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Sample records for computed protein anisotropic

  1. On characterization of anisotropic plant protein structures

    NARCIS (Netherlands)

    Krintiras, G.A.; Göbel, J.; Bouwman, W.G.; Goot, van der A.J.; Stefanidis, G.D.

    2014-01-01

    In this paper, a set of complementary techniques was used to characterize surface and bulk structures of an anisotropic Soy Protein Isolate (SPI)–vital wheat gluten blend after it was subjected to heat and simple shear flow in a Couette Cell. The structured biopolymer blend can form a basis for a

  2. Anisotropic biodegradable lipid coated particles for spatially dynamic protein presentation.

    Science.gov (United States)

    Meyer, Randall A; Mathew, Mohit P; Ben-Akiva, Elana; Sunshine, Joel C; Shmueli, Ron B; Ren, Qiuyin; Yarema, Kevin J; Green, Jordan J

    2018-05-01

    There has been growing interest in the use of particles coated with lipids for applications ranging from drug delivery, gene delivery, and diagnostic imaging to immunoengineering. To date, almost all particles with lipid coatings have been spherical despite emerging evidence that non-spherical shapes can provide important advantages including reduced non-specific elimination and increased target-specific binding. We combine control of core particle geometry with control of particle surface functionality by developing anisotropic, biodegradable ellipsoidal particles with lipid coatings. We demonstrate that these lipid coated ellipsoidal particles maintain advantageous properties of lipid polymer hybrid particles, such as the ability for modular protein conjugation to the particle surface using versatile bioorthogonal ligation reactions. In addition, they exhibit biomimetic membrane fluidity and demonstrate lateral diffusive properties characteristic of natural membrane proteins. These ellipsoidal particles simultaneously provide benefits of non-spherical particles in terms of stability and resistance to non-specific phagocytosis by macrophages as well as enhanced targeted binding. These biomaterials provide a novel and flexible platform for numerous biomedical applications. The research reported here documents the ability of non-spherical polymeric particles to be coated with lipids to form anisotropic biomimetic particles. In addition, we demonstrate that these lipid-coated biodegradable polymeric particles can be conjugated to a wide variety of biological molecules in a "click-like" fashion. This is of interest due to the multiple types of cellular mimicry enabled by this biomaterial based technology. These features include mimicry of the highly anisotropic shape exhibited by cells, surface presentation of membrane bound protein mimetics, and lateral diffusivity of membrane bound substrates comparable to that of a plasma membrane. This platform is demonstrated to

  3. Computational Study of Subdural Cortical Stimulation: Effects of Simulating Anisotropic Conductivity on Activation of Cortical Neurons.

    Directory of Open Access Journals (Sweden)

    Hyeon Seo

    Full Text Available Subdural cortical stimulation (SuCS is an appealing method in the treatment of neurological disorders, and computational modeling studies of SuCS have been applied to determine the optimal design for electrotherapy. To achieve a better understanding of computational modeling on the stimulation effects of SuCS, the influence of anisotropic white matter conductivity on the activation of cortical neurons was investigated in a realistic head model. In this paper, we constructed pyramidal neuronal models (layers 3 and 5 that showed primary excitation of the corticospinal tract, and an anatomically realistic head model reflecting complex brain geometry. The anisotropic information was acquired from diffusion tensor magnetic resonance imaging (DT-MRI and then applied to the white matter at various ratios of anisotropic conductivity. First, we compared the isotropic and anisotropic models; compared to the isotropic model, the anisotropic model showed that neurons were activated in the deeper bank during cathodal stimulation and in the wider crown during anodal stimulation. Second, several popular anisotropic principles were adapted to investigate the effects of variations in anisotropic information. We observed that excitation thresholds varied with anisotropic principles, especially with anodal stimulation. Overall, incorporating anisotropic conductivity into the anatomically realistic head model is critical for accurate estimation of neuronal responses; however, caution should be used in the selection of anisotropic information.

  4. Computational Protein Design

    DEFF Research Database (Denmark)

    Johansson, Kristoffer Enøe

    Proteins are the major functional group of molecules in biology. The impact of protein science on medicine and chemical productions is rapidly increasing. However, the greatest potential remains to be realized. The fi eld of protein design has advanced computational modeling from a tool of support...... to a central method that enables new developments. For example, novel enzymes with functions not found in natural proteins have been de novo designed to give enough activity for experimental optimization. This thesis presents the current state-of-the-art within computational design methods together...... with a novel method based on probability theory. With the aim of assembling a complete pipeline for protein design, this work touches upon several aspects of protein design. The presented work is the computational half of a design project where the other half is dedicated to the experimental part...

  5. Adaptive weighted anisotropic diffusion for computed tomography denoising

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Zhi; Silver, Michael D. [Toshiba Medical Research Institute USA, Inc., Vernon Hills, IL (United States); Noshi, Yasuhiro [Toshiba Medical System Corporation, Tokyo (Japan)

    2011-07-01

    With increasing awareness of radiation safety, dose reduction has become an important task of modern CT system development. This paper proposes an adaptive weighted anisotropic diffusion method and an adaptive weighted sharp source anisotropic diffusion method as image domain filters to potentially help dose reduction. Different from existing anisotropic diffusion methods, the proposed methods incorporate an edge-sensitive adaptive source term as part of the diffusion iteration. It provides better edge and detail preservation. Visual evaluation showed that the new methods can reduce noise substantially without apparent edge and detail loss. The quantitative evaluations also showed over 50% of noise reduction in terms of noise standard deviations, which is equivalent to over 75% of dose reduction for a normal dose image quality. (orig.)

  6. Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Opron, Kristopher [Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States); Xia, Kelin [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States); Department of Mathematics, Michigan State University, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, Michigan 48824 (United States)

    2014-06-21

    Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of O(N{sup 2}). This work introduces a fast FRI (fFRI) algorithm for the flexibility analysis of large macromolecules. The proposed fFRI further reduces the computational complexity to O(N). Additionally, we propose anisotropic FRI (aFRI) algorithms for the analysis of protein collective dynamics. The aFRI algorithms permit adaptive Hessian matrices, from a completely global 3N × 3N matrix to completely local 3 × 3 matrices. These 3 × 3 matrices, despite being calculated locally, also contain non-local correlation information. Eigenvectors obtained from the proposed aFRI algorithms are able to demonstrate collective motions. Moreover, we investigate the performance of FRI by employing four families of radial basis correlation functions. Both parameter optimized and parameter-free FRI methods are explored. Furthermore, we compare the accuracy and efficiency of FRI with some established approaches to flexibility analysis, namely

  7. Quantum computation in semiconductor quantum dots of electron-spin asymmetric anisotropic exchange

    International Nuclear Information System (INIS)

    Hao Xiang; Zhu Shiqun

    2007-01-01

    The universal quantum computation is obtained when there exists asymmetric anisotropic exchange between electron spins in coupled semiconductor quantum dots. The asymmetric Heisenberg model can be transformed into the isotropic model through the control of two local unitary rotations for the realization of essential quantum gates. The rotations on each qubit are symmetrical and depend on the strength and orientation of asymmetric exchange. The implementation of the axially symmetric local magnetic fields can assist the construction of quantum logic gates in anisotropic coupled quantum dots. This proposal can efficiently use each physical electron spin as a logical qubit in the universal quantum computation

  8. A Practical Computational Method for the Anisotropic Redshift-Space 3-Point Correlation Function

    Science.gov (United States)

    Slepian, Zachary; Eisenstein, Daniel J.

    2018-04-01

    We present an algorithm enabling computation of the anisotropic redshift-space galaxy 3-point correlation function (3PCF) scaling as N2, with N the number of galaxies. Our previous work showed how to compute the isotropic 3PCF with this scaling by expanding the radially-binned density field around each galaxy in the survey into spherical harmonics and combining these coefficients to form multipole moments. The N2 scaling occurred because this approach never explicitly required the relative angle between a galaxy pair about the primary galaxy. Here we generalize this work, demonstrating that in the presence of azimuthally-symmetric anisotropy produced by redshift-space distortions (RSD) the 3PCF can be described by two triangle side lengths, two independent total angular momenta, and a spin. This basis for the anisotropic 3PCF allows its computation with negligible additional work over the isotropic 3PCF. We also present the covariance matrix of the anisotropic 3PCF measured in this basis. Our algorithm tracks the full 5-D redshift-space 3PCF, uses an accurate line of sight to each triplet, is exact in angle, and easily handles edge correction. It will enable use of the anisotropic large-scale 3PCF as a probe of RSD in current and upcoming large-scale redshift surveys.

  9. 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)

  10. 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)

  11. 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.

  12. The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids

    Science.gov (United States)

    Newton, Arthur C.; Kools, Ramses; Swenson, David W. H.; Bolhuis, Peter G.

    2017-10-01

    The association and dissociation of particles via specific anisotropic interactions is a fundamental process, both in biology (proteins) and in soft matter (colloidal patchy particles). The presence of alternative binding sites can lead to multiple productive states and also to non-productive "decoy" or intermediate states. Besides anisotropic interactions, particles can experience non-specific isotropic interactions. We employ single replica transition interface sampling to investigate how adding a non-productive binding site or a nonspecific isotropic interaction alters the dimerization kinetics of a generic patchy particle model. The addition of a decoy binding site reduces the association rate constant, independent of the site's position, while adding an isotropic interaction increases it due to an increased rebinding probability. Surprisingly, the association kinetics becomes non-monotonic for a tetramer complex formed by multivalent patchy particles. While seemingly identical to two-particle binding with a decoy state, the cooperativity of binding multiple particles leads to a kinetic optimum. Our results are relevant for the understanding and modeling of biochemical networks and self-assembly processes.

  13. A novel anisotropic fast marching method and its application to blood flow computation in phase-contrast MRI.

    Science.gov (United States)

    Schwenke, M; Hennemuth, A; Fischer, B; Friman, O

    2012-01-01

    Phase-contrast MRI (PC MRI) can be used to assess blood flow dynamics noninvasively inside the human body. The acquired images can be reconstructed into flow vector fields. Traditionally, streamlines can be computed based on the vector fields to visualize flow patterns and particle trajectories. The traditional methods may give a false impression of precision, as they do not consider the measurement uncertainty in the PC MRI images. In our prior work, we incorporated the uncertainty of the measurement into the computation of particle trajectories. As a major part of the contribution, a novel numerical scheme for solving the anisotropic Fast Marching problem is presented. A computing time comparison to state-of-the-art methods is conducted on artificial tensor fields. A visual comparison of healthy to pathological blood flow patterns is given. The comparison shows that the novel anisotropic Fast Marching solver outperforms previous schemes in terms of computing time. The visual comparison of flow patterns directly visualizes large deviations of pathological flow from healthy flow. The novel anisotropic Fast Marching solver efficiently resolves even strongly anisotropic path costs. The visualization method enables the user to assess the uncertainty of particle trajectories derived from PC MRI images.

  14. Two-point anchoring of a lanthanide-binding peptide to a target protein enhances the paramagnetic anisotropic effect

    International Nuclear Information System (INIS)

    Saio, Tomohide; Ogura, Kenji; Yokochi, Masashi; Kobashigawa, Yoshihiro; Inagaki, Fuyuhiko

    2009-01-01

    Paramagnetic lanthanide ions fixed in a protein frame induce several paramagnetic effects such as pseudo-contact shifts and residual dipolar couplings. These effects provide long-range distance and angular information for proteins and, therefore, are valuable in protein structural analysis. However, until recently this approach had been restricted to metal-binding proteins, but now it has become applicable to non-metalloproteins through the use of a lanthanide-binding tag. Here we report a lanthanide-binding peptide tag anchored via two points to the target proteins. Compared to conventional single-point attached tags, the two-point linked tag provides two to threefold stronger anisotropic effects. Though there is slight residual mobility of the lanthanide-binding tag, the present tag provides a higher anisotropic paramagnetic effect

  15. 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.

  16. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages...

  17. 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.

  18. 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)

  19. 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.

  20. 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...

  1. 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

  2. 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.

  3. Disadvantage factor for anisotropic scattering

    International Nuclear Information System (INIS)

    Saad, E.A.; Abdel Krim, M.S.; EL-Dimerdash, A.A.

    1990-01-01

    The invariant embedding method is used to solve the problem for a two region reactor with anisotropic scattering and to compute the disadvantage factor necessary for calculating some reactor parameters

  4. 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

  5. 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.

  6. 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)

  7. Anisotropic elliptic optical fibers

    Science.gov (United States)

    Kang, Soon Ahm

    1991-05-01

    The exact characteristic equation for an anisotropic elliptic optical fiber is obtained for odd and even hybrid modes in terms of infinite determinants utilizing Mathieu and modified Mathieu functions. A simplified characteristic equation is obtained by applying the weakly guiding approximation such that the difference in the refractive indices of the core and the cladding is small. The simplified characteristic equation is used to compute the normalized guide wavelength for an elliptical fiber. When the anisotropic parameter is equal to unity, the results are compared with the previous research and they are in close agreement. For a fixed value normalized cross-section area or major axis, the normalized guide wavelength lambda/lambda(sub 0) for an anisotropic elliptic fiber is small for the larger value of anisotropy. This condition indicates that more energy is carried inside of the fiber. However, the geometry and anisotropy of the fiber have a smaller effect when the normalized cross-section area is very small or very large.

  8. 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

  9. 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.

  10. 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

  11. Computational Modeling of Complex Protein Activity Networks

    NARCIS (Netherlands)

    Schivo, Stefano; Leijten, Jeroen; Karperien, Marcel; Post, Janine N.; Prignet, Claude

    2017-01-01

    Because of the numerous entities interacting, the complexity of the networks that regulate cell fate makes it impossible to analyze and understand them using the human brain alone. Computational modeling is a powerful method to unravel complex systems. We recently described the development of a

  12. 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...

  13. Computing protein infrared spectroscopy with quantum chemistry.

    Science.gov (United States)

    Besley, Nicholas A

    2007-12-15

    Quantum chemistry is a field of science that has undergone unprecedented advances in the last 50 years. From the pioneering work of Boys in the 1950s, quantum chemistry has evolved from being regarded as a specialized and esoteric discipline to a widely used tool that underpins much of the current research in chemistry today. This achievement was recognized with the award of the 1998 Nobel Prize in Chemistry to John Pople and Walter Kohn. As the new millennium unfolds, quantum chemistry stands at the forefront of an exciting new era. Quantitative calculations on systems of the magnitude of proteins are becoming a realistic possibility, an achievement that would have been unimaginable to the early pioneers of quantum chemistry. In this article we will describe ongoing work towards this goal, focusing on the calculation of protein infrared amide bands directly with quantum chemical methods.

  14. Computational and theoretical studies of globular proteins

    Science.gov (United States)

    Pagan, Daniel L.

    Protein crystallization is often achieved in experiment through a trial and error approach. To date, there exists a dearth of theoretical understanding of the initial conditions necessary to promote crystallization. While a better understanding of crystallization will help to create good crystals suitable for structure analysis, it will also allow us to prevent the onset of certain diseases. The core of this thesis is to model and, ultimately, understand the phase behavior of protein particles in solution. Toward this goal, we calculate the fluid-fluid coexistence curve in the vicinity of the metastable critical point of the modified Lennard-Jones potential, where it has been shown that nucleation is increased by many orders of magnitude. We use finite-size scaling techniques and grand canonical Monte Carlo simulation methods. This has allowed us to pinpoint the critical point and subcritical region with high accuracy in spite of the critical fluctuations that hinder sampling using other Monte Carlo techniques. We also attempt to model the phase behavior of the gamma-crystallins, mutations of which have been linked to genetic cataracts. The complete phase behavior of the square well potential at the ranges of attraction lambda = 1.15 and lambda = 1.25 is calculated and compared with that of the gammaII-crystallin. The role of solvent is also important in the crystallization process and affects the phase behavior of proteins in solution. We study a model that accounts for the contribution of the solvent free-energy to the free-energy of globular proteins. This model allows us to model phase behavior that includes solvent.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. Efficient Wavefield Extrapolation In Anisotropic Media

    KAUST Repository

    Alkhalifah, Tariq; Ma, Xuxin; Waheed, Umair bin; Zuberi, Mohammad Akbar Hosain

    2014-01-01

    Various examples are provided for wavefield extrapolation in anisotropic media. In one example, among others, a method includes determining an effective isotropic velocity model and extrapolating an equivalent propagation of an anisotropic, poroelastic or viscoelastic wavefield. The effective isotropic velocity model can be based upon a kinematic geometrical representation of an anisotropic, poroelastic or viscoelastic wavefield. Extrapolating the equivalent propagation can use isotopic, acoustic or elastic operators based upon the determined effective isotropic velocity model. In another example, non-transitory computer readable medium stores an application that, when executed by processing circuitry, causes the processing circuitry to determine the effective isotropic velocity model and extrapolate the equivalent propagation of an anisotropic, poroelastic or viscoelastic wavefield. In another example, a system includes processing circuitry and an application configured to cause the system to determine the effective isotropic velocity model and extrapolate the equivalent propagation of an anisotropic, poroelastic or viscoelastic wavefield.

  1. Efficient Wavefield Extrapolation In Anisotropic Media

    KAUST Repository

    Alkhalifah, Tariq

    2014-07-03

    Various examples are provided for wavefield extrapolation in anisotropic media. In one example, among others, a method includes determining an effective isotropic velocity model and extrapolating an equivalent propagation of an anisotropic, poroelastic or viscoelastic wavefield. The effective isotropic velocity model can be based upon a kinematic geometrical representation of an anisotropic, poroelastic or viscoelastic wavefield. Extrapolating the equivalent propagation can use isotopic, acoustic or elastic operators based upon the determined effective isotropic velocity model. In another example, non-transitory computer readable medium stores an application that, when executed by processing circuitry, causes the processing circuitry to determine the effective isotropic velocity model and extrapolate the equivalent propagation of an anisotropic, poroelastic or viscoelastic wavefield. In another example, a system includes processing circuitry and an application configured to cause the system to determine the effective isotropic velocity model and extrapolate the equivalent propagation of an anisotropic, poroelastic or viscoelastic wavefield.

  2. Improved Discrete Ordinate Solutions in the Presence of an Anisotropically Reflecting Lower Boundary: Upgrades of the DISORT Computational Tool

    Science.gov (United States)

    Lin, Z.; Stamnes, S.; Jin, Z.; Laszlo, I.; Tsay, S. C.; Wiscombe, W. J.; Stamnes, K.

    2015-01-01

    A successor version 3 of DISORT (DISORT3) is presented with important upgrades that improve the accuracy, efficiency, and stability of the algorithm. Compared with version 2 (DISORT2 released in 2000) these upgrades include (a) a redesigned BRDF computation that improves both speed and accuracy, (b) a revised treatment of the single scattering correction, and (c) additional efficiency and stability upgrades for beam sources. In DISORT3 the BRDF computation is improved in the following three ways: (i) the Fourier decomposition is prepared "off-line", thus avoiding the repeated internal computations done in DISORT2; (ii) a large enough number of terms in the Fourier expansion of the BRDF is employed to guarantee accurate values of the expansion coefficients (default is 200 instead of 50 in DISORT2); (iii) in the post processing step the reflection of the direct attenuated beam from the lower boundary is included resulting in a more accurate single scattering correction. These improvements in the treatment of the BRDF have led to improved accuracy and a several-fold increase in speed. In addition, the stability of beam sources has been improved by removing a singularity occurring when the cosine of the incident beam angle is too close to the reciprocal of any of the eigenvalues. The efficiency for beam sources has been further improved from reducing by a factor of 2 (compared to DISORT2) the dimension of the linear system of equations that must be solved to obtain the particular solutions, and by replacing the LINPAK routines used in DISORT2 by LAPACK 3.5 in DISORT3. These beam source stability and efficiency upgrades bring enhanced stability and an additional 5-7% improvement in speed. Numerical results are provided to demonstrate and quantify the improvements in accuracy and efficiency of DISORT3 compared to DISORT2.

  3. Improved discrete ordinate solutions in the presence of an anisotropically reflecting lower boundary: Upgrades of the DISORT computational tool

    International Nuclear Information System (INIS)

    Lin, Z.; Stamnes, S.; Jin, Z.; Laszlo, I.; Tsay, S.-C.; Wiscombe, W.J.; Stamnes, K.

    2015-01-01

    A successor version 3 of DISORT (DISORT3) is presented with important upgrades that improve the accuracy, efficiency, and stability of the algorithm. Compared with version 2 (DISORT2 released in 2000) these upgrades include (a) a redesigned BRDF computation that improves both speed and accuracy, (b) a revised treatment of the single scattering correction, and (c) additional efficiency and stability upgrades for beam sources. In DISORT3 the BRDF computation is improved in the following three ways: (i) the Fourier decomposition is prepared “off-line”, thus avoiding the repeated internal computations done in DISORT2; (ii) a large enough number of terms in the Fourier expansion of the BRDF is employed to guarantee accurate values of the expansion coefficients (default is 200 instead of 50 in DISORT2); (iii) in the post-processing step the reflection of the direct attenuated beam from the lower boundary is included resulting in a more accurate single scattering correction. These improvements in the treatment of the BRDF have led to improved accuracy and a several-fold increase in speed. In addition, the stability of beam sources has been improved by removing a singularity occurring when the cosine of the incident beam angle is too close to the reciprocal of any of the eigenvalues. The efficiency for beam sources has been further improved from reducing by a factor of 2 (compared to DISORT2) the dimension of the linear system of equations that must be solved to obtain the particular solutions, and by replacing the LINPAK routines used in DISORT2 by LAPACK 3.5 in DISORT3. These beam source stability and efficiency upgrades bring enhanced stability and an additional 5–7% improvement in speed. Numerical results are provided to demonstrate and quantify the improvements in accuracy and efficiency of DISORT3 compared to DISORT2. - Highlights: • We present a successor version 3 of DISORT (DISORT3) with important upgrades. • Redesigned BRDF computation improves both

  4. 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.

  5. 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)

  6. 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)

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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)

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.)

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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

  12. Generalized Fractional Derivative Anisotropic Viscoelastic Characterization

    Directory of Open Access Journals (Sweden)

    Harry H. Hilton

    2012-01-01

    Full Text Available Isotropic linear and nonlinear fractional derivative constitutive relations are formulated and examined in terms of many parameter generalized Kelvin models and are analytically extended to cover general anisotropic homogeneous or non-homogeneous as well as functionally graded viscoelastic material behavior. Equivalent integral constitutive relations, which are computationally more powerful, are derived from fractional differential ones and the associated anisotropic temperature-moisture-degree-of-cure shift functions and reduced times are established. Approximate Fourier transform inversions for fractional derivative relations are formulated and their accuracy is evaluated. The efficacy of integer and fractional derivative constitutive relations is compared and the preferential use of either characterization in analyzing isotropic and anisotropic real materials must be examined on a case-by-case basis. Approximate protocols for curve fitting analytical fractional derivative results to experimental data are formulated and evaluated.

  13. 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

  14. 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.)

  15. 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

  16. 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.

  17. Computational Analysis of Uncharacterized Proteins of Environmental Bacterial Genome

    Science.gov (United States)

    Coxe, K. J.; Kumar, M.

    2017-12-01

    Betaproteobacteria strain CB is a gram-negative bacterium in the phylum Proteobacteria and are found naturally in soil and water. In this complex environment, bacteria play a key role in efficiently eliminating the organic material and other pollutants from wastewater. To investigate the process of pollutant removal from wastewater using bacteria, it is important to characterize the proteins encoded by the bacterial genome. Our study combines a number of bioinformatics tools to predict the function of unassigned proteins in the bacterial genome. The genome of Betaproteobacteria strain CB contains 2,112 proteins in which function of 508 proteins are unknown, termed as uncharacterized proteins (UPs). The localization of the UPs with in the cell was determined and the structure of 38 UPs was accurately predicted. These UPs were predicted to belong to various classes of proteins such as enzymes, transporters, binding proteins, signal peptides, transmembrane proteins and other proteins. The outcome of this work will help better understand wastewater treatment mechanism.

  18. 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.)

  19. 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.

  20. 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...

  1. Mechanical Modeling and Computer Simulation of Protein Folding

    Science.gov (United States)

    Prigozhin, Maxim B.; Scott, Gregory E.; Denos, Sharlene

    2014-01-01

    In this activity, science education and modern technology are bridged to teach students at the high school and undergraduate levels about protein folding and to strengthen their model building skills. Students are guided from a textbook picture of a protein as a rigid crystal structure to a more realistic view: proteins are highly dynamic…

  2. 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.

  3. In silico characterization of antifreeze proteins using computational ...

    Indian Academy of Sciences (India)

    WINTEC

    GRAVY, Grand Average Hydropathy. structure of protein (3D coordinates data). The 3D structure of AFPs Q01758 and P05140 were gener- ated by homology modelling using Esypred34 server. The similar 3D structures (for the AFPs Q01758 and. P05140 sequences) in the Protein Data bank. (www.rscb.org) were identified ...

  4. Computing wheat nitrogen requirements from grain yield and protein maps

    Science.gov (United States)

    Optical protein sensors and mass-flow yield monitors provide the opportunity to continuously measure grain quality and quantity during harvesting. This chapter illustrates how yield monitor and grain protein measurements may provide useful postharvest information for evaluating water or nitrogen (N)...

  5. 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...

  6. 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...

  7. 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.

  8. In silico characterization of antifreeze proteins using computational ...

    Indian Academy of Sciences (India)

    WINTEC

    structure. SOSUI server predicts one transmembrane region in winter flounder fish and atlantic cod and ..... result in a better interaction with water. The secon- ... structure of antifreeze protein P05140 (using PDB template 2AFP_A). The 10 ...

  9. 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.

  10. 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.

  11. A theory for the anisotropic interaction between two substitutional magnetic impurities and the magnetic anisotropic effect in dilute magnetic alloys

    International Nuclear Information System (INIS)

    Satter, M.A.

    1990-08-01

    In this paper, a formalism for studying the anisotropic interaction between two substitutional magnetic impurities and the magnetic anisotropic effect in a dilute noble metal- transition metal magnetic alloy has been developed from relativistic scattering theory. The theoretical development and the computational techniques of this formalism are based on relativistic spin-polarized scattering theory and relativistic band structure frameworks. For studying the magnetic anisotropic effect a convenient ''working'' frame of reference with its axes oriented along the fcc crystal axes is set up. This formalism is applied to study the situation for two Fe impurities in paramagnetic Au hosts. For AuFe dilute alloy, the two impurity site interaction as a function of separation is not oscillatory and the anisotropic effect is found to be less than the two site interaction itself only by an order of magnitude. Apart from the anisotropic coupling of the two impurity spins to the separation vector, for the first time, another weak anisotropic coupling to the crystal axes is also contained in the two site interaction. These anisotropic effects are the results of the relativistic spin-orbit interaction which are incorporated into the formalism. (author). 22 refs, 5 figs

  12. Connecting Protein Structure to Intermolecular Interactions: A Computer Modeling Laboratory

    Science.gov (United States)

    Abualia, Mohammed; Schroeder, Lianne; Garcia, Megan; Daubenmire, Patrick L.; Wink, Donald J.; Clark, Ginevra A.

    2016-01-01

    An understanding of protein folding relies on a solid foundation of a number of critical chemical concepts, such as molecular structure, intra-/intermolecular interactions, and relating structure to function. Recent reports show that students struggle on all levels to achieve these understandings and use them in meaningful ways. Further, several…

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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 ...

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 3-D waveform tomography sensitivity kernels for anisotropic media

    KAUST Repository

    Djebbi, Ramzi

    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 this ambiguity between the different parameters. We use dynamic ray tracing to efficiently handle the expensive computational cost for 3-D anisotropic models. Ray tracing provides also the ray direction information necessary for conditioning the sensitivity kernels to handle anisotropy. The NMO velocity and η parameter kernels showed a maximum sensitivity for diving waves which results in a relevant choice of those parameters in wave equation tomography. The δ parameter kernel showed zero sensitivity; therefore it can serve as a secondary parameter to fit the amplitude in the acoustic anisotropic inversion. Considering the limited penetration depth of diving waves, migration velocity analysis based kernels are introduced to fix the depth ambiguity with reflections and compute sensitivity maps in the deeper parts of the model.

  5. 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.

  6. Computational smart polymer design based on elastin protein mutability.

    Science.gov (United States)

    Tarakanova, Anna; Huang, Wenwen; Weiss, Anthony S; Kaplan, David L; Buehler, Markus J

    2017-05-01

    Soluble elastin-like peptides (ELPs) can be engineered into a range of physical forms, from hydrogels and scaffolds to fibers and artificial tissues, finding numerous applications in medicine and engineering as "smart polymers". Elastin-like peptides are attractive candidates as a platform for novel biomaterial design because they exhibit a highly tunable response spectrum, with reversible phase transition capabilities. Here, we report the design of the first virtual library of elastin-like protein models using methods for enhanced sampling to study the effect of peptide chemistry, chain length, and salt concentration on the structural transitions of ELPs, exposing associated molecular mechanisms. We describe the behavior of the local molecular structure under increasing temperatures and the effect of peptide interactions with nearest hydration shell water molecules on peptide mobility and propensity to exhibit structural transitions. Shifts in the magnitude of structural transitions at the single-molecule scale are explained from the perspective of peptide-ion-water interactions in a library of four unique elastin-like peptide systems. Predictions of structural transitions are subsequently validated in experiment. This library is a valuable resource for recombinant protein design and synthesis as it elucidates mechanisms at the single-molecule level, paving a feedback path between simulation and experiment for smart material designs, with applications in biomedicine and diagnostic devices. Copyright © 2017. Published by Elsevier Ltd.

  7. Computational multiscale modeling in protein--ligand docking.

    Science.gov (United States)

    Taufer, Michela; Armen, Roger; Chen, Jianhan; Teller, Patricia; Brooks, Charles

    2009-01-01

    In biological systems, the binding of small molecule ligands to proteins is a crucial process for almost every aspect of biochemistry and molecular biology. Enzymes are proteins that function by catalyzing specific biochemical reactions that convert reactants into products. Complex organisms are typically composed of cells in which thousands of enzymes participate in complex and interconnected biochemical pathways. Some enzymes serve as sequential steps in specific pathways (such as energy metabolism), while others function to regulate entire pathways and cellular functions [1]. Small molecule ligands can be designed to bind to a specific enzyme and inhibit the biochemical reaction. Inhibiting the activity of key enzymes may result in the entire biochemical pathways being turned on or off [2], [3]. Many small molecule drugs marketed today function in this generic way as enzyme inhibitors. If research identifies a specific enzyme as being crucial to the progress of disease, then this enzyme may be targeted with an inhibitor, which may slow down or reverse the progress of disease. In this way, enzymes are targeted from specific pathogens (e.g., virus, bacteria, fungi) for infectious diseases [4], [5], and human enzymes are targeted for noninfectious diseases such as cardiovascular disease, cancer, diabetes, and neurodegenerative diseases [6].

  8. Anisotropic Rabi model

    Science.gov (United States)

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

    2014-04-01

    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 the model. In this way, we provide a long-sought solution of a cascade of models with immediate relevance in different physical fields, including (i) quantum optics, a two-level atom in single-mode cross-electric and magnetic fields; (ii) solid-state physics, electrons in semiconductors with Rashba and Dresselhaus spin-orbit coupling; and (iii) mesoscopic physics, Josephson-junction flux-qubit quantum circuits.

  9. Anisotropic Rabi model

    Directory of Open Access Journals (Sweden)

    Qiong-Tao Xie

    2014-06-01

    Full Text Available 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 the model. In this way, we provide a long-sought solution of a cascade of models with immediate relevance in different physical fields, including (i quantum optics, a two-level atom in single-mode cross-electric and magnetic fields; (ii solid-state physics, electrons in semiconductors with Rashba and Dresselhaus spin-orbit coupling; and (iii mesoscopic physics, Josephson-junction flux-qubit quantum circuits.

  10. Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification

    Science.gov (United States)

    Wang, Jiaxin; Liang, Yanchun; Wang, Yan; Cui, Juan; Liu, Ming; Du, Wei; Xu, Ying

    2013-01-01

    Proteins can move from blood circulation into salivary glands through active transportation, passive diffusion or ultrafiltration, some of which are then released into saliva and hence can potentially serve as biomarkers for diseases if accurately identified. We present a novel computational method for predicting salivary proteins that come from circulation. The basis for the prediction is a set of physiochemical and sequence features we found to be discerning between human proteins known to be movable from circulation to saliva and proteins deemed to be not in saliva. A classifier was trained based on these features using a support-vector machine to predict protein secretion into saliva. The classifier achieved 88.56% average recall and 90.76% average precision in 10-fold cross-validation on the training data, indicating that the selected features are informative. Considering the possibility that our negative training data may not be highly reliable (i.e., proteins predicted to be not in saliva), we have also trained a ranking method, aiming to rank the known salivary proteins from circulation as the highest among the proteins in the general background, based on the same features. This prediction capability can be used to predict potential biomarker proteins for specific human diseases when coupled with the information of differentially expressed proteins in diseased versus healthy control tissues and a prediction capability for blood-secretory proteins. Using such integrated information, we predicted 31 candidate biomarker proteins in saliva for breast cancer. PMID:24324552

  11. 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.

  12. 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.

  13. A computational model of the LGI1 protein suggests a common binding site for ADAM proteins.

    Directory of Open Access Journals (Sweden)

    Emanuela Leonardi

    Full Text Available Mutations of human leucine-rich glioma inactivated (LGI1 gene encoding the epitempin protein cause autosomal dominant temporal lateral epilepsy (ADTLE, a rare familial partial epileptic syndrome. The LGI1 gene seems to have a role on the transmission of neuronal messages but the exact molecular mechanism remains unclear. In contrast to other genes involved in epileptic disorders, epitempin shows no homology with known ion channel genes but contains two domains, composed of repeated structural units, known to mediate protein-protein interactions.A three dimensional in silico model of the two epitempin domains was built to predict the structure-function relationship and propose a functional model integrating previous experimental findings. Conserved and electrostatic charged regions of the model surface suggest a possible arrangement between the two domains and identifies a possible ADAM protein binding site in the β-propeller domain and another protein binding site in the leucine-rich repeat domain. The functional model indicates that epitempin could mediate the interaction between proteins localized to different synaptic sides in a static way, by forming a dimer, or in a dynamic way, by binding proteins at different times.The model was also used to predict effects of known disease-causing missense mutations. Most of the variants are predicted to alter protein folding while several other map to functional surface regions. In agreement with experimental evidence, this suggests that non-secreted LGI1 mutants could be retained within the cell by quality control mechanisms or by altering interactions required for the secretion process.

  14. 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.

  15. 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.

  16. 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

  17. Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida.

    Science.gov (United States)

    Sander, C; Vriend, G; Bazan, F; Horovitz, A; Nakamura, H; Ribas, L; Finkelstein, A V; Lockhart, A; Merkl, R; Perry, L J

    1992-02-01

    What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four-stranded beta-sheets, a scaffold on which to explore variations in loop topology; Grendel, a four-helical membrane anchor, ready for fusion to water-soluble functional domains; Finger-clasp, a dimer of interdigitating beta-beta-alpha units, the simplest variant of the "handshake" structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather--a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three-dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.

  18. Anisotropic nonequilibrium hydrodynamic attractor

    Science.gov (United States)

    Strickland, Michael; Noronha, Jorge; Denicol, Gabriel S.

    2018-02-01

    We determine the dynamical attractors associated with anisotropic hydrodynamics (aHydro) and the DNMR equations for a 0 +1 d conformal system using kinetic theory in the relaxation time approximation. We compare our results to the nonequilibrium attractor obtained from the exact solution of the 0 +1 d conformal Boltzmann equation, the Navier-Stokes theory, and the second-order Mueller-Israel-Stewart theory. We demonstrate that the aHydro attractor equation resums an infinite number of terms in the inverse Reynolds number. The resulting resummed aHydro attractor possesses a positive longitudinal-to-transverse pressure ratio and is virtually indistinguishable from the exact attractor. This suggests that an optimized hydrodynamic treatment of kinetic theory involves a resummation not only in gradients (Knudsen number) but also in the inverse Reynolds number. We also demonstrate that the DNMR result provides a better approximation of the exact kinetic theory attractor than the Mueller-Israel-Stewart theory. Finally, we introduce a new method for obtaining approximate aHydro equations which relies solely on an expansion in the inverse Reynolds number. We then carry this expansion out to the third order, and compare these third-order results to the exact kinetic theory solution.

  19. Identification and analysis of potential targets in Streptococcus sanguinis using computer aided protein data analysis.

    Science.gov (United States)

    Chowdhury, Md Rabiul Hossain; Bhuiyan, Md IqbalKaiser; Saha, Ayan; Mosleh, Ivan Mhai; Mondol, Sobuj; Ahmed, C M Sabbir

    2014-01-01

    Streptococcus sanguinis is a Gram-positive, facultative aerobic bacterium that is a member of the viridans streptococcus group. It is found in human mouths in dental plaque, which accounts for both dental cavities and bacterial endocarditis, and which entails a mortality rate of 25%. Although a range of remedial mediators have been found to control this organism, the effectiveness of agents such as penicillin, amoxicillin, trimethoprim-sulfamethoxazole, and erythromycin, was observed. The emphasis of this investigation was on finding substitute and efficient remedial approaches for the total destruction of this bacterium. In this computational study, various databases and online software were used to ascertain some specific targets of S. sanguinis. Particularly, the Kyoto Encyclopedia of Genes and Genomes databases were applied to determine human nonhomologous proteins, as well as the metabolic pathways involved with those proteins. Different software such as Phyre2, CastP, DoGSiteScorer, the Protein Function Predictor server, and STRING were utilized to evaluate the probable active drug binding site with its known function and protein-protein interaction. In this study, among 218 essential proteins of this pathogenic bacterium, 81 nonhomologous proteins were accrued, and 15 proteins that are unique in several metabolic pathways of S. sanguinis were isolated through metabolic pathway analysis. Furthermore, four essentially membrane-bound unique proteins that are involved in distinct metabolic pathways were revealed by this research. Active sites and druggable pockets of these selected proteins were investigated with bioinformatic techniques. In addition, this study also mentions the activity of those proteins, as well as their interactions with the other proteins. Our findings helped to identify the type of protein to be considered as an efficient drug target. This study will pave the way for researchers to develop and discover more effective and specific

  20. 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

  1. The Sensitivity of Memory Consolidation and Reconsolidation to Inhibitors of Protein Synthesis and Kinases: Computational Analysis

    Science.gov (United States)

    Zhang, Yili; Smolen, Paul; Baxter, Douglas A.; Byrne, John H.

    2010-01-01

    Memory consolidation and reconsolidation require kinase activation and protein synthesis. Blocking either process during or shortly after training or recall disrupts memory stabilization, which suggests the existence of a critical time window during which these processes are necessary. Using a computational model of kinase synthesis and…

  2. 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

  3. 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.

  4. Identification and analysis of potential targets in Streptococcus sanguinis using computer aided protein data analysis

    Science.gov (United States)

    Chowdhury, Md Rabiul Hossain; Bhuiyan, Md IqbalKaiser; Saha, Ayan; Mosleh, Ivan MHAI; Mondol, Sobuj; Ahmed, C M Sabbir

    2014-01-01

    Purpose Streptococcus sanguinis is a Gram-positive, facultative aerobic bacterium that is a member of the viridans streptococcus group. It is found in human mouths in dental plaque, which accounts for both dental cavities and bacterial endocarditis, and which entails a mortality rate of 25%. Although a range of remedial mediators have been found to control this organism, the effectiveness of agents such as penicillin, amoxicillin, trimethoprim–sulfamethoxazole, and erythromycin, was observed. The emphasis of this investigation was on finding substitute and efficient remedial approaches for the total destruction of this bacterium. Materials and methods In this computational study, various databases and online software were used to ascertain some specific targets of S. sanguinis. Particularly, the Kyoto Encyclopedia of Genes and Genomes databases were applied to determine human nonhomologous proteins, as well as the metabolic pathways involved with those proteins. Different software such as Phyre2, CastP, DoGSiteScorer, the Protein Function Predictor server, and STRING were utilized to evaluate the probable active drug binding site with its known function and protein–protein interaction. Results In this study, among 218 essential proteins of this pathogenic bacterium, 81 nonhomologous proteins were accrued, and 15 proteins that are unique in several metabolic pathways of S. sanguinis were isolated through metabolic pathway analysis. Furthermore, four essentially membrane-bound unique proteins that are involved in distinct metabolic pathways were revealed by this research. Active sites and druggable pockets of these selected proteins were investigated with bioinformatic techniques. In addition, this study also mentions the activity of those proteins, as well as their interactions with the other proteins. Conclusion Our findings helped to identify the type of protein to be considered as an efficient drug target. This study will pave the way for researchers to

  5. 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.

  6. 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.

  7. An Integrated Bioinformatics and Computational Biology Approach Identifies New BH3-Only Protein Candidates.

    Science.gov (United States)

    Hawley, Robert G; Chen, Yuzhong; Riz, Irene; Zeng, Chen

    2012-05-04

    In this study, we utilized an integrated bioinformatics and computational biology approach in search of new BH3-only proteins belonging to the BCL2 family of apoptotic regulators. The BH3 (BCL2 homology 3) domain mediates specific binding interactions among various BCL2 family members. It is composed of an amphipathic α-helical region of approximately 13 residues that has only a few amino acids that are highly conserved across all members. Using a generalized motif, we performed a genome-wide search for novel BH3-containing proteins in the NCBI Consensus Coding Sequence (CCDS) database. In addition to known pro-apoptotic BH3-only proteins, 197 proteins were recovered that satisfied the search criteria. These were categorized according to α-helical content and predictive binding to BCL-xL (encoded by BCL2L1) and MCL-1, two representative anti-apoptotic BCL2 family members, using position-specific scoring matrix models. Notably, the list is enriched for proteins associated with autophagy as well as a broad spectrum of cellular stress responses such as endoplasmic reticulum stress, oxidative stress, antiviral defense, and the DNA damage response. Several potential novel BH3-containing proteins are highlighted. In particular, the analysis strongly suggests that the apoptosis inhibitor and DNA damage response regulator, AVEN, which was originally isolated as a BCL-xL-interacting protein, is a functional BH3-only protein representing a distinct subclass of BCL2 family members.

  8. 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/.

  9. 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.

  10. 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...

  11. 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.

  12. 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/ .

  13. Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors

    Science.gov (United States)

    Lagorce, David; Douguet, Dominique; Miteva, Maria A.; Villoutreix, Bruno O.

    2017-04-01

    The modulation of PPIs by low molecular weight chemical compounds, particularly by orally bioavailable molecules, would be very valuable in numerous disease indications. However, it is known that PPI inhibitors (iPPIs) tend to have properties that are linked to poor Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) and in some cases to poor clinical outcomes. Previously reported in silico analyses of iPPIs have essentially focused on physicochemical properties but several other ADMET parameters would be important to assess. In order to gain new insights into the ADMET properties of iPPIs, computations were carried out on eight datasets collected from several databases. These datasets involve compounds targeting enzymes, GPCRs, ion channels, nuclear receptors, allosteric modulators, oral marketed drugs, oral natural product-derived marketed drugs and iPPIs. Several trends are reported that should assist the design and optimization of future PPI inhibitors, either for drug discovery endeavors or for chemical biology projects.

  14. 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.

  15. 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.

  16. Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB)

    Science.gov (United States)

    Ghani, Nur Syatila Ab; Firdaus-Raih, Mohd

    2018-04-01

    The three-dimensional structure of a protein can provide insights regarding its function. Functional relationship between proteins can be inferred from fold and sequence similarities. In certain cases, sequence or fold comparison fails to conclude homology between proteins with similar mechanism. Since the structure is more conserved than the sequence, a constellation of functional residues can be similarly arranged among proteins of similar mechanism. Local structural similarity searches are able to detect such constellation of amino acids among distinct proteins, which can be useful to annotate proteins of unknown function. Detection of such patterns of amino acids on a large scale can increase the repertoire of important 3D motifs since available known 3D motifs currently, could not compensate the ever-increasing numbers of uncharacterized proteins to be annotated. Here, a computational platform for an automated detection of 3D motifs is described. A fuzzy-pattern searching algorithm derived from IMagine an Amino Acid 3D Arrangement search EnGINE (IMAAAGINE) was implemented to develop an automated method for searching of hypothetical patterns of amino acid side chains in Protein Data Bank (PDB), without the need for prior knowledge on related sequence or structure of pattern of interest. We present an example of the searches, which is the detection of a hypothetical pattern derived from known structural motif of C2H2 structural pattern from zinc fingers. The conservation of particular patterns of amino acid side chains in unrelated proteins is highlighted. This approach can act as a complementary method for available structure- and sequence-based platforms and may contribute in improving functional association between proteins.

  17. 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

  18. Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach.

    Science.gov (United States)

    Pan, Yuliang; Wang, Zixiang; Zhan, Weihua; Deng, Lei

    2018-05-01

    Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet, limited availability of experimentally recognized energy hot spots in protein-RNA crystal structures leads to the difficulties in developing empirical identification approaches. Computational prediction of RNA-binding hot spot residues is still in its infant stage. Here, we describe a computational method, PrabHot (Prediction of protein-RNA binding hot spots), that can effectively detect hot spot residues on protein-RNA binding interfaces using an ensemble of conceptually different machine learning classifiers. Residue interaction network features and new solvent exposure characteristics are combined together and selected for classification with the Boruta algorithm. In particular, two new reference datasets (benchmark and independent) have been generated containing 107 hot spots from 47 known protein-RNA complex structures. In 10-fold cross-validation on the training dataset, PrabHot achieves promising performances with an AUC score of 0.86 and a sensitivity of 0.78, which are significantly better than that of the pioneer RNA-binding hot spot prediction method HotSPRing. We also demonstrate the capability of our proposed method on the independent test dataset and gain a competitive advantage as a result. The PrabHot webserver is freely available at http://denglab.org/PrabHot/. leideng@csu.edu.cn. Supplementary data are available at Bioinformatics online.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.)

  4. 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.

  5. 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.

  6. 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

  7. Computational and statistical methods for high-throughput analysis of post-translational modifications of proteins

    DEFF Research Database (Denmark)

    Schwämmle, Veit; Braga, Thiago Verano; Roepstorff, Peter

    2015-01-01

    The investigation of post-translational modifications (PTMs) represents one of the main research focuses for the study of protein function and cell signaling. Mass spectrometry instrumentation with increasing sensitivity improved protocols for PTM enrichment and recently established pipelines...... for high-throughput experiments allow large-scale identification and quantification of several PTM types. This review addresses the concurrently emerging challenges for the computational analysis of the resulting data and presents PTM-centered approaches for spectra identification, statistical analysis...

  8. Identification and analysis of potential targets in Streptococcus sanguinis using computer aided protein data analysis

    Directory of Open Access Journals (Sweden)

    Chowdhury MRH

    2014-11-01

    Full Text Available Md Rabiul Hossain Chowdhury,1 Md IqbalKaiser Bhuiyan,2 Ayan Saha,2 Ivan MHAI Mosleh,2 Sobuj Mondol,2 C M Sabbir Ahmed3 1Department of Pharmacy, University of Science and Technology Chittagong, Chittagong, Bangladesh; 2Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh; 3Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh Purpose: Streptococcus sanguinis is a Gram-positive, facultative aerobic bacterium that is a member of the viridans streptococcus group. It is found in human mouths in dental plaque, which accounts for both dental cavities and bacterial endocarditis, and which entails a mortality rate of 25%. Although a range of remedial mediators have been found to control this organism, the effectiveness of agents such as penicillin, amoxicillin, trimethoprim–sulfamethoxazole, and erythromycin, was observed. The emphasis of this investigation was on finding substitute and efficient remedial approaches for the total destruction of this bacterium. Materials and methods: In this computational study, various databases and online software were used to ascertain some specific targets of S. sanguinis. Particularly, the Kyoto Encyclopedia of Genes and Genomes databases were applied to determine human nonhomologous proteins, as well as the metabolic pathways involved with those proteins. Different software such as Phyre2, CastP, DoGSiteScorer, the Protein Function Predictor server, and STRING were utilized to evaluate the probable active drug binding site with its known function and protein–protein interaction. Results: In this study, among 218 essential proteins of this pathogenic bacterium, 81 nonhomologous proteins were accrued, and 15 proteins that are unique in several metabolic pathways of S. sanguinis were isolated through metabolic pathway analysis. Furthermore, four essentially membrane-bound unique proteins that are involved in distinct metabolic

  9. 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)

  10. 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...

  11. 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....

  12. 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.

  13. 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.

  14. 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.

  15. Computer simulations and theoretical aspects of the depletion interaction in protein-oligomer mixtures.

    Science.gov (United States)

    Boncina, M; Rescic, J; Kalyuzhnyi, Yu V; Vlachy, V

    2007-07-21

    The depletion interaction between proteins caused by addition of either uncharged or partially charged oligomers was studied using the canonical Monte Carlo simulation technique and the integral equation theory. A protein molecule was modeled in two different ways: either as (i) a hard sphere of diameter 30.0 A with net charge 0, or +5, or (ii) as a hard sphere with discrete charges (depending on the pH of solution) of diameter 45.4 A. The oligomers were pictured as tangentially jointed, uncharged, or partially charged, hard spheres. The ions of a simple electrolyte present in solution were represented by charged hard spheres distributed in the dielectric continuum. In this study we were particularly interested in changes of the protein-protein pair-distribution function, caused by addition of the oligomer component. In agreement with previous studies we found that addition of a nonadsorbing oligomer reduces the phase stability of solution, which is reflected in the shape of the protein-protein pair-distribution function. The value of this function in protein-protein contact increases with increasing oligomer concentration, and is larger for charged oligomers. The range of the depletion interaction and its strength also depend on the length (number of monomer units) of the oligomer chain. The integral equation theory, based on the Wertheim Ornstein-Zernike approach applied in this study, was found to be in fair agreement with Monte Carlo results only for very short oligomers. The computer simulations for a model mimicking the lysozyme molecule (ii) are in qualitative agreement with small-angle neutron experiments for lysozyme-dextran mixtures.

  16. Discovery and annotation of small proteins using genomics, proteomics and computational approaches

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaohan; Tschaplinski, Timothy J.; Hurst, Gregory B.; Jawdy, Sara; Abraham, Paul E.; Lankford, Patricia K.; Adams, Rachel M.; Shah, Manesh B.; Hettich, Robert L.; Lindquist, Erika; Kalluri, Udaya C.; Gunter, Lee E.; Pennacchio, Christa; Tuskan, Gerald A.

    2011-03-02

    Small proteins (10 200 amino acids aa in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained 2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10 200 aa in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: (1) codingpotential prediction, (2) evolutionary conservation between P. deltoides and other plant species, and (3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were supported by proteomics data. Of the 611 highest-confidence candidate sORF genes, 56 were new to the current Populus genome annotation. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.

  17. 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

  18. Computational Modeling of Proteins based on Cellular Automata: A Method of HP Folding Approximation.

    Science.gov (United States)

    Madain, Alia; Abu Dalhoum, Abdel Latif; Sleit, Azzam

    2018-06-01

    The design of a protein folding approximation algorithm is not straightforward even when a simplified model is used. The folding problem is a combinatorial problem, where approximation and heuristic algorithms are usually used to find near optimal folds of proteins primary structures. Approximation algorithms provide guarantees on the distance to the optimal solution. The folding approximation approach proposed here depends on two-dimensional cellular automata to fold proteins presented in a well-studied simplified model called the hydrophobic-hydrophilic model. Cellular automata are discrete computational models that rely on local rules to produce some overall global behavior. One-third and one-fourth approximation algorithms choose a subset of the hydrophobic amino acids to form H-H contacts. Those algorithms start with finding a point to fold the protein sequence into two sides where one side ignores H's at even positions and the other side ignores H's at odd positions. In addition, blocks or groups of amino acids fold the same way according to a predefined normal form. We intend to improve approximation algorithms by considering all hydrophobic amino acids and folding based on the local neighborhood instead of using normal forms. The CA does not assume a fixed folding point. The proposed approach guarantees one half approximation minus the H-H endpoints. This lower bound guaranteed applies to short sequences only. This is proved as the core and the folds of the protein will have two identical sides for all short sequences.

  19. 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.

  20. LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise

    Directory of Open Access Journals (Sweden)

    Di Nicola Marta

    2007-03-01

    Full Text Available Abstract Background Mass spectrometry protein profiling is a promising tool for biomarker discovery in clinical proteomics. However, the development of a reliable approach for the separation of protein signals from noise is required. In this paper, LIMPIC, a computational method for the detection of protein peaks from linear-mode MALDI-TOF data is proposed. LIMPIC is based on novel techniques for background noise reduction and baseline removal. Peak detection is performed considering the presence of a non-homogeneous noise level in the mass spectrum. A comparison of the peaks collected from multiple spectra is used to classify them on the basis of a detection rate parameter, and hence to separate the protein signals from other disturbances. Results LIMPIC preprocessing proves to be superior than other classical preprocessing techniques, allowing for a reliable decomposition of the background noise and the baseline drift from the MALDI-TOF mass spectra. It provides lower coefficient of variation associated with the peak intensity, improving the reliability of the information that can be extracted from single spectra. Our results show that LIMPIC peak-picking is effective even in low protein concentration regimes. The analytical comparison with commercial and freeware peak-picking algorithms demonstrates its superior performances in terms of sensitivity and specificity, both on in-vitro purified protein samples and human plasma samples. Conclusion The quantitative information on the peak intensity extracted with LIMPIC could be used for the recognition of significant protein profiles by means of advanced statistic tools: LIMPIC might be valuable in the perspective of biomarker discovery.

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.)

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.)

  15. Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site

    Energy Technology Data Exchange (ETDEWEB)

    Strauch, Eva-Maria; Bernard, Steffen M.; La, David; Bohn, Alan J.; Lee, Peter S.; Anderson, Caitlin E.; Nieusma, Travis; Holstein, Carly A.; Garcia, Natalie K.; Hooper, Kathryn A.; Ravichandran, Rashmi; Nelson, Jorgen W.; Sheffler, William; Bloom, Jesse D.; Lee, Kelly K.; Ward, Andrew B.; Yager, Paul; Fuller, Deborah H.; Wilson, Ian A.; Baker , David (UWASH); (Scripps); (FHCRC)

    2017-06-12

    Many viral surface glycoproteins and cell surface receptors are homo-oligomers1, 2, 3, 4, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites5, 6, 7, 8. In the first step, a small protein is designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.

  16. Computer simulations of radiation damage in protein crystals; Simulationsrechnungen zu Strahlenschaeden an Proteinkristallen

    Energy Technology Data Exchange (ETDEWEB)

    Zehnder, M

    2007-03-15

    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.)

  17. Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins.

    Directory of Open Access Journals (Sweden)

    B Scott Perrin

    2014-07-01

    Full Text Available A module for fast determination of reduction potentials, E°, of redox-active proteins has been implemented in the CHARMM INterface and Graphics (CHARMMing web portal (www.charmming.org. The free energy of reduction, which is proportional to E°, is composed of an intrinsic contribution due to the redox site and an environmental contribution due to the protein and solvent. Here, the intrinsic contribution is selected from a library of pre-calculated density functional theory values for each type of redox site and redox couple, while the environmental contribution is calculated from a crystal structure of the protein using Poisson-Boltzmann continuum electrostatics. An accompanying lesson demonstrates a calculation of E°. In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent E° is identified, and the E° of a mutant that would test the identification is predicted. This demonstration is valuable to both computational chemistry students and researchers interested in predicting sequence determinants of E° for mutagenesis.

  18. The MELANIE project: from a biopsy to automatic protein map interpretation by computer.

    Science.gov (United States)

    Appel, R D; Hochstrasser, D F; Funk, M; Vargas, J R; Pellegrini, C; Muller, A F; Scherrer, J R

    1991-10-01

    The goals of the MELANIE project are to determine if disease-associated patterns can be detected in high resolution two-dimensional polyacrylamide gel electrophoresis (HR 2D-PAGE) images and if a diagnosis can be established automatically by computer. The ELSIE/MELANIE system is a set of computer programs which automatically detect, quantify, and compare protein spots shown on HR 2D-PAGE images. Classification programs help the physician to find disease-associated patterns from a given set of two-dimensional gel electrophoresis images and to form diagnostic rules. Prototype expert systems that use these rules to establish a diagnosis from new HR 2D-PAGE images have been developed. They successfully diagnosed cirrhosis of the liver and were able to distinguish a variety of cancer types from biopsies known to be cancerous.

  19. 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

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

    KAUST Repository

    Wang, Sheng

    2018-02-06

    Experimental determination of membrane protein (MP) structures is challenging as they are often too large for nuclear magnetic resonance (NMR) experiments and difficult to crystallize. Currently there are only about 510 non-redundant MPs with solved 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 and secondary structure, two-dimensional (2D) prediction of the contact/distance map, together with three-dimensional (3D) modeling of the MP structure in the lipid bilayer, for each MP target from a given model organism. The precision of the computationally constructed MP structures is leveraged by state-of-the-art deep learning methods as well as cutting-edge modeling strategies. In particular, (i) we annotate 1D property via DeepCNF (Deep Convolutional Neural Fields) that not only models complex sequence-structure relationship but also interdependency between adjacent property labels; (ii) we predict 2D contact/distance map through Deep Transfer Learning which learns the patterns as well as the complex relationship between contacts/distances and protein features from non-membrane proteins; and (iii) we model 3D structure by feeding its predicted contacts and secondary structure to the Crystallography & NMR System (CNS) suite combined with a membrane burial potential that is residue-specific and depth-dependent. PredMP currently contains more than 2,200 multi-pass transmembrane proteins (length<700 residues) from Human. These transmembrane proteins are classified according to IUPHAR/BPS Guide, which provides a hierarchical organization of receptors, channels, transporters, enzymes and other drug targets according to their molecular relationships and physiological functions. Among these MPs, we estimated that our approach could predict correct folds for 1

  1. 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)

  2. Aligator: A computational tool for optimizing total chemical synthesis of large proteins.

    Science.gov (United States)

    Jacobsen, Michael T; Erickson, Patrick W; Kay, Michael S

    2017-09-15

    The scope of chemical protein synthesis (CPS) continues to expand, driven primarily by advances in chemical ligation tools (e.g., reversible solubilizing groups and novel ligation chemistries). However, the design of an optimal synthesis route can be an arduous and fickle task due to the large number of theoretically possible, and in many cases problematic, synthetic strategies. In this perspective, we highlight recent CPS tool advances and then introduce a new and easy-to-use program, Aligator (Automated Ligator), for analyzing and designing the most efficient strategies for constructing large targets using CPS. As a model set, we selected the E. coli ribosomal proteins and associated factors for computational analysis. Aligator systematically scores and ranks all feasible synthetic strategies for a particular CPS target. The Aligator script methodically evaluates potential peptide segments for a target using a scoring function that includes solubility, ligation site quality, segment lengths, and number of ligations to provide a ranked list of potential synthetic strategies. We demonstrate the utility of Aligator by analyzing three recent CPS projects from our lab: TNFα (157 aa), GroES (97 aa), and DapA (312 aa). As the limits of CPS are extended, we expect that computational tools will play an increasingly important role in the efficient execution of ambitious CPS projects such as production of a mirror-image ribosome. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. 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

  4. Probing the mutational interplay between primary and promiscuous protein functions: a computational-experimental approach.

    Science.gov (United States)

    Garcia-Seisdedos, Hector; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2012-01-01

    Protein promiscuity is of considerable interest due its role in adaptive metabolic plasticity, its fundamental connection with molecular evolution and also because of its biotechnological applications. Current views on the relation between primary and promiscuous protein activities stem largely from laboratory evolution experiments aimed at increasing promiscuous activity levels. Here, on the other hand, we attempt to assess the main features of the simultaneous modulation of the primary and promiscuous functions during the course of natural evolution. The computational/experimental approach we propose for this task involves the following steps: a function-targeted, statistical coupling analysis of evolutionary data is used to determine a set of positions likely linked to the recruitment of a promiscuous activity for a new function; a combinatorial library of mutations on this set of positions is prepared and screened for both, the primary and the promiscuous activities; a partial-least-squares reconstruction of the full combinatorial space is carried out; finally, an approximation to the Pareto set of variants with optimal primary/promiscuous activities is derived. Application of the approach to the emergence of folding catalysis in thioredoxin scaffolds reveals an unanticipated scenario: diverse patterns of primary/promiscuous activity modulation are possible, including a moderate (but likely significant in a biological context) simultaneous enhancement of both activities. We show that this scenario can be most simply explained on the basis of the conformational diversity hypothesis, although alternative interpretations cannot be ruled out. Overall, the results reported may help clarify the mechanisms of the evolution of new functions. From a different viewpoint, the partial-least-squares-reconstruction/Pareto-set-prediction approach we have introduced provides the computational basis for an efficient directed-evolution protocol aimed at the simultaneous

  5. 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

  6. What can we learn by computing 13Cα chemical shifts for X-ray protein models?

    International Nuclear Information System (INIS)

    Arnautova, Yelena A.; Vila, Jorge A.; Martin, Osvaldo A.; Scheraga, Harold A.

    2009-01-01

    The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. The room-temperature X-ray structures of ubiquitin and of the RNA-binding domain of nonstructural protein 1 of influenza A virus solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R free factors similar to those of the deposited X-ray structure, the 13 C α chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13 C α chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13 C α chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13 C α chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13 C α chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with

  7. Neutron transfer with anisotropic scattering

    International Nuclear Information System (INIS)

    El Wakil, S.A.; Haggag, M.H.; Saad, E.A.

    1979-01-01

    The finite slab problem is reduced to a semi-infinite one by adding an infinitesimally thick layer such that both the added layer and the total layer are semi-infinite. The relation between the reflection and transmission functions for a finite slab and those for an infinite one are obtained in terms of an operator which satisfies a semigroup equation. The method is applied to anisotropic scattering with azimuthal dependence. Numerical calculations are made and the results compared with those of other workers. (author)

  8. Anisotropic densification of reference steel

    International Nuclear Information System (INIS)

    Garner, F.A.; Bates, J.F.; Gilbert, E.R.

    1975-09-01

    A correlation is presented for the densification expected during neutron irradiation of 20 percent CW 316 stainless steel cladding of FTR specification. The densification is known to be a function of time, prior heat treatment, cold work level, irradiation temperature and minor element composition. For FTR fuel pin use, the temperature and carbon composition were chosen as the only relevant variables on which to base the correlation. The densification of FTR cladding is expected to be slightly anisotropic, leading to a diameter change somewhat less than that predicted by the isotropic relationship ΔD = -D 0 /3

  9. Anisotropic and nonlinear optical waveguides

    CERN Document Server

    Someda, CG

    1992-01-01

    Dielectric optical waveguides have been investigated for more than two decades. In the last ten years they have had the unique position of being simultaneously the backbone of a very practical and fully developed technology, as well as an extremely exciting area of basic, forefront research. Existing waveguides can be divided into two sets: one consisting of waveguides which are already in practical use, and the second of those which are still at the laboratory stage of their evolution. This book is divided into two separate parts: the first dealing with anisotropic waveguides, an

  10. Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction.

    Science.gov (United States)

    Bandyopadhyay, Pradipta; Kuntz, Irwin D

    2009-01-01

    The determination of protein structure using distance constraints is a new and promising field of study. One implementation involves attaching residues of a protein using a cross-linking agent, followed by protease digestion, analysis of the resulting peptides by mass spectroscopy, and finally sequence threading to detect the protein folds. In the present work, we carry out computational modeling of the kinetics of cross-linking reactions in proteins using the master equation approach. The rate constants of the cross-linking reactions are estimated using the pKas and the solvent-accessible surface areas of the residues involved. This model is tested with fibroblast growth factor (FGF) and cytochrome C. It is consistent with the initial experimental rate data for individual lysine residues for cytochrome C. Our model captures all observed cross-links for FGF and almost 90% of the observed cross-links for cytochrome C, although it also predicts cross-links that were not observed experimentally (false positives). However, the analysis of the false positive results is complicated by the fact that experimental detection of cross-links can be difficult and may depend on specific experimental conditions such as pH, ionic strength. Receiver operator characteristic plots showed that our model does a good job in predicting the observed cross-links. Molecular dynamics simulations showed that for cytochrome C, in general, the two lysines come closer for the observed cross-links as compared to the false positive ones. For FGF, no such clear pattern exists. The kinetic model and MD simulation can be used to study proposed cross-linking protocols.

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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....

  16. 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).

  17. 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)

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. An iterative, fast-sweeping-based eikonal solver for 3D tilted anisotropic media

    KAUST Repository

    Waheed, Umair bin; Yarman, Can Evren; Flagg, Garret

    2015-01-01

    Computation of first-arrival traveltimes for quasi-P waves in the presence of anisotropy is important for high-end near-surface modeling, microseismic-source localization, and fractured-reservoir characterization - and it requires solving an anisotropic eikonal equation. Anisotropy deviating from elliptical anisotropy introduces higher order nonlinearity into the eikonal equation, which makes solving the eikonal equation a challenge. We addressed this challenge by iteratively solving a sequence of simpler tilted elliptically anisotropic eikonal equations. At each iteration, the source function was updated to capture the effects of the higher order nonlinear terms. We used Aitken's extrapolation to speed up convergence rate of the iterative algorithm. The result is an algorithm for computing first-arrival traveltimes in tilted anisotropic media. We evaluated the applicability and usefulness of our method on tilted transversely isotropic media and tilted orthorhombic media. Our numerical tests determined that the proposed method matches the first arrivals obtained by wavefield extrapolation, even for strongly anisotropic and highly complex subsurface structures. Thus, for the cases where two-point ray tracing fails, our method can be a potential substitute for computing traveltimes. The approach presented here can be easily extended to compute first-arrival traveltimes for anisotropic media with lower symmetries, such as monoclinic or even the triclinic media.

  3. An iterative, fast-sweeping-based eikonal solver for 3D tilted anisotropic media

    KAUST Repository

    Waheed, Umair bin

    2015-03-30

    Computation of first-arrival traveltimes for quasi-P waves in the presence of anisotropy is important for high-end near-surface modeling, microseismic-source localization, and fractured-reservoir characterization - and it requires solving an anisotropic eikonal equation. Anisotropy deviating from elliptical anisotropy introduces higher order nonlinearity into the eikonal equation, which makes solving the eikonal equation a challenge. We addressed this challenge by iteratively solving a sequence of simpler tilted elliptically anisotropic eikonal equations. At each iteration, the source function was updated to capture the effects of the higher order nonlinear terms. We used Aitken\\'s extrapolation to speed up convergence rate of the iterative algorithm. The result is an algorithm for computing first-arrival traveltimes in tilted anisotropic media. We evaluated the applicability and usefulness of our method on tilted transversely isotropic media and tilted orthorhombic media. Our numerical tests determined that the proposed method matches the first arrivals obtained by wavefield extrapolation, even for strongly anisotropic and highly complex subsurface structures. Thus, for the cases where two-point ray tracing fails, our method can be a potential substitute for computing traveltimes. The approach presented here can be easily extended to compute first-arrival traveltimes for anisotropic media with lower symmetries, such as monoclinic or even the triclinic media.

  4. Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.

    Science.gov (United States)

    Jiang, Peng; Singh, Mona; Coller, Hilary A

    2013-01-01

    Transcript degradation is a widespread and important mechanism for regulating protein abundance. Two major regulators of transcript degradation are RNA Binding Proteins (RBPs) and microRNAs (miRNAs). We computationally explored whether RBPs and miRNAs cooperate to promote transcript decay. We defined five RBP motifs based on the evolutionary conservation of their recognition sites in 3'UTRs as the binding motifs for Pumilio (PUM), U1A, Fox-1, Nova, and UAUUUAU. Recognition sites for some of these RBPs tended to localize at the end of long 3'UTRs. A specific group of miRNA recognition sites were enriched within 50 nts from the RBP recognition sites for PUM and UAUUUAU. The presence of both a PUM recognition site and a recognition site for preferentially co-occurring miRNAs was associated with faster decay of the associated transcripts. For PUM and its co-occurring miRNAs, binding of the RBP to its recognition sites was predicted to release nearby miRNA recognition sites from RNA secondary structures. The mammalian miRNAs that preferentially co-occur with PUM binding sites have recognition seeds that are reverse complements to the PUM recognition motif. Their binding sites have the potential to form hairpin secondary structures with proximal PUM binding sites that would normally limit RISC accessibility, but would be more accessible to miRNAs in response to the binding of PUM. In sum, our computational analyses suggest that a specific set of RBPs and miRNAs work together to affect transcript decay, with the rescue of miRNA recognition sites via RBP binding as one possible mechanism of cooperativity.

  5. 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.

  6. Computing Rates of Small Molecule Diffusion Through Protein Channels Using Markovian Milestoning

    Science.gov (United States)

    Abrams, Cameron

    2014-03-01

    Measuring diffusion rates of ligands plays a key role in understanding the kinetic processes inside proteins. For example, although many molecular simulation studies have reported free energy barriers to infer rates for CO diffusion in myoglobin (Mb), they typically do not include direct calculation of diffusion rates because of the long simulation times needed to infer these rates with statistical accuracy. We show in this talk how to apply Markovian milestoning along minimum free-energy pathways to calculate diffusion rates of CO inside Mb. In Markovian milestoning, one partitions a suitable reaction coordinate space into regions and performs restrained molecular dynamics in each region to accumulate kinetic statistics that, when assembled across regions, provides an estimate of the mean first-passage time between states. The mean escape time for CO directly from the so-called distal pocket (DP) through the histidine gate (HG) is estimated at about 24 ns, confirming the importance of this portal for CO. But Mb is known to contain several internal cavities, and cavity-to-cavity diffusion rates are also computed and used to build a complete kinetic network as a Markov state model. Within this framework, the effective mean time of escape to the solvent through HG increases to 30 ns. Our results suggest that carrier protein structure may have evolved under pressure to modulate dissolved gas release rates using a network of ligand-accessible cavities. Support: NIH R01GM100472.

  7. Computational Studies of pH Sensing Design Principles in Proteins

    Science.gov (United States)

    Garrido Ruiz, Diego

    Changes in pH are important regulatory signals for biological function, under physiological and pathological conditions. Recent advances in computer simulations strategies have made the exploration of the effects of charge titrations on protein function possible. In this work, I make use of these strategies to investigate the thermodynamic coupling between conformation and protonation states that give rise to pH-dependent function. As motivation for the rest of the work, I start by presenting a collaborative investigation on a pH-sensing mutant of the EGFR tyrosine kinase common to a set of distinct cancers. From then, I reduce the complexity of the systems under study to build models where exact enumeration of states is possible to inquire about the nature of the couplings between protonation states and conformation. Finally, I discuss detailed simulations of pH-sensing proteins for which I use the expectations and insights generated with simple models to identify and interpret couplings of interest for pH-dependent behavior.

  8. Computational Prediction of Atomic Structures of Helical Membrane Proteins Aided by EM Maps

    Science.gov (United States)

    Kovacs, Julio A.; Yeager, Mark; Abagyan, Ruben

    2007-01-01

    Integral membrane proteins pose a major challenge for protein-structure prediction because only ≈100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane α-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of α-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the α-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL. PMID:17496035

  9. Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.

    Directory of Open Access Journals (Sweden)

    Frank C Pickard

    2014-07-01

    Full Text Available A lesson utilizing a coarse-grained (CG Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing web portal (www.charmming.org to the Chemistry at HARvard Macromolecular Mechanics (CHARMM molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the Gō-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG Gō model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field.

  10. Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis.

    Science.gov (United States)

    Masso, Majid; Vaisman, Iosif I

    2008-09-15

    Accurate predictive models for the impact of single amino acid substitutions on protein stability provide insight into protein structure and function. Such models are also valuable for the design and engineering of new proteins. Previously described methods have utilized properties of protein sequence or structure to predict the free energy change of mutants due to thermal (DeltaDeltaG) and denaturant (DeltaDeltaG(H2O)) denaturations, as well as mutant thermal stability (DeltaT(m)), through the application of either computational energy-based approaches or machine learning techniques. However, accuracy associated with applying these methods separately is frequently far from optimal. We detail a computational mutagenesis technique based on a four-body, knowledge-based, statistical contact potential. For any mutation due to a single amino acid replacement in a protein, the method provides an empirical normalized measure of the ensuing environmental perturbation occurring at every residue position. A feature vector is generated for the mutant by considering perturbations at the mutated position and it's ordered six nearest neighbors in the 3-dimensional (3D) protein structure. These predictors of stability change are evaluated by applying machine learning tools to large training sets of mutants derived from diverse proteins that have been experimentally studied and described. Predictive models based on our combined approach are either comparable to, or in many cases significantly outperform, previously published results. A web server with supporting documentation is available at http://proteins.gmu.edu/automute.

  11. Stability of anisotropic stellar filaments

    Science.gov (United States)

    Bhatti, M. Zaeem-ul-Haq; Yousaf, Z.

    2017-12-01

    The study of perturbation of self-gravitating celestial cylindrical object have been carried out in this paper. We have designed a framework to construct the collapse equation by formulating the modified field equations with the background of f(R , T) theory as well as dynamical equations from the contracted form of Bianchi identities with anisotropic matter configuration. We have encapsulated the radial perturbations on metric and material variables of the geometry with some known static profile at Newtonian and post-Newtonian regimes. We examined a strong dependence of unstable regions on stiffness parameter which measures the rigidity of the fluid. Also, the static profile and matter variables with f(R , T) dark source terms control the instability of compact cylindrical system.

  12. Warm anisotropic inflationary universe model

    International Nuclear Information System (INIS)

    Sharif, M.; Saleem, Rabia

    2014-01-01

    This paper is devoted to the study of warm inflation using vector fields in the background of a locally rotationally symmetric Bianchi type I model of the universe. We formulate the field equations, and slow-roll and perturbation parameters (scalar and tensor power spectra as well as their spectral indices) in the slow-roll approximation. We evaluate all these parameters in terms of the directional Hubble parameter during the intermediate and logamediate inflationary regimes by taking the dissipation factor as a function of the scalar field as well as a constant. In each case, we calculate the observational parameter of interest, i.e., the tensor-scalar ratio in terms of the inflaton. The graphical behavior of these parameters shows that the anisotropic model is also compatible with WMAP7 and the Planck observational data. (orig.)

  13. Warm anisotropic inflationary universe model

    Energy Technology Data Exchange (ETDEWEB)

    Sharif, M.; Saleem, Rabia [University of the Punjab, Department of Mathematics, Lahore (Pakistan)

    2014-02-15

    This paper is devoted to the study of warm inflation using vector fields in the background of a locally rotationally symmetric Bianchi type I model of the universe. We formulate the field equations, and slow-roll and perturbation parameters (scalar and tensor power spectra as well as their spectral indices) in the slow-roll approximation. We evaluate all these parameters in terms of the directional Hubble parameter during the intermediate and logamediate inflationary regimes by taking the dissipation factor as a function of the scalar field as well as a constant. In each case, we calculate the observational parameter of interest, i.e., the tensor-scalar ratio in terms of the inflaton. The graphical behavior of these parameters shows that the anisotropic model is also compatible with WMAP7 and the Planck observational data. (orig.)

  14. 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.

  15. 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.

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

    Directory of Open Access Journals (Sweden)

    Beom Sik Kang

    2017-10-01

    Full Text Available 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.

  17. 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.

  18. Looking at the Green Fluorescent Protein (GFP) chromophore from a different perspective: A computational insight

    Science.gov (United States)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2013-02-01

    In the present contribution Density Functional Theory (DFT) has been applied to explore molecular dipole moment, frontier molecular orbital (FMO) features, chemical hardness, and the molecular electrostatic potential surface (MEPS) characteristics for optimized molecular geometry of the Green Fluorescent Protein (GFP) chromophore p-hydroxybenzylideneimidazolinone (HBDI) both in its protonated (neutral) and deprotonated (anion) forms. The distribution of atomic charges over the entire molecular framework as obtained from Natural Bond Orbital (NBO) analysis is found to faithfully replicate the predictions from the MEP map in respect of reactivity map of HBDI (neutral and anion) and possible sites for hydrogen bonding interactions etc. The three dimensional MEP map encompassing the entire molecule yields a reliable reactivity map of HBDI molecule also displaying the most probable regions for non-covalent interactions. The differential distribution of the electrostatic potential over the neutral and anionic species of HBDI is authentically reflected on MEP map and NBO charge distribution analysis. Thermodynamic properties such as heat capacity, thermal energy, enthalpy, entropy have been calculated and the correlation of the various thermodynamic functions with temperature has been established for neutral molecule. More importantly, however, the computational approach has been employed to unveil the nonlinear optical (NLO) properties of protonated (neutral) and deprotonated (anion) HBDI. Also in an endeavor to achieve a fuller understanding on this aspect the effect of basis set on the NLO properties of the title molecule has been investigated. Our computations delineate the discernible differences in NLO properties between the neutral and anionic species of HBDI whereby indicating the possibility of development of photoswitchable NLO device.

  19. Fast computational methods for predicting protein structure from primary amino acid sequence

    Science.gov (United States)

    Agarwal, Pratul Kumar [Knoxville, TN

    2011-07-19

    The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

  20. 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)

  1. 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.)

  2. 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

  3. 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

  4. 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 ...

  5. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.

    Directory of Open Access Journals (Sweden)

    Md Mehedi Hasan

    Full Text Available Prokaryotic proteins are regulated by pupylation, a type of post-translational modification that contributes to cellular function in bacterial organisms. In pupylation process, the prokaryotic ubiquitin-like protein (Pup tagging is functionally analogous to ubiquitination in order to tag target proteins for proteasomal degradation. To date, several experimental methods have been developed to identify pupylated proteins and their pupylation sites, but these experimental methods are generally laborious and costly. Therefore, computational methods that can accurately predict potential pupylation sites based on protein sequence information are highly desirable. In this paper, a novel predictor termed as pbPUP has been developed for accurate prediction of pupylation sites. In particular, a sophisticated sequence encoding scheme [i.e. the profile-based composition of k-spaced amino acid pairs (pbCKSAAP] is used to represent the sequence patterns and evolutionary information of the sequence fragments surrounding pupylation sites. Then, a Support Vector Machine (SVM classifier is trained using the pbCKSAAP encoding scheme. The final pbPUP predictor achieves an AUC value of 0.849 in 10-fold cross-validation tests and outperforms other existing predictors on a comprehensive independent test dataset. The proposed method is anticipated to be a helpful computational resource for the prediction of pupylation sites. The web server and curated datasets in this study are freely available at http://protein.cau.edu.cn/pbPUP/.

  6. 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.

  7. 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.

  8. 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.

  9. Rotational discontinuities in anisotropic plasmas

    International Nuclear Information System (INIS)

    Omidi, N.

    1992-01-01

    The kinetic structure of rotational discontinuities (RDs) in anisotropic plasmas with T perpendicular /T parallel > 1 is investigated by using a one-dimensional electromagnetic hybrid code. To form the RD, a new approach is used where the plasma is injected from one boundary and reflected from the other, resulting in the generation of a traveling fast shock and an RD. Unlike the previously used methods, no a priori assumptions are made regarding the initial structure (i.e. width or sense of rotation) of the rotational discontinuity. The results show that across the RD both the magnetic field strength and direction, as well as the plasma density change. Given that such a change can also be associated with an intermediate shock, the Rankine-Hugoniot relations are used to confirm that the observed structures are indeed RDs. It is found that the thickness of RDs is a few ion inertial lengths and is independent of the rotation angle. Also, the preferred sense of rotation is in the electron sense; however, RDs with a rotation angle larger than 180 degree are found to be unstable, changing their rotation to a stable ion sense

  10. Mechanics of anisotropic spring networks.

    Science.gov (United States)

    Zhang, T; Schwarz, J M; Das, Moumita

    2014-12-01

    We construct and analyze a model for a disordered linear spring network with anisotropy. The modeling is motivated by, for example, granular systems, nematic elastomers, and ultimately cytoskeletal networks exhibiting some underlying anisotropy. The model consists of a triangular lattice with two different bond occupation probabilities, p(x) and p(y), for the linear springs. We develop an effective medium theory (EMT) to describe the network elasticity as a function of p(x) and p(y). We find that the onset of rigidity in the EMT agrees with Maxwell constraint counting. We also find beyond linear behavior in the shear and bulk modulus as a function of occupation probability in the rigid phase for small strains, which differs from the isotropic case. We compare our EMT with numerical simulations to find rather good agreement. Finally, we discuss the implications of extending the reach of effective medium theory as well as draw connections with prior work on both anisotropic and isotropic spring networks.

  11. Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein.

    Science.gov (United States)

    Haarmeyer, Carolyn N; Smith, Matthew D; Chundawat, Shishir P S; Sammond, Deanne; Whitehead, Timothy A

    2017-04-01

    Biological-mediated conversion of pretreated lignocellulosic biomass to biofuels and biochemicals is a promising avenue toward energy sustainability. However, a critical impediment to the commercialization of cellulosic biofuel production is the high cost of cellulase enzymes needed to deconstruct biomass into fermentable sugars. One major factor driving cost is cellulase adsorption and inactivation in the presence of lignin, yet we currently have a poor understanding of the protein structure-function relationships driving this adsorption. In this work, we have systematically investigated the role of protein surface potential on lignin adsorption using a model monomeric fluorescent protein. We have designed and experimentally characterized 16 model protein variants spanning the physiological range of net charge (-24 to +16 total charges) and total charge density (0.28-0.40 charges per sequence length) typical for natural proteins. Protein designs were expressed, purified, and subjected to in silico and in vitro biophysical measurements to evaluate the relationship between protein surface potential and lignin adsorption properties. The designs were comparable to model fluorescent protein in terms of thermostability and heterologous expression yield, although the majority of the designs unexpectedly formed homodimers. Protein adsorption to lignin was studied at two different temperatures using Quartz Crystal Microbalance with Dissipation Monitoring and a subtractive mass balance assay. We found a weak correlation between protein net charge and protein-binding capacity to lignin. No other single characteristic, including apparent melting temperature and 2nd virial coefficient, showed correlation with lignin binding. Analysis of an unrelated cellulase dataset with mutations localized to a family I carbohydrate-binding module showed a similar correlation between net charge and lignin binding capacity. Overall, our study provides strategies to identify highly active, low

  12. 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

  13. Noise analysis of genome-scale protein synthesis using a discrete computational model of translation

    Energy Technology Data Exchange (ETDEWEB)

    Racle, Julien; Hatzimanikatis, Vassily, E-mail: vassily.hatzimanikatis@epfl.ch [Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne (Switzerland); Stefaniuk, Adam Jan [Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland)

    2015-07-28

    Noise in genetic networks has been the subject of extensive experimental and computational studies. However, very few of these studies have considered noise properties using mechanistic models that account for the discrete movement of ribosomes and RNA polymerases along their corresponding templates (messenger RNA (mRNA) and DNA). The large size of these systems, which scales with the number of genes, mRNA copies, codons per mRNA, and ribosomes, is responsible for some of the challenges. Additionally, one should be able to describe the dynamics of ribosome exchange between the free ribosome pool and those bound to mRNAs, as well as how mRNA species compete for ribosomes. We developed an efficient algorithm for stochastic simulations that addresses these issues and used it to study the contribution and trade-offs of noise to translation properties (rates, time delays, and rate-limiting steps). The algorithm scales linearly with the number of mRNA copies, which allowed us to study the importance of genome-scale competition between mRNAs for the same ribosomes. We determined that noise is minimized under conditions maximizing the specific synthesis rate. Moreover, sensitivity analysis of the stochastic system revealed the importance of the elongation rate in the resultant noise, whereas the translation initiation rate constant was more closely related to the average protein synthesis rate. We observed significant differences between our results and the noise properties of the most commonly used translation models. Overall, our studies demonstrate that the use of full mechanistic models is essential for the study of noise in translation and transcription.

  14. COMPUTING

    CERN Multimedia

    M. Kasemann

    Overview In autumn the main focus was to process and handle CRAFT data and to perform the Summer08 MC production. The operational aspects were well covered by regular Computing Shifts, experts on duty and Computing Run Coordination. At the Computing Resource Board (CRB) in October a model to account for service work at Tier 2s was approved. The computing resources for 2009 were reviewed for presentation at the C-RRB. The quarterly resource monitoring is continuing. Facilities/Infrastructure operations Operations during CRAFT data taking ran fine. This proved to be a very valuable experience for T0 workflows and operations. The transfers of custodial data to most T1s went smoothly. A first round of reprocessing started at the Tier-1 centers end of November; it will take about two weeks. The Computing Shifts procedure was tested full scale during this period and proved to be very efficient: 30 Computing Shifts Persons (CSP) and 10 Computing Resources Coordinators (CRC). The shift program for the shut down w...

  15. 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.

  16. 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

  17. COMPUTING

    CERN Multimedia

    I. Fisk

    2011-01-01

    Introduction CMS distributed computing system performed well during the 2011 start-up. The events in 2011 have more pile-up and are more complex than last year; this results in longer reconstruction times and harder events to simulate. Significant increases in computing capacity were delivered in April for all computing tiers, and the utilisation and load is close to the planning predictions. All computing centre tiers performed their expected functionalities. Heavy-Ion Programme The CMS Heavy-Ion Programme had a very strong showing at the Quark Matter conference. A large number of analyses were shown. The dedicated heavy-ion reconstruction facility at the Vanderbilt Tier-2 is still involved in some commissioning activities, but is available for processing and analysis. Facilities and Infrastructure Operations Facility and Infrastructure operations have been active with operations and several important deployment tasks. Facilities participated in the testing and deployment of WMAgent and WorkQueue+Request...

  18. COMPUTING

    CERN Multimedia

    P. McBride

    The Computing Project is preparing for a busy year where the primary emphasis of the project moves towards steady operations. Following the very successful completion of Computing Software and Analysis challenge, CSA06, last fall, we have reorganized and established four groups in computing area: Commissioning, User Support, Facility/Infrastructure Operations and Data Operations. These groups work closely together with groups from the Offline Project in planning for data processing and operations. Monte Carlo production has continued since CSA06, with about 30M events produced each month to be used for HLT studies and physics validation. Monte Carlo production will continue throughout the year in the preparation of large samples for physics and detector studies ramping to 50 M events/month for CSA07. Commissioning of the full CMS computing system is a major goal for 2007. Site monitoring is an important commissioning component and work is ongoing to devise CMS specific tests to be included in Service Availa...

  19. COMPUTING

    CERN Multimedia

    M. Kasemann

    Overview During the past three months activities were focused on data operations, testing and re-enforcing shift and operational procedures for data production and transfer, MC production and on user support. Planning of the computing resources in view of the new LHC calendar in ongoing. Two new task forces were created for supporting the integration work: Site Commissioning, which develops tools helping distributed sites to monitor job and data workflows, and Analysis Support, collecting the user experience and feedback during analysis activities and developing tools to increase efficiency. The development plan for DMWM for 2009/2011 was developed at the beginning of the year, based on the requirements from the Physics, Computing and Offline groups (see Offline section). The Computing management meeting at FermiLab on February 19th and 20th was an excellent opportunity discussing the impact and for addressing issues and solutions to the main challenges facing CMS computing. The lack of manpower is particul...

  20. 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.

  1. 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.

  2. Selection of symptomatic patients with Crohn's disease for abdominopelvic computed tomography: role of serum C-reactive protein.

    LENUS (Irish Health Repository)

    Desmond, Alan N

    2012-11-01

    Results of previous studies have shown that repeated abdominopelvic computed tomography (CT) examinations can lead to substantial cumulative diagnostic radiation exposure in patients with Crohn\\'s disease (CD). Improved selection of patients referred for CT will reduce unnecessary radiation exposure. This study examines if serum C-reactive protein (CRP) concentration predicts which symptomatic patients with CD are likely to have significant disease activity or disease complications (such as abscess) detected on abdominopelvic CT.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. Computational structural and functional analysis of hypothetical proteins of Staphylococcus aureus

    OpenAIRE

    Mohan, Ramadevi; Venugopal, Subhashree

    2012-01-01

    Genome sequencing projects has led to an explosion of large amount of gene products in which many are of hypothetical proteins with unknown function. Analyzing and annotating the functions of hypothetical proteins is important in Staphylococcus aureus which is a pathogenic bacterium that cause multiple types of diseases by infecting various sites in humans and animals. In this study, ten hypothetical proteins of Staphylococcus aureus were retrieved from NCBI and analyzed for their structural ...

  10. 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

  11. PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks.

    Science.gov (United States)

    Zhang, P; Tao, L; Zeng, X; Qin, C; Chen, S Y; Zhu, F; Yang, S Y; Li, Z R; Chen, W P; Chen, Y Z

    2017-02-03

    The studies of biological, disease, and pharmacological networks are facilitated by the systems-level investigations using computational tools. In particular, the network descriptors developed in other disciplines have found increasing applications in the study of the protein, gene regulatory, metabolic, disease, and drug-targeted networks. Facilities are provided by the public web servers for computing network descriptors, but many descriptors are not covered, including those used or useful for biological studies. We upgraded the PROFEAT web server http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi for computing up to 329 network descriptors and protein-protein interaction descriptors. PROFEAT network descriptors comprehensively describe the topological and connectivity characteristics of unweighted (uniform binding constants and molecular levels), edge-weighted (varying binding constants), node-weighted (varying molecular levels), edge-node-weighted (varying binding constants and molecular levels), and directed (oriented processes) networks. The usefulness of the network descriptors is illustrated by the literature-reported studies of the biological networks derived from the genome, interactome, transcriptome, metabolome, and diseasome profiles. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    DEFF Research Database (Denmark)

    Sastry, Anand; Monk, Jonathan M.; Tegel, Hanna

    2017-01-01

    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. Availability and implementation: 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...

  13. 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.

  14. COMPUTING

    CERN Multimedia

    I. Fisk

    2013-01-01

    Computing activity had ramped down after the completion of the reprocessing of the 2012 data and parked data, but is increasing with new simulation samples for analysis and upgrade studies. Much of the Computing effort is currently involved in activities to improve the computing system in preparation for 2015. Operations Office Since the beginning of 2013, the Computing Operations team successfully re-processed the 2012 data in record time, not only by using opportunistic resources like the San Diego Supercomputer Center which was accessible, to re-process the primary datasets HTMHT and MultiJet in Run2012D much earlier than planned. The Heavy-Ion data-taking period was successfully concluded in February collecting almost 500 T. Figure 3: Number of events per month (data) In LS1, our emphasis is to increase efficiency and flexibility of the infrastructure and operation. Computing Operations is working on separating disk and tape at the Tier-1 sites and the full implementation of the xrootd federation ...

  15. 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.)

  16. 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.

  17. 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.

  18. 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.

  19. 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)

  20. 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.

  1. Computational studies of G protein-coupled receptor complexes : Structure and dynamics

    NARCIS (Netherlands)

    Sensoy, Ozge; Almeida, Jose G; Shabbir, Javeria; de Sousa Moreira, Irina; Morra, Giulia

    2017-01-01

    G protein-coupled receptors (GPCRs) are ubiquitously expressed transmembrane proteins associated with a wide range of diseases such as Alzheimer's, Parkinson, schizophrenia, and also implicated in in several abnormal heart conditions. As such, this family of receptors is regarded as excellent drug

  2. LEAping to conclusions: a computational reanalysis of late embryogenesis abundant proteins and their possible roles.

    Science.gov (United States)

    Wise, Michael J

    2003-10-29

    The late embryogenesis abundant (LEA) proteins cover a number of loosely related groups of proteins, originally found in plants but now being found in non-plant species. Their precise function is unknown, though considerable evidence suggests that LEA proteins are involved in desiccation resistance. Using a number of statistically-based bioinformatics tools the classification of a large set of LEA proteins, covering all Groups, is reexamined together with some previous findings. Searches based on peptide composition return proteins with similar composition to different LEA Groups; keyword clustering is then applied to reveal keywords and phrases suggestive of the Groups' properties. Previous research has suggested that glycine is characteristic of LEA proteins, but it is only highly over-represented in Groups 1 and 2, while alanine, thought characteristic of Group 2, is over-represented in Group 3, 4 and 6 but under-represented in Groups 1 and 2. However, for LEA Groups 1 2 and 3 it is shown that glutamine is very significantly over-represented, while cysteine, phenylalanine, isoleucine, leucine and tryptophan are significantly under-represented. There is also evidence that the Group 4 LEA proteins are more appropriately redistributed to Group 2 and Group 3. Similarly, Group 5 is better found among the Group 3 LEA proteins. There is evidence that Group 2 and Group 3 LEA proteins, though distinct, might be related. This relationship is also evident in the overlapping sets of keywords for the two Groups, emphasising alpha-helical structure and, at a larger scale, filaments, all of which fits well with experimental evidence that proteins from both Groups are natively unstructured, but become structured under stress conditions. The keywords support localisation of LEA proteins both in the nucleus and associated with the cytoskeleton, and a mode of action similar to chaperones, perhaps the cold shock chaperones, via a role in DNA-binding. In general, non-globular and

  3. LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles

    Directory of Open Access Journals (Sweden)

    Wise Michael J

    2003-10-01

    Full Text Available Abstract Background The late embryogenesis abundant (LEA proteins cover a number of loosely related groups of proteins, originally found in plants but now being found in non-plant species. Their precise function is unknown, though considerable evidence suggests that LEA proteins are involved in desiccation resistance. Using a number of statistically-based bioinformatics tools the classification of a large set of LEA proteins, covering all Groups, is reexamined together with some previous findings. Searches based on peptide composition return proteins with similar composition to different LEA Groups; keyword clustering is then applied to reveal keywords and phrases suggestive of the Groups' properties. Results Previous research has suggested that glycine is characteristic of LEA proteins, but it is only highly over-represented in Groups 1 and 2, while alanine, thought characteristic of Group 2, is over-represented in Group 3, 4 and 6 but under-represented in Groups 1 and 2. However, for LEA Groups 1 2 and 3 it is shown that glutamine is very significantly over-represented, while cysteine, phenylalanine, isoleucine, leucine and tryptophan are significantly under-represented. There is also evidence that the Group 4 LEA proteins are more appropriately redistributed to Group 2 and Group 3. Similarly, Group 5 is better found among the Group 3 LEA proteins. Conclusions There is evidence that Group 2 and Group 3 LEA proteins, though distinct, might be related. This relationship is also evident in the overlapping sets of keywords for the two Groups, emphasising alpha-helical structure and, at a larger scale, filaments, all of which fits well with experimental evidence that proteins from both Groups are natively unstructured, but become structured under stress conditions. The keywords support localisation of LEA proteins both in the nucleus and associated with the cytoskeleton, and a mode of action similar to chaperones, perhaps the cold shock chaperones

  4. A TALE-inspired computational screen for proteins that contain approximate tandem repeats.

    Science.gov (United States)

    Perycz, Malgorzata; Krwawicz, Joanna; Bochtler, Matthias

    2017-01-01

    TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.

  5. COMPUTING

    CERN Multimedia

    I. Fisk

    2010-01-01

    Introduction It has been a very active quarter in Computing with interesting progress in all areas. The activity level at the computing facilities, driven by both organised processing from data operations and user analysis, has been steadily increasing. The large-scale production of simulated events that has been progressing throughout the fall is wrapping-up and reprocessing with pile-up will continue. A large reprocessing of all the proton-proton data has just been released and another will follow shortly. The number of analysis jobs by users each day, that was already hitting the computing model expectations at the time of ICHEP, is now 33% higher. We are expecting a busy holiday break to ensure samples are ready in time for the winter conferences. Heavy Ion An activity that is still in progress is computing for the heavy-ion program. The heavy-ion events are collected without zero suppression, so the event size is much large at roughly 11 MB per event of RAW. The central collisions are more complex and...

  6. COMPUTING

    CERN Multimedia

    M. Kasemann P. McBride Edited by M-C. Sawley with contributions from: P. Kreuzer D. Bonacorsi S. Belforte F. Wuerthwein L. Bauerdick K. Lassila-Perini M-C. Sawley

    Introduction More than seventy CMS collaborators attended the Computing and Offline Workshop in San Diego, California, April 20-24th to discuss the state of readiness of software and computing for collisions. Focus and priority were given to preparations for data taking and providing room for ample dialog between groups involved in Commissioning, Data Operations, Analysis and MC Production. Throughout the workshop, aspects of software, operating procedures and issues addressing all parts of the computing model were discussed. Plans for the CMS participation in STEP’09, the combined scale testing for all four experiments due in June 2009, were refined. The article in CMS Times by Frank Wuerthwein gave a good recap of the highly collaborative atmosphere of the workshop. Many thanks to UCSD and to the organizers for taking care of this workshop, which resulted in a long list of action items and was definitely a success. A considerable amount of effort and care is invested in the estimate of the comput...

  7. 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

  8. 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

  9. 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)

  10. 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.

  11. 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...

  12. 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

  13. 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

  14. 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

  15. Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics

    International Nuclear Information System (INIS)

    Villarreal, Oscar D.; Yu, Lili; Rodriguez, Roberto A.; Chen, Liao Y.

    2017-01-01

    Computing the ligand-protein binding affinity (or the Gibbs free energy) with chemical accuracy has long been a challenge for which many methods/approaches have been developed and refined with various successful applications. False positives and, even more harmful, false negatives have been and still are a common occurrence in practical applications. Inevitable in all approaches are the errors in the force field parameters we obtain from quantum mechanical computation and/or empirical fittings for the intra- and inter-molecular interactions. These errors propagate to the final results of the computed binding affinities even if we were able to perfectly implement the statistical mechanics of all the processes relevant to a given problem. And they are actually amplified to various degrees even in the mature, sophisticated computational approaches. In particular, the free energy perturbation (alchemical) approaches amplify the errors in the force field parameters because they rely on extracting the small differences between similarly large numbers. In this paper, we develop a hybrid steered molecular dynamics (hSMD) approach to the difficult binding problems of a ligand buried deep inside a protein. Sampling the transition along a physical (not alchemical) dissociation path of opening up the binding cavity- -pulling out the ligand- -closing back the cavity, we can avoid the problem of error amplifications by not relying on small differences between similar numbers. We tested this new form of hSMD on retinol inside cellular retinol-binding protein 1 and three cases of a ligand (a benzylacetate, a 2-nitrothiophene, and a benzene) inside a T4 lysozyme L99A/M102Q(H) double mutant. In all cases, we obtained binding free energies in close agreement with the experimentally measured values. This indicates that the force field parameters we employed are accurate and that hSMD (a brute force, unsophisticated approach) is free from the problem of error amplification suffered by

  16. New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces.

    Science.gov (United States)

    Simões, Inês C M; Costa, Inês P D; Coimbra, João T S; Ramos, Maria J; Fernandes, Pedro A

    2017-01-23

    Knowing how proteins make stable complexes enables the development of inhibitors to preclude protein-protein (P:P) binding. The identification of the specific interfacial residues that mostly contribute to protein binding, denominated as hot spots, is thus critical. Here, we refine an in silico alanine scanning mutagenesis protocol, based on a residue-dependent dielectric constant version of the Molecular Mechanics/Poisson-Boltzmann Surface Area method. We have used a large data set of structurally diverse P:P complexes to redefine the residue-dependent dielectric constants used in the determination of binding free energies. The accuracy of the method was validated through comparison with experimental data, considering the per-residue P:P binding free energy (ΔΔG binding ) differences upon alanine mutation. Different protocols were tested, i.e., a geometry optimization protocol and three molecular dynamics (MD) protocols: (1) one using explicit water molecules, (2) another with an implicit solvation model, and (3) a third where we have carried out an accelerated MD with explicit water molecules. Using a set of protein dielectric constants (within the range from 1 to 20) we showed that the dielectric constants of 7 for nonpolar and polar residues and 11 for charged residues (and histidine) provide optimal ΔΔG binding predictions. An overall mean unsigned error (MUE) of 1.4 kcal mol -1 relative to the experiment was achieved in 210 mutations only with geometry optimization, which was further reduced with MD simulations (MUE of 1.1 kcal mol -1 for the MD employing explicit solvent). This recalibrated method allows for a better computational identification of hot spots, avoiding expensive and time-consuming experiments or thermodynamic integration/ free energy perturbation/ uBAR calculations, and will hopefully help new drug discovery campaigns in their quest of searching spots of interest for binding small drug-like molecules at P:P interfaces.

  17. COMPUTING

    CERN Multimedia

    P. McBride

    It has been a very active year for the computing project with strong contributions from members of the global community. The project has focused on site preparation and Monte Carlo production. The operations group has begun processing data from P5 as part of the global data commissioning. Improvements in transfer rates and site availability have been seen as computing sites across the globe prepare for large scale production and analysis as part of CSA07. Preparations for the upcoming Computing Software and Analysis Challenge CSA07 are progressing. Ian Fisk and Neil Geddes have been appointed as coordinators for the challenge. CSA07 will include production tests of the Tier-0 production system, reprocessing at the Tier-1 sites and Monte Carlo production at the Tier-2 sites. At the same time there will be a large analysis exercise at the Tier-2 centres. Pre-production simulation of the Monte Carlo events for the challenge is beginning. Scale tests of the Tier-0 will begin in mid-July and the challenge it...

  18. COMPUTING

    CERN Multimedia

    M. Kasemann

    Introduction During the past six months, Computing participated in the STEP09 exercise, had a major involvement in the October exercise and has been working with CMS sites on improving open issues relevant for data taking. At the same time operations for MC production, real data reconstruction and re-reconstructions and data transfers at large scales were performed. STEP09 was successfully conducted in June as a joint exercise with ATLAS and the other experiments. It gave good indication about the readiness of the WLCG infrastructure with the two major LHC experiments stressing the reading, writing and processing of physics data. The October Exercise, in contrast, was conducted as an all-CMS exercise, where Physics, Computing and Offline worked on a common plan to exercise all steps to efficiently access and analyze data. As one of the major results, the CMS Tier-2s demonstrated to be fully capable for performing data analysis. In recent weeks, efforts were devoted to CMS Computing readiness. All th...

  19. COMPUTING

    CERN Multimedia

    I. Fisk

    2011-01-01

    Introduction It has been a very active quarter in Computing with interesting progress in all areas. The activity level at the computing facilities, driven by both organised processing from data operations and user analysis, has been steadily increasing. The large-scale production of simulated events that has been progressing throughout the fall is wrapping-up and reprocessing with pile-up will continue. A large reprocessing of all the proton-proton data has just been released and another will follow shortly. The number of analysis jobs by users each day, that was already hitting the computing model expectations at the time of ICHEP, is now 33% higher. We are expecting a busy holiday break to ensure samples are ready in time for the winter conferences. Heavy Ion The Tier 0 infrastructure was able to repack and promptly reconstruct heavy-ion collision data. Two copies were made of the data at CERN using a large CASTOR disk pool, and the core physics sample was replicated ...

  20. COMPUTING

    CERN Multimedia

    I. Fisk

    2012-01-01

    Introduction Computing continued with a high level of activity over the winter in preparation for conferences and the start of the 2012 run. 2012 brings new challenges with a new energy, more complex events, and the need to make the best use of the available time before the Long Shutdown. We expect to be resource constrained on all tiers of the computing system in 2012 and are working to ensure the high-priority goals of CMS are not impacted. Heavy ions After a successful 2011 heavy-ion run, the programme is moving to analysis. During the run, the CAF resources were well used for prompt analysis. Since then in 2012 on average 200 job slots have been used continuously at Vanderbilt for analysis workflows. Operations Office As of 2012, the Computing Project emphasis has moved from commissioning to operation of the various systems. This is reflected in the new organisation structure where the Facilities and Data Operations tasks have been merged into a common Operations Office, which now covers everything ...

  1. COMPUTING

    CERN Multimedia

    M. Kasemann

    CCRC’08 challenges and CSA08 During the February campaign of the Common Computing readiness challenges (CCRC’08), the CMS computing team had achieved very good results. The link between the detector site and the Tier0 was tested by gradually increasing the number of parallel transfer streams well beyond the target. Tests covered the global robustness at the Tier0, processing a massive number of very large files and with a high writing speed to tapes.  Other tests covered the links between the different Tiers of the distributed infrastructure and the pre-staging and reprocessing capacity of the Tier1’s: response time, data transfer rate and success rate for Tape to Buffer staging of files kept exclusively on Tape were measured. In all cases, coordination with the sites was efficient and no serious problem was found. These successful preparations prepared the ground for the second phase of the CCRC’08 campaign, in May. The Computing Software and Analysis challen...

  2. COMPUTING

    CERN Multimedia

    I. Fisk

    2010-01-01

    Introduction The first data taking period of November produced a first scientific paper, and this is a very satisfactory step for Computing. It also gave the invaluable opportunity to learn and debrief from this first, intense period, and make the necessary adaptations. The alarm procedures between different groups (DAQ, Physics, T0 processing, Alignment/calibration, T1 and T2 communications) have been reinforced. A major effort has also been invested into remodeling and optimizing operator tasks in all activities in Computing, in parallel with the recruitment of new Cat A operators. The teams are being completed and by mid year the new tasks will have been assigned. CRB (Computing Resource Board) The Board met twice since last CMS week. In December it reviewed the experience of the November data-taking period and could measure the positive improvements made for the site readiness. It also reviewed the policy under which Tier-2 are associated with Physics Groups. Such associations are decided twice per ye...

  3. COMPUTING

    CERN Multimedia

    M. Kasemann

    Introduction More than seventy CMS collaborators attended the Computing and Offline Workshop in San Diego, California, April 20-24th to discuss the state of readiness of software and computing for collisions. Focus and priority were given to preparations for data taking and providing room for ample dialog between groups involved in Commissioning, Data Operations, Analysis and MC Production. Throughout the workshop, aspects of software, operating procedures and issues addressing all parts of the computing model were discussed. Plans for the CMS participation in STEP’09, the combined scale testing for all four experiments due in June 2009, were refined. The article in CMS Times by Frank Wuerthwein gave a good recap of the highly collaborative atmosphere of the workshop. Many thanks to UCSD and to the organizers for taking care of this workshop, which resulted in a long list of action items and was definitely a success. A considerable amount of effort and care is invested in the estimate of the co...

  4. Computer simulation of protein—carbohydrate complexes: application to arabinose-binding protein and pea lectin

    Science.gov (United States)

    Rao, V. S. R.; Biswas, Margaret; Mukhopadhyay, Chaitali; Balaji, P. V.

    1989-03-01

    The CCEM method (Contact Criteria and Energy Minimisation) has been developed and applied to study protein-carbohydrate interactions. The method uses available X-ray data even on the native protein at low resolution (above 2.4 Å) to generate realistic models of a variety of proteins with various ligands. The two examples discussed in this paper are arabinose-binding protein (ABP) and pea lectin. The X-ray crystal structure data reported on ABP-β- L-arabinose complex at 2.8, 2.4 and 1.7 Å resolution differ drastically in predicting the nature of the interactions between the protein and ligand. It is shown that, using the data at 2.4 Å resolution, the CCEM method generates complexes which are as good as the higher (1.7 Å) resolution data. The CCEM method predicts some of the important hydrogen bonds between the ligand and the protein which are missing in the interpretation of the X-ray data at 2.4 Å resolution. The theoretically predicted hydrogen bonds are in good agreement with those reported at 1.7 Å resolution. Pea lectin has been solved only in the native form at 3 Å resolution. Application of the CCEM method also enables us to generate complexes of pea lectin with methyl-α- D-glucopyranoside and methyl-2,3-dimethyl-α- D-glucopyranoside which explain well the available experimental data in solution.

  5. ATP-Binding Cassette Proteins: Towards a Computational View of Mechanism

    Science.gov (United States)

    Liao, Jielou

    2004-03-01

    Many large machine proteins can generate mechanical force and undergo large-scale conformational changes (LSCC) to perform varying biological tasks in living cells by utilizing ATP. Important examples include ATP-binding cassette (ABC) transporters. They are membrane proteins that couple ATP binding and hydrolysis to the translocation of substrates across membranes [1]. To interpret how the mechanical force generated by ATP binding and hydrolysis is propagated, a coarse-grained ATP-dependent harmonic network model (HNM) [2,3] is applied to the ABC protein, BtuCD. This protein machine transports vitamin B12 across membranes. The analysis shows that subunits of the protein move against each other in a concerted manner. The lowest-frequency modes of the BtuCD protein are found to link the functionally critical domains, and are suggested to be responsible for large-scale ATP-coupled conformational changes. [1] K. P. Locher, A. T. Lee and D. C. Rees. Science 296, 1091-1098 (2002). [2] Atilgan, A. R., S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar. Biophys. J. 80, 505-515(2002); M. M Tirion, Phys. Rev. Lett. 77, 1905-1908 (1996). [3] J. -L. Liao and D. N. Beratan, 2003, to be published.

  6. Structure Prediction of Outer Membrane Protease Protein of Salmonella typhimurium Using Computational Techniques

    Directory of Open Access Journals (Sweden)

    Rozina Tabassum

    2016-03-01

    Full Text Available Salmonella typhimurium, a facultative gram-negative intracellular pathogen belonging to family Enterobacteriaceae, is the most frequent cause of human gastroenteritis worldwide. PgtE gene product, outer membrane protease emerges important in the intracellular phases of salmonellosis. The pgtE gene product of S. typhimurium was predicted to be capable of proteolyzing T7 RNA polymerase and localize in the outer membrane of these gram negative bacteria. PgtE product of S. enterica and OmpT of E. coli, having high sequence similarity have been revealed to degrade macrophages, causing salmonellosis and other diseases. The three-dimensional structure of the protein was not available through Protein Data Bank (PDB creating lack of structural information about E protein. In our study, by performing Comparative model building, the three dimensional structure of outer membrane protease protein was generated using the backbone of the crystal structure of Pla of Yersinia pestis, retrieved from PDB, with MODELLER (9v8. Quality of the model was assessed by validation tool PROCHECK, web servers like ERRAT and ProSA are used to certify the reliability of the predicted model. This information might offer clues for better understanding of E protein and consequently for developmet of better therapeutic treatment against pathogenic role of this protein in salmonellosis and other diseases.

  7. 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

  8. IN SILICO EVALUATION OF ANGIOTENSIN II RECEPTOR ANTAGONIST’S PLASMA PROTEIN BINDING USING COMPUTED MOLECULAR DESCRIPTORS

    Directory of Open Access Journals (Sweden)

    Jadranka Odović

    2014-03-01

    Full Text Available The discovery of new pharmacologically active substances and drugs modeling led to necessity of predicting drugs properties and its ADME data. Angiotensin II receptor antagonists are a group of pharmaceuticals which modulate the renin-angiotensin-aldosterone system and today represent the most commonly prescribed anti-hypertensive drugs. The aim of this study was to compare different molecular properties of seven angiotensin II receptor antagonists / blockers (ARBs, (eprosartan, irbesartan, losartan, olmesartan, telmisartan, valsartan and their plasma protein binding (PPB data. Several ARBs molecular descriptors were calculated using software package Molinspiration Depiction Software as well as Virtual Computational Chemistry Laboratory (electronic descriptor – PSA, constitutional parameter – Mw, geometric descriptor – Vol, lipophilicity descriptors - logP values, aqueous solubility data – logS. The correlations between all collected descriptors and plasma protein binding data obtained from relevant literature were established. In the simple linear regression poor correlations were obtained in relationships between PPB data and all calculated molecular descriptors. In the next stage of the study multiple linear regression (MLR was used for correlation of PPB data with two different descriptors as independent variables. The best correlation (R2=0.70 with P<0.05 was established between PPB data and molecular weight with addition of volume values as independent variables. The possible application of computed molecular descriptors in drugs protein binding evaluation can be of great importance in drug research.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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.)

  18. 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

  19. Algebraic solution of an anisotropic nonquadratic potential

    International Nuclear Information System (INIS)

    Boschi Filho, H.; Vaidya, A.N.

    1990-06-01

    We show that an anisotropic nonquadratic potential, for which a path integral treatment had been recently discussed in the literature, possesses the (SO(2,1)xSO(2,1))ΛSO(2,1) dynamical symmetry and constructs its Green function algebraically. A particular case which generates new eigenvalues and eigenfunctions is also discussed. (author). 11 refs

  20. 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].

  1. 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.

  2. 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

  3. 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...

  4. 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.

  5. 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

  6. 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 ...

  7. 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.

  8. COMPUTING

    CERN Multimedia

    2010-01-01

    Introduction Just two months after the “LHC First Physics” event of 30th March, the analysis of the O(200) million 7 TeV collision events in CMS accumulated during the first 60 days is well under way. The consistency of the CMS computing model has been confirmed during these first weeks of data taking. This model is based on a hierarchy of use-cases deployed between the different tiers and, in particular, the distribution of RECO data to T1s, who then serve data on request to T2s, along a topology known as “fat tree”. Indeed, during this period this model was further extended by almost full “mesh” commissioning, meaning that RECO data were shipped to T2s whenever possible, enabling additional physics analyses compared with the “fat tree” model. Computing activities at the CMS Analysis Facility (CAF) have been marked by a good time response for a load almost evenly shared between ALCA (Alignment and Calibration tasks - highest p...

  9. COMPUTING

    CERN Multimedia

    Contributions from I. Fisk

    2012-01-01

    Introduction The start of the 2012 run has been busy for Computing. We have reconstructed, archived, and served a larger sample of new data than in 2011, and we are in the process of producing an even larger new sample of simulations at 8 TeV. The running conditions and system performance are largely what was anticipated in the plan, thanks to the hard work and preparation of many people. Heavy ions Heavy Ions has been actively analysing data and preparing for conferences.  Operations Office Figure 6: Transfers from all sites in the last 90 days For ICHEP and the Upgrade efforts, we needed to produce and process record amounts of MC samples while supporting the very successful data-taking. This was a large burden, especially on the team members. Nevertheless the last three months were very successful and the total output was phenomenal, thanks to our dedicated site admins who keep the sites operational and the computing project members who spend countless hours nursing the...

  10. COMPUTING

    CERN Multimedia

    M. Kasemann

    Introduction A large fraction of the effort was focused during the last period into the preparation and monitoring of the February tests of Common VO Computing Readiness Challenge 08. CCRC08 is being run by the WLCG collaboration in two phases, between the centres and all experiments. The February test is dedicated to functionality tests, while the May challenge will consist of running at all centres and with full workflows. For this first period, a number of functionality checks of the computing power, data repositories and archives as well as network links are planned. This will help assess the reliability of the systems under a variety of loads, and identifying possible bottlenecks. Many tests are scheduled together with other VOs, allowing the full scale stress test. The data rates (writing, accessing and transfer¬ring) are being checked under a variety of loads and operating conditions, as well as the reliability and transfer rates of the links between Tier-0 and Tier-1s. In addition, the capa...

  11. COMPUTING

    CERN Multimedia

    Matthias Kasemann

    Overview The main focus during the summer was to handle data coming from the detector and to perform Monte Carlo production. The lessons learned during the CCRC and CSA08 challenges in May were addressed by dedicated PADA campaigns lead by the Integration team. Big improvements were achieved in the stability and reliability of the CMS Tier1 and Tier2 centres by regular and systematic follow-up of faults and errors with the help of the Savannah bug tracking system. In preparation for data taking the roles of a Computing Run Coordinator and regular computing shifts monitoring the services and infrastructure as well as interfacing to the data operations tasks are being defined. The shift plan until the end of 2008 is being put together. User support worked on documentation and organized several training sessions. The ECoM task force delivered the report on “Use Cases for Start-up of pp Data-Taking” with recommendations and a set of tests to be performed for trigger rates much higher than the ...

  12. COMPUTING

    CERN Multimedia

    P. MacBride

    The Computing Software and Analysis Challenge CSA07 has been the main focus of the Computing Project for the past few months. Activities began over the summer with the preparation of the Monte Carlo data sets for the challenge and tests of the new production system at the Tier-0 at CERN. The pre-challenge Monte Carlo production was done in several steps: physics generation, detector simulation, digitization, conversion to RAW format and the samples were run through the High Level Trigger (HLT). The data was then merged into three "Soups": Chowder (ALPGEN), Stew (Filtered Pythia) and Gumbo (Pythia). The challenge officially started when the first Chowder events were reconstructed on the Tier-0 on October 3rd. The data operations teams were very busy during the the challenge period. The MC production teams continued with signal production and processing while the Tier-0 and Tier-1 teams worked on splitting the Soups into Primary Data Sets (PDS), reconstruction and skimming. The storage sys...

  13. COMPUTING

    CERN Multimedia

    I. Fisk

    2013-01-01

    Computing operation has been lower as the Run 1 samples are completing and smaller samples for upgrades and preparations are ramping up. Much of the computing activity is focusing on preparations for Run 2 and improvements in data access and flexibility of using resources. Operations Office Data processing was slow in the second half of 2013 with only the legacy re-reconstruction pass of 2011 data being processed at the sites.   Figure 1: MC production and processing was more in demand with a peak of over 750 Million GEN-SIM events in a single month.   Figure 2: The transfer system worked reliably and efficiently and transferred on average close to 520 TB per week with peaks at close to 1.2 PB.   Figure 3: The volume of data moved between CMS sites in the last six months   The tape utilisation was a focus for the operation teams with frequent deletion campaigns from deprecated 7 TeV MC GEN-SIM samples to INVALID datasets, which could be cleaned up...

  14. COMPUTING

    CERN Multimedia

    I. Fisk

    2012-01-01

      Introduction Computing activity has been running at a sustained, high rate as we collect data at high luminosity, process simulation, and begin to process the parked data. The system is functional, though a number of improvements are planned during LS1. Many of the changes will impact users, we hope only in positive ways. We are trying to improve the distributed analysis tools as well as the ability to access more data samples more transparently.  Operations Office Figure 2: Number of events per month, for 2012 Since the June CMS Week, Computing Operations teams successfully completed data re-reconstruction passes and finished the CMSSW_53X MC campaign with over three billion events available in AOD format. Recorded data was successfully processed in parallel, exceeding 1.2 billion raw physics events per month for the first time in October 2012 due to the increase in data-parking rate. In parallel, large efforts were dedicated to WMAgent development and integrati...

  15. Impacts of Nonsynonymous Single Nucleotide Polymorphisms of Adiponectin Receptor 1 Gene on Corresponding Protein Stability: A Computational Approach

    Directory of Open Access Journals (Sweden)

    Md. Abu Saleh

    2016-01-01

    Full Text Available Despite the reported association of adiponectin receptor 1 (ADIPOR1 gene mutations with vulnerability to several human metabolic diseases, there is lack of computational analysis on the functional and structural impacts of single nucleotide polymorphisms (SNPs of the human ADIPOR1 at protein level. Therefore, sequence- and structure-based computational tools were employed in this study to functionally and structurally characterize the coding nsSNPs of ADIPOR1 gene listed in the dbSNP database. Our in silico analysis by SIFT, nsSNPAnalyzer, PolyPhen-2, Fathmm, I-Mutant 2.0, SNPs&GO, PhD-SNP, PANTHER, and SNPeffect tools identified the nsSNPs with distorting functional impacts, namely, rs765425383 (A348G, rs752071352 (H341Y, rs759555652 (R324L, rs200326086 (L224F, and rs766267373 (L143P from 74 nsSNPs of ADIPOR1 gene. Finally the aforementioned five deleterious nsSNPs were introduced using Swiss-PDB Viewer package within the X-ray crystal structure of ADIPOR1 protein, and changes in free energy for these mutations were computed. Although increased free energy was observed for all the mutants, the nsSNP H341Y caused the highest energy increase amongst all. RMSD and TM scores predicted that mutants were structurally similar to wild type protein. Our analyses suggested that the aforementioned variants especially H341Y could directly or indirectly destabilize the amino acid interactions and hydrogen bonding networks of ADIPOR1.

  16. Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.

    Science.gov (United States)

    Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

    2015-01-01

    Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and

  17. Proteomics computational analyses suggest that the bornavirus glycoprotein is a class III viral fusion protein (γ penetrene

    Directory of Open Access Journals (Sweden)

    Garry Robert F

    2009-09-01

    Full Text Available Abstract Background Borna disease virus (BDV is the type member of the Bornaviridae, a family of viruses that induce often fatal neurological diseases in horses, sheep and other animals, and have been proposed to have roles in certain psychiatric diseases of humans. The BDV glycoprotein (G is an extensively glycosylated protein that migrates with an apparent molecular mass of 84,000 to 94,000 kilodaltons (kDa. BDV G is post-translationally cleaved by the cellular subtilisin-like protease furin into two subunits, a 41 kDa amino terminal protein GP1 and a 43 kDa carboxyl terminal protein GP2. Results Class III viral fusion proteins (VFP encoded by members of the Rhabdoviridae, Herpesviridae and Baculoviridae have an internal fusion domain comprised of beta sheets, other beta sheet domains, an extended alpha helical domain, a membrane proximal stem domain and a carboxyl terminal anchor. Proteomics computational analyses suggest that the structural/functional motifs that characterize class III VFP are located collinearly in BDV G. Structural models were established for BDV G based on the post-fusion structure of a prototypic class III VFP, vesicular stomatitis virus glycoprotein (VSV G. Conclusion These results suggest that G encoded by members of the Bornavirdae are class III VFPs (gamma-penetrenes.

  18. COMPUTING

    CERN Multimedia

    I. Fisk

    2011-01-01

    Introduction The Computing Team successfully completed the storage, initial processing, and distribution for analysis of proton-proton data in 2011. There are still a variety of activities ongoing to support winter conference activities and preparations for 2012. Heavy ions The heavy-ion run for 2011 started in early November and has already demonstrated good machine performance and success of some of the more advanced workflows planned for 2011. Data collection will continue until early December. Facilities and Infrastructure Operations Operational and deployment support for WMAgent and WorkQueue+Request Manager components, routinely used in production by Data Operations, are provided. The GlideInWMS and components installation are now deployed at CERN, which is added to the GlideInWMS factory placed in the US. There has been new operational collaboration between the CERN team and the UCSD GlideIn factory operators, covering each others time zones by monitoring/debugging pilot jobs sent from the facto...

  19. Structure prediction and binding sites analysis of curcin protein of Jatropha curcas using computational approaches.

    Science.gov (United States)

    Srivastava, Mugdha; Gupta, Shishir K; Abhilash, P C; Singh, Nandita

    2012-07-01

    Ribosome inactivating proteins (RIPs) are defense proteins in a number of higher-plant species that are directly targeted toward herbivores. Jatropha curcas is one of the biodiesel plants having RIPs. The Jatropha seed meal, after extraction of oil, is rich in curcin, a highly toxic RIP similar to ricin, which makes it unsuitable for animal feed. Although the toxicity of curcin is well documented in the literature, the detailed toxic properties and the 3D structure of curcin has not been determined by X-ray crystallography, NMR spectroscopy or any in silico techniques to date. In this pursuit, the structure of curcin was modeled by a composite approach of 3D structure prediction using threading and ab initio modeling. Assessment of model quality was assessed by methods which include Ramachandran plot analysis and Qmean score estimation. Further, we applied the protein-ligand docking approach to identify the r-RNA binding residue of curcin. The present work provides the first structural insight into the binding mode of r-RNA adenine to the curcin protein and forms the basis for designing future inhibitors of curcin. Cloning of a future peptide inhibitor within J. curcas can produce non-toxic varieties of J. curcas, which would make the seed-cake suitable as animal feed without curcin detoxification.

  20. Proteomics computational analyses suggest that baculovirus GP64 superfamily proteins are class III penetrenes

    Directory of Open Access Journals (Sweden)

    Garry Robert F

    2008-02-01

    Full Text Available Abstract Background Members of the Baculoviridae encode two types of proteins that mediate virus:cell membrane fusion and penetration into the host cell. Alignments of primary amino acid sequences indicate that baculovirus fusion proteins of group I nucleopolyhedroviruses (NPV form the GP64 superfamily. The structure of these viral penetrenes has not been determined. The GP64 superfamily includes the glycoprotein (GP encoded by members of the Thogotovirus genus of the Orthomyxoviridae. The entry proteins of other baculoviruses, group II NPV and granuloviruses, are class I penetrenes. Results Class III penetrenes encoded by members of the Rhabdoviridae and Herpesviridae have an internal fusion domain comprised of beta sheets, other beta sheet domains, an extended alpha helical domain, a membrane proximal stem domain and a carboxyl terminal anchor. Similar sequences and structural/functional motifs that characterize class III penetrenes are located collinearly in GP64 of group I baculoviruses and related glycoproteins encoded by thogotoviruses. Structural models based on a prototypic class III penetrene, vesicular stomatitis virus glycoprotein (VSV G, were established for Thogoto virus (THOV GP and Autographa california multiple NPV (AcMNPV GP64 demonstrating feasible cysteine linkages. Glycosylation sites in THOV GP and AcMNPV GP64 appear in similar model locations to the two glycosylation sites of VSV G. Conclusion These results suggest that proteins in the GP64 superfamily are class III penetrenes.

  1. Computational exploration of single-protein mechanics by steered molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Sotomayor, Marcos [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio (United States)

    2015-12-31

    Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictions must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.

  2. 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.

  3. 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.

  4. 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

  5. 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.)

  6. 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.

  7. COMPUTING

    CERN Multimedia

    M. Kasemann

    CMS relies on a well functioning, distributed computing infrastructure. The Site Availability Monitoring (SAM) and the Job Robot submission have been very instrumental for site commissioning in order to increase availability of more sites such that they are available to participate in CSA07 and are ready to be used for analysis. The commissioning process has been further developed, including "lessons learned" documentation via the CMS twiki. Recently the visualization, presentation and summarizing of SAM tests for sites has been redesigned, it is now developed by the central ARDA project of WLCG. Work to test the new gLite Workload Management System was performed; a 4 times increase in throughput with respect to LCG Resource Broker is observed. CMS has designed and launched a new-generation traffic load generator called "LoadTest" to commission and to keep exercised all data transfer routes in the CMS PhE-DEx topology. Since mid-February, a transfer volume of about 12 P...

  8. Exploiting Large-Scale Drug-Protein Interaction Information for Computational Drug Repurposing

    Science.gov (United States)

    2014-06-20

    studies that have reported antimalarial activities of azole compounds [39-43] lend support to our model predictions. The highest-scored non-malarial...Table 4, verapamil and cimetidine, do not have antimal- arial activities themselves but exhibit synergism when used in combination with antimalarial ... activators . Because of their high frequencies among the antimalarial drugs, according to Eq. 3, the drug-protein interactions contributing most to the

  9. Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40

    Directory of Open Access Journals (Sweden)

    Muhammad Usman Mirza

    2016-10-01

    Full Text Available The Ebola virus (EBOV has been recognised for nearly 40 years, with the most recent EBOV outbreak being in West Africa, where it created a humanitarian crisis. Mortalities reported up to 30 March 2016 totalled 11,307. However, up until now, EBOV drugs have been far from achieving regulatory (FDA approval. It is therefore essential to identify parent compounds that have the potential to be developed into effective drugs. Studies on Ebola viral proteins have shown that some can elicit an immunological response in mice, and these are now considered essential components of a vaccine designed to protect against Ebola haemorrhagic fever. The current study focuses on chemoinformatic approaches to identify virtual hits against Ebola viral proteins (VP35 and VP40, including protein binding site prediction, drug-likeness, pharmacokinetic and pharmacodynamic properties, metabolic site prediction, and molecular docking. Retrospective validation was performed using a database of non-active compounds, and early enrichment of EBOV actives at different false positive rates was calculated. Homology modelling and subsequent superimposition of binding site residues on other strains of EBOV were carried out to check residual conformations, and hence to confirm the efficacy of potential compounds. As a mechanism for artefactual inhibition of proteins through non-specific compounds, virtual hits were assessed for their aggregator potential compared with previously reported aggregators. These systematic studies have indicated that a few compounds may be effective inhibitors of EBOV replication and therefore might have the potential to be developed as anti-EBOV drugs after subsequent testing and validation in experiments in vivo.

  10. Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40.

    Science.gov (United States)

    Mirza, Muhammad Usman; Ikram, Nazia

    2016-10-26

    The Ebola virus (EBOV) has been recognised for nearly 40 years, with the most recent EBOV outbreak being in West Africa, where it created a humanitarian crisis. Mortalities reported up to 30 March 2016 totalled 11,307. However, up until now, EBOV drugs have been far from achieving regulatory (FDA) approval. It is therefore essential to identify parent compounds that have the potential to be developed into effective drugs. Studies on Ebola viral proteins have shown that some can elicit an immunological response in mice, and these are now considered essential components of a vaccine designed to protect against Ebola haemorrhagic fever. The current study focuses on chemoinformatic approaches to identify virtual hits against Ebola viral proteins (VP35 and VP40), including protein binding site prediction, drug-likeness, pharmacokinetic and pharmacodynamic properties, metabolic site prediction, and molecular docking. Retrospective validation was performed using a database of non-active compounds, and early enrichment of EBOV actives at different false positive rates was calculated. Homology modelling and subsequent superimposition of binding site residues on other strains of EBOV were carried out to check residual conformations, and hence to confirm the efficacy of potential compounds. As a mechanism for artefactual inhibition of proteins through non-specific compounds, virtual hits were assessed for their aggregator potential compared with previously reported aggregators. These systematic studies have indicated that a few compounds may be effective inhibitors of EBOV replication and therefore might have the potential to be developed as anti-EBOV drugs after subsequent testing and validation in experiments in vivo.

  11. 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.

  12. 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.

  13. 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

  14. 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)

  15. Using affinity capillary electrophoresis and computational models for binding studies of heparinoids with p-selectin and other proteins.

    Science.gov (United States)

    Mozafari, Mona; Balasupramaniam, Shantheya; Preu, Lutz; El Deeb, Sami; Reiter, Christian G; Wätzig, Hermann

    2017-06-01

    A fast and precise affinity capillary electrophoresis (ACE) method has been developed and applied for the investigation of the binding interactions between P-selectin and heparinoids as potential P-selectin inhibitors in the presence and absence of calcium ions. Furthermore, model proteins and vitronectin were used to appraise the binding behavior of P-selectin. The normalized mobility ratios (∆R/R f ), which provided information about the binding strength and the overall charge of the protein-ligand complex, were used to evaluate the binding affinities. It was found that P-selectin interacts more strongly with heparinoids in the presence of calcium ions. P-selectin was affected by heparinoids at the concentration of 3 mg/L. In addition, the results of the ACE experiments showed that among other investigated proteins, albumins and vitronectin exhibited strong interactions with heparinoids. Especially with P-selectin and vitronectin, the interaction may additionally induce conformational changes. Subsequently, computational models were applied to interpret the ACE experiments. Docking experiments explained that the binding of heparinoids on P-selectin is promoted by calcium ions. These docking models proved to be particularly well suited to investigate the interaction of charged compounds, and are therefore complementary to ACE experiments. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Anisotropic conducting films for electromagnetic radiation applications

    Science.gov (United States)

    Cavallo, Francesca; Lagally, Max G.; Rojas-Delgado, Richard

    2015-06-16

    Electronic devices for the generation of electromagnetic radiation are provided. Also provided are methods for using the devices to generate electromagnetic radiation. The radiation sources include an anisotropic electrically conducting thin film that is characterized by a periodically varying charge carrier mobility in the plane of the film. The periodic variation in carrier mobility gives rise to a spatially varying electric field, which produces electromagnetic radiation as charged particles pass through the film.

  17. 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.

  18. 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.

  19. Entanglement of periodic anisotropic XY chains

    International Nuclear Information System (INIS)

    Zhang Lifa; Tong Peiqing

    2005-01-01

    By using the concept of concurrence, the entanglement of periodic anisotropic XY chains in a transverse field is studied numerically. It is found that the derivatives ∂ λ C(1) of nearest-neighbour concurrence diverge at quantum critical points. By proper scaling, we found that all the derivatives ∂ λ C(1) for periodic XY chains in the vicinity of quantum critical points have the same behaviours as that of a uniform chain

  20. Surface instabilities during straining of anisotropic materials

    DEFF Research Database (Denmark)

    Legarth, Brian Nyvang; Richelsen, Ann Bettina

    2006-01-01

    The development of instabilities in traction-free surfaces is investigated numerically using a unit cell model. Full finite strain analyses are conducted using isotropic as well as anisotropic yield criteria and both plane strain tension and compression are considered. In the load range of tensio...... of principal overall strain. For other orientations surface instabilities are seen when non-associated plastic flow is taken into account. Compared to tension, smaller compressive deformations are needed in order to initiate a surface instability....

  1. Symmetry analysis for anisotropic field theories

    International Nuclear Information System (INIS)

    Parra, Lorena; Vergara, J. David

    2012-01-01

    The purpose of this paper is to study with the help of Noether's theorem the symmetries of anisotropic actions for arbitrary fields which generally depend on higher order spatial derivatives, and to find the corresponding current densities and the Noether charges. We study in particular scale invariance and consider the cases of higher derivative extensions of the scalar field, electrodynamics and Chern-Simons theory.

  2. Electromagnetic effects on cracking of anisotropic polytropes

    Energy Technology Data Exchange (ETDEWEB)

    Sharif, Muhammad; Sadiq, Sobia [University of the Punjab, Department of Mathematics, Lahore (Pakistan)

    2016-10-15

    In this paper, we study the electromagnetic effects on the stability of a spherically symmetric anisotropic fluid distribution satisfying two polytropic equations of state and construct the corresponding generalized Tolman-Oppenheimer-Volkoff equations. We apply perturbations on matter variables via the polytropic constant as well as the polytropic index and formulate the force distribution function. It is found that the compact object is stable for a feasible choice of perturbed polytropic index in the presence of charge. (orig.)

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Protein thermal stability enhancement by designing salt bridges: a combined computational and experimental study.

    Directory of Open Access Journals (Sweden)

    Chi-Wen Lee

    Full Text Available Protein thermal stability is an important factor considered in medical and industrial applications. Many structural characteristics related to protein thermal stability have been elucidated, and increasing salt bridges is considered as one of the most efficient strategies to increase protein thermal stability. However, the accurate simulation of salt bridges remains difficult. In this study, a novel method for salt-bridge design was proposed based on the statistical analysis of 10,556 surface salt bridges on 6,493 X-ray protein structures. These salt bridges were first categorized based on pairing residues, secondary structure locations, and Cα-Cα distances. Pairing preferences generalized from statistical analysis were used to construct a salt-bridge pair index and utilized in a weighted electrostatic attraction model to find the effective pairings for designing salt bridges. The model was also coupled with B-factor, weighted contact number, relative solvent accessibility, and conservation prescreening to determine the residues appropriate for the thermal adaptive design of salt bridges. According to our method, eight putative salt-bridges were designed on a mesophilic β-glucosidase and 24 variants were constructed to verify the predictions. Six putative salt-bridges leaded to the increase of the enzyme thermal stability. A significant increase in melting temperature of 8.8, 4.8, 3.7, 1.3, 1.2, and 0.7°C of the putative salt-bridges N437K-D49, E96R-D28, E96K-D28, S440K-E70, T231K-D388, and Q277E-D282 was detected, respectively. Reversing the polarity of T231K-D388 to T231D-D388K resulted in a further increase in melting temperatures by 3.6°C, which may be caused by the transformation of an intra-subunit electrostatic interaction into an inter-subunit one depending on the local environment. The combination of the thermostable variants (N437K, E96R, T231D and D388K generated a melting temperature increase of 15.7°C. Thus, this study

  16. 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...

  17. 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)

  18. 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

  19. 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

  20. Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach

    KAUST Repository

    Guardiani, Carlo; Marino, Daniele Di; Tramontano, Anna; Chinappi, Mauro; Cecconi, Fabio

    2014-01-01

    © 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.

  1. Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach

    KAUST Repository

    Guardiani, Carlo

    2014-09-09

    © 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.

  2. Computational prediction of cAMP receptor protein (CRP binding sites in cyanobacterial genomes

    Directory of Open Access Journals (Sweden)

    Su Zhengchang

    2009-01-01

    Full Text Available Abstract Background Cyclic AMP receptor protein (CRP, also known as catabolite gene activator protein (CAP, is an important transcriptional regulator widely distributed in many bacteria. The biological processes under the regulation of CRP are highly diverse among different groups of bacterial species. Elucidation of CRP regulons in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. Previously, CRP has been experimentally studied in only two cyanobacterial strains: Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed. Results We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution. Conclusion The CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The

  3. 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.

  4. 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....

  5. 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....

  6. Development of Conformation Independent Computational Models for the Early Recognition of Breast Cancer Resistance Protein Substrates

    Directory of Open Access Journals (Sweden)

    Melisa Edith Gantner

    2013-01-01

    Full Text Available ABC efflux transporters are polyspecific members of the ABC superfamily that, acting as drug and metabolite carriers, provide a biochemical barrier against drug penetration and contribute to detoxification. Their overexpression is linked to multidrug resistance issues in a diversity of diseases. Breast cancer resistance protein (BCRP is the most expressed ABC efflux transporter throughout the intestine and the blood-brain barrier, limiting oral absorption and brain bioavailability of its substrates. Early recognition of BCRP substrates is thus essential to optimize oral drug absorption, design of novel therapeutics for central nervous system conditions, and overcome BCRP-mediated cross-resistance issues. We present the development of an ensemble of ligand-based machine learning algorithms for the early recognition of BCRP substrates, from a database of 262 substrates and nonsubstrates compiled from the literature. Such dataset was rationally partitioned into training and test sets by application of a 2-step clustering procedure. The models were developed through application of linear discriminant analysis to random subsamples of Dragon molecular descriptors. Simple data fusion and statistical comparison of partial areas under the curve of ROC curves were applied to obtain the best 2-model combination, which presented 82% and 74.5% of overall accuracy in the training and test set, respectively.

  7. 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

  8. Three-dimensional, Computer-tomographic Analysis of Membrane Proteins (TrkA, caveolin, clathrin) in PC12 Cells

    International Nuclear Information System (INIS)

    Nishida, Tomoki; Arii, Tatsuo; Takaoka, Akio; Yoshimura, Ryoichi; Endo, Yasuhisa

    2007-01-01

    Signaling of nerve growth factor (NGF) and its receptor (TrkA) promotes neuronal differentiation, synapse formation and survival. It has been known that the complex of NGF and TrkA is internalized into the cytoplasm and transported for further signal transduction, but the ultrastructural information of this process is virtually unknown. In order to clarify the relationship between the internalization of TrkA and the membrane-associated proteins (caveolin and clathrin), the localization and three-dimensional structures of those proteins were examined with computer tomography of high voltage electron microscopy in PC12 cells. TrkA immunoreactivity was found only at definite areas in the plasma membrane, as ring and cluster structures. Its 3D image indicated that those cluster structures contained small pits, which did not appear to be typical caveolae in size and shape. 3D images of clathrin and caveolin-1 immunoreactivities indicated that the formation of those small pits was associated with clathrin, but not with caveolin-1. Caveolin-1 immunoreactivity was found as a mesh-like structure just beneath the plasma membrane. These results suggest that clathrin rather than caveolin is mainly involved in the process of TrkA internalization, at least in differentiated PC12 cells

  9. Functional analysis of rare variants in mismatch repair proteins augments results from computation-based predictive methods

    Science.gov (United States)

    Arora, Sanjeevani; Huwe, Peter J.; Sikder, Rahmat; Shah, Manali; Browne, Amanda J.; Lesh, Randy; Nicolas, Emmanuelle; Deshpande, Sanat; Hall, Michael J.; Dunbrack, Roland L.; Golemis, Erica A.

    2017-01-01

    ABSTRACT The cancer-predisposing Lynch Syndrome (LS) arises from germline mutations in DNA mismatch repair (MMR) genes, predominantly MLH1, MSH2, MSH6, and PMS2. A major challenge for clinical diagnosis of LS is the frequent identification of variants of uncertain significance (VUS) in these genes, as it is often difficult to determine variant pathogenicity, particularly for missense variants. Generic programs such as SIFT and PolyPhen-2, and MMR gene-specific programs such as PON-MMR and MAPP-MMR, are often used to predict deleterious or neutral effects of VUS in MMR genes. We evaluated the performance of multiple predictive programs in the context of functional biologic data for 15 VUS in MLH1, MSH2, and PMS2. Using cell line models, we characterized VUS predicted to range from neutral to pathogenic on mRNA and protein expression, basal cellular viability, viability following treatment with a panel of DNA-damaging agents, and functionality in DNA damage response (DDR) signaling, benchmarking to wild-type MMR proteins. Our results suggest that the MMR gene-specific classifiers do not always align with the experimental phenotypes related to DDR. Our study highlights the importance of complementary experimental and computational assessment to develop future predictors for the assessment of VUS. PMID:28494185

  10. Computational study of elements of stability of a four-helix bundle protein biosurfactant

    Science.gov (United States)

    Schaller, Andrea; Connors, Natalie K.; Dwyer, Mirjana Dimitrijev; Oelmeier, Stefan A.; Hubbuch, Jürgen; Middelberg, Anton P. J.

    2015-01-01

    Biosurfactants are surface-active molecules produced principally by microorganisms. They are a sustainable alternative to chemically-synthesized surfactants, having the advantages of being non-toxic, highly functional, eco-friendly and biodegradable. However they are currently only used in a few industrial products due to costs associated with production and purification, which exceed those for commodity chemical surfactants. DAMP4, a member of a four-helix bundle biosurfactant protein family, can be produced in soluble form and at high yield in Escherichia coli, and can be recovered using a facile thermal phase-separation approach. As such, it encompasses an interesting synergy of biomolecular and chemical engineering with prospects for low-cost production even for industrial sectors. DAMP4 is highly functional, and due to its extraordinary thermal stability it can be purified in a simple two-step process, in which the combination of high temperature and salt leads to denaturation of all contaminants, whereas DAMP4 stays stable in solution and can be recovered by filtration. This study aimed to characterize and understand the fundamental drivers of DAMP4 stability to guide further process and surfactant design studies. The complementary use of experiments and molecular dynamics simulation revealed a broad pH and temperature tolerance for DAMP4, with a melting point of 122.4 °C, suggesting the hydrophobic core as the major contributor to thermal stability. Simulation of systematically created in silico variants of DAMP4 showed an influence of number and location of hydrophilic mutations in the hydrophobic core on stability, demonstrating a tolerance of up to three mutations before a strong loss in stability occurred. The results suggest a consideration of a balance of stability, functionality and kinetics for new designs according to their application, aiming for maximal functionality but at adequate stability to allow for cost-efficient production using thermal

  11. Detection of protease activity by fluorescent protein FRET sensors: from computer simulation to live cells

    Science.gov (United States)

    Goryashchenko, Alexander S.; Khrenova, Maria G.; Savitsky, Alexander P.

    2018-04-01

    Förster resonance energy transfer (FRET) sensors are widely used for the detection of protease activity in vitro and in vivo. Usually they consist of a FRET pair connected with a polypeptide linker containing a specific cleavage site for the relevant protease. Use of the fluorescent proteins as components of the FRET pair allows genetic encoding of such sensors and solves the problem of their delivery into live cells and animals. There are several ways to improve the properties of such sensors, mainly to increase FRET efficiency and therefore the dynamic range. One of the ways to achieve this is to use a non-fluorescent chromoprotein as an acceptor. Molecular dynamic simulations may assist in the construction of linker structures connecting donor and acceptor molecules. Estimation of the orientation factor κ 2 can be obtained by methods based on quantum theory and combined quantum mechanics/molecular mechanics approaches. The linker can be structured by hydrophobic interactions, bringing it into a closed conformation that shortens the distance between donor and acceptor and, consequently, increases FRET efficiency. We analyzed the effects of different linker structures on the detection of caspase-3 activity using a non-fluorescent acceptor. Also we have constructed the Tb3+- TagRFP sensor in which a complex of the terbium ion and terbium-binding peptide is used as a donor. This allowed us to use the unique property of lanthanide ions—fluorescence lifetime up to milliseconds—to perform measurements with time delay and exclude the nanosecond-order fluorescence. Using our systems as a starting point, by changing the recognition site in the linker it is possible to perform imaging of different protease activity in vitro or in vivo.

  12. Silicon as an anisotropic mechanical material

    DEFF Research Database (Denmark)

    Thomsen, Erik Vilain; Reck, Kasper; Skands, Gustav Erik

    2014-01-01

    While silicon is an anisotropic material it is often in literature treated as an isotropic material when it comes to plate calculations. This leads to considerable errors in the calculated deflection. To overcome this problem, we present an in-depth analysis of the bending behavior of thin crysta...... analytical models involving crystalline plates, such as those often found in the field of micro electro mechanical systems. The effect of elastic boundary conditions is taken into account by using an effective radius of the plate....

  13. Anisotropic perturbations due to dark energy

    International Nuclear Information System (INIS)

    Battye, Richard A.; Moss, Adam

    2006-01-01

    A variety of observational tests seem to suggest that the Universe is anisotropic. This is incompatible with the standard dogma based on adiabatic, rotationally invariant perturbations. We point out that this is a consequence of the standard decomposition of the stress-energy tensor for the cosmological fluids, and that rotational invariance need not be assumed, if there is elastic rigidity in the dark energy. The dark energy required to achieve this might be provided by point symmetric domain wall network with P/ρ=-2/3, although the concept is more general. We illustrate this with reference to a model with cubic symmetry and discuss various aspects of the model

  14. An approach to anisotropic cosmologies. 6

    International Nuclear Information System (INIS)

    Raychaudhuri, A.K.

    1989-01-01

    In this paper the motivation for the study of anisotropic cosmological models is set out. Then the mathematical basis for the study of such models as well as the description of some of the exact solutions of this genre are given. Killing vectors that spell out spacetime symmetries, are defined and the Bianchi classification of spacetimes based on the structure of the Killing vectors described. After a consideration of the kinematics of matter flow some of the known solutions are presented and their properties described. (author)

  15. The quantum cosmology of an anisotropic universe

    International Nuclear Information System (INIS)

    Duncan, M.J.; Jensen, L.G.

    1989-01-01

    Surveys of the microwave background indicate that the universe is isotropic to more than one part in 10 5 . Due to the arbitrariness of the initial conditions of the universe at the big bang singularity one cannot predict this; it is usually put in by hand. We therefore construct the quantum cosmology of an anisotropic universe according to the 'no-boundary' prescription of Hartle and Hawking. Such a model has a well-defined behavior at the classical singularity. We then show it also implies that a large universe, such as ours, is isotropic. (orig.)

  16. Quantum cosmology of an anisotropic universe

    Energy Technology Data Exchange (ETDEWEB)

    Duncan, M.J.; Jensen, L.G.

    1989-01-23

    Surveys of the microwave background indicate that the universe is isotropic to more than one part in 10/sup 5/. Due to the arbitrariness of the initial conditions of the universe at the big bang singularity one cannot predict this; it is usually put in by hand. We therefore construct the quantum cosmology of an anisotropic universe according to the 'no-boundary' prescription of Hartle and Hawking. Such a model has a well-defined behavior at the classical singularity. We then show it also implies that a large universe, such as ours, is isotropic.

  17. Critical state of anisotropic hard superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Romero-Salazar, C; Perez-RodrIguez, F [Instituto de FIsica, Universidad Autonoma de Puebla, Apdo Post J-48, Puebla, Pue 72570 (Mexico)

    2003-11-01

    The magnetic response of anisotropic irreversible type-II superconductors is investigated theoretically. Using an elliptic vertical law for the electric field E as a function of the current density J, we have reproduced available experimental magnetization curves of YBCO samples with the c axis lying in the sample plane. Specifically, we could reproduce quantitatively and interpret correctly the appearance of additional extrema and segments with relatively small slopes of the virgin magnetization curves when the direction of the applied magnetic field differs from the principal axes. The notable deformation of magnetization curves in a tilted magnetic field is connected to the strong coupling between the components of the magnetic induction.

  18. Generalised model for anisotropic 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, Uttar Pradesh (India); Ray, Saibal [Government College of Engineering and Ceramic Technology, Department of Physics, Kolkata, West Bengal (India); Deb, Debabrata [Indian Institute of Engineering Science and Technology, Shibpur, Department of Physics, Howrah, West Bengal (India)

    2016-12-15

    In the present investigation an exact generalised model for anisotropic compact stars of embedding class 1 is sought with a general relativistic background. The generic solutions are verified by exploring different physical aspects, viz. energy conditions, mass-radius relation, stability of the models, in connection to their validity. It is observed that the model presented here for compact stars is compatible with all these physical tests and thus physically acceptable as far as the compact star candidates RXJ 1856-37, SAX J 1808.4-3658 (SS1) and SAX J 1808.4-3658 (SS2) are concerned. (orig.)

  19. Many-dimensional anisotropic anharmonic oscillator

    International Nuclear Information System (INIS)

    Turbiner, A.V.

    1987-01-01

    Precision calculation of energies of several first states at d=2 and first 17 states at d=3 has been performed within the framework of a unique method based on ''nonlinearization'' method for d-dimension anisotropic an harmonic oscillator. Spectrum behaviour within the limit d → ∞ has been investigated and problems of the given approach accuracy have been studied. For the first time properties of nodal surfaces of the given task have been investigated. Routine perturbation theory in degrees of a perturbation parameter has been constructed for several first states

  20. Theory of Random Anisotropic Magnetic Alloys

    DEFF Research Database (Denmark)

    Lindgård, Per-Anker

    1976-01-01

    A mean-field-crystal-field theory is developed for random, multicomponent, anisotropic magnetic alloys. It is specially applicable to rare-earth alloys. A discussion is given of multicritical points and phase transitions between various states characterized by order parameters with different...... spatial directions or different ordering wave vectors. Theoretical predictions based on known parameters for the phase diagrams and magnetic moments for the binary rare-earth alloys of Tb, Dy, Ho, and Er, Tb-Tm, Nd-Pr, and pure double-hcp Nd agree qualitatively with the experimental observations...... fluctuation corrections in the mean-field results is also discussed....

  1. 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

  2. Local thermodynamics of a magnetized, anisotropic plasma

    International Nuclear Information System (INIS)

    Hazeltine, R. D.; Mahajan, S. M.; Morrison, P. J.

    2013-01-01

    An expression for the internal energy of a fluid element in a weakly coupled, magnetized, anisotropic plasma is derived from first principles. The result is a function of entropy, particle density and magnetic field, and as such plays the role of a thermodynamic potential: it determines in principle all thermodynamic properties of the fluid element. In particular it provides equations of state for the magnetized plasma. The derivation uses familiar fluid equations, a few elements of kinetic theory, the MHD version of Faraday's law, and certain familiar stability and regularity conditions.

  3. RELATIVISTIC CYCLOTRON INSTABILITY IN ANISOTROPIC PLASMAS

    Energy Technology Data Exchange (ETDEWEB)

    López, Rodrigo A.; Moya, Pablo S.; Muñoz, Víctor; Valdivia, J. Alejandro [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago (Chile); Navarro, Roberto E.; Araneda, Jaime A. [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Concepción, Casilla 160-C, Concepción (Chile); Viñas, Adolfo F., E-mail: rlopez186@gmail.com [NASA Goddard Space Flight Center, Heliophysics Science Division, Geospace Physics Laboratory, Mail Code 673, Greenbelt, MD 20771 (United States)

    2016-11-20

    A sufficiently large temperature anisotropy can sometimes drive various types of electromagnetic plasma micro-instabilities, which can play an important role in the dynamics of relativistic pair plasmas in space, astrophysics, and laboratory environments. Here, we provide a detailed description of the cyclotron instability of parallel propagating electromagnetic waves in relativistic pair plasmas on the basis of a relativistic anisotropic distribution function. Using plasma kinetic theory and particle-in-cell simulations, we study the influence of the relativistic temperature and the temperature anisotropy on the collective and noncollective modes of these plasmas. Growth rates and dispersion curves from the linear theory show a good agreement with simulations results.

  4. Creating an anisotropic plasma resistivity with waves

    International Nuclear Information System (INIS)

    Fisch, N.J.; Boozer, A.H.

    1980-05-01

    An anisotropic plasma resistivity may be created by preferential heating of electrons traveling in one direction. This can result in a steady-state toroidal current in a tokamak even in the absence of net wave momentum. In fact, at high wave phase velocities, the current associated with the change in resistivity is greater than that associated with net momentum input. An immediate implication is that other waves, such as electron cyclotron waves, may be competitive with lower-hybrid waves as a means for generating current. An analytical expression is derived for the current generated per power dissipated which agrees remarkably well with numerical calculations

  5. Analysis of anisotropic shells containing flowing fluid

    International Nuclear Information System (INIS)

    Lakis, A.A.

    1983-01-01

    A general theory for the dynamic analysis of anisotropic thin cylindrical shells containing flowing fluid is presented. The shell may be uniform or non-uniform, provided it is geometrically axially symmetric. This is a finite- element theory, using cylindrical finite elements, but the displacement functions are determined by using classical shell theory. A new solution of the wave equation of the liquid finite element leads to an expression of the fluid pressure, p, as a function of the nodal displacements of the element and three operative forces (inertia, centrifugal and Coriolis) of the moving fluid. (Author) [pt

  6. 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.

  7. 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)

  8. 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.

  9. 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.

  10. 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)

  11. Finite-difference schemes for anisotropic diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Es, Bram van, E-mail: es@cwi.nl [Centrum Wiskunde and Informatica, P.O. Box 94079, 1090GB Amsterdam (Netherlands); FOM Institute DIFFER, Dutch Institute for Fundamental Energy Research, Association EURATOM-FOM (Netherlands); Koren, Barry [Eindhoven University of Technology (Netherlands); Blank, Hugo J. de [FOM Institute DIFFER, Dutch Institute for Fundamental Energy Research, Association EURATOM-FOM (Netherlands)

    2014-09-01

    In fusion plasmas diffusion tensors are extremely anisotropic due to the high temperature and large magnetic field strength. This causes diffusion, heat conduction, and viscous momentum loss, to effectively be aligned with the magnetic field lines. This alignment leads to different values for the respective diffusive coefficients in the magnetic field direction and in the perpendicular direction, to the extent that heat diffusion coefficients can be up to 10{sup 12} times larger in the parallel direction than in the perpendicular direction. This anisotropy puts stringent requirements on the numerical methods used to approximate the MHD-equations since any misalignment of the grid may cause the perpendicular diffusion to be polluted by the numerical error in approximating the parallel diffusion. Currently the common approach is to apply magnetic field-aligned coordinates, an approach that automatically takes care of the directionality of the diffusive coefficients. This approach runs into problems at x-points and at points where there is magnetic re-connection, since this causes local non-alignment. It is therefore useful to consider numerical schemes that are tolerant to the misalignment of the grid with the magnetic field lines, both to improve existing methods and to help open the possibility of applying regular non-aligned grids. To investigate this, in this paper several discretization schemes are developed and applied to the anisotropic heat diffusion equation on a non-aligned grid.

  12. Anisotropic pressure and hyperons in neutron stars

    International Nuclear Information System (INIS)

    Sulaksono, A.

    2015-01-01

    We study the effects of anisotropic pressure (AI-P) on properties of the neutron stars (NSs) with hyperons inside its core within the framework of extended relativistic mean field. It is found that the main effects of AI-P on NS matter is to increase the stiffness of the equation of state EOS, which compensates for the softening of the EOS due to the hyperons. The maximum mass and redshift predictions of anisotropic neutron star with hyperonic core are quite compatible with the result of recent observational constraints if we use the parameter of AI-P model h ≤ 0.8 [L. Herrera and W. Barreto, Phys. Rev. D 88 (2013) 084022.] and Λ ≤ -1.15 [D. D. Doneva and S. S. Yazadjiev, Phys. Rev. D 85 (2012) 124023.]. The radius of the corresponding NS at M = 1.4 M ⊙ is more than 13 km, while the effect of AI-P on the minimum mass of NS is insignificant. Furthermore, due to the AI-P in the NS, the maximum mass limit of higher than 2.1 M ⊙ cannot rule out the presence of hyperons in the NS core. (author)

  13. Gravitomagnetic Instabilities in Anisotropically Expanding Fluids

    Science.gov (United States)

    Kleidis, Kostas; Kuiroukidis, Apostolos; Papadopoulos, Demetrios B.; Vlahos, Loukas

    Gravitational instabilities in a magnetized Friedman-Robertson-Walker (FRW) universe, in which the magnetic field was assumed to be too weak to destroy the isotropy of the model, are known and have been studied in the past. Accordingly, it became evident that the external magnetic field disfavors the perturbations' growth, suppressing the corresponding rate by an amount proportional to its strength. However, the spatial isotropy of the FRW universe is not compatible with the presence of large-scale magnetic fields. Therefore, in this paper we use the general-relativistic version of the (linearized) perturbed magnetohydrodynamic equations with and without resistivity, to discuss a generalized Jeans criterion and the potential formation of density condensations within a class of homogeneous and anisotropically expanding, self-gravitating, magnetized fluids in curved space-time. We find that, for a wide variety of anisotropic cosmological models, gravitomagnetic instabilities can lead to subhorizontal, magnetized condensations. In the nonresistive case, the power spectrum of the unstable cosmological perturbations suggests that most of the power is concentrated on large scales (small k), very close to the horizon. On the other hand, in a resistive medium, the critical wave-numbers so obtained, exhibit a delicate dependence on resistivity, resulting in the reduction of the corresponding Jeans lengths to smaller scales (well bellow the horizon) than the nonresistive ones, while increasing the range of cosmological models which admit such an instability.

  14. Electrically Anisotropic Layered Perovskite Single Crystal

    KAUST Repository

    Li, Ting-You

    2016-04-01

    Organic-inorganic hybrid perovskites (OIHPs), which are promising materials for electronic and optoelectronic applications (1-10), have made into layered organic-inorganic hybrid perovskites (LOIHPs). These LOIHPs have been applied to thin-film transistors, solar cells and tunable wavelength phosphors (11-18). It is known that devices fabricated with single crystal exhibit the superior performance, which makes the growth of large-sized single crystals critical for future device applications (19-23). However, the difficulty in growing large-sized LOIHPs single crystal with superior electrical properties limits their practical applications. Here, we report a method to grow the centimeter-scaled LOIHP single crystal of [(HOC2H4NH3)2PbI4], demonstrating the potentials in mass production. After that, we reveal anisotropic electrical and optoelectronic properties which proved the carrier propagating along inorganic framework. The carrier mobility of in-inorganic-plane (in-plane) devices shows the average value of 45 cm2 V–1 s–1 which is about 100 times greater than the record of LOIHP devices (15), showing the importance of single crystal in device application. Moreover, the LOIHP single crystals show its ultra-short carrier lifetime of 42.7 ps and photoluminescence quantum efficiency (PLQE) of 25.4 %. We expect this report to be a start of LOIHPs for advanced applications in which the anisotropic properties are needed (24-25), and meets the demand of high-speed applications and fast-response applications.

  15. The Effective Coherence Length in Anisotropic Superconductors

    International Nuclear Information System (INIS)

    Polturak, E.; Koren, G.; Nesher, O

    1999-01-01

    If electrons are transmitted from a normal conductor(N) into a superconductor(S), common wisdom has it that the electrons are converted into Cooper pairs within a coherence length from the interface. This is true in conventional superconductors with an isotropic order parameter. We have established experimentally that the situation is rather different in high Tc superconductors having an anisotropic order parameter. We used epitaxial thin film S/N bilayers having different interface orientations in order to inject carriers from S into N along different directions. The distance to which these carriers penetrate were determined through their effect on the Tc of the bilayers. We found that the effective coherence length is 20A only along the a or b directions, while in other directions we find a length of 250dr20A out of plane, and an even larger value for in-plane, off high symmetry directions. These observations can be explained using the Blonder-Tinkham-Klapwijk model adapted to anisotropic superconductivity. Several implications of our results on outstanding problems with high Tc junctions will be discussed

  16. Lyotropic Liquid Crystal Phases from Anisotropic Nanomaterials

    Directory of Open Access Journals (Sweden)

    Ingo Dierking

    2017-10-01

    Full Text Available Liquid crystals are an integral part of a mature display technology, also establishing themselves in other applications, such as spatial light modulators, telecommunication technology, photonics, or sensors, just to name a few of the non-display applications. In recent years, there has been an increasing trend to add various nanomaterials to liquid crystals, which is motivated by several aspects of materials development. (i addition of nanomaterials can change and thus tune the properties of the liquid crystal; (ii novel functionalities can be added to the liquid crystal; and (iii the self-organization of the liquid crystalline state can be exploited to template ordered structures or to transfer order onto dispersed nanomaterials. Much of the research effort has been concentrated on thermotropic systems, which change order as a function of temperature. Here we review the other side of the medal, the formation and properties of ordered, anisotropic fluid phases, liquid crystals, by addition of shape-anisotropic nanomaterials to isotropic liquids. Several classes of materials will be discussed, inorganic and mineral liquid crystals, viruses, nanotubes and nanorods, as well as graphene oxide.

  17. Scaling Argument of Anisotropic Random Walk

    International Nuclear Information System (INIS)

    Xu Bingzhen; Jin Guojun; Wang Feifeng

    2005-01-01

    In this paper, we analytically discuss the scaling properties of the average square end-to-end distance (R 2 ) for anisotropic random walk in D-dimensional space (D≥2), and the returning probability P n (r 0 ) for the walker into a certain neighborhood of the origin. We will not only give the calculating formula for (R 2 ) and P n (r 0 ), but also point out that if there is a symmetric axis for the distribution of the probability density of a single step displacement, we always obtain (R p erpendicular n 2 )∼n, where perpendicular refers to the projections of the displacement perpendicular to each symmetric axes of the walk; in D-dimensional space with D symmetric axes perpendicular to each other, we always have (R n 2 )∼n and the random walk will be like a purely random motion; if the number of inter-perpendicular symmetric axis is smaller than the dimensions of the space, we must have (R n 2 )∼n 2 for very large n and the walk will be like a ballistic motion. It is worth while to point out that unlike the isotropic random walk in one and two dimensions, which is certain to return into the neighborhood of the origin, generally there is only a nonzero probability for the anisotropic random walker in two dimensions to return to the neighborhood.

  18. 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.

  19. 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

  20. Making of Magnet Barium Ferit Anisotropic

    International Nuclear Information System (INIS)

    Idayati, Novrita; Dedi

    2003-01-01

    Barium Hexa ferrite (BaFe 12 O 19 ) is ceramic and materials which usually used for making of permanent magnet. In this research Barium Hexa ferrite were made Anisotropic, and applied for loudspeaker, electro motors, dynamo, KWh metre, etc. this Magnet is commonly used due to its high Induction of Remanen (Br) and coercivity (high Hc). Besides it applies a more simple and easier process technology, cheaper raw material, and easy to find it, hence the magnetic component is much cheaper. Powder Metallurgy was used for the process technology, by reacting all materials in the powder (oxide), with a certain size distribution and a tight preparation step. The next step was mixing ferrite and Barium Carbonate (in the form of oxide), calcination, compaction, cantering and characterisation. The Anisotropic particle effects a high Induce Remanen (Br) and of koersifitas (high Hc). All the process steps will is determine physical and chemical characteristics of the magnet. The best Magnet characteristic of the magnet produced in this research is Induction of Remanen (Br) = 4,27 kg, Coercivity (Hc) = 1,745 kOe, Energy Product max (BHmaks) = 2,31 MGOe

  1. Relativistic model for anisotropic strange stars

    Science.gov (United States)

    Deb, Debabrata; Chowdhury, Sourav Roy; Ray, Saibal; Rahaman, Farook; Guha, B. K.

    2017-12-01

    In this article, we attempt to find a singularity free solution of Einstein's field equations for compact stellar objects, precisely strange (quark) stars, considering Schwarzschild metric as the exterior spacetime. To this end, we consider that the stellar object is spherically symmetric, static and anisotropic in nature and follows the density profile given by Mak and Harko (2002) , which satisfies all the physical conditions. To investigate different properties of the ultra-dense strange stars we have employed the MIT bag model for the quark matter. Our investigation displays an interesting feature that the anisotropy of compact stars increases with the radial coordinate and attains its maximum value at the surface which seems an inherent property for the singularity free anisotropic compact stellar objects. In this connection we also perform several tests for physical features of the proposed model and show that these are reasonably acceptable within certain range. Further, we find that the model is consistent with the energy conditions and the compact stellar structure is stable with the validity of the TOV equation and Herrera cracking concept. For the masses below the maximum mass point in mass vs radius curve the typical behavior achieved within the framework of general relativity. We have calculated the maximum mass and radius of the strange stars for the three finite values of bag constant Bg.

  2. Building an Anisotropic Meniscus with Zonal Variations

    Science.gov (United States)

    Higashioka, Michael M.; Chen, Justin A.; Hu, Jerry C.

    2014-01-01

    Toward addressing the difficult problems of knee meniscus regeneration, a self-assembling process has been used to re-create the native morphology and matrix properties. A significant problem in such attempts is the recapitulation of the distinct zones of the meniscus, the inner, more cartilaginous and the outer, more fibrocartilaginous zones. In this study, an anisotropic and zonally variant meniscus was produced by self-assembly of the inner meniscus (100% chondrocytes) followed by cell seeding the outer meniscus (coculture of chondrocytes and meniscus cells). After 4 weeks in culture, the engineered, inner meniscus exhibited a 42% increase in both instantaneous and relaxation moduli and a 62% increase in GAG/DW, as compared to the outer meniscus. In contrast, the circumferential tensile modulus and collagen/DW of the outer zone was 101% and 129% higher, respectively, than the values measured for the inner zone. Furthermore, there was no difference in the radial tensile modulus between the control and zonal engineered menisci, suggesting that the inner and outer zones of the engineered zonal menisci successfully integrated. These data demonstrate that not only can biomechanical and biochemical properties be engineered to differ by the zone, but they can also recapitulate the anisotropic behavior of the knee meniscus. PMID:23931258

  3. 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.

  4. Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins

    Czech Academy of Sciences Publication Activity Database

    Palani, K.; Pfeiferová, L.; Boušová, Kristýna; Bednárová, L.; Obšilová, Veronika; Vondrášek, J.

    2016-01-01

    Roč. 84, č. 10 (2016), s. 1358-1374 ISSN 0887-3585 Institutional support: RVO:67985823 Keywords : protein design * fusion proteins * PDZ3 * SH3 * Trp-cage * two domain proteins * molecular dynamics simulation * circular dichroism Subject RIV: BO - Biophysics Impact factor: 2.289, year: 2016

  5. Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins

    Czech Academy of Sciences Publication Activity Database

    Palani, Kirubakaran; Pfeiferová, Lucie; Boušová, Kristýna; Bednárová, Lucie; Obšilová, V.; Vondrášek, Jiří

    2016-01-01

    Roč. 84, č. 10 (2016), s. 1358-1374 ISSN 0887-3585 Institutional support: RVO:61388963 Keywords : protein design * fusion proteins * PDZ3 * SH3 * Trp-cage * two domain proteins Subject RIV: CE - Biochemistry Impact factor: 2.289, year: 2016

  6. 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...

  7. 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.

  8. 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

  9. 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)

  10. 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.

  11. Using the Computer Game "FoldIt" to Entice Students to Explore External Representations of Protein Structure in a Biochemistry Course for Nonmajors

    Science.gov (United States)

    Farley, Peter C.

    2013-01-01

    This article describes a novel approach to teaching novice Biochemistry students visual literacy skills and understanding of some aspects of protein structure using the internet resource FoldIt and a worksheet based on selected Introductory Puzzles from this computer game. In responding to a questionnaire, students indicated that they (94%)…

  12. 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

  13. 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

  14. Anisotropic gradients in the upper mantle

    International Nuclear Information System (INIS)

    Garmany, J.

    1981-01-01

    Pn amplitudes in some widely spaced sets of orthogonal marine refraction lines on young oceanic crust are greater in the fast direction than in the slow direction. This is inconsistent with the predicted amplitude behavior for simple head waves, but can be explained by an increase in anisotropy with depth. It appears that these gradients are due to increasing olivine crystal orientation, although changes in the relative abundance of two anisotropic minerals without variable tectonization could also account for the observations. Depth variation of tectonization most probably indicates very high temperature gradients at the Moho. This would imply a substantial amount of convective heat transport in the whole oceanic crust near mid-ocean rises

  15. Long-range interaction of anisotropic systems

    KAUST Repository

    Zhang, Junyi

    2015-02-01

    The first-order electrostatic interaction energy between two far-apart anisotropic atoms depends not only on the distance between them but also on their relative orientation, according to Rayleigh-Schrödinger perturbation theory. Using the first-order interaction energy and the continuum model, we study the long-range interaction between a pair of parallel pristine graphene sheets at zero temperature. The asymptotic form of the obtained potential density, &epsi:(D) &prop: ?D ?3 ?O(D?4), is consistent with the random phase approximation and Lifshitz theory. Accordingly, neglectance of the anisotropy, especially the nonzero first-order interaction energy, is the reason why the widely used Lennard-Jones potential approach and dispersion corrections in density functional theory give a wrong asymptotic form ε(D) &prop: ?D?4. © EPLA, 2015.

  16. Spectral functions from anisotropic lattice QCD

    Energy Technology Data Exchange (ETDEWEB)

    Aarts, G.; Allton, C. [Department of Physics, Swansea University, Swansea SA2 8PP, Wales (United Kingdom); Amato, A. [Helsinki Institute of Physics and University of Helsinki, Helsinki (Finland); Evans, W. [Albert Einstein Center for Fundamental Physics, Institute for Theoretical Physics Universitat Bern, Sidlerstrasse 5, CH-3012 Bern (Switzerland); Giudice, P. [Institut für Theoretische Physik, Universität Münster, D–48149 Münster (Germany); Harris, T. [School of Mathematics, Trinity College, Dublin 2 (Ireland); Kelly, A. [Department of Mathematical Physics, Maynooth University, Maynooth, Co Kildare (Ireland); Kim, S.Y. [Department of Physics, Sejong University, Seoul 143-747 (Korea, Republic of); Lombardo, M.P. [INFN–Laboratori Nazionali di Frascati, I–00044 Frascati (RM) (Italy); Praki, K. [Department of Physics, Swansea University, Swansea SA2 8PP, Wales (United Kingdom); Ryan, S.M. [School of Mathematics, Trinity College, Dublin 2 (Ireland); Skullerud, J.-I. [Department of Mathematical Physics, Maynooth University, Maynooth, Co Kildare (Ireland)

    2016-12-15

    The FASTSUM collaboration has been carrying out lattice simulations of QCD for temperatures ranging from one third to twice the crossover temperature, investigating the transition region, as well as the properties of the Quark Gluon Plasma. In this contribution we concentrate on quarkonium correlators and spectral functions. We work in a fixed scale scheme and use anisotropic lattices which help achieving the desirable fine resolution in the temporal direction, thus facilitating the (ill posed) integral transform from imaginary time to frequency space. We contrast and compare results for the correlators obtained with different methods, and different temporal spacings. We observe robust features of the results, confirming the sequential dissociation scenario, but also quantitative differences indicating that the methods' systematic errors are not yet under full control. We briefly outline future steps towards accurate results for the spectral functions and their associated statistical and systematic errors.

  17. Long-range interaction of anisotropic systems

    KAUST Repository

    Zhang, Junyi; Schwingenschlö gl, Udo

    2015-01-01

    The first-order electrostatic interaction energy between two far-apart anisotropic atoms depends not only on the distance between them but also on their relative orientation, according to Rayleigh-Schrödinger perturbation theory. Using the first-order interaction energy and the continuum model, we study the long-range interaction between a pair of parallel pristine graphene sheets at zero temperature. The asymptotic form of the obtained potential density, &epsi:(D) &prop: ?D ?3 ?O(D?4), is consistent with the random phase approximation and Lifshitz theory. Accordingly, neglectance of the anisotropy, especially the nonzero first-order interaction energy, is the reason why the widely used Lennard-Jones potential approach and dispersion corrections in density functional theory give a wrong asymptotic form ε(D) &prop: ?D?4. © EPLA, 2015.

  18. Inverse anisotropic conductivity from internal current densities

    International Nuclear Information System (INIS)

    Bal, Guillaume; Guo, Chenxi; Monard, François

    2014-01-01

    This paper concerns the reconstruction of a fully anisotropic conductivity tensor γ from internal current densities of the form J = γ∇u, where u solves a second-order elliptic equation ∇ · (γ∇u) = 0 on a bounded domain X with prescribed boundary conditions. A minimum number of n + 2 such functionals known on Y⊂X, where n is the spatial dimension, is sufficient to guarantee a unique and explicit reconstruction of γ locally on Y. Moreover, we show that γ is reconstructed with a loss of one derivative compared to errors in the measurement of J in the general case and no loss of derivatives in the special case where γ is scalar. We also describe linear combinations of mixed partial derivatives of γ that exhibit better stability properties and hence can be reconstructed with better resolution in practice. (paper)

  19. Stability of anisotropic beams with space charge

    International Nuclear Information System (INIS)

    Hofmann, I.

    1997-07-01

    We calculate coherent frequencies and stability properties of anisotropic or ''non-equipartitioned'' beams with different focusing constants and emittances in the two transverse directions. Based on the self-consistent Vlasov-Poisson equations the dispersion relations of transverse multipole oscillations with quadrupolar, sextupolar and octupolar symmetry are solved numerically. The eigenfrequencies give the coherent space charge tune shift for linear or nonlinear resonances in circular accelerators. We find that for sufficiently large energy anisotropy some of the eigenmodes become unstable in the space-charge-dominated regime. The properties of these anisotropy instabilities are used to show that ''non-equipartitioned'' beams can be tolerated in high-current linear accelerators. It is only in beams with strongly space-charge-depressed betatron tunes where harmful instabilities leading to emittance exchange should be expected. (orig.)

  20. Anisotropic thermal expansion in flexible materials

    Science.gov (United States)

    Romao, Carl P.

    2017-10-01

    A definition of the Grüneisen parameters for anisotropic materials is derived based on the response of phonon frequencies to uniaxial stress perturbations. This Grüneisen model relates the thermal expansion in a given direction (αi i) to one element of the elastic compliance tensor, which corresponds to the Young's modulus in that direction (Yi i). The model is tested through ab initio prediction of thermal expansion in zinc, graphite, and calcite using density functional perturbation theory, indicating that it could lead to increased accuracy for structurally complex systems. The direct dependence of αi i on Yi i suggests that materials which are flexible along their principal axes but rigid in other directions will generally display both positive and negative thermal expansion.

  1. Effective stress law for anisotropic elastic deformation

    International Nuclear Information System (INIS)

    Carroll, M.M.

    1979-01-01

    An effective stress law is derived analytically to describe the effect of pore fluid pressure on the linearly elastic response of saturated porous rocks which exhibit anisotropy. For general anisotropy the difference between the effective stress and the applied stress is not hydrostatic. The effective stress law involves two constants for transversely isotropic response and three constants for orthotropic response; these constants can be expressed in terms of the moduli of the porous material and of the solid material. These expressions simplify considerably when the anisotropy is structural rather than intrinsic, i.e., in the case of an isotropic solid material with an anisotropic pore structure. In this case the effective stress law involves the solid or grain bulk modulus and two or three moduli of the porous material, for transverse isotropy and orthotropy, respectively. The law reduces, in the case of isotropic response, to that suggested by Geertsma (1957) and by Skempton (1961) and derived analytically by Nur and Byerlee

  2. Analytical study of anisotropic compact star models

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, B.V. [Bulgarian Academy of Science, Institute for Nuclear Research and Nuclear Energy, Sofia (Bulgaria)

    2017-11-15

    A simple classification is given of the anisotropic relativistic star models, resembling the one of charged isotropic solutions. On the ground of this database, and taking into account the conditions for physically realistic star models, a method is proposed for generating all such solutions. It is based on the energy density and the radial pressure as seeding functions. Numerous relations between the realistic conditions are found and the need for a graphic proof is reduced just to one pair of inequalities. This general formalism is illustrated with an example of a class of solutions with linear equation of state and simple energy density. It is found that the solutions depend on three free constants and concrete examples are given. Some other popular models are studied with the same method. (orig.)

  3. Derivation of the optical constants of anisotropic

    Science.gov (United States)

    Aronson, J. R.; Emslie, A. G.; Smith, E. M.; Strong, P. F.

    1985-07-01

    This report concerns the development of methods for obtaining the optical constants of anisotropic crystals of the triclinic and monoclinic systems. The principal method used, classical dispersion theory, is adapted to these crystal systems by extending the Lorentz line parameters to include the angles characterizing the individual resonances, and by replacing the dielectric constant by a dielectric tensor. The sample crystals are gypsium, orthoclase and chalcanthite. The derived optical constants are shown to be suitable for modeling the optical properties of particulate media in the infrared spectral region. For those materials where suitable size single crystals are not available, an extension of a previously used method is applied to alabaster, a polycrystalline material of the monoclinic crystal system.

  4. Anisotropic dynamic mass density for fluidsolid composites

    KAUST Repository

    Wu, Ying

    2012-10-01

    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-dependent dipole solution, to the leading-order of solid concentration. The angular dependence vanishes for the square lattice, but at high solid concentrations there is a structure-dependent factor that contributes to the leading-order solution. In all cases, Woods formula is found to be accurately valid for the effective bulk modulus, independent of the structures. Numerical evaluations from the solutions are shown to be in excellent agreement with finite-element simulations. © 2012 Elsevier B.V.

  5. An Anisotropic Hardening Model for Springback Prediction

    Science.gov (United States)

    Zeng, Danielle; Xia, Z. Cedric

    2005-08-01

    As more Advanced High-Strength Steels (AHSS) are heavily used for automotive body structures and closures panels, accurate springback prediction for these components becomes more challenging because of their rapid hardening characteristics and ability to sustain even higher stresses. In this paper, a modified Mroz hardening model is proposed to capture realistic Bauschinger effect at reverse loading, such as when material passes through die radii or drawbead during sheet metal forming process. This model accounts for material anisotropic yield surface and nonlinear isotropic/kinematic hardening behavior. Material tension/compression test data are used to accurately represent Bauschinger effect. The effectiveness of the model is demonstrated by comparison of numerical and experimental springback results for a DP600 straight U-channel test.

  6. An Anisotropic Hardening Model for Springback Prediction

    International Nuclear Information System (INIS)

    Zeng, Danielle; Xia, Z. Cedric

    2005-01-01

    As more Advanced High-Strength Steels (AHSS) are heavily used for automotive body structures and closures panels, accurate springback prediction for these components becomes more challenging because of their rapid hardening characteristics and ability to sustain even higher stresses. In this paper, a modified Mroz hardening model is proposed to capture realistic Bauschinger effect at reverse loading, such as when material passes through die radii or drawbead during sheet metal forming process. This model accounts for material anisotropic yield surface and nonlinear isotropic/kinematic hardening behavior. Material tension/compression test data are used to accurately represent Bauschinger effect. The effectiveness of the model is demonstrated by comparison of numerical and experimental springback results for a DP600 straight U-channel test

  7. Anisotropic magnetism in field-structured composites

    International Nuclear Information System (INIS)

    Martin, James E.; Venturini, Eugene; Odinek, Judy; Anderson, Robert A.

    2000-01-01

    Magnetic field-structured composites (FSCs) are made by structuring magnetic particle suspensions in uniaxial or biaxial (e.g., rotating) magnetic fields, while polymerizing the suspending resin. A uniaxial field produces chainlike particle structures, and a biaxial field produces sheetlike particle structures. In either case, these anisotropic structures affect the measured magnetic hysteresis loops, with the magnetic remanence and susceptibility increased significantly along the axis of the structuring field, and decreased slightly orthogonal to the structuring field, relative to the unstructured particle composite. The coercivity is essentially unaffected by structuring. We present data for FSCs of magnetically soft particles, and demonstrate that the altered magnetism can be accounted for by considering the large local fields that occur in FSCs. FSCs of magnetically hard particles show unexpectedly large anisotropies in the remanence, and this is due to the local field effects in combination with the large crystalline anisotropy of this material. (c) 2000 The American Physical Society

  8. Isotropic and anisotropic surface wave cloaking techniques

    International Nuclear Information System (INIS)

    McManus, T M; Spada, L La; Hao, Y

    2016-01-01

    In this paper we compare two different approaches for surface waves cloaking. The first technique is a unique application of Fermat’s principle and requires isotropic material properties, but owing to its derivation is limited in its applicability. The second technique utilises a geometrical optics approximation for dealing with rays bound to a two dimensional surface and requires anisotropic material properties, though it can be used to cloak any smooth surface. We analytically derive the surface wave scattering behaviour for both cloak techniques when applied to a rotationally symmetric surface deformation. Furthermore, we simulate both using a commercially available full-wave electromagnetic solver and demonstrate a good level of agreement with their analytically derived solutions. Our analytical solutions and simulations provide a complete and concise overview of two different surface wave cloaking techniques. (paper)

  9. Isotropic and anisotropic surface wave cloaking techniques

    Science.gov (United States)

    McManus, T. M.; La Spada, L.; Hao, Y.

    2016-04-01

    In this paper we compare two different approaches for surface waves cloaking. The first technique is a unique application of Fermat’s principle and requires isotropic material properties, but owing to its derivation is limited in its applicability. The second technique utilises a geometrical optics approximation for dealing with rays bound to a two dimensional surface and requires anisotropic material properties, though it can be used to cloak any smooth surface. We analytically derive the surface wave scattering behaviour for both cloak techniques when applied to a rotationally symmetric surface deformation. Furthermore, we simulate both using a commercially available full-wave electromagnetic solver and demonstrate a good level of agreement with their analytically derived solutions. Our analytical solutions and simulations provide a complete and concise overview of two different surface wave cloaking techniques.

  10. Recent developments in anisotropic heterogeneous shell theory

    CERN Document Server

    Grigorenko, Alexander Ya; Grigorenko, Yaroslav M; Vlaikov, Georgii G

    2016-01-01

    This volume focuses on the relevant general theory and presents some first applications, namely those based on classical shell theory. After a brief introduction, during which the history and state-of-the-art are discussed, the first chapter presents the mechanics of anisotropic heterogeneous shells, covering all relevant assumptions and the basic relations of 3D elasticity, classical and refined shell models. The second chapter examines the numerical techniques that are used, namely discrete orthogonalization, spline-collocation and Fourier series, while the third highlights applications based on classical theory, in particular, the stress-strain state of shallow shells, non-circular shells, shells of revolution, and free vibrations of conical shells. The book concludes with a summary and an outlook bridging the gap to the second volume.

  11. Measuring anisotropic muscle stiffness properties using elastography.

    Science.gov (United States)

    Green, M A; Geng, G; Qin, E; Sinkus, R; Gandevia, S C; Bilston, L E

    2013-11-01

    Physiological and pathological changes to the anisotropic mechanical properties of skeletal muscle are still largely unknown, with only a few studies quantifying changes in vivo. This study used the noninvasive MR elastography (MRE) technique, in combination with diffusion tensor imaging (DTI), to measure shear modulus anisotropy in the human skeletal muscle in the lower leg. Shear modulus measurements parallel and perpendicular to the fibre direction were made in 10 healthy subjects in the medial gastrocnemius, soleus and tibialis anterior muscles. The results showed significant differences in the medial gastrocnemius (μ‖ = 0.86 ± 0.15 kPa; μ⊥ = 0.66 ± 0.19 kPa, P < 0.001), soleus (μ‖ = 0.83 ± 0.22 kPa; μ⊥ = 0.65 ± 0.13 kPa, P < 0.001) and the tibialis anterior (μ‖ = 0.78 ± 0.24 kPa; μ⊥ = 0.66 ± 0.16 kPa, P = 0.03) muscles, where the shear modulus measured in the direction parallel is greater than that measured in the direction perpendicular to the muscle fibres. No significant differences were measured across muscle groups. This study provides the first direct estimates of the anisotropic shear modulus in the triceps surae muscle group, and shows that the technique may be useful for the probing of mechanical anisotropy changes caused by disease, aging and injury. Copyright © 2013 John Wiley & Sons, Ltd.

  12. Radial stability of anisotropic strange quark stars

    Energy Technology Data Exchange (ETDEWEB)

    Arbañil, José D.V.; Malheiro, M., E-mail: jose.arbanil@upn.pe, E-mail: malheiro@ita.br [ITA—Instituto Tecnológico de Aeronáutica—Departamento de Física, 12228-900, São José dos Campos, São Paulo (Brazil)

    2016-11-01

    The influence of the anisotropy in the equilibrium and stability of strange stars is investigated through the numerical solution of the hydrostatic equilibrium equation and the radial oscillation equation, both modified from their original version to include this effect. The strange matter inside the quark stars is described by the MIT bag model equation of state. For the anisotropy two different kinds of local anisotropic σ = p {sub t} − p {sub r} are considered, where p {sub t} and p {sub r} are respectively the tangential and the radial pressure: one that is null at the star's surface defined by p {sub r} ( R ) = 0, and one that is nonnull at the surface, namely, σ {sub s} = 0 and σ {sub s} {sub ≠} {sub 0}. In the case σ {sub s} = 0, the maximum mass value and the zero frequency of oscillation are found at the same central energy density, indicating that the maximum mass marks the onset of the instability. For the case σ {sub s} {sub ≠} {sub 0}, we show that the maximum mass point and the zero frequency of oscillation coincide in the same central energy density value only in a sequence of equilibrium configurations with the same value of σ {sub s} . Thus, the stability star regions are determined always by the condition dM / d ρ {sub c} {sub >} {sub 0} only when the tangential pressure is maintained fixed at the star surface's p {sub t} ( R ). These results are also quite important to analyze the stability of other anisotropic compact objects such as neutron stars, boson stars and gravastars.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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).

  19. Anisotropic properties of the enamel organic extracellular matrix.

    Science.gov (United States)

    do Espírito Santo, Alexandre R; Novaes, Pedro D; Line, Sérgio R P

    2006-05-01

    Enamel biosynthesis is initiated by the secretion, processing, and self-assembly of a complex mixture of proteins. This supramolecular ensemble controls the nucleation of the crystalline mineral phase. The detection of anisotropic properties by polarizing microscopy has been extensively used to detect macromolecular organizations in ordinary histological sections. The aim of this work was to study the birefringence of enamel organic matrix during the development of rat molar and incisor teeth. Incisor and molar teeth of rats were fixed in 2% paraformaldehyde/0.5% glutaraldehyde in 0.2 M phosphate-buffered saline (PBS), pH 7.2, and decalcified in 5% nitric acid/4% formaldehyde. After paraffin embedding, 5-microm-thick sections were obtained, treated with xylene, and hydrated. Form birefringence curves were obtained after measuring optical retardations in imbibing media, with different refractive indices. Our observations showed that enamel organic matrix of rat incisor and molar teeth is strongly birefringent, presenting an ordered supramolecular structure. The birefringence starts during the early secretion phase and disappears at the maturation phase. The analysis of enamel organic matrix birefringence may be used to detect the effects of genetic and environmental factors on the supramolecular orientation of enamel matrix and their effects on the structure of mature enamel.

  20. Noise-induced drift in two-dimensional anisotropic systems

    Science.gov (United States)

    Farago, Oded

    2017-10-01

    We study the isothermal Brownian dynamics of a particle in a system with spatially varying diffusivity. Due to the heterogeneity of the system, the particle's mean displacement does not vanish even if it does not experience any physical force. This phenomenon has been termed "noise-induced drift," and has been extensively studied for one-dimensional systems. Here, we examine the noise-induced drift in a two-dimensional anisotropic system, characterized by a symmetric diffusion tensor with unequal diagonal elements. A general expression for the mean displacement vector is derived and presented as a sum of two vectors, depicting two distinct drifting effects. The first vector describes the tendency of the particle to drift toward the high diffusivity side in each orthogonal principal diffusion direction. This is a generalization of the well-known expression for the noise-induced drift in one-dimensional systems. The second vector represents a novel drifting effect, not found in one-dimensional systems, originating from the spatial rotation in the directions of the principal axes. The validity of the derived expressions is verified by using Langevin dynamics simulations. As a specific example, we consider the relative diffusion of two transmembrane proteins, and demonstrate that the average distance between them increases at a surprisingly fast rate of several tens of micrometers per second.

  1. Computational study on the inhibitor binding mode and allosteric regulation mechanism in hepatitis C virus NS3/4A protein.

    Directory of Open Access Journals (Sweden)

    Weiwei Xue

    Full Text Available HCV NS3/4A protein is an attractive therapeutic target responsible for harboring serine protease and RNA helicase activities during the viral replication. Small molecules binding at the interface between the protease and helicase domains can stabilize the closed conformation of the protein and thus block the catalytic function of HCV NS3/4A protein via an allosteric regulation mechanism. But the detailed mechanism remains elusive. Here, we aimed to provide some insight into the inhibitor binding mode and allosteric regulation mechanism of HCV NS3/4A protein by using computational methods. Four simulation systems were investigated. They include: apo state of HCV NS3/4A protein, HCV NS3/4A protein in complex with an allosteric inhibitor and the truncated form of the above two systems. The molecular dynamics simulation results indicate HCV NS3/4A protein in complex with the allosteric inhibitor 4VA adopts a closed conformation (inactive state, while the truncated apo protein adopts an open conformation (active state. Further residue interaction network analysis suggests the communication of the domain-domain interface play an important role in the transition from closed to open conformation of HCV NS3/4A protein. However, the inhibitor stabilizes the closed conformation through interaction with several key residues from both the protease and helicase domains, including His57, Asp79, Asp81, Asp168, Met485, Cys525 and Asp527, which blocks the information communication between the functional domains interface. Finally, a dynamic model about the allosteric regulation and conformational changes of HCV NS3/4A protein was proposed and could provide fundamental insights into the allosteric mechanism of HCV NS3/4A protein function regulation and design of new potent inhibitors.

  2. 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.

  3. FDTD modeling of anisotropic nonlinear optical phenomena in silicon waveguides.

    Science.gov (United States)

    Dissanayake, Chethiya M; Premaratne, Malin; Rukhlenko, Ivan D; Agrawal, Govind P

    2010-09-27

    A deep insight into the inherent anisotropic optical properties of silicon is required to improve the performance of silicon-waveguide-based photonic devices. It may also lead to novel device concepts and substantially extend the capabilities of silicon photonics in the future. In this paper, for the first time to the best of our knowledge, we present a three-dimensional finite-difference time-domain (FDTD) method for modeling optical phenomena in silicon waveguides, which takes into account fully the anisotropy of the third-order electronic and Raman susceptibilities. We show that, under certain realistic conditions that prevent generation of the longitudinal optical field inside the waveguide, this model is considerably simplified and can be represented by a computationally efficient algorithm, suitable for numerical analysis of complex polarization effects. To demonstrate the versatility of our model, we study polarization dependence for several nonlinear effects, including self-phase modulation, cross-phase modulation, and stimulated Raman scattering. Our FDTD model provides a basis for a full-blown numerical simulator that is restricted neither by the single-mode assumption nor by the slowly varying envelope approximation.

  4. 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

  5. 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%

  6. 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%.

  7. 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.

  8. 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.

  9. Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers.

    Science.gov (United States)

    Gunasekaran, K; Gomathi, L; Ramakrishnan, C; Chandrasekhar, J; Balaram, P

    1998-12-18

    The two most important beta-turn features in peptides and proteins are the type I and type II turns, which differ mainly in the orientation of the central peptide unit. Facile conformational interconversion is possible, in principle, by a flip of the central peptide unit. Homologous crystal structures afford an opportunity to structurally characterize both possible conformational states, thus allowing identification of sites that are potentially stereochemically mobile. A representative data set of 250 high-resolution (turns that are assigned different conformational types (type I/type II) in related structures. A total of 55 examples of beta-turns were identified as possible candidates for a stereochemically mobile site. Of the 55 examples, 45 could be classified as a potential site for interconversion between type I and type II beta-turns, while ten correspond to flips from type I' to type II' structures. As a further check, the temperature factors of the central peptide unit carbonyl oxygen atom of the 55 examples were examined. The analysis reveals that the turn assignments are indeed reliable. Examination of the secondary structures at the flanking positions of the flippable beta-turns reveals that seven examples occur in the loop region of beta-hairpins, indicating that the formation of ordered secondary structures on either side of the beta-turn does not preclude local conformational variations. In these beta-turns, Pro (11 examples), Lys (nine examples) and Ser (seven examples) were most often found at the i+1 position. Glycine was found to occur overwhelmingly at position i+2 (28 examples), while Ser (seven examples) and Asn (six examples) were amongst the most frequent residues. Activation energy barriers for the interconversion between type I and type II beta-turns were computed using the peptide models Ac-Pro-Aib-NHMe and Ac-Pro-Gly-NHMe within the framework of the AM1 semi-empirical molecular orbital procedure. In order to have a uniform basis for

  10. Efficient computational model for classification of protein localization images using Extended Threshold Adjacency Statistics and Support Vector Machines.

    Science.gov (United States)

    Tahir, Muhammad; Jan, Bismillah; Hayat, Maqsood; Shah, Shakir Ullah; Amin, Muhammad

    2018-04-01

    Discriminative and informative feature extraction is the core requirement for accurate and efficient classification of protein subcellular localization images so that drug development could be more effective. The objective of this paper is to propose a novel modification in the Threshold Adjacency Statistics technique and enhance its discriminative power. In this work, we utilized Threshold Adjacency Statistics from a novel perspective to enhance its discrimination power and efficiency. In this connection, we utilized seven threshold ranges to produce seven distinct feature spaces, which are then used to train seven SVMs. The final prediction is obtained through the majority voting scheme. The proposed ETAS-SubLoc system is tested on two benchmark datasets using 5-fold cross-validation technique. We observed that our proposed novel utilization of TAS technique has improved the discriminative power of the classifier. The ETAS-SubLoc system has achieved 99.2% accuracy, 99.3% sensitivity and 99.1% specificity for Endogenous dataset outperforming the classical Threshold Adjacency Statistics technique. Similarly, 91.8% accuracy, 96.3% sensitivity and 91.6% specificity values are achieved for Transfected dataset. Simulation results validated the effectiveness of ETAS-SubLoc that provides superior prediction performance compared to the existing technique. The proposed methodology aims at providing support to pharmaceutical industry as well as research community towards better drug designing and innovation in the fields of bioinformatics and computational biology. The implementation code for replicating the experiments presented in this paper is available at: https://drive.google.com/file/d/0B7IyGPObWbSqRTRMcXI2bG5CZWs/view?usp=sharing. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins.

    Science.gov (United States)

    Ruiz-Blanco, Yasser B; Paz, Waldo; Green, James; Marrero-Ponce, Yovani

    2015-05-16

    The exponential growth of protein structural and sequence databases is enabling multifaceted approaches to understanding the long sought sequence-structure-function relationship. Advances in computation now make it possible to apply well-established data mining and pattern recognition techniques to these data to learn models that effectively relate structure and function. However, extracting meaningful numerical descriptors of protein sequence and structure is a key issue that requires an efficient and widely available solution. We here introduce ProtDCal, a new computational software suite capable of generating tens of thousands of features considering both sequence-based and 3D-structural descriptors. We demonstrate, by means of principle component analysis and Shannon entropy tests, how ProtDCal's sequence-based descriptors provide new and more relevant information not encoded by currently available servers for sequence-based protein feature generation. The wide diversity of the 3D-structure-based features generated by ProtDCal is shown to provide additional complementary information and effectively completes its general protein encoding capability. As demonstration of the utility of ProtDCal's features, prediction models of N-linked glycosylation sites are trained and evaluated. Classification performance compares favourably with that of contemporary predictors of N-linked glycosylation sites, in spite of not using domain-specific features as input information. ProtDCal provides a friendly and cross-platform graphical user interface, developed in the Java programming language and is freely available at: http://bioinf.sce.carleton.ca/ProtDCal/ . ProtDCal introduces local and group-based encoding which enhances the diversity of the information captured by the computed features. Furthermore, we have shown that adding structure-based descriptors contributes non-redundant additional information to the features-based characterization of polypeptide systems. This

  12. 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.

  13. Anisotropic nature of radially strained metal tubes

    Science.gov (United States)

    Strickland, Julie N.

    Metal pipes are sometimes swaged by a metal cone to enlarge them, which increases the strain in the material. The amount of strain is important because it affects the burst and collapse strength. Burst strength is the amount of internal pressure that a pipe can withstand before failure, while collapse strength is the amount of external pressure that a pipe can withstand before failure. If the burst or collapse strengths are exceeded, the pipe may fracture, causing critical failure. Such an event could cost the owners and their customers millions of dollars in clean up, repair, and lost time, in addition to the potential environmental damage. Therefore, a reliable way of estimating the burst and collapse strength of strained pipe is desired and valuable. The sponsor currently rates strained pipes using the properties of raw steel, because those properties are easily measured (for example, yield strength). In the past, the engineers assumed that the metal would be work-hardened when swaged, so that yield strength would increase. However, swaging introduces anisotropic strain, which may decrease the yield strength. This study measured the yield strength of strained material in the transverse and axial direction and compared them to raw material, to determine the amount of anisotropy. This information will be used to more accurately determine burst and collapse ratings for strained pipes. More accurate ratings mean safer products, which will minimize risk for the sponsor's customers. Since the strained metal has a higher yield strength than the raw material, using the raw yield strength to calculate burst and collapse ratings is a conservative method. The metal has even higher yield strength after strain aging, which indicates that the stresses are relieved. Even with the 12% anisotropy in the strained and 9% anisotropy in the strain aged specimens, the raw yield strengths are lower and therefore more conservative. I recommend that the sponsor continue using the raw

  14. 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.

  15. Timescales of isotropic and anisotropic cluster collapse

    Science.gov (United States)

    Bartelmann, M.; Ehlers, J.; Schneider, P.

    1993-12-01

    From a simple estimate for the formation time of galaxy clusters, Richstone et al. have recently concluded that the evidence for non-virialized structures in a large fraction of observed clusters points towards a high value for the cosmological density parameter Omega0. This conclusion was based on a study of the spherical collapse of density perturbations, assumed to follow a Gaussian probability distribution. In this paper, we extend their treatment in several respects: first, we argue that the collapse does not start from a comoving motion of the perturbation, but that the continuity equation requires an initial velocity perturbation directly related to the density perturbation. This requirement modifies the initial condition for the evolution equation and has the effect that the collapse proceeds faster than in the case where the initial velocity perturbation is set to zero; the timescale is reduced by a factor of up to approximately equal 0.5. Our results thus strengthens the conclusion of Richstone et al. for a high Omega0. In addition, we study the collapse of density fluctuations in the frame of the Zel'dovich approximation, using as starting condition the analytically known probability distribution of the eigenvalues of the deformation tensor, which depends only on the (Gaussian) width of the perturbation spectrum. Finally, we consider the anisotropic collapse of density perturbations dynamically, again with initial conditions drawn from the probability distribution of the deformation tensor. We find that in both cases of anisotropic collapse, in the Zel'dovich approximation and in the dynamical calculations, the resulting distribution of collapse times agrees remarkably well with the results from spherical collapse. We discuss this agreement and conclude that it is mainly due to the properties of the probability distribution for the eigenvalues of the Zel'dovich deformation tensor. Hence, the conclusions of Richstone et al. on the value of Omega0 can be

  16. 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

  17. 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

  18. 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.

  19. Propagation of waves in a gravitating and rotating anisotropic heat ...

    African Journals Online (AJOL)

    Bheema

    astrophysical plasmas. These plasmas are usually self-gravitating, rotating and embedded in a .... gravitational potential, and P denotes the anisotropic pressure tensor defined as. ൌ ୄ ൅ ሺ צǦ ..... Nonlinear Processes Geophysics, 11 :731.

  20. 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.

  1. 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.

  2. Anisotropic Third-Order Regularization for Sparse Digital Elevation Models

    KAUST Repository

    Lellmann, Jan; Morel, Jean-Michel; Schö nlieb, Carola-Bibiane

    2013-01-01

    features of the contours while ensuring smoothness across level lines. We propose an anisotropic third-order model and an efficient method to adaptively estimate both the surface and the anisotropy. Our experiments show that the approach outperforms AMLE

  3. 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

  4. On plasma stability under anisotropic random electric field influence

    International Nuclear Information System (INIS)

    Rabich, L.N.; Sosenko, P.P.

    1987-01-01

    The influence of anisotropic random field on plasma stability is studied. The thresholds and instability increments are obtained. The stabilizing influence of frequency missmatch and external magnetic field is pointed out

  5. 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.)

  6. 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.

  7. 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.

  8. 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

  9. Finite-difference modelling of anisotropic wave scattering in discrete ...

    Indian Academy of Sciences (India)

    A M Ekanem

    2018-04-05

    Apr 5, 2018 ... scattering characteristics in fractured media and thus, validate the practical utility of using anisotropic .... to fluid flow. ... account the porosity of the host rock and assumes .... The free surface boundary conditions generally.

  10. 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.

  11. 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.

  12. 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...

  13. 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

  14. 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.)

  15. 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)

  16. 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....

  17. 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

  18. Identification of putative drug targets in Vancomycin-resistant Staphylococcus aureus (VRSA) using computer aided protein data analysis.

    Science.gov (United States)

    Hasan, Md Anayet; Khan, Md Arif; Sharmin, Tahmina; Hasan Mazumder, Md Habibul; Chowdhury, Afrin Sultana

    2016-01-01

    Vancomycin-resistant Staphylococcus aureus (VRSA) is a Gram-positive, facultative aerobic bacterium which is evolved from the extensive exposure of Vancomycin to Methicillin resistant S. aureus (MRSA) that had become the most common cause of hospital and community-acquired infections. Due to the emergence of different antibiotic resistance strains, there is an exigency to develop novel drug targets to address the provocation of multidrug-resistant bacteria. In this study, in-silico genome subtraction methodology was used to design potential and pathogen specific drug targets against VRSA. Our study divulged 1987 proteins from the proteome of 34,549 proteins, which have no homologues in human genome after sequential analysis through CD-HIT and BLASTp. The high stringency analysis of the remaining proteins against database of essential genes (DEG) resulted in 169 proteins which are essential for S. aureus. Metabolic pathway analysis of human host and pathogen by KAAS at the KEGG server sorted out 19 proteins involved in unique metabolic pathways. 26 human non-homologous membrane-bound essential proteins including 4 which were also involved in unique metabolic pathway were deduced through PSORTb, CELLO v.2.5, ngLOC. Functional classification of uncharacterized proteins through SVMprot derived 7 human non-homologous membrane-bound hypothetical essential proteins. Study of potential drug target against Drug Bank revealed pbpA-penicillin-binding protein 1 and hypothetical protein MQW_01796 as the best drug target candidate. 2D structure was predicted by PRED-TMBB, 3D structure and functional analysis was also performed. Protein-protein interaction network of potential drug target proteins was analyzed by using STRING. The identified drug targets are expected to have great potential for designing novel drugs against VRSA infections and further screening of the compounds against these new targets may result in the discovery of novel therapeutic compounds that can be

  19. 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.)

  20. Schroedinger covariance states in anisotropic waveguides

    International Nuclear Information System (INIS)

    Angelow, A.; Trifonov, D.

    1995-03-01

    In this paper Squeezed and Covariance States based on Schroedinger inequality and their connection with other nonclassical states are considered for particular case of anisotropic waveguide in LiNiO 3 . Here, the problem of photon creation and generation of squeezed and Schroedinger covariance states in optical waveguides is solved in two steps: 1. Quantization of electromagnetic field is provided in the presence of dielectric waveguide using normal-mode expansion. The photon creation and annihilation operators are introduced, expanding the solution A-vector(r-vector,t) in a series in terms of the Sturm - Liouville mode-functions. 2. In terms of these operators the Hamiltonian of the field in a nonlinear waveguide is derived. For such Hamiltonian we construct the covariance states as stable (with nonzero covariance), which minimize the Schroedinger uncertainty relation. The evolutions of the three second momenta of q-circumflex j and p-circumflex j are calculated. For this Hamiltonian all three momenta are expressed in terms of one real parameters s only. It is found out how covariance, via this parameter s, depends on the waveguide profile n(x,y), on the mode-distributions u-vector j (x,y), and on the waveguide phase mismatching Δβ. (author). 37 refs

  1. Polarization dynamics in nonlinear anisotropic fibers

    International Nuclear Information System (INIS)

    Komarov, Andrey; Komarov, Konstantin; Meshcheriakov, Dmitry; Amrani, Foued; Sanchez, Francois

    2010-01-01

    We give an extensive study of polarization dynamics in anisotropic fibers exhibiting a third-order index nonlinearity. The study is performed in the framework of the Stokes parameters with the help of the Poincare sphere. Stationary states are determined, and their stability is investigated. The number of fixed points and their stability depend on the respective magnitude of the linear and nonlinear birefringence. A conservation relation analogous to the energy conservation in mechanics allows evidencing a close analogy between the movement of the polarization in the Poincare sphere and the motion of a particle in a potential well. Two distinct potentials are found, leading to the existence of two families of solutions, according to the sign of the total energy of the equivalent mechanical system. The mechanical analogy allows us to fully characterize the solutions and also to determine analytically the associated beat lengths. General analytical solutions are given for the two families in terms of Jacobi's functions. The intensity-dependent transmission of a fiber placed between two crossed polarizers is calculated. Optimal conditions for efficient nonlinear switching compatible with mode-locking applications are determined. The general case of a nonlinear fiber ring with an intracavity polarizer placed between two polarization controllers is also considered.

  2. Zonal flows in tokamaks with anisotropic pressure

    International Nuclear Information System (INIS)

    Ren, Haijun

    2014-01-01

    Zonal flows (ZFs) in a tokamak plasma with anisotropic pressure are investigated. The dynamics of perpendicular and parallel pressures are determined by the Chew-Goldberger-Low double equations and low-β condition is adopted, where β is the ratio of plasma pressure to the magnetic field pressure. The dispersion relation is analytically derived and illustrates two branches of ZFs. The low frequency zonal flow (LFZF) branch becomes unstable when χ, the ratio of the perpendicular pressure to the parallel one, is greater than a threshold value χ c , which is about 3.8. In the stable region, its frequency increases first and then decreases with increasing χ. For χ = 1, the frequency of LFZF agrees well with the experimental observation. For the instability, the growth rate of LFZF increases with χ. The geodesic acoustic mode branch is shown to be always stable with a frequency increasing with χ. The safety factor is shown to diminish the frequencies of both branches or the growth rate of LFZF

  3. Gauge unification in highly anisotropic string compactifications

    International Nuclear Information System (INIS)

    Hebecker, A.; Trapletti, M.

    2005-01-01

    It is well known that heterotic string compactifications have, in spite of their conceptual simplicity and aesthetic appeal, a serious problem with precision gauge coupling unification in the perturbative regime of string theory. Using both a duality-based and a field-theoretic definition of the boundary of the perturbative regime, we reevaluate the situation in a quantitative manner. We conclude that the simplest and most promising situations are those where some of the compactification radii are exceptionally large, corresponding to highly anisotropic orbifold models. Thus, one is led to consider constructions which are known to the effective field-theorist as higher-dimensional or orbifold grand unified theories (orbifold GUTs). In particular, if the discrete symmetry used to break the GUT group acts freely, a non-local breaking in the larger compact dimensions can be realized, leading to a precise gauge coupling unification as expected on the basis of the MSSM particle spectrum. Furthermore, a somewhat more model dependent but nevertheless very promising scenario arises if the GUT breaking is restricted to certain singular points within the manifold spanned by the larger compactification radii

  4. Birkeland currents in an anisotropic, magnetostatic plasma

    International Nuclear Information System (INIS)

    Birmingham, T.J.

    1992-01-01

    An expression for the parallel current density is derived for a plasma characterized by negligible bulk flow (magnetostatic) velocity and a two-component (anisotropic) pressure tensor by expanding the equilibrium Vlasov equation for each species in the adiabatic parameter until such point as a nonvanishing moment j parallel = ∫ d 3 vv parallel is identified. The result is a nonlocal one: it relates j parallel at one point s along a field line to j parallel at another (reference) point s 0 plus an integral function of the pressure and magnetic field between them. It is a generalization and elaboration of results obtained by Bostrom (1975), Heinemann (1990), and Heinemann and Pontius (1991). The expression could have been obtained by integrating the current continuity equation with -∇ x j perpendicular as a source term and j perpendicular given by perpendicular momentum balance. The authors explicitly show the equivalency. The widely used Vasyliunas (1970) equation follows when P perpendicular is set equal to P parallel and s and s 0 are taken to be at the ionosphere and the equator. An extended discussion of the relationship of results derived here to others in the literature is carried out in an effort to bring unity and perspective to this problem area

  5. Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches.

    Directory of Open Access Journals (Sweden)

    Abbas Khan

    Full Text Available High-risk human papillomaviruses (hrHPVs are the most prevalent viruses in human diseases including cervical cancers. Expression of E6 protein has already been reported in cervical cancer cases, excluding normal tissues. Continuous expression of E6 protein is making it ideal to develop therapeutic vaccines against hrHPVs infection and cervical cancer. Therefore, we carried out a meta-analysis of multiple hrHPVs to predict the most potential prophylactic peptide vaccines. In this study, immunoinformatics approach was employed to predict antigenic epitopes of hrHPVs E6 proteins restricted to 12 Human HLAs to aid the development of peptide vaccines against hrHPVs. Conformational B-cell and CTL epitopes were predicted for hrHPVs E6 proteins using ElliPro and NetCTL. The potential of the predicted peptides were tested and validated by using systems biology approach considering experimental concentration. We also investigated the binding interactions of the antigenic CTL epitopes by using docking. The stability of the resulting peptide-MHC I complexes was further studied by molecular dynamics simulations. The simulation results highlighted the regions from 46-62 and 65-76 that could be the first choice for the development of prophylactic peptide vaccines against hrHPVs. To overcome the worldwide distribution, the predicted epitopes restricted to different HLAs could cover most of the vaccination and would help to explore the possibility of these epitopes for adaptive immunotherapy against HPVs infections.

  6. Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study.

    Science.gov (United States)

    Taghizadeh, Mohammad; Goliaei, Bahram; Madadkar-Sobhani, Armin

    2016-06-01

    addition, it could provide a better computational calculation of the protein flexibility, which is, especially important in the comparative studies of the proteins' flexibility.

  7. 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.

  8. 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.

  9. Experimental and computational analysis of a large protein network that controls fat storage reveals the design principles of a signaling network.

    Directory of Open Access Journals (Sweden)

    Bader Al-Anzi

    2015-05-01

    Full Text Available An approach combining genetic, proteomic, computational, and physiological analysis was used to define a protein network that regulates fat storage in budding yeast (Saccharomyces cerevisiae. A computational analysis of this network shows that it is not scale-free, and is best approximated by the Watts-Strogatz model, which generates "small-world" networks with high clustering and short path lengths. The network is also modular, containing energy level sensing proteins that connect to four output processes: autophagy, fatty acid synthesis, mRNA processing, and MAP kinase signaling. The importance of each protein to network function is dependent on its Katz centrality score, which is related both to the protein's position within a module and to the module's relationship to the network as a whole. The network is also divisible into subnetworks that span modular boundaries and regulate different aspects of fat metabolism. We used a combination of genetics and pharmacology to simultaneously block output from multiple network nodes. The phenotypic results of this blockage define patterns of communication among distant network nodes, and these patterns are consistent with the Watts-Strogatz model.

  10. Experimental and computational analysis of a large protein network that controls fat storage reveals the design principles of a signaling network.

    Science.gov (United States)

    Al-Anzi, Bader; Arpp, Patrick; Gerges, Sherif; Ormerod, Christopher; Olsman, Noah; Zinn, Kai

    2015-05-01

    An approach combining genetic, proteomic, computational, and physiological analysis was used to define a protein network that regulates fat storage in budding yeast (Saccharomyces cerevisiae). A computational analysis of this network shows that it is not scale-free, and is best approximated by the Watts-Strogatz model, which generates "small-world" networks with high clustering and short path lengths. The network is also modular, containing energy level sensing proteins that connect to four output processes: autophagy, fatty acid synthesis, mRNA processing, and MAP kinase signaling. The importance of each protein to network function is dependent on its Katz centrality score, which is related both to the protein's position within a module and to the module's relationship to the network as a whole. The network is also divisible into subnetworks that span modular boundaries and regulate different aspects of fat metabolism. We used a combination of genetics and pharmacology to simultaneously block output from multiple network nodes. The phenotypic results of this blockage define patterns of communication among distant network nodes, and these patterns are consistent with the Watts-Strogatz model.

  11. 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

  12. 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

  13. Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore.

    Science.gov (United States)

    Fry, H Christopher; Lehmann, Andreas; Saven, Jeffery G; DeGrado, William F; Therien, Michael J

    2010-03-24

    The first example of a computationally de novo designed protein that binds an emissive abiological chromophore is presented, in which a sophisticated level of cofactor discrimination is pre-engineered. This heterotetrameric, C(2)-symmetric bundle, A(His):B(Thr), uniquely binds (5,15-di[(4-carboxymethyleneoxy)phenyl]porphinato)zinc [(DPP)Zn] via histidine coordination and complementary noncovalent interactions. The A(2)B(2) heterotetrameric protein reflects ligand-directed elements of both positive and negative design, including hydrogen bonds to second-shell ligands. Experimental support for the appropriate formulation of [(DPP)Zn:A(His):B(Thr)](2) is provided by UV/visible and circular dichroism spectroscopies, size exclusion chromatography, and analytical ultracentrifugation. Time-resolved transient absorption and fluorescence spectroscopic data reveal classic excited-state singlet and triplet PZn photophysics for the A(His):B(Thr):(DPP)Zn protein (k(fluorescence) = 4 x 10(8) s(-1); tau(triplet) = 5 ms). The A(2)B(2) apoprotein has immeasurably low binding affinities for related [porphinato]metal chromophores that include a (DPP)Fe(III) cofactor and the zinc metal ion hemin derivative [(PPIX)Zn], underscoring the exquisite active-site binding discrimination realized in this computationally designed protein. Importantly, elements of design in the A(His):B(Thr) protein ensure that interactions within the tetra-alpha-helical bundle are such that only the heterotetramer is stable in solution; corresponding homomeric bundles present unfavorable ligand-binding environments and thus preclude protein structural rearrangements that could lead to binding of (porphinato)iron cofactors.

  14. Toward Bridging the Mechanistic Gap between Genes and Traits by Emphasizing the Role of Proteins in a Computational Environment

    Science.gov (United States)

    Haskel-Ittah, Michal; Yarden, Anat

    2017-01-01

    Previous studies have shown that students often ignore molecular mechanisms when describing genetic phenomena. Specifically, students tend to directly link genes to their encoded traits, ignoring the role of proteins as mediators in this process. We tested the ability of 10th grade students to connect genes to traits through proteins, using…

  15. 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

  16. Computer-aided model analysis for ionic strength-dependent effective charge of protein in ion-exchange chromatography

    DEFF Research Database (Denmark)

    Lim, Young-il; Jørgensen, Sten Bay; Kim, In-Ho

    2005-01-01

    differential algebraic equation (PDAE) system, a fast and accurate numerical method (i.e., conservation element/solution element (CE/SE) method), is proposed. Sensitivity and elasticity of the model parameters (e.g., steric/shape factors, adsorption heat coefficient, effective protein charge, equilibrium...... constant, mass transfer coefficient, axial dispersion coefficient and bed voidage) are analyzed for a BSA-salt system in a low protein concentration range. Within a low concentration range of bovine serum albumin (BSA) where linear adsorption isotherms are shown, the adsorption heat coefficient, shape...... salt concentrations, it is proposed that the effective protein charge could depend upon the salt concentration (or ionic strength). The reason for this dependence may be a steric hindrance of protein binding sites combined with a salt shielding effect neutralizing the surface charges of the protein. (c...

  17. 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.

  18. Anisotropic mesh adaptation for marine ice-sheet modelling

    Science.gov (United States)

    Gillet-Chaulet, Fabien; Tavard, Laure; Merino, Nacho; Peyaud, Vincent; Brondex, Julien; Durand, Gael; Gagliardini, Olivier

    2017-04-01

    Improving forecasts of ice-sheets contribution to sea-level rise requires, amongst others, to correctly model the dynamics of the grounding line (GL), i.e. the line where the ice detaches from its underlying bed and goes afloat on the ocean. Many numerical studies, including the intercomparison exercises MISMIP and MISMIP3D, have shown that grid refinement in the GL vicinity is a key component to obtain reliable results. Improving model accuracy while maintaining the computational cost affordable has then been an important target for the development of marine icesheet models. Adaptive mesh refinement (AMR) is a method where the accuracy of the solution is controlled by spatially adapting the mesh size. It has become popular in models using the finite element method as they naturally deal with unstructured meshes, but block-structured AMR has also been successfully applied to model GL dynamics. The main difficulty with AMR is to find efficient and reliable estimators of the numerical error to control the mesh size. Here, we use the estimator proposed by Frey and Alauzet (2015). Based on the interpolation error, it has been found effective in practice to control the numerical error, and has some flexibility, such as its ability to combine metrics for different variables, that makes it attractive. Routines to compute the anisotropic metric defining the mesh size have been implemented in the finite element ice flow model Elmer/Ice (Gagliardini et al., 2013). The mesh adaptation is performed using the freely available library MMG (Dapogny et al., 2014) called from Elmer/Ice. Using a setup based on the inter-comparison exercise MISMIP+ (Asay-Davis et al., 2016), we study the accuracy of the solution when the mesh is adapted using various variables (ice thickness, velocity, basal drag, …). We show that combining these variables allows to reduce the number of mesh nodes by more than one order of magnitude, for the same numerical accuracy, when compared to uniform mesh

  19. Scalar particle creation in an anisotropic universe

    International Nuclear Information System (INIS)

    Berger, B.K.

    1975-01-01

    The problem of quantized scalar field creation in an anisotropic spatially homogeneous background universe is reexamined from a Schroedinger-picture point of view. For each mode a complete set of orthonormal wave functions, psi/subN/, is obtained using the method of Salusti and Zirilli. These wave functions are valid at all times even if there is an initial cosmological singularity and depend only on the solution of the classical equation of motion. The wave functions are fixed completely by requiring the classical solution to have positive-frequency WKB form when the universe reaches the stage of adiabatic expansion. These wave functions are eigenfunctions of a conserved number operator which has the usual particle interpretation in the adiabatic regime. An intitial state near the singularity is chosen as a superposition of the wave functions, psi/subN/, and the particle number in the adiabatic regime is calculated. For plane-wave initial states, which follow the classical behavior near the singularity, the final particle number depends only on the parameters of the initial wave packet. For an initial state which instantaneously diagonalizes the Hamiltonian, an (arbitrary) initial time must be chosen. If the mode in question is in the adiabatic regime at that time almost no particle creation occurs. If it is not adiabatic, creation occurs and becomes infinite if the initial time is taken to be that of the singularity. This creation is a consequence of the failure of particle number to be well defined in this regime. Comparisons with other particle-creation studies are made

  20. Theory of Langmuir probes in anisotropic plasmas

    International Nuclear Information System (INIS)

    Sudit, I.D.; Woods, R.C.

    1994-01-01

    A theory has been developed for electron retardation by Langmuir probes of several geometries in a general anisotropic plasma with arbitrary probe orientation and valid for any sheath thickness. Electron densities and electron velocity distribution functions (EVDFs) are obtained from the second derivative of probe I-V curves, as in Druyvesteyn's original method, which was developed for isotropic plasmas. Fedorov had extended the latter method in the context of a thin sheath approximation, to axisymmetric plasmas, in which the EVDF is expanded in a series of Legendary polynomials. In the present work an expansion in a series of spherical harmonics is employed, and the coordinate transformations are handled using the irreducible representation of the three dimensional rotation group. It is shown that the Volterra integral equations that must be solved to obtain the expansion coefficients of the EVDF from the second derivative data are no more complicated in the general case that hose for the axisymmetric plasma. Furthermore in the latter case the results can be shown to be equivalent to Fedrov's thin sheath expression. For the case of planar probes a formulation based on first derivatives of the I-V curves has been obtained. If data is obtained at enough different probe orientation of a one sided planar disc probe, any number of spherical harmonic coefficient functions may be obtained by inverting a set of linear equations and the complete EVDF deduced. For a cylindrical probe or a two-sided planar disc probe the integration of the second derivative of the probe current gives the exact electron density with any arbitrary probe orientation and any degree of plasma anisotropy