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  • Electronic books.  (1)
  • Polymer and Materials Science  (1)
  • 1
    Online Resource
    Online Resource
    Newark :John Wiley & Sons, Incorporated,
    Keywords: Crystallography. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (306 pages)
    Edition: 1st ed.
    ISBN: 9783527802258
    DDC: 548
    Language: English
    Note: Cover -- Title Page -- Copyright -- Contents -- Chapter 1 Crystallography Open Database: History, Development, and Perspectives -- 1.1 Introduction -- 1.2 Open Databases for Science -- 1.3 Building COD -- 1.3.1 Scope and Contents -- 1.3.2 Data Sources -- 1.3.3 Data Maintenance -- 1.3.3.1 Version Control -- 1.3.3.2 Data Curation Policies -- 1.3.3.3 Quarterly Releases -- 1.3.4 Sister Databases (PCOD, TCOD) -- 1.4 Use of COD -- 1.4.1 Data Search and Retrieval -- 1.4.1.1 Data Identification -- 1.4.1.2 Web Search Interface -- 1.4.1.3 RESTful Interfaces -- 1.4.1.4 Output Formats -- 1.4.1.5 Accessing COD Records -- 1.4.1.6 MySQL Interface -- 1.4.1.7 Alternative Implementations of COD Search on the Web -- 1.4.1.8 Installing a Local Copy of the COD -- 1.4.1.9 File System‐Based Queries -- 1.4.1.10 Programmatic Use of COD CIFs -- 1.4.2 Data Deposition -- 1.5 Applications -- 1.5.1 Material Identification -- 1.5.2 Applications for the Mining Industry -- 1.5.3 Extracting Chemical Information -- 1.5.4 Property Search -- 1.5.5 Geometry Statistics -- 1.5.6 High‐Throughput Computations -- 1.5.7 Applications in College Education and Complementing Outreach Activities -- 1.6 Perspectives -- 1.6.1 Historic Structures -- 1.6.2 Theoretical Data in (T)COD -- 1.6.3 Conclusion -- Acknowledgments -- References -- Chapter 2 The Inorganic Crystal Structure Database (ICSD): A Tool for Materials Sciences -- 2.1 Introduction -- 2.2 Content of ICSD -- 2.3 Interfaces -- 2.4 Applications of ICSD -- 2.4.1 Prediction of Ferroelectricity -- 2.4.2 Using the Concept of Structure Types -- 2.4.3 Two Examples of Training Machine Learning Algorithms with ICSD Data -- 2.4.4 High‐Throughput Calculation -- 2.5 Outlook -- References -- Chapter 3 Pauling File: Toward a Holistic View -- 3.1 Introduction -- 3.1.1 Creation and Development of the PAULING FILE -- 3.2 PAULING FILE: Crystal Structures. , 3.2.1 Data Selection -- 3.2.2 Categories of Crystal Structure Entries -- 3.2.3 Database Fields -- 3.2.4 Structure Prototypes -- 3.2.5 Standardized Crystallographic Data -- 3.2.5.1 Checking of Symmetry -- 3.2.5.2 Standardization -- 3.2.5.3 Comparison with the Type‐Defining Data Set -- 3.2.6 Assigned Atom Coordinates -- 3.2.7 Atomic Environment Types (AETs) -- 3.2.8 Cell Parameters from Plots -- 3.3 PAULING FILE: Phase Diagrams -- 3.4 PAULING FILE: Physical Properties -- 3.4.1 Data Selection -- 3.4.2 Database Fields -- 3.4.3 Physical Properties Considered in the PAULING FILE -- 3.5 Data Quality -- 3.5.1 Computer‐Aided Checking -- 3.6 Distinct Phases -- 3.6.1 Chemical Formulas and Phase Names -- 3.6.2 Phase Classifications -- 3.7 Toward a Megadatabase -- 3.8 Applications -- 3.8.1 Products Containing PAULING FILE Data -- 3.8.2 Holistic Overviews Based on the PAULING FILE -- 3.8.3 Principles Defining Ordering of Chemical Elements -- 3.9 Lessons to Learn from Experience -- 3.10 Conclusion -- References -- Chapter 4 From Topological Descriptors to Expert Systems: A Route to Predictable Materials -- 4.1 Introduction -- 4.2 Topological Tools for Developing Knowledge Databases -- 4.2.1 Why Topological? -- 4.2.2 Topological vs. Other Descriptors of Crystal Structures -- 4.2.3 Topological vs. Crystallographic Databases -- 4.2.4 Deriving Topological Knowledge from Crystallographic Data -- 4.2.4.1 Algorithms for Topological Analysis -- 4.2.4.2 Building Distributions of Descriptors -- 4.2.4.3 Finding Correlations Between Descriptors -- 4.2.5 Universal Data Storage -- 4.3 Applications of Topological Tools in Crystal Chemistry and Materials Science -- 4.3.1 Network Topology Prediction -- 4.3.2 Prediction of Properties -- 4.4 Conclusions -- References. , Chapter 5 A High‐Throughput Computational Study Driven by the AiiDA Materials Informatics Framework and the PAULING FILE as Reference Database -- 5.1 Introduction -- 5.1.1 Three Key Developments Opened Up Unprecedented Opportunities -- 5.1.2 Relative Few Inorganic Solids Have Been Experimentally Investigated -- 5.2 Nature Defines Cornerstones Providing a Marvelously Rich but Still Very Rigid Systematic Framework of Restraint Conditions -- 5.3 The First, Second, and Third Paradigms -- 5.4 The Realization of the Fourth and Fifth Paradigms Requires Three Preconditions -- 5.4.1 Introduction of the Prototype Classification to Link Crystallographic Databases Created by Different Groups -- 5.4.2 Introduction of the Distinct Phases Concept to Link Different Kinds of Inorganic Solids Data -- 5.4.3 The Existence of a Comprehensive, Critically Evaluated Inorganic Solids Database Concept (DBMS) of Experimentally Determined Single‐Phase Inorganic Solids Data to Be Used as Reference -- 5.5 The Core Idea of the Fifth Paradigm -- 5.6 Restraint Conditions Revealed by "Inorganic Solids Overview-Governing Factor Spaces (Maps)" Discovered by Data‐Mining Techniques -- 5.6.1 Compound Formation Maps -- 5.6.2 Atomic Environment Type Stability Maps for AB Inorganic Solids -- 5.6.3 Twelve Principles in Materials Science Supporting Three Cornerstones Given by Nature -- 5.7 Quantum Simulation Strategy -- 5.8 Workflows Engine in AiiDA to Carry Out High‐Throughput Calculation for the Creation of the Materials Cloud, Binaries Edition -- 5.8.1 AiiDA -- 5.8.2 SSSP (Standard Solid State Pseudopotentials) Library -- 5.8.3 Workflows -- 5.8.4 Workfunctions -- 5.8.5 Workchains -- 5.8.6 Workflows Used in This Project -- 5.9 Conclusions -- Acknowledgment -- References -- Chapter 6 Modeling Materials Quantum Properties with Machine Learning -- 6.1 Introduction -- 6.2 Kernel Ridge Regression. , 6.3 Model Assessment -- 6.3.1 Learning Curve -- 6.3.2 Speedup -- 6.4 Representations -- 6.5 Recent Developments -- References -- Chapter 7 Automated Computation of Materials Properties -- 7.1 Introduction -- 7.2 Automated Computational Materials Design Frameworks -- 7.2.1 Generating and Using Databases for Materials Discovery -- 7.2.2 Standardized Protocols for Automated Data Generation -- 7.3 Integrated Calculation of Materials Properties -- 7.3.1 Autonomous Symmetry Analysis -- 7.3.2 Elastic Constants -- 7.3.3 Quasi‐harmonic Debye-Grüneisen Model -- 7.3.4 Harmonic Phonons -- 7.3.5 Quasi‐harmonic Phonons -- 7.3.6 Anharmonic Phonons -- 7.4 Online Data Repositories -- 7.4.1 Computational Materials Data Web Portals -- 7.4.2 Programmatically Accessible Online Repositories of Computed Materials Properties -- 7.5 Materials Applications -- 7.5.1 Disordered Materials -- 7.5.1.1 High Entropy Materials -- 7.5.1.2 Metallic Glasses -- 7.5.1.3 Modeling Off‐Stoichiometry Materials -- 7.5.2 Superalloys -- 7.5.3 Thermoelectrics -- 7.5.4 Magnetic Materials -- 7.6 Conclusion -- Acknowledgments -- References -- Chapter 8 Cognitive Chemistry: The Marriage of Machine Learning and Chemistry to Accelerate Materials Discovery -- 8.1 Introduction -- 8.2 Describing Molecules for Machine Learning Algorithms -- 8.3 Building Fast and Accurate Models with Machine Learning -- 8.3.1 Squared Exponential Kernel -- 8.3.2 Rational Quadratic Kernel -- 8.4 Searching Through Chemical Libraries -- 8.5 Conclusion -- References -- Chapter 9 Machine Learning Interatomic Potentials for Global Optimization and Molecular Dynamics Simulation -- 9.1 Introduction -- 9.2 Machine Learning Potential for Global Optimization -- 9.2.1 Lattice Sums Method -- 9.2.2 Feature Vector -- 9.2.3 Feature Vector Analysis -- 9.2.4 Examples of Machine Learning Interatomic Potentials -- 9.2.4.1 Aluminum. , 9.2.4.2 Carbon -- 9.2.4.3 Helium and Xenon -- 9.2.5 Discussion -- 9.3 Interatomic Potential for Molecular Dynamics -- 9.3.1 General Form of the Potential -- 9.3.2 Parameters Selection -- 9.3.3 Thermodynamic Quantities and Phase Transitions -- 9.3.4 Interatomic Potential for System of Two (or More) Atomic Types -- 9.4 Statistical Approach for Constructing ML Potentials -- 9.4.1 Two‐Body Potential -- 9.4.2 Three‐Body Potential -- Acknowledgements -- References -- Index -- EULA.
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  • 2
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 39 (1996), S. 479-489 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using molecular dynamics simulations to calculate free energies of molecular transformation, we have computed helix-coil transition free energies for alanine oligomers up to 14 residues long. The simulations have been done on the model in vacuo with dielectric constant, ε = 1, 5, 25, and ∞ and on the model in solution with explicit representation of water molecules and with partial charges on the oligomer set to zero. (The analogous simulations of the solvated model with full charges on the oligomer were reported elsewhere [L. Wang et al. (1995) Proceedings of the National Academy of Science USA 92, 10924-10928]). In vacuo, both entropic and electrostatic contributions oppose formation of a 3-residue helical nucleus in the helix initiation step. The entropy change opposing helix growth is found to be 3 e.u., van der Waals interactions favor helix growth by 1.9 kcal/mol, and electrostatic interactions favor helix growth by 3 kcal/mol (for ε = 1; all these values are per residue). In water, helix stability is slightly greater for the zero-charge model than for the full-charge model, i.e., the polypeptide's electrostatic interactions, which include hydrogen bonds, slightly destabilize the helix. The helix stabilizing contribution of the hydrophobic effect was found to be identical to that of the van der Waals interactions in vacuo (i.e., 1.9 kcal/mol per residue). The zero-charge model has nearly identical helix stability in vacuo and in water; the almost identical free energies of transfer of helix and coil state of the zero-charge oligomer from vacuum to water are found to be small. Thus, the results of this systematic variation of the force field afford a meaningful decomposition of the free energies for helix initiation and growth. © 1996 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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