is defined and introduced within both the damage criterion and the delay-damage evolution law. At the structural level, strain localization often leads to spurious mesh dependency. Three-dimensional Finite Element computations of dynamic tensile tests by spalling are presented, with visco-damage and either without or with non-local enhancement. Delay-damage, as introduced, regularizes the solution in fast dynamics. The location of the macro-crack initiated is found influenced by non-local regularization. The strain rate range in which each enhancement, delay-damage or non-local enhancement, has a regularizing effect is studied. (authors)

A methodology for interpretation of overcoring stress measurements in anisotropic rock

International Nuclear Information System (INIS)

Hakala, M.; Sjoeberg, J.

2006-11-01

The in situ state of stress is an important parameter for the design of a repository for final disposal of spent nuclear fuel. This report presents work conducted to improve the quality of overcoring stress measurements, focused on the interpretation of overcoring rock stress measurements when accounting for possible anisotropic behavior of the rock. The work comprised: (i) development/upgrading of a computer code for calculating stresses from overcoring strains for anisotropic materials and for a general overcoring probe configuration (up to six strain rosettes with six gauges each), (ii) development of a computer code for determining elastic constants for transversely isotropic rocks from biaxial testing, and (iii) analysis of case studies of selected overcoring measurements in both isotropic and anisotropic rocks from the Posiva and SKB sites in Finland and Sweden, respectively. The work was principally limited to transversely isotropic materials, although the stress calculation code is applicable also to orthotropic materials. The developed computer codes have been geared to work primarily with the Borre and CSIRO HI three-dimensional overcoring measurement probes. Application of the codes to selected case studies, showed that the developed tools were practical and useful for interpreting overcoring stress measurements conducted in anisotropic rock. A quantitative assessment of the effects of anisotropy may thus be obtained, which provides increased reliability in the stress data. Potential gaps in existing data and/or understanding can also be identified. (orig.)

3-D waveform tomography sensitivity kernels for anisotropic media

KAUST Repository

Djebbi, Ramzi; Alkhalifah, Tariq Ali

2014-01-01

The complications in anisotropic multi-parameter inversion lie in the trade-off between the different anisotropy parameters. We compute the tomographic waveform sensitivity kernels for a VTI acoustic medium perturbation as a tool to investigate

SO-FDTD analysis of anisotropic magnetized plasma

International Nuclear Information System (INIS)

Yang Hongwei; Nanjing Univ. of Science and Technology, Nanjing; Yuan Hong; Chen Rushan; Yang Yang

2007-01-01

A novel finite-difference time-domain (FDTD) method, called shift operator FDTD (SO-FDTD) method is developed for anisotropic magnetized dispersive media. The recursive relation between operators is used. In this paper, some expressions containing the dielectric constants of magnetized dispersive media are written as rational polynomial function. The SO-FDTD formulation for anisotropic magnetized plasma is derived. The high efficiency and effectiveness of the method are confirmed by computing the reflection and transmission through a magnetized plasma layer, with the direction of the propagation parallel to the direction of the biasing field. A comparison with frequency domain analytic results is included. The CPU time was several times shorter than that of the JEC method. (authors)

Preconditioned conjugate gradient technique for the analysis of symmetric anisotropic structures

Science.gov (United States)

Noor, Ahmed K.; Peters, Jeanne M.

1987-01-01

An efficient preconditioned conjugate gradient (PCG) technique and a computational procedure are presented for the analysis of symmetric anisotropic structures. The technique is based on selecting the preconditioning matrix as the orthotropic part of the global stiffness matrix of the structure, with all the nonorthotropic terms set equal to zero. This particular choice of the preconditioning matrix results in reducing the size of the analysis model of the anisotropic structure to that of the corresponding orthotropic structure. The similarities between the proposed PCG technique and a reduction technique previously presented by the authors are identified and exploited to generate from the PCG technique direct measures for the sensitivity of the different response quantities to the nonorthotropic (anisotropic) material coefficients of the structure. The effectiveness of the PCG technique is demonstrated by means of a numerical example of an anisotropic cylindrical panel.

An Anisotropic Model for Magnetostriction and Magnetization Computing for Noise Generation in Electric Devices.

Science.gov (United States)

Mbengue, Serigne Saliou; Buiron, Nicolas; Lanfranchi, Vincent

2016-04-16

During the manufacturing process and use of ferromagnetic sheets, operations such as rolling, cutting, and tightening induce anisotropy that changes the material's behavior. Consequently for more accuracy in magnetization and magnetostriction calculations in electric devices such as transformers, anisotropic effects should be considered. In the following sections, we give an overview of a macroscopic model which takes into account the magnetic and magnetoelastic anisotropy of the material for both magnetization and magnetostriction computing. Firstly, a comparison between the model results and measurements from a Single Sheet Tester (SST) and values will be shown. Secondly, the model is integrated in a finite elements code to predict magnetostrictive deformation of an in-house test bench which is a stack of 40 sheets glued together by the Vacuum-Pressure Impregnation (VPI) method. Measurements on the test bench and Finite Elements results are presented.

Anisotropic colloids: bulk phase behavior and equilibrium sedimentation

NARCIS (Netherlands)

Marechal, M.A.T.

2009-01-01

This thesis focuses on the phase behavior of anisotropically shaped (i.e. non-spherical) colloids using computer simulations. Only hard-core interactions between the colloids are taken into account to investigate the effects of shape alone. The bulk phase behavior of three different shapes of

Anisotropic diffusion tensor applied to temporal mammograms

DEFF Research Database (Denmark)

Karemore, Gopal; Brandt, Sami; Sporring, Jon

2010-01-01

changes related to  specific  effects  like  Hormonal  Replacement  Therapy  (HRT) and aging. Given effect-grouped patient data, we demonstrated how  anisotropic  diffusion  tensor  and  its  coherence  features computed in an anatomically oriented breast coordinate system followed by statistical learning...

Computational protein design: a review

International Nuclear Information System (INIS)

Coluzza, Ivan

2017-01-01

Proteins are one of the most versatile modular assembling systems in nature. Experimentally, more than 110 000 protein structures have been identified and more are deposited every day in the Protein Data Bank. Such an enormous structural variety is to a first approximation controlled by the sequence of amino acids along the peptide chain of each protein. Understanding how the structural and functional properties of the target can be encoded in this sequence is the main objective of protein design. Unfortunately, rational protein design remains one of the major challenges across the disciplines of biology, physics and chemistry. The implications of solving this problem are enormous and branch into materials science, drug design, evolution and even cryptography. For instance, in the field of drug design an effective computational method to design protein-based ligands for biological targets such as viruses, bacteria or tumour cells, could give a significant boost to the development of new therapies with reduced side effects. In materials science, self-assembly is a highly desired property and soon artificial proteins could represent a new class of designable self-assembling materials. The scope of this review is to describe the state of the art in computational protein design methods and give the reader an outline of what developments could be expected in the near future. (topical review)

Cosmological signatures of anisotropic spatial curvature

International Nuclear Information System (INIS)

Pereira, Thiago S.; Marugán, Guillermo A. Mena; Carneiro, Saulo

2015-01-01

If one is willing to give up the cherished hypothesis of spatial isotropy, many interesting cosmological models can be developed beyond the simple anisotropically expanding scenarios. One interesting possibility is presented by shear-free models in which the anisotropy emerges at the level of the curvature of the homogeneous spatial sections, whereas the expansion is dictated by a single scale factor. We show that such models represent viable alternatives to describe the large-scale structure of the inflationary universe, leading to a kinematically equivalent Sachs-Wolfe effect. Through the definition of a complete set of spatial eigenfunctions we compute the two-point correlation function of scalar perturbations in these models. In addition, we show how such scenarios would modify the spectrum of the CMB assuming that the observations take place in a small patch of a universe with anisotropic curvature

Cosmological signatures of anisotropic spatial curvature

Energy Technology Data Exchange (ETDEWEB)

Pereira, Thiago S. [Departamento de Física, Universidade Estadual de Londrina, 86057-970, Londrina – PR (Brazil); Marugán, Guillermo A. Mena [Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006, Madrid (Spain); Carneiro, Saulo, E-mail: tspereira@uel.br, E-mail: mena@iem.cfmac.csic.es, E-mail: saulo.carneiro@pq.cnpq.br [Instituto de Física, Universidade Federal da Bahia, 40210-340, Salvador – BA (Brazil)

2015-07-01

If one is willing to give up the cherished hypothesis of spatial isotropy, many interesting cosmological models can be developed beyond the simple anisotropically expanding scenarios. One interesting possibility is presented by shear-free models in which the anisotropy emerges at the level of the curvature of the homogeneous spatial sections, whereas the expansion is dictated by a single scale factor. We show that such models represent viable alternatives to describe the large-scale structure of the inflationary universe, leading to a kinematically equivalent Sachs-Wolfe effect. Through the definition of a complete set of spatial eigenfunctions we compute the two-point correlation function of scalar perturbations in these models. In addition, we show how such scenarios would modify the spectrum of the CMB assuming that the observations take place in a small patch of a universe with anisotropic curvature.

The traces of anisotropic dark energy in light of Planck

Energy Technology Data Exchange (ETDEWEB)

Cardona, Wilmar; Kunz, Martin [Département de Physique Théorique and Center for Astroparticle Physics, Université de Genève, 24 Quai Ernest Ansermet, 1211 Genève 4 (Switzerland); Hollenstein, Lukas, E-mail: wilmar.cardona@unige.ch, E-mail: lukas.hollenstein@zhaw.ch, E-mail: martin.kunz@unige.ch [IAS Institute of Applied Simulation, ZHAW Zurich University of Applied Sciences, Grüental, PO Box, 8820 Wädenswil (Switzerland)

2014-07-01

We study a dark energy model with non-zero anisotropic stress, either linked to the dark energy density or to the dark matter density. We compute approximate solutions that allow to characterise the behaviour of the dark energy model and to assess the stability of the perturbations. We also determine the current limits on such an anisotropic stress from the cosmic microwave background data by the Planck satellite, and derive the corresponding constraints on the modified growth parameters like the growth index, the effective Newton's constant and the gravitational slip.

Timoshenko beam element with anisotropic cross-sectional properties

DEFF Research Database (Denmark)

Stäblein, Alexander; Hansen, Morten Hartvig

2016-01-01

Beam models are used for the aeroelastic time and frequency domain analysis of wind turbines due to their computational efficiency. Many current aeroelastic tools for the analysis of wind turbines rely on Timoshenko beam elements with classical crosssectional properties (EA, EI, etc.). Those cross......-sectional properties do not reflect the various couplings arising from the anisotropic behaviour of the blade material. A twonoded, three-dimensional Timoshenko beam element was therefore extended to allow for anisotropic cross-sectional properties. For an uncoupled beam, the resulting shape functions are identical...... to the original formulation. The new element was implemented into a co-rotational formulation and validated against natural frequencies and several static load cases of previous works....

Generalized analytic solutions and response characteristics of magnetotelluric fields on anisotropic infinite faults

Science.gov (United States)

Bing, Xue; Yicai, Ji

2018-06-01

In order to understand directly and analyze accurately the detected magnetotelluric (MT) data on anisotropic infinite faults, two-dimensional partial differential equations of MT fields are used to establish a model of anisotropic infinite faults using the Fourier transform method. A multi-fault model is developed to expand the one-fault model. The transverse electric mode and transverse magnetic mode analytic solutions are derived using two-infinite-fault models. The infinite integral terms of the quasi-analytic solutions are discussed. The dual-fault model is computed using the finite element method to verify the correctness of the solutions. The MT responses of isotropic and anisotropic media are calculated to analyze the response functions by different anisotropic conductivity structures. The thickness and conductivity of the media, influencing MT responses, are discussed. The analytic principles are also given. The analysis results are significant to how MT responses are perceived and to the data interpretation of the complex anisotropic infinite faults.

δ M formalism and anisotropic chaotic inflation power spectrum

Science.gov (United States)

Talebian-Ashkezari, A.; Ahmadi, N.

2018-05-01

A new analytical approach to linear perturbations in anisotropic inflation has been introduced in [A. Talebian-Ashkezari, N. Ahmadi and A.A. Abolhasani, JCAP 03 (2018) 001] under the name of δ M formalism. In this paper we apply the mentioned approach to a model of anisotropic inflation driven by a scalar field, coupled to the kinetic term of a vector field with a U(1) symmetry. The δ M formalism provides an efficient way of computing tensor-tensor, tensor-scalar as well as scalar-scalar 2-point correlations that are needed for the analysis of the observational features of an anisotropic model on the CMB. A comparison between δ M results and the tedious calculations using in-in formalism shows the aptitude of the δ M formalism in calculating accurate two point correlation functions between physical modes of the system.

Anisotropic gravitational instability

International Nuclear Information System (INIS)

Polyachenko, V.L.; Fridman, A.M.

1988-01-01

Exact solutions of stability problems are obtained for two anisotropic gravitational systems of different geometries - a layer of finite thickness at rest and a rotating cylinder of finite radius. It is shown that the anisotropic gravitational instability which develops in both cases is of Jeans type. However, in contrast to the classical aperiodic Jeans instability, this instability is oscillatory. The physics of the anisotropic gravitational instability is investigated. It is shown that in a gravitating layer this instability is due, in particular, to excitation of previously unknown interchange-Jeans modes. In the cylinder, the oscillatory Jeans instability is associated with excitation of a rotational branch, this also being responsible for the beam gravitational instability. This is the reason why this instability and the anisotropic gravitational instability have so much in common

Anisotropic constant-roll inflation

Energy Technology Data Exchange (ETDEWEB)

Ito, Asuka; Soda, Jiro [Kobe University, Department of Physics, Kobe (Japan)

2018-01-15

We study constant-roll inflation in the presence of a gauge field coupled to an inflaton. By imposing the constant anisotropy condition, we find new exact anisotropic constant-roll inflationary solutions which include anisotropic power-law inflation as a special case. We also numerically show that the new anisotropic solutions are attractors in the phase space. (orig.)

Modelling of ultrasonic nondestructive testing in anisotropic materials - Rectangular crack

International Nuclear Information System (INIS)

Bostroem, A.

2001-12-01

Nondestructive testing with ultrasound is a standard procedure in the nuclear power industry when searching for defects, in particular cracks. To develop and qualify testing procedures extensive experimental work on test blocks is usually required. This can take a lot of time and therefore be quite costly. A good mathematical model of the testing situation is therefore of great value as it can reduce the experimental work to a great extent. A good model can be very useful for parametric studies and as a pedagogical tool. A further use of a model is as a tool in the qualification of personnel. In anisotropic materials, e.g. austenitic welds, the propagation of ultrasound becomes much more complicated as compared to isotropic materials. Therefore, modelling is even more useful for anisotropic materials, and it in particular has a greater pedagogical value. The present project has been concerned with a further development of the anisotropic capabilities of the computer program UTDefect, which has so far only contained a strip-like crack as the single defect type for anisotropic materials. To be more specific, the scattering by a rectangular crack in an anisotropic component has been studied and the result is adapted to include transmitting and receiving ultrasonic probes. The component under study is assumed to be anisotropic with arbitrary anisotropy. On the other hand, it is assumed to be homogeneous, and this in particular excludes most welds, where it is seldom an adequate approximation to assume homogeneity. The anisotropy may be arbitrarily oriented and the same is true of the rectangular crack. The crack may also be located near a backside of the component. To solve the scattering problem for the crack an integral equation method is used. The probe model has been developed in an earlier project and to compute the signal response in the receiving probe an electromechanical reciprocity argument is employed. As a rectangle is a truly 3D scatterer the sizes of the

A resistor interpretation of general anisotropic cardiac tissue.

Science.gov (United States)

Shao, Hai; Sampson, Kevin J; Pormann, John B; Rose, Donald J; Henriquez, Craig S

2004-02-01

This paper describes a spatial discretization scheme for partial differential equation systems that contain anisotropic diffusion. The discretization method uses unstructured finite volumes, or the boxes, that are formed as a secondary geometric structure from an underlying triangular mesh. We show how the discretization can be interpreted as a resistive circuit network, where each resistor is assigned at each edge of the triangular element. The resistor is computed as an anisotropy dependent geometric quantity of the local mesh structure. Finally, we show that under certain conditions, the discretization gives rise to negative resistors that can produce non-physical hyperpolarizations near depolarizing stimuli. We discuss how the proper choice of triangulation (anisotropic Delaunay triangulation) can ensure monotonicity (i.e. all resistors are positive).

A numerical method for two-dimensional anisotropic transport problem in cylindrical geometry

International Nuclear Information System (INIS)

Du Mingsheng; Feng Tiekai; Fu Lianxiang; Cao Changshu; Liu Yulan

1988-01-01

The authors deal with the triangular mesh-discontinuous finite element method for solving the time-dependent anisotropic neutron transport problem in two-dimensional cylindrical geometry. A prior estimate of the numerical solution is given. Stability is proved. The authors have computed a two dimensional anisotropic neutron transport problem and a Tungsten-Carbide critical assembly problem by using the numerical method. In comparision with DSN method and the experimental results obtained by others both at home and abroad, the method is satisfactory

Importance of anisotropy in detachment rates for force production and cargo transport by a team of motor proteins.

Science.gov (United States)

Takshak, Anjneya; Kunwar, Ambarish

2016-05-01

Many cellular processes are driven by collective forces generated by a team consisting of multiple molecular motor proteins. One aspect that has received less attention is the detachment rate of molecular motors under mechanical force/load. While detachment rate of kinesin motors measured under backward force increases rapidly for forces beyond stall-force; this scenario is just reversed for non-yeast dynein motors where detachment rate from microtubule decreases, exhibiting a catch-bond type behavior. It has been shown recently that yeast dynein responds anisotropically to applied load, i.e. detachment rates are different under forward and backward pulling. Here, we use computational modeling to show that these anisotropic detachment rates might help yeast dynein motors to improve their collective force generation in the absence of catch-bond behavior. We further show that the travel distance of cargos would be longer if detachment rates are anisotropic. Our results suggest that anisotropic detachment rates could be an alternative strategy for motors to improve the transport properties and force production by the team. © 2016 The Protein Society.

Finite frequency traveltime sensitivity kernels for acoustic anisotropic media: Angle dependent bananas

KAUST Repository

Djebbi, Ramzi

2013-08-19

Anisotropy is an inherent character of the Earth subsurface. It should be considered for modeling and inversion. The acoustic VTI wave equation approximates the wave behavior in anisotropic media, and especially it\\'s kinematic characteristics. To analyze which parts of the model would affect the traveltime for anisotropic traveltime inversion methods, especially for wave equation tomography (WET), we drive the sensitivity kernels for anisotropic media using the VTI acoustic wave equation. A Born scattering approximation is first derived using the Fourier domain acoustic wave equation as a function of perturbations in three anisotropy parameters. Using the instantaneous traveltime, which unwraps the phase, we compute the kernels. These kernels resemble those for isotropic media, with the η kernel directionally dependent. They also have a maximum sensitivity along the geometrical ray, which is more realistic compared to the cross-correlation based kernels. Focusing on diving waves, which is used more often, especially recently in waveform inversion, we show sensitivity kernels in anisotropic media for this case.

Finite frequency traveltime sensitivity kernels for acoustic anisotropic media: Angle dependent bananas

KAUST Repository

Djebbi, Ramzi; Alkhalifah, Tariq Ali

2013-01-01

Anisotropy is an inherent character of the Earth subsurface. It should be considered for modeling and inversion. The acoustic VTI wave equation approximates the wave behavior in anisotropic media, and especially it's kinematic characteristics. To analyze which parts of the model would affect the traveltime for anisotropic traveltime inversion methods, especially for wave equation tomography (WET), we drive the sensitivity kernels for anisotropic media using the VTI acoustic wave equation. A Born scattering approximation is first derived using the Fourier domain acoustic wave equation as a function of perturbations in three anisotropy parameters. Using the instantaneous traveltime, which unwraps the phase, we compute the kernels. These kernels resemble those for isotropic media, with the η kernel directionally dependent. They also have a maximum sensitivity along the geometrical ray, which is more realistic compared to the cross-correlation based kernels. Focusing on diving waves, which is used more often, especially recently in waveform inversion, we show sensitivity kernels in anisotropic media for this case.

Anisotropic spheres with Van der Waals-type equation of state

Indian Academy of Sciences (India)

We study static spherically symmetric space-time to describe relativistic compact objects with anisotropic matter distribution and derive two classes of exact models to the Einstein–Maxwell system ... Proceedings of the International Workshop/Conference on Computational Condensed Matter Physics and Materials Science

Computational design of proteins with novel structure and functions

International Nuclear Information System (INIS)

Yang Wei; Lai Lu-Hua

2016-01-01

Computational design of proteins is a relatively new field, where scientists search the enormous sequence space for sequences that can fold into desired structure and perform desired functions. With the computational approach, proteins can be designed, for example, as regulators of biological processes, novel enzymes, or as biotherapeutics. These approaches not only provide valuable information for understanding of sequence–structure–function relations in proteins, but also hold promise for applications to protein engineering and biomedical research. In this review, we briefly introduce the rationale for computational protein design, then summarize the recent progress in this field, including de novo protein design, enzyme design, and design of protein–protein interactions. Challenges and future prospects of this field are also discussed. (topical review)

Imaging the Earth's anisotropic structure with Bayesian Inversion of fundamental and higher mode surface-wave dispersion data

Science.gov (United States)

Ravenna, Matteo; Lebedev, Sergei; Celli, Nicolas

2017-04-01

We develop a Markov Chain Monte Carlo inversion of fundamental and higher mode phase-velocity curves for radially and azimuthally anisotropic structure of the crust and upper mantle. In the inversions of Rayleigh- and Love-wave dispersion curves for radially anisotropic structure, we obtain probabilistic 1D radially anisotropic shear-velocity profiles of the isotropic average Vs and anisotropy (or Vsv and Vsh) as functions of depth. In the inversions for azimuthal anisotropy, Rayleigh-wave dispersion curves at different azimuths are inverted for the vertically polarized shear-velocity structure (Vsv) and the 2-phi component of azimuthal anisotropy. The strength and originality of the method is in its fully non-linear approach. Each model realization is computed using exact forward calculations. The uncertainty of the models is a part of the output. In the inversions for azimuthal anisotropy, in particular, the computation of the forward problem is performed separately at different azimuths, with no linear approximations on the relation of the Earth's elastic parameters to surface wave phase velocities. The computations are performed in parallel in order reduce the computing time. We compare inversions of the fundamental mode phase-velocity curves alone with inversions that also include overtones. The addition of higher modes enhances the resolving power of the anisotropic structure of the deep upper mantle. We apply the inversion method to phase-velocity curves in a few regions, including the Hangai dome region in Mongolia. Our models provide constraints on the Moho depth, the Lithosphere-Asthenosphere Boundary, and the alignment of the anisotropic fabric and the direction of current and past flow, from the crust down to the deep asthenosphere.

Soft Computing Techniques for the Protein Folding Problem on High Performance Computing Architectures.

Science.gov (United States)

Llanes, Antonio; Muñoz, Andrés; Bueno-Crespo, Andrés; García-Valverde, Teresa; Sánchez, Antonia; Arcas-Túnez, Francisco; Pérez-Sánchez, Horacio; Cecilia, José M

2016-01-01

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.

Multiresolution, Multi-Scale Target Identification and Tracking using the Anisotropic Diffusion Pyramid

National Research Council Canada - National Science Library

Acton, Scott

1998-01-01

...: the anisotropic diffusion pyramid and the morphological pyramid. Coarse-to-fine target searches are implemented within the image pyramids, providing a lOOX improvement in computational expense over standard correlation-based approaches...

DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins.

Science.gov (United States)

Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Banchariya, Anjali; Rao, Atmakuri Ramakrishna

2017-03-24

Insecticide resistance is a major challenge for the control program of insect pests in the fields of crop protection, human and animal health etc. Resistance to different insecticides is conferred by the proteins encoded from certain class of genes of the insects. To distinguish the insecticide resistant proteins from non-resistant proteins, no computational tool is available till date. Thus, development of such a computational tool will be helpful in predicting the insecticide resistant proteins, which can be targeted for developing appropriate insecticides. Five different sets of feature viz., amino acid composition (AAC), di-peptide composition (DPC), pseudo amino acid composition (PAAC), composition-transition-distribution (CTD) and auto-correlation function (ACF) were used to map the protein sequences into numeric feature vectors. The encoded numeric vectors were then used as input in support vector machine (SVM) for classification of insecticide resistant and non-resistant proteins. Higher accuracies were obtained under RBF kernel than that of other kernels. Further, accuracies were observed to be higher for DPC feature set as compared to others. The proposed approach achieved an overall accuracy of >90% in discriminating resistant from non-resistant proteins. Further, the two classes of resistant proteins i.e., detoxification-based and target-based were discriminated from non-resistant proteins with >95% accuracy. Besides, >95% accuracy was also observed for discrimination of proteins involved in detoxification- and target-based resistance mechanisms. The proposed approach not only outperformed Blastp, PSI-Blast and Delta-Blast algorithms, but also achieved >92% accuracy while assessed using an independent dataset of 75 insecticide resistant proteins. This paper presents the first computational approach for discriminating the insecticide resistant proteins from non-resistant proteins. Based on the proposed approach, an online prediction server DIRProt has

Effective orthorhombic anisotropic models for wavefield extrapolation

KAUST Repository

Ibanez-Jacome, W.

2014-07-18

Wavefield extrapolation in orthorhombic anisotropic media incorporates complicated but realistic models to reproduce wave propagation phenomena in the Earth\\'s subsurface. Compared with the representations used for simpler symmetries, such as transversely isotropic or isotropic, orthorhombic models require an extended and more elaborated formulation that also involves more expensive computational processes. The acoustic assumption yields more efficient description of the orthorhombic wave equation that also provides a simplified representation for the orthorhombic dispersion relation. However, such representation is hampered by the sixth-order nature of the acoustic wave equation, as it also encompasses the contribution of shear waves. To reduce the computational cost of wavefield extrapolation in such media, we generate effective isotropic inhomogeneous models that are capable of reproducing the firstarrival kinematic aspects of the orthorhombic wavefield. First, in order to compute traveltimes in vertical orthorhombic media, we develop a stable, efficient and accurate algorithm based on the fast marching method. The derived orthorhombic acoustic dispersion relation, unlike the isotropic or transversely isotropic ones, is represented by a sixth order polynomial equation with the fastest solution corresponding to outgoing P waves in acoustic media. The effective velocity models are then computed by evaluating the traveltime gradients of the orthorhombic traveltime solution, and using them to explicitly evaluate the corresponding inhomogeneous isotropic velocity field. The inverted effective velocity fields are source dependent and produce equivalent first-arrival kinematic descriptions of wave propagation in orthorhombic media. We extrapolate wavefields in these isotropic effective velocity models using the more efficient isotropic operator, and the results compare well, especially kinematically, with those obtained from the more expensive anisotropic extrapolator.

Effective orthorhombic anisotropic models for wavefield extrapolation

KAUST Repository

Ibanez-Jacome, W.; Alkhalifah, Tariq Ali; Waheed, Umair bin

2014-01-01

Wavefield extrapolation in orthorhombic anisotropic media incorporates complicated but realistic models to reproduce wave propagation phenomena in the Earth's subsurface. Compared with the representations used for simpler symmetries, such as transversely isotropic or isotropic, orthorhombic models require an extended and more elaborated formulation that also involves more expensive computational processes. The acoustic assumption yields more efficient description of the orthorhombic wave equation that also provides a simplified representation for the orthorhombic dispersion relation. However, such representation is hampered by the sixth-order nature of the acoustic wave equation, as it also encompasses the contribution of shear waves. To reduce the computational cost of wavefield extrapolation in such media, we generate effective isotropic inhomogeneous models that are capable of reproducing the firstarrival kinematic aspects of the orthorhombic wavefield. First, in order to compute traveltimes in vertical orthorhombic media, we develop a stable, efficient and accurate algorithm based on the fast marching method. The derived orthorhombic acoustic dispersion relation, unlike the isotropic or transversely isotropic ones, is represented by a sixth order polynomial equation with the fastest solution corresponding to outgoing P waves in acoustic media. The effective velocity models are then computed by evaluating the traveltime gradients of the orthorhombic traveltime solution, and using them to explicitly evaluate the corresponding inhomogeneous isotropic velocity field. The inverted effective velocity fields are source dependent and produce equivalent first-arrival kinematic descriptions of wave propagation in orthorhombic media. We extrapolate wavefields in these isotropic effective velocity models using the more efficient isotropic operator, and the results compare well, especially kinematically, with those obtained from the more expensive anisotropic extrapolator.

Anisotropic contrast optical microscope.

Science.gov (United States)

Peev, D; Hofmann, T; Kananizadeh, N; Beeram, S; Rodriguez, E; Wimer, S; Rodenhausen, K B; Herzinger, C M; Kasputis, T; Pfaunmiller, E; Nguyen, A; Korlacki, R; Pannier, A; Li, Y; Schubert, E; Hage, D; Schubert, M

2016-11-01

An optical microscope is described that reveals contrast in the Mueller matrix images of a thin, transparent, or semi-transparent specimen located within an anisotropic object plane (anisotropic filter). The specimen changes the anisotropy of the filter and thereby produces contrast within the Mueller matrix images. Here we use an anisotropic filter composed of a semi-transparent, nanostructured thin film with sub-wavelength thickness placed within the object plane. The sample is illuminated as in common optical microscopy but the light is modulated in its polarization using combinations of linear polarizers and phase plate (compensator) to control and analyze the state of polarization. Direct generalized ellipsometry data analysis approaches permit extraction of fundamental Mueller matrix object plane images dispensing with the need of Fourier expansion methods. Generalized ellipsometry model approaches are used for quantitative image analyses. These images are obtained from sets of multiple images obtained under various polarizer, analyzer, and compensator settings. Up to 16 independent Mueller matrix images can be obtained, while our current setup is limited to 11 images normalized by the unpolarized intensity. We demonstrate the anisotropic contrast optical microscope by measuring lithographically defined micro-patterned anisotropic filters, and we quantify the adsorption of an organic self-assembled monolayer film onto the anisotropic filter. Comparison with an isotropic glass slide demonstrates the image enhancement obtained by our method over microscopy without the use of an anisotropic filter. In our current instrument, we estimate the limit of detection for organic volumetric mass within the object plane of ≈49 fg within ≈7 × 7 μm 2 object surface area. Compared to a quartz crystal microbalance with dissipation instrumentation, where contemporary limits require a total load of ≈500 pg for detection, the instrumentation demonstrated here improves

Simple types of anisotropic inflation

International Nuclear Information System (INIS)

Barrow, John D.; Hervik, Sigbjoern

2010-01-01

We display some simple cosmological solutions of gravity theories with quadratic Ricci curvature terms added to the Einstein-Hilbert Lagrangian which exhibit anisotropic inflation. The Hubble expansion rates are constant and unequal in three orthogonal directions. We describe the evolution of the simplest of these homogeneous and anisotropic cosmological models from its natural initial state and evaluate the deviations they will create from statistical isotropy in the fluctuations produced during a period of anisotropic inflation. The anisotropic inflation is not a late-time attractor in these models but the rate of approach to a final isotropic de Sitter state is slow and is conducive to the creation of observable anisotropic statistical effects in the microwave background. The statistical anisotropy would not be scale invariant and the level of statistical anisotropy will grow with scale.

Monte carlo simulation of anisotropic grain growth in liquid phase sintering

International Nuclear Information System (INIS)

Han, Yoon Soo; Kim, Do Kyung

2003-01-01

One of the key techniques in modern engineering ceramic system is microstructural control of anisotropic grain growth because grain orientation and shape proved to have an influence on mechanic, dielectric and electric behavior of ceramics. But until now, computer simulation for grain growth has not sufficiently addressed to this subject. The reason is that simulation algorithm was laborious because it has to contain mass transfer through liquid phase and especially anisotropic grain growth has to be considered based on interfacial properties in real system. The goal of present study is simulation of anisotropic grain growth in liquid phase by Q-states model. To give anisotropic inherency to grains, constraint on mobility to specific boundaries was applied. For comparison, we measured grain size distribution and deduced grain growth kinetics from relation ship between average grain size and time. As a result, the grain size distribution functions become broader and the peak height decreases as the anisotropy is increased. The growth exponent 0.67 and 0.47 found by linear fitting have slightly different values in comparison with work of Grest et al. but similar is trend to the decrease of exponent with anisotropy

Computational methods for protein identification from mass spectrometry data.

Directory of Open Access Journals (Sweden)

Leo McHugh

2008-02-01

Full Text Available Protein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods for protein identification. A wide range of computational methods, each with various implementations, are available to complement different proteomic approaches. A solid knowledge of the range of algorithms available and, more critically, the accuracy and effectiveness of these techniques is essential to ensure as many of the proteins as possible, within any particular experiment, are correctly identified. Here, we undertake a systematic review of the currently available methods and algorithms for interpreting, managing, and analyzing biological data associated with protein identification. We summarize the advances in computational solutions as they have responded to corresponding advances in mass spectrometry hardware. The evolution of scoring algorithms and metrics for automated protein identification are also discussed with a focus on the relative performance of different techniques. We also consider the relative advantages and limitations of different techniques in particular biological contexts. Finally, we present our perspective on future developments in the area of computational protein identification by considering the most recent literature on new and promising approaches to the problem as well as identifying areas yet to be explored and the potential application of methods from other areas of computational biology.

A large-scale evaluation of computational protein function prediction

NARCIS (Netherlands)

Radivojac, P.; Clark, W.T.; Oron, T.R.; Schnoes, A.M.; Wittkop, T.; Kourmpetis, Y.A.I.; Dijk, van A.D.J.; Friedberg, I.

2013-01-01

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be

3D anisotropic modeling and identification for airborne EM systems based on the spectral-element method

Science.gov (United States)

Huang, Xin; Yin, Chang-Chun; Cao, Xiao-Yue; Liu, Yun-He; Zhang, Bo; Cai, Jing

2017-09-01

The airborne electromagnetic (AEM) method has a high sampling rate and survey flexibility. However, traditional numerical modeling approaches must use high-resolution physical grids to guarantee modeling accuracy, especially for complex geological structures such as anisotropic earth. This can lead to huge computational costs. To solve this problem, we propose a spectral-element (SE) method for 3D AEM anisotropic modeling, which combines the advantages of spectral and finite-element methods. Thus, the SE method has accuracy as high as that of the spectral method and the ability to model complex geology inherited from the finite-element method. The SE method can improve the modeling accuracy within discrete grids and reduce the dependence of modeling results on the grids. This helps achieve high-accuracy anisotropic AEM modeling. We first introduced a rotating tensor of anisotropic conductivity to Maxwell's equations and described the electrical field via SE basis functions based on GLL interpolation polynomials. We used the Galerkin weighted residual method to establish the linear equation system for the SE method, and we took a vertical magnetic dipole as the transmission source for our AEM modeling. We then applied fourth-order SE calculations with coarse physical grids to check the accuracy of our modeling results against a 1D semi-analytical solution for an anisotropic half-space model and verified the high accuracy of the SE. Moreover, we conducted AEM modeling for different anisotropic 3D abnormal bodies using two physical grid scales and three orders of SE to obtain the convergence conditions for different anisotropic abnormal bodies. Finally, we studied the identification of anisotropy for single anisotropic abnormal bodies, anisotropic surrounding rock, and single anisotropic abnormal body embedded in an anisotropic surrounding rock. This approach will play a key role in the inversion and interpretation of AEM data collected in regions with anisotropic

Anisotropic magnetotelluric inversion using a mutual information constraint

Science.gov (United States)

Mandolesi, E.; Jones, A. G.

2012-12-01

In recent years, several authors pointed that the electrical conductivity of many subsurface structures cannot be described properly by a scalar field. With the development of field devices and techniques, data quality improved to the point that the anisotropy in conductivity of rocks (microscopic anisotropy) and tectonic structures (macroscopic anisotropy) cannot be neglected. Therefore a correct use of high quality data has to include electrical anisotropy and a correct interpretation of anisotropic data characterizes directly a non-negligible part of the subsurface. In this work we test an inversion routine that takes advantage of the classic Levenberg-Marquardt (LM) algorithm to invert magnetotelluric (MT) data generated from a bi-dimensional (2D) anisotropic domain. The LM method is routinely used in inverse problems due its performance and robustness. In non-linear inverse problems -such the MT problem- the LM method provides a spectacular compromise betwee quick and secure convergence at the price of the explicit computation and storage of the sensitivity matrix. Regularization in inverse MT problems has been used extensively, due to the necessity to constrain model space and to reduce the ill-posedness of the anisotropic MT problem, which makes MT inversions extremely challenging. In order to reduce non-uniqueness of the MT problem and to reach a model compatible with other different tomographic results from the same target region, we used a mutual information (MI) based constraint. MI is a basic quantity in information theory that can be used to define a metric between images, and it is routinely used in fields as computer vision, image registration and medical tomography, to cite some applications. We -thus- inverted for the model that best fits the anisotropic data and that is the closest -in a MI sense- to a tomographic model of the target area. The advantage of this technique is that the tomographic model of the studied region may be produced by any

Large-scale transmission-type multifunctional anisotropic coding metasurfaces in millimeter-wave frequencies

Science.gov (United States)

Cui, Tie Jun; Wu, Rui Yuan; Wu, Wei; Shi, Chuan Bo; Li, Yun Bo

2017-10-01

We propose fast and accurate designs to large-scale and low-profile transmission-type anisotropic coding metasurfaces with multiple functions in the millimeter-wave frequencies based on the antenna-array method. The numerical simulation of an anisotropic coding metasurface with the size of 30λ × 30λ by the proposed method takes only 20 min, which however cannot be realized by commercial software due to huge memory usage in personal computers. To inspect the performance of coding metasurfaces in the millimeter-wave band, the working frequency is chosen as 60 GHz. Based on the convolution operations and holographic theory, the proposed multifunctional anisotropic coding metasurface exhibits different effects excited by y-polarized and x-polarized incidences. This study extends the frequency range of coding metasurfaces, filling the gap between microwave and terahertz bands, and implying promising applications in millimeter-wave communication and imaging.

Long-wave model for strongly anisotropic growth of a crystal step.

Science.gov (United States)

Khenner, Mikhail

2013-08-01

A continuum model for the dynamics of a single step with the strongly anisotropic line energy is formulated and analyzed. The step grows by attachment of adatoms from the lower terrace, onto which atoms adsorb from a vapor phase or from a molecular beam, and the desorption is nonnegligible (the "one-sided" model). Via a multiscale expansion, we derived a long-wave, strongly nonlinear, and strongly anisotropic evolution PDE for the step profile. Written in terms of the step slope, the PDE can be represented in a form similar to a convective Cahn-Hilliard equation. We performed the linear stability analysis and computed the nonlinear dynamics. Linear stability depends on whether the stiffness is minimum or maximum in the direction of the step growth. It also depends nontrivially on the combination of the anisotropy strength parameter and the atomic flux from the terrace to the step. Computations show formation and coarsening of a hill-and-valley structure superimposed onto a long-wavelength profile, which independently coarsens. Coarsening laws for the hill-and-valley structure are computed for two principal orientations of a maximum step stiffness, the increasing anisotropy strength, and the varying atomic flux.

Effective Orthorhombic Anisotropic Models for Wave field Extrapolation

KAUST Repository

Ibanez Jacome, Wilson

2013-05-01

Wavefield extrapolation in orthorhombic anisotropic media incorporates complicated but realistic models, to reproduce wave propagation phenomena in the Earth\\'s subsurface. Compared with the representations used for simpler symmetries, such as transversely isotropic or isotropic, orthorhombic models require an extended and more elaborated formulation that also involves more expensive computational processes. The acoustic assumption yields more efficient description of the orthorhombic wave equation that also provides a simplified representation for the orthorhombic dispersion relation. However, such representation is hampered by the sixth-order nature of the acoustic wave equation, as it also encompasses the contribution of shear waves. To reduce the computational cost of wavefield extrapolation in such media, I generate effective isotropic inhomogeneous models that are capable of reproducing the first-arrival kinematic aspects of the orthorhombic wavefield. First, in order to compute traveltimes in vertical orthorhombic media, I develop a stable, efficient and accurate algorithm based on the fast marching method. The derived orthorhombic acoustic dispersion relation, unlike the isotropic or transversely isotropic one, is represented by a sixth order polynomial equation that includes the fastest solution corresponding to outgoing P-waves in acoustic media. The effective velocity models are then computed by evaluating the traveltime gradients of the orthorhombic traveltime solution, which is done by explicitly solving the isotropic eikonal equation for the corresponding inhomogeneous isotropic velocity field. The inverted effective velocity fields are source dependent and produce equivalent first-arrival kinematic descriptions of wave propagation in orthorhombic media. I extrapolate wavefields in these isotropic effective velocity models using the more efficient isotropic operator, and the results compare well, especially kinematically, with those obtained from the

3D MRI-based anisotropic FSI models with cyclic bending for human coronary atherosclerotic plaque mechanical analysis.

Science.gov (United States)

Tang, Dalin; Yang, Chun; Kobayashi, Shunichi; Zheng, Jie; Woodard, Pamela K; Teng, Zhongzhao; Billiar, Kristen; Bach, Richard; Ku, David N

2009-06-01

Heart attack and stroke are often caused by atherosclerotic plaque rupture, which happens without warning most of the time. Magnetic resonance imaging (MRI)-based atherosclerotic plaque models with fluid-structure interactions (FSIs) have been introduced to perform flow and stress/strain analysis and identify possible mechanical and morphological indices for accurate plaque vulnerability assessment. For coronary arteries, cyclic bending associated with heart motion and anisotropy of the vessel walls may have significant influence on flow and stress/strain distributions in the plaque. FSI models with cyclic bending and anisotropic vessel properties for coronary plaques are lacking in the current literature. In this paper, cyclic bending and anisotropic vessel properties were added to 3D FSI coronary plaque models so that the models would be more realistic for more accurate computational flow and stress/strain predictions. Six computational models using one ex vivo MRI human coronary plaque specimen data were constructed to assess the effects of cyclic bending, anisotropic vessel properties, pulsating pressure, plaque structure, and axial stretch on plaque stress/strain distributions. Our results indicate that cyclic bending and anisotropic properties may cause 50-800% increase in maximum principal stress (Stress-P1) values at selected locations. The stress increase varies with location and is higher when bending is coupled with axial stretch, nonsmooth plaque structure, and resonant pressure conditions (zero phase angle shift). Effects of cyclic bending on flow behaviors are more modest (9.8% decrease in maximum velocity, 2.5% decrease in flow rate, 15% increase in maximum flow shear stress). Inclusion of cyclic bending, anisotropic vessel material properties, accurate plaque structure, and axial stretch in computational FSI models should lead to a considerable improvement of accuracy of computational stress/strain predictions for coronary plaque vulnerability

Anisotropic Galaxy-Galaxy Lensing in the Illustris-1 Simulation

Science.gov (United States)

Brainerd, Tereasa G.

2017-06-01

In Cold Dark Matter universes, the dark matter halos of galaxies are expected to be triaxial, leading to a surface mass density that is not circularly symmetric. In principle, this "flattening" of the dark matter halos of galaxies should be observable as an anisotropy in the weak galaxy-galaxy lensing signal. The degree to which the weak lensing signal is observed to be anisotropic, however, will depend strongly on the degree to which mass (i.e., the dark matter) is aligned with light in the lensing galaxies. That is, the anisotropy will be maximized when the major axis of the projected mass distribution is well aligned with the projected light distribution of the lens galaxies. Observational studies of anisotropic galaxy-galaxy lensing have found an anisotropic weak lensing signal around massive, red galaxies. Detecting the signal around blue, disky galaxies has, however, been more elusive. A possible explanation for this is that mass and light are well aligned within red galaxies and poorly aligned within blue galaxies (an explanation that is supported by studies of the locations of satellites of large, relatively isolated galaxies). Here we compute the weak lensing signal of isolated central galaxies in the Illustris-1 simulation. We compute the anisotropy of the weak lensing signal using two definitions of the geometry: [1] the major axis of the projected dark matter mass distribution and [2] the major axis of the projected stellar mass. On projected scales less than 15% of the virial radius, an anisotropy of order 10% is found for both definitions of the geometry. On larger scales, the anisotropy computed relative to the major axis of the projected light distribution is less than the anisotropy computed relative to the major axis of the projected dark matter. On projected scales of order the virial radius, the anisotropy obtained when using the major axis of the light is an order of magnitude less than the anisotropy obtained when using the major axis of the

APC: A New Code for Atmospheric Polarization Computations

Science.gov (United States)

Korkin, Sergey V.; Lyapustin, Alexei I.; Rozanov, Vladimir V.

2014-01-01

A new polarized radiative transfer code Atmospheric Polarization Computations (APC) is described. The code is based on separation of the diffuse light field into anisotropic and smooth (regular) parts. The anisotropic part is computed analytically. The smooth regular part is computed numerically using the discrete ordinates method. Vertical stratification of the atmosphere, common types of bidirectional surface reflection and scattering by spherical particles or spheroids are included. A particular consideration is given to computation of the bidirectional polarization distribution function (BPDF) of the waved ocean surface.

Short intergranular cracks in the piecewise anisotropic continuum model of the microstructure

International Nuclear Information System (INIS)

Cizelj, L.; Kovse, I.

2001-01-01

Computational algorithms aiming at modeling and visualization of the initiation and growth of intergranular stress corrosion cracks (e.g., in the steam generator tubes) on the grain-size scale have already been proposed [6]. The main focus of the paper is given to the influence of randomly oriented neighboring grains on the microscopic stress fields at crack tips. The incompatibility strains, which develop along the boundaries of randomly oriented anisotropic grains, are shown to influence the local stress fields at crack tips significantly. Special attention has been paid to the implementation and comparison of different numerical methods estimating the local stress fields at crack tips, aiming at optimizing the computational time and the numerical accuracy of the results. The limited number of calculations indicate that the anisotropic arrangement of grains with local incompatibility strains causes on average about 10% (plane strain) and 26% (plane stress) higher J-integral values at the crack tips than expected from the calculations in the isotropic case.(author)

PCE: web tools to compute protein continuum electrostatics

Science.gov (United States)

Miteva, Maria A.; Tufféry, Pierre; Villoutreix, Bruno O.

2005-01-01

PCE (protein continuum electrostatics) is an online service for protein electrostatic computations presently based on the MEAD (macroscopic electrostatics with atomic detail) package initially developed by D. Bashford [(2004) Front Biosci., 9, 1082–1099]. This computer method uses a macroscopic electrostatic model for the calculation of protein electrostatic properties, such as pKa values of titratable groups and electrostatic potentials. The MEAD package generates electrostatic energies via finite difference solution to the Poisson–Boltzmann equation. Users submit a PDB file and PCE returns potentials and pKa values as well as color (static or animated) figures displaying electrostatic potentials mapped on the molecular surface. This service is intended to facilitate electrostatics analyses of proteins and thereby broaden the accessibility to continuum electrostatics to the biological community. PCE can be accessed at . PMID:15980492

Determination of phase diagrams via computer simulation: methodology and applications to water, electrolytes and proteins

International Nuclear Information System (INIS)

Vega, C; Sanz, E; Abascal, J L F; Noya, E G

2008-01-01

. Moreover, the possibility of obtaining fluid-solid equilibria for simple protein models will be discussed. In these primitive models, the protein is described by a spherical potential with certain anisotropic bonding sites (patchy sites). (topical review)

CT reconstruction from few-views with anisotropic edge-guided total variance

International Nuclear Information System (INIS)

Rong, Junyan; Liu, Wenlei; Gao, Peng; Liao, Qimei; Jiao, Chun; Ma, Jianhua; Lu, Hongbing

2016-01-01

To overcome the oversmoothing drawback in the edge areas when reconstructing few-view CT with total variation (TV) minimization, in this paper, we propose an anisotropic edge-guided TV minimization framework for few-view CT reconstruction. In the framework, anisotropic TV is summed with pre-weighted image gradient and then used as the object function for minimizing. It includes edge-guided TV minimization (EGTV) and edge-guided adaptive-weighted TV minimization (EGAwTV) algorithms. For EGTV algorithm, the weights of the TV discretization term are updated by anisotropic edge information detected from the image, whereas the weights for EGAwTV are determined based on edge information and local image-intensity gradients. To solve the minimization problem of the proposed algorithm, a similar TV-based minimization implementation is developed to address the raw data fidelity and other constraints. The evaluation results using both computer simulations with the Shepp-Logan phantom and experimental data from a physical phantom demonstrate that the proposed algorithms exhibit noticeable gains in the merits of spatial resolution compared with the conventional TV and other modified TV algorithms.

Computational protein design-the next generation tool to expand synthetic biology applications.

Science.gov (United States)

Gainza-Cirauqui, Pablo; Correia, Bruno Emanuel

2018-05-02

One powerful approach to engineer synthetic biology pathways is the assembly of proteins sourced from one or more natural organisms. However, synthetic pathways often require custom functions or biophysical properties not displayed by natural proteins, limitations that could be overcome through modern protein engineering techniques. Structure-based computational protein design is a powerful tool to engineer new functional capabilities in proteins, and it is beginning to have a profound impact in synthetic biology. Here, we review efforts to increase the capabilities of synthetic biology using computational protein design. We focus primarily on computationally designed proteins not only validated in vitro, but also shown to modulate different activities in living cells. Efforts made to validate computational designs in cells can illustrate both the challenges and opportunities in the intersection of protein design and synthetic biology. We also highlight protein design approaches, which although not validated as conveyors of new cellular function in situ, may have rapid and innovative applications in synthetic biology. We foresee that in the near-future, computational protein design will vastly expand the functional capabilities of synthetic cells. Copyright © 2018. Published by Elsevier Ltd.

Tokamak plasma equilibrium problems with anisotropic pressure and rotation and their numerical solution

International Nuclear Information System (INIS)

Ivanov, A. A.; Martynov, A. A.; Medvedev, S. Yu.; Poshekhonov, Yu. Yu.

2015-01-01

In the MHD tokamak plasma theory, the plasma pressure is usually assumed to be isotropic. However, plasma heating by neutral beam injection and RF heating can lead to a strong anisotropy of plasma parameters and rotation of the plasma. The development of MHD equilibrium theory taking into account the plasma inertia and anisotropic pressure began a long time ago, but until now it has not been consistently applied in computational codes for engineering calculations of the plasma equilibrium and evolution in tokamak. This paper contains a detailed derivation of the axisymmetric plasma equilibrium equation in the most general form (with arbitrary rotation and anisotropic pressure) and description of the specialized version of the SPIDER code. The original method of calculation of the equilibrium with an anisotropic pressure and a prescribed rotational transform profile is proposed. Examples of calculations and discussion of the results are also presented

Effective Elliptic Models for Efficient Wavefield Extrapolation in Anisotropic Media

KAUST Repository

Waheed, Umair bin

2014-05-01

Wavefield extrapolation operator for elliptically anisotropic media offers significant cost reduction compared to that of transversely isotropic media (TI), especially when the medium exhibits tilt in the symmetry axis (TTI). However, elliptical anisotropy does not provide accurate focusing for TI media. Therefore, we develop effective elliptically anisotropic models that correctly capture the kinematic behavior of the TTI wavefield. Specifically, we use an iterative elliptically anisotropic eikonal solver that provides the accurate traveltimes for a TI model. The resultant coefficients of the elliptical eikonal provide the effective models. These effective models allow us to use the cheaper wavefield extrapolation operator for elliptic media to obtain approximate wavefield solutions for TTI media. Despite the fact that the effective elliptic models are obtained by kinematic matching using high-frequency asymptotic, the resulting wavefield contains most of the critical wavefield components, including the frequency dependency and caustics, if present, with reasonable accuracy. The methodology developed here offers a much better cost versus accuracy tradeoff for wavefield computations in TTI media, considering the cost prohibitive nature of the problem. We demonstrate the applicability of the proposed approach on the BP TTI model.

Effective Elliptic Models for Efficient Wavefield Extrapolation in Anisotropic Media

KAUST Repository

Waheed, Umair bin; Alkhalifah, Tariq Ali

2014-01-01

Wavefield extrapolation operator for elliptically anisotropic media offers significant cost reduction compared to that of transversely isotropic media (TI), especially when the medium exhibits tilt in the symmetry axis (TTI). However, elliptical anisotropy does not provide accurate focusing for TI media. Therefore, we develop effective elliptically anisotropic models that correctly capture the kinematic behavior of the TTI wavefield. Specifically, we use an iterative elliptically anisotropic eikonal solver that provides the accurate traveltimes for a TI model. The resultant coefficients of the elliptical eikonal provide the effective models. These effective models allow us to use the cheaper wavefield extrapolation operator for elliptic media to obtain approximate wavefield solutions for TTI media. Despite the fact that the effective elliptic models are obtained by kinematic matching using high-frequency asymptotic, the resulting wavefield contains most of the critical wavefield components, including the frequency dependency and caustics, if present, with reasonable accuracy. The methodology developed here offers a much better cost versus accuracy tradeoff for wavefield computations in TTI media, considering the cost prohibitive nature of the problem. We demonstrate the applicability of the proposed approach on the BP TTI model.

Three-dimensional protein structure prediction: Methods and computational strategies.

Science.gov (United States)

Dorn, Márcio; E Silva, Mariel Barbachan; Buriol, Luciana S; Lamb, Luis C

2014-10-12

A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction. Copyright © 2014 Elsevier Ltd. All rights reserved.

Computer Simulations of Lipid Bilayers and Proteins

DEFF Research Database (Denmark)

Sonne, Jacob

2006-01-01

The importance of computer simulations in lipid bilayer research has become more prominent for the last couple of decades and as computers get even faster, simulations will play an increasingly important part of understanding the processes that take place in and across cell membranes. This thesis...... entitled Computer simulations of lipid bilayers and proteins describes two molecular dynamics (MD) simulation studies of pure lipid bilayers as well as a study of a transmembrane protein embedded in a lipid bilayer matrix. Below follows a brief overview of the thesis. Chapter 1. This chapter is a short...... in the succeeding chapters is presented. Details on system setups, simulation parameters and other technicalities can be found in the relevant chapters. Chapter 3, DPPC lipid parameters: The quality of MD simulations is intimately dependent on the empirical potential energy function and its parameters, i...

Oligomerization of G protein-coupled receptors: computational methods.

Science.gov (United States)

Selent, J; Kaczor, A A

2011-01-01

Recent research has unveiled the complexity of mechanisms involved in G protein-coupled receptor (GPCR) functioning in which receptor dimerization/oligomerization may play an important role. Although the first high-resolution X-ray structure for a likely functional chemokine receptor dimer has been deposited in the Protein Data Bank, the interactions and mechanisms of dimer formation are not yet fully understood. In this respect, computational methods play a key role for predicting accurate GPCR complexes. This review outlines computational approaches focusing on sequence- and structure-based methodologies as well as discusses their advantages and limitations. Sequence-based approaches that search for possible protein-protein interfaces in GPCR complexes have been applied with success in several studies, but did not yield always consistent results. Structure-based methodologies are a potent complement to sequence-based approaches. For instance, protein-protein docking is a valuable method especially when guided by experimental constraints. Some disadvantages like limited receptor flexibility and non-consideration of the membrane environment have to be taken into account. Molecular dynamics simulation can overcome these drawbacks giving a detailed description of conformational changes in a native-like membrane. Successful prediction of GPCR complexes using computational approaches combined with experimental efforts may help to understand the role of dimeric/oligomeric GPCR complexes for fine-tuning receptor signaling. Moreover, since such GPCR complexes have attracted interest as potential drug target for diverse diseases, unveiling molecular determinants of dimerization/oligomerization can provide important implications for drug discovery.

Anisotropic structure of the mantle wedge beneath the Ryukyu arc from teleseismic receiver function analysis

Science.gov (United States)

McCormack, K. A.; Wirth, E. A.; Long, M. D.

2011-12-01

The recycling of oceanic plates back into the mantle through subduction is an important process taking place within our planet. However, many fundamental aspects of subduction systems, such as the dynamics of mantle flow, have yet to be completely understood. Subducting slabs transport water down into the mantle, but how and where that water is released, as well as how it affects mantle flow, is still an open question. In this study, we focus on the Ryukyu subduction zone in southwestern Japan and use anisotropic receiver function analysis to characterize the structure of the mantle wedge. We compute radial and transverse P-to-S receiver functions for eight stations of the broadband F-net array using a multitaper receiver function estimator. We observe coherent P-to-SV converted energy in the radial receiver functions at ~6 sec for most of the stations analyzed consistent with conversions originating at the top of the slab. We also observe conversions on the transverse receiver functions that are consistent with the presence of multiple anisotropic and/or dipping layers. The character of the transverse receiver functions varies significantly along strike, with the northernmost three stations exhibiting markedly different behavior than stations located in the center of the Ryukyu arc. We compute synthetic receiver functions using a forward modeling scheme that can handle dipping interfaces and anisotropic layers to create models for the depths, thicknesses, and strengths of anisotropic layers in the mantle wedge beneath Ryukyu.

An efficient wave extrapolation method for anisotropic media with tilt

KAUST Repository

Waheed, Umair bin

2015-03-23

Wavefield extrapolation operators for elliptically anisotropic media offer significant cost reduction compared with that for the transversely isotropic case, particularly when the axis of symmetry exhibits tilt (from the vertical). However, elliptical anisotropy does not provide accurate wavefield representation or imaging for transversely isotropic media. Therefore, we propose effective elliptically anisotropic models that correctly capture the kinematic behaviour of wavefields for transversely isotropic media. Specifically, we compute source-dependent effective velocities for the elliptic medium using kinematic high-frequency representation of the transversely isotropic wavefield. The effective model allows us to use cheaper elliptic wave extrapolation operators. Despite the fact that the effective models are obtained by matching kinematics using high-frequency asymptotic, the resulting wavefield contains most of the critical wavefield components, including frequency dependency and caustics, if present, with reasonable accuracy. The methodology developed here offers a much better cost versus accuracy trade-off for wavefield computations in transversely isotropic media, particularly for media of low to moderate complexity. In addition, the wavefield solution is free from shear-wave artefacts as opposed to the conventional finite-difference-based transversely isotropic wave extrapolation scheme. We demonstrate these assertions through numerical tests on synthetic tilted transversely isotropic models.

An efficient wave extrapolation method for anisotropic media with tilt

KAUST Repository

Waheed, Umair bin; Alkhalifah, Tariq Ali

2015-01-01

Wavefield extrapolation operators for elliptically anisotropic media offer significant cost reduction compared with that for the transversely isotropic case, particularly when the axis of symmetry exhibits tilt (from the vertical). However, elliptical anisotropy does not provide accurate wavefield representation or imaging for transversely isotropic media. Therefore, we propose effective elliptically anisotropic models that correctly capture the kinematic behaviour of wavefields for transversely isotropic media. Specifically, we compute source-dependent effective velocities for the elliptic medium using kinematic high-frequency representation of the transversely isotropic wavefield. The effective model allows us to use cheaper elliptic wave extrapolation operators. Despite the fact that the effective models are obtained by matching kinematics using high-frequency asymptotic, the resulting wavefield contains most of the critical wavefield components, including frequency dependency and caustics, if present, with reasonable accuracy. The methodology developed here offers a much better cost versus accuracy trade-off for wavefield computations in transversely isotropic media, particularly for media of low to moderate complexity. In addition, the wavefield solution is free from shear-wave artefacts as opposed to the conventional finite-difference-based transversely isotropic wave extrapolation scheme. We demonstrate these assertions through numerical tests on synthetic tilted transversely isotropic models.

Investigate the effect of anisotropic order parameter on the specific heat of anisotropic two-band superconductors

International Nuclear Information System (INIS)

Udomsamuthirun, P.; Peamsuwan, R.; Kumvongsa, C.

2009-01-01

The effect of anisotropic order parameter on the specific heat of anisotropic two-band superconductors in BCS weak-coupling limit is investigated. An analytical specific heat jump and the numerical specific heat are shown by using anisotropic order parameters, and the electron-phonon interaction and non-electron-phonon interaction. The two models of anisotropic order parameters are used for numerical calculation that we find little effect on the numerical results. The specific heat jump of MgB 2 , Lu 2 Fe 3 Si 5 and Nb 3 Sn superconductors can fit well with both of them. By comparing the experimental data with overall range of temperature, the best fit is Nb 3 Sn, MgB 2 , and Lu 2 Fe 3 Si 5 superconductors.

Anisotropic Elastoplastic Damage Mechanics Method to Predict Fatigue Life of the Structure

Directory of Open Access Journals (Sweden)

Hualiang Wan

2016-01-01

Full Text Available New damage mechanics method is proposed to predict the low-cycle fatigue life of metallic structures under multiaxial loading. The microstructure mechanical model is proposed to simulate anisotropic elastoplastic damage evolution. As the micromodel depends on few material parameters, the present method is very concise and suitable for engineering application. The material parameters in damage evolution equation are determined by fatigue experimental data of standard specimens. By employing further development on the ANSYS platform, the anisotropic elastoplastic damage mechanics-finite element method is developed. The fatigue crack propagation life of satellite structure is predicted using the present method and the computational results comply with the experimental data very well.

Anisotropic elastic plates

CERN Document Server

Hwu, Chyanbin

2010-01-01

As structural elements, anisotropic elastic plates find wide applications in modern technology. The plates here are considered to be subjected to not only in plane load but also transverse load. In other words, both plane and plate bending problems as well as the stretching-bending coupling problems are all explained in this book. In addition to the introduction of the theory of anisotropic elasticity, several important subjects have are discussed in this book such as interfaces, cracks, holes, inclusions, contact problems, piezoelectric materials, thermoelastic problems and boundary element a

Non-uniform self-assembly : On the anisotropic architecture of α-synuclein supra-fibrillar aggregates

NARCIS (Netherlands)

Semerdzhiev, Slav A.; Shvadchak, Volodymyr V.; Subramaniam, Vinod; Claessens, Mireille M.A.E.

2017-01-01

Although the function of biopolymer hydrogels in nature depends on structural anisotropy at mesoscopic length scales, the self-assembly of such anisotropic structures in vitro is challenging. Here we show that fibrils of the protein α-synuclein spontaneously self-assemble into structurally

A new anisotropic mesh adaptation method based upon hierarchical a posteriori error estimates

Science.gov (United States)

Huang, Weizhang; Kamenski, Lennard; Lang, Jens

2010-03-01

A new anisotropic mesh adaptation strategy for finite element solution of elliptic differential equations is presented. It generates anisotropic adaptive meshes as quasi-uniform ones in some metric space, with the metric tensor being computed based on hierarchical a posteriori error estimates. A global hierarchical error estimate is employed in this study to obtain reliable directional information of the solution. Instead of solving the global error problem exactly, which is costly in general, we solve it iteratively using the symmetric Gauß-Seidel method. Numerical results show that a few GS iterations are sufficient for obtaining a reasonably good approximation to the error for use in anisotropic mesh adaptation. The new method is compared with several strategies using local error estimators or recovered Hessians. Numerical results are presented for a selection of test examples and a mathematical model for heat conduction in a thermal battery with large orthotropic jumps in the material coefficients.

TU-A-9A-05: First Experimental Demonstration of the Anisotropic Detection Principle in X-Ray Fluorescence Computed Tomography

International Nuclear Information System (INIS)

Ahmad, M; Bazalova, M; Fahrig, R; Xing, L

2014-01-01

Purpose: To improve the sensitivity of X-ray fluorescence computed tomography (XFCT) for in vivo molecular imaging. Is the maximum sensitivity achieved with an isotropic (4π) detector configuration? We prove that this is not necessarily true, and that a greater sensitivity is possible with anisotropic detector configuration. Methods: An XFCT imaging system was constructed consisting of 1) a collimated pencil beam x-ray source using a fluoroscopy grade x-ray tube; 2) a CdTe x-ray photon counting detector to detect fluorescent x-rays; and 3) a rotation/translation stage for tomographic imaging. We created a 6.5-cm diameter water phantom with 2-cm inserts of low gold concentration (0.25%–1%) to simulate tumors targeted by gold nano-particles. The placement of x-ray fluorescence detector were chosen to minimize scatter x-rays. XFCT imaging was performed at three different detector positions (60°, 90°, 145°) to determine the impact of forward-scatter, side-scatter, and back-scatter on imaging performance. The three data sets were also combined to estimate the imaging performance with an isotropic detector. Results: The highest imaging performance was achieved when the XF detector was in the backscatter 145° configuration. The signal-to-noise ratio (SNR) was 5.5 for the 0.25% gold concentration compared to SNRs of 1.4, 0, and 2.4 for 60°, 90°, and combined (60°+90°+145°) datasets. Only the 145° detector arrangement alone could detect the 0.25% concentration. The imaging dose was 14 mGy for each detector arrangement experiment. Conclusion: This study experimentally proves, for the fist time, the Anisotropic Detection Principle in XF imaging, which holds that optimized anisotropic x-ray fluorescence detection provides greater sensitivity than isotropic detection. The optimized detection arrangement was used to improve the sensitivity of the XFCT experiment. The achieved XFCT sensitivity is the highest ever for a phantom at least this large using a benchtop x

Efficient Modeling and Migration in Anisotropic Media Based on Prestack Exploding Reflector Model and Effective Anisotropy

KAUST Repository

Wang, Hui

2014-05-01

This thesis addresses the efficiency improvement of seismic wave modeling and migration in anisotropic media. This improvement becomes crucial in practice as the process of imaging complex geological structures of the Earth\\'s subsurface requires modeling and migration as building blocks. The challenge comes from two aspects. First, the underlying governing equations for seismic wave propagation in anisotropic media are far more complicated than that in isotropic media which demand higher computational costs to solve. Second, the usage of whole prestack seismic data still remains a burden considering its storage volume and the existing wave equation solvers. In this thesis, I develop two approaches to tackle the challenges. In the first part, I adopt the concept of prestack exploding reflector model to handle the whole prestack data and bridge the data space directly to image space in a single kernel. I formulate the extrapolation operator in a two-way fashion to remove he restriction on directions that waves propagate. I also develop a generic method for phase velocity evaluation within anisotropic media used in this extrapolation kernel. The proposed method provides a tool for generating prestack images without wavefield cross correlations. In the second part of this thesis, I approximate the anisotropic models using effective isotropic models. The wave phenomena in these effective models match that in anisotropic models both kinematically and dynamically. I obtain the effective models through equating eikonal equations and transport equations of anisotropic and isotropic models, thereby in the high frequency asymptotic approximation sense. The wavefields extrapolation costs are thus reduced using isotropic wave equation solvers while the anisotropic effects are maintained through this approach. I benchmark the two proposed methods using synthetic datasets. Tests on anisotropic Marmousi model and anisotropic BP2007 model demonstrate the applicability of my

Computational prediction of protein hot spot residues.

Science.gov (United States)

Morrow, John Kenneth; Zhang, Shuxing

2012-01-01

Most biological processes involve multiple proteins interacting with each other. It has been recently discovered that certain residues in these protein-protein interactions, which are called hot spots, contribute more significantly to binding affinity than others. Hot spot residues have unique and diverse energetic properties that make them challenging yet important targets in the modulation of protein-protein complexes. Design of therapeutic agents that interact with hot spot residues has proven to be a valid methodology in disrupting unwanted protein-protein interactions. Using biological methods to determine which residues are hot spots can be costly and time consuming. Recent advances in computational approaches to predict hot spots have incorporated a myriad of features, and have shown increasing predictive successes. Here we review the state of knowledge around protein-protein interactions, hot spots, and give an overview of multiple in silico prediction techniques of hot spot residues.

Anisotropic evaluation of synthetic surgical meshes.

Science.gov (United States)

Saberski, E R; Orenstein, S B; Novitsky, Y W

2011-02-01

The material properties of meshes used in hernia repair contribute to the overall mechanical behavior of the repair. The anisotropic potential of synthetic meshes, representing a difference in material properties (e.g., elasticity) in different material axes, is not well defined to date. Haphazard orientation of anisotropic mesh material can contribute to inconsistent surgical outcomes. We aimed to characterize and compare anisotropic properties of commonly used synthetic meshes. Six different polypropylene (Trelex(®), ProLite™, Ultrapro™), polyester (Parietex™), and PTFE-based (Dualmesh(®), Infinit) synthetic meshes were selected. Longitudinal and transverse axes were defined for each mesh, and samples were cut in each axis orientation. Samples underwent uniaxial tensile testing, from which the elastic modulus (E) in each axis was determined. The degree of anisotropy (λ) was calculated as a logarithmic expression of the ratio between the elastic modulus in each axis. Five of six meshes displayed significant anisotropic behavior. Ultrapro™ and Infinit exhibited approximately 12- and 20-fold differences between perpendicular axes, respectively. Trelex(®), ProLite™, and Parietex™ were 2.3-2.4 times. Dualmesh(®) was the least anisotropic mesh, without marked difference between the axes. Anisotropy of synthetic meshes has been underappreciated. In this study, we found striking differences between elastic properties of perpendicular axes for most commonly used synthetic meshes. Indiscriminate orientation of anisotropic mesh may adversely affect hernia repairs. Proper labeling of all implants by manufacturers should be mandatory. Understanding the specific anisotropic behavior of synthetic meshes should allow surgeons to employ rational implant orientation to maximize outcomes of hernia repair.

Application of distributed point source method (DPSM) to wave propagation in anisotropic media

Science.gov (United States)

Fooladi, Samaneh; Kundu, Tribikram

2017-04-01

Distributed Point Source Method (DPSM) was developed by Placko and Kundu1, as a technique for modeling electromagnetic and elastic wave propagation problems. DPSM has been used for modeling ultrasonic, electrostatic and electromagnetic fields scattered by defects and anomalies in a structure. The modeling of such scattered field helps to extract valuable information about the location and type of defects. Therefore, DPSM can be used as an effective tool for Non-Destructive Testing (NDT). Anisotropy adds to the complexity of the problem, both mathematically and computationally. Computation of the Green's function which is used as the fundamental solution in DPSM is considerably more challenging for anisotropic media, and it cannot be reduced to a closed-form solution as is done for isotropic materials. The purpose of this study is to investigate and implement DPSM for an anisotropic medium. While the mathematical formulation and the numerical algorithm will be considered for general anisotropic media, more emphasis will be placed on transversely isotropic materials in the numerical example presented in this paper. The unidirectional fiber-reinforced composites which are widely used in today's industry are good examples of transversely isotropic materials. Development of an effective and accurate NDT method based on these modeling results can be of paramount importance for in-service monitoring of damage in composite structures.

Computed tomography in severe protein energy malnutrition.

OpenAIRE

Househam, K C; de Villiers, J F

1987-01-01

Computed tomography of the brain was performed on eight children aged 1 to 4 years with severe protein energy malnutrition. Clinical features typical of kwashiorkor were present in all the children studied. Severe cerebral atrophy or brain shrinkage according to standard radiological criteria was present in every case. The findings of this study suggest considerable cerebral insult associated with severe protein energy malnutrition.

Cracking on anisotropic neutron stars

Science.gov (United States)

Setiawan, A. M.; Sulaksono, A.

2017-07-01

We study the effect of cracking of a local anisotropic neutron star (NS) due to small density fluctuations. It is assumed that the neutron star core consists of leptons, nucleons and hyperons. The relativistic mean field model is used to describe the core of equation of state (EOS). For the crust, we use the EOS introduced by Miyatsu et al. [1]. Furthermore, two models are used to describe pressure anisotropic in neutron star matter. One is proposed by Doneva-Yazadjiev (DY) [2] and the other is proposed by Herrera-Barreto (HB) [3]. The anisotropic parameter of DY and HB models are adjusted in order the predicted maximum mass compatible to the mass of PSR J1614-2230 [4] and PSR J0348+0432 [5]. We have found that cracking can potentially present in the region close to the neutron star surface. The instability due cracking is quite sensitive to the NS mass and anisotropic parameter used.

Anisotropic resonator analysis using the Fourier-Bessel mode solver

Science.gov (United States)

Gauthier, Robert C.

2018-03-01

A numerical mode solver for optical structures that conform to cylindrical symmetry using Faraday's and Ampere's laws as starting expressions is developed when electric or magnetic anisotropy is present. The technique builds on the existing Fourier-Bessel mode solver which allows resonator states to be computed exploiting the symmetry properties of the resonator and states to reduce the matrix system. The introduction of anisotropy into the theoretical frame work facilitates the inclusion of PML borders permitting the computation of open ended structures and a better estimation of the resonator state quality factor. Matrix populating expressions are provided that can accommodate any material anisotropy with arbitrary orientation in the computation domain. Several example of electrical anisotropic computations are provided for rationally symmetric structures such as standard optical fibers, axial Bragg-ring fibers and bottle resonators. The anisotropy present in the materials introduces off diagonal matrix elements in the permittivity tensor when expressed in cylindrical coordinates. The effects of the anisotropy of computed states are presented and discussed.

Analysis of Crack Propagation Path on the Anisotropic Bi-Material Rock

Directory of Open Access Journals (Sweden)

Chao-Shi Chen

2010-01-01

Full Text Available This paper presents a single-domain boundary element method (SDBEM for linear elastic fracture mechanics analysis in the 2D anisotropic bimaterial. In this formulation, the displacement integral equation is collocated on the uncracked boundary only, and the traction integral equation is collocated on one side of the crack surface only. The complete fundamental solution (Green's function for anisotropic bi-materials was also derived and implemented into the boundary integral formulation so the discretization along the interface can be avoided except for the interfacial crack part. A special crack-tip element was introduced to capture exactly the crack-tip behavior. A computer program with the FORTRAN code has been developed to effectively calculate the stress intensity factors, crack initiation angle, and propagation path of an anisotropic bi-material. This SDBEM program has been verified having a good accuracy with the previous researches. In addition, a rock of type (1/(2 disk specimen with a central crack was made to conduct the Brazilian test under diametrical loading. The result shows that the numerical analysis can predict relatively well the direction of crack initiation and the path of crack propagation.

Anisotropic Weyl invariance

Energy Technology Data Exchange (ETDEWEB)

Perez-Nadal, Guillem [Universidad de Buenos Aires, Buenos Aires (Argentina)

2017-07-15

We consider a non-relativistic free scalar field theory with a type of anisotropic scale invariance in which the number of coordinates ''scaling like time'' is generically greater than one. We propose the Cartesian product of two curved spaces, the metric of each space being parameterized by the other space, as a notion of curved background to which the theory can be extended. We study this type of geometries, and find a family of extensions of the theory to curved backgrounds in which the anisotropic scale invariance is promoted to a local, Weyl-type symmetry. (orig.)

Holographic quark–antiquark potential in hot, anisotropic Yang–Mills plasma

International Nuclear Information System (INIS)

Chakraborty, Somdeb; Haque, Najmul

2013-01-01

Using the gauge/gravity duality we calculate the heavy quark–antiquark potential in a hot, anisotropic and strongly coupled Yang–Mills plasma in (3+1)-dimensions. As the anisotropic medium we take a deformed version of N=4 super Yang–Mills theory at finite temperature following a recent work where the dual type IIB supergravity solution is also proposed. We turn on a small value of the anisotropy parameter, for which the gravity dual is known analytically (perturbatively), and compute the velocity-dependent quark–antiquark interaction potential when the pair is moving through the plasma with a velocity v. By setting v=0 we recover the static quark–antiquark potential. We numerically study how the potential is modified in the presence of anisotropy. We further show numerically how the quark–antiquark separation (both in the static and the velocity-dependent case) and hence, the screening length gets modified by anisotropy. We discuss various cases depending upon the direction of the dipole and the direction of its propagation and make a comparative study of these cases. We are also able to obtain an analytical expression for the screening length of the dipole moving in a hot, anisotropic plasma in a special case

Anisotropic power spectrum and bispectrum in the f(ϕ)F2 mechanism

Science.gov (United States)

Bartolo, Nicola; Matarrese, Sabino; Peloso, Marco; Ricciardone, Angelo

2013-01-01

A suitable coupling of the inflaton φ to a vector kinetic term F2 gives frozen and scale invariant vector perturbations. We compute the cosmological perturbations ζ that result from such coupling by taking into account the classical vector field that unavoidably gets generated at large scales during inflation. This generically results in a too-anisotropic power spectrum of ζ. Specifically, the anisotropy exceeds the 1% level (10% level) if inflation lasts ˜5 e-folds (˜50 e-folds) more than the minimal amount required to produce the cosmic microwave background modes. This conclusion applies, among others, to the application of this mechanism for magnetogenesis, for anisotropic inflation, and for the generation of anisotropic perturbations at the end of inflation through a waterfall field coupled to the vector (in this case, the unavoidable contribution that we obtain is effective all throughout inflation, and it is independent of the waterfall field). For a tuned duration of inflation, a 1% (10%) anisotropy in the power spectrum corresponds to an anisotropic bispectrum which is enhanced like the local one in the squeezed limit, and with an effective local fNL˜3(˜30). More in general, a significant anisotropy of the perturbations may be a natural outcome of all models that sustain higher than 0 spin fields during inflation.

Cloud computing for protein-ligand binding site comparison.

Science.gov (United States)

Hung, Che-Lun; Hua, Guan-Jie

2013-01-01

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

Anisotropic phenomena in gauge/gravity duality

International Nuclear Information System (INIS)

Zeller, Hansjoerg

2014-01-01

In this thesis we use gauge/gravity duality to model anisotropic effects realised in nature. Firstly we analyse transport properties in holographic systems with a broken rotational invariance. Secondly we discuss geometries dual to IR fixed points with anisotropic scaling behaviour, which are related to quantum critical points in condensed matter systems. Gauge/gravity duality relates a gravity theory in Anti-de Sitter space to a lower dimensional strongly coupled quantum field theory in Minkowski space. Over the past decade this duality provided many insights into systems at strong coupling, e.g. quark-gluon plasma and condensed matter close to quantum critical points. One very important result computed in this framework is the value of the shear viscosity divided by the entropy density in strongly coupled theories. The quantitative result agrees very well with measurements of the ratio in quark-gluon plasma. However, for isotropic two derivative Einstein gravity it is temperature independent. We show that by breaking the rotational symmetry of a system we obtain a temperature dependent shear viscosity over entropy density. This is important to make contact with real world systems, since substances in nature display such dependence. In addition, we derive various transport properties in strongly coupled anisotropic systems using the gauge/gravity dictionary. The most notable results include an electrical conductivity with Drude behaviour in the low frequency region. This resembles conductors with broken translational invariance. However, we did not implement the breaking explicitly. Furthermore, our analysis shows that this setup models effects, resembling the piezoelectric and exoelectric effects, known from liquid crystals. In a second project we discuss a geometry with non-trivial scaling behaviour in order to model an IR fixed point of condensed matter theories. We construct the UV completion of this geometry and analyse its properties by computing the

Anisotropic phenomena in gauge/gravity duality

Energy Technology Data Exchange (ETDEWEB)

Zeller, Hansjoerg

2014-05-26

In this thesis we use gauge/gravity duality to model anisotropic effects realised in nature. Firstly we analyse transport properties in holographic systems with a broken rotational invariance. Secondly we discuss geometries dual to IR fixed points with anisotropic scaling behaviour, which are related to quantum critical points in condensed matter systems. Gauge/gravity duality relates a gravity theory in Anti-de Sitter space to a lower dimensional strongly coupled quantum field theory in Minkowski space. Over the past decade this duality provided many insights into systems at strong coupling, e.g. quark-gluon plasma and condensed matter close to quantum critical points. One very important result computed in this framework is the value of the shear viscosity divided by the entropy density in strongly coupled theories. The quantitative result agrees very well with measurements of the ratio in quark-gluon plasma. However, for isotropic two derivative Einstein gravity it is temperature independent. We show that by breaking the rotational symmetry of a system we obtain a temperature dependent shear viscosity over entropy density. This is important to make contact with real world systems, since substances in nature display such dependence. In addition, we derive various transport properties in strongly coupled anisotropic systems using the gauge/gravity dictionary. The most notable results include an electrical conductivity with Drude behaviour in the low frequency region. This resembles conductors with broken translational invariance. However, we did not implement the breaking explicitly. Furthermore, our analysis shows that this setup models effects, resembling the piezoelectric and exoelectric effects, known from liquid crystals. In a second project we discuss a geometry with non-trivial scaling behaviour in order to model an IR fixed point of condensed matter theories. We construct the UV completion of this geometry and analyse its properties by computing the

Computational Studies of Protein Hydration Methods

Science.gov (United States)

Morozenko, Aleksandr

It is widely appreciated that water plays a vital role in proteins' functions. The long-range proton transfer inside proteins is usually carried out by the Grotthuss mechanism and requires a chain of hydrogen bonds that is composed of internal water molecules and amino acid residues of the protein. In other cases, water molecules can facilitate the enzymes catalytic reactions by becoming a temporary proton donor/acceptor. Yet a reliable way of predicting water protein interior is still not available to the biophysics community. This thesis presents computational studies that have been performed to gain insights into the problems of fast and accurate prediction of potential water sites inside internal cavities of protein. Specifically, we focus on the task of attainment of correspondence between results obtained from computational experiments and experimental data available from X-ray structures. An overview of existing methods of predicting water molecules in the interior of a protein along with a discussion of the trustworthiness of these predictions is a second major subject of this thesis. A description of differences of water molecules in various media, particularly, gas, liquid and protein interior, and theoretical aspects of designing an adequate model of water for the protein environment are widely discussed in chapters 3 and 4. In chapter 5, we discuss recently developed methods of placement of water molecules into internal cavities of a protein. We propose a new methodology based on the principle of docking water molecules to a protein body which allows to achieve a higher degree of matching experimental data reported in protein crystal structures than other techniques available in the world of biophysical software. The new methodology is tested on a set of high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules and applied to bovine heart cytochrome c oxidase in the fully

Non-uniform self-assembly: On the anisotropic architecture of α-synuclein supra-fibrillar aggregates.

Science.gov (United States)

Semerdzhiev, Slav A; Shvadchak, Volodymyr V; Subramaniam, Vinod; Claessens, Mireille M A E

2017-08-09

Although the function of biopolymer hydrogels in nature depends on structural anisotropy at mesoscopic length scales, the self-assembly of such anisotropic structures in vitro is challenging. Here we show that fibrils of the protein α-synuclein spontaneously self-assemble into structurally anisotropic hydrogel particles. While the fibrils in the interior of these supra-fibrillar aggregates (SFAs) are randomly oriented, the fibrils in the periphery prefer to cross neighboring fibrils at high angles. This difference in organization coincides with a significant difference in polarity of the environment in the central and peripheral parts of the SFA. We rationalize the structural anisotropy of SFAs in the light of the observation that αS fibrils bind a substantial amount of counterions. We propose that, with the progress of protein polymerization into fibrils, this binding of counterions changes the ionic environment which triggers a change in fibril organization resulting in anisotropy in the architecture of hydrogel particles.

Continuum mechanics of anisotropic materials

CERN Document Server

Cowin, Stephen C

2013-01-01

Continuum Mechanics of Anisotropic Materials(CMAM) presents an entirely new and unique development of material anisotropy in the context of an appropriate selection and organization of continuum mechanics topics. These features will distinguish this continuum mechanics book from other books on this subject. Textbooks on continuum mechanics are widely employed in engineering education, however, none of them deal specifically with anisotropy in materials. For the audience of Biomedical, Chemical and Civil Engineering students, these materials will be dealt with more frequently and greater accuracy in their analysis will be desired. Continuum Mechanics of Anisotropic Materials' author has been a leader in the field of developing new approaches for the understanding of anisotropic materials.

Dynamics of anisotropic tissue growth

Energy Technology Data Exchange (ETDEWEB)

Bittig, Thomas; Juelicher, Frank [Max Planck Institute for the Physics of Complex Systems, Noethnitzer Strasse 38, 01187 Dresden (Germany); Wartlick, Ortrud; Kicheva, Anna; Gonzalez-Gaitan, Marcos [Department of Biochemistry and Department of Molecular Biology, Geneva University, Sciences II, Quai Ernest-Ansermet 30, 1211 Geneva 4 (Switzerland)], E-mail: Marcos.Gonzalez@biochem.unige.ch, E-mail: julicher@pks.mpg.de

2008-06-15

We study the mechanics of tissue growth via cell division and cell death (apoptosis). The rearrangements of cells can on large scales and times be captured by a continuum theory which describes the tissue as an effective viscous material with active stresses generated by cell division. We study the effects of anisotropies of cell division on cell rearrangements and show that average cellular trajectories exhibit anisotropic scaling behaviors. If cell division and apoptosis balance, there is no net growth, but for anisotropic cell division the tissue undergoes spontaneous shear deformations. Our description is relevant for the study of developing tissues such as the imaginal disks of the fruit fly Drosophila melanogaster, which grow anisotropically.

APC: A new code for Atmospheric Polarization Computations

International Nuclear Information System (INIS)

Korkin, Sergey V.; Lyapustin, Alexei I.; Rozanov, Vladimir V.

2013-01-01

A new polarized radiative transfer code Atmospheric Polarization Computations (APC) is described. The code is based on separation of the diffuse light field into anisotropic and smooth (regular) parts. The anisotropic part is computed analytically. The smooth regular part is computed numerically using the discrete ordinates method. Vertical stratification of the atmosphere, common types of bidirectional surface reflection and scattering by spherical particles or spheroids are included. A particular consideration is given to computation of the bidirectional polarization distribution function (BPDF) of the waved ocean surface. -- Highlights: •A new code, APC, has been developed. •The code was validated against well-known codes. •The BPDF for an arbitrary Mueller matrix is computed

Nonlinear constitutive relations for anisotropic elastic materials

Science.gov (United States)

Sokolova, Marina; Khristich, Dmitrii

2018-03-01

A general approach to constructing of nonlinear variants of connection between stresses and strains in anisotropic materials with different types of symmetry of properties is considered. This approach is based on the concept of elastic proper subspaces of anisotropic materials introduced in the mechanics of solids by J. Rychlewski and on the particular postulate of isotropy proposed by A. A. Il’yushin. The generalization of the particular postulate on the case of nonlinear anisotropic materials is formulated. Systems of invariants of deformations as lengths of projections of the strain vector into proper subspaces are developed. Some variants of nonlinear constitutive relations for anisotropic materials are offered. The analysis of these relations from the point of view of their satisfaction to general and limit forms of generalization of partial isotropy postulate on anisotropic materials is performed. The relations for particular cases of anisotropy are written.

Characterization of Anisotropic Behavior for High Grade Pipes

Science.gov (United States)

Yang, Kun; Huo, Chunyong; Ji, Lingkang; Li, Yang; Zhang, Jiming; Ma, Qiurong

With the developing requirement of nature gas, the property needs of steel for pipe line are higher and higher, especially in strength and toughness. It is necessary to improve the steel grade in order to ensure economic demand and safety. However, with the rise of steel grade, the differences on properties in different orientations (anisotropic behaviors) become more and more obvious after the process of hot rolling, which may affect the prediction of fracture for the pipes seriously (Thinking of isotropic mechanical properties for material in traditional predict way). In order to get the reason for anisotropic mechanics, a series of tests are carried out for high grade steel pipes, including not only mechanical properties but also microstructures. Result indicates that there are obviously anisotropic behaviors for high grade steel pipes in two orientations (rolling orientation and transverse orientation). Strength is better in T orientation because Rm is higher and Rt 0.5 rises more in T orientation, and toughness is better in L orientation because of the higher Akv and SA in L orientation under a same temperature. Banded structures are formed in T orientation, and the spatial distribution of inclusion and precipitated phases are different in T, L and S orientation. The anisotropic arrangement for the matrix in space (banded structures), which is formed after the process of hot rolling, may affect the mechanical properties in different orientation. Moreover, the elasticity modulus of particles is different from the elasticity modulus of matrix, deformation between particles and matrix may cause stress concentration, and damage forms in this place. Because of the different distribution of particles in space, the level of damage is anisotropic in different orientations, and the anisotropic mechanical properties occur finally. Therefore, the anisotropic mechanical properties are determined by the anisotropic microstructures, both the anisotropic of matrix and the

Computational analysis of RNA-protein interaction interfaces via the Voronoi diagram.

Science.gov (United States)

Mahdavi, Sedigheh; Mohades, Ali; Salehzadeh Yazdi, Ali; Jahandideh, Samad; Masoudi-Nejad, Ali

2012-01-21

Cellular functions are mediated by various biological processes including biomolecular interactions, such as protein-protein, DNA-protein and RNA-protein interactions in which RNA-Protein interactions are indispensable for many biological processes like cell development and viral replication. Unlike the protein-protein and protein-DNA interactions, accurate mechanisms and structures of the RNA-Protein complexes are not fully understood. A large amount of theoretical evidence have shown during the past several years that computational geometry is the first pace in understanding the binding profiles and plays a key role in the study of intricate biological structures, interactions and complexes. In this paper, RNA-Protein interaction interface surface is computed via the weighted Voronoi diagram of atoms. Using two filter operations provides a natural definition for interface atoms as classic methods. Unbounded parts of Voronoi facets that are far from the complex are trimmed using modified convex hull of atom centers. This algorithm is implemented to a database with different RNA-Protein complexes extracted from Protein Data Bank (PDB). Afterward, the features of interfaces have been computed and compared with classic method. The results show high correlation coefficients between interface size in the Voronoi model and the classical model based on solvent accessibility, as well as high accuracy and precision in comparison to classical model. Copyright © 2011 Elsevier Ltd. All rights reserved.

Orthonormal bases for anisotropic α-modulation spaces

DEFF Research Database (Denmark)

Rasmussen, Kenneth Niemann

2012-01-01

In this article we construct orthonormal bases for bi-variate anisotropic α-modulation spaces. The construction is based on generating a nice anisotropic α-covering and using carefully selected tensor products of univariate brushlet functions with regards to this covering. As an application, we...... show that n-term nonlinear approximation with the orthonormal bases in certain anisotropic α-modulation spaces can be completely characterized....

Orthonormal bases for anisotropic α-modulation spaces

DEFF Research Database (Denmark)

Rasmussen, Kenneth Niemann

In this article we construct orthonormal bases for bi-variate anisotropic α-modulation spaces. The construction is based on generating a nice anisotropic α-covering and using carefully selected tensor products of univariate brushlet functions with regards to this covering. As an application, we...... show that n-term nonlinear approximation with the orthonormal bases in certain anisotropic α-modulation spaces can be completely characterized....

Finite-volume scheme for anisotropic diffusion

Energy Technology Data Exchange (ETDEWEB)

Es, Bram van, E-mail: bramiozo@gmail.com [Centrum Wiskunde & Informatica, P.O. Box 94079, 1090GB Amsterdam (Netherlands); FOM Institute DIFFER, Dutch Institute for Fundamental Energy Research, The Netherlands" 1 (Netherlands); Koren, Barry [Eindhoven University of Technology (Netherlands); Blank, Hugo J. de [FOM Institute DIFFER, Dutch Institute for Fundamental Energy Research, The Netherlands" 1 (Netherlands)

2016-02-01

In this paper, we apply a special finite-volume scheme, limited to smooth temperature distributions and Cartesian grids, to test the importance of connectivity of the finite volumes. The area of application is nuclear fusion plasma with field line aligned temperature gradients and extreme anisotropy. We apply the scheme to the anisotropic heat-conduction equation, and compare its results with those of existing finite-volume schemes for anisotropic diffusion. Also, we introduce a general model adaptation of the steady diffusion equation for extremely anisotropic diffusion problems with closed field lines.

Dilepton production from the quark-gluon plasma using (3 +1 )-dimensional anisotropic dissipative hydrodynamics

Science.gov (United States)

Ryblewski, Radoslaw; Strickland, Michael

2015-07-01

We compute dilepton production from the deconfined phase of the quark-gluon plasma using leading-order (3 +1 )-dimensional anisotropic hydrodynamics. The anisotropic hydrodynamics equations employed describe the full spatiotemporal evolution of the transverse temperature, spheroidal momentum-space anisotropy parameter, and the associated three-dimensional collective flow of the matter. The momentum-space anisotropy is also taken into account in the computation of the dilepton production rate, allowing for a self-consistent description of dilepton production from the quark-gluon plasma. For our final results, we present predictions for high-energy dilepton yields as a function of invariant mass, transverse momentum, and pair rapidity. We demonstrate that high-energy dilepton production is extremely sensitive to the assumed level of initial momentum-space anisotropy of the quark-gluon plasma. As a result, it may be possible to experimentally constrain the early-time momentum-space anisotropy of the quark-gluon plasma generated in relativistic heavy-ion collisions using high-energy dilepton yields.

Achievements and Challenges in Computational Protein Design.

Science.gov (United States)

Samish, Ilan

2017-01-01

Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs. Future challenges also include dissemination of CPD software to the general use of life-sciences researchers and the emphasis of success within an in vivo milieu. CPD increases our understanding of protein structure and function and the relationships between the two along with the application of such know-how for the benefit of mankind. Applied aspects range from biological drugs, via healthier and tastier food products to nanotechnology and environmentally friendly enzymes replacing toxic chemicals utilized in the industry.

Analysis of electromagnetic scattering by uniaxial anisotropic bispheres.

Science.gov (United States)

Li, Zheng-Jun; Wu, Zhen-Sen; Li, Hai-Ying

2011-02-01

Based on the generalized multiparticle Mie theory and the Fourier transformation approach, electromagnetic (EM) scattering of two interacting homogeneous uniaxial anisotropic spheres with parallel primary optical axes is investigated. By introducing the Fourier transformation, the EM fields in the uniaxial anisotropic spheres are expanded in terms of the spherical vector wave functions. The interactive scattering coefficients and the expansion coefficients of the internal fields are derived through the continuous boundary conditions on which the interaction of the bispheres is considered. Some selected calculations on the effects of the size parameter, the uniaxial anisotropic absorbing dielectric, and the sphere separation distance are described. The backward radar cross section of two uniaxial anisotropic spheres with a complex permittivity tensor changing with the sphere separation distance is numerically studied. The authors are hopeful that the work in this paper will help provide an effective calibration for further research on the scattering characteristic of an aggregate of anisotropic spheres or other shaped anisotropic particles.

Transient anisotropic magnetic field calculation

International Nuclear Information System (INIS)

Jesenik, Marko; Gorican, Viktor; Trlep, Mladen; Hamler, Anton; Stumberger, Bojan

2006-01-01

For anisotropic magnetic material, nonlinear magnetic characteristics of the material are described with magnetization curves for different magnetization directions. The paper presents transient finite element calculation of the magnetic field in the anisotropic magnetic material based on the measured magnetization curves for different magnetization directions. For the verification of the calculation method some results of the calculation are compared with the measurement

Turbulent Output-Based Anisotropic Adaptation

Science.gov (United States)

Park, Michael A.; Carlson, Jan-Renee

2010-01-01

Controlling discretization error is a remaining challenge for computational fluid dynamics simulation. Grid adaptation is applied to reduce estimated discretization error in drag or pressure integral output functions. To enable application to high O(10(exp 7)) Reynolds number turbulent flows, a hybrid approach is utilized that freezes the near-wall boundary layer grids and adapts the grid away from the no slip boundaries. The hybrid approach is not applicable to problems with under resolved initial boundary layer grids, but is a powerful technique for problems with important off-body anisotropic features. Supersonic nozzle plume, turbulent flat plate, and shock-boundary layer interaction examples are presented with comparisons to experimental measurements of pressure and velocity. Adapted grids are produced that resolve off-body features in locations that are not known a priori.

Views on the Anisotropic Nature of Ilva Valley Region

Directory of Open Access Journals (Sweden)

GABRIELA-ALINA MUREŞAN

2012-01-01

Full Text Available There are two concepts important for the authors of this article: anisotropic region and anisotropic space. Anisotropic region is defined by A. Dauphiné, the geographer (-mathematician, as a territorial unit whose structure results from the organisation of space along one or more axes. From the point of view of a territorial system, this type of region has some characteristics which differentiate it both from the homogeneous region and from the polarised one. These specificities have been analysed for Ilva Valley. The region of Ilva Valley is formed along the morphological axis represented by the Ilva River. The aim is to identify these specificities or their absence within this region. In this way we can determine whether this region is an anisotropic one or just an anisotropic space, namely whether it can be considered as evolving towards an anisotropic region, not yet complying with all characteristics of anisotropic regions.

Effective medium theory for anisotropic metamaterials

KAUST Repository

Zhang, Xiujuan

2015-01-20

Materials with anisotropic material parameters can be utilized to fabricate many fascinating devices, such as hyperlenses, metasolids, and one-way waveguides. In this study, we analyze the effects of geometric anisotropy on a two-dimensional metamaterial composed of a rectangular array of elliptic cylinders and derive an effective medium theory for such a metamaterial. We find that it is possible to obtain a closed-form analytical solution for the anisotropic effective medium parameters, provided the aspect ratio of the lattice and the eccentricity of the elliptic cylinder satisfy certain conditions. The derived effective medium theory not only recovers the well-known Maxwell-Garnett results in the quasi-static regime, but is also valid beyond the long-wavelength limit, where the wavelength in the host medium is comparable to the size of the lattice so that previous anisotropic effective medium theories fail. Such an advance greatly broadens the applicable realm of the effective medium theory and introduces many possibilities in the design of structures with desired anisotropic material characteristics. A real sample of a recently theoretically proposed anisotropic medium, with a near-zero index to control the flux, is achieved using the derived effective medium theory, and control of the electromagnetic waves in the sample is clearly demonstrated.

Nanoscale Rheology and Anisotropic Diffusion Using Single Gold Nanorod Probes

Science.gov (United States)

Molaei, Mehdi; Atefi, Ehsan; Crocker, John C.

2018-03-01

The complex rotational and translational Brownian motion of anisotropic particles depends on their shape and the viscoelasticity of their surroundings. Because of their strong optical scattering and chemical versatility, gold nanorods would seem to provide the ultimate probes of rheology at the nanoscale, but the suitably accurate orientational tracking required to compute rheology has not been demonstrated. Here we image single gold nanorods with a laser-illuminated dark-field microscope and use optical polarization to determine their three-dimensional orientation to better than one degree. We convert the rotational diffusion of single nanorods in viscoelastic polyethylene glycol solutions to rheology and obtain excellent agreement with bulk measurements. Extensions of earlier models of anisotropic translational diffusion to three dimensions and viscoelastic fluids give excellent agreement with the observed motion of single nanorods. We find that nanorod tracking provides a uniquely capable approach to microrheology and provides a powerful tool for probing nanoscale dynamics and structure in a range of soft materials.

Tunneling anisotropic magnetoresistance driven by magnetic phase transition.

Science.gov (United States)

Chen, X Z; Feng, J F; Wang, Z C; Zhang, J; Zhong, X Y; Song, C; Jin, L; Zhang, B; Li, F; Jiang, M; Tan, Y Z; Zhou, X J; Shi, G Y; Zhou, X F; Han, X D; Mao, S C; Chen, Y H; Han, X F; Pan, F

2017-09-06

The independent control of two magnetic electrodes and spin-coherent transport in magnetic tunnel junctions are strictly required for tunneling magnetoresistance, while junctions with only one ferromagnetic electrode exhibit tunneling anisotropic magnetoresistance dependent on the anisotropic density of states with no room temperature performance so far. Here, we report an alternative approach to obtaining tunneling anisotropic magnetoresistance in α'-FeRh-based junctions driven by the magnetic phase transition of α'-FeRh and resultantly large variation of the density of states in the vicinity of MgO tunneling barrier, referred to as phase transition tunneling anisotropic magnetoresistance. The junctions with only one α'-FeRh magnetic electrode show a magnetoresistance ratio up to 20% at room temperature. Both the polarity and magnitude of the phase transition tunneling anisotropic magnetoresistance can be modulated by interfacial engineering at the α'-FeRh/MgO interface. Besides the fundamental significance, our finding might add a different dimension to magnetic random access memory and antiferromagnet spintronics.Tunneling anisotropic magnetoresistance is promising for next generation memory devices but limited by the low efficiency and functioning temperature. Here the authors achieved 20% tunneling anisotropic magnetoresistance at room temperature in magnetic tunnel junctions with one α'-FeRh magnetic electrode.

A Variational Approach to Perturbed Discrete Anisotropic Equations

Directory of Open Access Journals (Sweden)

Amjad Salari

2016-01-01

Full Text Available We continue the study of discrete anisotropic equations and we will provide new multiplicity results of the solutions for a discrete anisotropic equation. We investigate the existence of infinitely many solutions for a perturbed discrete anisotropic boundary value problem. The approach is based on variational methods and critical point theory.

An auxiliary differential equation FDTD method for anisotropic magnetized plasmas

International Nuclear Information System (INIS)

Liu Shaobin; Mo Jinjun; Yuan Naichang

2004-01-01

An auxiliary differential equation finite-difference time-domain (ADE-FDTD) methodology for anisotropic magnetized plasmas is derived. The method is based on a difference approximation of the auxiliary differential equation. A comparison with the JEC method is included. The CPU time saving by several times and accuracy of the method are confirmed by computing the reflection and transmission through a magnetized plasma layer with the direction of propagation parallel to the direction of the biasing field

An anisotropic elastoplasticity model implemented in FLAG

Energy Technology Data Exchange (ETDEWEB)

Buechler, Miles Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Canfield, Thomas R. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-10-12

Many metals, including Tantalum and Zirconium, exhibit anisotropic elastoplastic behavior at the single crystal level, and if components are manufactured from these metals through forming processes the polycrystal (component) may also exhibit anisotropic elastoplastic behavior. This is because the forming can induce a preferential orientation of the crystals in the polycrystal. One example is a rolled plate of Uranium where the sti /strong orientation of the crystal (c-axis) tends to align itself perpendicular to the rolling direction. If loads are applied to this plate in di erent orientations the sti ness as well as the ow strength of the material will be greater in the through thickness direction than in other directions. To better accommodate simulations of such materials, an anisotropic elastoplasticity model has been implemented in FLAG. The model includes an anisotropic elastic stress model as well as an anisotropic plasticity model. The model could represent single crystals of any symmetry, though it should not be confused with a high- delity crystal plasticity model with multiple slip planes and evolutions. The model is most appropriate for homogenized polycrystalline materials. Elastic rotation of the material due to deformation is captured, so the anisotropic models are appropriate for arbitrary large rotations, but currently they do not account for signi cant change in material texture beyond the elastic rotation of the entire polycrystal.

The role of shape vs. patches in protein crystallization

Science.gov (United States)

Glaser, Jens; Glotzer, Sharon C.

Proteins fold into a multitude of three-dimensional native structures. The structures of over 100,000 known proteins are deposited in the protein data bank, and most of them have been determined through X-ray crystallography. We ask the question if the role of shape in protein crystallization can be isolated using simulation. Current computational studies show that patchy complementary contacts stabilize experimentally observed P212121 crystal structures for relatively globular protein using spherical protein models. Here we study an anisotropic rigid shape model of green fluorescent protein based on a coarse-grained representation of the atomic coordinates. Using GPU-accelerated molecular dynamics simulations, we find that the experimentally found crystal structure can be stabilized in self-assembly by using complementary attractive patches, confirming the earlier findings. However, we discuss the additional roles of solvent mediated and electrostatic interactions, depletion effects and the self-assembly properties of a purely hard shape model in stabilizing different assemblies. Our findings shed light on fundamental assembly mechanisms in colloidal systems with many competing interactions.

PSPP: a protein structure prediction pipeline for computing clusters.

Directory of Open Access Journals (Sweden)

Michael S Lee

2009-07-01

Full Text Available Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of prediction methodologies. Therefore, we present a standalone protein structure prediction software package suitable for high-throughput structural genomic applications that performs all three classes of prediction methodologies: comparative modeling, fold recognition, and ab initio. This software can be deployed on a user's own high-performance computing cluster.The pipeline consists of a Perl core that integrates more than 20 individual software packages and databases, most of which are freely available from other research laboratories. The query protein sequences are first divided into domains either by domain boundary recognition or Bayesian statistics. The structures of the individual domains are then predicted using template-based modeling or ab initio modeling. The predicted models are scored with a statistical potential and an all-atom force field. The top-scoring ab initio models are annotated by structural comparison against the Structural Classification of Proteins (SCOP fold database. Furthermore, secondary structure, solvent accessibility, transmembrane helices, and structural disorder are predicted. The results are generated in text, tab-delimited, and hypertext markup language (HTML formats. So far, the pipeline has been used to study viral and bacterial proteomes.The standalone pipeline that we introduce here, unlike protein structure prediction Web servers, allows users to devote their own computing assets to process a potentially unlimited number of queries as well as perform

Theoretical and numerical study of highly anisotropic turbulent flows

NARCIS (Netherlands)

Biferale, L.; Daumont, I.; Lanotte, A.; Toschi, F.

2004-01-01

We present a detailed numerical study of anisotropic statistical fluctuations in stationary, homogeneous turbulent flows. We address both problems of intermittency in anisotropic sectors, and the relative importance of isotropic and anisotropic fluctuations at different scales on a direct numerical

Numerical simulation of anisotropic polymeric foams

Directory of Open Access Journals (Sweden)

Volnei Tita

Full Text Available This paper shows in detail the modelling of anisotropic polymeric foam under compression and tension loadings, including discussions on isotropic material models and the entire procedure to calibrate the parameters involved. First, specimens of poly(vinyl chloride (PVC foam were investigated through experimental analyses in order to understand the mechanical behavior of this anisotropic material. Then, isotropic material models available in the commercial software AbaqusTM were investigated in order to verify their ability to model anisotropic foams and how the parameters involved can influence the results. Due to anisotropy, it is possible to obtain different values for the same parameter in the calibration process. The obtained set of parameters are used to calibrate the model according to the application of the structure. The models investigated showed minor and major limitations to simulate the mechanical behavior of anisotropic PVC foams under compression, tension and multi-axial loadings. Results show that the calibration process and the choice of the material model applied to the polymeric foam can provide good quantitative results and save project time. Results also indicate what kind and order of error one will get if certain choices are made throughout the modelling process. Finally, even though the developed calibration procedure is applied to specific PVC foam, it still outlines a very broad drill to analyze other anisotropic cellular materials.

Polarization ray tracing in anisotropic optically active media. I. Algorithms

International Nuclear Information System (INIS)

McClain, S.C.; Hillman, L.W.; Chipman, R.A.

1993-01-01

Procedures for performing polarization ray tracing through birefringent media are presented in a form compatible with the standard methods of geometrical ray tracing. The birefringent materials treated include the following: anisotropic optically active materials such as quartz, non-optically active uniaxial materials such as calcite, and isotropic optically active materials such as mercury sulfide and organic liquids. Refraction and reflection algorithms are presented that compute both ray directions and wave directions. Methods for computing polarization modes, refractive indices, optical path lengths, and Fresnel transmission and reflection coefficients are also specified. A numerical example of these algorithms is given for analyzing the field of view of a quartz rotator. 37 refs., 3 figs

Computational identification of MoRFs in protein sequences.

Science.gov (United States)

Malhis, Nawar; Gsponer, Jörg

2015-06-01

Intrinsically disordered regions of proteins play an essential role in the regulation of various biological processes. Key to their regulatory function is the binding of molecular recognition features (MoRFs) to globular protein domains in a process known as a disorder-to-order transition. Predicting the location of MoRFs in protein sequences with high accuracy remains an important computational challenge. In this study, we introduce MoRFCHiBi, a new computational approach for fast and accurate prediction of MoRFs in protein sequences. MoRFCHiBi combines the outcomes of two support vector machine (SVM) models that take advantage of two different kernels with high noise tolerance. The first, SVMS, is designed to extract maximal information from the general contrast in amino acid compositions between MoRFs, their surrounding regions (Flanks), and the remainders of the sequences. The second, SVMT, is used to identify similarities between regions in a query sequence and MoRFs of the training set. We evaluated the performance of our predictor by comparing its results with those of two currently available MoRF predictors, MoRFpred and ANCHOR. Using three test sets that have previously been collected and used to evaluate MoRFpred and ANCHOR, we demonstrate that MoRFCHiBi outperforms the other predictors with respect to different evaluation metrics. In addition, MoRFCHiBi is downloadable and fast, which makes it useful as a component in other computational prediction tools. http://www.chibi.ubc.ca/morf/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Anisotropic wave-equation traveltime and waveform inversion

KAUST Repository

Feng, Shihang; Schuster, Gerard T.

2016-01-01

The wave-equation traveltime and waveform inversion (WTW) methodology is developed to invert for anisotropic parameters in a vertical transverse isotropic (VTI) meidum. The simultaneous inversion of anisotropic parameters v0, ε and δ is initially

Obtuse triangle suppression in anisotropic meshes

KAUST Repository

Sun, Feng; Choi, Yi King; Wang, Wen Ping; Yan, Dongming; Liu, Yang; Lé vy, Bruno L.

2011-01-01

Anisotropic triangle meshes are used for efficient approximation of surfaces and flow data in finite element analysis, and in these applications it is desirable to have as few obtuse triangles as possible to reduce the discretization error. We present a variational approach to suppressing obtuse triangles in anisotropic meshes. Specifically, we introduce a hexagonal Minkowski metric, which is sensitive to triangle orientation, to give a new formulation of the centroidal Voronoi tessellation (CVT) method. Furthermore, we prove several relevant properties of the CVT method with the newly introduced metric. Experiments show that our algorithm produces anisotropic meshes with much fewer obtuse triangles than using existing methods while maintaining mesh anisotropy. © 2011 Elsevier B.V. All rights reserved.

Obtuse triangle suppression in anisotropic meshes

KAUST Repository

Sun, Feng

2011-12-01

Anisotropic triangle meshes are used for efficient approximation of surfaces and flow data in finite element analysis, and in these applications it is desirable to have as few obtuse triangles as possible to reduce the discretization error. We present a variational approach to suppressing obtuse triangles in anisotropic meshes. Specifically, we introduce a hexagonal Minkowski metric, which is sensitive to triangle orientation, to give a new formulation of the centroidal Voronoi tessellation (CVT) method. Furthermore, we prove several relevant properties of the CVT method with the newly introduced metric. Experiments show that our algorithm produces anisotropic meshes with much fewer obtuse triangles than using existing methods while maintaining mesh anisotropy. © 2011 Elsevier B.V. All rights reserved.

Aeroelastic modal dynamics of wind turbines including anisotropic effects

Energy Technology Data Exchange (ETDEWEB)

Fisker Skjoldan, P.

2011-03-15

Several methods for aeroelastic modal analysis of a rotating wind turbine are developed and used to analyse the modal dynamics of two simplified models and a complex model in isotropic and anisotropic conditions. The Coleman transformation is used to enable extraction of the modal frequencies, damping, and periodic mode shapes of a rotating wind turbine by describing the rotor degrees of freedom in the inertial frame. This approach is valid only for an isotropic system. Anisotropic systems, e.g., with an unbalanced rotor or operating in wind shear, are treated with the general approaches of Floquet analysis or Hill's method which do not provide a unique reference frame for observing the modal frequency, to which any multiple of the rotor speed can be added. This indeterminacy is resolved by requiring that the periodic mode shape be as constant as possible in the inertial frame. The modal frequency is thus identified as the dominant frequency in the response of a pure excitation of the mode observed in the inertial frame. A modal analysis tool based directly on the complex aeroelastic wind turbine code BHawC is presented. It uses the Coleman approach in isotropic conditions and the computationally efficient implicit Floquet analysis in anisotropic conditions. The tool is validated against system identifications with the partial Floquet method on the nonlinear BHawC model of a 2.3 MW wind turbine. System identification results show that nonlinear effects on the 2.3 MW turbine in most cases are small, but indicate that the controller creates nonlinear damping. In isotropic conditions the periodic mode shape contains up to three harmonic components, but in anisotropic conditions it can contain an infinite number of harmonic components with frequencies that are multiples of the rotor speed. These harmonics appear in calculated frequency responses of the turbine. Extreme wind shear changes the modal damping when the flow is separated due to an interaction between

Band gaps in periodically magnetized homogeneous anisotropic media

Science.gov (United States)

Merzlikin, A. M.; Levy, M.; Vinogradov, A. P.; Wu, Z.; Jalali, A. A.

2010-11-01

In [A. M. Merzlikin, A. P. Vinogradov, A. V. Dorofeenko, M. Inoue, M. Levy, A. B. Granovsky, Physica B 394 (2007) 277] it is shown that in anisotropic magnetophotonic crystal made of anisotropic dielectric layers and isotropic magneto-optical layers the magnetization leads to formation of additional band gaps (BG) inside the Brillouin zones. Due to the weakness of the magneto-optical effects the width of these BG is much smaller than that of usual BG forming on the boundaries of Brillouin zones. In the present communication we show that though the anisotropy suppresses magneto-optical effects. An anisotropic magnetophotonic crystal made of anisotropic dielectric layers and anisotropic magneto-optical; the width of additional BG may be much greater than the width of the usual Brillouin BG. Anisotropy tends to suppress Brillouin zone boundary band gap formation because the anisotropy suppresses magneto-optical properties, while degenerate band gap formation occurs around points of effective isotropy and is not suppressed.

Single-molecule protein sequencing through fingerprinting: computational assessment

Science.gov (United States)

Yao, Yao; Docter, Margreet; van Ginkel, Jetty; de Ridder, Dick; Joo, Chirlmin

2015-10-01

Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we propose a method for single-molecule (SM) protein sequencing. A major challenge lies in the fact that proteins are composed of 20 different amino acids, which demands 20 molecular reporters. We computationally demonstrate that it suffices to measure only two types of amino acids to identify proteins and suggest an experimental scheme using SM fluorescence. When achieved, this highly sensitive approach will result in a paradigm shift in proteomics, with major impact in the biological and medical sciences.

Single-molecule protein sequencing through fingerprinting: computational assessment

International Nuclear Information System (INIS)

Yao, Yao; Docter, Margreet; Van Ginkel, Jetty; Joo, Chirlmin; De Ridder, Dick

2015-01-01

Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we propose a method for single-molecule (SM) protein sequencing. A major challenge lies in the fact that proteins are composed of 20 different amino acids, which demands 20 molecular reporters. We computationally demonstrate that it suffices to measure only two types of amino acids to identify proteins and suggest an experimental scheme using SM fluorescence. When achieved, this highly sensitive approach will result in a paradigm shift in proteomics, with major impact in the biological and medical sciences. (paper)

Computational design of binding proteins to EGFR domain II.

Directory of Open Access Journals (Sweden)

Yoon Sup Choi

Full Text Available We developed a process to produce novel interactions between two previously unrelated proteins. This process selects protein scaffolds and designs protein interfaces that bind to a surface patch of interest on a target protein. Scaffolds with shapes complementary to the target surface patch were screened using an exhaustive computational search of the human proteome and optimized by directed evolution using phage display. This method was applied to successfully design scaffolds that bind to epidermal growth factor receptor (EGFR domain II, the interface of EGFR dimerization, with high reactivity toward the target surface patch of EGFR domain II. One potential application of these tailor-made protein interactions is the development of therapeutic agents against specific protein targets.

COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation.

Science.gov (United States)

Roudier, François; Fernandez, Anita G; Fujita, Miki; Himmelspach, Regina; Borner, Georg H H; Schindelman, Gary; Song, Shuang; Baskin, Tobias I; Dupree, Paul; Wasteneys, Geoffrey O; Benfey, Philip N

2005-06-01

The orientation of cell expansion is a process at the heart of plant morphogenesis. Cellulose microfibrils are the primary anisotropic material in the cell wall and thus are likely to be the main determinant of the orientation of cell expansion. COBRA (COB) has been identified previously as a potential regulator of cellulose biogenesis. In this study, characterization of a null allele, cob-4, establishes the key role of COB in controlling anisotropic expansion in most developing organs. Quantitative polarized-light and field-emission scanning electron microscopy reveal that loss of anisotropic expansion in cob mutants is accompanied by disorganization of the orientation of cellulose microfibrils and subsequent reduction of crystalline cellulose. Analyses of the conditional cob-1 allele suggested that COB is primarily implicated in microfibril deposition during rapid elongation. Immunodetection analysis in elongating root cells revealed that, in agreement with its substitution by a glycosylphosphatidylinositol anchor, COB was polarly targeted to both the plasma membrane and the longitudinal cell walls and was distributed in a banding pattern perpendicular to the longitudinal axis via a microtubule-dependent mechanism. Our observations suggest that COB, through its involvement in cellulose microfibril orientation, is an essential factor in highly anisotropic expansion during plant morphogenesis.

Singular problems in shell theory. Computing and asymptotics

Energy Technology Data Exchange (ETDEWEB)

Sanchez-Palencia, Evariste [Institut Jean Le Rond d' Alembert, Paris (France); Millet, Olivier [La Rochelle Univ. (France). LEPTIAB; Bechet, Fabien [Metz Univ. (France). LPMM

2010-07-01

It is known that deformations of thin shells exhibit peculiarities such as propagation of singularities, edge and internal layers, piecewise quasi inextensional deformations, sensitive problems and others, leading in most cases to numerical locking phenomena under several forms, and very poor quality of computations for small relative thickness. Most of these phenomena have a local and often anisotropic character (elongated in some directions), so that efficient numerical schemes should take them in consideration. This book deals with various topics in this context: general geometric formalism, analysis of singularities, numerical computing of thin shell problems, estimates for finite element approximation (including non-uniform and anisotropic meshes), mathematical considerations on boundary value problems in connection with sensitive problems encountered for very thin shells; and others. Most of numerical computations presented here use an adaptive anisotropic mesh procedure which allows a good computation of the physical peculiarities on one hand, and the possibility to perform automatic computations (without a previous mathematical description of the singularities) on the other. The book is recommended for PhD students, postgraduates and researchers who want to improve their knowledge in shell theory and in particular in the areas addressed (analysis of singularities, numerical computing of thin and very thin shell problems, sensitive problems). The lecture of the book may not be continuous and the reader may refer directly to the chapters concerned. (orig.)

Magnetostatics of anisotropic superconducting ellipsoid

International Nuclear Information System (INIS)

Saif, A.G.

1987-09-01

The magnetization and the magnetic field distribution inside (outside) an anisotropic type II superconducting ellipsoid, with filamentary structure, is formulated. We have shown that the magnetic field in this case is different from that of the general anisotropic one. The nucleations of the flux lines for specimens with large demagnetization factors are theoretically studied. We have shown that the nucleations of the flux lines, for specimens with large demagnetization factor, appears at a field larger than that of ellipsoidal shape. (author). 15 refs

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

Science.gov (United States)

Gur, M.; Zomot, E.; Bahar, I.

2013-09-01

The Anton supercomputing technology recently developed for efficient molecular dynamics simulations permits us to examine micro- to milli-second events at full atomic resolution for proteins in explicit water and lipid bilayer. It also permits us to investigate to what extent the collective motions predicted by network models (that have found broad use in molecular biophysics) agree with those exhibited by full-atomic long simulations. The present study focuses on Anton trajectories generated for two systems: the bovine pancreatic trypsin inhibitor, and an archaeal aspartate transporter, GltPh. The former, a thoroughly studied system, helps benchmark the method of comparative analysis, and the latter provides new insights into the mechanism of function of glutamate transporters. The principal modes of motion derived from both simulations closely overlap with those predicted for each system by the anisotropic network model (ANM). Notably, the ANM modes define the collective mechanisms, or the pathways on conformational energy landscape, that underlie the passage between the crystal structure and substates visited in simulations. In particular, the lowest frequency ANM modes facilitate the conversion between the most probable substates, lending support to the view that easy access to functional substates is a robust determinant of evolutionarily selected native contact topology.

Hybrid hydrogels containing vertically aligned carbon nanotubes with anisotropic electrical conductivity for muscle myofiber fabrication.

Science.gov (United States)

Ahadian, Samad; Ramón-Azcón, Javier; Estili, Mehdi; Liang, Xiaobin; Ostrovidov, Serge; Shiku, Hitoshi; Ramalingam, Murugan; Nakajima, Ken; Sakka, Yoshio; Bae, Hojae; Matsue, Tomokazu; Khademhosseini, Ali

2014-03-19

Biological scaffolds with tunable electrical and mechanical properties are of great interest in many different fields, such as regenerative medicine, biorobotics, and biosensing. In this study, dielectrophoresis (DEP) was used to vertically align carbon nanotubes (CNTs) within methacrylated gelatin (GelMA) hydrogels in a robust, simple, and rapid manner. GelMA-aligned CNT hydrogels showed anisotropic electrical conductivity and superior mechanical properties compared with pristine GelMA hydrogels and GelMA hydrogels containing randomly distributed CNTs. Skeletal muscle cells grown on vertically aligned CNTs in GelMA hydrogels yielded a higher number of functional myofibers than cells that were cultured on hydrogels with randomly distributed CNTs and horizontally aligned CNTs, as confirmed by the expression of myogenic genes and proteins. In addition, the myogenic gene and protein expression increased more profoundly after applying electrical stimulation along the direction of the aligned CNTs due to the anisotropic conductivity of the hybrid GelMA-vertically aligned CNT hydrogels. We believe that platform could attract great attention in other biomedical applications, such as biosensing, bioelectronics, and creating functional biomedical devices.

Computational prediction of protein-protein interactions in Leishmania predicted proteomes.

Directory of Open Access Journals (Sweden)

Antonio M Rezende

Full Text Available The Trypanosomatids parasites Leishmania braziliensis, Leishmania major and Leishmania infantum are important human pathogens. Despite of years of study and genome availability, effective vaccine has not been developed yet, and the chemotherapy is highly toxic. Therefore, it is clear just interdisciplinary integrated studies will have success in trying to search new targets for developing of vaccines and drugs. An essential part of this rationale is related to protein-protein interaction network (PPI study which can provide a better understanding of complex protein interactions in biological system. Thus, we modeled PPIs for Trypanosomatids through computational methods using sequence comparison against public database of protein or domain interaction for interaction prediction (Interolog Mapping and developed a dedicated combined system score to address the predictions robustness. The confidence evaluation of network prediction approach was addressed using gold standard positive and negative datasets and the AUC value obtained was 0.94. As result, 39,420, 43,531 and 45,235 interactions were predicted for L. braziliensis, L. major and L. infantum respectively. For each predicted network the top 20 proteins were ranked by MCC topological index. In addition, information related with immunological potential, degree of protein sequence conservation among orthologs and degree of identity compared to proteins of potential parasite hosts was integrated. This information integration provides a better understanding and usefulness of the predicted networks that can be valuable to select new potential biological targets for drug and vaccine development. Network modularity which is a key when one is interested in destabilizing the PPIs for drug or vaccine purposes along with multiple alignments of the predicted PPIs were performed revealing patterns associated with protein turnover. In addition, around 50% of hypothetical protein present in the networks

A fast algorithm for 3D azimuthally anisotropic velocity scan

KAUST Repository

Hu, Jingwei; Fomel, Sergey; Ying, Lexing

2014-01-01

© 2014 European Association of Geoscientists & Engineers. The conventional velocity scan can be computationally expensive for large-scale seismic data sets, particularly when the presence of anisotropy requires multiparameter scanning. We introduce a fast algorithm for 3D azimuthally anisotropic velocity scan by generalizing the previously proposed 2D butterfly algorithm for hyperbolic Radon transforms. To compute semblance in a two-parameter residual moveout domain, the numerical complexity of our algorithm is roughly O(N3logN) as opposed to O(N5) of the straightforward velocity scan, with N being the representative of the number of points in a particular dimension of either data space or parameter space. Synthetic and field data examples demonstrate the superior efficiency of the proposed algorithm.

A fast algorithm for 3D azimuthally anisotropic velocity scan

KAUST Repository

Hu, Jingwei

2014-11-11

© 2014 European Association of Geoscientists & Engineers. The conventional velocity scan can be computationally expensive for large-scale seismic data sets, particularly when the presence of anisotropy requires multiparameter scanning. We introduce a fast algorithm for 3D azimuthally anisotropic velocity scan by generalizing the previously proposed 2D butterfly algorithm for hyperbolic Radon transforms. To compute semblance in a two-parameter residual moveout domain, the numerical complexity of our algorithm is roughly O(N3logN) as opposed to O(N5) of the straightforward velocity scan, with N being the representative of the number of points in a particular dimension of either data space or parameter space. Synthetic and field data examples demonstrate the superior efficiency of the proposed algorithm.

Anisotropic hydrodynamics, holography and the chiral magnetic effect

International Nuclear Information System (INIS)

Gahramanov, Ilmar; Kalaydzhyan, Tigran; Kirsch, Ingo; Hamburg Univ.

2012-03-01

We discuss a possible dependence of the chiral magnetic effect (CME) on the elliptic flow coefficient υ 2 . We first study this in a hydrodynamic model for a static anisotropic plasma with multiple anomalous U(1) currents. In the case of two charges, one axial and one vector, the CME formally appears as a first-order transport coefficient in the vector current. We compute this transport coefficient and show its dependence on υ 2 . We also determine the CME-coefficient from first-order corrections to the dual AdS background using the fluid-gravity duality. For small anisotropies, we find numerical agreement with the hydrodynamic result. (orig.)

Anisotropic hydrodynamics, holography and the chiral magnetic effect

Energy Technology Data Exchange (ETDEWEB)

Gahramanov, Ilmar; Kalaydzhyan, Tigran; Kirsch, Ingo [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Hamburg Univ. (Germany). Zentrum fuer Mathematische Physik

2012-03-15

We discuss a possible dependence of the chiral magnetic effect (CME) on the elliptic flow coefficient {upsilon}{sub 2}. We first study this in a hydrodynamic model for a static anisotropic plasma with multiple anomalous U(1) currents. In the case of two charges, one axial and one vector, the CME formally appears as a first-order transport coefficient in the vector current. We compute this transport coefficient and show its dependence on {upsilon}{sub 2}. We also determine the CME-coefficient from first-order corrections to the dual AdS background using the fluid-gravity duality. For small anisotropies, we find numerical agreement with the hydrodynamic result. (orig.)

Efficient anisotropic quasi-P wavefield extrapolation using an isotropic low-rank approximation

KAUST Repository

Zhang, Zhendong

2017-12-17

The computational cost of quasi-P wave extrapolation depends on the complexity of the medium, and specifically the anisotropy. Our effective-model method splits the anisotropic dispersion relation into an isotropic background and a correction factor to handle this dependency. The correction term depends on the slope (measured using the gradient) of current wavefields and the anisotropy. As a result, the computational cost is independent of the nature of anisotropy, which makes the extrapolation efficient. A dynamic implementation of this approach decomposes the original pseudo-differential operator into a Laplacian, handled using the low-rank approximation of the spectral operator, plus an angular dependent correction factor applied in the space domain to correct for anisotropy. We analyze the role played by the correction factor and propose a new spherical decomposition of the dispersion relation. The proposed method provides accurate wavefields in phase and more balanced amplitudes than a previous spherical decomposition. Also, it is free of SV-wave artifacts. Applications to a simple homogeneous transverse isotropic medium with a vertical symmetry axis (VTI) and a modified Hess VTI model demonstrate the effectiveness of the approach. The Reverse Time Migration (RTM) applied to a modified BP VTI model reveals that the anisotropic migration using the proposed modeling engine performs better than an isotropic migration.

Oscillating electromagnetic soliton in an anisotropic ferromagnetic medium

Energy Technology Data Exchange (ETDEWEB)

Sathishkumar, P., E-mail: perumal_sathish@yahoo.co.in [Department of Physics, K.S.R. College of Engineering (Autonomous), Tiruchengode 637215, Tamilnadu (India); Senjudarvannan, R. [Department of Physics, Jansons Institute of Technology, Karumathampatty, Coimbatore 641659 (India)

2017-05-01

We investigate theoretically the propagation of electromagnetic oscillating soliton in the form of breather in an anisotropic ferromagnetic medium. The interaction of magnetization with the magnetic field component of the electromagnetic (EM) wave has been studied by solving Maxwell's equations coupled with a Landau–Lifshitz equation for the magnetization of the medium. We made a small perturbation on the magnetization and magnetic field along the direction of propagation of EM wave in the framework of reductive perturbation method and the associated nonlinear magnetization dynamics is governed by a generalized derivative nonlinear Schrödinger (DNLS) equation. In order to understand the dynamics of the concerned system, we employ the Jacobi elliptic function method to solve the DNLS equation and deduce breatherlike soliton modes for the EM wave in the medium. - Highlights: • The propagation of electromagnetic oscillating soliton in an anisotropic ferromagnetic medium is investigated in the presence of varying external magnetic field. • The magnetization and electromagnetic wave modulates in the form of breathing like oscillating solitons. • The governing nonlinear spin dynamical equation is studied through a reductive perturbation method. • The magnetization components of the ferromagnetic medium are derived using Jacobi elliptic functions method with the aid of symbolic computation.

Jet quenching in a strongly coupled anisotropic plasma

Science.gov (United States)

Chernicoff, Mariano; Fernández, Daniel; Mateos, David; Trancanelli, Diego

2012-08-01

The jet quenching parameter of an anisotropic plasma depends on the relative orientation between the anisotropic direction, the direction of motion of the parton, and the direction along which the momentum broadening is measured. We calculate the jet quenching parameter of an anisotropic, strongly coupled {N} = 4 plasma by means of its gravity dual. We present the results for arbitrary orientations and arbitrary values of the anisotropy. The anisotropic value can be larger or smaller than the isotropic one, and this depends on whether the comparison is made at equal temperatures or at equal entropy densities. We compare our results to analogous calculations for the real-world quark-gluon plasma and find agreement in some cases and disagreement in others.

Anisotropic solutions by gravitational decoupling

Science.gov (United States)

Ovalle, J.; Casadio, R.; da Rocha, R.; Sotomayor, A.

2018-02-01

We investigate the extension of isotropic interior solutions for static self-gravitating systems to include the effects of anisotropic spherically symmetric gravitational sources by means of the gravitational decoupling realised via the minimal geometric deformation approach. In particular, the matching conditions at the surface of the star with the outer Schwarzschild space-time are studied in great detail, and we describe how to generate, from a single physically acceptable isotropic solution, new families of anisotropic solutions whose physical acceptability is also inherited from their isotropic parent.

Anisotropic solutions by gravitational decoupling

Energy Technology Data Exchange (ETDEWEB)

Ovalle, J. [Silesian University in Opava, Institute of Physics and Research Centre of Theoretical Physics and Astrophysics, Faculty of Philosophy and Science, Opava (Czech Republic); Universidad Simon Bolivar, Departamento de Fisica, Caracas (Venezuela, Bolivarian Republic of); Casadio, R. [Alma Mater Universita di Bologna, Dipartimento di Fisica e Astronomia, Bologna (Italy); Istituto Nazionale di Fisica Nucleare, Bologna (Italy); Rocha, R. da [Universidade Federal do ABC (UFABC), Centro de Matematica, Computacao e Cognicao, Santo Andre, SP (Brazil); Sotomayor, A. [Universidad de Antofagasta, Departamento de Matematicas, Antofagasta (Chile)

2018-02-15

We investigate the extension of isotropic interior solutions for static self-gravitating systems to include the effects of anisotropic spherically symmetric gravitational sources by means of the gravitational decoupling realised via the minimal geometric deformation approach. In particular, the matching conditions at the surface of the star with the outer Schwarzschild space-time are studied in great detail, and we describe how to generate, from a single physically acceptable isotropic solution, new families of anisotropic solutions whose physical acceptability is also inherited from their isotropic parent. (orig.)

Jets in a strongly coupled anisotropic plasma

Energy Technology Data Exchange (ETDEWEB)

Fadafan, Kazem Bitaghsir [Shahrood University of Technology, Faculty of Physics, Shahrood (Iran, Islamic Republic of); University of Southampton, STAG Research Centre Physics and Astronomy, Southampton (United Kingdom); Morad, Razieh [University of Cape Town, Department of Physics, Rondebosch (South Africa)

2018-01-15

In this paper, we study the dynamics of the light quark jet moving through the static, strongly coupled N = 4, anisotropic plasma with and without charge. The light quark is presented by a 2-parameters point-like initial condition falling string in the context of the AdS/CFT. We calculate the stopping distance of the light quark in the anisotropic medium and compare it with its isotropic value. We study the dependency of the stopping distance to the both string initial conditions and background parameters such as anisotropy parameter or chemical potential. Although the typical behavior of the string in the anisotropic medium is similar to the one in the isotropic AdS-Sch background, the string falls faster to the horizon depending on the direction of moving. Particularly, the enhancement of quenching is larger in the beam direction. We find that the suppression of stopping distance is more prominent when the anisotropic plasma have the same temperature as the isotropic plasma. (orig.)

The spatially anisotropic triangular lattice antiferromagnet: Popov-Fedotov method

International Nuclear Information System (INIS)

Nga, Pham Thi Thanh; Trang, Phan Thu; Thang, Nguyen Toan

2017-01-01

We present an analysis of the antiferromagnetic Heisenberg model on an triangular lattice with spatially anisotropic J 1 - J 2 exchange interactions. We apply the Popov-Fedotov method based on introducing an imaginary valued chemical potential to enforce the auxiliary fermion constraint exactly. The staggered magnetization, magnon spectra, free energy are computed in one loop approximation and compared using two different constraints: exact and on average. In the limit of zero temperature the results are identical, whereas at higher temperature significant differences are found. The comparisons with the results obtained by other methods are discussed. (paper)

Quantitative multi-waves migration in elastic anisotropic media; Migration quantitative multi-ondes en milieu elastique anisotrope

Energy Technology Data Exchange (ETDEWEB)

Borgne, H.

2004-12-01

Seismic imaging is an important tool for ail exploration. From the filtered seismic traces and a subsurface velocity model, migration allows to localize the reflectors and to estimate physical properties of these interfaces. The subsurface is split up into a reference medium, corresponding to the low spatial frequencies (a smooth medium), and a perturbation medium, corresponding to the high spatial frequencies. The propagation of elastic waves in the medium of reference is modelled by the ray theory. The association of this theory with a principle of diffraction or reflection allows to take into account the high spatial frequencies: the Kirchhoff approach represents so the medium of perturbations with continuous surfaces, characterized by reflection coefficients. The target of the quantitative migration is to reconstruct this reflection coefficient, notably its behaviour according to the incidence angle. These information will open the way to seismic characterization of the reservoir domain, with. a stratigraphic inversion for instance. In order to improve the qualitative and quantitative migration results, one of the current challenges is to take into account the anisotropy of the subsurface. Taking into account rocks anisotropy in the imaging process of seismic data requires two improvements from the isotropic case. The first one roughly concerns the modelling aspect: an anisotropic propagator should be used to avoid a mis-positioning or bad focusing of the imaged reflectors. The second correction concerns the migration aspect: as anisotropy affects the reflectivity of subsurface, a specific anisotropic imaging formula should be applied in the migration kernel, in order to recover the correct A V A behavior of the subsurface reflectors, If the first correction is DOW made in most so-called anisotropic imaging algorithms, the second one is currently ignored. The first part of my work concerns theoretical aspects. 1 study first the preservation of amplitudes in the

Theoretical investigations on a class of double-focus planar lens on the anisotropic material

Science.gov (United States)

Bozorgi, Mahdieh; Atlasbaf, Zahra

2017-05-01

We study a double-focus lens constituted of V-shaped plasmonic nano-antennas (VSPNAs) on the anisotropic TiO2 thin film. The phase and amplitude variations of cross-polarized scattered wave from a unit cell are computed by the developed fast Method of Moments (MoM) in which the dyadic Green's function is evaluated with the transmission line model in the spectral domain. Using the calculated phase and amplitude diagrams, a double-focus lens on the anisotropic thin film is designed in 2 μm. To validate the numerical results, the designed lens is analysed using a full-wave EM-solver. The obtained results show a tunable asymmetric behavior in the focusing intensity of the focal spots for different incident polarizations. It is shown that changing the thickness of anisotropic thin film leads to the changing in such an asymmetric behavior and also the intensity ratio of two focal spots. In addition, the lens performance is examined in the broadband wavelength range from 1.76 to 2.86 μm. It is achieved that the increasing the wavelength leads to decreasing the focal distances of the designed lens and increasing its numerical aperture (NA).

Effective-field treatment of an anisotropic Ising ferromagnet: thermodynamical properties

International Nuclear Information System (INIS)

Sarmento, E.F.; Honmura, R.; Tsallis, C.

1982-01-01

The anisotropic square lattice spin -1/2 Ising ferromagnet is discussed. Through this system it is illustrated how all relevant thermodynamical quantities (phase diagram, magnetization, short range order parameter, specific heat and susceptibility) can be approximatively calculated within an effective-field unified procedure (which substantially improves the Mean Field Approximation). Two slightly different approximations for the susceptibility (whose exact computation is still lacking) are presented. The (square lattice) - (linear chain) crossover is exhibited. The present (mathematically simple) procedures could be useful in the study of complex Ising problems. (Author) [pt

Screening of the field of a static charge in an anisotropic magnetized plasma

International Nuclear Information System (INIS)

Arsenin, V.V.; Puzitskii, M.L.

1991-01-01

The field of a static charge placed in an equilibrium plasma is screened at a distance of the order of the Debye radius. Debye screening occurs both with and without an external magnetic field. This property also persists when the plasma is not an equilibrium plasma but the velocity distribution function of the particles is isotropic (the screening radius in this case contains the characteristic value of the energy instead of the temperature). The situation can change if the distribution is anisotropic. First, the drop in the field can become non-Debye. In particular, in an unmagnetized plasma some distribution functions are characterized by a power-law decrease of the field. Second, a static test charge induces a magnetic as well as an electrostatic field in an anisotropic plasma. In this communication the authors describe the anomalies of screening of the field of a static charge in a magnetized plasma. For definiteness they consider a situation (typical, e.g., of magnetic mirror systems) when the ionic component is anisotropic. The simplifications for the sake of computations are limited to the case of a charge which extends along the magnetic field and only harmonics much longer than the Debye length are significant in the Fourier expansion of the density of this charge in the longitudinal coordinate

Computational methods for constructing protein structure models from 3D electron microscopy maps.

Science.gov (United States)

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2013-10-01

Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

Computational Approaches for Prediction of Pathogen-Host Protein-Protein Interactions

Directory of Open Access Journals (Sweden)

Esmaeil eNourani

2015-02-01

Full Text Available Infectious diseases are still among the major and prevalent health problems, mostly because of the drug resistance of novel variants of pathogens. Molecular interactions between pathogens and their hosts are the key part of the infection mechanisms. Novel antimicrobial therapeutics to fight drug resistance is only possible in case of a thorough understanding of pathogen-host interaction (PHI systems. Existing databases, which contain experimentally verified PHI data, suffer from scarcity of reported interactions due to the technically challenging and time consuming process of experiments. This has motivated many researchers to address the problem by proposing computational approaches for analysis and prediction of PHIs. The computational methods primarily utilize sequence information, protein structure and known interactions. Classic machine learning techniques are used when there are sufficient known interactions to be used as training data. On the opposite case, transfer and multi task learning methods are preferred. Here, we present an overview of these computational approaches for PHI prediction, discussing their weakness and abilities, with future directions.

Computing a new family of shape descriptors for protein structures

DEFF Research Database (Denmark)

Røgen, Peter; Sinclair, Robert

2003-01-01

The large-scale 3D structure of a protein can be represented by the polygonal curve through the carbon a atoms of the protein backbone. We introduce an algorithm for computing the average number of times that a given configuration of crossings on such polygonal curves is seen, the average being...

Waves and discontinuities in relativistic and anisotropic magnetohydrodynamics

International Nuclear Information System (INIS)

Cissoko, Mahdy

1975-01-01

This work is devoted to the relativistic study of a non-dissipative anisotropic fluid diagram of infinite conductivity. Such a fluid diagram is constructed in part one. Starting from a macroscopic viewpoint a hydrothermodynamic study of the fluid diagram considered is carried out and the fundamental differential system of anisotropic magnetohydrodynamics is deduced. Part two concerns the study of characteristic varieties and propagation of waves for a polytropic anisotropic fluid diagram. Three types of characteristic varieties are revealed: entropy waves (or material waves), magnetosonic waves and Alfven waves. The propagation rates of Alfven and magnetosonic waves are situated with respect to each other. The study of wave cones showed up on the one hand certain special features of wave propagation in anisotropic magnetohydrodynamics and on the other hand the hyperbolic nature of differential operators associated with the various waves [fr

Anisotropic interpolation theorems of Musielak-Orlicz type

Directory of Open Access Journals (Sweden)

Jinxia Li

2016-10-01

Full Text Available Abstract Anisotropy is a common attribute of Nature, which shows different characterizations in different directions of all or part of the physical or chemical properties of an object. The anisotropic property, in mathematics, can be expressed by a fairly general discrete group of dilations { A k : k ∈ Z } $\\{A^{k}: k\\in\\mathbb{Z}\\}$ , where A is a real n × n $n\\times n$ matrix with all its eigenvalues λ satisfy | λ | > 1 $|\\lambda|>1$ . Let φ : R n × [ 0 , ∞ → [ 0 , ∞ $\\varphi: \\mathbb{R}^{n}\\times[0, \\infty\\to[0,\\infty$ be an anisotropic Musielak-Orlicz function such that φ ( x , ⋅ $\\varphi(x,\\cdot$ is an Orlicz function and φ ( ⋅ , t $\\varphi(\\cdot,t$ is a Muckenhoupt A ∞ ( A $\\mathbb {A}_{\\infty}(A$ weight. The aim of this article is to obtain two anisotropic interpolation theorems of Musielak-Orlicz type, which are weighted anisotropic extension of Marcinkiewicz interpolation theorems. The above results are new even for the isotropic weighted settings.

Anisotropic conductivity imaging with MREIT using equipotential projection algorithm

Energy Technology Data Exchange (ETDEWEB)

Degirmenci, Evren [Department of Electrical and Electronics Engineering, Mersin University, Mersin (Turkey); Eyueboglu, B Murat [Department of Electrical and Electronics Engineering, Middle East Technical University, 06531, Ankara (Turkey)

2007-12-21

Magnetic resonance electrical impedance tomography (MREIT) combines magnetic flux or current density measurements obtained by magnetic resonance imaging (MRI) and surface potential measurements to reconstruct images of true conductivity with high spatial resolution. Most of the biological tissues have anisotropic conductivity; therefore, anisotropy should be taken into account in conductivity image reconstruction. Almost all of the MREIT reconstruction algorithms proposed to date assume isotropic conductivity distribution. In this study, a novel MREIT image reconstruction algorithm is proposed to image anisotropic conductivity. Relative anisotropic conductivity values are reconstructed iteratively, using only current density measurements without any potential measurement. In order to obtain true conductivity values, only either one potential or conductivity measurement is sufficient to determine a scaling factor. The proposed technique is evaluated on simulated data for isotropic and anisotropic conductivity distributions, with and without measurement noise. Simulation results show that the images of both anisotropic and isotropic conductivity distributions can be reconstructed successfully.

Extended phase graphs with anisotropic diffusion

Science.gov (United States)

Weigel, M.; Schwenk, S.; Kiselev, V. G.; Scheffler, K.; Hennig, J.

2010-08-01

The extended phase graph (EPG) calculus gives an elegant pictorial description of magnetization response in multi-pulse MR sequences. The use of the EPG calculus enables a high computational efficiency for the quantitation of echo intensities even for complex sequences with multiple refocusing pulses with arbitrary flip angles. In this work, the EPG concept dealing with RF pulses with arbitrary flip angles and phases is extended to account for anisotropic diffusion in the presence of arbitrary varying gradients. The diffusion effect can be expressed by specific diffusion weightings of individual magnetization pathways. This can be represented as an action of a linear operator on the magnetization state. The algorithm allows easy integration of diffusion anisotropy effects. The formalism is validated on known examples from literature and used to calculate the effective diffusion weighting in multi-echo sequences with arbitrary refocusing flip angles.

Calculation of anisotropic few-group constants in asymptotic cells: the code ANICELL

International Nuclear Information System (INIS)

Devenyi, A.

1985-10-01

The theoretical background of the ANICELL computer program together with a user's manual is presented. ANICELL is a nuclear reactor neutron transport code which solves the traditional asymptotic and the so-called tilted flux transport problems in one-dimensional cylindrical geometry using linearly anisotropic scattering. The method of solution used is the first flight collision probability technique. Few-group constants including radial and axial diffusion coefficients for the cell are also prepared by the program. (author)

Stability conditions for the Bianchi type II anisotropically inflating universes

International Nuclear Information System (INIS)

Kao, W.F.; Lin, Ing-Chen

2009-01-01

Stability conditions for a class of anisotropically inflating solutions in the Bianchi type II background space are shown explicitly in this paper. These inflating solutions were known to break the cosmic no-hair theorem such that they do not approach the de Sitter universe at large times. It can be shown that unstable modes of the anisotropic perturbations always exist for this class of expanding solutions. As a result, we show that these set of anisotropically expanding solutions are unstable against anisotropic perturbations in the Bianchi type II space

Anisotropic hydrodynamics: Motivation and methodology

Energy Technology Data Exchange (ETDEWEB)

Strickland, Michael

2014-06-15

In this proceedings contribution I review recent progress in our understanding of the bulk dynamics of relativistic systems that possess potentially large local rest frame momentum-space anisotropies. In order to deal with these momentum-space anisotropies, a reorganization of relativistic viscous hydrodynamics can be made around an anisotropic background, and the resulting dynamical framework has been dubbed “anisotropic hydrodynamics”. I also discuss expectations for the degree of momentum-space anisotropy of the quark–gluon plasma generated in relativistic heavy ion collisions at RHIC and LHC from second-order viscous hydrodynamics, strong-coupling approaches, and weak-coupling approaches.

Cartesian anisotropic mesh adaptation for compressible flow

International Nuclear Information System (INIS)

Keats, W.A.; Lien, F.-S.

2004-01-01

Simulating transient compressible flows involving shock waves presents challenges to the CFD practitioner in terms of the mesh quality required to resolve discontinuities and prevent smearing. This paper discusses a novel two-dimensional Cartesian anisotropic mesh adaptation technique implemented for compressible flow. This technique, developed for laminar flow by Ham, Lien and Strong, is efficient because it refines and coarsens cells using criteria that consider the solution in each of the cardinal directions separately. In this paper the method will be applied to compressible flow. The procedure shows promise in its ability to deliver good quality solutions while achieving computational savings. The convection scheme used is the Advective Upstream Splitting Method (Plus), and the refinement/ coarsening criteria are based on work done by Ham et al. Transient shock wave diffraction over a backward step and shock reflection over a forward step are considered as test cases because they demonstrate that the quality of the solution can be maintained as the mesh is refined and coarsened in time. The data structure is explained in relation to the computational mesh, and the object-oriented design and implementation of the code is presented. Refinement and coarsening algorithms are outlined. Computational savings over uniform and isotropic mesh approaches are shown to be significant. (author)

Magnetoelastic shear wave propagation in pre-stressed anisotropic media under gravity

Science.gov (United States)

Kumari, Nirmala; Chattopadhyay, Amares; Singh, Abhishek K.; Sahu, Sanjeev A.

2017-03-01

The present study investigates the propagation of shear wave (horizontally polarized) in two initially stressed heterogeneous anisotropic (magnetoelastic transversely isotropic) layers in the crust overlying a transversely isotropic gravitating semi-infinite medium. Heterogeneities in both the anisotropic layers are caused due to exponential variation (case-I) and linear variation (case-II) in the elastic constants with respect to the space variable pointing positively downwards. The dispersion relations have been established in closed form using Whittaker's asymptotic expansion and were found to be in the well-agreement to the classical Love wave equations. The substantial effects of magnetoelastic coupling parameters, heterogeneity parameters, horizontal compressive initial stresses, Biot's gravity parameter, and wave number on the phase velocity of shear waves have been computed and depicted by means of a graph. As a special case, dispersion equations have been deduced when the two layers and half-space are isotropic and homogeneous. The comparative study for both cases of heterogeneity of the layers has been performed and also depicted by means of graphical illustrations.

Computational design of chimeric protein libraries for directed evolution.

Science.gov (United States)

Silberg, Jonathan J; Nguyen, Peter Q; Stevenson, Taylor

2010-01-01

The best approach for creating libraries of functional proteins with large numbers of nondisruptive amino acid substitutions is protein recombination, in which structurally related polypeptides are swapped among homologous proteins. Unfortunately, as more distantly related proteins are recombined, the fraction of variants having a disrupted structure increases. One way to enrich the fraction of folded and potentially interesting chimeras in these libraries is to use computational algorithms to anticipate which structural elements can be swapped without disturbing the integrity of a protein's structure. Herein, we describe how the algorithm Schema uses the sequences and structures of the parent proteins recombined to predict the structural disruption of chimeras, and we outline how dynamic programming can be used to find libraries with a range of amino acid substitution levels that are enriched in variants with low Schema disruption.

Hydrodynamic cavitation in Stokes flow of anisotropic fluids

Science.gov (United States)

Stieger, Tillmann; Agha, Hakam; Schoen, Martin; Mazza, Marco G.; Sengupta, Anupam

2017-05-01

Cavitation, the nucleation of vapour in liquids, is ubiquitous in fluid dynamics, and is often implicated in a myriad of industrial and biomedical applications. Although extensively studied in isotropic liquids, corresponding investigations in anisotropic liquids are largely lacking. Here, by combining liquid crystal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments, we report flow-induced cavitation in an anisotropic fluid. The cavitation domain nucleates due to sudden pressure drop upon flow past a cylindrical obstacle within a microchannel. For an anisotropic fluid, the inception and growth of the cavitation domain ensued in the Stokes regime, while no cavitation was observed in isotropic liquids flowing under similar hydrodynamic parameters. Using simulations we identify a critical value of the Reynolds number for cavitation inception that scales inversely with the order parameter of the fluid. Strikingly, the critical Reynolds number for anisotropic fluids can be 50% lower than that of isotropic fluids.

A pull-back algorithm to determine the unloaded vascular geometry in anisotropic hyperelastic AAA passive mechanics.

Science.gov (United States)

Riveros, Fabián; Chandra, Santanu; Finol, Ender A; Gasser, T Christian; Rodriguez, Jose F

2013-04-01

Biomechanical studies on abdominal aortic aneurysms (AAA) seek to provide for better decision criteria to undergo surgical intervention for AAA repair. More accurate results can be obtained by using appropriate material models for the tissues along with accurate geometric models and more realistic boundary conditions for the lesion. However, patient-specific AAA models are generated from gated medical images in which the artery is under pressure. Therefore, identification of the AAA zero pressure geometry would allow for a more realistic estimate of the aneurysmal wall mechanics. This study proposes a novel iterative algorithm to find the zero pressure geometry of patient-specific AAA models. The methodology allows considering the anisotropic hyperelastic behavior of the aortic wall, its thickness and accounts for the presence of the intraluminal thrombus. Results on 12 patient-specific AAA geometric models indicate that the procedure is computational tractable and efficient, and preserves the global volume of the model. In addition, a comparison of the peak wall stress computed with the zero pressure and CT-based geometries during systole indicates that computations using CT-based geometric models underestimate the peak wall stress by 59 ± 64 and 47 ± 64 kPa for the isotropic and anisotropic material models of the arterial wall, respectively.

Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein-Protein Interactions.

Science.gov (United States)

Kang, Beom Sik; Pugalendhi, GaneshKumar; Kim, Ku-Jin

2017-10-13

Interactions between protein molecules are essential for the assembly, function, and regulation of proteins. The contact region between two protein molecules in a protein complex is usually complementary in shape for both molecules and the area of the contact region can be used to estimate the binding strength between two molecules. Although the area is a value calculated from the three-dimensional surface, it cannot represent the three-dimensional shape of the surface. Therefore, we propose an original concept of two-dimensional contact area which provides further information such as the ruggedness of the contact region. We present a novel algorithm for calculating the binding direction between two molecules in a protein complex, and then suggest a method to compute the two-dimensional flattened area of the contact region between two molecules based on the binding direction.

Anisotropic thermal conductivity in epoxy-bonded magnetocaloric composites

Science.gov (United States)

Weise, Bruno; Sellschopp, Kai; Bierdel, Marius; Funk, Alexander; Bobeth, Manfred; Krautz, Maria; Waske, Anja

2016-09-01

Thermal management is one of the crucial issues in the development of magnetocaloric refrigeration technology for application. In order to ensure optimal exploitation of the materials "primary" properties, such as entropy change and temperature lift, thermal properties (and other "secondary" properties) play an important role. In magnetocaloric composites, which show an increased cycling stability in comparison to their bulk counterparts, thermal properties are strongly determined by the geometric arrangement of the corresponding components. In the first part of this paper, the inner structure of a polymer-bonded La(Fe, Co, Si)13-composite was studied by X-ray computed tomography. Based on this 3D data, a numerical study along all three spatial directions revealed anisotropic thermal conductivity of the composite: Due to the preparation process, the long-axis of the magnetocaloric particles is aligned along the xy plane which is why the in-plane thermal conductivity is larger than the thermal conductivity along the z-axis. Further, the study is expanded to a second aspect devoted to the influence of particle distribution and alignment within the polymer matrix. Based on an equivalent ellipsoids model to describe the inner structure of the composite, numerical simulation of the thermal conductivity in different particle arrangements and orientation distributions were performed. This paper evaluates the possibilities of microstructural design for inducing and adjusting anisotropic thermal conductivity in magnetocaloric composites.

A Morphing framework to couple non-local and local anisotropic continua

KAUST Repository

Azdoud, Yan

2013-05-01

In this article, we develop a method to couple anisotropic local continua with anisotropic non-local continua with central long-range forces. First, we describe anisotropic non-local models based on spherical harmonic descriptions. We then derive compatible classic continuum models. Finally, we apply the morphing method to these anisotropic non-local models and present three-dimensional numerical examples to validate the efficiency of the technique. © 2013 Elsevier Ltd. All rights reserved.

Elastic properties of spherically anisotropic piezoelectric composites

International Nuclear Information System (INIS)

En-Bo, Wei; Guo-Qing, Gu; Ying-Ming, Poon

2010-01-01

Effective elastic properties of spherically anisotropic piezoelectric composites, whose spherically anisotropic piezoelectric inclusions are embedded in an infinite non-piezoelectric matrix, are theoretically investigated. Analytical solutions for the elastic displacements and the electric potentials under a uniform external strain are derived exactly. Taking into account of the coupling effects of elasticity, permittivity and piezoelectricity, the formula is derived for estimating the effective elastic properties based on the average field theory in the dilute limit. An elastic response mechanism is revealed, in which the effective elastic properties increase as inclusion piezoelectric properties increase and inclusion dielectric properties decrease. Moreover, a piezoelectric response mechanism, of which the effective piezoelectric response vanishes due to the symmetry of spherically anisotropic composite, is also disclosed. (condensed matter: structure, thermal and mechanical properties)

A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein.

Science.gov (United States)

Agrawal, Neeraj J; Helk, Bernhard; Trout, Bernhardt L

2014-01-21

Identifying hot-spot residues - residues that are critical to protein-protein binding - can help to elucidate a protein's function and assist in designing therapeutic molecules to target those residues. We present a novel computational tool, termed spatial-interaction-map (SIM), to predict the hot-spot residues of an evolutionarily conserved protein-protein interaction from the structure of an unbound protein alone. SIM can predict the protein hot-spot residues with an accuracy of 36-57%. Thus, the SIM tool can be used to predict the yet unknown hot-spot residues for many proteins for which the structure of the protein-protein complexes are not available, thereby providing a clue to their functions and an opportunity to design therapeutic molecules to target these proteins. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Acoustic frequency filter based on anisotropic topological phononic crystals

KAUST Repository

Chen, Zeguo

2017-11-02

We present a design of acoustic frequency filter based on a two-dimensional anisotropic phononic crystal. The anisotropic band structure exhibits either a directional or a combined (global + directional) bandgap at certain frequency regions, depending on the geometry. When the time-reversal symmetry is broken, it may introduce a topologically nontrivial bandgap. The induced nontrivial bandgap and the original directional bandgap result in various interesting wave propagation behaviors, such as frequency filter. We develop a tight-binding model to characterize the effective Hamiltonian of the system, from which the contribution of anisotropy is explicitly shown. Different from the isotropic cases, the Zeeman-type splitting is not linear and the anisotropic bandgap makes it possible to achieve anisotropic propagation characteristics along different directions and at different frequencies.

Acoustic frequency filter based on anisotropic topological phononic crystals

KAUST Repository

Chen, Zeguo; Zhao, Jiajun; Mei, Jun; Wu, Ying

2017-01-01

We present a design of acoustic frequency filter based on a two-dimensional anisotropic phononic crystal. The anisotropic band structure exhibits either a directional or a combined (global + directional) bandgap at certain frequency regions, depending on the geometry. When the time-reversal symmetry is broken, it may introduce a topologically nontrivial bandgap. The induced nontrivial bandgap and the original directional bandgap result in various interesting wave propagation behaviors, such as frequency filter. We develop a tight-binding model to characterize the effective Hamiltonian of the system, from which the contribution of anisotropy is explicitly shown. Different from the isotropic cases, the Zeeman-type splitting is not linear and the anisotropic bandgap makes it possible to achieve anisotropic propagation characteristics along different directions and at different frequencies.

Anisotropic nanomaterials preparation, properties, and applications

CERN Document Server

Li, Quan

2015-01-01

In this book anisotropic one-dimensional and two-dimensional nanoscale building blocks and their assembly into fascinating and qualitatively new functional structures embracing both hard and soft components are explained. Contributions from leading experts regarding important aspects like synthesis, assembly, properties and applications of the above materials are compiled into a reference book. The anisotropy, i.e. the direction-dependent physical properties, of materials is fascinating and elegant and has sparked the quest for anisotropic materials with useful properties. With such a curiosi

Lipid-protein interaction induced domains: Kinetics and conformational changes in multicomponent vesicles

Science.gov (United States)

Sreeja, K. K.; Sunil Kumar, P. B.

2018-04-01

The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been investigated in the past. We show, using Monte Carlo simulations, that the affinity of proteins for specific lipids can hasten their aggregation kinetics. The lipid membrane is modeled as a dynamically triangulated surface with the proteins defined as in-plane fields at the vertices. We show that, even at low protein concentrations, strong lipid-protein interactions can result in large protein clusters indicating a route to lipid mediated signal amplification. At high protein concentrations, the domains form buds similar to that seen in lipid-lipid interaction induced phase separation. Protein interaction induced domain budding is suppressed when proteins act as anisotropic inclusions and exhibit nematic orientational order. The kinetics of protein clustering and resulting conformational changes are shown to be significantly different for the isotropic and anisotropic curvature inducing proteins.

Performance of an anisotropic Allman/DKT 3-node thin triangular flat shell element

Science.gov (United States)

Ertas, A.; Krafcik, J. T.; Ekwaro-Osire, S.

1992-05-01

A simple, explicit formulation of the stiffness matrix for an anisotropic, 3-node, thin triangular flat shell element in global coordinates is presented. An Allman triangle (AT) is used for membrane stiffness. The membrane stiffness matrix is explicitly derived by applying an Allman transformation to a Felippa 6-node linear strain triangle (LST). Bending stiffness is incorporated by the use of a discrete Kirchhoff triangle (DKT) bending element. Stiffness terms resulting from anisotropic membrane-bending coupling are included by integrating, in area coordinates, the membrane and bending strain-displacement matrices. Using the aforementioned approach, the objective of this study is to develop and test the performance of a practical 3-node flat shell element that could be used in plate problems with unsymmetrically stacked composite laminates. The performance of the latter element is tested on plates of varying aspect ratios. The developed 3-node shell element should simplify the programming task and have the potential of reducing the computational time.

Composite Fermi surface in the half-filled Landau level with anisotropic electron mass

Science.gov (United States)

Ippoliti, Matteo; Geraedts, Scott; Bhatt, Ravindra

We study the problem of interacting electrons in the lowest Landau level at half filling in the quantum Hall regime, when the electron dispersion is given by an anisotropic mass tensor. Based on experimental observations and theoretical arguments, the ground state of the system is expected to consist of composite Fermions filling an elliptical Fermi sea, with the anisotropy of the ellipse determined by the competing effects of the isotropic Coulomb interaction and anisotropic electron mass tensor. We test this idea quantitatively by using a numerical density matrix renormalization group method for quantum Hall systems on an infinitely long cylinder. Singularities in the structure factor allow us to map the Fermi surface of the composite Fermions. We compute the composite Fermi surface anisotropy for several values of the electron mass anisotropy which allow us to deduce the functional dependence of the former on the latter. This research was supported by Department of Energy Office of Basic Energy Sciences through Grant No. DE-SC0002140.

Computing and Comparing Effective Properties for Flow and Transport in Computer-Generated Porous Media

KAUST Repository

Allen, Rebecca; Sun, Shuyu

2017-01-01

We compute effective properties (i.e., permeability, hydraulic tortuosity, and diffusive tortuosity) of three different digital porous media samples, including in-line array of uniform shapes, staggered-array of squares, and randomly distributed squares. The permeability and hydraulic tortuosity are computed by solving a set of rescaled Stokes equations obtained by homogenization, and the diffusive tortuosity is computed by solving a homogenization problem given for the effective diffusion coefficient that is inversely related to diffusive tortuosity. We find that hydraulic and diffusive tortuosity can be quantitatively different by up to a factor of ten in the same pore geometry, which indicates that these tortuosity terms cannot be used interchangeably. We also find that when a pore geometry is characterized by an anisotropic permeability, the diffusive tortuosity (and correspondingly the effective diffusion coefficient) can also be anisotropic. This finding has important implications for reservoir-scale modeling of flow and transport, as it is more realistic to account for the anisotropy of both the permeability and the effective diffusion coefficient.

Computing and Comparing Effective Properties for Flow and Transport in Computer-Generated Porous Media

KAUST Repository

Allen, Rebecca

2017-02-13

We compute effective properties (i.e., permeability, hydraulic tortuosity, and diffusive tortuosity) of three different digital porous media samples, including in-line array of uniform shapes, staggered-array of squares, and randomly distributed squares. The permeability and hydraulic tortuosity are computed by solving a set of rescaled Stokes equations obtained by homogenization, and the diffusive tortuosity is computed by solving a homogenization problem given for the effective diffusion coefficient that is inversely related to diffusive tortuosity. We find that hydraulic and diffusive tortuosity can be quantitatively different by up to a factor of ten in the same pore geometry, which indicates that these tortuosity terms cannot be used interchangeably. We also find that when a pore geometry is characterized by an anisotropic permeability, the diffusive tortuosity (and correspondingly the effective diffusion coefficient) can also be anisotropic. This finding has important implications for reservoir-scale modeling of flow and transport, as it is more realistic to account for the anisotropy of both the permeability and the effective diffusion coefficient.

Anisotropic Intervalley Plasmon Excitations in Graphene

International Nuclear Information System (INIS)

Chen Jian; Xu Huai-Zhe

2015-01-01

We investigate theoretically the intervalley plasmon excitations (IPEs) in graphene monolayer within the random-phase approximation. We derive an analytical expression of the real part of the dielectric function. We find a low-energy plasmon mode with a linear anisotropic dispersion which depends on the Fermi energy and the dielectric constant of substrate. The IPEs show strongly anisotropic behavior, which becomes significant around the zigzag crystallographic direction. More interestingly, the group velocity of IPE varies from negative to positive, and vanishes at special energy. (paper)

Modelling of CMUTs with Anisotropic Plates

DEFF Research Database (Denmark)

la Cour, Mette Funding; Christiansen, Thomas Lehrmann; Jensen, Jørgen Arendt

2012-01-01

Traditionally, CMUTs are modelled using the isotropic plate equation and this leads to deviations between analytical calculations and FEM simulations. In this paper, the deflection profile and material parameters are calculated using the anisotropic plate equation. It is shown that the anisotropic...... calculations match perfectly with FEM while an isotropic approach causes up to 10% deviations in deflection profile. Furthermore, we show how commonly used analytic modelling methods such as static calculations of the pull-in voltage and dynamic modelling through an equivalent circuit representation can...

On Pokrovskii's anisotropic gap equations in superconductivity theory

Science.gov (United States)

Yang, Yisong

2003-11-01

An existence and uniqueness theorem for Pokrovskii's zero-temperature anisotropic gap equation is proved. Furthermore, it is shown that Pokrovskii's finite-temperature equation is inconsistent with the Bardeen-Cooper-Schrieffer (BCS) theory. A reformulation of the anisotropic gap equation is presented along the line of Pokrovskii and it is shown that the new equation is consistent with the BCS theory for the whole temperature range. As an application, the Markowitz-Kadanoff model for anisotropic superconductivity is considered and a rigorous proof of the half-integer-exponent isotope effect is obtained. Furthermore, a sharp estimate of the gap solution near the transition temperature is established.

Data-driven imaging in anisotropic media

Energy Technology Data Exchange (ETDEWEB)

Volker, Arno; Hunter, Alan [TNO Stieltjes weg 1, 2600 AD, Delft (Netherlands)

2012-05-17

Anisotropic materials are being used increasingly in high performance industrial applications, particularly in the aeronautical and nuclear industries. Some important examples of these materials are composites, single-crystal and heavy-grained metals. Ultrasonic array imaging in these materials requires exact knowledge of the anisotropic material properties. Without this information, the images can be adversely affected, causing a reduction in defect detection and characterization performance. The imaging operation can be formulated in two consecutive and reciprocal focusing steps, i.e., focusing the sources and then focusing the receivers. Applying just one of these focusing steps yields an interesting intermediate domain. The resulting common focus point gather (CFP-gather) can be interpreted to determine the propagation operator. After focusing the sources, the observed travel-time in the CFP-gather describes the propagation from the focus point to the receivers. If the correct propagation operator is used, the measured travel-times should be the same as the time-reversed focusing operator due to reciprocity. This makes it possible to iteratively update the focusing operator using the data only and allows the material to be imaged without explicit knowledge of the anisotropic material parameters. Furthermore, the determined propagation operator can also be used to invert for the anisotropic medium parameters. This paper details the proposed technique and demonstrates its use on simulated array data from a specimen of Inconel single-crystal alloy commonly used in the aeronautical and nuclear industries.

Introducing Anisotropic Minkowski Functionals and Quantitative Anisotropy Measures for Local Structure Analysis in Biomedical Imaging

Science.gov (United States)

Wismüller, Axel; De, Titas; Lochmüller, Eva; Eckstein, Felix; Nagarajan, Mahesh B.

2017-01-01

The ability of Minkowski Functionals to characterize local structure in different biological tissue types has been demonstrated in a variety of medical image processing tasks. We introduce anisotropic Minkowski Functionals (AMFs) as a novel variant that captures the inherent anisotropy of the underlying gray-level structures. To quantify the anisotropy characterized by our approach, we further introduce a method to compute a quantitative measure motivated by a technique utilized in MR diffusion tensor imaging, namely fractional anisotropy. We showcase the applicability of our method in the research context of characterizing the local structure properties of trabecular bone micro-architecture in the proximal femur as visualized on multi-detector CT. To this end, AMFs were computed locally for each pixel of ROIs extracted from the head, neck and trochanter regions. Fractional anisotropy was then used to quantify the local anisotropy of the trabecular structures found in these ROIs and to compare its distribution in different anatomical regions. Our results suggest a significantly greater concentration of anisotropic trabecular structures in the head and neck regions when compared to the trochanter region (p < 10−4). We also evaluated the ability of such AMFs to predict bone strength in the femoral head of proximal femur specimens obtained from 50 donors. Our results suggest that such AMFs, when used in conjunction with multi-regression models, can outperform more conventional features such as BMD in predicting failure load. We conclude that such anisotropic Minkowski Functionals can capture valuable information regarding directional attributes of local structure, which may be useful in a wide scope of biomedical imaging applications. PMID:29170580

Recent developments of the MARC/PN transport theory code including a treatment of anisotropic scatter

International Nuclear Information System (INIS)

Fletcher, J.K.

1987-12-01

The computer code MARC/PN provides a solution of the multigroup transport equation by expanding the flux in spherical harmonics. The coefficients of the series so obtained satisfy linked first order differential equations, and on eliminating terms associated with odd parity harmonics a second order system results which can be solved by established finite difference or finite element techniques. This report describes modifications incorporated in MARC/PN to allow for anisotropic scattering, and the modelling of irregular exterior boundaries in the finite element option. The latter development leads to substantial reductions in problem size, particularly for three dimensions. Also, links to an interactive graphics mesh generator (SUPERTAB) have been added. The final section of the report contains results from problems showing the effects of anisotropic scatter and the ability of the code to model irregular geometries. (author)

Protein adsorption on nanoparticles: model development using computer simulation

International Nuclear Information System (INIS)

Shao, Qing; Hall, Carol K

2016-01-01

The adsorption of proteins on nanoparticles results in the formation of the protein corona, the composition of which determines how nanoparticles influence their biological surroundings. We seek to better understand corona formation by developing models that describe protein adsorption on nanoparticles using computer simulation results as data. Using a coarse-grained protein model, discontinuous molecular dynamics simulations are conducted to investigate the adsorption of two small proteins (Trp-cage and WW domain) on a model nanoparticle of diameter 10.0 nm at protein concentrations ranging from 0.5 to 5 mM. The resulting adsorption isotherms are well described by the Langmuir, Freundlich, Temkin and Kiselev models, but not by the Elovich, Fowler–Guggenheim and Hill–de Boer models. We also try to develop a generalized model that can describe protein adsorption equilibrium on nanoparticles of different diameters in terms of dimensionless size parameters. The simulation results for three proteins (Trp-cage, WW domain, and GB3) on four nanoparticles (diameter  =  5.0, 10.0, 15.0, and 20.0 nm) illustrate both the promise and the challenge associated with developing generalized models of protein adsorption on nanoparticles. (paper)

Studying protein assembly with reversible Brownian dynamics of patchy particles

International Nuclear Information System (INIS)

Klein, Heinrich C. R.; Schwarz, Ulrich S.

2014-01-01

Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly

Studying protein assembly with reversible Brownian dynamics of patchy particles

Energy Technology Data Exchange (ETDEWEB)

Klein, Heinrich C. R. [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); Schwarz, Ulrich S., E-mail: ulrich.schwarz@bioquant.uni-heidelberg.de [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); BioQuant, Heidelberg University, 69120 Heidelberg (Germany)

2014-05-14

Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly.

Computation of temperature-dependent legendre moments of a double-differential elastic cross section

International Nuclear Information System (INIS)

Arbanas, G.; Dunn, M.E.; Larson, N.M.; Leal, L.C.; Williams, M.L.; Becker, B.; Dagan, R.

2011-01-01

A general expression for temperature-dependent Legendre moments of a double-differential elastic scattering cross section was derived by Ouisloumen and Sanchez [Nucl. Sci. Eng. 107, 189-200 (1991)]. Attempts to compute this expression are hindered by the three-fold nested integral, limiting their practical application to just the zeroth Legendre moment of an isotropic scattering. It is shown that the two innermost integrals could be evaluated analytically to all orders of Legendre moments, and for anisotropic scattering, by a recursive application of the integration by parts method. For this method to work, the anisotropic angular distribution in the center of mass is expressed as an expansion in Legendre polynomials. The first several Legendre moments of elastic scattering of neutrons on 238 U are computed at T=1000 K at incoming energy 6.5 eV for isotropic scattering in the center of mass frame. Legendre moments of the anisotropic angular distribution given via Blatt-Biedenharn coefficients are computed at 1 keV. The results are in agreement with those computed by the Monte Carlo method. (author)

Anisotropic characterization of magnetorheological materials

Energy Technology Data Exchange (ETDEWEB)

Dohmen, E., E-mail: eike.dohmen@tu-dresden.de; Modler, N.; Gude, M.

2017-06-01

For the development of energy efficient lightweight parts novel function integrating materials are needed. Concerning this field of application magnetorheological (MR) fluids, MR elastomers and MR composites are promising materials allowing the adjustment of mechanical properties by an external magnetic field. A key issue for operating such structures in praxis is the magneto-mechanical description. Most rheological properties are gathered at laboratory conditions for high magnetic flux densities and a single field direction, which does not correspond to real praxis conditions. Although anisotropic formation of superstructures can be observed in MR suspensions (Fig. 1) or experimenters intentionally polymerize MR elastomers with anisotropic superstructures these MR materials are usually described in an external magnetic field as uniform, isotropic materials. This is due to missing possibilities for experimentally measuring field angle dependent properties and ways of distinguishing between material properties and frictional effects. Just a few scientific works experimentally investigated the influence of different field angles (Ambacher et al., 1992; Grants et al., 1990; Kuzhir et al., 2003) or the influence of surface roughness on the shear behaviour of magnetic fluids (Tang and Conrad, 1996) . The aim of this work is the introduction of a novel field angle cell allowing the determination of anisotropic mechanical properties for various MR materials depending on the applied magnetic field angle. - Highlights: • Novel magnetic field angle testing device (MFATD) presented. • Determination of magnetic field dependent anisotropic mechanical properties. • Experimental data for different field directions shown for a commercial MR fluid. • Material description of MR fluids as transversal-isotropic solids. • Magnetic field angle dependent variations in shear stresses experimentally measured. • Determination of frictional coefficients between the MR fluid and

A unified theoretical and experimental study of anisotropic hardening

International Nuclear Information System (INIS)

Boehler, J.P.; Raclin, J.

1981-01-01

The purpose of this work is to develop a consistent formulation of the constitutive relations regarding anisotropic hardening materials. Attention is focused on the appearance and the evolution of mechanical anisotropies during irreversible processes, such as plastic forming and inelastic deformation of structures. The representation theorems for anisotropic tensor functions constitute a theoretical basis, allowing to reduce arbitrariness and to obtain a unified formulation of anisotropic hardening. In this approach, a general three-dimensional constitutive law is developed for prestrained initially orthotropic materials. Introduction of the plastic behavior results in the general forms of both the flow-law and the yield criterion. The developed theory is then specialized for the case of plane stress and different modes of anisotropic hardening are analyzed. A new generalization of the Von Mises criterion is proposed, in considering a homogeneous form of order two in stress and employing the simplest combinations of the basic invariants entering the general form of the yield condition. The proposed criterion involves specific terms accounting for the initial anisotropy, the deformation induced anisotropy and correlative terms between initial and induced anisotropy. The effects of prestrainings result in both isotropic and anisotropic hardening. An adequate experimental program, consisting of uniaxial tensile tests on oriented specimens of prestrained sheet-metal, was performed, in order to determine the specific form and the evolution of the anisotropic failure criterion for soft-steel subjected to different irreversible prestrainings. (orig.)

Anisotropic magnetoresistance and piezoelectric effect in GaAs Hall samples

Science.gov (United States)

Ciftja, Orion

2017-02-01

Application of a strong magnetic field perpendicular to a two-dimensional electron system leads to a variety of quantum phases ranging from incompressible quantum Hall liquid to Wigner solid, charge density wave, and exotic non-Abelian states. A few quantum phases seen in past experiments on GaAs Hall samples of electrons show pronounced anisotropic magnetoresistance values at certain weak magnetic fields. We argue that this might be due to the piezoelectric effect that is inherent in a semiconductor host such as GaAs. Such an effect has the potential to create a sufficient in-plane internal strain that will be felt by electrons and will determine the direction of high and low resistance. When Wigner solid, charge density wave, and isotropic liquid phases are very close in energy, the overall stability of the system is very sensitive to local order and, thus, can be strongly influenced even by a weak perturbation such as the piezoelectric-induced effective electron-electron interaction, which is anisotropic. In this work, we argue that an anisotropic interaction potential may stabilize anisotropic liquid phases of electrons even in a strong magnetic field regime where normally one expects to see only isotropic quantum Hall or isotropic Fermi liquid states. We use this approach to support a theoretical framework that envisions the possibility of an anisotropic liquid crystalline state of electrons in the lowest Landau level. In particular, we argue that an anisotropic liquid state of electrons may stabilize in the lowest Landau level close to the liquid-solid transition region at filling factor ν =1 /6 for a given anisotropic Coulomb interaction potential. Quantum Monte Carlo simulations for a liquid crystalline state with broken rotational symmetry indicate stability of liquid crystalline order consistent with the existence of an anisotropic liquid state of electrons stabilized by anisotropy at filling factor ν =1 /6 of the lowest Landau level.

Development of laser ablation plasma by anisotropic self-radiation

Directory of Open Access Journals (Sweden)

Ohnishi Naofumi

2013-11-01

Full Text Available We have proposed a method for reproducing an accurate solution of low-density ablation plasma by properly treating anisotropic radiation. Monte-Carlo method is employed for estimating Eddington tensor with limited number of photon samples in each fluid time step. Radiation field from ablation plasma is significantly affected by the anisotropic Eddington tensor. Electron temperature around the ablation surface changes with the radiation field and is responsible for the observed emission. An accurate prediction of the light emission from the laser ablation plasma requires a careful estimation of the anisotropic radiation field.

Anisotropic inflation with derivative couplings

Science.gov (United States)

Holland, Jonathan; Kanno, Sugumi; Zavala, Ivonne

2018-05-01

We study anisotropic power-law inflationary solutions when the inflaton and its derivative couple to a vector field. This type of coupling is motivated by D-brane inflationary models, in which the inflaton, and a vector field living on the D-brane, couple disformally (derivatively). We start by studying a phenomenological model where we show the existence of anisotropic solutions and demonstrate their stability via a dynamical system analysis. Compared to the case without a derivative coupling, the anisotropy is reduced and thus can be made consistent with current limits, while the value of the slow-roll parameter remains almost unchanged. We also discuss solutions for more general cases, including D-brane-like couplings.

Anisotropic charged generalized polytropic models

Science.gov (United States)

Nasim, A.; Azam, M.

2018-06-01

In this paper, we found some new anisotropic charged models admitting generalized polytropic equation of state with spherically symmetry. An analytic solution of the Einstein-Maxwell field equations is obtained through the transformation introduced by Durgapal and Banerji (Phys. Rev. D 27:328, 1983). The physical viability of solutions corresponding to polytropic index η =1/2, 2/3, 1, 2 is analyzed graphically. For this, we plot physical quantities such as radial and tangential pressure, anisotropy, speed of sound which demonstrated that these models achieve all the considerable physical conditions required for a relativistic star. Further, it is mentioned here that previous results for anisotropic charged matter with linear, quadratic and polytropic equation of state can be retrieved.

Polarization ray tracing in anisotropic optically active media. II. Theory and physics

International Nuclear Information System (INIS)

McClain, S.C.; Hillman, L.W.; Chipman, R.A.

1993-01-01

Refraction, reflection, and amplitude relations are derived that apply to polarization ray tracing in anisotropic, optically active media such as quartz. The constitutive relations for quartz are discussed. The refractive indices and polarization states associated with the two modes of propagation are derived as a function of wave direction. A procedure for refracting at any uniaxial or optically active interface is derived that computes both the ray direction and the wave direction. A method for computing the optical path length is given, and Fresnel transmission and ref lection equations are derived from boundary conditions on the electromagnetic fields. These ray-tracing formulas apply to uniaxial, optically active media and therefore encompass uniaxial, non-optically active materials and isotropic, optically active materials

Pulse splitting in nonlinear media with anisotropic dispersion properties

DEFF Research Database (Denmark)

Bergé, L.; Juul Rasmussen, J.; Schmidt, M.R.

1998-01-01

The nonlinear self-focusing of beams in media with anisotropic (mix-signed) dispersion is investigated. Theoretical predictions employing virial-type arguments and self-similar techniques suggest that a pulse propagating in a nonlinear medium with anisotropic dispersion will not collapse...

A new technique for generating the isotropic and linearly anisotropic components of elastic and discrete inelastic transfer matrices

International Nuclear Information System (INIS)

Garcia, R.D.M.

1984-01-01

A new technique for generating the isotropic and linearly anisotropic componets of elastic and discrete inelastic transfer matrices is proposed. The technique allows certain angular integrals to be expressed in terms of functions that can be computed by recursion relations or series expansions alternatively to the use of numerical quadratures. (Author) [pt

Anisotropic rectangular metric for polygonal surface remeshing

KAUST Repository

Pellenard, Bertrand

2013-06-18

We propose a new method for anisotropic polygonal surface remeshing. Our algorithm takes as input a surface triangle mesh. An anisotropic rectangular metric, defined at each triangle facet of the input mesh, is derived from both a user-specified normal-based tolerance error and the requirement to favor rectangle-shaped polygons. Our algorithm uses a greedy optimization procedure that adds, deletes and relocates generators so as to match two criteria related to partitioning and conformity.

Anisotropic rectangular metric for polygonal surface remeshing

KAUST Repository

Pellenard, Bertrand; Morvan, Jean-Marie; Alliez, Pierre

2013-01-01

We propose a new method for anisotropic polygonal surface remeshing. Our algorithm takes as input a surface triangle mesh. An anisotropic rectangular metric, defined at each triangle facet of the input mesh, is derived from both a user-specified normal-based tolerance error and the requirement to favor rectangle-shaped polygons. Our algorithm uses a greedy optimization procedure that adds, deletes and relocates generators so as to match two criteria related to partitioning and conformity.

Temperature-Responsive Anisotropic Slippery Surface for Smart Control of the Droplet Motion.

Science.gov (United States)

Wang, By Lili; Heng, Liping; Jiang, Lei

2018-02-28

Development of stimulus-responsive anisotropic slippery surfaces is important because of the high demand for such materials in the field of liquid directional-driven systems. However, current studies in the field of slippery surfaces are mainly conducted to prepare isotropic slippery surfaces. Although we have developed electric-responsive anisotropic slippery surfaces that enable smart control of the droplet motion, there remain challenges for designing temperature-responsive anisotropic slippery surfaces to control the liquid droplet motion on the surface and in the tube. In this work, temperature-responsive anisotropic slippery surfaces have been prepared by using paraffin, a thermo-responsive phase-transition material, as a lubricating fluid and directional porous polystyrene (PS) films as the substrate. The smart regulation of the droplet motion of several liquids on this surface was accomplished by tuning the substrate temperature. The uniqueness of this surface lies in the use of an anisotropic structure and temperature-responsive lubricating fluids to achieve temperature-driven smart control of the anisotropic motion of the droplets. Furthermore, this surface was used to design temperature-driven anisotropic microreactors and to manipulate liquid transfer in tubes. This work advances the understanding of the principles underlying anisotropic slippery surfaces and provides a promising material for applications in the biochip and microreactor system.

An Efficient FPGA Implementation of Optimized Anisotropic Diffusion Filtering of Images

Directory of Open Access Journals (Sweden)

Chandrajit Pal

2016-01-01

Full Text Available Digital image processing is an exciting area of research with a variety of applications including medical, surveillance security systems, defence, and space applications. Noise removal as a preprocessing step helps to improve the performance of the signal processing algorithms, thereby enhancing image quality. Anisotropic diffusion filtering proposed by Perona and Malik can be used as an edge-preserving smoother, removing high-frequency components of images without blurring their edges. In this paper, we present the FPGA implementation of an edge-preserving anisotropic diffusion filter for digital images. The designed architecture completely replaced the convolution operation and implemented the same using simple arithmetic subtraction of the neighboring intensities within a kernel, preceded by multiple operations in parallel within the kernel. To improve the image reconstruction quality, the diffusion coefficient parameter, responsible for controlling the filtering process, has been properly analyzed. Its signal behavior has been studied by subsequently scaling and differentiating the signal. The hardware implementation of the proposed design shows better performance in terms of reconstruction quality and accelerated performance with respect to its software implementation. It also reduces computation, power consumption, and resource utilization with respect to other related works.

Manipulation of surface plasmon polariton propagation on isotropic and anisotropic two-dimensional materials coupled to boron nitride heterostructures

Energy Technology Data Exchange (ETDEWEB)

Inampudi, Sandeep; Nazari, Mina; Forouzmand, Ali; Mosallaei, Hossein, E-mail: hosseinm@coe.neu.edu [Department of Electrical and Computer Engineering, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 (United States)

2016-01-14

We present a comprehensive analysis of surface plasmon polariton dispersion characteristics associated with isotropic and anisotropic two-dimensional atomically thin layered materials (2D sheets) coupled to h-BN heterostructures. A scattering matrix based approach is presented to compute the electromagnetic fields and related dispersion characteristics of stacked layered systems composed of anisotropic 2D sheets and uniaxial bulk materials. We analyze specifically the surface plasmon polariton (SPP) dispersion characteristics in case of isolated and coupled two-dimensional layers with isotropic and anisotropic conductivities. An analysis based on residue theorem is utilized to identify optimum optical parameters (surface conductivity) and geometrical parameters (separation between layers) to maximize the SPP field at a given position. The effect of type and degree of anisotropy on the shapes of iso-frequency curves and propagation characteristics is discussed in detail. The analysis presented in this paper gives an insight to identify optimum setup to enhance the SPP field at a given position and in a given direction on the surface of two-dimensional materials.

Modeling of anisotropic wound healing

Science.gov (United States)

Valero, C.; Javierre, E.; García-Aznar, J. M.; Gómez-Benito, M. J.; Menzel, A.

2015-06-01

Biological soft tissues exhibit non-linear complex properties, the quantification of which presents a challenge. Nevertheless, these properties, such as skin anisotropy, highly influence different processes that occur in soft tissues, for instance wound healing, and thus its correct identification and quantification is crucial to understand them. Experimental and computational works are required in order to find the most precise model to replicate the tissues' properties. In this work, we present a wound healing model focused on the proliferative stage that includes angiogenesis and wound contraction in three dimensions and which relies on the accurate representation of the mechanical behavior of the skin. Thus, an anisotropic hyperelastic model has been considered to analyze the effect of collagen fibers on the healing evolution of an ellipsoidal wound. The implemented model accounts for the contribution of the ground matrix and two mechanically equivalent families of fibers. Simulation results show the evolution of the cellular and chemical species in the wound and the wound volume evolution. Moreover, the local strain directions depend on the relative wound orientation with respect to the fibers.

Method of moving frames to solve time-dependent Maxwell's equations on anisotropic curved surfaces: Applications to invisible cloak and ELF propagation

Science.gov (United States)

Chun, Sehun

2017-07-01

Applying the method of moving frames to Maxwell's equations yields two important advancements for scientific computing. The first is the use of upwind flux for anisotropic materials in Maxwell's equations, especially in the context of discontinuous Galerkin (DG) methods. Upwind flux has been available only to isotropic material, because of the difficulty of satisfying the Rankine-Hugoniot conditions in anisotropic media. The second is to solve numerically Maxwell's equations on curved surfaces without the metric tensor and composite meshes. For numerical validation, spectral convergences are displayed for both two-dimensional anisotropic media and isotropic spheres. In the first application, invisible two-dimensional metamaterial cloaks are simulated with a relatively coarse mesh by both the lossless Drude model and the piecewisely-parametered layered model. In the second application, extremely low frequency propagation on various surfaces such as spheres, irregular surfaces, and non-convex surfaces is demonstrated.

Anisotropic permeable porous facing and slip velocity on squeeze film in an axially undefined journal bearing with ferrofluid lubricant

International Nuclear Information System (INIS)

Shah, R.C.; Bhat, M.V.

2004-01-01

Ferrofluid squeeze film in an axially undefined porous journal bearing was analyzed to determine its performance considering anisotropic permeability of the porous facing and slip velocity at the interface of porous matrix and film region using Jenkins flow model. Expressions were obtained for dimensionless pressure, load capacity and response time of the squeeze film. How to deduce results for no-slip case, isotropic porous case and for Neuringer-Rosensweig model case were indicated. The computed values of dimensionless load capacity and response time were displayed in graphical form. They increased with increasing values of eccentricity ratio and anisotropic parameter while they decreased with increasing values of slip parameter or material parameter of Jenkins model

Anisotropic wave-equation traveltime and waveform inversion

KAUST Repository

Feng, Shihang

2016-09-06

The wave-equation traveltime and waveform inversion (WTW) methodology is developed to invert for anisotropic parameters in a vertical transverse isotropic (VTI) meidum. The simultaneous inversion of anisotropic parameters v0, ε and δ is initially performed using the wave-equation traveltime inversion (WT) method. The WT tomograms are then used as starting background models for VTI full waveform inversion. Preliminary numerical tests on synthetic data demonstrate the feasibility of this method for multi-parameter inversion.

Anisotropic microporous supports impregnated with polymeric ion-exchange materials

Science.gov (United States)

Friesen, Dwayne; Babcock, Walter C.; Tuttle, Mark

1985-05-07

Novel ion-exchange media are disclosed, the media comprising polymeric anisotropic microporous supports containing polymeric ion-exchange or ion-complexing materials. The supports are anisotropic, having small exterior pores and larger interior pores, and are preferably in the form of beads, fibers and sheets.

Fast algorithms for evaluating the stress field of dislocation lines in anisotropic elastic media

Science.gov (United States)

Chen, C.; Aubry, S.; Oppelstrup, T.; Arsenlis, A.; Darve, E.

2018-06-01

In dislocation dynamics (DD) simulations, the most computationally intensive step is the evaluation of the elastic interaction forces among dislocation ensembles. Because the pair-wise interaction between dislocations is long-range, this force calculation step can be significantly accelerated by the fast multipole method (FMM). We implemented and compared four different methods in isotropic and anisotropic elastic media: one based on the Taylor series expansion (Taylor FMM), one based on the spherical harmonics expansion (Spherical FMM), one kernel-independent method based on the Chebyshev interpolation (Chebyshev FMM), and a new kernel-independent method that we call the Lagrange FMM. The Taylor FMM is an existing method, used in ParaDiS, one of the most popular DD simulation softwares. The Spherical FMM employs a more compact multipole representation than the Taylor FMM does and is thus more efficient. However, both the Taylor FMM and the Spherical FMM are difficult to derive in anisotropic elastic media because the interaction force is complex and has no closed analytical formula. The Chebyshev FMM requires only being able to evaluate the interaction between dislocations and thus can be applied easily in anisotropic elastic media. But it has a relatively large memory footprint, which limits its usage. The Lagrange FMM was designed to be a memory-efficient black-box method. Various numerical experiments are presented to demonstrate the convergence and the scalability of the four methods.

Green synthesis of anisotropic gold nanoparticles for photothermal therapy of cancer.

Science.gov (United States)

Fazal, Sajid; Jayasree, Aswathy; Sasidharan, Sisini; Koyakutty, Manzoor; Nair, Shantikumar V; Menon, Deepthy

2014-06-11

Nanoparticles of varying composition, size, shape, and architecture have been explored for use as photothermal agents in the field of cancer nanomedicine. Among them, gold nanoparticles provide a simple platform for thermal ablation owing to its biocompatibility in vivo. However, the synthesis of such gold nanoparticles exhibiting suitable properties for photothermal activity involves cumbersome routes using toxic chemicals as capping agents, which can cause concerns in vivo. Herein, gold nanoparticles, synthesized using green chemistry routes possessing near-infrared (NIR) absorbance facilitating photothermal therapy, would be a viable alternative. In this study, anisotropic gold nanoparticles were synthesized using an aqueous route with cocoa extract which served both as a reducing and stabilizing agent. The as-prepared gold nanoparticles were subjected to density gradient centrifugation to maximize its NIR absorption in the wavelength range of 800-1000 nm. The particles also showed good biocompatibility when tested in vitro using A431, MDA-MB231, L929, and NIH-3T3 cell lines up to concentrations of 200 μg/mL. Cell death induced in epidermoid carcinoma A431 cells upon irradiation with a femtosecond laser at 800 nm at a low power density of 6 W/cm(2) proved the suitability of green synthesized NIR absorbing anisotropic gold nanoparticles for photothermal ablation of cancer cells. These gold nanoparticles also showed good X-ray contrast when tested using computed tomography (CT), proving their feasibility for use as a contrast agent as well. This is the first report on green synthesized anisotropic and cytocompatible gold nanoparticles without any capping agents and their suitability for photothermal therapy.

Infinitely dilute partial molar properties of proteins from computer simulation.

Science.gov (United States)

Ploetz, Elizabeth A; Smith, Paul E

2014-11-13

A detailed understanding of temperature and pressure effects on an infinitely dilute protein's conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method's feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.

Modelling of anisotropic compact stars of embedding class one

Energy Technology Data Exchange (ETDEWEB)

Bhar, Piyali [Government General Degree College, Department of Mathematics, Singur, Hooghly, West Bengal (India); Maurya, S.K. [University of Nizwa, Department of Mathematical and Physical Sciences, College of Arts and Science, Nizwa (Oman); Gupta, Y.K. [Raj Kumar Goel Institute of Technology, Department of Mathematics, Ghaziabad, U.P. (India); Manna, Tuhina [St. Xavier' s College, Department of Commerce (Evening), Kolkata, West Bengal (India)

2016-10-15

In the present article, we have constructed static anisotropic compact star models of Einstein field equations for the spherical symmetric metric of embedding class one. By assuming the particular form of the metric function ν, we have solved the Einstein field equations for anisotropic matter distribution. The anisotropic models represent the realistic compact objects such as SAX J 1808.4-3658 (SS1), Her X-1, Vela X-12, PSR J1614-2230 and Cen X-3. We have reported our results in details for the compact star Her X-1 on the ground of physical properties such as pressure, density, velocity of sound, energy conditions, TOV equation and red-shift etc. Along with these, we have also discussed about the stability of the compact star models. Finally we made a comparison between our anisotropic stars with the realistic objects on the key aspects as central density, central pressure, compactness and surface red-shift. (orig.)

Microseismic Full Waveform Modeling in Anisotropic Media with Moment Tensor Implementation

Science.gov (United States)

Shi, Peidong; Angus, Doug; Nowacki, Andy; Yuan, Sanyi; Wang, Yanyan

2018-03-01

Seismic anisotropy which is common in shale and fractured rocks will cause travel-time and amplitude discrepancy in different propagation directions. For microseismic monitoring which is often implemented in shale or fractured rocks, seismic anisotropy needs to be carefully accounted for in source location and mechanism determination. We have developed an efficient finite-difference full waveform modeling tool with an arbitrary moment tensor source. The modeling tool is suitable for simulating wave propagation in anisotropic media for microseismic monitoring. As both dislocation and non-double-couple source are often observed in microseismic monitoring, an arbitrary moment tensor source is implemented in our forward modeling tool. The increments of shear stress are equally distributed on the staggered grid to implement an accurate and symmetric moment tensor source. Our modeling tool provides an efficient way to obtain the Green's function in anisotropic media, which is the key of anisotropic moment tensor inversion and source mechanism characterization in microseismic monitoring. In our research, wavefields in anisotropic media have been carefully simulated and analyzed in both surface array and downhole array. The variation characteristics of travel-time and amplitude of direct P- and S-wave in vertical transverse isotropic media and horizontal transverse isotropic media are distinct, thus providing a feasible way to distinguish and identify the anisotropic type of the subsurface. Analyzing the travel-times and amplitudes of the microseismic data is a feasible way to estimate the orientation and density of the induced cracks in hydraulic fracturing. Our anisotropic modeling tool can be used to generate and analyze microseismic full wavefield with full moment tensor source in anisotropic media, which can help promote the anisotropic interpretation and inversion of field data.

Thermodynamic analysis on an anisotropically superhydrophobic surface with a hierarchical structure

Energy Technology Data Exchange (ETDEWEB)

Zhao, Jieliang [Division of Intelligent and Biomechanical Systems, State Key Laboratory of Tribology, Tsinghua University, Room 3407, Building 9003, 100084 Beijing (China); Su, Zhengliang [Division of Intelligent and Biomechanical Systems, State Key Laboratory of Tribology, Tsinghua University, Room 3407, Building 9003, 100084 Beijing (China); Department of Automotive Engineering, Tsinghua University, Beijing 100084 (China); Yan, Shaoze, E-mail: yansz@mail.tsinghua.edu.cn [Division of Intelligent and Biomechanical Systems, State Key Laboratory of Tribology, Tsinghua University, Room 3407, Building 9003, 100084 Beijing (China)

2015-12-01

Graphical abstract: - Highlights: • We model the superhydrophobic surface with anisotropic and hierarchical structure. • Anisotropic wetting only shows in noncomposite state (not in composite state). • Transition from noncomposite to composite state on dual-scale structure is hard. • Droplets tend to roll in the particular direction. • Droplets tend to stably remain in one preferred thermodynamic state. - Abstract: Superhydrophobic surfaces, which refer to the surfaces with contact angle higher than 150° and hysteresis less than 10°, have been reported in various studies. However, studies on the superhydrophobicity of anisotropic, hierarchical surfaces are limited and the corresponding thermodynamic mechanisms could not be explained thoroughly. Here we propose a simplified surface model of anisotropic patterned surface with dual scale roughness. Based on the thermodynamic method, we calculate the equilibrium contact angle (ECA) and the contact angle hysteresis (CAH) on the given surface. We show here that the hierarchical structure has much better anisotropic wetting properties than the single-scale one, and the results shed light on the potential application in controllable micro-/nano-fluidic systems. Our studies can be potentially applied for the fabrication of anisotropically superhydrophobic surfaces.

Thermodynamic analysis on an anisotropically superhydrophobic surface with a hierarchical structure

International Nuclear Information System (INIS)

Zhao, Jieliang; Su, Zhengliang; Yan, Shaoze

2015-01-01

Graphical abstract: - Highlights: • We model the superhydrophobic surface with anisotropic and hierarchical structure. • Anisotropic wetting only shows in noncomposite state (not in composite state). • Transition from noncomposite to composite state on dual-scale structure is hard. • Droplets tend to roll in the particular direction. • Droplets tend to stably remain in one preferred thermodynamic state. - Abstract: Superhydrophobic surfaces, which refer to the surfaces with contact angle higher than 150° and hysteresis less than 10°, have been reported in various studies. However, studies on the superhydrophobicity of anisotropic, hierarchical surfaces are limited and the corresponding thermodynamic mechanisms could not be explained thoroughly. Here we propose a simplified surface model of anisotropic patterned surface with dual scale roughness. Based on the thermodynamic method, we calculate the equilibrium contact angle (ECA) and the contact angle hysteresis (CAH) on the given surface. We show here that the hierarchical structure has much better anisotropic wetting properties than the single-scale one, and the results shed light on the potential application in controllable micro-/nano-fluidic systems. Our studies can be potentially applied for the fabrication of anisotropically superhydrophobic surfaces.

Pseudo-spectral method using rotated staggered grid for elastic wave propagation in 3D arbitrary anisotropic media

KAUST Repository

Zou, Peng

2017-05-10

Staggering grid is a very effective way to reduce the Nyquist errors and to suppress the non-causal ringing artefacts in the pseudo-spectral solution of first-order elastic wave equations. However, the straightforward use of a staggered-grid pseudo-spectral method is problematic for simulating wave propagation when the anisotropy level is greater than orthorhombic or when the anisotropic symmetries are not aligned with the computational grids. Inspired by the idea of rotated staggered-grid finite-difference method, we propose a modified pseudo-spectral method for wave propagation in arbitrary anisotropic media. Compared with an existing remedy of staggered-grid pseudo-spectral method based on stiffness matrix decomposition and a possible alternative using the Lebedev grids, the rotated staggered-grid-based pseudo-spectral method possesses the best balance between the mitigation of artefacts and efficiency. A 2D example on a transversely isotropic model with tilted symmetry axis verifies its effectiveness to suppress the ringing artefacts. Two 3D examples of increasing anisotropy levels demonstrate that the rotated staggered-grid-based pseudo-spectral method can successfully simulate complex wavefields in such anisotropic formations.

Anisotropic Concrete Compressive Strength

DEFF Research Database (Denmark)

Gustenhoff Hansen, Søren; Jørgensen, Henrik Brøner; Hoang, Linh Cao

2017-01-01

When the load carrying capacity of existing concrete structures is (re-)assessed it is often based on compressive strength of cores drilled out from the structure. Existing studies show that the core compressive strength is anisotropic; i.e. it depends on whether the cores are drilled parallel...

Computational and biological characterization of fusion proteins of two insecticidal proteins for control of insect pests.

Science.gov (United States)

Javaid, Shaista; Naz, Sehrish; Amin, Imran; Jander, Georg; Ul-Haq, Zaheer; Mansoor, Shahid

2018-03-19

Sucking pests pose a serious agricultural challenge, as available transgenic technologies such as Bacillus thuringiensis crystal toxins (Bt) are not effective against them. One approach is to produce fusion protein toxins for the control of these pests. Two protein toxins, Hvt (ω-atracotoxin from Hadronyche versuta) and onion leaf lectin, were translationally fused to evaluate the negative effects of fusion proteins on Phenacoccus solenopsis (mealybug), a phloem-feeding insect pest. Hvt was cloned both N-terminally (HL) and then C-terminally (LH) in the fusion protein constructs, which were expressed transiently in Nicotiana tabacum using a Potato Virus X (PVX) vector. The HL fusion protein was found to be more effective against P. solenopsis, with an 83% mortality rate, as compared to the LH protein, which caused 65% mortality. Hvt and lectin alone caused 42% and 45%, respectively, under the same conditions. Computational studies of both fusion proteins showed that the HL protein is more stable than the LH protein. Together, these results demonstrate that translational fusion of two insecticidal proteins improved the insecticidal activity relative to each protein individually and could be expressed in transgenic plants for effective control of sucking pests.

Three-dimensional anisotropic adaptive filtering of projection data for noise reduction in cone beam CT

Energy Technology Data Exchange (ETDEWEB)

Maier, Andreas; Wigstroem, Lars; Hofmann, Hannes G.; Hornegger, Joachim; Zhu Lei; Strobel, Norbert; Fahrig, Rebecca [Department of Radiology, Stanford University, Stanford, California 94305 (United States); Department of Radiology, Stanford University, Stanford, California 94305 (United States) and Center for Medical Image Science and Visualization, Linkoeping University, Linkoeping (Sweden); Pattern Recognition Laboratory, Department of Computer Science, Friedrich-Alexander University of Erlangen-Nuremberg, 91054, Erlangen (Germany); Nuclear and Radiological Engineering and Medical Physics Programs, George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Siemens AG Healthcare, Forchheim 91301 (Germany); Department of Radiology, Stanford University, Stanford, California 94305 (United States)

2011-11-15

Purpose: The combination of quickly rotating C-arm gantry with digital flat panel has enabled the acquisition of three-dimensional data (3D) in the interventional suite. However, image quality is still somewhat limited since the hardware has not been optimized for CT imaging. Adaptive anisotropic filtering has the ability to improve image quality by reducing the noise level and therewith the radiation dose without introducing noticeable blurring. By applying the filtering prior to 3D reconstruction, noise-induced streak artifacts are reduced as compared to processing in the image domain. Methods: 3D anisotropic adaptive filtering was used to process an ensemble of 2D x-ray views acquired along a circular trajectory around an object. After arranging the input data into a 3D space (2D projections + angle), the orientation of structures was estimated using a set of differently oriented filters. The resulting tensor representation of local orientation was utilized to control the anisotropic filtering. Low-pass filtering is applied only along structures to maintain high spatial frequency components perpendicular to these. The evaluation of the proposed algorithm includes numerical simulations, phantom experiments, and in-vivo data which were acquired using an AXIOM Artis dTA C-arm system (Siemens AG, Healthcare Sector, Forchheim, Germany). Spatial resolution and noise levels were compared with and without adaptive filtering. A human observer study was carried out to evaluate low-contrast detectability. Results: The adaptive anisotropic filtering algorithm was found to significantly improve low-contrast detectability by reducing the noise level by half (reduction of the standard deviation in certain areas from 74 to 30 HU). Virtually no degradation of high contrast spatial resolution was observed in the modulation transfer function (MTF) analysis. Although the algorithm is computationally intensive, hardware acceleration using Nvidia's CUDA Interface provided an 8

Three-dimensional anisotropic adaptive filtering of projection data for noise reduction in cone beam CT

International Nuclear Information System (INIS)

Maier, Andreas; Wigstroem, Lars; Hofmann, Hannes G.; Hornegger, Joachim; Zhu Lei; Strobel, Norbert; Fahrig, Rebecca

2011-01-01

Purpose: The combination of quickly rotating C-arm gantry with digital flat panel has enabled the acquisition of three-dimensional data (3D) in the interventional suite. However, image quality is still somewhat limited since the hardware has not been optimized for CT imaging. Adaptive anisotropic filtering has the ability to improve image quality by reducing the noise level and therewith the radiation dose without introducing noticeable blurring. By applying the filtering prior to 3D reconstruction, noise-induced streak artifacts are reduced as compared to processing in the image domain. Methods: 3D anisotropic adaptive filtering was used to process an ensemble of 2D x-ray views acquired along a circular trajectory around an object. After arranging the input data into a 3D space (2D projections + angle), the orientation of structures was estimated using a set of differently oriented filters. The resulting tensor representation of local orientation was utilized to control the anisotropic filtering. Low-pass filtering is applied only along structures to maintain high spatial frequency components perpendicular to these. The evaluation of the proposed algorithm includes numerical simulations, phantom experiments, and in-vivo data which were acquired using an AXIOM Artis dTA C-arm system (Siemens AG, Healthcare Sector, Forchheim, Germany). Spatial resolution and noise levels were compared with and without adaptive filtering. A human observer study was carried out to evaluate low-contrast detectability. Results: The adaptive anisotropic filtering algorithm was found to significantly improve low-contrast detectability by reducing the noise level by half (reduction of the standard deviation in certain areas from 74 to 30 HU). Virtually no degradation of high contrast spatial resolution was observed in the modulation transfer function (MTF) analysis. Although the algorithm is computationally intensive, hardware acceleration using Nvidia's CUDA Interface provided an 8.9-fold

Hydrodynamic cavitation in Stokes flow of anisotropic fluids

OpenAIRE

Stieger, Tillmann; Agha, Hakam; Schoen, Martin; Mazza, Marco G.; Sengupta, Anupam

2017-01-01

Cavitation, the nucleation of vapour in liquids, is ubiquitous in fluid dynamics, and is often implicated in a myriad of industrial and biomedical applications. Although extensively studied in isotropic liquids, corresponding investigations in anisotropic liquids are largely lacking. Here, by combining liquid crystal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments, we report flow-induced cavitation in an anisotropic fluid. The cavitation domai...

Transfer by anisotropic scattering between subsets of the unit sphere of directions in linear transport theory

International Nuclear Information System (INIS)

Trombetti, T.

1990-01-01

The exact kernel method is presented for linear transport problems with azimuth-dependent angular fluxes. It is based on the evaluation of average scattering densities (ASD's) that fully describe the neutron (or particle) transfer between subsets of the unit sphere of directions by anisotropic scattering. Reciprocity and other ASD functional properties are proved and combined with the symmetry properties of suitable SN quadrature sets. This greatly reduces the number of independent ASD's to be computed and stored. An approach for performing ASD computations with reciprocity checks is presented. ASD expressions of the scattering source for typical 2D geometries are explicitly given. (author)

General PFG signal attenuation expressions for anisotropic anomalous diffusion by modified-Bloch equations

Science.gov (United States)

Lin, Guoxing

2018-05-01

Anomalous diffusion exists widely in polymer and biological systems. Pulsed-field gradient (PFG) anomalous diffusion is complicated, especially in the anisotropic case where limited research has been reported. A general PFG signal attenuation expression, including the finite gradient pulse (FGPW) effect for free general anisotropic fractional diffusion { 0 integral modified-Bloch equation, were extended to obtain general PFG signal attenuation expressions for anisotropic anomalous diffusion. Various cases of PFG anisotropic anomalous diffusion were investigated, including coupled and uncoupled anisotropic anomalous diffusion. The continuous-time random walk (CTRW) simulation was also carried out to support the theoretical results. The theory and the CTRW simulation agree with each other. The obtained signal attenuation expressions and the three-dimensional fractional modified-Bloch equations are important for analyzing PFG anisotropic anomalous diffusion in NMR and MRI.

Anisotropic elasticity of silicon and its application to the modelling of X-ray optics

International Nuclear Information System (INIS)

Zhang, Lin; Barrett, Raymond; Cloetens, Peter; Detlefs, Carsten; Sanchez del Rio, Manuel

2014-01-01

Anisotropic elasticity of single-crystal silicon, applications to modelling of a bent X-ray mirror, and thermal deformation of a liquid-nitrogen-cooled monochromator crystal are presented. The crystal lattice of single-crystal silicon gives rise to anisotropic elasticity. The stiffness and compliance coefficient matrix depend on crystal orientation and, consequently, Young’s modulus, the shear modulus and Poisson’s ratio as well. Computer codes (in Matlab and Python) have been developed to calculate these anisotropic elasticity parameters for a silicon crystal in any orientation. These codes facilitate the evaluation of these anisotropy effects in silicon for applications such as microelectronics, microelectromechanical systems and X-ray optics. For mechanically bent X-ray optics, it is shown that the silicon crystal orientation is an important factor which may significantly influence the optics design and manufacturing phase. Choosing the appropriate crystal orientation can both lead to improved performance whilst lowering mechanical bending stresses. The thermal deformation of the crystal depends on Poisson’s ratio. For an isotropic constant Poisson’s ratio, ν, the thermal deformation (RMS slope) is proportional to (1 + ν). For a cubic anisotropic material, the thermal deformation of the X-ray optics can be approximately simulated by using the average of ν 12 and ν 13 as an effective isotropic Poisson’s ratio, where the direction 1 is normal to the optic surface, and the directions 2 and 3 are two normal orthogonal directions parallel to the optical surface. This average is independent of the direction in the optical surface (the crystal plane) for Si(100), Si(110) and Si(111). Using the effective isotropic Poisson’s ratio for these orientations leads to an error in thermal deformation smaller than 5.5%

Anisotropic elasticity of silicon and its application to the modelling of X-ray optics

Energy Technology Data Exchange (ETDEWEB)

Zhang, Lin, E-mail: zhang@esrf.fr; Barrett, Raymond; Cloetens, Peter; Detlefs, Carsten; Sanchez del Rio, Manuel [European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP 220, 38043 Grenoble (France)

2014-04-04

Anisotropic elasticity of single-crystal silicon, applications to modelling of a bent X-ray mirror, and thermal deformation of a liquid-nitrogen-cooled monochromator crystal are presented. The crystal lattice of single-crystal silicon gives rise to anisotropic elasticity. The stiffness and compliance coefficient matrix depend on crystal orientation and, consequently, Young’s modulus, the shear modulus and Poisson’s ratio as well. Computer codes (in Matlab and Python) have been developed to calculate these anisotropic elasticity parameters for a silicon crystal in any orientation. These codes facilitate the evaluation of these anisotropy effects in silicon for applications such as microelectronics, microelectromechanical systems and X-ray optics. For mechanically bent X-ray optics, it is shown that the silicon crystal orientation is an important factor which may significantly influence the optics design and manufacturing phase. Choosing the appropriate crystal orientation can both lead to improved performance whilst lowering mechanical bending stresses. The thermal deformation of the crystal depends on Poisson’s ratio. For an isotropic constant Poisson’s ratio, ν, the thermal deformation (RMS slope) is proportional to (1 + ν). For a cubic anisotropic material, the thermal deformation of the X-ray optics can be approximately simulated by using the average of ν{sub 12} and ν{sub 13} as an effective isotropic Poisson’s ratio, where the direction 1 is normal to the optic surface, and the directions 2 and 3 are two normal orthogonal directions parallel to the optical surface. This average is independent of the direction in the optical surface (the crystal plane) for Si(100), Si(110) and Si(111). Using the effective isotropic Poisson’s ratio for these orientations leads to an error in thermal deformation smaller than 5.5%.

New methodology for mechanical characterization of human superficial facial tissue anisotropic behaviour in vivo.

Science.gov (United States)

Then, C; Stassen, B; Depta, K; Silber, G

2017-07-01

Mechanical characterization of human superficial facial tissue has important applications in biomedical science, computer assisted forensics, graphics, and consumer goods development. Specifically, the latter may include facial hair removal devices. Predictive accuracy of numerical models and their ability to elucidate biomechanically relevant questions depends on the acquisition of experimental data and mechanical tissue behavior representation. Anisotropic viscoelastic behavioral characterization of human facial tissue, deformed in vivo with finite strain, however, is sparse. Employing an experimental-numerical approach, a procedure is presented to evaluate multidirectional tensile properties of superficial tissue layers of the face in vivo. Specifically, in addition to stress relaxation, displacement-controlled multi-step ramp-and-hold protocols were performed to separate elastic from inelastic properties. For numerical representation, an anisotropic hyperelastic material model in conjunction with a time domain linear viscoelasticity formulation with Prony series was employed. Model parameters were inversely derived, employing finite element models, using multi-criteria optimization. The methodology provides insight into mechanical superficial facial tissue properties. Experimental data shows pronounced anisotropy, especially with large strain. The stress relaxation rate does not depend on the loading direction, but is strain-dependent. Preconditioning eliminates equilibrium hysteresis effects and leads to stress-strain repeatability. In the preconditioned state tissue stiffness and hysteresis insensitivity to strain rate in the applied range is evident. The employed material model fits the nonlinear anisotropic elastic results and the viscoelasticity model reasonably reproduces time-dependent results. Inversely deduced maximum anisotropic long-term shear modulus of linear elasticity is G ∞,max aniso =2.43kPa and instantaneous initial shear modulus at an

Anisotropic surface chemistry properties and adsorption behavior of silicate mineral crystals.

Science.gov (United States)

Xu, Longhua; Tian, Jia; Wu, Houqin; Fang, Shuai; Lu, Zhongyuan; Ma, Caifeng; Sun, Wei; Hu, Yuehua

2018-03-07

Anisotropic surface properties of minerals play an important role in a variety of fields. With a focus on the two most intensively investigated silicate minerals (i.e., phyllosilicate minerals and pegmatite aluminosilicate minerals), this review highlights the research on their anisotropic surface properties based on their crystal structures. Four surface features comprise the anisotropic surface chemistry of minerals: broken bonds, energy, wettability, and charge. Analysis of surface broken bond and energy anisotropy helps to explain the cleavage and growth properties of mineral crystals, and understanding surface wettability and charge anisotropy is critical to the analysis of minerals' solution behavior, such as their flotation performance and rheological properties. In a specific reaction, the anisotropic surface properties of minerals are reflected in the adsorption strengths of reagents on different mineral surfaces. Combined with the knowledge of mineral crushing and grinding, a thorough understanding of the anisotropic surface chemistry properties and the anisotropic adsorption behavior of minerals will lead to the development of effective relational models comprising their crystal structure, surface chemistry properties, and targeted reagent adsorption. Overall, such a comprehensive approach is expected to firmly establish the connection between selective cleavage of mineral crystals for desired surfaces and designing novel reagents selectively adsorbed on the mineral surfaces. As tools to characterize the anisotropic surface chemistry properties of minerals, DLVO theory, atomic force microscopy (AFM), and molecular dynamics (MD) simulations are also reviewed. Copyright © 2017 Elsevier B.V. All rights reserved.

Acoustic anisotropic wavefields through perturbation theory

KAUST Repository

Alkhalifah, Tariq Ali

2013-09-01

Solving the anisotropic acoustic wave equation numerically using finite-difference methods introduces many problems and media restriction requirements, and it rarely contributes to the ability to resolve the anisotropy parameters. Among these restrictions are the inability to handle media with η<0 and the presence of shear-wave artifacts in the solution. Both limitations do not exist in the solution of the elliptical anisotropic acoustic wave equation. Using perturbation theory in developing the solution of the anisotropic acoustic wave equation allows direct access to the desired limitation-free solutions, that is, solutions perturbed from the elliptical anisotropic background medium. It also provides a platform for parameter estimation because of the ability to isolate the wavefield dependency on the perturbed anisotropy parameters. As a result, I derive partial differential equations that relate changes in the wavefield to perturbations in the anisotropy parameters. The solutions of the perturbation equations represented the coefficients of a Taylor-series-type expansion of the wavefield as a function of the perturbed parameter, which is in this case η or the tilt of the symmetry axis. The expansion with respect to the symmetry axis allows use of an acoustic transversely isotropic media with a vertical symmetry axis (VTI) kernel to estimate the background wavefield and the corresponding perturbation coefficients. The VTI extrapolation kernel is about one-fourth the cost of the transversely isotropic model with a tilt in the symmetry axis kernel. Thus, for a small symmetry axis tilt, the cost of migration using a first-order expansion can be reduced. The effectiveness of the approach was demonstrated on the Marmousi model.

Bryan's effect and anisotropic nonlinear damping

Science.gov (United States)

Joubert, Stephan V.; Shatalov, Michael Y.; Fay, Temple H.; Manzhirov, Alexander V.

2018-03-01

In 1890, G. H. Bryan discovered the following: "The vibration pattern of a revolving cylinder or bell revolves at a rate proportional to the inertial rotation rate of the cylinder or bell." We call this phenomenon Bryan's law or Bryan's effect. It is well known that any imperfections in a vibratory gyroscope (VG) affect Bryan's law and this affects the accuracy of the VG. Consequently, in this paper, we assume that all such imperfections are either minimised or eliminated by some known control method and that only damping is present within the VG. If the damping is isotropic (linear or nonlinear), then it has been recently demonstrated in this journal, using symbolic analysis, that Bryan's law remains invariant. However, it is known that linear anisotropic damping does affect Bryan's law. In this paper, we generalise Rayleigh's dissipation function so that anisotropic nonlinear damping may be introduced into the equations of motion. Using a mixture of numeric and symbolic analysis on the ODEs of motion of the VG, for anisotropic light nonlinear damping, we demonstrate (up to an approximate average), that Bryan's law is affected by any form of such damping, causing pattern drift, compromising the accuracy of the VG.

Anisotropic hydrodynamics for conformal Gubser flow

Energy Technology Data Exchange (ETDEWEB)

Strickland, Michael; Nopoush, Mohammad [Kent State University, Kent OH 44242 (United States); Ryblewski, Radoslaw [The H. Niewodniczański Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków (Poland)

2016-12-15

In this proceedings contribution, we review the exact solution of the anisotropic hydrodynamics equations for a system subject to Gubser flow. For this purpose, we use the leading-order anisotropic hydrodynamics equations which assume that the distribution function is ellipsoidally symmetric in local-rest-frame momentum. We then prove that the SO(3){sub q} symmetry in de Sitter space constrains the anisotropy tensor to be of spheroidal form with only one independent anisotropy parameter remaining. As a consequence, the exact solution reduces to the problem of solving two coupled non-linear differential equations. We show that, in the limit that the relaxation time goes to zero, one obtains Gubser's ideal hydrodynamic solution and, in the limit that the relaxation time goes to infinity, one obtains the exact free streaming solution obtained originally by Denicol et al. For finite relaxation time, we solve the equations numerically and compare to the exact solution of the relaxation-time-approximation Boltzmann equation subject to Gubser flow. Using this as our standard, we find that anisotropic hydrodynamics describes the spatio-temporal evolution of the system better than all currently known dissipative hydrodynamics approaches.

Anisotropic hydrodynamics for conformal Gubser flow

International Nuclear Information System (INIS)

Strickland, Michael; Nopoush, Mohammad; Ryblewski, Radoslaw

2016-01-01

In this proceedings contribution, we review the exact solution of the anisotropic hydrodynamics equations for a system subject to Gubser flow. For this purpose, we use the leading-order anisotropic hydrodynamics equations which assume that the distribution function is ellipsoidally symmetric in local-rest-frame momentum. We then prove that the SO(3)_q symmetry in de Sitter space constrains the anisotropy tensor to be of spheroidal form with only one independent anisotropy parameter remaining. As a consequence, the exact solution reduces to the problem of solving two coupled non-linear differential equations. We show that, in the limit that the relaxation time goes to zero, one obtains Gubser's ideal hydrodynamic solution and, in the limit that the relaxation time goes to infinity, one obtains the exact free streaming solution obtained originally by Denicol et al. For finite relaxation time, we solve the equations numerically and compare to the exact solution of the relaxation-time-approximation Boltzmann equation subject to Gubser flow. Using this as our standard, we find that anisotropic hydrodynamics describes the spatio-temporal evolution of the system better than all currently known dissipative hydrodynamics approaches.

CASTp 3.0: computed atlas of surface topography of proteins.

Science.gov (United States)

Tian, Wei; Chen, Chang; Lei, Xue; Zhao, Jieling; Liang, Jie

2018-06-01

Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.

Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

Science.gov (United States)

2015-01-01

Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

Textile-templated electrospun anisotropic scaffolds for regenerative cardiac tissue engineering.

Science.gov (United States)

Şenel Ayaz, H Gözde; Perets, Anat; Ayaz, Hasan; Gilroy, Kyle D; Govindaraj, Muthu; Brookstein, David; Lelkes, Peter I

2014-10-01

For patients with end-stage heart disease, the access to heart transplantation is limited due to the shortage of donor organs and to the potential for rejection of the donated organ. Therefore, current studies focus on bioengineering approaches for creating biomimetic cardiac patches that will assist in restoring cardiac function, by repairing and/or regenerating the intrinsically anisotropic myocardium. In this paper we present a simplified, straightforward approach for creating bioactive anisotropic cardiac patches, based on a combination of bioengineering and textile-manufacturing techniques in concert with nano-biotechnology based tissue-engineering stratagems. Using knitted conventional textiles, made of cotton or polyester yarns as template targets, we successfully electrospun anisotropic three-dimensional scaffolds from poly(lactic-co-glycolic) acid (PLGA), and thermoplastic polycarbonate-urethane (PCU, Bionate(®)). The surface topography and mechanical properties of textile-templated anisotropic scaffolds significantly differed from those of scaffolds electrospun from the same materials onto conventional 2-D flat-target electrospun scaffolds. Anisotropic textile-templated scaffolds electrospun from both PLGA and PCU, supported the adhesion and proliferation of H9C2 cardiac myoblasts cell line, and guided the cardiac tissue-like anisotropic organization of these cells in vitro. All cell-seeded PCU scaffolds exhibited mechanical properties comparable to those of a human heart, but only the cells on the polyester-templated scaffolds exhibited prolonged spontaneous synchronous contractility on the entire engineered construct for 10 days in vitro at a near physiologic frequency of ∼120 bpm. Taken together, the methods described here take advantage of straightforward established textile manufacturing strategies as an efficient and cost-effective approach to engineering 3D anisotropic, elastomeric PCU scaffolds that can serve as a cardiac patch. Copyright �

Polarized Raman anisotropic response of collagen in tendon: towards 3D orientation mapping of collagen in tissues.

Directory of Open Access Journals (Sweden)

Leonardo Galvis

Full Text Available In this study, polarized Raman spectroscopy (PRS was used to characterize the anisotropic response of the amide I band of collagen as a basis for evaluating three-dimensional collagen fibril orientation in tissues. Firstly, the response was investigated theoretically by applying classical Raman theory to collagen-like peptide crystal structures. The theoretical methodology was then tested experimentally, by measuring amide I intensity anisotropy in rat tail as a function of the orientation of the incident laser polarization. For the theoretical study, several collagen-like triple-helical peptide crystal structures obtained from the Protein Data Bank were rotated "in plane" and "out of plane" to evaluate the role of molecular orientation on the intensity of the amide I band. Collagen-like peptides exhibit a sinusoidal anisotropic response when rotated "in plane" with respect to the polarized incident laser. Maximal intensity was obtained when the polarization of the incident light is perpendicular to the molecule and minimal when parallel. In the case of "out of plane" rotation of the molecular structure a decreased anisotropic response was observed, becoming completely isotropic when the structure was perpendicular to the plane of observation. The theoretical Raman response of collagen was compared to that of alpha helical protein fragments. In contrast to collagen, alpha helices have a maximal signal when incident light is parallel to the molecule and minimal when perpendicular. For out-of-plane molecular orientations alpha-helix structures display a decreased average intensity. Results obtained from experiments on rat tail tendon are in excellent agreement with the theoretical predictions, thus demonstrating the high potential of PRS for experimental evaluation of the three-dimensional orientation of collagen fibers in biological tissues.

The anisotropic network model web server at 2015 (ANM 2.0).

Science.gov (United States)

Eyal, Eran; Lum, Gengkon; Bahar, Ivet

2015-05-01

The anisotropic network model (ANM) is one of the simplest yet powerful tools for exploring protein dynamics. Its main utility is to predict and visualize the collective motions of large complexes and assemblies near their equilibrium structures. The ANM server, introduced by us in 2006 helped making this tool more accessible to non-sophisticated users. We now provide a new version (ANM 2.0), which allows inclusion of nucleic acids and ligands in the network model and thus enables the investigation of the collective motions of protein-DNA/RNA and -ligand systems. The new version offers the flexibility of defining the system nodes and the interaction types and cutoffs. It also includes extensive improvements in hardware, software and graphical interfaces. ANM 2.0 is available at http://anm.csb.pitt.edu eran.eyal@sheba.health.gov.il, eyal.eran@gmail.com. © The Author 2015. Published by Oxford University Press.

Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding.

Science.gov (United States)

Montalvo-Acosta, Joel José; Cecchini, Marco

2016-12-01

The physiological role played by protein-ligand recognition has motivated the development of several computational approaches to the ligand binding affinity. Some of them, termed rigorous, have a strong theoretical foundation but involve too much computation to be generally useful. Some others alleviate the computational burden by introducing strong approximations and/or empirical calibrations, which also limit their general use. Most importantly, there is no straightforward correlation between the predictive power and the level of approximation introduced. Here, we present a general framework for the quantitative interpretation of protein-ligand binding based on statistical mechanics. Within this framework, we re-derive self-consistently the fundamental equations of some popular approaches to the binding constant and pinpoint the inherent approximations. Our analysis represents a first step towards the development of variants with optimum accuracy/efficiency ratio for each stage of the drug discovery pipeline. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Anisotropic, Mixed-Norm Lizorkin-Triebel Spaces and Diffeomorphic Maps

DEFF Research Database (Denmark)

Johnsen, Jon; Hansen, Sabrina Munch; Sickel, Winfried

2014-01-01

This paper gives general results on invariance of anisotropic Lizorkin-Triebel spaces with mixed norms under coordinate transformations on Euclidean space, open sets, and cylindrical domains.......This paper gives general results on invariance of anisotropic Lizorkin-Triebel spaces with mixed norms under coordinate transformations on Euclidean space, open sets, and cylindrical domains....

Anisotropically Swelling Gels Attained through Axis-Dependent Crosslinking of MOF Crystals.

Science.gov (United States)

Ishiwata, Takumi; Kokado, Kenta; Sada, Kazuki

2017-03-01

Anisotropically deforming objects have attracted considerable interest for use in molecular machines and artificial muscles. Herein, we focus on a new approach based on the crystal crosslinking of organic ligands in a pillared-layer metal-organic framework (PLMOF). The approach involves the transformation from crosslinked PLMOF to polymer gels through hydrolysis of the coordination bonds between the organic ligands and metal ions, giving a network polymer that exhibits anisotropic swelling. The anisotropic monomer arrangement in the PLMOF underwent axis-dependent crosslinking to yield anisotropically swelling gels. Therefore, the crystal crosslinking of MOFs should be a useful method for creating actuators with designable deformation properties. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The anisotropic Ising correlations as elliptic integrals: duality and differential equations

International Nuclear Information System (INIS)

McCoy, B M; Maillard, J-M

2016-01-01

We present the reduction of the correlation functions of the Ising model on the anisotropic square lattice to complete elliptic integrals of the first, second and third kind, the extension of Kramers–Wannier duality to anisotropic correlation functions, and the linear differential equations for these anisotropic correlations. More precisely, we show that the anisotropic correlation functions are homogeneous polynomials of the complete elliptic integrals of the first, second and third kind. We give the exact dual transformation matching the correlation functions and the dual correlation functions. We show that the linear differential operators annihilating the general two-point correlation functions are factorized in a very simple way, in operators of decreasing orders. (paper)

Hybrid localized waves supported by resonant anisotropic metasurfaces

DEFF Research Database (Denmark)

Bogdanov, A. A.; Yermakov, O. Y.; Ovcharenko, A. I.

2016-01-01

We study both theoretically and experimentally a new class of surface electromagnetic waves supported by resonant anisotropic metasurface. At certain frequency this type of metasurface demonstrates the topological transition from elliptical to hyperbolic regime.......We study both theoretically and experimentally a new class of surface electromagnetic waves supported by resonant anisotropic metasurface. At certain frequency this type of metasurface demonstrates the topological transition from elliptical to hyperbolic regime....

Proteins of unknown function in the Protein Data Bank (PDB): an inventory of true uncharacterized proteins and computational tools for their analysis.

Science.gov (United States)

Nadzirin, Nurul; Firdaus-Raih, Mohd

2012-10-08

Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB). Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files) that were categorized under "unknown function" are true examples of proteins of unknown function at this point in time. The remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, based on the availability of direct functional characterization experiments for the protein itself, or for homologous sequences or structures thus enabling computational function inference.

Proteins of Unknown Function in the Protein Data Bank (PDB: An Inventory of True Uncharacterized Proteins and Computational Tools for Their Analysis

Directory of Open Access Journals (Sweden)

Nurul Nadzirin

2012-10-01

Full Text Available Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB. Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files that were categorized under “unknown function” are true examples of proteins of unknown function at this point in time. The remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, based on the availability of direct functional characterization experiments for the protein itself, or for homologous sequences or structures thus enabling computational function inference.

Computer-simulation study of a disordered classical spin system in one dimension with long-range anisotropic ferromagnetic interactions

Science.gov (United States)

Romano, S.

1992-01-01

The present paper considers a classical system, consisting of n-component unit vectors (n=2 or 3), associated with a one-dimensional lattice \\{uk||k∈openZ\\}, and interacting via a translationally invariant pair potential of the long-range, ferromagnetic and anisotropic form W=Wjk=-ɛ||j-k||-2(auj,nuk,n +b tsumλuk,λ denotes the Cartesian components of the unit vectors. According to the available rigorous results, the system disorders at all finite temperatures when a=b, or n=3, a=0, and possesses an ordering transition at finite temperature when b=0. Approximate arguments and simulation results suggest that the isotropic models (a=b) produce a transition to a low-temperature phase with infinite susceptibility and power-law decay of the correlation function. If this is true, the available correlation inequalities entail that it also happens in the anisotropic but O(2)-invariant case n=3, b=0. We report here Monte Carlo calculations for this latter potential model; simulation results were found to be consistent with this conjecture, and to suggest that T*c=0.65+/-0.01.

A new model for spherically symmetric anisotropic compact star

Energy Technology Data Exchange (ETDEWEB)

Maurya, S.K.; Dayanandan, Baiju [University of Nizwa, Department of Mathematical and Physical Sciences, College of Arts and Science, Nizwa (Oman); Gupta, Y.K. [Raj Kumar Goel Institute of Technology, Department of Mathematics, Ghaziabad, UP (India); Ray, Saibal [Government College of Engineering and Ceramic Technology, Department of Physics, Kolkata, West Bengal (India)

2016-05-15

In this article we obtain a new anisotropic solution for Einstein's field equations of embedding class one metric. The solution represents realistic objects such as Her X-1 and RXJ 1856-37. We perform a detailed investigation of both objects by solving numerically the Einstein field equations with anisotropic pressure. The physical features of the parameters depend on the anisotropic factor i.e. if the anisotropy is zero everywhere inside the star then the density and pressures will become zero and the metric turns out to be flat. We report our results and compare with the above mentioned two compact objects as regards a number of key aspects: the central density, the surface density onset and the critical scaling behaviour, the effective mass and radius ratio, the anisotropization with isotropic initial conditions, adiabatic index and red shift. Along with this we have also made a comparison between the classical limit and theoretical model treatment of the compact objects. Finally we discuss the implications of our findings for the stability condition in a relativistic compact star. (orig.)

Prestack exploding reflector modelling and migration for anisotropic media

KAUST Repository

Alkhalifah, Tariq Ali

2014-10-09

The double-square-root equation is commonly used to image data by downward continuation using one-way depth extrapolation methods. A two-way time extrapolation of the double-square-root-derived phase operator allows for up and downgoing wavefields but suffers from an essential singularity for horizontally travelling waves. This singularity is also associated with an anisotropic version of the double-square-root extrapolator. Perturbation theory allows us to separate the isotropic contribution, as well as the singularity, from the anisotropic contribution to the operator. As a result, the anisotropic residual operator is free from such singularities and can be applied as a stand alone operator to correct for anisotropy. We can apply the residual anisotropy operator even if the original prestack wavefield was obtained using, for example, reverse-time migration. The residual correction is also useful for anisotropic parameter estimation. Applications to synthetic data demonstrate the accuracy of the new prestack modelling and migration approach. It also proves useful in approximately imaging the Vertical Transverse Isotropic Marmousi model.

Dynamical anisotropic response of black phosphorus under magnetic field

Science.gov (United States)

Liu, Xuefeng; Lu, Wei; Zhou, Xiaoying; Zhou, Yang; Zhang, Chenglong; Lai, Jiawei; Ge, Shaofeng; Sekhar, M. Chandra; Jia, Shuang; Chang, Kai; Sun, Dong

2018-04-01

Black phosphorus (BP) has emerged as a promising material candidate for next generation electronic and optoelectronic devices due to its high mobility, tunable band gap and highly anisotropic properties. In this work, polarization resolved ultrafast mid-infrared transient reflection spectroscopy measurements are performed to study the dynamical anisotropic optical properties of BP under magnetic fields up to 9 T. The relaxation dynamics of photoexcited carrier is found to be insensitive to the applied magnetic field due to the broadening of the Landau levels and large effective mass of carriers. While the anisotropic optical response of BP decreases with increasing magnetic field, its enhancement due to the excitation of hot carriers is similar to that without magnetic field. These experimental results can be well interpreted by the magneto-optical conductivity of the Landau levels of BP thin film, based on an effective k · p Hamiltonian and linear response theory. These findings suggest attractive possibilities of multi-dimensional control of anisotropic response (AR) of BP with light, electric and magnetic field, which further introduces BP to the fantastic magnetic field sensitive applications.

Computational design of protein interactions: designing proteins that neutralize influenza by inhibiting its hemagglutinin surface protein

Science.gov (United States)

Fleishman, Sarel

2012-02-01

Molecular recognition underlies all life processes. Design of interactions not seen in nature is a test of our understanding of molecular recognition and could unlock the vast potential of subtle control over molecular interaction networks, allowing the design of novel diagnostics and therapeutics for basic and applied research. We developed the first general method for designing protein interactions. The method starts by computing a region of high affinity interactions between dismembered amino acid residues and the target surface and then identifying proteins that can harbor these residues. Designs are tested experimentally for binding the target surface and successful ones are affinity matured using yeast cell surface display. Applied to the conserved stem region of influenza hemagglutinin we designed two unrelated proteins that, following affinity maturation, bound hemagglutinin at subnanomolar dissociation constants. Co-crystal structures of hemagglutinin bound to the two designed binders were within 1Angstrom RMSd of their models, validating the accuracy of the design strategy. One of the designed proteins inhibits the conformational changes that underlie hemagglutinin's cell-invasion functions and blocks virus infectivity in cell culture, suggesting that such proteins may in future serve as diagnostics and antivirals against a wide range of pathogenic influenza strains. We have used this method to obtain experimentally validated binders of several other target proteins, demonstrating the generality of the approach. We discuss the combination of modeling and high-throughput characterization of design variants which has been key to the success of this approach, as well as how we have used the data obtained in this project to enhance our understanding of molecular recognition. References: Science 332:816 JMB, in press Protein Sci 20:753

Anisotropic light scattering of individual sickle red blood cells.

Science.gov (United States)

Kim, Youngchan; Higgins, John M; Dasari, Ramachandra R; Suresh, Subra; Park, YongKeun

2012-04-01

We present the anisotropic light scattering of individual red blood cells (RBCs) from a patient with sickle cell disease (SCD). To measure light scattering spectra along two independent axes of elongated-shaped sickle RBCs with arbitrary orientation, we introduce the anisotropic Fourier transform light scattering (aFTLS) technique and measured both the static and dynamic anisotropic light scattering. We observed strong anisotropy in light scattering patterns of elongated-shaped sickle RBCs along its major axes using static aFTLS. Dynamic aFTLS analysis reveals the significantly altered biophysical properties in individual sickle RBCs. These results provide evidence that effective viscosity and elasticity of sickle RBCs are significantly different from those of the healthy RBCs.

Modeling of charged anisotropic compact stars in general relativity

Energy Technology Data Exchange (ETDEWEB)

Dayanandan, Baiju; Maurya, S.K.; T, Smitha T. [University of Nizwa, Department of Mathematical and Physical Sciences, College of Arts and Science, Nizwa (Oman)

2017-06-15

A charged compact star model has been determined for anisotropic fluid distribution. We have solved the Einstein-Maxwell field equations to construct the charged compact star model by using the radial pressure, the metric function e{sup λ} and the electric charge function. The generic charged anisotropic solution is verified by exploring different physical conditions like causality condition, mass-radius relation and stability of the solution (via the adiabatic index, TOV equations and the Herrera cracking concept). It is observed that the present charged anisotropic compact star model is compatible with the star PSR 1937+21. Moreover, we also presented the EOS ρ = f(p) for the present charged compact star model. (orig.)

Anisotropic mechanical properties and Stone-Wales defects in graphene monolayer: A theoretical study

International Nuclear Information System (INIS)

Fan, B.B.; Yang, X.B.; Zhang, R.

2010-01-01

We investigate the mechanical properties of graphene monolayer via the density functional theoretical (DFT) method. We find that the strain energies are anisotropic for the graphene under large strain. We attribute the anisotropic feature to the anisotropic sp 2 hybridization in the hexagonal lattice. We further identify that the formation energies of Stone-Wales (SW) defects in the graphene monolayer are determined by the defect concentration and also the direction of applied tensile strain, correlating with the anisotropic feature.

Q-P Wave traveltime computation by an iterative approach

KAUST Repository

Ma, Xuxin; Alkhalifah, Tariq Ali

2013-01-01

In this work, we present a new approach to compute anisotropic traveltime based on solving successively elliptical isotropic traveltimes. The method shows good accuracy and is very simple to implement.

An anisotropic elasto-viscoplastic model for short-fiber reinforced polymers

NARCIS (Netherlands)

Amiri Rad, A.; Govaert, L.E.; van Dommelen, J.A.W.

2017-01-01

The influence of flow on the fiber orientation in injection molding of short-fiber composites leads to both anisotropy and inhomogeneity of the mechanical response. An anisotropic elasto-viscoplastic constitutive model is developed to capture the anisotropic and time-dependent behavior and

An Anisotropic Elasto-Viscoplastic Model for Short-Fiber Reinforced Polymers

NARCIS (Netherlands)

Amiri Rad, A.; Govaert, L.E.; van Dommelen, J.A.W.

2018-01-01

The influence of flow on the fiber orientation in injection molding of short-fiber composites leads to both anisotropy and inhomogeneity of the mechanical response. An anisotropic elasto-viscoplastic constitutive model is developed to capture the anisotropic and time-dependent behavior and

Bianchi-type II spacetime and anisotropic brane-world cosmology

International Nuclear Information System (INIS)

Sevinc, O.

2010-01-01

Anisotropic generalization of Randall and Sundrum brane-world model is considered. I studied a bulk with an anisotropic space of motion of the brane, depending on both time and extra coordinate. Then I discussed possibility of obtaining the fine-tuning condition of Randall and Sundrum following the method of Andrei V. Frolov (Phys. Lett. B, 514,213).

Remarks on the relativistic magnetohydrodynamics of an anisotropic fluid

International Nuclear Information System (INIS)

Ignat, M.

1980-01-01

Considering a pressure tensor of a general form, a relativistic rarefied, anisotropic, infinite electrically conducting and nondissipative plasma is studied. For this purpose, the method of the orthonormal frame of reference is used. The choice of the frame of reference is made adequately to the problem. Some thermodynamical properties of such a relativistic, anisotropic plasma are also given. (author)

VASCo: computation and visualization of annotated protein surface contacts

Directory of Open Access Journals (Sweden)

Thallinger Gerhard G

2009-01-01

Full Text Available Abstract Background Structural data from crystallographic analyses contain a vast amount of information on protein-protein contacts. Knowledge on protein-protein interactions is essential for understanding many processes in living cells. The methods to investigate these interactions range from genetics to biophysics, crystallography, bioinformatics and computer modeling. Also crystal contact information can be useful to understand biologically relevant protein oligomerisation as they rely in principle on the same physico-chemical interaction forces. Visualization of crystal and biological contact data including different surface properties can help to analyse protein-protein interactions. Results VASCo is a program package for the calculation of protein surface properties and the visualization of annotated surfaces. Special emphasis is laid on protein-protein interactions, which are calculated based on surface point distances. The same approach is used to compare surfaces of two aligned molecules. Molecular properties such as electrostatic potential or hydrophobicity are mapped onto these surface points. Molecular surfaces and the corresponding properties are calculated using well established programs integrated into the package, as well as using custom developed programs. The modular package can easily be extended to include new properties for annotation. The output of the program is most conveniently displayed in PyMOL using a custom-made plug-in. Conclusion VASCo supplements other available protein contact visualisation tools and provides additional information on biological interactions as well as on crystal contacts. The tool provides a unique feature to compare surfaces of two aligned molecules based on point distances and thereby facilitates the visualization and analysis of surface differences.

Anisotropic wetting characteristics versus roughness on machined surfaces of hydrophilic and hydrophobic materials

International Nuclear Information System (INIS)

Liang, Yande; Shu, Liming; Natsu, Wataru; He, Fuben

2015-01-01

Graphical abstract: - Highlights: • The aim is to investigate the influence of roughness on anisotropic wetting on machined surfaces. • The relationship between roughness and anisotropic wetting is modeled by thermodynamical analysis. • The effect of roughness on anisotropic wetting on hydrophilic materials is stronger than that on hydrophobic materials. • The energy barrier existing in the direction perpendicular to the lay is one of the main reasons for the anisotropic wetting. • The contact angle in the parallel direction is larger than that in the perpendicular direction. - Abstract: Anisotropic wetting of machined surfaces is widely applied in industries which can be greatly affected by roughness and solid's chemical properties. However, there has not been much work on it. A free-energy thermodynamic model is presented by analyzing geometry morphology of machined surfaces (2-D model surfaces), which demonstrates the influence of roughness on anisotropic wetting. It can be concluded that the energy barrier is one of the main reasons for the anisotropic wetting existing in the direction perpendicular to the lay. In addition, experiments in investigating anisotropic wetting, which was characterized by the static contact angle and droplet's distortion, were performed on machined surfaces with different roughness on hydrophilic and hydrophobic materials. The droplet's anisotropy found on machined surfaces increased with mean slope of roughness profile Kr. It indicates that roughness on anisotropic wetting on hydrophilic materials has a stronger effect than that on hydrophobic materials. Furthermore, the contact angles predicted by the model are basically consistent with the experimentally ones

Anisotropic plasma with flows in tokamak: Steady state and stability

International Nuclear Information System (INIS)

Ilgisonis, V.I.

1996-01-01

An adequate description of equilibrium and stability of anisotropic plasma with macroscopic flows in tokamaks is presented. The Chew-Goldberger-Low (CGL) approximation is consistently used to analyze anisotropic plasma dynamics. The admissible structure of a stationary flow is found to be the same as in the ideal magnetohydrodynamics with isotropic pressure (MHD), which means an allowance for the same relabeling symmetry as in ideal MHD systems with toroidally nested magnetic surfaces. A generalization of the Grad-Shafranov equation for the case of anisotropic plasma with flows confined in the axisymmetric magnetic field is derived. A variational principle was obtained, which allows for a stability analysis of anisotropic pressure plasma with flows, and takes into account the conservation laws resulting from the relabeling symmetry. This principle covers the previous stability criteria for static CGL plasma and for ideal MHD flows in isotropic plasma as well. copyright 1996 American Institute of Physics

Anisotropic Ripple Deformation in Phosphorene.

Science.gov (United States)

Kou, Liangzhi; Ma, Yandong; Smith, Sean C; Chen, Changfeng

2015-05-07

Two-dimensional materials tend to become crumpled according to the Mermin-Wagner theorem, and the resulting ripple deformation may significantly influence electronic properties as observed in graphene and MoS2. Here, we unveil by first-principles calculations a new, highly anisotropic ripple pattern in phosphorene, a monolayer black phosphorus, where compression-induced ripple deformation occurs only along the zigzag direction in the strain range up to 10%, but not the armchair direction. This direction-selective ripple deformation mode in phosphorene stems from its puckered structure with coupled hinge-like bonding configurations and the resulting anisotropic Poisson ratio. We also construct an analytical model using classical elasticity theory for ripple deformation in phosphorene under arbitrary strain. The present results offer new insights into the mechanisms governing the structural and electronic properties of phosphorene crucial to its device applications.

On cracking of charged anisotropic polytropes

Energy Technology Data Exchange (ETDEWEB)

Azam, M. [Division of Science and Technology, University of Education, Township Campus, Lahore-54590 (Pakistan); Mardan, S.A., E-mail: azam.math@ue.edu.pk, E-mail: syedalimardanazmi@yahoo.com [Department of Mathematics, University of the Management and Technology, C-II, Johar Town, Lahore-54590 (Pakistan)

2017-01-01

Recently in [1], the role of electromagnetic field on the cracking of spherical polytropes has been investigated without perturbing charge parameter explicitly. In this study, we have examined the occurrence of cracking of anisotropic spherical polytropes through perturbing parameters like anisotropic pressure, energy density and charge. We consider two different types of polytropes in this study. We discuss the occurrence of cracking in two different ways ( i ) by perturbing polytropic constant, anisotropy and charge parameter ( ii ) by perturbing polytropic index, anisotropy and charge parameter for each case. We conclude that cracking appears for a wide range of parameters in both cases. Also, our results are reduced to [2] in the absence of charge.

Black Holes with Anisotropic Fluid in Lyra Scalar-Tensor Theory

Directory of Open Access Journals (Sweden)

Melis ULU DOĞRU

2018-02-01

Full Text Available In this paper, we investigate distribution of anisotropic fluid which is a resource of black holes in regard to Lyra scalar-tensor theory. As part of the theory, we obtain field equations of spherically symmetric space-time with anisotropic fluid. By using field equations, we suggest distribution of anisotropic fluid, responsible for space-time geometries such as Schwarzschild, Reissner-Nordström, Minkowski type, de Sitter type, Anti-de Sitter type, BTZ and charged BTZ black holes. Finally, we discuss obtained pressures and density of the fluid for different values of arbitrary constants, geometrically and physically.

Veselago focusing of anisotropic massless Dirac fermions

Science.gov (United States)

Zhang, Shu-Hui; Yang, Wen; Peeters, F. M.

2018-05-01

Massless Dirac fermions (MDFs) emerge as quasiparticles in various novel materials such as graphene and topological insulators, and they exhibit several intriguing properties, of which Veselago focusing is an outstanding example with a lot of possible applications. However, up to now Veselago focusing merely occurred in p-n junction devices based on the isotropic MDF, which lacks the tunability needed for realistic applications. Here, motivated by the emergence of novel Dirac materials, we investigate the propagation behaviors of anisotropic MDFs in such a p-n junction structure. By projecting the Hamiltonian of the anisotropic MDF to that of the isotropic MDF and deriving an exact analytical expression for the propagator, precise Veselago focusing is demonstrated without the need for mirror symmetry of the electron source and its focusing image. We show a tunable focusing position that can be used in a device to probe masked atom-scale defects. This study provides an innovative concept to realize Veselago focusing relevant for potential applications, and it paves the way for the design of novel electron optics devices by exploiting the anisotropic MDF.

An accurate anisotropic adaptation method for solving the level set advection equation

International Nuclear Information System (INIS)

Bui, C.; Dapogny, C.; Frey, P.

2012-01-01

In the present paper, a mesh adaptation process for solving the advection equation on a fully unstructured computational mesh is introduced, with a particular interest in the case it implicitly describes an evolving surface. This process mainly relies on a numerical scheme based on the method of characteristics. However, low order, this scheme lends itself to a thorough analysis on the theoretical side. It gives rise to an anisotropic error estimate which enjoys a very natural interpretation in terms of the Hausdorff distance between the exact and approximated surfaces. The computational mesh is then adapted according to the metric supplied by this estimate. The whole process enjoys a good accuracy as far as the interface resolution is concerned. Some numerical features are discussed and several classical examples are presented and commented in two or three dimensions. (authors)

Cloud4Psi: cloud computing for 3D protein structure similarity searching.

Science.gov (United States)

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

2014-10-01

Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. © The Author 2014. Published by Oxford University Press.

Anomalously large anisotropic magnetoresistance in a perovskite manganite

Science.gov (United States)

Li, Run-Wei; Wang, Huabing; Wang, Xuewen; Yu, X. Z.; Matsui, Y.; Cheng, Zhao-Hua; Shen, Bao-Gen; Plummer, E. Ward; Zhang, Jiandi

2009-01-01

The signature of correlated electron materials (CEMs) is the coupling between spin, charge, orbital and lattice resulting in exotic functionality. This complexity is directly responsible for their tunability. We demonstrate here that the broken symmetry, through cubic to orthorhombic distortion in the lattice structure in a prototype manganite single crystal, La0.69Ca0.31MnO3, leads to an anisotropic magneto-elastic response to an external field, and consequently to remarkable magneto-transport behavior. An anomalous anisotropic magnetoresistance (AMR) effect occurs close to the metal-insulator transition (MIT) in the system, showing a direct correlation with the anisotropic field-tuned MIT in the system and can be understood by means of a simple phenomenological model. A small crystalline anisotropy stimulates a “colossal” AMR near the MIT phase boundary of the system, thus revealing the intimate interplay between magneto- and electronic-crystalline couplings. PMID:19706504

Sign rules for anisotropic quantum spin systems

International Nuclear Information System (INIS)

Bishop, R. F.; Farnell, D. J. J.; Parkinson, J. B.

2000-01-01

We present exact ''sign rules'' for various spin-s anisotropic spin-lattice models. It is shown that, after a simple transformation which utilizes these sign rules, the ground-state wave function of the transformed Hamiltonian is positive definite. Using these results exact statements for various expectation values of off-diagonal operators are presented, and transitions in the behavior of these expectation values are observed at particular values of the anisotropy. Furthermore, the importance of such sign rules in variational calculations and quantum Monte Carlo calculations is emphasized. This is illustrated by a simple variational treatment of a one-dimensional anisotropic spin model

Variational principles for the static electric and magnetic polarizabilities of anisotropic media with perfect electric conductor inclusions

International Nuclear Information System (INIS)

Sjoeberg, Daniel

2009-01-01

We present four variational principles for the electric and magnetic polarizabilities for a structure consisting of anisotropic media with perfect electric conductor (PEC) inclusions. From these principles, we derive monotonicity results and upper and lower bounds on the electric and magnetic polarizabilities. When computing the polarizabilities numerically, the bounds can be used as error bounds. The variational principles demonstrate important differences between electrostatics and magnetostatics when PEC bodies are present.

Anisotropic Flow Measurements in ALICE at the Large Hadron Collider

NARCIS (Netherlands)

Bilandzic, A.

2012-01-01

Anisotropic flow is one of the observables which is sensitive to the properties of the created hot and dense system in heavy-ion collisions. In noncentral heavy-ion collisions the initial volume of the interacting system is anisotropic in coordinate space. Due to multiple interactions this anisotropy

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling.

Science.gov (United States)

Politis, Argyris; Schmidt, Carla

2018-03-20

Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution. These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease. In this review we summarise the techniques of structural mass spectrometry often applied when studying protein-ligand complexes. We exemplify these techniques through recent examples from literature that helped in the understanding of medically relevant protein assemblies. We further provide a detailed introduction into various computational approaches that can be integrated with these mass spectrometric techniques. Last but not least we discuss case studies that integrated mass spectrometry and computational modelling approaches and yielded models of medically important protein assembly states such as fibrils and amyloids. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Double anisotropic electrically conductive flexible Janus-typed membranes.

Science.gov (United States)

Li, Xiaobing; Ma, Qianli; Tian, Jiao; Xi, Xue; Li, Dan; Dong, Xiangting; Yu, Wensheng; Wang, Xinlu; Wang, Jinxian; Liu, Guixia

2017-12-07

Novel type III anisotropic conductive films (ACFs), namely flexible Janus-typed membranes, were proposed, designed and fabricated for the first time. Flexible Janus-typed membranes composed of ordered Janus nanobelts were constructed by electrospinning, which simultaneously possess fluorescence and double electrically conductive anisotropy. For the fabrication of the Janus-typed membrane, Janus nanobelts comprising a conductive side and an insulative-fluorescent side were primarily fabricated, and then the Janus nanobelts are arranged into parallel arrays using an aluminum rotary drum as the collector to obtain a single anisotropically conductive film. Subsequently, a secondary electrospinning process was applied to the as-prepared single anisotropically conductive films to acquire the final Janus-typed membrane. For this Janus-typed membrane, namely its left-to-right structure, anisotropic electrical conduction synchronously exists on both sides, and furthermore, the two electrically conductive directions are perpendicular. By modulating the amount of Eu(BA) 3 phen complex and conducting polyaniline (PANI), the characteristics and intensity of the fluorescence-electricity dual-function in the membrane can be tuned. The high integration of this peculiar Janus-typed membrane with simultaneous double electrically conductive anisotropy-fluorescent dual-functionality is successfully realized in this study. This design philosophy and preparative technique will provide support for the design and construction of new types of special nanostructures with multi-functionality.

Conductivity tensor of anisotropic composite media from the microstructure

International Nuclear Information System (INIS)

Torquato, S.; Sen, A.K.

1990-01-01

Perturbation expansions and rigorous bounds on the effective conductivity tensor σ e of d-dimensional anisotropic two-phase composite media of arbitrary topology have recently been shown by the authors to depend upon the set of n-point probability functions S (i) 1 ,..., S (i) n . S (i) n gives the probability of simultaneously finding n points in phase i (i=1,2). Here we describe a means of representing these statistical quantities for distributions of identical, oriented inclusions of arbitrary shape. Our results are applied by computing second-order perturbation expansions and bounds for a certain distribution of oriented cylinders with a finite aspect ratio. We examine both cases of conducting cylindrical inclusions in an insulating matrix and of insulating cracks or voids in a conducting matrix

Holographic models with anisotropic scaling

Science.gov (United States)

Brynjolfsson, E. J.; Danielsson, U. H.; Thorlacius, L.; Zingg, T.

2013-12-01

We consider gravity duals to d+1 dimensional quantum critical points with anisotropic scaling. The primary motivation comes from strongly correlated electron systems in condensed matter theory but the main focus of the present paper is on the gravity models in their own right. Physics at finite temperature and fixed charge density is described in terms of charged black branes. Some exact solutions are known and can be used to obtain a maximally extended spacetime geometry, which has a null curvature singularity inside a single non-degenerate horizon, but generic black brane solutions in the model can only be obtained numerically. Charged matter gives rise to black branes with hair that are dual to the superconducting phase of a holographic superconductor. Our numerical results indicate that holographic superconductors with anisotropic scaling have vanishing zero temperature entropy when the back reaction of the hair on the brane geometry is taken into account.

Anisotropic models for compact stars

Energy Technology Data Exchange (ETDEWEB)

Maurya, S.K.; Dayanandan, Baiju [University of Nizwa, Department of Mathematical and Physical Sciences, College of Arts and Science, Nizwa (Oman); Gupta, Y.K. [Jaypee Institute of Information Technology University, Department of Mathematics, Noida, Uttar Pradesh (India); Ray, Saibal [Government College of Engineering and Ceramic Technology, Department of Physics, Kolkata, West Bengal (India)

2015-05-15

In the present paper we obtain an anisotropic analog of the Durgapal and Fuloria (Gen Relativ Gravit 17:671, 1985) perfect fluid solution. The methodology consists of contraction of the anisotropic factor Δ with the help of both metric potentials e{sup ν} and e{sup λ}. Here we consider e{sup λ} the same as Durgapal and Fuloria (Gen Relativ Gravit 17:671, 1985) did, whereas e{sup ν} is as given by Lake (Phys Rev D 67:104015, 2003). The field equations are solved by the change of dependent variable method. The solutions set mathematically thus obtained are compared with the physical properties of some of the compact stars, strange star as well as white dwarf. It is observed that all the expected physical features are available related to the stellar fluid distribution, which clearly indicates the validity of the model. (orig.)

Hybrid anisotropic materials for wind power turbine blades

CERN Document Server

Golfman, Yosif

2012-01-01

Based on rapid technological developments in wind power, governments and energy corporations are aggressively investing in this natural resource. Illustrating some of the crucial new breakthroughs in structural design and application of wind energy generation machinery, Hybrid Anisotropic Materials for Wind Power Turbine Blades explores new automated, repeatable production techniques that expand the use of robotics and process controls. These practices are intended to ensure cheaper fabrication of less-defective anisotropic material composites used to manufacture power turbine blades. This boo

Anisotropic behavior of quantum transport in graphene superlattices

DEFF Research Database (Denmark)

Pedersen, Jesper Goor; Cummings, Aron W.; Roche, Stephan

2014-01-01

We report on the possibility to generate highly anisotropic quantum conductivity in disordered graphene-based superlattices. Our quantum simulations, based on an efficient real-space implementation of the Kubo-Greenwood formula, show that in disordered graphene superlattices the strength of multi......We report on the possibility to generate highly anisotropic quantum conductivity in disordered graphene-based superlattices. Our quantum simulations, based on an efficient real-space implementation of the Kubo-Greenwood formula, show that in disordered graphene superlattices the strength...

Variational Multiscale error estimator for anisotropic adaptive fluid mechanic simulations: application to convection-diffusion problems

OpenAIRE

Bazile , Alban; Hachem , Elie; Larroya-Huguet , Juan-Carlos; Mesri , Youssef

2018-01-01

International audience; In this work, we present a new a posteriori error estimator based on the Variational Multiscale method for anisotropic adaptive fluid mechanics problems. The general idea is to combine the large scale error based on the solved part of the solution with the sub-mesh scale error based on the unresolved part of the solution. We compute the latter with two different methods: one using the stabilizing parameters and the other using bubble functions. We propose two different...

DichroCalc: Improvements in Computing Protein Circular Dichroism Spectroscopy in the Near-Ultraviolet.

Science.gov (United States)

Jasim, Sarah B; Li, Zhuo; Guest, Ellen E; Hirst, Jonathan D

2017-12-16

A fully quantitative theory connecting protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. The web server DichroCalc (http://comp.chem.nottingham.ac.uk/dichrocalc) allows one to compute from first principles the electronic circular dichroism spectrum of a (modeled or experimental) protein structure or ensemble of structures. The regular, repeating, chiral nature of secondary structure elements leads to intense bands in the far-ultraviolet (UV). The near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, realized through the consideration of the vibrational structure of the electronic transitions of aromatic side chains. The improvements have been assessed over a set of diverse proteins. We illustrate them using bovine pancreatic trypsin inhibitor and present a new, detailed analysis of the interactions which are most important in determining the near-UV circular dichroism spectrum. Copyright © 2018. Published by Elsevier Ltd.

Computational identification of strain-, species- and genus-specific proteins

Directory of Open Access Journals (Sweden)

Thiagarajan Rathi

2005-11-01

Full Text Available Abstract Background The identification of unique proteins at different taxonomic levels has both scientific and practical value. Strain-, species- and genus-specific proteins can provide insight into the criteria that define an organism and its relationship with close relatives. Such proteins can also serve as taxon-specific diagnostic targets. Description A pipeline using a combination of computational and manual analyses of BLAST results was developed to identify strain-, species-, and genus-specific proteins and to catalog the closest sequenced relative for each protein in a proteome. Proteins encoded by a given strain are preliminarily considered to be unique if BLAST, using a comprehensive protein database, fails to retrieve (with an e-value better than 0.001 any protein not encoded by the query strain, species or genus (for strain-, species- and genus-specific proteins respectively, or if BLAST, using the best hit as the query (reverse BLAST, does not retrieve the initial query protein. Results are manually inspected for homology if the initial query is retrieved in the reverse BLAST but is not the best hit. Sequences unlikely to retrieve homologs using the default BLOSUM62 matrix (usually short sequences are re-tested using the PAM30 matrix, thereby increasing the number of retrieved homologs and increasing the stringency of the search for unique proteins. The above protocol was used to examine several food- and water-borne pathogens. We find that the reverse BLAST step filters out about 22% of proteins with homologs that would otherwise be considered unique at the genus and species levels. Analysis of the annotations of unique proteins reveals that many are remnants of prophage proteins, or may be involved in virulence. The data generated from this study can be accessed and further evaluated from the CUPID (Core and Unique Protein Identification system web site (updated semi-annually at http://pir.georgetown.edu/cupid. Conclusion CUPID

Simulation of ultrasonic wave propagation in anisotropic poroelastic bone plate using hybrid spectral/finite element method.

Science.gov (United States)

Nguyen, Vu-Hieu; Naili, Salah

2012-08-01

This paper deals with the modeling of guided waves propagation in in vivo cortical long bone, which is known to be anisotropic medium with functionally graded porosity. The bone is modeled as an anisotropic poroelastic material by using Biot's theory formulated in high frequency domain. A hybrid spectral/finite element formulation has been developed to find the time-domain solution of ultrasonic waves propagating in a poroelastic plate immersed in two fluid halfspaces. The numerical technique is based on a combined Laplace-Fourier transform, which allows to obtain a reduced dimension problem in the frequency-wavenumber domain. In the spectral domain, as radiation conditions representing infinite fluid halfspaces may be exactly introduced, only the heterogeneous solid layer needs to be analyzed by using finite element method. Several numerical tests are presented showing very good performance of the proposed procedure. A preliminary study on the first arrived signal velocities computed by using equivalent elastic and poroelastic models will be presented. Copyright © 2012 John Wiley & Sons, Ltd.

Anisotropic Rabi model

OpenAIRE

Xie, Qiong-Tao; Cui, Shuai; Cao, Jun-Peng; Amico, Luigi; Fan, Heng

2014-01-01

We define the anisotropic Rabi model as the generalization of the spin-boson Rabi model: The Hamiltonian system breaks the parity symmetry; the rotating and counterrotating interactions are governed by two different coupling constants; a further parameter introduces a phase factor in the counterrotating terms. The exact energy spectrum and eigenstates of the generalized model are worked out. The solution is obtained as an elaboration of a recently proposed method for the isotropic limit of th...

Effective material parameter retrieval of anisotropic elastic metamaterials with inherent nonlocality

Science.gov (United States)

Lee, Hyung Jin; Lee, Heung Son; Ma, Pyung Sik; Kim, Yoon Young

2016-09-01

In this paper, the scattering (S-) parameter retrieval method is presented specifically for anisotropic elastic metamaterials; so far, no retrieval has been accomplished when elastic metamaterials exhibit fully anisotropic behavior. Complex constitutive property and intrinsic scattering behavior of elastic metamaterials make their characterization far more complicated than that for acoustic and electromagnetic metamaterials. In particular, elastic metamaterials generally exhibit anisotropic scattering behavior due to higher scattering modes associated with shear deformation. They also exhibit nonlocal responses to some degrees, which originate from strong multiple scattering interactions even in the long wavelength limit. Accordingly, the conventional S-parameter retrieval methods cannot be directly used for elastic metamaterials, because they determine only the diagonal components in effective tensor property. Also, the conventional methods simply use the analytic inversion formulae for the material characterization so that inherent nonlocality cannot be taken into account. To establish a retrieval method applicable to anisotropic elastic metamaterials, we propose an alternative S-parameter method to deal with full anisotropy of elastic metamaterials. To retrieve the whole effective anisotropic parameter, we utilize not only normal but also oblique wave incidences. For the retrieval, we first retrieve the ratio of the effective stiffness tensor to effective density and then determine the effective density. The proposed retrieval method is validated by characterizing the effective material parameters of various types of non-resonant anisotropic metamaterials. It is found that the whole effective parameters are retrieved consistently regardless of used retrieval conditions in spite of inherent nonlocality.

Speckle Suppression by Weighted Euclidean Distance Anisotropic Diffusion

Directory of Open Access Journals (Sweden)

Fengcheng Guo

2018-05-01

Full Text Available To better reduce image speckle noise while also maintaining edge information in synthetic aperture radar (SAR images, we propose a novel anisotropic diffusion algorithm using weighted Euclidean distance (WEDAD. Presented here is a modified speckle reducing anisotropic diffusion (SRAD method, which constructs a new edge detection operator using weighted Euclidean distances. The new edge detection operator can adaptively distinguish between homogenous and heterogeneous image regions, effectively generate anisotropic diffusion coefficients for each image pixel, and filter each pixel at different scales. Additionally, the effects of two different weighting methods (Gaussian weighting and non-linear weighting of de-noising were analyzed. The effect of different adjustment coefficient settings on speckle suppression was also explored. A series of experiments were conducted using an added noise image, GF-3 SAR image, and YG-29 SAR image. The experimental results demonstrate that the proposed method can not only significantly suppress speckle, thus improving the visual effects, but also better preserve the edge information of images.

Self-force on dislocation segments in anisotropic crystals

International Nuclear Information System (INIS)

Fitzgerald, S P; Aubry, S

2010-01-01

A dislocation segment in a crystal experiences a 'self-force', by virtue of the orientation dependence of its elastic energy. If the crystal is elastically isotropic, this force is manifested as a couple acting to rotate the segment toward the lower energy of the pure screw orientation (i.e. acting to align the dislocation line with its Burgers vector). If the crystal is anisotropic, there are additional contributions to the couple, arising from the more complex energy landscape of the lattice itself. These effects can strongly influence the dynamic evolution of dislocation networks, and via their governing role in dislocation multiplication phenomena, control plastic flow in metals. In this paper we develop a model for dislocation self-forces in a general anisotropic crystal, and briefly consider the technologically important example of α-iron, which becomes increasingly anisotropic as the temperature approaches that of the α-γ phase transition at 912 0 C.

Synthetic acceleration methods for linear transport problems with highly anisotropic scattering

International Nuclear Information System (INIS)

Khattab, K.M.; Larsen, E.W.

1992-01-01

The diffusion synthetic acceleration (DSA) algorithm effectively accelerates the iterative solution of transport problems with isotropic or mildly anisotropic scattering. However, DSA loses its effectiveness for transport problems that have strongly anisotropic scattering. Two generalizations of DSA are proposed, which, for highly anisotropic scattering problems, converge at least an order of magnitude (clock time) faster than the DSA method. These two methods are developed, the results of Fourier analysis that theoretically predict their efficiency are described, and numerical results that verify the theoretical predictions are presented. (author). 10 refs., 7 figs., 5 tabs

Synthetic acceleration methods for linear transport problems with highly anisotropic scattering

International Nuclear Information System (INIS)

Khattab, K.M.; Larsen, E.W.

1991-01-01

This paper reports on the diffusion synthetic acceleration (DSA) algorithm that effectively accelerates the iterative solution of transport problems with isotropic or mildly anisotropic scattering. However, DSA loses its effectiveness for transport problems that have strongly anisotropic scattering. Two generalizations of DSA are proposed, which, for highly anisotropic scattering problems, converge at least an order of magnitude (clock time) faster than the DSA method. These two methods are developed, the results of Fourier analyses that theoretically predict their efficiency are described, and numerical results that verify the theoretical predictions are presented

Effective modeling and reverse-time migration for novel pure acoustic wave in arbitrary orthorhombic anisotropic media

Science.gov (United States)

Xu, Shigang; Liu, Yang

2018-03-01

The conventional pseudo-acoustic wave equations (PWEs) in arbitrary orthorhombic anisotropic (OA) media usually have coupled P- and SV-wave modes. These coupled equations may introduce strong SV-wave artifacts and numerical instabilities in P-wave simulation results and reverse-time migration (RTM) profiles. However, pure acoustic wave equations (PAWEs) completely decouple the P-wave component from the full elastic wavefield and naturally solve all the aforementioned problems. In this article, we present a novel PAWE in arbitrary OA media and compare it with the conventional coupled PWEs. Through decomposing the solution of the corresponding eigenvalue equation for the original PWE into an ellipsoidal differential operator (EDO) and an ellipsoidal scalar operator (ESO), the new PAWE in time-space domain is constructed by applying the combination of these two solvable operators and can effectively describe P-wave features in arbitrary OA media. Furthermore, we adopt the optimal finite-difference method (FDM) to solve the newly derived PAWE. In addition, the three-dimensional (3D) hybrid absorbing boundary condition (HABC) with some reasonable modifications is developed for reducing artificial edge reflections in anisotropic media. To improve computational efficiency in 3D case, we adopt graphic processing unit (GPU) with Compute Unified Device Architecture (CUDA) instead of traditional central processing unit (CPU) architecture. Several numerical experiments for arbitrary OA models confirm that the proposed schemes can produce pure, stable and accurate P-wave modeling results and RTM images with higher computational efficiency. Moreover, the 3D numerical simulations can provide us with a comprehensive and real description of wave propagation.

ANALYSIS OF DEFORMABILITY OF ANISOTROPIC AGRILLITE CLAYSTONES

Directory of Open Access Journals (Sweden)

Ponomaryov Andrey Budimirovicn

2017-08-01

Full Text Available In the paper, the results of deformability study of agrillite claystones are used for determination of the Jointed rock model parameters. The number of stamp, pressuremeter and compressive tests allowed to research anisotropic deformability of argillite claystone in vertical and horizontal direction. The following problems were solved during the study: 1 the in-place and laboratory experiments to calculate the anisotropy coefficient were done for anisotropic agrillite claystones with both natural moisture and total water saturation; 2 the deformation parameters were determined and the numerical simulation of the stress-strain state of claystone in field tests was carried out with the use of Plaxis 2D software application; 3 the comparative analysis was done for calculated claystone deformation and the values obtained during the in-place tests. The authors proved that agrillite claystones shows two times less deformation under loading in the horizontal direction than vertically. The ratio is obtained to determine the parameters for numerical simulation of the Jointed Rock model used as a practical tool for analysis of stress-strain behavior of anisotropic soils. The authors provided a recommended practice for consideration of specific properties of argillite claystones when carrying out foundation works.

A systematic study of head tissue inhomogeneity and anisotropy on EEG forward problem computing

International Nuclear Information System (INIS)

Bashar, M.R.; Li, Y.; Wen, P.

2010-01-01

Full text: In this study, we propose a stochastic method to analyze the effects of inhomogeneous anisotropic tissue conductivity on electroencephalogram (EEG) in forward computation. We apply this method to an inhomogeneous and anisotropic spherical human head model. We apply stochastic finite element method based on Legendre polynomials, Karhunen-Loeve expansion and stochastic Galerkin methods. We apply Volume and Wang's constraints to restrict the anisotropic conductivities for both the white matter (WM) and the skull tissue compartments. The EEGs resulting from deterministic and stochastic FEMs are compared using statistical measurement techniques. Based on these comparisons, we find that EEGs generated by incorporating WM and skull inhomogeneous anisotropic tissue properties individually result in an average of 56.5 and 57.5% relative errors, respectively. Incorporating these tissue properties for both layers together generate 43.5% average relative error. Inhomogeneous scalp tissue causes 27% average relative error and a full inhomogeneous anisotropic model brings in an average of 45.5% relative error. The study results demonstrate that the effects of inhomogeneous anisotropic tissue conductivity are significant on EEG.

3-D direct current resistivity anisotropic modelling by goal-oriented adaptive finite element methods

Science.gov (United States)

Ren, Zhengyong; Qiu, Lewen; Tang, Jingtian; Wu, Xiaoping; Xiao, Xiao; Zhou, Zilong

2018-01-01

Although accurate numerical solvers for 3-D direct current (DC) isotropic resistivity models are current available even for complicated models with topography, reliable numerical solvers for the anisotropic case are still an open question. This study aims to develop a novel and optimal numerical solver for accurately calculating the DC potentials for complicated models with arbitrary anisotropic conductivity structures in the Earth. First, a secondary potential boundary value problem is derived by considering the topography and the anisotropic conductivity. Then, two a posteriori error estimators with one using the gradient-recovery technique and one measuring the discontinuity of the normal component of current density are developed for the anisotropic cases. Combing the goal-oriented and non-goal-oriented mesh refinements and these two error estimators, four different solving strategies are developed for complicated DC anisotropic forward modelling problems. A synthetic anisotropic two-layer model with analytic solutions verified the accuracy of our algorithms. A half-space model with a buried anisotropic cube and a mountain-valley model are adopted to test the convergence rates of these four solving strategies. We found that the error estimator based on the discontinuity of current density shows better performance than the gradient-recovery based a posteriori error estimator for anisotropic models with conductivity contrasts. Both error estimators working together with goal-oriented concepts can offer optimal mesh density distributions and highly accurate solutions.

Failure in imperfect anisotropic materials

DEFF Research Database (Denmark)

Legarth, Brian Nyvang

2005-01-01

The fundamental cause of crack growth, namely nucleation and growth of voids, is investigated numerically for a two phase imperfect anisotropic material. A unit cell approach is adopted from which the overall stress strain is evaluated. Failure is observed as a sudden stress drop and depending...

Field theoretic approach to structure formation in an anisotropic medium

International Nuclear Information System (INIS)

Joy, Minu; Kuriakose, V.C.

2003-01-01

Considering a real scalar field distribution which is assumed to be locally anisotropic and coupled to a Bianchi type-I background spacetime, the energy density and pressure associated with the anisotropic matter field distribution are evaluated. The vanishing of the expectation values of the nondiagonal components of T μν allows us to treat the scalar field in complete analogy with the distribution of fluid. The primeval density perturbations produced by the vacuum fluctuations of the scalar field are considered and the Jeans criterion for structure formation is obtained. The metric and matter field perturbations are considered and it is found that for the present anisotropic case the perturbations of the pressure in the radial and tangential directions are different. The Jeans instability is discussed and the Jeans wave number for the present case is evaluated. It is found that for the anisotropic case the Jeans length depends on the velocity of the fluctuations in the radial and transverse directions and thus on the direction of propagation of the perturbations

Effective Medium Theory for Anisotropic Metamaterials

KAUST Repository

Zhang, Xiujuan

2017-11-12

This dissertation includes the study of effective medium theories (EMTs) and their applications in describing wave propagation in anisotropic metamaterials, which can guide the design of metamaterials. An EMT based on field averaging is proposed to describe a peculiar anisotropic dispersion relation that is linear along the symmetry line but quadratic in the perpendicular direction. This dispersion relation is associated with the topological transition of the iso-frequency contours (IFCs), suggesting interesting wave propagation behaviors from beam shaping to beam splitting. In the framework of coherent potential approximation, an analytical EMT is further developed, with the ability to build a direct connection between the microscopic structure and the macroscopic material properties, which overcomes the requirement of prior knowledge of the field distributions. The derived EMT is valid beyond the long-wavelength limit. Using the EMT, an anisotropic zero-index metamaterial is designed. Moreover, the derived EMT imposes a condition that no scattered wave is generated in the ambient medium, which suggests the input signal cannot detect any object that might exist, making it invisible. Such correspondence between the EMT and the invisibilityinspires us to explore the wave cloaking in the same framework of coherent potential approximation. To further broaden the application realm of EMT, an EMT using the parameter retrieval method is studied in the regimes where the previously-developed EMTs are no longer accurate. Based on this study, in conjunction with the EMT mentioned above, a general scheme to realize coherent perfect absorption (CPA) in anisotropic metamaterials is proposed. As an exciting area in metamaterials, the field of metasurfaces has drawn great attention recently. As an easily attainable device, a grating may be the simplest version of metasurfaces. Here, an analytical EMT for gratings made of cylinders is developed by using the multiple scattering

An anisotropic standing wave braneworld and associated Sturm-Liouville problem

International Nuclear Information System (INIS)

Gogberashvili, Merab; Herrera-Aguilar, Alfredo; Malagón-Morejón, Dagoberto

2012-01-01

We present a consistent derivation of the recently proposed 5D anisotropic standing wave braneworld generated by gravity coupled to a phantom-like scalar field. We explicitly solve the corresponding junction conditions, a fact that enables us to give a physical interpretation to the anisotropic energy-momentum tensor components of the brane. So matter on the brane represents an oscillating fluid which emits anisotropic waves into the bulk. We also analyze the Sturm-Liouville problem associated with the correct localization condition of the transverse to the brane metric and scalar fields. It is shown that this condition restricts the physically meaningful space of solutions for the localization of the fluctuations of the model. (paper)

Experimental evidence for anisotropic double exchange interaction driven anisotropic transport in manganite heterostructures

NARCIS (Netherlands)

Liao, Zhaoliang; Koster, Gertjan; Huijben, Mark; Rijnders, A.J.H.M.

2017-01-01

An anisotropic double exchange interaction driven giant transport anisotropy is demonstrated in a canonic double exchange system of La2/3Sr1/3MnO3 ultrathin films epitaxially grown on NdGaO3 (110) substrates. The oxygen octahedral coupling at the La2/3Sr1/3MnO3/NdGaO3 interface induces a planar

Characterization of highly anisotropic three-dimensionally nanostructured surfaces

International Nuclear Information System (INIS)

Schmidt, Daniel

2014-01-01

Generalized ellipsometry, a non-destructive optical characterization technique, is employed to determine geometrical structure parameters and anisotropic dielectric properties of highly spatially coherent three-dimensionally nanostructured thin films grown by glancing angle deposition. The (piecewise) homogeneous biaxial layer model approach is discussed, which can be universally applied to model the optical response of sculptured thin films with different geometries and from diverse materials, and structural parameters as well as effective optical properties of the nanostructured thin films are obtained. Alternative model approaches for slanted columnar thin films, anisotropic effective medium approximations based on the Bruggeman formalism, are presented, which deliver results comparable to the homogeneous biaxial layer approach and in addition provide film constituent volume fraction parameters as well as depolarization or shape factors. Advantages of these ellipsometry models are discussed on the example of metal slanted columnar thin films, which have been conformally coated with a thin passivating oxide layer by atomic layer deposition. Furthermore, the application of an effective medium approximation approach to in-situ growth monitoring of this anisotropic thin film functionalization process is presented. It was found that structural parameters determined with the presented optical model equivalents for slanted columnar thin films agree very well with scanning electron microscope image estimates. - Highlights: • Summary of optical model strategies for sculptured thin films with arbitrary geometries • Application of the rigorous anisotropic Bruggeman effective medium applications • In-situ growth monitoring of atomic layer deposition on biaxial metal slanted columnar thin film

On a hierarchical construction of the anisotropic LTSN solution from the isotropic LTSN solution

International Nuclear Information System (INIS)

Foletto, Taline; Segatto, Cynthia F.; Bodmann, Bardo E.; Vilhena, Marco T.

2015-01-01

In this work, we present a recursive scheme targeting the hierarchical construction of anisotropic LTS N solution from the isotropic LTS N solution. The main idea relies in the decomposition of the associated LTS N anisotropic matrix as a sum of two matrices in which one matrix contains the isotropic and the other anisotropic part of the problem. The matrix containing the anisotropic part is considered as the source of the isotropic problem. The solution of this problem is made by the decomposition of the angular flux as a truncated series of intermediate functions and replace in the isotropic equation. After the replacement of these into the split isotropic equation, we construct a set of isotropic recursive problems, that are readily solved by the classic LTS N isotropic method. We apply this methodology to solve problems considering homogeneous and heterogeneous anisotropic regions. Numerical results are presented and compared with the classical LTS N anisotropic solution. (author)

Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information.

Science.gov (United States)

An, Ji-Yong; Zhang, Lei; Zhou, Yong; Zhao, Yu-Jun; Wang, Da-Fu

2017-08-18

Self-interactions Proteins (SIPs) is important for their biological activity owing to the inherent interaction amongst their secondary structures or domains. However, due to the limitations of experimental Self-interactions detection, one major challenge in the study of prediction SIPs is how to exploit computational approaches for SIPs detection based on evolutionary information contained protein sequence. In the work, we presented a novel computational approach named WELM-LAG, which combined the Weighed-Extreme Learning Machine (WELM) classifier with Local Average Group (LAG) to predict SIPs based on protein sequence. The major improvement of our method lies in presenting an effective feature extraction method used to represent candidate Self-interactions proteins by exploring the evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix (PSSM); and then employing a reliable and robust WELM classifier to carry out classification. In addition, the Principal Component Analysis (PCA) approach is used to reduce the impact of noise. The WELM-LAG method gave very high average accuracies of 92.94 and 96.74% on yeast and human datasets, respectively. Meanwhile, we compared it with the state-of-the-art support vector machine (SVM) classifier and other existing methods on human and yeast datasets, respectively. Comparative results indicated that our approach is very promising and may provide a cost-effective alternative for predicting SIPs. In addition, we developed a freely available web server called WELM-LAG-SIPs to predict SIPs. The web server is available at http://219.219.62.123:8888/WELMLAG/ .

Brazilian Tensile Strength of Anisotropic Rocks: Review and New Insights

Directory of Open Access Journals (Sweden)

Tianshou Ma

2018-01-01

Full Text Available Strength anisotropy is one of the most distinct features of anisotropic rocks, and it also normally reveals strong anisotropy in Brazilian test Strength (“BtS”. Theoretical research on the “BtS” of anisotropic rocks is seldom performed, and in particular some significant factors, such as the anisotropic tensile strength of anisotropic rocks, the initial Brazilian disc fracture points, and the stress distribution on the Brazilian disc, are often ignored. The aim of the present paper is to review the state of the art in the experimental studies on the “BtS” of anisotropic rocks since the pioneering work was introduced in 1964, and to propose a novel theoretical method to underpin the failure mechanisms and predict the “BtS” of anisotropic rocks under Brazilian test conditions. The experimental data of Longmaxi Shale-I and Jixi Coal were utilized to verify the proposed method. The results show the predicted “BtS” results show strong agreement with experimental data, the maximum error is only ~6.55% for Longmaxi Shale-I and ~7.50% for Jixi Coal, and the simulated failure patterns of the Longmaxi Shale-I are also consistent with the test results. For the Longmaxi Shale-I, the Brazilian disc experiences tensile failure of the intact rock when 0° ≤ βw ≤ 24°, shear failure along the weakness planes when 24° ≤ βw ≤ 76°, and tensile failure along the weakness planes when 76° ≤ βw ≤ 90°. For the Jixi Coal, the Brazilian disc experiences tensile failure when 0° ≤ βw ≤ 23° or 76° ≤ βw ≤ 90°, shear failure along the butt cleats when 23° ≤ βw ≤ 32°, and shear failure along the face cleats when 32° ≤ βw ≤ 76°. The proposed method can not only be used to predict the “BtS” and underpin the failure mechanisms of anisotropic rocks containing a single group of weakness planes, but can also be generalized for fractured rocks containing multi-groups of weakness planes.

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

Science.gov (United States)

Duan, Lili; Liu, Xiao; Zhang, John Z H

2016-05-04

Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

Debonding analyses in anisotropic materials with strain- gradient effects

DEFF Research Database (Denmark)

Legarth, Brian Nyvang

2012-01-01

A unit cell approach is adopted to numerically analyze the effect of plastic anisotropy on damage evolution in a micro-reinforced composite. The matrix material exhibit size effects and a visco-plastic anisotropic strain gradient plasticity model accounting for such size effects is adopted....... A conventional cohesive law is extended such that both the average as well as the jump in plastic strain across the fiber-matrix interface are accounted for. Results are shown for both conventional isotropic and anisotropic materials as well as for higher order isotropic and anisotropic materials...... with and without debonding. Generally, the strain gradient enhanced material exhibits higher load carry capacity compared to the corresponding conventional material. A sudden stress drop occurs in the macroscopic stress-strain response curve due to fiber-matrix debonding and the results show that a change in yield...

Two-relaxation-time lattice Boltzmann method for the anisotropic dispersive Henry problem

Science.gov (United States)

Servan-Camas, Borja; Tsai, Frank T.-C.

2010-02-01

This study develops a lattice Boltzmann method (LBM) with a two-relaxation-time collision operator (TRT) to cope with anisotropic heterogeneous hydraulic conductivity and anisotropic velocity-dependent hydrodynamic dispersion in the saltwater intrusion problem. The directional-speed-of-sound technique is further developed to address anisotropic hydraulic conductivity and dispersion tensors. Forcing terms are introduced in the LBM to correct numerical errors that arise during the recovery procedure and to describe the sink/source terms in the flow and transport equations. In order to facilitate the LBM implementation, the forcing terms are combined with the equilibrium distribution functions (EDFs) to create pseudo-EDFs. This study performs linear stability analysis and derives LBM stability domains to solve the anisotropic advection-dispersion equation. The stability domains are used to select the time step at which the lattice Boltzmann method provides stable solutions to the numerical examples. The LBM was implemented for the anisotropic dispersive Henry problem with high ratios of longitudinal to transverse dispersivities, and the results compared well to the solutions in the work of Abarca et al. (2007).

Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks.

Science.gov (United States)

Yeh, Chun-Ting; Brunette, T J; Baker, David; McIntosh-Smith, Simon; Parmeggiani, Fabio

2018-02-01

Computational protein design methods have enabled the design of novel protein structures, but they are often still limited to small proteins and symmetric systems. To expand the size of designable proteins while controlling the overall structure, we developed Elfin, a genetic algorithm for the design of novel proteins with custom shapes using structural building blocks derived from experimentally verified repeat proteins. By combining building blocks with compatible interfaces, it is possible to rapidly build non-symmetric large structures (>1000 amino acids) that match three-dimensional geometric descriptions provided by the user. A run time of about 20min on a laptop computer for a 3000 amino acid structure makes Elfin accessible to users with limited computational resources. Protein structures with controlled geometry will allow the systematic study of the effect of spatial arrangement of enzymes and signaling molecules, and provide new scaffolds for functional nanomaterials. Copyright © 2017 Elsevier Inc. All rights reserved.

Fabrication of an Anisotropic Superhydrophobic Polymer Surface Using Compression Molding and Dip Coating

Directory of Open Access Journals (Sweden)

Kyong-Min Lee

2017-11-01

Full Text Available Many studies of anisotropic wetting surfaces with directional structures inspired from rice leaves, bamboo leaves, and butterfly wings have been carried out because of their unique liquid shape control and transportation. In this study, a precision mechanical cutting process, ultra-precision machining using a single crystal diamond tool, was used to fabricate a mold with microscale directional patterns of triangular cross-sectional shape for good moldability, and the patterns were duplicated on a flat thermoplastic polymer plate by compression molding for the mass production of an anisotropic wetting polymer surface. Anisotropic wetting was observed only with microscale patterns, but the sliding of water could not be achieved because of the pinning effect of the micro-structure. Therefore, an additional dip coating process with 1H, 1H, 2H, 2H-perfluorodecythricholosilanes, and TiO2 nanoparticles was applied for a small sliding angle with nanoscale patterns and a low surface energy. The anisotropic superhydrophobic surface was fabricated and the surface morphology and anisotropic wetting behaviors were investigated. The suggested fabrication method can be used to mass produce an anisotropic superhydrophobic polymer surface, demonstrating the feasibility of liquid shape control and transportation.

Anisotropic spin motive force in multi-layered Dirac fermion system, α-(BEDT-TTF)2I3

International Nuclear Information System (INIS)

Kubo, K; Morinari, T

2015-01-01

We investigate the anisotropic spin motive force in α-(BEDT-TTF) 2 I 3 , which is a multi-layered massless Dirac fermion system under pressure. Assuming the interlayer antiferromagnetic interaction and the interlayer anisotropic ferromagnetic interaction, we numerically examine the spin ordered state of the ground state using the steepest descent method. The anisotropic interaction leads to the anisotropic spin ordered state. We calculate the spin motive force produced by the anisotropic spin texture. The result quantitatively agrees with the experiment. (paper)

Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions.

Science.gov (United States)

Nagao, Chioko; Izako, Nozomi; Soga, Shinji; Khan, Samia Haseeb; Kawabata, Shigeki; Shirai, Hiroki; Mizuguchi, Kenji

2012-10-01

Proteins interact with different partners to perform different functions and it is important to elucidate the determinants of partner specificity in protein complex formation. Although methods for detecting specificity determining positions have been developed previously, direct experimental evidence for these amino acid residues is scarce, and the lack of information has prevented further computational studies. In this article, we constructed a dataset that is likely to exhibit specificity in protein complex formation, based on available crystal structures and several intuitive ideas about interaction profiles and functional subclasses. We then defined a "structure-based specificity determining position (sbSDP)" as a set of equivalent residues in a protein family showing a large variation in their interaction energy with different partners. We investigated sequence and structural features of sbSDPs and demonstrated that their amino acid propensities significantly differed from those of other interacting residues and that the importance of many of these residues for determining specificity had been verified experimentally. Copyright © 2012 Wiley Periodicals, Inc.

Analytical theory and method for longitudinal magneto-optical Kerr effect of optically anisotropic magnetic film

Energy Technology Data Exchange (ETDEWEB)

Wang, Xiao, E-mail: sps_wangx@ujn.edu.cn [School of Physics and Technology, University of Jinan, Jinan 250022 (China); School of Material Science and Engineering, University of Jinan, Jinan 250022 (China); Lian, Jie [School of Information Science and Engineering, Shandong University, Jinan 250100 (China); Li, Ping; Xu, XiJin [School of Physics and Technology, University of Jinan, Jinan 250022 (China); Li, MengMeng [School of Information Science and Engineering, Shandong University, Jinan 250100 (China)

2017-01-15

The Fresnel equations are solved to analyze the reflection and propagation properties of the ordinary and extraordinary light of the optically anisotropic magnetic film. Using the boundary and propagation matrix, the longitudinal magneto-optical Kerr rotation expression is derived. After that, simulations are performed on optically anisotropic and isotropic Co/SiO{sub 2} film. Results show that for Co material in the thin-film limit, the anisotropic Co can provide larger max rotations than the isotropic Co in the visible region. This is because that the refractive index discrepancy of optically anisotropic Co film reduces the Fresnel reflective coefficient r{sub pp,} which improves the Kerr rotation. This makes the optically anisotropic Co film more effective in magneto optical sensor design and device fabrication. - Highlights: • In this work, using the boundary matrix and media propagation matrix developed by Zak and S.D.Bader,we get the analytical solution of the magneto-optical Kerr rotation of the optical anisotropic magnetic film. • Results show that for film in the thin-film limit, the anisotropic Co can provide larger maximum rotations than the isotropic Co. • The improvement of Kerr rotation can be attributed to the refractive index discrepancy of optically anisotropic Co film which reduce the Fresnel reflective coefficient rpp.

Collision-induced absorption with exchange effects and anisotropic interactions: theory and application to H2 - H2.

Science.gov (United States)

Karman, Tijs; van der Avoird, Ad; Groenenboom, Gerrit C

2015-02-28

We discuss three quantum mechanical formalisms for calculating collision-induced absorption spectra. First, we revisit the established theory of collision-induced absorption, assuming distinguishable molecules which interact isotropically. Then, the theory is rederived incorporating exchange effects between indistinguishable molecules. It is shown that the spectrum can no longer be written as an incoherent sum of the contributions of the different spherical components of the dipole moment. Finally, we derive an efficient method to include the effects of anisotropic interactions in the computation of the absorption spectrum. This method calculates the dipole coupling on-the-fly, which allows for the uncoupled treatment of the initial and final states without the explicit reconstruction of the many-component wave functions. The three formalisms are applied to the collision-induced rotation-translation spectra of hydrogen molecules in the far-infrared. Good agreement with experimental data is obtained. Significant effects of anisotropic interactions are observed in the far wing.

Anisotropic cosmological solutions in massive vector theories

Energy Technology Data Exchange (ETDEWEB)

Heisenberg, Lavinia [Institute for Theoretical Studies, ETH Zurich, Clausiusstrasse 47, 8092 Zurich (Switzerland); Kase, Ryotaro; Tsujikawa, Shinji, E-mail: Lavinia.heisenberg@googlemail.com, E-mail: r.kase@rs.tus.ac.jp, E-mail: shinji@rs.kagu.tus.ac.jp [Department of Physics, Faculty of Science, Tokyo University of Science, 1-3, Kagurazaka, Shinjuku-ku, Tokyo 162-8601 (Japan)

2016-11-01

In beyond-generalized Proca theories including the extension to theories higher than second order, we study the role of a spatial component v of a massive vector field on the anisotropic cosmological background. We show that, as in the case of the isotropic cosmological background, there is no additional ghostly degrees of freedom associated with the Ostrogradski instability. In second-order generalized Proca theories we find the existence of anisotropic solutions on which the ratio between the anisotropic expansion rate Σ and the isotropic expansion rate H remains nearly constant in the radiation-dominated epoch. In the regime where Σ/ H is constant, the spatial vector component v works as a dark radiation with the equation of state close to 1/3. During the matter era, the ratio Σ/ H decreases with the decrease of v . As long as the conditions |Σ| || H and v {sup 2} || φ{sup 2} are satisfied around the onset of late-time cosmic acceleration, where φ is the temporal vector component, we find that the solutions approach the isotropic de Sitter fixed point (Σ = 0 = v ) in accordance with the cosmic no-hair conjecture. In the presence of v and Σ the early evolution of the dark energy equation of state w {sub DE} in the radiation era is different from that in the isotropic case, but the approach to the isotropic value w {sub DE}{sup (iso)} typically occurs at redshifts z much larger than 1. Thus, apart from the existence of dark radiation, the anisotropic cosmological dynamics at low redshifts is similar to that in isotropic generalized Proca theories. In beyond-generalized Proca theories the only consistent solution to avoid the divergence of a determinant of the dynamical system corresponds to v = 0, so Σ always decreases in time.

Anisotropic cosmological solutions in massive vector theories

International Nuclear Information System (INIS)

Heisenberg, Lavinia; Kase, Ryotaro; Tsujikawa, Shinji

2016-01-01

In beyond-generalized Proca theories including the extension to theories higher than second order, we study the role of a spatial component v of a massive vector field on the anisotropic cosmological background. We show that, as in the case of the isotropic cosmological background, there is no additional ghostly degrees of freedom associated with the Ostrogradski instability. In second-order generalized Proca theories we find the existence of anisotropic solutions on which the ratio between the anisotropic expansion rate Σ and the isotropic expansion rate H remains nearly constant in the radiation-dominated epoch. In the regime where Σ/ H is constant, the spatial vector component v works as a dark radiation with the equation of state close to 1/3. During the matter era, the ratio Σ/ H decreases with the decrease of v . As long as the conditions |Σ| || H and v 2 || φ 2 are satisfied around the onset of late-time cosmic acceleration, where φ is the temporal vector component, we find that the solutions approach the isotropic de Sitter fixed point (Σ = 0 = v ) in accordance with the cosmic no-hair conjecture. In the presence of v and Σ the early evolution of the dark energy equation of state w DE in the radiation era is different from that in the isotropic case, but the approach to the isotropic value w DE (iso) typically occurs at redshifts z much larger than 1. Thus, apart from the existence of dark radiation, the anisotropic cosmological dynamics at low redshifts is similar to that in isotropic generalized Proca theories. In beyond-generalized Proca theories the only consistent solution to avoid the divergence of a determinant of the dynamical system corresponds to v = 0, so Σ always decreases in time.

A simple strategy to realize biomimetic surfaces with controlled anisotropic wetting

Science.gov (United States)

Wu, Dong; Chen, Qi-Dai; Yao, Jia; Guan, Yong-Chao; Wang, Jian-Nan; Niu, Li-Gang; Fang, Hong-Hua; Sun, Hong-Bo

2010-02-01

The study of anisotropic wetting has become one of the most important research areas in biomimicry. However, realization of controlled anisotropic surfaces remains challenging. Here we investigated anisotropic wetting on grooves with different linewidth, period, and height fabricated by laser interference lithography and found that the anisotropy strongly depended on the height. The anisotropy significantly increased from 9° to 48° when the height was changed from 100 nm to 1.3 μm. This was interpreted by a thermodynamic model as a consequence of the increase of free energy barriers versus the height increase. According to the relationship, controlled anisotropic surfaces were rapidly realized by adjusting the grooves' height that was simply accomplished by changing the resin thickness. Finally, the perpendicular contact angle was further enhanced to 131°±2° by surface modification, which was very close to 135°±3° of a common grass leaf.

Protein 3D structure computed from evolutionary sequence variation.

Directory of Open Access Journals (Sweden)

Debora S Marks

Full Text Available The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org. This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of

Pattern formation of a nonlocal, anisotropic interaction model

KAUST Repository

Burger, Martin

2017-11-24

We consider a class of interacting particle models with anisotropic, repulsive–attractive interaction forces whose orientations depend on an underlying tensor field. An example of this class of models is the so-called Kücken–Champod model describing the formation of fingerprint patterns. This class of models can be regarded as a generalization of a gradient flow of a nonlocal interaction potential which has a local repulsion and a long-range attraction structure. In contrast to isotropic interaction models the anisotropic forces in our class of models cannot be derived from a potential. The underlying tensor field introduces an anisotropy leading to complex patterns which do not occur in isotropic models. This anisotropy is characterized by one parameter in the model. We study the variation of this parameter, describing the transition between the isotropic and the anisotropic model, analytically and numerically. We analyze the equilibria of the corresponding mean-field partial differential equation and investigate pattern formation numerically in two dimensions by studying the dependence of the parameters in the model on the resulting patterns.

Pattern formation of a nonlocal, anisotropic interaction model

KAUST Repository

Burger, Martin; Dü ring, Bertram; Kreusser, Lisa Maria; Markowich, Peter A.; Schö nlieb, Carola-Bibiane

2017-01-01

We consider a class of interacting particle models with anisotropic, repulsive–attractive interaction forces whose orientations depend on an underlying tensor field. An example of this class of models is the so-called Kücken–Champod model describing the formation of fingerprint patterns. This class of models can be regarded as a generalization of a gradient flow of a nonlocal interaction potential which has a local repulsion and a long-range attraction structure. In contrast to isotropic interaction models the anisotropic forces in our class of models cannot be derived from a potential. The underlying tensor field introduces an anisotropy leading to complex patterns which do not occur in isotropic models. This anisotropy is characterized by one parameter in the model. We study the variation of this parameter, describing the transition between the isotropic and the anisotropic model, analytically and numerically. We analyze the equilibria of the corresponding mean-field partial differential equation and investigate pattern formation numerically in two dimensions by studying the dependence of the parameters in the model on the resulting patterns.

DNA-nanoparticle superlattices formed from anisotropic building blocks

Science.gov (United States)

Jones, Matthew R.; Macfarlane, Robert J.; Lee, Byeongdu; Zhang, Jian; Young, Kaylie L.; Senesi, Andrew J.; Mirkin, Chad A.

2010-11-01

Directional bonding interactions in solid-state atomic lattices dictate the unique symmetries of atomic crystals, resulting in a diverse and complex assortment of three-dimensional structures that exhibit a wide variety of material properties. Methods to create analogous nanoparticle superlattices are beginning to be realized, but the concept of anisotropy is still largely underdeveloped in most particle assembly schemes. Some examples provide interesting methods to take advantage of anisotropic effects, but most are able to make only small clusters or lattices that are limited in crystallinity and especially in lattice parameter programmability. Anisotropic nanoparticles can be used to impart directional bonding interactions on the nanoscale, both through face-selective functionalization of the particle with recognition elements to introduce the concept of valency, and through anisotropic interactions resulting from particle shape. In this work, we examine the concept of inherent shape-directed crystallization in the context of DNA-mediated nanoparticle assembly. Importantly, we show how the anisotropy of these particles can be used to synthesize one-, two- and three-dimensional structures that cannot be made through the assembly of spherical particles.

Surface Waves Propagating on Grounded Anisotropic Dielectric Slab

Directory of Open Access Journals (Sweden)

Zhuozhu Chen

2018-01-01

Full Text Available This paper investigates the characteristics of surface waves propagating on a grounded anisotropic dielectric slab. Distinct from the existing analyses that generally assume that the fields of surface wave uniformly distribute along the transverse direction of the infinitely large grounded slab, our method takes into account the field variations along the transverse direction of a finite-width slab. By solving Maxwell’s equations in closed-form, it is revealed that no pure transverse magnetic (TM or transverse electric (TE mode exists if the fields are non-uniformly distributed along the transverse direction of the grounded slab. Instead, two hybrid modes, namely quasi-TM and quasi-TE modes, are supported. In addition, the propagation characteristics of two hybrid modes supported by the grounded anisotropic slab are analyzed in terms of the slab thickness, slab width, as well as the relative permittivity tensor of the anisotropic slab. Furthermore, different methods are employed to compare the analyses, as well as to validate our derivations. The proposed method is very suitable for practical engineering applications.

Newton–Hooke-type symmetry of anisotropic oscillators

International Nuclear Information System (INIS)

Zhang, P.M.; Horvathy, P.A.; Andrzejewski, K.; Gonera, J.; Kosiński, P.

2013-01-01

Rotation-less Newton–Hooke-type symmetry, found recently in the Hill problem, and instrumental for explaining the center-of-mass decomposition, is generalized to an arbitrary anisotropic oscillator in the plane. Conversely, the latter system is shown, by the orbit method, to be the most general one with such a symmetry. Full Newton–Hooke symmetry is recovered in the isotropic case. Star escape from a galaxy is studied as an application. -- Highlights: ► Rotation-less Newton–Hooke (NH) symmetry is generalized to an arbitrary anisotropic oscillator. ► The orbit method is used to find the most general case for rotation-less NH symmetry. ► The NH symmetry is decomposed into Heisenberg algebras based on chiral decomposition

Inflationary perturbations in anisotropic, shear-free universes

International Nuclear Information System (INIS)

Pereira, Thiago S.; Carneiro, Saulo; Marugan, Guillermo A. Mena

2012-01-01

In this work, the linear and gauge-invariant theory of cosmological perturbations in a class of anisotropic and shear-free spacetimes is developed. After constructing an explicit set of complete eigenfunctions in terms of which perturbations can be expanded, we identify the effective degrees of freedom during a generic slow-roll inflationary phase. These correspond to the anisotropic equivalent of the standard Mukhanov-Sasaki variables. The associated equations of motion present a remarkable resemblance to those found in perturbed Friedmann-Robertson-Walker spacetimes with curvature, apart from the spectrum of the Laplacian, which exhibits the characteristic frequencies of the underlying geometry. In particular, it is found that the perturbations cannot develop arbitrarily large super-Hubble modes

Computational enzyme design: transitioning from catalytic proteins to enzymes.

Science.gov (United States)

Mak, Wai Shun; Siegel, Justin B

2014-08-01

The widespread interest in enzymes stem from their ability to catalyze chemical reactions under mild and ecologically friendly conditions with unparalleled catalytic proficiencies. While thousands of naturally occurring enzymes have been identified and characterized, there are still numerous important applications for which there are no biological catalysts capable of performing the desired chemical transformation. In order to engineer enzymes for which there is no natural starting point, efforts using a combination of quantum chemistry and force-field based protein molecular modeling have led to the design of novel proteins capable of catalyzing chemical reactions not catalyzed by naturally occurring enzymes. Here we discuss the current status and potential avenues to pursue as the field of computational enzyme design moves forward. Published by Elsevier Ltd.

A magnetic relaxation study on anisotropic reorientation in aqueous polyelectrolyte solutions

International Nuclear Information System (INIS)

Mulder, C.W.R.

1984-01-01

The present thesis proposes a study on anisotropic reorientation of aqueous polyelectrolyte solutions. In particular, it is directed to the question to what extent information may be obtained on anisotropic reorientation by nuclear magnetic relaxation experiments. The polymethacrylic acid/water system has been chosen as probe system. (Auth.)

Anisotropic magnetoresistance in a Fermi glass

International Nuclear Information System (INIS)

Ovadyahu, Z.; Physics Department, Ben-Gurion University of the Negev, Beer-Sheva, Israel 84120)

1986-01-01

Insulating thin films of indium oxide exhibit negative, anisotropic magnetoresistance. The systematics of these results imply that the magnetoresistance mechanism may give different weight to the distribution of the localization lengths than that given by the hopping conductivity

Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding.

Science.gov (United States)

Isvoran, Adriana; Craciun, Dana; Martiny, Virginie; Sperandio, Olivier; Miteva, Maria A

2013-06-14

Protein-Protein Interactions (PPIs) are key for many cellular processes. The characterization of PPI interfaces and the prediction of putative ligand binding sites and hot spot residues are essential to design efficient small-molecule modulators of PPI. Terphenyl and its derivatives are small organic molecules known to mimic one face of protein-binding alpha-helical peptides. In this work we focus on several PPIs mediated by alpha-helical peptides. We performed computational sequence- and structure-based analyses in order to evaluate several key physicochemical and surface properties of proteins known to interact with alpha-helical peptides and/or terphenyl and its derivatives. Sequence-based analysis revealed low sequence identity between some of the analyzed proteins binding alpha-helical peptides. Structure-based analysis was performed to calculate the volume, the fractal dimension roughness and the hydrophobicity of the binding regions. Besides the overall hydrophobic character of the binding pockets, some specificities were detected. We showed that the hydrophobicity is not uniformly distributed in different alpha-helix binding pockets that can help to identify key hydrophobic hot spots. The presence of hydrophobic cavities at the protein surface with a more complex shape than the entire protein surface seems to be an important property related to the ability of proteins to bind alpha-helical peptides and low molecular weight mimetics. Characterization of similarities and specificities of PPI binding sites can be helpful for further development of small molecules targeting alpha-helix binding proteins.

Adaptive anisotropic diffusion filtering of Monte Carlo dose distributions

International Nuclear Information System (INIS)

Miao Binhe; Jeraj, Robert; Bao Shanglian; Mackie, Thomas R

2003-01-01

The Monte Carlo method is the most accurate method for radiotherapy dose calculations, if used correctly. However, any Monte Carlo dose calculation is burdened with statistical noise. In this paper, denoising of Monte Carlo dose distributions with a three-dimensional adaptive anisotropic diffusion method was investigated. The standard anisotropic diffusion method was extended by changing the filtering parameters adaptively according to the local statistical noise. Smoothing of dose distributions with different noise levels in an inhomogeneous phantom, a conventional and an IMRT treatment case is shown. The resultant dose distributions were analysed using several evaluating criteria. It is shown that the adaptive anisotropic diffusion method can reduce statistical noise significantly (two to five times, corresponding to the reduction of simulation time by a factor of up to 20), while preserving important gradients of the dose distribution well. The choice of free parameters of the method was found to be fairly robust

Inhomogeneous anisotropic cosmology

International Nuclear Information System (INIS)

Kleban, Matthew; Senatore, Leonardo

2016-01-01

In homogeneous and isotropic Friedmann-Robertson-Walker cosmology, the topology of the universe determines its ultimate fate. If the Weak Energy Condition is satisfied, open and flat universes must expand forever, while closed cosmologies can recollapse to a Big Crunch. A similar statement holds for homogeneous but anisotropic (Bianchi) universes. Here, we prove that arbitrarily inhomogeneous and anisotropic cosmologies with “flat” (including toroidal) and “open” (including compact hyperbolic) spatial topology that are initially expanding must continue to expand forever at least in some region at a rate bounded from below by a positive number, despite the presence of arbitrarily large density fluctuations and/or the formation of black holes. Because the set of 3-manifold topologies is countable, a single integer determines the ultimate fate of the universe, and, in a specific sense, most 3-manifolds are “flat” or “open”. Our result has important implications for inflation: if there is a positive cosmological constant (or suitable inflationary potential) and initial conditions for the inflaton, cosmologies with “flat” or “open” topology must expand forever in some region at least as fast as de Sitter space, and are therefore very likely to begin inflationary expansion eventually, regardless of the scale of the inflationary energy or the spectrum and amplitude of initial inhomogeneities and gravitational waves. Our result is also significant for numerical general relativity, which often makes use of periodic (toroidal) boundary conditions.

Longitudinal fluctuations and decorrelation of anisotropic flow

Energy Technology Data Exchange (ETDEWEB)

Pang, Long-Gang [Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, 60438 Frankfurt am Main (Germany); Petersen, Hannah [Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, 60438 Frankfurt am Main (Germany); Institute for Theoretical Physics, Goethe University, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main (Germany); GSI Helmholtzzentrum für Schwerionenforschung, Planckstr. 1, 64291 Darmstadt (Germany); Qin, Guang-You [Key Laboratory of Quark & Lepton Physics (MOE) and Institute of Particle Physics, Central China Normal University, Wuhan 430079 (China); Roy, Victor [Institute for Theoretical Physics, Goethe University, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main (Germany); Wang, Xin-Nian [Key Laboratory of Quark & Lepton Physics (MOE) and Institute of Particle Physics, Central China Normal University, Wuhan 430079 (China); Nuclear Science Division MS70R0319, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)

2016-12-15

We investigate the decorrelation of 2nd and 3rd order anisotropic flow for charged particles in two different pseudo rapidity (η) windows by varying the pseudo rapidity gap, in an event-by-event (3+1)D ideal hydrodynamic model, with fluctuating initial conditions from A Multi-Phase Transport (AMPT) model. We visualize the parton distribution at initial state for Pb+Pb collisions at LHC and Au+Au collisions at RHIC, and demonstrate the longitudinal fluctuations originating from the asymmetry between forward and backward going participants, the fluctuations of the string length and the fluctuations due to finite number of partons at different beam energies. The decorrelation of anisotropic flow of final hadrons with large η gaps is found to originate from the spatial decorrelation along the longitudinal direction in the AMPT initial conditions through hydrodynamic evolution. The agreement between our results and recent CMS data in most centralities suggests that the string-like mechanism of initial parton production in AMPT model captures the initial longitudinal fluctuation that is responsible for the measured decorrelation of anisotropic flow in Pb+Pb collisions at LHC. Our predictions for Au+Au collisions at the highest RHIC energy show stronger longitudinal decorrelation than at LHC, indicating larger longitudinal fluctuations at lower beam energies.

Magnetic relaxation in anisotropic magnets

DEFF Research Database (Denmark)

Lindgård, Per-Anker

1971-01-01

The line shape and the kinematic and thermodynamic slowing down of the critical and paramagnetic relaxation in axially anisotropic materials are discussed. Kinematic slowing down occurs only in the longitudinal relaxation function. The thermodynamic slowing down occurs in either the transverse...... or longitudinal relaxation function depending on the sign of the axial anisotropy....

Anisotropic stress as a signature of nonstandard propagation of gravitational waves.

Science.gov (United States)

Saltas, Ippocratis D; Sawicki, Ignacy; Amendola, Luca; Kunz, Martin

2014-11-07

We make precise the heretofore ambiguous statement that anisotropic stress is a sign of a modification of gravity. We show that in cosmological solutions of very general classes of models extending gravity-all scalar-tensor theories (Horndeski), Einstein-aether models, and bimetric massive gravity-a direct correspondence exists between perfect fluids apparently carrying anisotropic stress and a modification in the propagation of gravitational waves. Since the anisotropic stress can be measured in a model-independent manner, a comparison of the behavior of gravitational waves from cosmological sources with large-scale-structure formation could, in principle, lead to new constraints on the theory of gravity.

Anisotropic Failure Strength of Shale with Increasing Confinement: Behaviors, Factors and Mechanism.

Science.gov (United States)

Cheng, Cheng; Li, Xiao; Qian, Haitao

2017-11-15

Some studies reported that the anisotropic failure strength of shale will be weakened by increasing confinement. In this paper, it is found that there are various types of anisotropic strength behaviors. Four types of anisotropic strength ratio ( S A 1 ) behaviors and three types of anisotropic strength difference ( S A 2 ) behaviors have been classified based on laboratory experiments on nine groups of different shale samples. The cohesion c w and friction angle ϕ w of the weak planes are proven to be two dominant factors according to a series of bonded-particle discrete element modelling analyses. It is observed that shale is more prone to a slight increase of S A 1 and significant increase of S A 2 with increasing confinement for higher cohesion c w and lower to medium friction angle ϕ w . This study also investigated the mechanism of the anisotropic strength behaviors with increasing confinement. Owing to different contributions of c w and ϕ w under different confinements, different combinations of c w and ϕ w may have various types of influences on the minimum failure strength with the increasing confinement; therefore, different types of anisotropic behaviors occur for different shale specimens as the confinement increases. These findings are very important to understand the stability of wellbore and underground tunneling in the shale rock mass, and should be helpful for further studies on hydraulic fracture propagations in the shale reservoir.

An optimization-based framework for anisotropic simplex mesh adaptation

Science.gov (United States)

Yano, Masayuki; Darmofal, David L.

2012-09-01

We present a general framework for anisotropic h-adaptation of simplex meshes. Given a discretization and any element-wise, localizable error estimate, our adaptive method iterates toward a mesh that minimizes error for a given degrees of freedom. Utilizing mesh-metric duality, we consider a continuous optimization problem of the Riemannian metric tensor field that provides an anisotropic description of element sizes. First, our method performs a series of local solves to survey the behavior of the local error function. This information is then synthesized using an affine-invariant tensor manipulation framework to reconstruct an approximate gradient of the error function with respect to the metric tensor field. Finally, we perform gradient descent in the metric space to drive the mesh toward optimality. The method is first demonstrated to produce optimal anisotropic meshes minimizing the L2 projection error for a pair of canonical problems containing a singularity and a singular perturbation. The effectiveness of the framework is then demonstrated in the context of output-based adaptation for the advection-diffusion equation using a high-order discontinuous Galerkin discretization and the dual-weighted residual (DWR) error estimate. The method presented provides a unified framework for optimizing both the element size and anisotropy distribution using an a posteriori error estimate and enables efficient adaptation of anisotropic simplex meshes for high-order discretizations.

Study of anisotropic mechanical properties for aeronautical PMMA

Directory of Open Access Journals (Sweden)

Wei Shang

Full Text Available For the properties of polymer are relative to its structure, the main purpose of the present work is to investigate the mechanical properties of the aeronautical PMMA which has been treated by the directional tensile technology. Isodyne images reveal the stress state in directional PMMA. And then, an anisotropic mechanical model is established. Furthermore, all mechanical parameters are measured by the digital image correlation method. Finally, based on the anisotropic mechanical model and mechanical parameters, the FEM numerical simulation and experimental methods are applied to analyze the fracture mechanical properties along different directions.

Understanding nanoparticle-mediated nucleation pathways of anisotropic nanoparticles

Science.gov (United States)

Laramy, Christine R.; Fong, Lam-Kiu; Jones, Matthew R.; O'Brien, Matthew N.; Schatz, George C.; Mirkin, Chad A.

2017-09-01

Several seed-mediated syntheses of low symmetry anisotropic nanoparticles yield broad product distributions with multiple defect structures. This observation challenges the role of the nanoparticle precursor as a seed for certain syntheses and suggests the possibility of alternate nucleation pathways. Herein, we report a method to probe the role of the nanoparticle precursor in anisotropic nanoparticle nucleation with compositional and structural 'labels' to track their fate. We use the synthesis of gold triangular nanoprisms (Au TPs) as a model system. We propose a mechanism in which, rather than acting as a template, the nanoparticle precursor catalyzes homogenous nucleation of Au TPs.

MHz gravitational waves from short-term anisotropic inflation

International Nuclear Information System (INIS)

Ito, Asuka; Soda, Jiro

2016-01-01

We reveal the universality of short-term anisotropic inflation. As a demonstration, we study inflation with an exponential type gauge kinetic function which is ubiquitous in models obtained by dimensional reduction from higher dimensional fundamental theory. It turns out that an anisotropic inflation universally takes place in the later stage of conventional inflation. Remarkably, we find that primordial gravitational waves with a peak amplitude around 10 −26 ∼10 −27 are copiously produced in high-frequency bands 10 MHz∼100 MHz. If we could detect such gravitational waves in future, we would be able to probe higher dimensional fundamental theory.

Thermal fluctuations and critical behavior in a magnetized, anisotropic plasma

International Nuclear Information System (INIS)

Hazeltine, R. D.; Mahajan, S. M.

2013-01-01

Thermal fluctuations in a magnetized, anisotropic plasma are studied by applying standard methods, based on the Einstein rule, to the known thermodynamic potential of the system. It is found in particular that magnetic fluctuations become critical when the anisotropy p ∥ −p ⊥ changes sign. By examining the critical region, additional insight on the equations of state for near-critical anisotropic plasma is obtained

Subsurface Flow Modeling in Single and Dual Continuum Anisotropic Porous Media using the Multipoint Flux Approximation Method

KAUST Repository

Negara, Ardiansyah

2015-05-01

phases, migrates upwards and the anisotropy aligns the flow directions closer to the principal direction of anisotropy. Lastly, for the gas flow modeling in anisotropic shale reservoirs, we observe that anisotropy affects the pressure fields and the velocity fields of the matrix and fracture systems as well as the production rate and cumulative production. It is observed from the results that all of the anisotropic cases produce higher amount of gas compared to isotropic case during the same production time. Furthermore, we have also examined the performance of MPFA with respect to mixed finite element (MFE) method over the lowest-order Raviart-Thomas (RT0) space and the first-order Brezzi-Douglas-Marini (BDM1) space. From the comparison of the numerical results we observe that MPFA method show very good agreement with the BDM1 than RT0. In terms of numerical implementation, however, MPFA method is easier than BDM1 and it also offers explicit discrete fluxes that are advantageous. Combining MPFA with the experimenting pressure field approach will certainly adds another advantage of implementing MPFA method as compared with RT0 and BDM1. Moreover, the computational cost (CPU cost) of the three different methods are also discussed.

Effective medium theory for anisotropic metamaterials

KAUST Repository

Zhang, Xiujuan; Wu, Ying

2015-01-01

-dimensional metamaterial composed of a rectangular array of elliptic cylinders and derive an effective medium theory for such a metamaterial. We find that it is possible to obtain a closed-form analytical solution for the anisotropic effective medium parameters, provided

Casimir interactions for anisotropic magnetodielectric metamaterials

Energy Technology Data Exchange (ETDEWEB)

Da Rosa, Felipe S [Los Alamos National Laboratory; Dalvit, Diego A [Los Alamos National Laboratory; Milonni, Peter W [Los Alamos National Laboratory

2008-01-01

We extend our previous work on the generalization of the Casimir-Lifshitz theory to treat anisotropic magnetodielectric media, focusing on the forces between metals and magnetodielectric metamaterials and on the possibility of inferring magnetic effects by measurements of these forces.

Acoustic anisotropic wavefields through perturbation theory

KAUST Repository

Alkhalifah, Tariq Ali

2013-01-01

these restrictions are the inability to handle media with η<0 and the presence of shear-wave artifacts in the solution. Both limitations do not exist in the solution of the elliptical anisotropic acoustic wave equation. Using perturbation theory in developing

Anisotropic modelling of the electrical conductivity of fractured bedrock

International Nuclear Information System (INIS)

Flykt, M.J.; Sihvola, A.H.; Eloranta, E.H.

1995-01-01

The electromagnetic characterization of fractured bedrock is of importance when studying the final disposal of nuclear waste. The different types of discontinuities at all scales in rocks can be viewed as an inhomogeneity. In some cases there are reasons to assume the influence of the discontinuities on electrical conductivity is anisotropic in character. The effort has been made to use electromagnetic mixing rules in the definition of an equivalent homogeneous anisotropic conductivity tensor for such fractured rock mass. (author) (16 refs., 6 figs.)

Fourier Multipliers on Anisotropic Mixed-Norm Spaces of Distributions

DEFF Research Database (Denmark)

Cleanthous, Galatia; Georgiadis, Athanasios; Nielsen, Morten

2018-01-01

A new general Hormander type condition involving anisotropies and mixed norms is introduced, and boundedness results for Fourier multi- pliers on anisotropic Besov and Triebel-Lizorkin spaces of distributions with mixed Lebesgue norms are obtained. As an application, the continuity of such operat......A new general Hormander type condition involving anisotropies and mixed norms is introduced, and boundedness results for Fourier multi- pliers on anisotropic Besov and Triebel-Lizorkin spaces of distributions with mixed Lebesgue norms are obtained. As an application, the continuity...

Features of the electric-field distribution in anisotropic semiconductor wafers in a transverse magnetic field

International Nuclear Information System (INIS)

Filippov, V. V.; Bormontov, E. N.

2013-01-01

A macroscopic model of the Hall effects and magnetoresistance in anisotropic semiconductor wafers is developed. The results obtained by solving the electrodynamic boundary problem allow the potential and eddy currents in anisotropic semiconductors to be calculated at different current-contact locations, depending on the parameters of the sample material’s anisotropy. The results of this study are of great practical importance for investigating the physical properties of anisotropic semiconductors and simulating the electron-transport phenomena in devices based on anisotropic semiconductors

Features of the electric-field distribution in anisotropic semiconductor wafers in a transverse magnetic field

Energy Technology Data Exchange (ETDEWEB)

Filippov, V. V., E-mail: wwfilippow@mail.ru [Lipetsk State Pedagogical University (Russian Federation); Bormontov, E. N. [Voronezh State University (Russian Federation)

2013-07-15

A macroscopic model of the Hall effects and magnetoresistance in anisotropic semiconductor wafers is developed. The results obtained by solving the electrodynamic boundary problem allow the potential and eddy currents in anisotropic semiconductors to be calculated at different current-contact locations, depending on the parameters of the sample material's anisotropy. The results of this study are of great practical importance for investigating the physical properties of anisotropic semiconductors and simulating the electron-transport phenomena in devices based on anisotropic semiconductors.

1-D DC Resistivity Modeling and Interpretation in Anisotropic Media Using Particle Swarm Optimization

Science.gov (United States)

Pekşen, Ertan; Yas, Türker; Kıyak, Alper

2014-09-01

We examine the one-dimensional direct current method in anisotropic earth formation. We derive an analytic expression of a simple, two-layered anisotropic earth model. Further, we also consider a horizontally layered anisotropic earth response with respect to the digital filter method, which yields a quasi-analytic solution over anisotropic media. These analytic and quasi-analytic solutions are useful tests for numerical codes. A two-dimensional finite difference earth model in anisotropic media is presented in order to generate a synthetic data set for a simple one-dimensional earth. Further, we propose a particle swarm optimization method for estimating the model parameters of a layered anisotropic earth model such as horizontal and vertical resistivities, and thickness. The particle swarm optimization is a naturally inspired meta-heuristic algorithm. The proposed method finds model parameters quite successfully based on synthetic and field data. However, adding 5 % Gaussian noise to the synthetic data increases the ambiguity of the value of the model parameters. For this reason, the results should be controlled by a number of statistical tests. In this study, we use probability density function within 95 % confidence interval, parameter variation of each iteration and frequency distribution of the model parameters to reduce the ambiguity. The result is promising and the proposed method can be used for evaluating one-dimensional direct current data in anisotropic media.

Nonlinear, anisotropic, and giant photoconductivity in intrinsic and doped graphene

Science.gov (United States)

Singh, Ashutosh; Ghosh, Saikat; Agarwal, Amit

2018-01-01

We present a framework to calculate the anisotropic and nonlinear photoconductivity for two band systems with application to graphene. In contrast to the usual perturbative (second order in the optical field strength) techniques, we calculate photoconductivity to all orders in the optical field strength. In particular, for graphene, we find the photoresponse to be giant (at large optical field strengths) and anisotropic. The anisotropic photoresponse in graphene is correlated with polarization of the incident field, with the response being similar to that of a half-wave plate. We predict that the anisotropy in the simultaneous measurement of longitudinal (σx x) and transverse (σy x) photoconductivity, with four probes, offers a unique experimental signature of the photovoltaic response, distinguishing it from the thermal-Seebeck and bolometric effects in photoresponse.

Anisotropic Margin Expansions in 6 Anatomic Directions for Oropharyngeal Image Guided Radiation Therapy

International Nuclear Information System (INIS)

Yock, Adam D.; Garden, Adam S.; Court, Laurence E.; Beadle, Beth M.; Zhang, Lifei; Dong, Lei

2013-01-01

Purpose: The purpose of this work was to determine the expansions in 6 anatomic directions that produced optimal margins considering nonrigid setup errors and tissue deformation for patients receiving image-guided radiation therapy (IGRT) of the oropharynx. Methods and Materials: For 20 patients who had received IGRT to the head and neck, we deformably registered each patient's daily images acquired with a computed tomography (CT)-on-rails system to his or her planning CT. By use of the resulting vector fields, the positions of volume elements within the clinical target volume (CTV) (target voxels) or within a 1-cm shell surrounding the CTV (normal tissue voxels) on the planning CT were identified on each daily CT. We generated a total of 15,625 margins by dilating the CTV by 1, 2, 3, 4, or 5 mm in the posterior, anterior, lateral, medial, inferior, and superior directions. The optimal margins were those that minimized the relative volume of normal tissue voxels positioned within the margin while satisfying 1 of 4 geometric target coverage criteria and 1 of 3 population criteria. Results: Each pair of geometric target coverage and population criteria resulted in a unique, anisotropic, optimal margin. The optimal margin expansions ranged in magnitude from 1 to 5 mm depending on the anatomic direction of the expansion and on the geometric target coverage and population criteria. Typically, the expansions were largest in the medial direction, were smallest in the lateral direction, and increased with the demand of the criteria. The anisotropic margin resulting from the optimal set of expansions always included less normal tissue than did any isotropic margin that satisfied the same pair of criteria. Conclusions: We demonstrated the potential of anisotropic margins to reduce normal tissue exposure without compromising target coverage in IGRT to the head and neck

A novel 2.5D finite difference scheme for simulations of resistivity logging in anisotropic media

Science.gov (United States)

Zeng, Shubin; Chen, Fangzhou; Li, Dawei; Chen, Ji; Chen, Jiefu

2018-03-01

The objective of this study is to develop a method to model 3D resistivity well logging problems in 2D formation with anisotropy, known as 2.5D modeling. The traditional 1D forward modeling extensively used in practice lacks the capability of modeling 2D formation. A 2.5D finite difference method (FDM) solving all the electric and magnetic field components simultaneously is proposed. Compared to other previous 2.5D FDM schemes, this method is more straightforward in modeling fully anisotropic media and easy to be implemented. Fourier transform is essential to this FDM scheme, and by employing Gauss-Legendre (GL) quadrature rule the computational time of this step can be greatly reduced. In the numerical examples, we first demonstrate the validity of the FDM scheme with GL rule by comparing with 1D forward modeling for layered anisotropic problems, and then we model a complicated 2D formation case and find that the proposed 2.5D FD scheme is much more efficient than 3D numerical methods.

Computer simulations of radiation damage in protein crystals

International Nuclear Information System (INIS)

Zehnder, M.

2007-03-01

The achievable resolution and the quality of the dataset of an intensity data collection for structure analysis of protein crystals with X-rays is limited among other factors by radiation damage. The aim of this work is to obtain a better quantitative understanding of the radiation damage process in proteins. Since radiation damage is unavoidable it was intended to look for the optimum ratio between elastically scattered intensity and radiation damage. Using a Monte Carlo algorithm physical processes after an inelastic photon interaction are studied. The main radiation damage consists of ionizations of the atoms through the electron cascade following any inelastic photon interaction. Results of the method introduced in this investigation and results of an earlier theoretical studies of the influence of Auger-electron transport in diamond are in a good agreement. The dependence of the radiation damage as a function of the energy of the incident photon was studied by computer-aided simulations. The optimum energy range for diffraction experiments on the protein myoglobin is 10-40 keV. Studies of radiation damage as a function of crystal volume and shape revealed that very small plate or rod shaped crystals suffer less damage than crystals formed like a cube with the same volume. Furthermore the influence of a few heavy atoms in the protein molecule on radiation damage was examined. Already two iron atoms in the unit cell of myoglobin increase radiation damage significantly. (orig.)

Low-loss single-mode hollow-core fiber with anisotropic anti-resonant elements

DEFF Research Database (Denmark)

Habib, Selim; Bang, Ole; Bache, Morten

2016-01-01

A hollow-core fiber using anisotropic anti-resonant tubes in thecladding is proposed for low loss and effectively single-mode guidance. We show that the loss performance and higher-order mode suppression is significantly improved by using symmetrically distributed anisotropic antiresonant tubes i...

Algebraic collapsing acceleration of the characteristics method with anisotropic scattering

International Nuclear Information System (INIS)

Le Tellier, R.; Hebert, A.; Roy, R.

2004-01-01

In this paper, the characteristics solvers implemented in the lattice code Dragon are extended to allow a complete anisotropic treatment of the collision operator. An efficient synthetic acceleration method, called Algebraic Collapsing Acceleration (ACA), is presented. Tests show that this method can substantially speed up the convergence of scattering source iterations. The effect of boundary conditions, either specular or white reflections, on anisotropic scattering lattice-cell problems is also considered. (author)

A study on the effective hydraulic conductivity of an anisotropic porous medium

International Nuclear Information System (INIS)

Seong, Kwan Jae

2002-01-01

Effective hydraulic conductivity of a statistically anisotropic heterogeneous medium is obtained for steady two-dimensional flows employing stochastic analysis. Flow equations are solved up to second order and the effective conductivity is obtained in a semi-analytic form depending only on the spatial correlation function and the anisotropy ratio of the hydraulic conductivity field, hence becoming a true intrinsic property independent of the flow field. Results are obtained using a statistically anisotropic Gaussian correlation function where the anisotropic is defined as the ratio of integral scales normal and parallel to the mean flow direction. Second order results indicate that the effective conductivity of an anisotropic medium is greater than that of an isotropic one when the anisotropy ratio is less than one and vice versa. It is also found that the effective conductivity has upper and lower bounds of the arithmetic and the harmonic mean conductivities

Analytical Method and Semianalytical Method for Analysis of Scattering by Anisotropic Sphere: A Review

Directory of Open Access Journals (Sweden)

Chao Wan

2012-01-01

Full Text Available The history of methods for the electromagnetic scattering by an anisotropic sphere has been reviewed. Two main methods, angular expansion method and T-matrix method, which are widely used for the anisotropic sphere, are expressed in Cartesian coordinate firstly. The comparison of those and the further exploration on the scattering field are illustrated afterwards. Based on the most general form concluded by variable separation method, the coupled electric field and magnetic field of radial anisotropic sphere can be derived. By simplifying the condition, simpler case of uniaxial anisotropic media is expressed with confirmed coefficients for the internal and external field. Details of significant phenomenon are presented.

Lipopolysaccharide Membranes and Membrane Proteins of Pseudomonas aeruginosa Studied by Computer Simulation

Energy Technology Data Exchange (ETDEWEB)

Straatsma, TP

2006-12-01

Pseudomonas aeruginosa is a ubiquitous environmental Gram-negative bacterium with high metabolic versatility and an exceptional ability to adapt to a wide range of ecological environments, including soil, marches, coastal habitats, plant and animal tissues. Gram-negative microbes are characterized by the asymmetric lipopolysaccharide outer membrane, the study of which is important for a number of applications. The adhesion to mineral surfaces plays a central role in characterizing their contribution to the fate of contaminants in complex environmental systems by effecting microbial transport through soils, respiration redox chemistry, and ion mobility. Another important application stems from the fact that it is also a major opportunistic human pathogen that can result in life-threatening infections in many immunocompromised patients, such as lung infections in children with cystic fibrosis, bacteraemia in burn victims, urinary-tract infections in catheterized patients, hospital-acquired pneumonia in patients on respirators, infections in cancer patients receiving chemotherapy, and keratitis and corneal ulcers in users of extended-wear soft contact lenses. The inherent resistance against antibiotics which has been linked with the specific interactions in the outer membrane of P. aeruginosa makes these infections difficult to treat. Developments in simulation methodologies as well as computer hardware have enabled the molecular simulation of biological systems of increasing size and with increasing accuracy, providing detail that is difficult or impossible to obtain experimentally. Computer simulation studies contribute to our understanding of the behavior of proteins, protein-protein and protein-DNA complexes. In recent years, a number of research groups have made significant progress in applying these methods to the study of biological membranes. However, these applications have been focused exclusively on lipid bilayer membranes and on membrane proteins in lipid

Odd number of coupled antiferromagnetic anisotropic Heisenberg chains: Spin wave theory

International Nuclear Information System (INIS)

Benyoussef, A.

1996-10-01

The effect of the chain and perpendicular anisotropies on the energy gap for odd number of coupled quantum spin-1/2 antiferromagnetic anisotropic Heisenberg chains is investigated using a spin wave theory. The energy gap opens above a critical anisotropic value. The known results of the isotropic case have been obtained. (author). 11 refs, 4 figs

Van der Waals Attraction of Vortices in Anisotropic and Layered Superconductors

International Nuclear Information System (INIS)

Blatter, G.; Geshkenbein, V.

1996-01-01

We show that in anisotropic and layered superconductors the fluctuations of vortex lines produce an attractive long-range vortex-vortex interaction of the van der Waals type. This attraction follows from the anisotropic screening properties of the material and has profound consequences for the low-field phase diagram of these materials. copyright 1996 The American Physical Society

Anisotropic silk fibroin/gelatin scaffolds from unidirectional freezing

Energy Technology Data Exchange (ETDEWEB)

Asuncion, Maria Christine Tankeh, E-mail: christine.asuncion@u.nus.edu [National University of Singapore, Department of Biomedical Engineering (Singapore); Goh, James Cho-Hong [National University of Singapore, Department of Biomedical Engineering (Singapore); National University of Singapore, Department of Orthopedic Surgery (Singapore); Toh, Siew-Lok [National University of Singapore, Department of Biomedical Engineering (Singapore); National University of Singapore, Department of Mechanical Engineering (Singapore)

2016-10-01

Recent studies have underlined the importance of matching scaffold properties to the biological milieu. Tissue, and thus scaffold, anisotropy is one such property that is important yet sometimes overlooked. Methods that have been used to achieve anisotropic scaffolds present challenges such as complicated fabrication steps, harsh processing conditions and toxic chemicals involved. In this study, unidirectional freezing was employed to fabricate anisotropic silk fibroin/gelatin scaffolds in a simple and mild manner. Morphological, mechanical, chemical and cellular compatibility properties were investigated, as well as the effect of the addition of gelatin to certain properties of the scaffold. It was shown that scaffold properties were suitable for cell proliferation and that mesenchymal stem cells were able to align themselves along the directed fibers. The fabricated scaffolds present a platform that can be used for anisotropic tissue engineering applications such as cardiac patches. - Highlights: • Silk/gelatin scaffolds with unidirectional alignment were fabricated using a simple and scalable process • Presence of gelatin in silk resulted to lesser shrinkage, better water retention and improved cell proliferation. • Mesenchymal stem cells were shown to align themselves according to the fiber alignment.

Double-grooved nanofibre surfaces with enhanced anisotropic hydrophobicity.

Science.gov (United States)

Liang, Meimei; Chen, Xin; Xu, Yang; Zhu, Lei; Jin, Xiangyu; Huang, Chen

2017-11-02

This study reports a facile method for fabricating double-grooved fibrous surfaces. The primary grooves of the surface are formed by aligned fibres, while the secondary grooves are achieved by oriented nanogrooves on the fibre surface. Investigation into the formation mechanism reveals that the nanogrooves can be readily tailored through adjusting the solvent ratio and relative humidity. With this understanding, a variety of polymers have been successfully electrospun into fibres having the same nanogrooved feature. These fibres show high resemblance to natural hierarchical structures, and thereby endowing the corresponding double-grooved surface with enhanced anisotropic hydrophobicity. A water droplet at a parallel direction to the grooves exhibits a much higher contact angle and a lower roll-off angle than the droplet at a perpendicular direction. The application potential of such anisotropic hydrophobicity has been demonstrated via a fog collection experiment, in which the double-grooved surface can harvest the largest amount of water. Moreover, the fabrication method requires neither post-treatment nor sophisticated equipment, making us anticipate that the double-grooved surface would be competitive in areas where a highly ordered surface, a large surface area and an anisotropic hydrophobicity are preferred.

Isothermal anisotropic magnetoresistance in antiferromagnetic metallic IrMn.

Science.gov (United States)

Galceran, R; Fina, I; Cisneros-Fernández, J; Bozzo, B; Frontera, C; López-Mir, L; Deniz, H; Park, K-W; Park, B-G; Balcells, Ll; Martí, X; Jungwirth, T; Martínez, B

2016-10-20

Antiferromagnetic spintronics is an emerging field; antiferromagnets can improve the functionalities of ferromagnets with higher response times, and having the information shielded against external magnetic field. Moreover, a large list of aniferromagnetic semiconductors and metals with Néel temperatures above room temperature exists. In the present manuscript, we persevere in the quest for the limits of how large can anisotropic magnetoresistance be in antiferromagnetic materials with very large spin-orbit coupling. We selected IrMn as a prime example of first-class moment (Mn) and spin-orbit (Ir) combination. Isothermal magnetotransport measurements in an antiferromagnetic-metal(IrMn)/ferromagnetic-insulator thin film bilayer have been performed. The metal/insulator structure with magnetic coupling between both layers allows the measurement of the modulation of the transport properties exclusively in the antiferromagnetic layer. Anisotropic magnetoresistance as large as 0.15% has been found, which is much larger than that for a bare IrMn layer. Interestingly, it has been observed that anisotropic magnetoresistance is strongly influenced by the field cooling conditions, signaling the dependence of the found response on the formation of domains at the magnetic ordering temperature.

Effective wavefield extrapolation in anisotropic media: Accounting for resolvable anisotropy

KAUST Repository

Alkhalifah, Tariq Ali

2014-04-30

Spectral methods provide artefact-free and generally dispersion-free wavefield extrapolation in anisotropic media. Their apparent weakness is in accessing the medium-inhomogeneity information in an efficient manner. This is usually handled through a velocity-weighted summation (interpolation) of representative constant-velocity extrapolated wavefields, with the number of these extrapolations controlled by the effective rank of the original mixed-domain operator or, more specifically, by the complexity of the velocity model. Conversely, with pseudo-spectral methods, because only the space derivatives are handled in the wavenumber domain, we obtain relatively efficient access to the inhomogeneity in isotropic media, but we often resort to weak approximations to handle the anisotropy efficiently. Utilizing perturbation theory, I isolate the contribution of anisotropy to the wavefield extrapolation process. This allows us to factorize as much of the inhomogeneity in the anisotropic parameters as possible out of the spectral implementation, yielding effectively a pseudo-spectral formulation. This is particularly true if the inhomogeneity of the dimensionless anisotropic parameters are mild compared with the velocity (i.e., factorized anisotropic media). I improve on the accuracy by using the Shanks transformation to incorporate a denominator in the expansion that predicts the higher-order omitted terms; thus, we deal with fewer terms for a high level of accuracy. In fact, when we use this new separation-based implementation, the anisotropy correction to the extrapolation can be applied separately as a residual operation, which provides a tool for anisotropic parameter sensitivity analysis. The accuracy of the approximation is high, as demonstrated in a complex tilted transversely isotropic model. © 2014 European Association of Geoscientists & Engineers.

Effective wavefield extrapolation in anisotropic media: Accounting for resolvable anisotropy

KAUST Repository

Alkhalifah, Tariq Ali

2014-01-01

Spectral methods provide artefact-free and generally dispersion-free wavefield extrapolation in anisotropic media. Their apparent weakness is in accessing the medium-inhomogeneity information in an efficient manner. This is usually handled through a velocity-weighted summation (interpolation) of representative constant-velocity extrapolated wavefields, with the number of these extrapolations controlled by the effective rank of the original mixed-domain operator or, more specifically, by the complexity of the velocity model. Conversely, with pseudo-spectral methods, because only the space derivatives are handled in the wavenumber domain, we obtain relatively efficient access to the inhomogeneity in isotropic media, but we often resort to weak approximations to handle the anisotropy efficiently. Utilizing perturbation theory, I isolate the contribution of anisotropy to the wavefield extrapolation process. This allows us to factorize as much of the inhomogeneity in the anisotropic parameters as possible out of the spectral implementation, yielding effectively a pseudo-spectral formulation. This is particularly true if the inhomogeneity of the dimensionless anisotropic parameters are mild compared with the velocity (i.e., factorized anisotropic media). I improve on the accuracy by using the Shanks transformation to incorporate a denominator in the expansion that predicts the higher-order omitted terms; thus, we deal with fewer terms for a high level of accuracy. In fact, when we use this new separation-based implementation, the anisotropy correction to the extrapolation can be applied separately as a residual operation, which provides a tool for anisotropic parameter sensitivity analysis. The accuracy of the approximation is high, as demonstrated in a complex tilted transversely isotropic model. © 2014 European Association of Geoscientists & Engineers.

Longitudinal disordering of vortex lattices in anisotropic superconductors

International Nuclear Information System (INIS)

Harshman, D.R.; Brandt, E.H.; Fiory, A.T.; Inui, M.; Mitzi, D.B.; Schneemeyer, L.F.; Waszczak, J.V.

1993-01-01

Vortex disordering in superconducting crystals is shown to be markedly sensitive to penetration-depth anisotropy. At low temperature and high magnetic field, the muon-spin-rotation spectra for the highly anisotropic Bi 2 Sr 2 CaCu 2 O 8+δ material are found to be anomalously narrow and symmetric about the applied field, in a manner consistent with a layered vortex sublattice structure with pinning-induced misalignment between layers. In contrast, spectra for the less-anisotropic YBa 2 Cu 3 O 7-δ compounds taken at comparable fields are broader and asymmetric, showing that the vortex lattices are aligned parallel to the applied-field direction

An anisotropic diffusion approximation to thermal radiative transfer

International Nuclear Information System (INIS)

Johnson, Seth R.; Larsen, Edward W.

2011-01-01

This paper describes an anisotropic diffusion (AD) method that uses transport-calculated AD coefficients to efficiently and accurately solve the thermal radiative transfer (TRT) equations. By assuming weak gradients and angular moments in the radiation intensity, we derive an expression for the radiation energy density that depends on a non-local function of the opacity. This nonlocal function is the solution of a transport equation that can be solved with a single steady-state transport sweep once per time step, and the function's second angular moment is the anisotropic diffusion tensor. To demonstrate the AD method's efficacy, we model radiation flow down a channel in 'flatland' geometry. (author)

Tunable waveguide bends with graphene-based anisotropic metamaterials

KAUST Repository

Chen, Zhao-xian; Chen, Ze-guo; Ming, Yang; Wu, Ying; Lu, Yan-qing

2016-01-01

We design tunable waveguide bends filled with graphene-based anisotropic metamaterials to achieve a nearly perfect bending effect. The anisotropic properties of the metamaterials can be described by the effective medium theory. The nearly perfect bending effect is demonstrated by finite element simulations of various structures with different bending curvatures and shapes. This effect is attributed to zero effective permittivity along the direction of propagation and matched effective impedance at the interfaces between the bending part and the dielectric waveguides. We envisage that the design will be applicable in the far-infrared and terahertz frequency ranges owing to the tunable dielectric responses of graphene.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

Energy Technology Data Exchange (ETDEWEB)

Mannix, A. J.; Zhou, X. -F.; Kiraly, B.; Wood, J. D.; Alducin, D.; Myers, B. D.; Liu, X.; Fisher, B. L.; Santiago, U.; Guest, J. R.; Yacaman, M. J.; Ponce, A.; Oganov, A. R.; Hersam, M. C.; Guisinger, N. P.

2015-12-17

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

Tunable waveguide bends with graphene-based anisotropic metamaterials

KAUST Repository

Chen, Zhao-xian

2016-01-15

We design tunable waveguide bends filled with graphene-based anisotropic metamaterials to achieve a nearly perfect bending effect. The anisotropic properties of the metamaterials can be described by the effective medium theory. The nearly perfect bending effect is demonstrated by finite element simulations of various structures with different bending curvatures and shapes. This effect is attributed to zero effective permittivity along the direction of propagation and matched effective impedance at the interfaces between the bending part and the dielectric waveguides. We envisage that the design will be applicable in the far-infrared and terahertz frequency ranges owing to the tunable dielectric responses of graphene.

Anisotropic and Hierarchical Porosity in Multifunctional Ceramics

Science.gov (United States)

Lichtner, Aaron Zev

The performance of multifunctional porous ceramics is often hindered by the seemingly contradictory effects of porosity on both mechanical and non-structural properties and yet a sufficient body of knowledge linking microstructure to these properties does not exist. Using a combination of tailored anisotropic and hierarchical materials, these disparate effects may be reconciled. In this project, a systematic investigation of the processing, characterization and properties of anisotropic and isotropic hierarchically porous ceramics was conducted. The system chosen was a composite ceramic intended as the cathode for a solid oxide fuel cell (SOFC). Comprehensive processing investigations led to the development of approaches to make hierarchical, anisotropic porous microstructures using directional freeze-casting of well dispersed slurries. The effect of all the important processing parameters was investigated. This resulted in an ability to tailor and control the important microstructural features including the scale of the microstructure, the macropore size and total porosity. Comparable isotropic porous ceramics were also processed using fugitive pore formers. A suite of characterization techniques including x-ray tomography and 3-D sectional scanning electron micrographs (FIB-SEM) was used to characterize and quantify the green and partially sintered microstructures. The effect of sintering temperature on the microstructure was quantified and discrete element simulations (DEM) were used to explain the experimental observations. Finally, the comprehensive mechanical properties, at room temperature, were investigated, experimentally and using DEM, for the different microstructures.

Anisotropic swim stress in active matter with nematic order

Science.gov (United States)

Yan, Wen; Brady, John F.

2018-05-01

Active Brownian particles (ABPs) transmit a swim pressure {{{\\Pi }}}{{swim}}=n\\zeta {D}{{swim}} to the container boundaries, where ζ is the drag coefficient, D swim is the swim diffusivity and n is the uniform bulk number density far from the container walls. In this work we extend the notion of the isotropic swim pressure to the anisotropic tensorial swim stress {{\\boldsymbol{σ }}}{{swim}}=-n\\zeta {{\\boldsymbol{D}}}{{swim}}, which is related to the anisotropic swim diffusivity {{\\boldsymbol{D}}}{{swim}}. We demonstrate this relationship with ABPs that achieve nematic orientational order via a bulk external field. The anisotropic swim stress is obtained analytically for dilute ABPs in both 2D and 3D systems. The anisotropy, defined as the ratio of the maximum to the minimum of the three principal stresses, is shown to grow exponentially with the strength of the external field. We verify that the normal component of the anisotropic swim stress applies a pressure {{{\\Pi }}}{{swim}}=-({{\\boldsymbol{σ }}}{{swim}}\\cdot {\\boldsymbol{n}})\\cdot {\\boldsymbol{n}} on a wall with normal vector {\\boldsymbol{n}}, and, through Brownian dynamics simulations, this pressure is shown to be the force per unit area transmitted by the active particles. Since ABPs have no friction with a wall, the difference between the normal and tangential stress components—the normal stress difference—generates a net flow of ABPs along the wall, which is a generic property of active matter systems.

Anisotropic temperature relaxation of plasmas in an external magnetic field

International Nuclear Information System (INIS)

Hassan, M.H.A.

1977-01-01

The magnetized kinetic equation derived in an earlier paper (Hassan and Watson, 1977) is used to study the problem of relaxation of anisotropic electron and ion temperatures in a magnetized plasma. In the case of anisotropic electron temperature relaxation, it is shown that for small anisotropies the exchange of energy within the electrons between the components parallel and perpendicular to the magnetic field direction determine the relaxation rate. For anisotropic ion temperature relaxation it is shown that the essential mechanism for relaxation is provided by energy transfer between ions and electrons, and that the expression for the relaxation rate perpendicular to the magnetic field contains a significant term proportional to ln eta 0 ln (msub(e)/msub(i)) (where eta 0 = Ωsub(e)/ksub(D)Vsub(e perpendicular to)), in addition to the term proportional to the Coulomb logarithm. (author)

Anisotropic magnetoelectric characteristics in five-layer magnetization-graded multiferroic composites

Directory of Open Access Journals (Sweden)

Lei Chen

2017-05-01

Full Text Available We investigate the anisotropic magnetoelectric(ME characteristics for the five-layer magnetization-graded multiferroic composites(MGMC. The magnetic anisotropy and corresponding anisotropic magnetomechanical effect, demagnetization effect and magneto-mechanical damping’s dependence on magnetic field direction result in an obvious anisotropic ME coupling effect. The experimental results show that ME voltage coefficient in H33 mode is remarkably larger than the other ones (H11, H31 and H13 over the whole Hdc range. Correspondingly, ∂VME/∂Hdc arrives about 420mV/Oe at an optimum bias magnetic field of 46Oe, which is approximately 40 times larger than that of the previous reported composite. Furthermore, it also demonstrates an obvious angular dependence on dc magnetic field. Taking advantage of these specifications, the MGMC can be used to detect weak dc magnetic field and its spatial orientation.

Radiation of planar electromagnetic waves by a line source in anisotropic metamaterials

International Nuclear Information System (INIS)

Cheng Qiang; Jiang Weixiang; Cui Tiejun

2010-01-01

We show experimentally that a line source in an anisotropic metamaterial directly radiates planar electromagnetic waves instead of cylindrical waves, when one component of the permeability tensor approaches zero. The impedance of this material can be perfectly matched to that of free space, which can significantly reduce the reflections between the source and the superstrate, as in traditional highly directive antennas based on zero index metamaterials. Such a unique property determines the two-way propagation of electromagnetic waves excited by a line source, instead of all-way propagation. From this feature, a highly directive emission of electromagnetic waves is achieved using the anisotropic metamaterial with arbitrary shape. We have designed and fabricated the anisotropic metamaterial in the microwave region, and observed the generation of plane waves and their highly directive emission. The proposed plane-wave emission is independent of the shape variance of the anisotropic metamaterial, which can be utilized in the design of conformal antennas.

Spectrum of perturbations in anisotropic inflationary universe with vector hair

Energy Technology Data Exchange (ETDEWEB)

Himmetoglu, Burak, E-mail: burak@physics.umn.edu [School of Physics and Astronomy, University of Minnesota, 116 Church Street S.E., Minneapolis, MN 55455 (United States)

2010-03-01

We study both the background evolution and cosmological perturbations of anisotropic inflationary models supported by coupled scalar and vector fields. The models we study preserve the U(1) gauge symmetry associated with the vector field, and therefore do not possess instabilities associated with longitudinal modes (which instead plague some recently proposed models of vector inflation and curvaton). We first intoduce a model in which the background anisotropy slowly decreases during inflation; we then confirm the stability of the background solution by studying the quadratic action for all the perturbations of the model. We then compute the spectrum of the h{sub ×} gravitational wave polarization. The spectrum we find breaks statistical isotropy at the largest scales and reduces to the standard nearly scale invariant form at small scales. We finally discuss the possible relevance of our results to the large scale CMB anomalies.

A continuum anisotropic damage model with unilateral effect

Directory of Open Access Journals (Sweden)

A. Alliche

2016-02-01

Full Text Available A continuum damage mechanics model has been derived within the framework of irreversible thermodynamics with internal variables in order to describe the behaviour of quasi-brittle materials under various loading paths. The anisotropic character induced by the progressive material degradation is explicitly taken into account, and the Helmholtz free energy is a scalar function of the basic invariants of the second order strain and damage tensors. The elastic response varies depending on the closed or open configuration of defects. The constitutive laws derived within the framework of irreversible thermodynamics theory display a dissymmetry as well as unilateral effects under tensile and compressive loading conditions. This approach verifies continuity and uniqueness of the potential energy. An application to uniaxial tension-compression loading shows a good adequacy with experimental results when available, and realistic evolutions for computed stresses and strains otherwise.

Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution.

Energy Technology Data Exchange (ETDEWEB)

Dantas, Gautam; Watters, Alexander L.; Lunde, Bradley; Eletr, Ziad; Isern, Nancy G.; Roseman, Toby; Lipfert, Jan; Doniach, Sebastian; Tompa, Martin; Kuhlman, Brian; Stoddard, Barry L.; Varani, Gabriele; Baker, David

2006-10-06

We recently used computational protein design to create an extremely stable, globular protein, Top7, with a sequence and fold not observed previously in nature. Since Top7 was created in the absence of genetic selection, it provides a rare opportunity to investigate aspects of the cellular protein production and surveillance machinery that are subject to natural selection. Here we show that a portion of the Top7 protein corresponding to the final 49 C-terminal residues is efficiently mistranslated and accumulates at high levels in E. coli. We used circular dichroism spectroscopy, size-exclusion chromatography, small-angle x-ray scattering, analytical ultra-centrifugation, and NMR spectroscopy to show that the resulting CFr protein adopts a compact, extremely-stable, obligate, symmetric, homo-dimeric structure. Based on the solution structure, we engineered an even more stable variant of CFr by disulfide-induced covalent circularisation that should be an excellent platform for design of novel functions. The accumulation of high levels of CFr exposes the high error rate of the protein translation machinery, and the rarity of correspondingly stable fragments in natural proteins implies a stringent evolutionary pressure against protein sub-fragments that can independently fold into stable structures. The symmetric self-association between two identical mistranslated CFr sub-units to generate an extremely stable structure parallels a mechanism for natural protein-fold evolution by modular recombination of stable protein sub-structures.

Anisotropic Interactions between Cold Rydberg Atoms

Science.gov (United States)

2015-09-28

AFRL-AFOSR-CL-TR-2015-0002 Anisotropic interactions between cold Rydberg atoms Luis Marcassa INSTITUTO DE FISICA DE SAO CARLOS Final Report 09/28...problem with the report +551633739806 Organization / Institution name Instituto de Fisica de Sao Carlos Grant/Contract Title The full title of the

Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media

Energy Technology Data Exchange (ETDEWEB)

Gao, Kai, E-mail: kaigao87@gmail.com [Department of Geology and Geophysics, Texas A& M University, College Station, TX 77843 (United States); Fu, Shubin, E-mail: shubinfu89@gmail.com [Department of Mathematics, Texas A& M University, College Station, TX 77843 (United States); Gibson, Richard L., E-mail: gibson@tamu.edu [Department of Geology and Geophysics, Texas A& M University, College Station, TX 77843 (United States); Chung, Eric T., E-mail: tschung@math.cuhk.edu.hk [Department of Mathematics, The Chinese University of Hong Kong, Shatin, NT (Hong Kong); Efendiev, Yalchin, E-mail: efendiev@math.tamu.edu [Department of Mathematics, Texas A& M University, College Station, TX 77843 (United States); Numerical Porous Media SRI Center (NumPor), King Abdullah University of Science and Technology, Thuwal (Saudi Arabia)

2015-08-15

It is important to develop fast yet accurate numerical methods for seismic wave propagation to characterize complex geological structures and oil and gas reservoirs. However, the computational cost of conventional numerical modeling methods, such as finite-difference method and finite-element method, becomes prohibitively expensive when applied to very large models. We propose a Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media, where we construct basis functions from multiple local problems for both the boundaries and interior of a coarse node support or coarse element. The application of multiscale basis functions can capture the fine scale medium property variations, and allows us to greatly reduce the degrees of freedom that are required to implement the modeling compared with conventional finite-element method for wave equation, while restricting the error to low values. We formulate the continuous Galerkin and discontinuous Galerkin formulation of the multiscale method, both of which have pros and cons. Applications of the multiscale method to three heterogeneous models show that our multiscale method can effectively model the elastic wave propagation in anisotropic media with a significant reduction in the degrees of freedom in the modeling system.

Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media

International Nuclear Information System (INIS)

Gao, Kai; Fu, Shubin; Gibson, Richard L.; Chung, Eric T.; Efendiev, Yalchin

2015-01-01

It is important to develop fast yet accurate numerical methods for seismic wave propagation to characterize complex geological structures and oil and gas reservoirs. However, the computational cost of conventional numerical modeling methods, such as finite-difference method and finite-element method, becomes prohibitively expensive when applied to very large models. We propose a Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media, where we construct basis functions from multiple local problems for both the boundaries and interior of a coarse node support or coarse element. The application of multiscale basis functions can capture the fine scale medium property variations, and allows us to greatly reduce the degrees of freedom that are required to implement the modeling compared with conventional finite-element method for wave equation, while restricting the error to low values. We formulate the continuous Galerkin and discontinuous Galerkin formulation of the multiscale method, both of which have pros and cons. Applications of the multiscale method to three heterogeneous models show that our multiscale method can effectively model the elastic wave propagation in anisotropic media with a significant reduction in the degrees of freedom in the modeling system

Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media

KAUST Repository

Gao, Kai

2015-04-14

It is important to develop fast yet accurate numerical methods for seismic wave propagation to characterize complex geological structures and oil and gas reservoirs. However, the computational cost of conventional numerical modeling methods, such as finite-difference method and finite-element method, becomes prohibitively expensive when applied to very large models. We propose a Generalized Multiscale Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media, where we construct basis functions from multiple local problems for both boundaries and the interior of a coarse node support or coarse element. The application of multiscale basis functions can capture the fine scale medium property variations, and allows us to greatly reduce the degrees of freedom that are required to implement the modeling compared with conventional finite-element method for wave equation, while restricting the error to low values. We formulate the continuous Galerkin and discontinuous Galerkin formulation of the multiscale method, both of which have pros and cons. Applications of the multiscale method to three heterogeneous models show that our multiscale method can effectively model the elastic wave propagation in anisotropic media with a significant reduction in the degrees of freedom in the modeling system.

TOPICAL REVIEW Textured silicon nitride: processing and anisotropic properties

Directory of Open Access Journals (Sweden)

Xinwen Zhu and Yoshio Sakka

2008-01-01

Full Text Available Textured silicon nitride (Si3N4 has been intensively studied over the past 15 years because of its use for achieving its superthermal and mechanical properties. In this review we present the fundamental aspects of the processing and anisotropic properties of textured Si3N4, with emphasis on the anisotropic and abnormal grain growth of β-Si3N4, texture structure and texture analysis, processing methods and anisotropic properties. On the basis of the texturing mechanisms, the processing methods described in this article have been classified into two types: hot-working (HW and templated grain growth (TGG. The HW method includes the hot-pressing, hot-forging and sinter-forging techniques, and the TGG method includes the cold-pressing, extrusion, tape-casting and strong magnetic field alignment techniques for β-Si3N4 seed crystals. Each processing technique is thoroughly discussed in terms of theoretical models and experimental data, including the texturing mechanisms and the factors affecting texture development. Also, methods of synthesizing the rodlike β-Si3N4 single crystals are presented. Various anisotropic properties of textured Si3 N4 and their origins are thoroughly described and discussed, such as hardness, elastic modulus, bending strength, fracture toughness, fracture energy, creep behavior, tribological and wear behavior, erosion behavior, contact damage behavior and thermal conductivity. Models are analyzed to determine the thermal anisotropy by considering the intrinsic thermal anisotropy, degree of orientation and various microstructure factors. Textured porous Si3N4 with a unique microstructure composed of oriented elongated β-Si3N4 and anisotropic pores is also described for the first time, with emphasis on its unique mechanical and thermal-mechanical properties. Moreover, as an important related material, textured α-Sialon is also reviewed, because the presence of elongated α-Sialon grains allows the production of textured �

Machine learning in computational biology to accelerate high-throughput protein expression.

Science.gov (United States)

Sastry, Anand; Monk, Jonathan; Tegel, Hanna; Uhlen, Mathias; Palsson, Bernhard O; Rockberg, Johan; Brunk, Elizabeth

2017-08-15

The Human Protein Atlas (HPA) enables the simultaneous characterization of thousands of proteins across various tissues to pinpoint their spatial location in the human body. This has been achieved through transcriptomics and high-throughput immunohistochemistry-based approaches, where over 40 000 unique human protein fragments have been expressed in E. coli. These datasets enable quantitative tracking of entire cellular proteomes and present new avenues for understanding molecular-level properties influencing expression and solubility. Combining computational biology and machine learning identifies protein properties that hinder the HPA high-throughput antibody production pipeline. We predict protein expression and solubility with accuracies of 70% and 80%, respectively, based on a subset of key properties (aromaticity, hydropathy and isoelectric point). We guide the selection of protein fragments based on these characteristics to optimize high-throughput experimentation. We present the machine learning workflow as a series of IPython notebooks hosted on GitHub (https://github.com/SBRG/Protein_ML). The workflow can be used as a template for analysis of further expression and solubility datasets. ebrunk@ucsd.edu or johanr@biotech.kth.se. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Ultraviolet laser-induced voltage in anisotropic shale

Science.gov (United States)

Miao, Xinyang; Zhu, Jing; Li, Yizhang; Zhao, Kun; Zhan, Honglei; Yue, Wenzheng

2018-01-01

The anisotropy of shales plays a significant role in oil and gas exploration and engineering. Owing to various problems and limitations, anisotropic properties were seldom investigated by direct current resistivity methods. Here in this work, a 248 nm ultraviolet laser was employed to assess the anisotropic electrical response of a dielectric shale. Angular dependence of laser-induced voltages (V p) were obtained, with a data symmetry at the location of 180° and a ~62.2% V p anisotropy of the sample. The double-exponential functions have provided an explanation for the electrical field controlled carrier transportation process in horizontal and vertical directions. The results demonstrate that the combination of optics and electrical logging analysis (Opti-electrical Logging) is a promising technology for the investigation of unconventional reservoirs.

Transient electromagnetic scattering on anisotropic media

International Nuclear Information System (INIS)

Stewart, R.D.

1990-01-01

This dissertation treats the problem of transient scattering of obliquely incident electromagnetic plane waves on a stratified anisotropic dielectric slab. Scattering operators are derived for the reflective response of the medium. The internal fields are calculated. Wave splitting and invariant imbedding techniques are used. These techniques are first presented for fields normally incident on a stratified, isotropic dielectric medium. The techniques of wave splitting and invariant imbedding are applied to normally incident plane waves on an anisotropic medium. An integro-differential equation is derived for the reflective response and the direct and inverse scattering problems are discussed. These techniques are applied to the case of obliquely incident plane waves. The reflective response is derived and the direct and inverse problems discussed and compared to those for the normal incidence case. The internal fields are investigated for the oblique incidence via a Green's function approach. A numerical scheme is presented to calculate the Green's function. Finally, symmetry relations of the reflective response are discussed

FDTD analysis of 3-D conducting target coated by anisotropic magnetized plasma

International Nuclear Information System (INIS)

Xu Lijun; Liu Shaobin; Mo Jinjun; Yuan Naichang

2006-01-01

The JEC finite-difference time-domain (JEC-FDTD) method is extended to three dimensional anisotropic dispersive media- the magnetized plasma. The problem which incorporates both anisotropy and frequency dispersion at the same time is solved for the electromagnetic wave propagation. The three dimensional JEC-FDTD formulations for anisotropic magnetized plasma are derived. The method is applied to the electromagnetic scattering of dihedral corner reflector and sphere-cone coated with anisotropic magnetized plasma. By simulating the interaction of electromagnetic wave with magnetized plasma, some numerical results are obtained, which indicate that an appropriate plasma coating may efficiently reduce the RCS of a metallic target. (authors)

Anisotropic fractal media by vector calculus in non-integer dimensional space

Energy Technology Data Exchange (ETDEWEB)

Tarasov, Vasily E., E-mail: tarasov@theory.sinp.msu.ru [Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow 119991 (Russian Federation)

2014-08-15

A review of different approaches to describe anisotropic fractal media is proposed. In this paper, differentiation and integration non-integer dimensional and multi-fractional spaces are considered as tools to describe anisotropic fractal materials and media. We suggest a generalization of vector calculus for non-integer dimensional space by using a product measure method. The product of fractional and non-integer dimensional spaces allows us to take into account the anisotropy of the fractal media in the framework of continuum models. The integration over non-integer-dimensional spaces is considered. In this paper differential operators of first and second orders for fractional space and non-integer dimensional space are suggested. The differential operators are defined as inverse operations to integration in spaces with non-integer dimensions. Non-integer dimensional space that is product of spaces with different dimensions allows us to give continuum models for anisotropic type of the media. The Poisson's equation for fractal medium, the Euler-Bernoulli fractal beam, and the Timoshenko beam equations for fractal material are considered as examples of application of suggested generalization of vector calculus for anisotropic fractal materials and media.

Anisotropic fractal media by vector calculus in non-integer dimensional space

Science.gov (United States)

Tarasov, Vasily E.

2014-08-01

A review of different approaches to describe anisotropic fractal media is proposed. In this paper, differentiation and integration non-integer dimensional and multi-fractional spaces are considered as tools to describe anisotropic fractal materials and media. We suggest a generalization of vector calculus for non-integer dimensional space by using a product measure method. The product of fractional and non-integer dimensional spaces allows us to take into account the anisotropy of the fractal media in the framework of continuum models. The integration over non-integer-dimensional spaces is considered. In this paper differential operators of first and second orders for fractional space and non-integer dimensional space are suggested. The differential operators are defined as inverse operations to integration in spaces with non-integer dimensions. Non-integer dimensional space that is product of spaces with different dimensions allows us to give continuum models for anisotropic type of the media. The Poisson's equation for fractal medium, the Euler-Bernoulli fractal beam, and the Timoshenko beam equations for fractal material are considered as examples of application of suggested generalization of vector calculus for anisotropic fractal materials and media.

Anisotropic fractal media by vector calculus in non-integer dimensional space

International Nuclear Information System (INIS)

Tarasov, Vasily E.

2014-01-01

A review of different approaches to describe anisotropic fractal media is proposed. In this paper, differentiation and integration non-integer dimensional and multi-fractional spaces are considered as tools to describe anisotropic fractal materials and media. We suggest a generalization of vector calculus for non-integer dimensional space by using a product measure method. The product of fractional and non-integer dimensional spaces allows us to take into account the anisotropy of the fractal media in the framework of continuum models. The integration over non-integer-dimensional spaces is considered. In this paper differential operators of first and second orders for fractional space and non-integer dimensional space are suggested. The differential operators are defined as inverse operations to integration in spaces with non-integer dimensions. Non-integer dimensional space that is product of spaces with different dimensions allows us to give continuum models for anisotropic type of the media. The Poisson's equation for fractal medium, the Euler-Bernoulli fractal beam, and the Timoshenko beam equations for fractal material are considered as examples of application of suggested generalization of vector calculus for anisotropic fractal materials and media

Influence of copper foil polycrystalline structure on graphene anisotropic etching

Energy Technology Data Exchange (ETDEWEB)

Sharma, Kamal P. [Department of Frontier Materials, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan); Mahyavanshi, Rakesh D. [Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan); Kalita, Golap, E-mail: kalita.golap@nitech.ac.jp [Department of Frontier Materials, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan); Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan); Tanemura, Masaki [Department of Frontier Materials, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan); Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan)

2017-01-30

Graphical abstract: Hexagonal hole formation with anisotropic etching independent of the stripes and wrinkles in the synthesized graphene. We also observed variation in etched pattern of the graphene depending on the base Cu grain orientations, attributing to difference in nucleation and growth process. - Highlights: • Reveal the influence of copper polycrystalline structure on anisotropic etching of graphene. • Hexagonal hole formation with etching is observed to be independent of stripes and wrinkles in graphene. • Variation in etched pattern of graphene depending on the base Cu grain is confirmed. • This finding will help to understand the nature of microscopic etched pattern in graphene. - Abstract: Anisotropic etching of graphene and other two dimensional materials is an important tool to understand the growth process as well as enabling fabrication of various well-defined structures. Here, we reveal the influence of copper foil polycrystalline structure on anisotropic etching process of as-synthesized graphene. Graphene crystals were synthesized on the polycrystalline Cu foil by a low-pressure chemical vapor deposition (LPCVD) system. Microscopic analysis shows difference in shape, size and stripes alignment of graphene crystals with dissimilar nucleation within closure vicinity of neighboring Cu grains. Post-growth etching of such graphene crystals also significantly affected by the crystallographic nature of Cu grains as observed by the field emission scanning electron microscope (FE-SEM) and electron back scattered diffraction (EBSD) analysis. Hexagonal hole formation with anisotropic etching is observed to be independent of the stripes and wrinkles in the synthesized graphene. We also observed variation in etched pattern of the graphene depending on the base Cu grain orientations, attributing to difference in nucleation and growth process. The findings can facilitate to understand the nature of microscopic etched pattern depending on metal

Influence of copper foil polycrystalline structure on graphene anisotropic etching

International Nuclear Information System (INIS)

Sharma, Kamal P.; Mahyavanshi, Rakesh D.; Kalita, Golap; Tanemura, Masaki

2017-01-01

Graphical abstract: Hexagonal hole formation with anisotropic etching independent of the stripes and wrinkles in the synthesized graphene. We also observed variation in etched pattern of the graphene depending on the base Cu grain orientations, attributing to difference in nucleation and growth process. - Highlights: • Reveal the influence of copper polycrystalline structure on anisotropic etching of graphene. • Hexagonal hole formation with etching is observed to be independent of stripes and wrinkles in graphene. • Variation in etched pattern of graphene depending on the base Cu grain is confirmed. • This finding will help to understand the nature of microscopic etched pattern in graphene. - Abstract: Anisotropic etching of graphene and other two dimensional materials is an important tool to understand the growth process as well as enabling fabrication of various well-defined structures. Here, we reveal the influence of copper foil polycrystalline structure on anisotropic etching process of as-synthesized graphene. Graphene crystals were synthesized on the polycrystalline Cu foil by a low-pressure chemical vapor deposition (LPCVD) system. Microscopic analysis shows difference in shape, size and stripes alignment of graphene crystals with dissimilar nucleation within closure vicinity of neighboring Cu grains. Post-growth etching of such graphene crystals also significantly affected by the crystallographic nature of Cu grains as observed by the field emission scanning electron microscope (FE-SEM) and electron back scattered diffraction (EBSD) analysis. Hexagonal hole formation with anisotropic etching is observed to be independent of the stripes and wrinkles in the synthesized graphene. We also observed variation in etched pattern of the graphene depending on the base Cu grain orientations, attributing to difference in nucleation and growth process. The findings can facilitate to understand the nature of microscopic etched pattern depending on metal

Analysis of High Tc Superconducting Rectangular Microstrip Patches over Ground Planes with Rectangular Apertures in Substrates Containing Anisotropic Materials

Directory of Open Access Journals (Sweden)

Abderraouf Messai

2013-01-01

Full Text Available A rigorous full-wave analysis of high Tc superconducting rectangular microstrip patch over ground plane with rectangular aperture in the case where the patch is printed on a uniaxially anisotropic substrate material is presented. The dyadic Green’s functions of the considered structure are efficiently determined in the vector Fourier transform domain. The effect of the superconductivity of the patch is taken into account using the concept of the complex resistive boundary condition. The accuracy of the analysis is tested by comparing the computed results with measurements and previously published data for several anisotropic substrate materials. Numerical results showing variation of the resonant frequency and the quality factor of the superconducting antenna with regard to operating temperature are given. Finally, the effects of uniaxial anisotropy in the substrate on the resonant frequencies of different TM modes of the superconducting microstrip antenna with rectangular aperture in the ground plane are presented.

Anisotropic dynamic mass density for fluidsolid composites

KAUST Repository

Wu, Ying; Mei, Jun; Sheng, Ping

2012-01-01

By taking the low frequency limit of multiple-scattering theory, we obtain the dynamic effective mass density of fluidsolid composites with a two-dimensional rectangular lattice structure. The anisotropic mass density can be described by an angle

On the computation of molecular surface correlations for protein docking using fourier techniques.

Science.gov (United States)

Sakk, Eric

2007-08-01

The computation of surface correlations using a variety of molecular models has been applied to the unbound protein docking problem. Because of the computational complexity involved in examining all possible molecular orientations, the fast Fourier transform (FFT) (a fast numerical implementation of the discrete Fourier transform (DFT)) is generally applied to minimize the number of calculations. This approach is rooted in the convolution theorem which allows one to inverse transform the product of two DFTs in order to perform the correlation calculation. However, such a DFT calculation results in a cyclic or "circular" correlation which, in general, does not lead to the same result as the linear correlation desired for the docking problem. In this work, we provide computational bounds for constructing molecular models used in the molecular surface correlation problem. The derived bounds are then shown to be consistent with various intuitive guidelines previously reported in the protein docking literature. Finally, these bounds are applied to different molecular models in order to investigate their effect on the correlation calculation.

3-D anisotropic neutron diffusion in optically thick media with optically thin channels

International Nuclear Information System (INIS)

Trahan, Travis J.; Larsen, Edward W.

2011-01-01

Standard neutron diffusion theory accurately approximates the neutron transport process for optically thick, scattering-dominated systems in which the angular neutron flux is a weak (nearly linear) function of angle. Therefore, standard diffusion theory is not directly applicable for Very High Temperature Reactor (VHTR) cores, which contain numerous narrow, axially-oriented, nearly-voided coolant channels. However, we have derived a new, accurate diffusion equation for such problems, which contains nonstandard anisotropic diffusion coefficients near and within the channels, but which reduces to the standard diffusion approximation away from the channels. The new diffusion approximation significantly improves the accuracy of VHTR diffusion simulations, while having lower computational cost than higher-order transport methods. (author)

Nonlinear anisotropic parabolic equations in Lm

Directory of Open Access Journals (Sweden)

Fares Mokhtari

2014-01-01

Full Text Available In this paper, we give a result of regularity of weak solutions for a class of nonlinear anisotropic parabolic equations with lower-order term when the right-hand side is an Lm function, with m being ”small”. This work generalizes some results given in [2] and [3].

Stoner–Wohlfarth model for the anisotropic case

Energy Technology Data Exchange (ETDEWEB)

Campos, Marcos F. de, E-mail: mcampos@metal.eeimvr.uff.br [Programa de Pós-graduação em Engenharia Metalúrgica-PUVR, Universidade Federal Fluminense, Av dos Trabalhadores 420,27255-125 Volta Redonda, Rio de Janeiro (Brazil); Sampaio da Silva, Fernanda A. [Programa de Pós-graduação em Engenharia Metalúrgica-PUVR, Universidade Federal Fluminense, Av dos Trabalhadores 420,27255-125 Volta Redonda, Rio de Janeiro (Brazil); Perigo, Elio A. [Laboratory for the Physics of Advanced Materials, University of Luxembourg, L1511 Luxembourg (Luxembourg); Castro, José A. de [Programa de Pós-graduação em Engenharia Metalúrgica-PUVR, Universidade Federal Fluminense, Av dos Trabalhadores 420,27255-125 Volta Redonda, Rio de Janeiro (Brazil)

2013-11-15

The Stoner–Wohlfarth (SW) model was calculated for the anisotropic case, by assuming crystallographical texture distributions as Gaussian, Lorentzian and Cos{sup n} (alpha). All these distributions were tested and both Gaussian and Cos{sup n} (alpha) give similar results for M{sub r}/M{sub s} above 0.8. However, the use of Cos{sup n} (alpha) makes it easier to find analytical expressions representing texture. The Lorentzian distribution is a suitable choice for not well aligned magnets, or magnets with a high fraction of misaligned grains. It is discussed how to obtain the alignment degree M{sub r}/M{sub s} directly from two measurements of magnetic remanence at the transverse and parallel directions to the alignment direction of the magnet. It is demonstrated that even the well aligned magnets with M{sub r}/M{sub s}=0.96 present coercive field of 60–70% of the anisotropy field, depending on the chosen distribution. The anisotropic SW model was used for discussing hysteresis squareness. Improving the crystalographical texture, the loop squareness also increases. - Highlights: • The Stoner–Wohlfarth model was calculated for the anisotropic case. • Different distribution functions for texture description were compared and discussed. • Lorentzian distribution is adequate for not well oriented magnets. • Determination of the alignment ratio M{sub r}/M{sub s} from 2 remanence measurements. • Prediction of the coercive field in Stoner–Wohlfarth aligned magnets.

Anisotropic stars obeying Chaplygin equation of state

Indian Academy of Sciences (India)

P Bhar

2017-12-14

Dec 14, 2017 ... Anisotropic effects may also originate from slow rotation of the core ... to include the effects of pressure anisotropy, electric charge, scalar field, dark energy and the cosmological constant in .... Generating solutions. In order to ...

Computational studies on the interactions of nanomaterials with proteins and their impacts

International Nuclear Information System (INIS)

An De-Yi; Li Jing-Yuan; Su Ji-Guo; Li Chun-Hua

2015-01-01

The intensive concern over the biosafety of nanomaterials demands the systematic study of the mechanisms underlying their biological effects. Many of the effects of nanomaterials can be attributed to their interactions with proteins and their impacts on protein function. On the other hand, nanomaterials show potential for a variety of biomedical applications, many of which also involve direct interactions with proteins. In this paper, we review some recent computational studies on this subject, especially those investigating the interactions of carbon and gold nanomaterials. Beside hydrophobic and π-stacking interactions, the mode of interaction of carbon nanomaterials can also be regulated by their functional groups. The coatings of gold nanomaterials similarly adjust their mode of interaction, in addition to coordination interactions with the sulfur groups of cysteine residues and the imidazole groups of histidine residues. Nanomaterials can interact with multiple proteins and their impacts on protein activity are attributed to a wide spectrum of mechanisms. These findings on the mechanisms of nanomaterial–protein interactions can further guide the design and development of nanomaterials to realize their application in disease diagnosis and treatment. (paper)

Ballistic Anisotropic Magnetoresistance of Single-Atom Contacts.

Science.gov (United States)

Schöneberg, J; Otte, F; Néel, N; Weismann, A; Mokrousov, Y; Kröger, J; Berndt, R; Heinze, S

2016-02-10

Anisotropic magnetoresistance, that is, the sensitivity of the electrical resistance of magnetic materials on the magnetization direction, is expected to be strongly enhanced in ballistic transport through nanoscale junctions. However, unambiguous experimental evidence of this effect is difficult to achieve. We utilize single-atom junctions to measure this ballistic anisotropic magnetoresistance (AMR). Single Co and Ir atoms are deposited on domains and domain walls of ferromagnetic Fe layers on W(110) to control their magnetization directions. They are contacted with nonmagnetic tips in a low-temperature scanning tunneling microscope to measure the junction conductances. Large changes of the magnetoresistance occur from the tunneling to the ballistic regime due to the competition of localized and delocalized d-orbitals, which are differently affected by spin-orbit coupling. This work shows that engineering the AMR at the single atom level is feasible.

Selective optical transmission in anisotropic multilayers structure

International Nuclear Information System (INIS)

Ouchani, N.; Bria, D.; Nougaoui, A.; Merad, A.E.

2007-08-01

We developed a Green's function method to study theoretically a single-defect photonic crystal composed of anisotropic dielectric materials. This structure can trap light of a given frequency range and filter only a certain frequency light with a very high quality. It is shown that the defect modes appear as peaks in the transmission spectrum. Their intensities and frequency positions depend on the incidence angle and the orientation of the principal axes of layers consisting of the superlattice and the layer defect. Our structure offers a great variety of possibilities for creating and controlling the number and transmitted intensities of defect modes. It can be a good candidate for realizing a selective electromagnetic filter. In addition to this filtration process, the defective anisotropic photonic crystal can be used to switch the modes when appropriate geometry is selected. (author)

Superstrate loading effects on the resonant characteristics of high Tc superconducting circular patch printed on anisotropic materials

Science.gov (United States)

Bedra, Sami; Bedra, Randa; Benkouda, Siham; Fortaki, Tarek

2017-12-01

In this paper, the effects of both anisotropies in the substrate and superstrate loading on the resonant frequency and bandwidth of high-Tc superconducting circular microstrip patch in a substrate-superstrate configuration are investigated. A rigorous analysis is performed using a dyadic Galerkin's method in the vector Hankel transform domain. Galerkin's procedure is employed in the spectral domain where the TM and TE modes of the cylindrical cavity with magnetic side walls are used in the expansion of the disk current. The effect of the superconductivity of the patch is taken into account using the concept of the complex resistive boundary condition. London's equations and the two-fluid model of Gorter and Casimir are used in the calculation of the complex surface impedance of the superconducting circular disc. The accuracy of the analysis is tested by comparing the computed results with previously published data for several anisotropic substrate-superstrate materials. Good agreement is found among all sets of results. The numerical results obtained show that important errors can be made in the computation of the resonant frequencies and bandwidths of the superconducting resonators when substrate dielectric anisotropy, and/or superstrate anisotropy are ignored. Other theoretical results obtained show that the superconducting circular microstrip patch on anisotropic substrate-superstrate with properly selected permittivity values along the optical and the non-optical axes combined with optimally chosen structural parameters is more advantageous than the one on isotropic substrate-superstrate by exhibiting wider bandwidth characteristic.

An accurate discontinuous Galerkin method for solving point-source Eikonal equation in 2-D heterogeneous anisotropic media

Science.gov (United States)

Le Bouteiller, P.; Benjemaa, M.; Métivier, L.; Virieux, J.

2018-03-01

Accurate numerical computation of wave traveltimes in heterogeneous media is of major interest for a large range of applications in seismics, such as phase identification, data windowing, traveltime tomography and seismic imaging. A high level of precision is needed for traveltimes and their derivatives in applications which require quantities such as amplitude or take-off angle. Even more challenging is the anisotropic case, where the general Eikonal equation is a quartic in the derivatives of traveltimes. Despite their efficiency on Cartesian meshes, finite-difference solvers are inappropriate when dealing with unstructured meshes and irregular topographies. Moreover, reaching high orders of accuracy generally requires wide stencils and high additional computational load. To go beyond these limitations, we propose a discontinuous-finite-element-based strategy which has the following advantages: (1) the Hamiltonian formalism is general enough for handling the full anisotropic Eikonal equations; (2) the scheme is suitable for any desired high-order formulation or mixing of orders (p-adaptivity); (3) the solver is explicit whatever Hamiltonian is used (no need to find the roots of the quartic); (4) the use of unstructured meshes provides the flexibility for handling complex boundary geometries such as topographies (h-adaptivity) and radiation boundary conditions for mimicking an infinite medium. The point-source factorization principles are extended to this discontinuous Galerkin formulation. Extensive tests in smooth analytical media demonstrate the high accuracy of the method. Simulations in strongly heterogeneous media illustrate the solver robustness to realistic Earth-sciences-oriented applications.

An analytical model of anisotropic low-field electron mobility in wurtzite indium nitride

International Nuclear Information System (INIS)

Wang, Shulong; Liu, Hongxia; Song, Xin; Guo, Yulong; Yang, Zhaonian

2014-01-01

This paper presents a theoretical analysis of anisotropic transport properties and develops an anisotropic low-field electron analytical mobility model for wurtzite indium nitride (InN). For the different effective masses in the Γ-A and Γ-M directions of the lowest valley, both the transient and steady state transport behaviors of wurtzite InN show different transport characteristics in the two directions. From the relationship between velocity and electric field, the difference is more obvious when the electric field is low in the two directions. To make an accurate description of the anisotropic transport properties under low field, for the first time, we present an analytical model of anisotropic low-field electron mobility in wurtzite InN. The effects of different ionized impurity scattering models on the low-field mobility calculated by Monte Carlo method (Conwell-Weisskopf and Brooks-Herring method) are also considered. (orig.)

Anisotropic Characteristics of Turbulence Dissipation in Swirling Flow: A Direct Numerical Simulation Study

Directory of Open Access Journals (Sweden)

Xingtuan Yang

2015-01-01

Full Text Available This study investigates the anisotropic characteristics of turbulent energy dissipation rate in a rotating jet flow via direct numerical simulation. The turbulent energy dissipation tensor, including its eigenvalues in the swirling flows with different rotating velocities, is analyzed to investigate the anisotropic characteristics of turbulence and dissipation. In addition, the probability density function of the eigenvalues of turbulence dissipation tensor is presented. The isotropic subrange of PDF always exists in swirling flows relevant to small-scale vortex structure. Thus, with remarkable large-scale vortex breakdown, the isotropic subrange of PDF is reduced in strongly swirling flows, and anisotropic energy dissipation is proven to exist in the core region of the vortex breakdown. More specifically, strong anisotropic turbulence dissipation occurs concentratively in the vortex breakdown region, whereas nearly isotropic turbulence dissipation occurs dispersively in the peripheral region of the strong swirling flows.

A computer graphics program system for protein structure representation.

Science.gov (United States)

Ross, A M; Golub, E E

1988-01-01

We have developed a computer graphics program system for the schematic representation of several protein secondary structure analysis algorithms. The programs calculate the probability of occurrence of alpha-helix, beta-sheet and beta-turns by the method of Chou and Fasman and assign unique predicted structure to each residue using a novel conflict resolution algorithm based on maximum likelihood. A detailed structure map containing secondary structure, hydrophobicity, sequence identity, sequence numbering and the location of putative N-linked glycosylation sites is then produced. In addition, helical wheel diagrams and hydrophobic moment calculations can be performed to further analyze the properties of selected regions of the sequence. As they require only structure specification as input, the graphics programs can easily be adapted for use with other secondary structure prediction schemes. The use of these programs to analyze protein structure-function relationships is described and evaluated. PMID:2832829

Experimental and computational laser tissue welding using a protein patch.

Science.gov (United States)

Small, W; Heredia, N J; Maitland, D J; Eder, D C; Celliers, P M; Da Silva, L B; London, R A; Matthews, D L

1998-01-01

An in vitro study of laser tissue welding mediated with a dye-enhanced protein patch was conducted. Fresh sections of porcine aorta were used for the experiments. Arteriotomies were treated using an indocyanine green dye-enhanced collagen patch activated by an 805-nm continuous-wave fiber-delivered diode laser. Temperature histories of the surface of the weld site were obtained using a hollow glass optical fiber-based two-color infrared thermometer. The experimental effort was complemented by simulations with the LATIS (LAser-TISsue) computer code, which uses coupled Monte Carlo, thermal transport, and mass transport models. Comparison of simulated and experimental thermal data indicated that evaporative cooling clamped the surface temperature of the weld site below 100 °C. For fluences of approximately 200 J/cm2, peak surface temperatures averaged 74°C and acute burst strengths consistently exceeded 0.14×106 dyn/cm (hoop tension). The combination of experimental and simulation results showed that the inclusion of water transport and evaporative losses in the computer code has a significant impact on the thermal distributions and hydration levels throughout the tissue volume. The solid-matrix protein patch provided a means of controllable energy delivery and yielded consistently strong welds. © 1998 Society of Photo-Optical Instrumentation Engineers.

Measurement of Anisotropic Particle Interactions with Nonuniform ac Electric Fields.

Science.gov (United States)

Rupp, Bradley; Torres-Díaz, Isaac; Hua, Xiaoqing; Bevan, Michael A

2018-02-20

Optical microscopy measurements are reported for single anisotropic polymer particles interacting with nonuniform ac electric fields. The present study is limited to conditions where gravity confines particles with their long axis parallel to the substrate such that particles can be treated using quasi-2D analysis. Field parameters are investigated that result in particles residing at either electric field maxima or minima and with long axes oriented either parallel or perpendicular to the electric field direction. By nonintrusively observing thermally sampled positions and orientations at different field frequencies and amplitudes, a Boltzmann inversion of the time-averaged probability of states yields kT-scale energy landscapes (including dipole-field, particle-substrate, and gravitational potentials). The measured energy landscapes show agreement with theoretical potentials using particle conductivity as the sole adjustable material property. Understanding anisotropic particle-field energy landscapes vs field parameters enables quantitative control of local forces and torques on single anisotropic particles to manipulate their position and orientation within nonuniform fields.

Analytical modeling of pressure transient behavior for coalbed methane transport in anisotropic media

International Nuclear Information System (INIS)

Wang, Lei; Wang, Xiaodong

2014-01-01

Resulting from the nature of anisotropy of coal media, it is a meaningful work to evaluate pressure transient behavior and flow characteristics within coals. In this article, a complete analytical model called the elliptical flow model is established by combining the theory of elliptical flow in anisotropic media and Fick's laws about the diffusion of coalbed methane. To investigate pressure transient behavior, analytical solutions were first obtained through introducing a series of special functions (Mathieu functions), which are extremely complex and are hard to calculate. Thus, a computer program was developed to establish type curves, on which the effects of the parameters, including anisotropy coefficient, storage coefficient, transfer coefficient and rate constant, were analyzed in detail. Calculative results show that the existence of anisotropy would cause great pressure depletion. To validate new analytical solutions, previous results were used to compare with the new results. It is found that a better agreement between the solutions obtained in this work and the literature was achieved. Finally, a case study is used to explain the effects of the parameters, including rock total compressibility coefficient, coal medium porosity and anisotropic permeability, sorption time constant, Langmuir volume and fluid viscosity, on bottom-hole pressure behavior. It is necessary to coordinate these parameters so as to reduce the pressure depletion. (paper)

The influence of the anisotropic stress state on the intermediate strain properties of granular material

KAUST Repository

Goudarzy, M.

2017-07-20

This paper shows the effect of anisotropic stress state on intermediate strain properties of cylindrical samples containing spherical glass particles. Tests were carried out with the modified resonant column device available at Ruhr-Universität Bochum. Dry samples were subjected to two anisotropic stress states: (a) cell pressure, σ′h, constant and vertical stress, σ′v, increased (stress state GB-I) and (b) σ′v/σ′h equal to 2 (stress state GB-II). The experimental results revealed that the effect of stress state GB-II on the modulus and damping ratio was more significant and obvious than stress state GB-I. The effect of the anisotropic stress state was explained through the impact of confining pressure and anisotropic stress components on the stiffness and damping ratio. The results showed that: (a) G(γ) increased, η(γ) decreased and their strain non-linearity decreased with an increase in the confining pressure component σ′vσ′h; (b) G(γ) decreased, η(γ) increased and their strain non-linearity increased with an increase in the anisotropic stress component, σ′v/σ′h. The analysis of results revealed that reference shear strain was also affected by anisotropic stress state. Therefore, an empirical relationship was developed to predict the reference shear strain, as a function of confining pressure and anisotropic stress components. Additionally, the damping ratio was written as a function of the minimum damping ratio and the reference shear strain.

A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.

Directory of Open Access Journals (Sweden)

Brittany Burton

Full Text Available Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. However, to date, no studies have attempted to elucidate these conformational changes. The present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of the ribosome. Ribosomal proteins are known to be positively charged and we find the percentage of positive residues in r-proteins to be about twice that of the average protein: Lys+Arg is 18.7% for E. coli and 21.2% for T. thermophilus. Also, positive residues constitute a large proportion of RNA contacting residues: 39% for E. coli and 46% for T. thermophilus. This affirms the known importance of charge-charge interactions in the assembly of the ribosome. We studied the dynamics of three primary proteins from E. coli and T. thermophilus 30S subunits that bind early in the assembly (S15, S17, and S20 with atomic molecular dynamic simulations, followed by a study of all r-proteins using elastic network models. Molecular dynamics simulations show that solvent-exposed proteins (S15 and S17 tend to adopt more stable solution conformations than an RNA-embedded protein (S20. We also find protein residues that contact the 16S rRNA are generally more mobile in comparison with the other residues. This is because there is a larger proportion of contacting residues located in flexible loop regions. By the use of elastic network models, which are computationally more efficient, we show that this trend holds for most of the 30S r-proteins.

Characterization of optical anisotropy in quantum wells under compressive anisotropic in-plane strain

Energy Technology Data Exchange (ETDEWEB)

Biermann, Mark L [Physics Department, 566 Brownson Rd., U.S. Naval Academy, Annapolis, MD 21402 (United States); Walters, Matthew [Physics Department, 566 Brownson Rd., U.S. Naval Academy, Annapolis, MD 21402 (United States); Diaz-Barriga, James [Physics Department, 566 Brownson Rd., U.S. Naval Academy, Annapolis, MD 21402 (United States); Rabinovich, W S [Naval Research Laboratory, Code 5652, 4555 Overlook Ave. SW, Washington, DC 20375-5320 (United States)

2003-10-21

Anisotropic in-plane strain in quantum wells leads to an optical polarization anisotropy that can be exploited for device applications. We have determined that for many anisotropic compressive strain cases, the dependence of the optical anisotropy is linear in the strain anisotropy. This result holds for a variety of well and barrier materials and widths and for various overall strain conditions. Further, the polarization anisotropy per strain anisotropy varies as the reciprocal of the energy separation of the relevant hole sub-bands. Hence, a general result for the polarization anisotropy per strain anisotropy is available for cases of compressive anisotropic in-plane strain.

Characterization of optical anisotropy in quantum wells under compressive anisotropic in-plane strain

International Nuclear Information System (INIS)

Biermann, Mark L; Walters, Matthew; Diaz-Barriga, James; Rabinovich, W S

2003-01-01

Anisotropic in-plane strain in quantum wells leads to an optical polarization anisotropy that can be exploited for device applications. We have determined that for many anisotropic compressive strain cases, the dependence of the optical anisotropy is linear in the strain anisotropy. This result holds for a variety of well and barrier materials and widths and for various overall strain conditions. Further, the polarization anisotropy per strain anisotropy varies as the reciprocal of the energy separation of the relevant hole sub-bands. Hence, a general result for the polarization anisotropy per strain anisotropy is available for cases of compressive anisotropic in-plane strain

Adaptive slices for acquisition of anisotropic BRDF

Czech Academy of Sciences Publication Activity Database

Vávra, Radomír; Filip, Jiří

(2018) ISSN 2096-0433 R&D Projects: GA ČR GA17-18407S Institutional support: RVO:67985556 Keywords : anisotropic BRDF * slice * sampling Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2018/RO/vavra-0486116.pdf

Multiscale coarse-graining of the protein energy landscape.

Directory of Open Access Journals (Sweden)

Ronald D Hills

2010-06-01

Full Text Available A variety of coarse-grained (CG models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states.

The Role of Anisotropic Exchange in Single Molecule Magnets: A CASSCF/NEVPT2 Study of the Fe4 SMM Building Block [Fe2(OCH32(dbm4] Dimer

Directory of Open Access Journals (Sweden)

Alessandro Lunghi

2016-09-01

Full Text Available The rationalisation of single molecule magnets’ (SMMs magnetic properties by quantum mechanical approaches represents a major task in the field of the Molecular Magnetism. The fundamental interpretative key of molecular magnetism is the phenomenological Spin Hamiltonian and the understanding of the role of its different terms by electronic structure calculations is expected to steer the rational design of new and more performing SMMs. This paper deals with the ab initio calculation of isotropic and anisotropic exchange contributions in the Fe(III dimer [Fe 2 (OCH 3 2 (dbm 4 ]. This system represents the building block of one of the most studied Single Molecule Magnets ([Fe 4 RC(CH 2 O 3 2 (dpm 6 ] where R can be an aliphatic chain or a phenyl group just to name the most common functionalization groups and its relatively reduced size allows the use of a high computational level of theory. Calculations were performed using CASSCF and NEVPT2 approaches on the X-ray geometry as assessment of the computational protocol, which has then be used to evinced the importance of the outer coordination shell nature through organic ligand modelization. Magneto-structural correlations as function of internal degrees of freedom for isotropic and anisotropic exchange contributions are also presented, outlining, for the first time, the extremely rapidly changing nature of the anisotropic exchange coupling.

Ellipsometric studies of synthetic albumin-binding chitosan-derivatives and selected blood plasma proteins

Science.gov (United States)

Sarkar, Sabyasachi

This dissertation summarizes work on the synthesis of chitosan-derivatives and the development of ellipsometric methods to characterize materials of biological origin. Albumin-binding chitosan-derivatives were synthesized via addition reactions that involve amine groups naturally present in chitosan. These surfaces were shown to have an affinity towards human serum albumin via ELISA, UV spectroscopy and SDS PAGE. Modified surfaces were characterized with IR ellipsometry at various stages of their synthesis using appropriate optical models. It was found that spin cast chitosan films were anisotropic in nature. All optical models used for characterizing chitosan-derivatives were thus anisotropic. Chemical signal dependence on molecular structure and composition was illustrated via IR spectroscopic ellipsometry (IRSE). An anisotropic optical model of an ensemble of Lorentz oscillators were used to approximate material behavior. The presence of acetic acid in spin-cast non-neutralized chitosan samples was thus shown. IRSE application to biomaterials was also demonstrated by performing a step-wise chemical characterizations during synthesis stages. Protein adsorbed from single protein solutions on these modified surfaces was monitored by visible in-situ variable wavelength ellipsometry. Based on adsorption profiles obtained from single protein adsorption onto silicon surfaces, lumped parameter kinetic models were developed. These models were used to fit experimental data of immunoglobulin-G of different concentrations and approximate conformational changes in fibrinogen adsorption. Biomaterial characterization by ellipsometry was further extended to include characterization of individual protein solutions in the IR range. Proteins in an aqueous environment were characterized by attenuated total internal reflection (ATR) IR ellipsometry using a ZnSe prism. Parameterized dielectric functions were created for individual proteins using Lorentz oscillators. These

Highly Enhanced Many-Body Interactions in Anisotropic 2D Semiconductors.

Science.gov (United States)

Sharma, Ankur; Yan, Han; Zhang, Linglong; Sun, Xueqian; Liu, Boqing; Lu, Yuerui

2018-05-15

Atomically thin two-dimensional (2D) semiconductors have presented a plethora of opportunities for future optoelectronic devices and photonics applications, made possible by the strong light matter interactions at the 2D quantum limit. Many body interactions between fundamental particles in 2D semiconductors are strongly enhanced compared with those in bulk semiconductors because of the reduced dimensionality and, thus, reduced dielectric screening. These enhanced many body interactions lead to the formation of robust quasi-particles, such as excitons, trions, and biexcitons, which are extremely important for the optoelectronics device applications of 2D semiconductors, such as light emitting diodes, lasers, and optical modulators, etc. Recently, the emerging anisotropic 2D semiconductors, such as black phosphorus (termed as phosphorene) and phosphorene-like 2D materials, such as ReSe 2 , 2D-perovskites, SnS, etc., show strong anisotropic optical and electrical properties, which are different from conventional isotropic 2D semiconductors, such as transition metal dichalcogenide (TMD) monolayers. This anisotropy leads to the formation of quasi-one-dimensional (quasi-1D) excitons and trions in a 2D system, which results in even stronger many body interactions in anisotropic 2D materials, arising from the further reduced dimensionality of the quasi-particles and thus reduced dielectric screening. Many body interactions have been heavily investigated in TMD monolayers in past years, but not in anisotropic 2D materials yet. The quasi-particles in anisotropic 2D materials have fractional dimensionality which makes them perfect candidates to serve as a platform to study fundamental particle interactions in fractional dimensional space. In this Account, we present our recent progress related to 2D phosphorene, a 2D system with quasi-1D excitons and trions. Phosphorene, because of its unique anisotropic properties, provides a unique 2D platform for investigating the

Dipole estimation errors due to not incorporating anisotropic conductivities in realistic head models for EEG source analysis

Science.gov (United States)

Hallez, Hans; Staelens, Steven; Lemahieu, Ignace

2009-10-01

EEG source analysis is a valuable tool for brain functionality research and for diagnosing neurological disorders, such as epilepsy. It requires a geometrical representation of the human head or a head model, which is often modeled as an isotropic conductor. However, it is known that some brain tissues, such as the skull or white matter, have an anisotropic conductivity. Many studies reported that the anisotropic conductivities have an influence on the calculated electrode potentials. However, few studies have assessed the influence of anisotropic conductivities on the dipole estimations. In this study, we want to determine the dipole estimation errors due to not taking into account the anisotropic conductivities of the skull and/or brain tissues. Therefore, head models are constructed with the same geometry, but with an anisotropically conducting skull and/or brain tissue compartment. These head models are used in simulation studies where the dipole location and orientation error is calculated due to neglecting anisotropic conductivities of the skull and brain tissue. Results show that not taking into account the anisotropic conductivities of the skull yields a dipole location error between 2 and 25 mm, with an average of 10 mm. When the anisotropic conductivities of the brain tissues are neglected, the dipole location error ranges between 0 and 5 mm. In this case, the average dipole location error was 2.3 mm. In all simulations, the dipole orientation error was smaller than 10°. We can conclude that the anisotropic conductivities of the skull have to be incorporated to improve the accuracy of EEG source analysis. The results of the simulation, as presented here, also suggest that incorporation of the anisotropic conductivities of brain tissues is not necessary. However, more studies are needed to confirm these suggestions.

Dipole estimation errors due to not incorporating anisotropic conductivities in realistic head models for EEG source analysis

International Nuclear Information System (INIS)

Hallez, Hans; Staelens, Steven; Lemahieu, Ignace

2009-01-01

EEG source analysis is a valuable tool for brain functionality research and for diagnosing neurological disorders, such as epilepsy. It requires a geometrical representation of the human head or a head model, which is often modeled as an isotropic conductor. However, it is known that some brain tissues, such as the skull or white matter, have an anisotropic conductivity. Many studies reported that the anisotropic conductivities have an influence on the calculated electrode potentials. However, few studies have assessed the influence of anisotropic conductivities on the dipole estimations. In this study, we want to determine the dipole estimation errors due to not taking into account the anisotropic conductivities of the skull and/or brain tissues. Therefore, head models are constructed with the same geometry, but with an anisotropically conducting skull and/or brain tissue compartment. These head models are used in simulation studies where the dipole location and orientation error is calculated due to neglecting anisotropic conductivities of the skull and brain tissue. Results show that not taking into account the anisotropic conductivities of the skull yields a dipole location error between 2 and 25 mm, with an average of 10 mm. When the anisotropic conductivities of the brain tissues are neglected, the dipole location error ranges between 0 and 5 mm. In this case, the average dipole location error was 2.3 mm. In all simulations, the dipole orientation error was smaller than 10 deg. We can conclude that the anisotropic conductivities of the skull have to be incorporated to improve the accuracy of EEG source analysis. The results of the simulation, as presented here, also suggest that incorporation of the anisotropic conductivities of brain tissues is not necessary. However, more studies are needed to confirm these suggestions.

Phase space analysis for anisotropic universe with nonlinear bulk viscosity

Science.gov (United States)

Sharif, M.; Mumtaz, Saadia

2018-06-01

In this paper, we discuss phase space analysis of locally rotationally symmetric Bianchi type I universe model by taking a noninteracting mixture of dust like and viscous radiation like fluid whose viscous pressure satisfies a nonlinear version of the Israel-Stewart transport equation. An autonomous system of equations is established by defining normalized dimensionless variables. In order to investigate stability of the system, we evaluate corresponding critical points for different values of the parameters. We also compute power-law scale factor whose behavior indicates different phases of the universe model. It is found that our analysis does not provide a complete immune from fine-tuning because the exponentially expanding solution occurs only for a particular range of parameters. We conclude that stable solutions exist in the presence of nonlinear model for bulk viscosity with different choices of the constant parameter m for anisotropic universe.

Symbolic computation of nonlinear wave interactions on MACSYMA

International Nuclear Information System (INIS)

Bers, A.; Kulp, J.L.; Karney, C.F.F.

1976-01-01

In this paper the use of a large symbolic computation system - MACSYMA - in determining approximate analytic expressions for the nonlinear coupling of waves in an anisotropic plasma is described. MACSYMA was used to implement the solutions of a fluid plasma model nonlinear partial differential equations by perturbation expansions and subsequent iterative analytic computations. By interacting with the details of the symbolic computation, the physical processes responsible for particular nonlinear wave interactions could be uncovered and appropriate approximations introduced so as to simplify the final analytic result. Details of the MACSYMA system and its use are discussed and illustrated. (Auth.)

Instabilities of collisionless current sheets revisited: The role of anisotropic heating

International Nuclear Information System (INIS)

Muñoz, P. A.; Kilian, P.; Büchner, J.

2014-01-01

In this work, we investigate the influence of the anisotropic heating on the spontaneous instability and evolution of thin Harris-type collisionless current sheets, embedded in antiparallel magnetic fields. In particular, we explore the influence of the macroparticle shape-function using a 2D version of the PIC code ACRONYM. We also investigate the role of the numerical collisionality due to the finite number of macroparticles in PIC codes. It is shown that it is appropriate to choose higher order shape functions of the macroparticles compared to a larger number of macroparticles per cell. This allows to estimate better the anisotropic electron heating due to the collisions of macroparticles in a PIC code. Temperature anisotropies can stabilize the tearing mode instability and trigger additional current sheet instabilities. We found a good agreement between the analytically derived threshold for the stabilization of the anisotropic tearing mode and other instabilities, either spontaneously developing or initially triggered ones. Numerical effects causing anisotropic heating at electron time scales become especially important for higher mass ratios (above m i /m e =180). If numerical effects are carefully taken into account, one can recover the theoretical estimated linear growth rates of the tearing instability of thin isotropic collisionless current sheets, also for higher mass ratios

Multivariate statistical analysis of electron energy-loss spectroscopy in anisotropic materials

International Nuclear Information System (INIS)

Hu Xuerang; Sun Yuekui; Yuan Jun

2008-01-01

Recently, an expression has been developed to take into account the complex dependence of the fine structure in core-level electron energy-loss spectroscopy (EELS) in anisotropic materials on specimen orientation and spectral collection conditions [Y. Sun, J. Yuan, Phys. Rev. B 71 (2005) 125109]. One application of this expression is the development of a phenomenological theory of magic-angle electron energy-loss spectroscopy (MAEELS), which can be used to extract the isotropically averaged spectral information for materials with arbitrary anisotropy. Here we use this expression to extract not only the isotropically averaged spectral information, but also the anisotropic spectral components, without the restriction of MAEELS. The application is based on a multivariate statistical analysis of core-level EELS for anisotropic materials. To demonstrate the applicability of this approach, we have conducted a study on a set of carbon K-edge spectra of multi-wall carbon nanotube (MWCNT) acquired with energy-loss spectroscopic profiling (ELSP) technique and successfully extracted both the averaged and dichroic spectral components of the wrapped graphite-like sheets. Our result shows that this can be a practical alternative to MAEELS for the study of electronic structure of anisotropic materials, in particular for those nanostructures made of layered materials

Anisotropic cosmological constant and the CMB quadrupole anomaly

International Nuclear Information System (INIS)

Rodrigues, Davi C.

2008-01-01

There are evidences that the cosmic microwave background (CMB) large-angle anomalies imply a departure from statistical isotropy and hence from the standard cosmological model. We propose a ΛCDM model extension whose dark energy component preserves its nondynamical character but wields anisotropic vacuum pressure. Exact solutions for the cosmological scale factors are presented, upper bounds for the deformation parameter are evaluated and its value is estimated considering the elliptical universe proposal to solve the quadrupole anomaly. This model can be constructed from a Bianchi I cosmology with a cosmological constant from two different ways: (i) a straightforward anisotropic modification of the vacuum pressure consistently with energy-momentum conservation; (ii) a Poisson structure deformation between canonical momenta such that the dynamics remain invariant under scale factors rescalings

Anisotropic non-Fermi liquids

Science.gov (United States)

Sur, Shouvik; Lee, Sung-Sik

2016-11-01

We study non-Fermi-liquid states that arise at the quantum critical points associated with the spin density wave (SDW) and charge density wave (CDW) transitions in metals with twofold rotational symmetry. We use the dimensional regularization scheme, where a one-dimensional Fermi surface is embedded in (3 -ɛ ) -dimensional momentum space. In three dimensions, quasilocal marginal Fermi liquids arise both at the SDW and CDW critical points: the speed of the collective mode along the ordering wave vector is logarithmically renormalized to zero compared to that of Fermi velocity. Below three dimensions, however, the SDW and CDW critical points exhibit drastically different behaviors. At the SDW critical point, a stable anisotropic non-Fermi-liquid state is realized for small ɛ , where not only time but also different spatial coordinates develop distinct anomalous dimensions. The non-Fermi liquid exhibits an emergent algebraic nesting as the patches of Fermi surface are deformed into a universal power-law shape near the hot spots. Due to the anisotropic scaling, the energy of incoherent spin fluctuations disperse with different power laws in different momentum directions. At the CDW critical point, on the other hand, the perturbative expansion breaks down immediately below three dimensions as the interaction renormalizes the speed of charge fluctuations to zero within a finite renormalization group scale through a two-loop effect. The difference originates from the fact that the vertex correction antiscreens the coupling at the SDW critical point whereas it screens at the CDW critical point.

Anisotropic Hanle line shape via magnetothermoelectric phenomena

NARCIS (Netherlands)

Das, Kumar; Dejene, Fasil; van Wees, Bart; Vera Marun, Ivan

2016-01-01

We observe anisotropic Hanle line shape with unequal in-plane and out-of-plane nonlocal signals for spin precession measurements carried out on lateral metallic spin valves with transparent interfaces. The conventional interpretation for this anisotropy corresponds to unequal spin relaxation times

Analytical results for entanglement in the five-qubit anisotropic Heisenberg model

International Nuclear Information System (INIS)

Wang Xiaoguang

2004-01-01

We solve the eigenvalue problem of the five-qubit anisotropic Heisenberg model, without use of Bethe's ansatz, and give analytical results for entanglement and mixedness of two nearest-neighbor qubits. The entanglement takes its maximum at Δ=1 (Δ>1) for the case of zero (finite) temperature with Δ being the anisotropic parameter. In contrast, the mixedness takes its minimum at Δ=1 (Δ>1) for the case of zero (finite) temperature

Integral superposition of paraxial Gaussian beams in inhomogeneous anisotropic layered structures in Cartesian coordinates

Czech Academy of Sciences Publication Activity Database

Červený, V.; Pšenčík, Ivan

2015-01-01

Roč. 25, - (2015), s. 109-155 ISSN 2336-3827 Institutional support: RVO:67985530 Keywords : integral superposition of paraxial Gaussian beams * inhomogeneous anisotropic media * S waves in weakly anisotropic media Subject RIV: DC - Siesmology, Volcanology, Earth Structure

Lower critical field of an anisotropic type-II superconductor

International Nuclear Information System (INIS)

Klemm, R.A.; Clem, J.R.

1980-01-01

We consider the Ginzburg-Landau free energy of the anisotropic mass form in the presence of a magnetic field of arbitrary fixed direction. It is shown that the free energy may be transformed into the isotropic Ginsburg-Landau form with a kappa that depends upon the direction of the magnetic induction B relative to the crystal lattice. The lower critical field H/sub c/1 is then found for arbitrary direction of B. For highly anisotropic crystals the angular dependence of H/sub c/1 can exhibit a discontinuity or a cusp. The special case of a crystal with uniaxial symmetry is considered in detail

All spherically symmetric charged anisotropic solutions for compact stars

Energy Technology Data Exchange (ETDEWEB)

Maurya, S.K. [University of Nizwa, Department of Mathematical and Physical Sciences, College of Arts and Science, Nizwa (Oman); Gupta, Y.K. [Raj Kumar Goel Institute of Technology, Department of Mathematics, Ghaziabad, UP (India); Ray, Saibal [Government College of Engineering and Ceramic Technology, Department of Physics, Kolkata, West Bengal (India)

2017-06-15

In the present paper we develop an algorithm for all spherically symmetric anisotropic charged fluid distributions. Considering a new source function ν(r) we find a set of solutions which is physically well behaved and represents compact stellar models. A detailed study specifically shows that the models actually correspond to strange stars in terms of their mass and radius. In this connection we investigate several physical properties like energy conditions, stability, mass-radius ratio, electric charge content, anisotropic nature and surface redshift through graphical plots and mathematical calculations. All the features from these studies are in excellent agreement with the already available evidence in theory as well as observations. (orig.)

Anisotropic hypersonic phonon propagation in films of aligned ellipsoids.

Science.gov (United States)

Beltramo, Peter J; Schneider, Dirk; Fytas, George; Furst, Eric M

2014-11-14

A material with anisotropic elastic mechanical properties and a direction-dependent hypersonic band gap is fabricated using ac electric field-directed convective self-assembly of colloidal ellipsoids. The frequency of the gap, which is detected in the direction perpendicular to particle alignment and entirely absent parallel to alignment, and the effective sound velocities can be tuned by the particle aspect ratio. We hypothesize that the band gap originates from the primary eigenmode peak, the m-splitted (s,1,2) mode, of the particle resonating with the effective medium. These results reveal the potential for powerful control of the hypersonic phononic band diagram by combining anisotropic particles and self-assembly.

Necking of anisotropic micro-films with strain-gradient effects

DEFF Research Database (Denmark)

Legarth, Brian Nyvang

2008-01-01

Necking of stubby micro-films of aluminum is investigated numerically by considering tension of a specimen with an initial imperfection used to onset localisation. Plastic anisotropy is represented by two different yield criteria and strain-gradient effects are accounted for using the visco......-plastic finite strain model. Furthermore, the model is extended to isotropic anisotropic hardening (evolving anisotropy). For isotropic hardening plastic anisotropy affects the predicted overall nominal stress level, while the peak stress remains at an overall logarithmic strain corresponding to the hardening...... exponent. This holds true for both local and nonlocal materials. Anisotropic hardening delays the point of maximum overall nominal stress....

PredMP: A Web Resource for Computationally Predicted Membrane Proteins via Deep Learning

KAUST Repository

Wang, Sheng; Fei, Shiyang; Zongan, Wang; Li, Yu; Zhao, Feng; Gao, Xin

2018-01-01

structures in Protein Data Bank (PDB). To elucidate the MP structures computationally, we developed a novel web resource, denoted as PredMP (http://52.87.130.56:3001/#/proteinindex), that delivers one-dimensional (1D) annotation of the membrane topology

Electromagnetism on anisotropic fractal media

Science.gov (United States)

Ostoja-Starzewski, Martin

2013-04-01

Basic equations of electromagnetic fields in anisotropic fractal media are obtained using a dimensional regularization approach. First, a formulation based on product measures is shown to satisfy the four basic identities of the vector calculus. This allows a generalization of the Green-Gauss and Stokes theorems as well as the charge conservation equation on anisotropic fractals. Then, pursuing the conceptual approach, we derive the Faraday and Ampère laws for such fractal media, which, along with two auxiliary null-divergence conditions, effectively give the modified Maxwell equations. Proceeding on a separate track, we employ a variational principle for electromagnetic fields, appropriately adapted to fractal media, so as to independently derive the same forms of these two laws. It is next found that the parabolic (for a conducting medium) and the hyperbolic (for a dielectric medium) equations involve modified gradient operators, while the Poynting vector has the same form as in the non-fractal case. Finally, Maxwell's electromagnetic stress tensor is reformulated for fractal systems. In all the cases, the derived equations for fractal media depend explicitly on fractal dimensions in three different directions and reduce to conventional forms for continuous media with Euclidean geometries upon setting these each of dimensions equal to unity.

Anisotropic magnetocrystalline coupling of the skyrmion lattice in MnSi

Science.gov (United States)

Luo, Yongkang; Lin, Shi-Zeng; Fobes, D. M.; Liu, Zhiqi; Bauer, E. D.; Betts, J. B.; Migliori, A.; Thompson, J. D.; Janoschek, M.; Maiorov, B.

2018-03-01

We investigate the anisotropic nature of magnetocrystalline coupling between the crystallographic and skyrmion crystal (SKX) lattices in the chiral magnet MnSi by magnetic field-angle resolved resonant ultrasound spectroscopy. Abrupt changes are observed in the elastic moduli and attenuation when the magnetic field is parallel to the [011] crystallographic direction. These observations are interpreted in a phenomenological Ginzburg-Landau theory that identifies switching of the SKX orientation to be the result of an anisotropic magnetocrystalline coupling potential. Our paper sheds new light on the nature of magnetocrystalline coupling potential relevant to future spintronic applications.

Anisotropic Magnus Force in Type-II Superconductors with Planar Defects

Science.gov (United States)

Monroy, Ricardo Vega; Gomez, Eliceo Cortés

2015-02-01

The effect of planar defects on the Magnus force in type-II superconductors is studied. It is shown that the deformation of the vortex due to the presence of a planar defect leads to a local decrease in the mean free path of electrons in the vortex. This effect reduces the effective Magnus coefficient in normal direction to the planar defect, leading to an anisotropic regime of the Hall effect. The presented developments here can qualitatively explain experimental observations of the anisotropic Hall effect in high- T c superconductors in the mixed state.

Design and development of anisotropic inorganic/polystyrene nanocomposites by surface modification of zinc oxide nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Han, Xiao [School of Materials Science and Engineering, Tongji University, Shanghai 200092 (China); Research Center for Translational Medicine, East Hospital, the Institute for Biomedical Engineering & Nano Science, Tongji University School of Medicine, Shanghai 200092 (China); Huang, Shiming [Department of Physics, Tongji University, Shanghai 200092 (China); Wang, Yilong, E-mail: yilongwang@tongji.edu.cn [Research Center for Translational Medicine, East Hospital, the Institute for Biomedical Engineering & Nano Science, Tongji University School of Medicine, Shanghai 200092 (China); Shi, Donglu, E-mail: shid@ucmail.uc.edu [Research Center for Translational Medicine, East Hospital, the Institute for Biomedical Engineering & Nano Science, Tongji University School of Medicine, Shanghai 200092 (China); The Materials Science and Engineering Program, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH 45221 (United States)

2016-07-01

Anisotropic yolk/shell or Janus inorganic/polystyrene nanocomposites were prepared by combining miniemulsion polymerization and sol–gel reaction. The morphologies of the anisotropic composites were found to be greatly influenced by surface modification of zinc oxide (ZnO) nanoparticle seeds. Two different types of the oleic acid modified ZnO nanoparticles (OA-ZnO) were prepared by post-treatment of commercial ZnO powder and homemade OA-ZnO nanoparticles. The morphologies and properties of the nanocomposites were investigated by transmission electron microscope (TEM), thermogravimetric analysis (TGA), Fourier transform infrared spectroscopy (FT-IR), dynamic light scattering (DLS), and energy dispersive X-ray spectroscopy (EDX). It was found that both post-treated OA-ZnO and in-situ prepared OA-ZnO nanoparticles resulted in the yolk–shell and Janus structure nanocomposites, but with varied size and morphology. These nanocomposites showed stable and strong fluorescence by introducing quantum dots as the co-seeds. The fluorescent anisotropic nanocomposites were decorated separately with surface carboxyl and hydroxyl groups. These composites with unique anisotropic properties will have high potential in biomedical applications, particularly in bio-detection. - Graphical abstract: Design and development of anisotropic inorganic/polystyrene nanocomposites by surface modification of zinc oxide nanoparticles. - Highlights: • Non-magnetic anisotropic yolk/shell or Janus nanocomposites are prepared and characterized. • Different surface modification of zinc oxide (ZnO) nanoparticles results in varied morphology and size of the final product. • Fluorescent anisotropic nanocomposites embodying quantum dots are an ideal candidate for bio-detection applications.

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

Science.gov (United States)

Maguire, Jack B; Boyken, Scott E; Baker, David; Kuhlman, Brian

2018-05-08

Hydrogen bond networks play a critical role in determining the stability and specificity of biomolecular complexes, and the ability to design such networks is important for engineering novel structures, interactions, and enzymes. One key feature of hydrogen bond networks that makes them difficult to rationally engineer is that they are highly cooperative and are not energetically favorable until the hydrogen bonding potential has been satisfied for all buried polar groups in the network. Existing computational methods for protein design are ill-equipped for creating these highly cooperative networks because they rely on energy functions and sampling strategies that are focused on pairwise interactions. To enable the design of complex hydrogen bond networks, we have developed a new sampling protocol in the molecular modeling program Rosetta that explicitly searches for sets of amino acid mutations that can form self-contained hydrogen bond networks. For a given set of designable residues, the protocol often identifies many alternative sets of mutations/networks, and we show that it can readily be applied to large sets of residues at protein-protein interfaces or in the interior of proteins. The protocol builds on a recently developed method in Rosetta for designing hydrogen bond networks that has been experimentally validated for small symmetric systems but was not extensible to many larger protein structures and complexes. The sampling protocol we describe here not only recapitulates previously validated designs with performance improvements but also yields viable hydrogen bond networks for cases where the previous method fails, such as the design of large, asymmetric interfaces relevant to engineering protein-based therapeutics.

Application of empirical hydration distribution functions around polar atoms for assessing hydration structures of proteins

International Nuclear Information System (INIS)

Matsuoka, Daisuke; Nakasako, Masayoshi

2013-01-01

Highlights: ► Empirical distribution functions of water molecules in protein hydration are made. ► The functions measure how hydrogen-bond geometry in hydration deviate from ideal. ► The functions assess experimentally identified hydration structures of protein. - Abstract: To quantitatively characterize hydrogen-bond geometry in local hydration structures of proteins, we constructed a set of empirical hydration distribution functions (EHDFs) around polar protein atoms in the main and side chains of 11 types of hydrophilic amino acids (D. Matsuoka, M. Nakasako, Journal of Physical Chemistry B 113 (2009) 11274). The functions are the ensemble average of possible hydration patterns around the polar atoms, and describe the anisotropic deviations from ideal hydrogen bond geometry. In addition, we defined probability distribution function of hydration water molecules (PDFH) over the hydrophilic surface of a protein as the sum of EHDFs of solvent accessible polar protein atoms. The functions envelop most of hydration sites identified in crystal structures of proteins (D. Matsuoka, M. Nakasako, Journal of Physical Chemistry B 114 (2010) 4652). Here we propose the application of EHDFs and PDFHs for assessing crystallographically identified hydration structures of proteins. First, hydration water molecules are classified with respect to the geometry in hydrogen bonds in referring EHDFs. Difference Fourier electron density map weighted by PDFH of protein is proposed to identify easily density peaks as candidates of hydration water molecules. A computer program implementing those ideas was developed and used for assessing hydration structures of proteins

An experimental and computational framework to build a dynamic protein atlas of human cell division

OpenAIRE

Kavur, Marina; Kavur, Marina; Kavur, Marina; Ellenberg, Jan; Peters, Jan-Michael; Ladurner, Rene; Martinic, Marina; Kueblbeck, Moritz; Nijmeijer, Bianca; Wachsmuth, Malte; Koch, Birgit; Walther, Nike; Politi, Antonio; Heriche, Jean-Karim; Hossain, M.

2017-01-01

Essential biological functions of human cells, such as division, require the tight coordination of the activity of hundreds of proteins in space and time. While live cell imaging is a powerful tool to study the distribution and dynamics of individual proteins after fluorescence tagging, it has not yet been used to map protein networks due to the lack of systematic and quantitative experimental and computational approaches. Using the cell and nuclear boundaries as landmarks, we generated a 4D ...

Wide-azimuth angle gathers for anisotropic wave-equation migration

KAUST Repository

Sava, Paul C.

2012-10-15

Extended common-image-point gathers (CIP) constructed by wide-azimuth TI wave-equation migration contain all the necessary information for angle decomposition as a function of the reflection and azimuth angles at selected locations in the subsurface. The aperture and azimuth angles are derived from the extended images using analytic relations between the space- and time-lag extensions using information which is already available at the time of migration, i.e. the anisotropic model parameters. CIPs are cheap to compute because they can be distributed in the image at the most relevant positions, as indicated by the geologic structure. If the reflector dip is known at the CIP locations, then the computational cost can be reduced by evaluating only two components of the space-lag vector. The transformation from extended images to angle gathers is a planar Radon transform which depends on the local medium parameters. This transformation allows us to separate all illumination directions for a given experiment, or between different experiments. We do not need to decompose the reconstructed wavefields or to choose the most energetic directions for decomposition. Applications of the method include illumination studies in complex areas where ray-based methods fail, and assuming that the subsurface illumination is sufficiently dense, the study of amplitude variation with aperture and azimuth angles. © 2012 European Association of Geoscientists & Engineers.

Wide-azimuth angle gathers for anisotropic wave-equation migration

KAUST Repository

Sava, Paul C.; Alkhalifah, Tariq Ali

2012-01-01

Extended common-image-point gathers (CIP) constructed by wide-azimuth TI wave-equation migration contain all the necessary information for angle decomposition as a function of the reflection and azimuth angles at selected locations in the subsurface. The aperture and azimuth angles are derived from the extended images using analytic relations between the space- and time-lag extensions using information which is already available at the time of migration, i.e. the anisotropic model parameters. CIPs are cheap to compute because they can be distributed in the image at the most relevant positions, as indicated by the geologic structure. If the reflector dip is known at the CIP locations, then the computational cost can be reduced by evaluating only two components of the space-lag vector. The transformation from extended images to angle gathers is a planar Radon transform which depends on the local medium parameters. This transformation allows us to separate all illumination directions for a given experiment, or between different experiments. We do not need to decompose the reconstructed wavefields or to choose the most energetic directions for decomposition. Applications of the method include illumination studies in complex areas where ray-based methods fail, and assuming that the subsurface illumination is sufficiently dense, the study of amplitude variation with aperture and azimuth angles. © 2012 European Association of Geoscientists & Engineers.

Anisotropic diffusion in a toroidal geometry

International Nuclear Information System (INIS)

Fischer, Paul F

2005-01-01

As part of the Department of Energy's applications oriented SciDAC project, three model problems have been proposed by the Center for Extended Magnetohydrodynamics Modeling to test the potential of numerical algorithms for challenging magnetohydrodynamics (MHD) problems that are required for future fusion development. The first of these, anisotropic diffusion in a toroidal geometry, is considered in this note

The unfolding effects on the protein hydration shell and partial molar volume: a computational study.

Science.gov (United States)

Del Galdo, Sara; Amadei, Andrea

2016-10-12

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process.

Protein consensus-based surface engineering (ProCoS): a computer-assisted method for directed protein evolution.

Science.gov (United States)

Shivange, Amol V; Hoeffken, Hans Wolfgang; Haefner, Stefan; Schwaneberg, Ulrich

2016-12-01

Protein consensus-based surface engineering (ProCoS) is a simple and efficient method for directed protein evolution combining computational analysis and molecular biology tools to engineer protein surfaces. ProCoS is based on the hypothesis that conserved residues originated from a common ancestor and that these residues are crucial for the function of a protein, whereas highly variable regions (situated on the surface of a protein) can be targeted for surface engineering to maximize performance. ProCoS comprises four main steps: ( i ) identification of conserved and highly variable regions; ( ii ) protein sequence design by substituting residues in the highly variable regions, and gene synthesis; ( iii ) in vitro DNA recombination of synthetic genes; and ( iv ) screening for active variants. ProCoS is a simple method for surface mutagenesis in which multiple sequence alignment is used for selection of surface residues based on a structural model. To demonstrate the technique's utility for directed evolution, the surface of a phytase enzyme from Yersinia mollaretii (Ymphytase) was subjected to ProCoS. Screening just 1050 clones from ProCoS engineering-guided mutant libraries yielded an enzyme with 34 amino acid substitutions. The surface-engineered Ymphytase exhibited 3.8-fold higher pH stability (at pH 2.8 for 3 h) and retained 40% of the enzyme's specific activity (400 U/mg) compared with the wild-type Ymphytase. The pH stability might be attributed to a significantly increased (20 percentage points; from 9% to 29%) number of negatively charged amino acids on the surface of the engineered phytase.

Effective computation of stochastic protein kinetic equation by reducing stiffness via variable transformation

Energy Technology Data Exchange (ETDEWEB)

Wang, Lijin, E-mail: ljwang@ucas.ac.cn [School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049 (China)

2016-06-08

The stochastic protein kinetic equations can be stiff for certain parameters, which makes their numerical simulation rely on very small time step sizes, resulting in large computational cost and accumulated round-off errors. For such situation, we provide a method of reducing stiffness of the stochastic protein kinetic equation by means of a kind of variable transformation. Theoretical and numerical analysis show effectiveness of this method. Its generalization to a more general class of stochastic differential equation models is also discussed.

Possibility to explain the temperature distribution in sunspots by an anisotropic heat transfer

Energy Technology Data Exchange (ETDEWEB)

Eschrich, K O; Krause, F [Akademie der Wissenschaften der DDR, Potsdam. Zentralinstitut fuer Astrophysik

1977-01-01

Numerical solutions of a heat conduction problem in an anisotropic medium are used for a discussion of the possibility to explain the temperature distribution in sunspots and their environment. The anisotropy is assumed being due to the strong magnetic field in sunspots and the region below. This magnetic field forces the convection to take an anisotropic structure (two-dimensional turbulence) and thus the region gets anisotropic conduction properties, on the average. The discussion shows that the observed temperature profiles can be explained in the case the depth of the region of anisotropy is about as large as the diameter of the spot or larger.

Hydraulic fracturing in anisotropic and heterogeneous rocks

NARCIS (Netherlands)

Valliappan, V.; Remmers, J.J.C.; Barnhoorn, A.; Smeulders, D.M.J.

2017-01-01

In this paper, we present a two dimensional model for modelling the hydraulic fracture process in anisotropic and heterogeneous rocks. The model is formulated using extended finite elements (XFEM) in combination with Newton-Raphson method for spatial and Euler's implicit scheme for time. The

Spin Wave Theory of Strongly Anisotropic Magnets

DEFF Research Database (Denmark)

Lindgård, Per-Anker

1977-01-01

A strong anisotropy gives rise to a non-spherical precession of the spins with different amplitudes in the x and y directions. The highly anharmonic exchange interaction thereby becomes effectively anisotropic. The possibility of detecting a genuine two-ion anisotropy is discussed, and comments...

Cracking of anisotropic cylindrical polytropes

Energy Technology Data Exchange (ETDEWEB)

Mardan, S.A. [University of the Management and Technology, Department of Mathematics, Lahore (Pakistan); Azam, M. [University of Education, Division of Science and Technology, Lahore (Pakistan)

2017-06-15

We study the appearance of cracking in charged anisotropic cylindrical polytropes with generalized polytropic equation. We investigate the existence of cracking in two different kinds of polytropes existing in the literature through two different assumptions: (a) local density perturbation with conformally flat condition, and (b) perturbing polytropic index, charge and anisotropy parameters. We conclude that cracking appears in both kinds of polytropes for a specific range of density and model parameters. (orig.)

Layered Black Phosphorus: Strongly Anisotropic Magnetic, Electronic, and Electron-Transfer Properties.

Science.gov (United States)

Sofer, Zdeněk; Sedmidubský, David; Huber, Štěpán; Luxa, Jan; Bouša, Daniel; Boothroyd, Chris; Pumera, Martin

2016-03-01

Layered elemental materials, such as black phosphorus, exhibit unique properties originating from their highly anisotropic layered structure. The results presented herein demonstrate an anomalous anisotropy for the electrical, magnetic, and electrochemical properties of black phosphorus. It is shown that heterogeneous electron transfer from black phosphorus to outer- and inner-sphere molecular probes is highly anisotropic. The electron-transfer rates differ at the basal and edge planes. These unusual properties were interpreted by means of calculations, manifesting the metallic character of the edge planes as compared to the semiconducting properties of the basal plane. This indicates that black phosphorus belongs to a group of materials known as topological insulators. Consequently, these effects render the magnetic properties highly anisotropic, as both diamagnetic and paramagnetic behavior can be observed depending on the orientation in the magnetic field. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of Protein by Spectrophotometric and Computer Colour Based Intensity Method from Stem of Pea (Pisum sativum at Different Stages

Directory of Open Access Journals (Sweden)

Afsheen Mushtaque Shah

2010-12-01

Full Text Available In this study proteins were analyzed from pea plants at three different growth stages of stem by spectrophotometric i.e Lowry and Bradford quantitative methods and computer colour intensity based method. Though Spectrophotometric methods are regarded as classical methods, we report an alternate computer based method which gave comparable results. Computer software was developed the for protein analysis which is easier, time and money saving method as compared to the classical methods.

Efficient anisotropic wavefield extrapolation using effective isotropic models

KAUST Repository

Alkhalifah, Tariq Ali; Ma, X.; Waheed, Umair bin; Zuberi, Mohammad

2013-01-01

Isotropic wavefield extrapolation is more efficient than anisotropic extrapolation, and this is especially true when the anisotropy of the medium is tilted (from the vertical). We use the kinematics of the wavefield, appropriately represented

Angle-domain common-image gathers from anisotropic Gaussian ...

Indian Academy of Sciences (India)

3State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Chengdu University of Technology,. Chengdu ... studied the extraction scheme of ADCIGs by using. Kirchhoff ..... The effect of shale properties on anisotropic brittleness.

MATHEMATICAL AND COMPUTATIONAL MODELLING OF RIBOSOMAL MOVEMENT AND PROTEIN SYNTHESIS: AN OVERVIEW

Directory of Open Access Journals (Sweden)

Tobias von der Haar

2012-04-01

Full Text Available Translation or protein synthesis consists of a complex system of chemical reactions, which ultimately result in decoding of the mRNA and the production of a protein. The complexity of this reaction system makes it difficult to quantitatively connect its input parameters (such as translation factor or ribosome concentrations, codon composition of the mRNA, or energy availability to output parameters (such as protein synthesis rates or ribosome densities on mRNAs. Mathematical and computational models of translation have now been used for nearly five decades to investigate translation, and to shed light on the relationship between the different reactions in the system. This review gives an overview over the principal approaches used in the modelling efforts, and summarises some of the major findings that were made.

Anisotropic Josephson-vortex dynamics in layered organic superconductors

International Nuclear Information System (INIS)

Yasuzuka, S.; Uji, S.; Satsukawa, H.; Kimata, M.; Terashima, T.; Koga, H.; Yamamura, Y.; Saito, K.; Akutsu, H.; Yamada, J.

2010-01-01

To study the anisotropic Josephson-vortex dynamics in the d-wave superconductors, the interplane resistance has been measured on layered organic superconductors κ-(ET) 2 Cu(NCS) 2 and β-(BDA-TTP) 2 SbF 6 under magnetic fields precisely parallel to the conducting planes. For κ-(ET) 2 Cu(NCS) 2 , in-plane angular dependence of the Josephson-vortex flow resistance is mainly described by the fourfold symmetry and dip structures appear when the magnetic field is applied parallel to the b- and c-axes. The obtained results have a relation to the d-wave superconducting gap symmetry. However, the absence of in-plane fourfold anisotropy was found for β-(BDA-TTP) 2 SbF 6 . The different anisotropic behavior is discussed in terms of the interlayer coupling strength.

Computational tools for experimental determination and theoretical prediction of protein structure

Energy Technology Data Exchange (ETDEWEB)

O`Donoghue, S.; Rost, B.

1995-12-31

This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.

Anisotropic power spectrum of refractive-index fluctuation in hypersonic turbulence.

Science.gov (United States)

Li, Jiangting; Yang, Shaofei; Guo, Lixin; Cheng, Mingjian

2016-11-10

An anisotropic power spectrum of the refractive-index fluctuation in hypersonic turbulence was obtained by processing the experimental image of the hypersonic plasma sheath and transforming the generalized anisotropic von Kármán spectrum. The power spectrum suggested here can provide as good a fit to measured spectrum data for hypersonic turbulence as that recorded from the nano-planar laser scattering image. Based on the newfound anisotropic hypersonic turbulence power spectrum, Rytov approximation was employed to establish the wave structure function and the spatial coherence radius model of electromagnetic beam propagation in hypersonic turbulence. Enhancing the anisotropy characteristics of the hypersonic turbulence led to a significant improvement in the propagation performance of electromagnetic beams in hypersonic plasma sheath. The influence of hypersonic turbulence on electromagnetic beams increases with the increase of variance of the refractive-index fluctuation and the decrease of turbulence outer scale and anisotropy parameters. The spatial coherence radius was much smaller than that in atmospheric turbulence. These results are fundamental to understanding electromagnetic wave propagation in hypersonic turbulence.

Modelling anisotropic water transport in polymer composite

Indian Academy of Sciences (India)

This work reports anisotropic water transport in a polymer composite consisting of an epoxy matrix reinforced with aligned triangular bars made of vinyl ester. By gravimetric experiments, water diffusion in resin and polymer composites were characterized. Parameters for Fickian diffusion and polymer relaxation models were ...

Illusion thermal device based on material with constant anisotropic thermal conductivity for location camouflage

Science.gov (United States)

Hou, Quanwen; Zhao, Xiaopeng; Meng, Tong; Liu, Cunliang

2016-09-01

Thermal metamaterials and devices based on transformation thermodynamics often require materials with anisotropic and inhomogeneous thermal conductivities. In this study, still based on the concept of transformation thermodynamics, we designed a planar illusion thermal device, which can delocalize a heat source in the device such that the temperature profile outside the device appears to be produced by a virtual source at another position. This device can be constructed by only one kind of material with constant anisotropic thermal conductivity. The condition which should be satisfied by the device is provided, and the required anisotropic thermal conductivity is then deduced theoretically. This study may be useful for the designs of metamaterials or devices since materials with constant anisotropic parameters have great facility in fabrication. A prototype device has been fabricated based on a composite composed by two naturally occurring materials. The experimental results validate the effectiveness of the device.

In situ anisotropic parameter determination using refraction seismic and VSP methods

Energy Technology Data Exchange (ETDEWEB)

Leslie, J.M.; Lawton, D.C. (Calgary Univ., AB (Canada))

1999-01-01

A prime concern in the time-to-depth conversion of reflection seismic data is seismic anisotropy, because it can produce velocity anomalies in seismic data that mimic the structural plays of interest to the petroleum prospector in both size and shape. Ongoing techniques of time-to-depth conversion of P-wave seismic data do not handle the travel time and velocity distortions caused by seismic anisotropy, particularly in areas of complex geologic structures. To address this problem, the first step is to know which rock units are anisotropic and measure their anisotropic parameters. Laboratory means are available, but there are problems with these mainly with shales because of their fissile nature. In situ measurements are preferable because they yield a more robust value, and at the University of Calgary such measurements were undertaken using refraction seismic and vertical seismic profiling (VSP) methods. Results indicate that the two Thomsen anisotropic parameters of interest can be determined from the VSP experiment, but these values are slightly less than those obtained using the refraction technique. This may be because of the sensitivity of the shot statics which arises from the direct travel time measurement of the technique. The experiment yields another method to measure velocity anisotropy, in situ, where steeply dipping strata outcrop, which allows for the accurate measurement of the anisotropic parameters for use in depth migration routines. 4 refs.

In situ anisotropic parameter determination using refraction seismic and VSP methods

Energy Technology Data Exchange (ETDEWEB)

Leslie, J.M.; Lawton, D.C. [Calgary Univ., AB (Canada)

1999-11-01

A prime concern in the time-to-depth conversion of reflection seismic data is seismic anisotropy, because it can produce velocity anomalies in seismic data that mimic the structural plays of interest to the petroleum prospector in both size and shape. Ongoing techniques of time-to-depth conversion of P-wave seismic data do not handle the travel time and velocity distortions caused by seismic anisotropy, particularly in areas of complex geologic structures. To address this problem, the first step is to know which rock units are anisotropic and measure their anisotropic parameters. Laboratory means are available, but there are problems with these mainly with shales because of their fissile nature. In situ measurements are preferable because they yield a more robust value, and at the University of Calgary such measurements were undertaken using refraction seismic and vertical seismic profiling (VSP) methods. Results indicate that the two Thomsen anisotropic parameters of interest can be determined from the VSP experiment, but these values are slightly less than those obtained using the refraction technique. This may be because of the sensitivity of the shot statics which arises from the direct travel time measurement of the technique. The experiment yields another method to measure velocity anisotropy, in situ, where steeply dipping strata outcrop, which allows for the accurate measurement of the anisotropic parameters for use in depth migration routines. 4 refs.

Wireless energy transfer between anisotropic metamaterials shells

Energy Technology Data Exchange (ETDEWEB)

Díaz-Rubio, Ana; Carbonell, Jorge; Sánchez-Dehesa, José, E-mail: jsdehesa@upv.es

2014-06-15

The behavior of strongly coupled Radial Photonic Crystals shells is investigated as a potential alternative to transfer electromagnetic energy wirelessly. These sub-wavelength resonant microstructures, which are based on anisotropic metamaterials, can produce efficient coupling phenomena due to their high quality factor. A configuration of selected constitutive parameters (permittivity and permeability) is analyzed in terms of its resonant characteristics. The coupling to loss ratio between two coupled resonators is calculated as a function of distance, the maximum (in excess of 300) is obtained when the shells are separated by three times their radius. Under practical conditions an 83% of maximum power transfer has been also estimated. -- Highlights: •Anisotropic metamaterial shells exhibit high quality factors and sub-wavelength size. •Exchange of electromagnetic energy between shells with high efficiency is analyzed. •Strong coupling is supported with high wireless transfer efficiency. •End-to-end energy transfer efficiencies higher than 83% can be predicted.

Wireless energy transfer between anisotropic metamaterials shells

International Nuclear Information System (INIS)

Díaz-Rubio, Ana; Carbonell, Jorge; Sánchez-Dehesa, José

2014-01-01

The behavior of strongly coupled Radial Photonic Crystals shells is investigated as a potential alternative to transfer electromagnetic energy wirelessly. These sub-wavelength resonant microstructures, which are based on anisotropic metamaterials, can produce efficient coupling phenomena due to their high quality factor. A configuration of selected constitutive parameters (permittivity and permeability) is analyzed in terms of its resonant characteristics. The coupling to loss ratio between two coupled resonators is calculated as a function of distance, the maximum (in excess of 300) is obtained when the shells are separated by three times their radius. Under practical conditions an 83% of maximum power transfer has been also estimated. -- Highlights: •Anisotropic metamaterial shells exhibit high quality factors and sub-wavelength size. •Exchange of electromagnetic energy between shells with high efficiency is analyzed. •Strong coupling is supported with high wireless transfer efficiency. •End-to-end energy transfer efficiencies higher than 83% can be predicted

Anisotropic hydrodynamics with a scalar collisional kernel

Science.gov (United States)

Almaalol, Dekrayat; Strickland, Michael

2018-04-01

Prior studies of nonequilibrium dynamics using anisotropic hydrodynamics have used the relativistic Anderson-Witting scattering kernel or some variant thereof. In this paper, we make the first study of the impact of using a more realistic scattering kernel. For this purpose, we consider a conformal system undergoing transversally homogenous and boost-invariant Bjorken expansion and take the collisional kernel to be given by the leading order 2 ↔2 scattering kernel in scalar λ ϕ4 . We consider both classical and quantum statistics to assess the impact of Bose enhancement on the dynamics. We also determine the anisotropic nonequilibrium attractor of a system subject to this collisional kernel. We find that, when the near-equilibrium relaxation-times in the Anderson-Witting and scalar collisional kernels are matched, the scalar kernel results in a higher degree of momentum-space anisotropy during the system's evolution, given the same initial conditions. Additionally, we find that taking into account Bose enhancement further increases the dynamically generated momentum-space anisotropy.

Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe): A new radiomics descriptor.

Science.gov (United States)

Prasanna, Prateek; Tiwari, Pallavi; Madabhushi, Anant

2016-11-22

In this paper, we introduce a new radiomic descriptor, Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe) for capturing subtle differences between benign and pathologic phenotypes which may be visually indistinguishable on routine anatomic imaging. CoLlAGe seeks to capture and exploit local anisotropic differences in voxel-level gradient orientations to distinguish similar appearing phenotypes. CoLlAGe involves assigning every image voxel an entropy value associated with the co-occurrence matrix of gradient orientations computed around every voxel. The hypothesis behind CoLlAGe is that benign and pathologic phenotypes even though they may appear similar on anatomic imaging, will differ in their local entropy patterns, in turn reflecting subtle local differences in tissue microarchitecture. We demonstrate CoLlAGe's utility in three clinically challenging classification problems: distinguishing (1) radiation necrosis, a benign yet confounding effect of radiation treatment, from recurrent tumors on T1-w MRI in 42 brain tumor patients, (2) different molecular sub-types of breast cancer on DCE-MRI in 65 studies and (3) non-small cell lung cancer (adenocarcinomas) from benign fungal infection (granulomas) on 120 non-contrast CT studies. For each of these classification problems, CoLlAGE in conjunction with a random forest classifier outperformed state of the art radiomic descriptors (Haralick, Gabor, Histogram of Gradient Orientations).

Thick-walled anisotropic elliptic tube analyzed via curvilinear tensor calculus

Directory of Open Access Journals (Sweden)

Mareš T.

2007-10-01

Full Text Available After a brief introduction into the tensor calculus, the thick-walled anisotropic elliptic tube is analyzed. A procedure of the analysis is described in a stepwise manner. A choice of the appropriate coordinate systems is the first step. The second step consists of the determination of corresponding metric tensors. Then the elasticity tensor of a local orthotropy is transformed into a global computational coordinate system. Next the appropriate Christoffel symbols of the second kind are determined and the total potential energy of the system is expressed. At the end the solution is approximated by a Fourier series and for given geometrical values and loading the numerical results are obtained and graphically represented.It must be said that throughout the calculation the free software only was used and for the numerical operations an old laptop is sufficient. The author regards both the former and the latter as a great advantage of the demonstrated method.

A novel anisotropic inversion approach for magnetotelluric data from subsurfaces with orthogonal geoelectric strike directions

Science.gov (United States)

Schmoldt, Jan-Philipp; Jones, Alan G.

2013-12-01

The key result of this study is the development of a novel inversion approach for cases of orthogonal, or close to orthogonal, geoelectric strike directions at different depth ranges, for example, crustal and mantle depths. Oblique geoelectric strike directions are a well-known issue in commonly employed isotropic 2-D inversion of MT data. Whereas recovery of upper (crustal) structures can, in most cases, be achieved in a straightforward manner, deriving lower (mantle) structures is more challenging with isotropic 2-D inversion in the case of an overlying region (crust) with different geoelectric strike direction. Thus, investigators may resort to computationally expensive and more limited 3-D inversion in order to derive the electric resistivity distribution at mantle depths. In the novel approaches presented in this paper, electric anisotropy is used to image 2-D structures in one depth range, whereas the other region is modelled with an isotropic 1-D or 2-D approach, as a result significantly reducing computational costs of the inversion in comparison with 3-D inversion. The 1- and 2-D versions of the novel approach were tested using a synthetic 3-D subsurface model with orthogonal strike directions at crust and mantle depths and their performance was compared to results of isotropic 2-D inversion. Structures at crustal depths were reasonably well recovered by all inversion approaches, whereas recovery of mantle structures varied significantly between the different approaches. Isotropic 2-D inversion models, despite decomposition of the electric impedance tensor and using a wide range of inversion parameters, exhibited severe artefacts thereby confirming the requirement of either an enhanced or a higher dimensionality inversion approach. With the anisotropic 1-D inversion approach, mantle structures of the synthetic model were recovered reasonably well with anisotropy values parallel to the mantle strike direction (in this study anisotropy was assigned to the

Homogenization of linearly anisotropic scattering cross sections in a consistent B1 heterogeneous leakage model

International Nuclear Information System (INIS)

Marleau, G.; Debos, E.

1998-01-01

One of the main problems encountered in cell calculations is that of spatial homogenization where one associates to an heterogeneous cell an homogeneous set of cross sections. The homogenization process is in fact trivial when a totally reflected cell without leakage is fully homogenized since it involved only a flux-volume weighting of the isotropic cross sections. When anisotropic leakages models are considered, in addition to homogenizing isotropic cross sections, the anisotropic scattering cross section must also be considered. The simple option, which consists of using the same homogenization procedure for both the isotropic and anisotropic components of the scattering cross section, leads to inconsistencies between the homogeneous and homogenized transport equation. Here we will present a method for homogenizing the anisotropic scattering cross sections that will resolve these inconsistencies. (author)

Anisotropic superfluidity of hadronic matter

International Nuclear Information System (INIS)

Chela Flores, J.

1977-10-01

From a model of strong interactions with important general features (f-g model) and from recent experiments of Rudnick and co-workers on thin films of helium II, hadronic matter is considered as a new manifestation of anisotropic superfluidity. In order to test the validity of the suggestion, some qualitative features of multiparticle production of hadrons are considered, and found to have a natural explanation. A prediction is made following a recent experiment on π + p collisions

Complex Anisotropic Structure of the Mantle Wedge Beneath Kamchatka Volcanoes

Science.gov (United States)

Levin, V.; Park, J.; Gordeev, E.; Droznin, D.

2002-12-01

A wedge of mantle material above the subducting lithospheric plate at a convergent margin is among the most dynamic environments of the Earth's interior. Deformation and transport of solid and volatile phases within this region control the fundamental process of elemental exchange between the surficial layers and the interior of the planet. A helpful property in the study of material deformation and transport within the upper mantle is seismic anisotropy, which may reflect both microscopic effects of preferentialy aligned crystals of olivine and orthopyroxene and macroscopic effects of systematic cracks, melt lenses, layering etc. Through the mapping of anisotropic properties within the mantle wedge we can establish patterns of deformation. Volatile content affects olivine alignment, so regions of anomalous volatile content may be evident. Indicators of seismic anisotropy commonly employed in upper mantle studies include shear wave birefringence and mode-conversion between compressional and shear body waves. When combined together, these techniques offer complementary constraints on the location and intensity of anisotropic properties. The eastern coast of southern Kamchatka overlies a vigorous convergent margin where the Pacific plate descends at a rate of almost 80 mm/yr towards the northwest. We extracted seismic anisotropy indicators from two data sets sensitive to the anisotropic properties of the uppermost mantle. Firstly, we evaluated teleseismic receiver functions for a number of sites, and found ample evidence for anisotropicaly-influenced P-to-S mode conversion. Secondly, we measured splitting in S waves of earthquakes with sources within the downgoing slab. The first set of observations provides constraints on the depth ranges where strong changes in anisotropic properties take place. The local splitting data provides constraints on the cumulative strength of anisotropic properties along specific pathways through the mantle wedge and possibly parts of

Numerically stable finite difference simulation for ultrasonic NDE in anisotropic composites

Science.gov (United States)

Leckey, Cara A. C.; Quintanilla, Francisco Hernando; Cole, Christina M.

2018-04-01

Simulation tools can enable optimized inspection of advanced materials and complex geometry structures. Recent work at NASA Langley is focused on the development of custom simulation tools for modeling ultrasonic wave behavior in composite materials. Prior work focused on the use of a standard staggered grid finite difference type of mathematical approach, by implementing a three-dimensional (3D) anisotropic Elastodynamic Finite Integration Technique (EFIT) code. However, observations showed that the anisotropic EFIT method displays numerically unstable behavior at the locations of stress-free boundaries for some cases of anisotropic materials. This paper gives examples of the numerical instabilities observed for EFIT and discusses the source of instability. As an alternative to EFIT, the 3D Lebedev Finite Difference (LFD) method has been implemented. The paper briefly describes the LFD approach and shows examples of stable behavior in the presence of stress-free boundaries for a monoclinic anisotropy case. The LFD results are also compared to experimental results and dispersion curves.

A numerical homogenization method for heterogeneous, anisotropic elastic media based on multiscale theory

KAUST Repository

Gao, Kai

2015-06-05

The development of reliable methods for upscaling fine-scale models of elastic media has long been an important topic for rock physics and applied seismology. Several effective medium theories have been developed to provide elastic parameters for materials such as finely layered media or randomly oriented or aligned fractures. In such cases, the analytic solutions for upscaled properties can be used for accurate prediction of wave propagation. However, such theories cannot be applied directly to homogenize elastic media with more complex, arbitrary spatial heterogeneity. Therefore, we have proposed a numerical homogenization algorithm based on multiscale finite-element methods for simulating elastic wave propagation in heterogeneous, anisotropic elastic media. Specifically, our method used multiscale basis functions obtained from a local linear elasticity problem with appropriately defined boundary conditions. Homogenized, effective medium parameters were then computed using these basis functions, and the approach applied a numerical discretization that was similar to the rotated staggered-grid finite-difference scheme. Comparisons of the results from our method and from conventional, analytical approaches for finely layered media showed that the homogenization reliably estimated elastic parameters for this simple geometry. Additional tests examined anisotropic models with arbitrary spatial heterogeneity in which the average size of the heterogeneities ranged from several centimeters to several meters, and the ratio between the dominant wavelength and the average size of the arbitrary heterogeneities ranged from 10 to 100. Comparisons to finite-difference simulations proved that the numerical homogenization was equally accurate for these complex cases.

Linearly polarized photoluminescence of anisotropically strained c-plane GaN layers on stripe-shaped cavity-engineered sapphire substrate

Science.gov (United States)

Kim, Jongmyeong; Moon, Daeyoung; Lee, Seungmin; Lee, Donghyun; Yang, Duyoung; Jang, Jeonghwan; Park, Yongjo; Yoon, Euijoon

2018-05-01

Anisotropic in-plane strain and resultant linearly polarized photoluminescence (PL) of c-plane GaN layers were realized by using a stripe-shaped cavity-engineered sapphire substrate (SCES). High resolution X-ray reciprocal space mapping measurements revealed that the GaN layers on the SCES were under significant anisotropic in-plane strain of -0.0140% and -0.1351% along the directions perpendicular and parallel to the stripe pattern, respectively. The anisotropic in-plane strain in the GaN layers was attributed to the anisotropic strain relaxation due to the anisotropic arrangement of cavity-incorporated membranes. Linearly polarized PL behavior such as the observed angle-dependent shift in PL peak position and intensity comparable with the calculated value based on k.p perturbation theory. It was found that the polarized PL behavior was attributed to the modification of valence band structures induced by anisotropic in-plane strain in the GaN layers on the SCES.

Predicting sintering deformation of ceramic film constrained by rigid substrate using anisotropic constitutive law

International Nuclear Information System (INIS)

Li Fan; Pan Jingzhe; Guillon, Olivier; Cocks, Alan

2010-01-01

Sintering of ceramic films on a solid substrate is an important technology for fabricating a range of products, including solid oxide fuel cells, micro-electronic PZT films and protective coatings. There is clear evidence that the constrained sintering process is anisotropic in nature. This paper presents a study of the constrained sintering deformation using an anisotropic constitutive law. The state of the material is described using the sintering strains rather than the relative density. In the limiting case of free sintering, the constitutive law reduces to a conventional isotropic constitutive law. The anisotropic constitutive law is used to calculate sintering deformation of a constrained film bonded to a rigid substrate and the compressive stress required in a sinter-forging experiment to achieve zero lateral shrinkage. The results are compared with experimental data in the literature. It is shown that the anisotropic constitutive law can capture the behaviour of the materials observed in the sintering experiments.

Evaluation of the Anisotropic Radiative Conductivity of a Low-Density Carbon Fiber Material from Realistic Microscale Imaging

Science.gov (United States)

Nouri, Nima; Panerai, Francesco; Tagavi, Kaveh A.; Mansour, Nagi N.; Martin, Alexandre

2015-01-01

The radiative heat transfer inside a low-density carbon fiber insulator is analyzed using a three-dimensional direct simulation model. A robust procedure is presented for the numerical calculation of the geometric configuration factor to compute the radiative energy exchange processes among the small discretized surface areas of the fibrous material. The methodology is applied to a polygonal mesh of a fibrous insulator obtained from three-dimensional microscale imaging of the real material. The anisotropic values of the radiative conductivity are calculated for that geometry. The results yield both directional and thermal dependence of the radiative conductivity.