supercomputing for molecular dynamics simulations handling multi trillion particles in nanofluidics springerbriefs in computer science

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Supercomputing For Molecular Dynamics Simulations

Author : Alexander Heinecke
ISBN : 9783319171487
Genre : Computers
File Size : 44. 58 MB
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This work presents modern implementations of relevant molecular dynamics algorithms using ls1 mardyn, a simulation program for engineering applications. The text focuses strictly on HPC-related aspects, covering implementation on HPC architectures, taking Intel Xeon and Intel Xeon Phi clusters as representatives of current platforms. The work describes distributed and shared-memory parallelization on these platforms, including load balancing, with a particular focus on the efficient implementation of the compute kernels. The text also discusses the software-architecture of the resulting code.

Euro Par 2015 Parallel Processing Workshops

Author : Sascha Hunold
ISBN : 9783319273082
Genre : Computers
File Size : 88. 16 MB
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This book constitutes the thoroughly refereed post-conference proceedings of 12 workshops held at the 21st International Conference on Parallel and Distributed Computing, Euro-Par 2015, in Vienna, Austria, in August 2015. The 67 revised full papers presented were carefully reviewed and selected from 121 submissions. The volume includes papers from the following workshops: BigDataCloud: 4th Workshop on Big Data Management in Clouds - Euro-EDUPAR: First European Workshop on Parallel and Distributed Computing Education for Undergraduate Students - Hetero Par: 13th International Workshop on Algorithms, Models and Tools for Parallel Computing on Heterogeneous Platforms - LSDVE: Third Workshop on Large Scale Distributed Virtual Environments - OMHI: 4th International Workshop on On-chip Memory Hierarchies and Interconnects - PADAPS: Third Workshop on Parallel and Distributed Agent-Based Simulations - PELGA: Workshop on Performance Engineering for Large-Scale Graph Analytics - REPPAR: Second International Workshop on Reproducibility in Parallel Computing - Resilience: 8th Workshop on Resiliency in High Performance Computing in Clusters, Clouds, and Grids - ROME: Third Workshop on Runtime and Operating Systems for the Many Core Era - UCHPC: 8th Workshop on UnConventional High Performance Computing - and VHPC: 10th Workshop on Virtualization in High-Performance Cloud Computing.

First Socialist Schism

Author : Wolfgang Eckhardt
ISBN : 9781629633084
Genre : Political Science
File Size : 77. 74 MB
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The First Socialist Schism chronicles the conflicts in the International Working Men’s Association (First International, 1864–1877), which represents an important milestone in the history of political ideas and socialist theory. The separate movements in the International—which would later develop into social democracy, communism, and anarchism—found their greatest advocates in Mikhail Bakunin and Karl Marx. What made the conflict between Bakunin and Marx so important was that it heralded the first socialist schism between parliamentary party politics aiming to conquer political power and social-revolutionary concepts. Instead of focusing exclusively on what Marx and Bakunin said, many other contributions to this debate are examined, making this the first reconstruction of a dispute that gripped the entire organization. This book also provides the first detailed account of the International’s Congress of The Hague (September, 1872), famous for the expulsion of Bakunin; including the background, the sequence of events, and international reaction. The book sets new standards when it comes to source material, taking into account documents from numerous archives and libraries that have previously gone unnoticed or were completely unknown.

Machine Learning For Text

Author : Charu C. Aggarwal
ISBN : 9783319735313
Genre : Computers
File Size : 46. 83 MB
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Text analytics is a field that lies on the interface of information retrieval,machine learning, and natural language processing, and this textbook carefully covers a coherently organized framework drawn from these intersecting topics. The chapters of this textbook is organized into three categories: - Basic algorithms: Chapters 1 through 7 discuss the classical algorithms for machine learning from text such as preprocessing, similarity computation, topic modeling, matrix factorization, clustering, classification, regression, and ensemble analysis. - Domain-sensitive mining: Chapters 8 and 9 discuss the learning methods from text when combined with different domains such as multimedia and the Web. The problem of information retrieval and Web search is also discussed in the context of its relationship with ranking and machine learning methods. - Sequence-centric mining: Chapters 10 through 14 discuss various sequence-centric and natural language applications, such as feature engineering, neural language models, deep learning, text summarization, information extraction, opinion mining, text segmentation, and event detection. This textbook covers machine learning topics for text in detail. Since the coverage is extensive,multiple courses can be offered from the same book, depending on course level. Even though the presentation is text-centric, Chapters 3 to 7 cover machine learning algorithms that are often used indomains beyond text data. Therefore, the book can be used to offer courses not just in text analytics but also from the broader perspective of machine learning (with text as a backdrop). This textbook targets graduate students in computer science, as well as researchers, professors, and industrial practitioners working in these related fields. This textbook is accompanied with a solution manual for classroom teaching.

Computer Simulation Of Liquids

Author : M. P. Allen
ISBN : 0198556454
Genre : History
File Size : 50. 14 MB
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This book describes how to use computers to simulate the properties of liquids. It provides an introduction and practical guide to the molecular dynamics and Monte Carlo methods. 'The book is comprehensive, thorough and readable' Chemistry in Britain

The Art Of Molecular Dynamics Simulation

Author : D. C. Rapaport
ISBN : 0521825687
Genre : Science
File Size : 86. 57 MB
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The extremely powerful technique of molecular dynamics simulation involves solving the classical many-body problem in contexts relevant to the study of matter at the atomistic level. Since there is no alternative approach capable of handling this extremely broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This book, first published in 2004, is a blend of tutorial and recipe collection, providing both an introduction to the subject for beginners and a reference manual for the more experienced practitioner. It is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. The second edition of the book includes a substantial amount of new material as well as completely rewritten software.

Numerical Simulation In Molecular Dynamics

Author : Michael Griebel
ISBN : 9783540680956
Genre : Science
File Size : 69. 91 MB
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This book details the necessary numerical methods, the theoretical background and foundations and the techniques involved in creating computer particle models, including linked-cell method, SPME-method, tree codes, amd multipol technique. It illustrates modeling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. The text offers step-by-step explanations of numerical simulation, providing illustrative code examples. With the description of the algorithms and the presentation of the results of various simulations from fields such as material science, nanotechnology, biochemistry and astrophysics, the reader of this book will learn how to write programs capable of running successful experiments for molecular dynamics.

Multiscale Molecular Methods In Applied Chemistry

Author : Barbara Kirchner
ISBN : 9783642249679
Genre : Science
File Size : 74. 45 MB
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First-Principles-Based Multiscale, Multiparadigm Molecular Mechanics and Dynamics Methods for Describing Complex Chemical Processes, by A. Jaramillo-Botero, R. Nielsen, R. Abrol, J. Su, T. Pascal, J. Mueller and W. A. Goddard.- Dynamic QM/MM: A Hybrid Approach to Simulating Gas–Liquid Interactions, by S. Yockel and G. C. Schatz.- Multiscale Modelling in Computational Heterogeneous Catalysis, by F. J. Keil.- Real-World Predictions from Ab Initio Molecular Dynamics Simulations, by B. Kirchner, P. J. di Dio and J. Hutter.- Nanoscale Wetting Under Electric Field from Molecular Simulations, by C. D. Daub, D. Bratko and A. Luzar.- Molecular Simulations of Retention in Chromatographic Systems: Use of Biased Monte Carlo Techniques to Access Multiple Time and Length Scales, by J. L. Rafferty, J. I. Siepmann, M. R. Schure.- Thermodynamic Properties for Applications in Chemical Industry via Classical Force Fields, by G. Guevara-Carrion, H. Hasse and J. Vrabec.- Multiscale Approaches and Perspectives to Modeling Aqueous Electrolytes and Polyelectrolytes, by L. Delle Site, C. Holm and N. F. A. van der Vegt.- Coarse-Grained Modeling for Macromolecular Chemistry, by H. A. Karimi-Varzaneh and F. Müller-Plathe.-

Data Mining Techniques In Sensor Networks

Author : Annalisa Appice
ISBN : 9781447154549
Genre : Computers
File Size : 39. 94 MB
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Sensor networks comprise of a number of sensors installed across a spatially distributed network, which gather information and periodically feed a central server with the measured data. The server monitors the data, issues possible alarms and computes fast aggregates. As data analysis requests may concern both present and past data, the server is forced to store the entire stream. But the limited storage capacity of a server may reduce the amount of data stored on the disk. One solution is to compute summaries of the data as it arrives, and to use these summaries to interpolate the real data. This work introduces a recently defined spatio-temporal pattern, called trend cluster, to summarize, interpolate and identify anomalies in a sensor network. As an example, the application of trend cluster discovery to monitor the efficiency of photovoltaic power plants is discussed. The work closes with remarks on new possibilities for surveillance enabled by recent developments in sensing technology.

Multiscale Modeling Of Complex Molecular Structure And Dynamics With Mbn Explorer

Author : Ilia A. Solov’yov
ISBN : 9783319560878
Genre : Science
File Size : 75. 86 MB
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This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the mesoscale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational efficiency of MBN Explorer is comparable to that of other, more specialized software packages, making it a viable multi-purpose alternative for the computational modeling of complex molecular systems. A number of detailed case studies presented in the second part of this book demonstrate MBN Explorer’s usefulness and efficiency in the fields of atomic clusters and nanoparticles, biomolecular systems, nanostructured materials, composite materials and hybrid systems, crystals, liquids and gases, as well as in providing modeling support for novel and emerging technologies. Last but not least, with the release of the 3rd edition of MBN Explorer in spring 2017, a free trial version will be available from the MBN Research Center website (mbnresearch.com).

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