1,721,199 research outputs found
Physics-based adaptivity of a spectral method for the Vlasov-Poisson equations based on the asymmetrically-weighted Hermite expansion in velocity space
Get PDFWe propose a spectral method for the 1D-1V Vlasov-Poisson system where the
discretization in velocity space is based on asymmetrically-weighted Hermite
functions, dynamically adapted via a scaling and shifting of the
velocity variable. Specifically, at each time instant an adaptivity criterion
selects new values of and based on the numerical solution of the
discrete Vlasov-Poisson system obtained at that time step. Once the new values
of the Hermite parameters and are fixed, the Hermite expansion is
updated and the discrete system is further evolved for the next time step. The
procedure is applied iteratively over the desired temporal interval. The key
aspects of the adaptive algorithm are: the map between approximation spaces
associated with different values of the Hermite parameters that preserves total
mass, momentum and energy; and the adaptivity criterion to update and
based on physics considerations relating the Hermite parameters to the
average velocity and temperature of each plasma species. For the discretization
of the spatial coordinate, we rely on Fourier functions and use the implicit
midpoint rule for time stepping. The resulting numerical method possesses
intrinsically the property of fluid-kinetic coupling, where the low-order terms
of the expansion are akin to the fluid moments of a macroscopic description of
the plasma, while kinetic physics is retained by adding more spectral terms.
Moreover, the scheme features conservation of total mass, momentum and energy
associated in the discrete, for periodic boundary conditions. A set of
numerical experiments confirms that the adaptive method outperforms the
non-adaptive one in terms of accuracy and stability of the numerical solution
Understanding the I/O Impact on the Performance of High-Throughput Molecular Docking
Get PDFHigh-throughput molecular docking is a data-driven simulation methodology to estimate millions of molecules’ position and interaction strength (ligands) when interacting with a given protein site. Because of its data-driven nature, the highthroughput molecular docking performance depends on how fast we can ingest data into the processing pipeline and how efficiently we can write molecular docking results to a shared file. This work characterizes the I/O performance of a high-performance, high-throughput molecular docking application, called DockerHT, running on a supercomputer up to 512 computing nodes with two different parallel I/O configurations. We show that a tuned I/O configuration can improve the overall parallel efficiency from 71% to 90% on 512 nodes and identify and solve a performance degradation observed when running on 16 and 32 nodes
A Review on Parallel Virtual Screening Softwares for High-Performance Computers
Get PDFDrug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high-affinity binding and specificity for a target associated with a disease, and, in addition, they should have favorable pharmacodynamic and pharmacokinetic properties (grouped as ADMET properties). Overall, drug discovery is a multivariable optimization and can be carried out in supercomputers using a reliable scoring function which is a measure of binding affinity or inhibition potential of the drug-like compound. The major problem is that the number of compounds in the chemical spaces is huge, making the computational drug discovery very demanding. However, it is cheaper and less time-consuming when compared to experimental high-throughput screening. As the problem is to find the most stable (global) minima for numerous protein–ligand complexes (on the order of 106 to 1012), the parallel implementation of in silico virtual screening can be exploited to ensure drug discovery in affordable time. In this review, we discuss such implementations of parallelization algorithms in virtual screening programs. The nature of different scoring functions and search algorithms are discussed, together with a performance analysis of several docking softwares ported on high-performance computing architectures
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Multischaal kinetische simulaties met iPic3D: van de analyse van satellietoplading tot de zonnewind-interactie met magnetische anomalieën op de Maan
No full textLong before the advent of spaceflight, it was realized that space is not empty. The Universe hosts a harsh plasma environment and understandingthe complex interactions of bodies immersed in it is therefore indispensable to make progress in space science, especially with the eye of society looking ever further into and beyond our Solar system. In this thesis, we focus on three important topics in the field of space plasma physics connected through their need for detailed simulation studies.
First, we present the initial results of a comparative performance studybetween the new Intel Xeon-Phi (MIC) architecture, the Intel Xeon (Sandy Bridge, SB) and a Nvidia graphical processing unit (GPU) running CUDA,for which we use a 1-D explicit electrostatic Vlasov-Ampère particle-in-cell code. Computing times and speedup of the code for the three different architectures are compared for various number of cores/threadsand compiler options. We find that the GPU consistently obtains shortercomputing times than both the MIC and SB architectures for an increasing numbers of threads as well as better scaling. At this stage, then, we have to conclude that the GPU out-performs the MIC in terms of speed.
Secondly, the full-kinetic implicit multi-scale plasma simulation code iPic3D is adapted for the analysis of solar wind-spacecraft interactions. We successfully implement a suitable electrostatic solver to enclose the immersed boundary algorithm and create the possibility to handle complex spacecraft geometries. Additionally we discuss a cross-comparison of spacecraft-environment interaction model predictions from five different spacecraft-plasma codes applied to a simplified geometry of the Solar Probe Plus (SPP) spacecraft near perihelion, predicting that SPP will operate in a saturated emission regime with a negative floating potential Φ ≈ −10 V.
Last but not least, we present the first three-dimensional full-kinetic and electromagnetic simulations of the solar wind interaction with Lunar crustal magnetic anomalies (LMAs). We confirm that LMAs may indeed be strong enough to stand off the solar wind from directly impacting the Lunar surface forming a so-called ‘mini-magnetosphere’, as suggested by spacecraft observations and theory. We develop electromagnetic open boundary conditions and, studying in detail the field structure and particle dynamics, we show that the LMA configuration is driven by electron motion because its scale size is small with respect to the gyroradius of the solar wind ions. We identify a population of backstreaming ions, the deflection of magnetized electrons viathe E × B drift motion and the subsequent formation of a halo region ofelevated density around the dipole source. Finally, it is shown that the presence and efficiency of the latter mechanisms are heavily impacted by the upstream plasma conditions and, on their turn, influence the overall structure and evolution of the LMA system.
Each of the subjects discussed in this work extends our current scientific knowledge and helps pave the way to new and exciting research and to future human exploration on and beyond our precious planet.status: Publishe
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