Parallel Domain Research Articles

MICROBIAL PECTINASES: A REVIEW ON MOLECULAR AND BIOTECHNOLOGICAL PERSPECTIVES

Pectinases are upcoming enzymes in the biotechnological sector. This large group of enzymes involves in break down of pectic polysaccharides, the major component of middle lamella in plant cell wall. The pectin degrading enzymes are categorized according to their mode of action and release of degradative products. Various filamentous fungi, yeast, and bacteria are the common sources of microbial pectinases. Solid state fermentation is more preferable for extracellular microbial pectinases production over the submerged fermentation. A group of genes regulates the expression of pectinolytic enzymes. Mostly, all the enzymes share a common parallel  helix topology which consists of a single domain of parallel -strands folded into a large right-handed cylinder. These enzymes are eco-friendly tools for industrial applications and being used in various sectors like wine, food, paper industry, waste paper recycling, fruit juice preparation, processing of tea–coffee, animal feed preparation.

Coercive gifts: Ritual and electoral transactions and political value in village Tamil Nadu1

This article considers the gift as a medium of politics in two parallel domains, namely the electoral and the ritual. Juxtaposing the material transactions during a rural election campaign and the distribution of meat after a sacrifice in a vernacular polity, it traces the continuing interpenetrations between philanthropy and politics in lubricating political associations. The properties of the political gift and the proprieties of its giving are what create political value. The right to govern is premised upon the prerogative to give. The right to give, however, is premised on the obligation to receive. The coercive gift—which one is not allowed to reciprocate but more importantly does not want and is forced to receive—is the animus of a politics that is premised upon caste and class hierarchies that also reverberate through democratic governance. What compels the political gift’s receiving, and deliberately negates its reciprocity—its spirit or force—is the implicit threat of violence that it harbours.

Overlapping communication and computation of GPU/CPU heterogeneous parallel spatial domain decomposition MOC method

GPU/CPU heterogeneous parallel calculation has been widely used and great performance has been achieved. Recently it also has been introduced into whole-core transport calculation. Considering the ability to solve the large-scale problem, the spatial domain decomposition (SDD) technique has been applied in the whole-core transport application. However, the communication burden becomes an important bottleneck in heterogeneous parallel SDD calculation and the parallel efficiency decreases dramatically when the number of the calculation domains increasing. GPU brings great acceleration meanwhile the communication time doesn’t change, which makes the parallel efficiency of the heterogeneous parallel calculation worse. In this work, heterogeneous parallel SDD calculation is performed by applying both the spatial domain decomposition and ray parallelization and the parallel performance is analyzed. In addition, a new scheme of the communication is implemented to overlap the MPI communication time and the neutron transport sweep on GPU. In order to accomplish this scheme, both MPI, CUDA protocols are introduced. Numerical results show that the new scheme successfully hide the communication time and the data copy time between GPU and CPU, which brings significant improvement of the parallel efficiency. With the new communication scheme, the large-scale whole-core transport calculation is more practicable.

Observation of the Magnetization Reorientation in Self-Assembled Metallic Fe-Silicide Nanowires at Room Temperature by Spin-Polarized Scanning Tunneling Spectromicroscopy

The quasi-periodic magnetic domains in metallic Fe-silicide nanowires self-assembled on the Si(110)-16 × 2 surface have been observed at room temperature by direct imaging of both the topographic and magnetic structures using spin-polarized scanning tunneling microscopy/spectroscopy. The spin-polarized differential conductance (dI/dV) map of the rectangular-sectional Fe-silicide nanowire with a width and height larger than 36 and 4 nm, respectively, clearly shows an array of almost parallel streak domains that alternate an enhanced (reduced) density of states over in-plane (out-of-plane) magnetized domains with a magnetic period of 5.0 ± 1.0 nm. This heterostructure of magnetic Fe-silicide nanowires epitaxially integrated with the Si(110)-16 × 2 surface will have a significant impact on the development of Si-based spintronic nanodevices.

Highly parallel space-time domain decomposition methods for parabolic problems

In the past few years, the number of processor cores of top ranked supercomputers has increased drastically. It is challenging to design efficient parallel algorithms that offer such a high degree of parallelism, especially for certain time-dependent problems because of the sequential nature of “time”. To increase the degree of parallelization, some parallel-in-time algorithms have been developed. In this paper, we give an overview of some recently introduced parallel-in-time methods, and present in detail the class of space-time Schwarz methods, including the standard and the restricted versions, for solving parabolic partial differential equations. Some numerical experiments carried out on a parallel computer with a large number of processor cores for three-dimensional problems are given to show the parallel scalability of the methods. In the end of the paper, we provide a comparison of the parallel-in-time algorithms with a traditional algorithm that is parallelized only in space.

A parallel non-invasive mixed domain decomposition - Implementation and applications to mechanical assemblies

This paper proposes to confront a mixed domain decomposition method with industrial computations, in particular the simulation of quasi-static assemblies with frictional contact between the parts. The method is implemented in a non-invasive manner around an industrial finite element software. The performance of the algorithm is studied on industrial assemblies.

Parallel Integral Equation-Based Nonoverlapping DDM for Solving Challenging Electromagnetic Scattering Problems of Two Thousand Wavelengths

In this paper, a parallel nonoverlapping and nonconformal domain decomposition method (DDM) is proposed for fast and accurate analysis of electrically large objects in the condition of limited resources. The formulation of nonoverlapping DDM for PEC bodies is derived from combined-field integral equation (CFIE), and an explicit boundary condition is applied to ensure the continuity of electric currents across the boundary. A parallel multilevel fast multipole algorithm (MLFMA) is extended to accelerate matrix-vector multiplications of subdomains as well as the coupling between them, and the coupling between different subdomains is computed in the manner of near field to avoid the storage of the mutual impedance. An improved adaptive direction partitioning scheme is applied to the oct-tree of MLFMA to achieve high parallel efficiency. Numerical examples demonstrate that the proposed method is able to simulate realistic problems with a maximum dimension greater than 2000 wavelengths.

Visualizing a Moving Target: A Design Study on Task Parallel Programs in the Presence of Evolving Data and Concerns.

Common pitfalls in visualization projects include lack of data availability and the domain users' needs and focus changing too rapidly for the design process to complete. While it is often prudent to avoid such projects, we argue it can be beneficial to engage them in some cases as the visualization process can help refine data collection, solving a "chicken and egg" problem of having the data and tools to analyze it. We found this to be the case in the domain of task parallel computing where such data and tooling is an open area of research. Despite these hurdles, we conducted a design study. Through a tightly-coupled iterative design process, we built Atria, a multi-view execution graph visualization to support performance analysis. Atria simplifies the initial representation of the execution graph by aggregating nodes as related to their line of code. We deployed Atria on multiple platforms, some requiring design alteration. We describe how we adapted the design study methodology to the "moving target" of both the data and the domain experts' concerns and how this movement kept both the visualization and programming project healthy. We reflect on our process and discuss what factors allow the project to be successful in the presence of changing data and user needs.

A parallel domain decomposition algorithm for large scale image denoising

Total variation denoising (TVD) is an effective technique for image denoising, in particular, for recovering blocky, discontinuous images from noisy background. The problem is formulated as an optimization problem in the space of bounded variation functions, and the solution is obtained by solving the associated Euler–Lagrange equation defined on the domain occupied by the entire image. The method offers high quality results, but is computationally expensive for large images, especially for three-dimensional problems. In this paper, we introduce a highly parallel version of the algorithm which formulates the problem as multiple overlapping, but independent, optimization problems, and each is defined on a portion of the image domain. This approach is similar to the overlapping Schwarz type domain decomposition method, but is non-iterative, for solving partial differential equations, and is highly scalable, without using any coarse grids, for parallel computers with a large number of processors. We show by a theory and also by some two- and three-dimensional numerical experiments that the new approach has similar numerical accuracy as the classical TVD approach, but is much more efficient on parallel computers.

A Parallel Domain Decomposition Method for the Helmholtz Equation in Layered Media

An efficient domain decomposition method and its parallel implementation for the solution of the Helmholtz equation in three-dimensional layered media are considered. A modified trilinear finite el...

The PX Motif of DNA Binds Specifically to Escherichia coli DNA Polymerase I.

The PX motif of DNA is a four-stranded structure in which two parallel juxtaposed double-helical domains are fused by crossovers at every point where the strands approach each other. Consequently, its twist and writhe are approximately half of those of conventional DNA. This property has been shown to relax supercoiled plasmid DNA under circumstances in which head-to-head homology exists within the plasmid; the homology can be either complete homology or every-other-half-turn homology, known as PX homology. It is clearly of interest to establish whether the cell contains proteins that interact with this unusual and possibly functional motif. We have examined Escherichia coli extracts to seek such a protein. We find by gel mobility studies that the PX motif is apparently bound by a cellular component. Fractionation of this binding activity reveals that the component is DNA polymerase I (Pol I). Although the PX motif binds to Pol I, we find that PX-DNA is not able to serve as a substrate for the extension of a shortened strand. We cannot say at this time whether the binding is a coincidence or whether it represents an activity of Pol I that is currently unknown. We have modeled the interaction of Pol I and PX-DNA using symmetry considerations and molecular dynamics.

Explicit/implicit and Crank–Nicolson domain decomposition methods for parabolic partial differential equations

Two parallel non-overlapping domain decomposition algorithms for solving parabolic partial differential equations are proposed. The algorithms combine Crank–Nicolson scheme with implicit Galerkin finite element methods in sub-domains and explicit flux approximation along inner boundaries at each time step. Thus, parallelism can be easily achieved. L2-norm error estimates for these explicit/implicit procedures are presented, in which time step constraints are proved to be less severe than that of fully explicit schemes. Numerical experiments are also performed to verify the theoretical analysis.

A parallel implicit domain decomposition algorithm for the large eddy simulation of incompressible turbulent flows on 3D unstructured meshes

SummaryWe present a parallel fully implicit algorithm for the large eddy simulation (LES) of incompressible turbulent flows on unstructured meshes in three dimensions. The LES governing equations are discretized by a stabilized Galerkin finite element method in space and an implicit second‐order backward differentiation scheme in time. To efficiently solve the resulting large nonlinear systems, we present a highly parallel Newton‐Krylov‐Schwarz algorithm based on domain decomposition techniques. Analytic Jacobian is applied in order to obtain the best achievable performance. Two benchmark problems of lid‐driven cavity and flow passing a square cylinder are employed to validate the proposed algorithm. We then apply the algorithm to the LES of turbulent flows passing a full‐size high‐speed train with realistic geometry and operating conditions. The numerical results show that the algorithm is both accurate and efficient and exhibits a good scalability and parallel efficiency with tens of millions of degrees of freedom on a computer with up to 4096 processors. To understand the numerical behavior of the proposed fully implicit scheme, we study several important issues, including the choices of linear solvers, the overlapping size of the subdomains, and, especially, the accuracy of the Jacobian matrix. The results show that an exact Jacobian is necessary for the efficiency and the robustness of the proposed LES solver.

Feasibility and validity of the Health Status Classification System-Preschool (HSCS-PS) in a large community sample: the Generation R study

ObjectivesTo evaluate the feasibility, discriminant validity and concurrent validity of the Health Status Classification System-Preschool (HSCS-PS) in children aged 3 years in a large community sample in the Netherlands.Design/settingA prospective...

Ball characterizations in spaces of constant curvature

High proved the following theorem. If the intersections of any two congruent copies of a plane convex body are centrally symmetric, then this body is a circle. In our paper we extend the theorem of High to spherical, Euclidean and hyperbolic spaces, under some regularity assumptions. Suppose that in any of these spaces there is a pair of closed convex sets of class C+2 with interior points, different from the whole space, and the intersections of any congruent copies of these sets are centrally symmetric (provided they have non-empty interiors). Then our sets are congruent balls. Under the same hypotheses, but if we require only central symmetry of small intersections, then our sets are either congruent balls, or paraballs, or have as connected components of their boundaries congruent hyperspheres (and the converse implication also holds). Under the same hypotheses, if we require central symmetry of all compact intersections, then either our sets are congruent balls or paraballs, or have as connected components of their boundaries congruent hyperspheres, and either d ≥ 3, or d = 2 and one of the sets is bounded by one hypercycle, or both sets are congruent parallel domains of straight lines, or there are no more compact intersections than those bounded by two finite hypercycle arcs (and the converse implication also holds). We also prove a dual theorem. If in any of these spaces there is a pair of smooth closed convex sets, such that both of them have supporting spheres at any of their boundary points Sd for Sd of radius less than π/2- and the closed convex hulls of any congruent copies of these sets are centrally symmetric, then our sets are congruent balls.

Accurate semiempirical analytical formulas for spontaneous polarization by crystallographic parameters of SrTiO3-BaTiO3 system by ab initio calculations

Spontaneous polarizations (PS’s) of BaTiO3 and SrTiO3 under various conditions are calculated ab initio using different exchange-correlation functionals. The extensive theoretical sets of PS vs. ion positions are found to lie on a single curve, despite the chemical differences and the wide variations of PS and lattice parameters. This uncovers accurate simple analytical formulas of PS of SrTiO3-BaTiO3 system expressed by ion positions; a single formula predicts both macroscopic and atomic-scale PS of SrTiO3, BaTiO3 and SrTiO3-BaTiO alloys. The accuracy of the formula is demonstrated by the application to experiments, BaTiO3-SrTiO3 (-CaTiO3) alloys, Sr4Ti4O12 with PS // a-axis, a parallel domain, and a headon domain. In addition, the present results verify empirically that oxygen displacement is the primary identifier and the origin of PS of SrTiO3 and BaTiO3 and indicate that BaTiO3 and SrTiO3 may transforms into new state by an extremely large strain, e.g., −3%. Furthermore, the earlier prediction of headon domain without aid of defects was confirmed. The present procedures for finding formulas can be applied to other materials.

A Novel Approach for Building Adaptive Components using Top-Down Analysis

Developing reusable components are one of the main objectives of component-based software engineering. They play a crucial role in the field of application development and support. CBSE use certain architectural patterns and infrastructures of standard software to increase overall product quality. CBSE apply two parallel engineering activities, domain engineering and component-based development (CBD). Domain analysis explores the application domain with the intent of finding functional, behavioural, and data components that are candidates for reuse and places them in the reuse repository. Strategies for developing adaptive reusable components using top-down domain analysis leads to good quality in the component. Domain analysis promotes strategies and models that have been developed for their specific areas. Therefore, these models are suitable for their own domain, but may not be entirely suitable for domain analysis of other domains. So, developing the reusable components using the top down domain analyses existing components. This paper describes how to build a domain to use top-down analysis of reusable software components.

Control of spin-wave transmission by a programmable domain wall

Active manipulation of spin waves is essential for the development of magnon-based technologies. Here, we demonstrate programmable spin-wave filtering by resetting the spin structure of pinned 90° Néel domain walls in a continuous CoFeB film with abrupt rotations of uniaxial magnetic anisotropy. Using micro-focused Brillouin light scattering and micromagnetic simulations, we show that broad 90° head-to-head or tail-to-tail magnetic domain walls are transparent to spin waves over a broad frequency range. In contrast, magnetic switching to a 90° head-to-tail configuration produces much narrower and strongly reflecting domain walls at the same pinning locations. Based on these results, we propose a magnetic spin-wave valve with two parallel domain walls. Switching the spin-wave valve from an open to a closed state changes the transmission of spin waves from nearly 100 to 0%. Active control over spin-wave transport through programmable domain walls could be utilized in magnonic logic devices or non-volatile memory elements.

Parallel domain decomposition methods for a quantum-corrected drift–diffusion model for MOSFET devices

In this paper, we describe parallel domain decomposition methods based on the restricted additive Schwarz (RAS) method for a quantum-corrected drift–diffusion (QCDD) model for MOSFET devices. We have developed hybrid Message Passing Interface (MPI)/OpenMP parallelization algorithms of the QCDD system. For internode parallelization, two extensions of the RAS method are newly developed for the QCDD model. For intranode parallelization, we combine the conjugate gradient (CG) and BiCGSTAB procedures with a splitting-up operator method to realize parallelization of the incomplete factorization. The parallel numerical results for a three-dimensional Si bulk n-MOSFET on a multi-core NEC SX-ACE parallel computer are demonstrated. The intranode parallel numerical results are further evaluated on a many-core Cray XC40 parallel computer.

Thin film confinement reduces compatibility in symmetric ternary block copolymer/homopolymer blends

ABSTRACTThe thin film phase behavior of ternary blends consisting of symmetric poly(styrene) (PS)‐b‐poly(dimethylsiloxane)(PDMS), PS, and PDMS was investigated using X‐ray reflectivity (XRR) and atomic force microscopy (AFM). This system is strongly segregated, and the homopolymers are approximately the same length as the corresponding blocks of the copolymer. The XRR and AFM data are used to quantify changes in domain spacing (L) and morphology evolution with increasing homopolymer content (Φ H). In 100 nm thick films, from Φ H = 0 to 0.20, the system maintains a perfect parallel lamellar structure and domains swell as predicted based on theory; however, from Φ H = 0.30 to 0.50, a morphology transition to a “dot pattern” morphology (tentatively identified as perforated lamellae) and mixed morphologies were observed before macrophase separation. In thicker films, dot patterns were observed for a broad range of Φ H before macrophase separation. The absence of the bicontinuous microemulsion phase reported for bulk blends and thin films of perpendicular lamellae and the presence of dot patterns/perforated lamellae are attributed to preferential migration of the PDMS homopolymer to the wetting layers located at the substrate and free air interfaces, which leads to an asymmetric composition within the film and morphology transition. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018, 56, 1443–1451