Multiscale modeling : from atoms to devices / edited by Pedro Derosa, Tahir Cagin
- Published:
- Boca Raton : CRC Press, [2011]
- Copyright Date:
- ©2011
- Physical Description:
- xiv, 271 pages : illustrations (some color) ; 25 cm
- Additional Creators:
- Derosa, Pedro and Cagin, Tahir
- Contents:
- Machine generated contents note: ch. 1 Overcoming Large Time-and Length-Scale Challenges in Molecular Modeling: A Review of Atomistic to Mesoscale Coarse-Graining Methods / Timothy Morrow -- 1.1.Introduction -- 1.2.Rigorous Coarse-Graining Method -- 1.2.1.Coarse-Graining by Matching Correlation Functions: Potential of Mean and Intetgral Equation Approaches -- 1.2.2.Coarse-Graining by Matching Correlation Functions -- 1.3.Coarse-Graining by Matching Forces -- 1.4.Empirical Coarse-Graining Techniques -- 1.5.Summary -- References -- ch. 2 Coarse-Graining Parameterization and Multiscale Simulation of Hierarchical Systems. Part I: Theory and Model Formulation / Markus J. Buehler -- 2.1.Introduction -- 2.1.1.Motivation: Hierarchical Systems and Empirical Links -- 2.1.2.Diversity of Systems and Applications: Need for a System-Dependent Approach -- 2.1.3.Alternative Coarse-Graining Advantages: Pragmatic System Simplification -- 2.1.4.When to Coarse-Grain: Appropriate Systems and Considerations -- 2.2.Examples of Coarse-Graining Methods -- 2.2.1.Elastic Network Models -- 2.2.2.Two Potential Freely Jointed Chain Polymer Models -- 2.2.3.Generalization of Interactions: The Martini Force Field -- 2.2.4.Universal Framework, Diverse Applications -- 2.3.Model Formulation -- 2.3.1.Characterize the System: Coarse-Grain Potential Type and Quantity -- 2.3.2.Full Atomistic Test Suite -- 2.3.3.Fitting Coarse-Grain Potentials -- 2.3.4.Direct Energy Equivalence -- 2.3.4.1.Consistent Mechanical Behavior -- 2.3.5.Validation -- 2.4.Summary and Conclusions -- Acknowledgments -- References -- ch. 3 Coarse-Graining Parameterization and Multiscale Simulation of Hierarchical Systems. Part II: Case Studies / Markus J. Buehler -- 3.1.Introduction -- 3.1.1.Investigate the Structure-Property Relation at the Mesoscale -- 3.1.2.Extend Atomistic Behavior to Inaccessible Time- and Length-Scales -- 3.1.3.Minimize Degrees of Freedom for Large Systems -- 3.2.Case Study I: Carbon Nanotubes and Tropocollagen -- 3.2.1.Model Development -- 3.2.2.Model Applications -- 3.2.2.1.Application 1: Self-Folding of Large Aspect Ratio Carbon Nanotubes and Nanotube Bundles -- 3.2.2.2.Application 2: Mechanical and Surface Properties of Vertically Aligned CNT Arrays -- 3.2.2.3.Application 3: Mechancial Property Veriation through Collagen Fibrial Crosslink Density -- 3.3.Case Study II: Folding/Unfolding of Alpha-Helical Protein Domains -- 3.3.1.Model Development -- 3.3.2.Model Applications -- 3.3.2.1.Application 1: Time Scale Extension -- 3.3.2.2.Application 2: Length Dependence -- 3.3.2.3.Application 3: Characterizing Intermediate Filament Networks -- 3.4.Case Study III: Mesoscopic Aggregation of Fullerene-Polymer Clusters -- 3.4.1.Model Development -- 3.4.2.Model Applications -- 3.4.2.1.Application 1: Large Systems of Aqueous C60-PEO Nanoparticles -- 3.4.2.2.Application 2: Systematic Variation of Polymer Architecture on C60-PEO Nanoparticles -- 3.5.Summary and Conclusions -- Acknowledgments -- References -- ch. 4 Coarse Molecular-Dynamics Analysis of Structural Transitions in Solid Materials / Ioannis G. Kevrekidis -- 4.1.Introduction -- 4.2.Coarse Molecular Dynamics -- 4.3.Melting of a Silicon Slab -- 4.4.Polymorphic Transitions in Metallic Crystals -- 4.5.Order-to-Disorder Transitions in Physisorbed Layers of Noble-Gas Adsorbates on Graphite -- 4.6.Summary and Conclusions -- Acknowledgments -- References -- ch. 5 Multiscale Modeling Approach for Studying MDH-Catalyzed Methanol Oxidation / Daniela Silvia Mainardi -- 5.1.Multiscale Modeling of Biological Systems -- 5.2.Monte Carlo Modeling -- 5.3.Modeling of an Enzyme-Assisted Reaction -- 5.4.Methanol Dehydrogenase Enzyme -- 5.4.1.Methanol Oxidation Mechanism by Methanol Dehydrogenase Enzymes -- 5.5.Components of the Multiscale Model -- 5.5.1.Density Functional Theory -- 5.5.2.Transition State Theory -- 5.5.3.Molecular Mechanics -- 5.6.Implementation of the Multiscale Approach to Study MDH-Assisted Methanol Oxidation -- 5.6.1.Molecular Mechanics for Lattice Preparation -- 5.6.2.Adsorption Models for Docking Site Information -- 5.6.3.Kinetic Monte Carlo Modeling of MDH-Assisted Methanol Oxidation Containing Multiscale Components -- 5.7.Conclusion -- References -- ch. 6 First-Principles Alloy Thermodynamics / Axel van de Walle -- 6.1.Introduction -- 6.2.Overview -- 6.3.Thermodynamics of Ordered Alloys -- 6.4.Thermodynamics of Disordered Alloys -- 6.4.1.Cluster Expansion Formalism -- 6.4.2.Determining Ground-State Structures -- 6.4.3.Free Energy Calculations -- 6.4.4.Free Energy of Phases with Dilute Disorder -- 6.5.Conclusion -- Acknowledgments -- References -- ch. 7 Nonlinear Finite Element Model for the Determination of Elastic and Thermal Properties of Nanocomposites / Pol Spanos -- 7.1.Introduction -- 7.2.Methodology -- 7.3.RVE Geometry Generation -- 7.3.1.Fiber Partitioning -- 7.3.2.Embedded Fiber Method -- 7.4.Nonlinear Model -- 7.4.1.Nonlinear Properties of Carbon Nanotubes -- 7.4.2.Nonlinear Properties of Epoxies -- 7.4.3.Choice and Implementation of Nonlinear Approaches -- 7.5.Results and Discussion -- 7.5.1.Elastic Results -- 7.5.2.Thermal Results -- 7.6.Concluding Remarks -- References -- ch. 8 Ensemble Monte Carlo Device Modeling: High-Field Transport in Nitrides / Cem Sevik -- 8.1.Introduction -- 8.2.Boltzmann Transport Equation -- 8.3.Ensemble Monte Carlo Charge Transport Simulation -- 8.3.1.EMC Flow Chart -- 8.3.1.1.Free Flight -- 8.3.1.2.Scattering Event -- 8.3.1.3.Carrier Energy -- 8.3.2.Scattering -- 8.4.Device Applications -- 8.4.1.Hot-Electron Effects in n-Type Structures -- 8.4.1.1.Computational Details -- 8.4.1.2.Alloy Scattering -- 8.4.1.3.Results -- 8.4.2.AlGaN Solar-Blind Avalanche Photodiodes -- 8.4.2.1.Computational Details -- 8.4.2.2.Results -- 8.4.3.Gunn Oscillations in GaN Channels -- 8.4.3.1.Basics -- 8.4.3.2.Motivation -- 8.4.3.3.Computational Details -- 8.4.3.4.Results -- 8.5.Concluding Remarks -- References -- ch. 9 Modeling Two-Dimensional Charge Devices / Afif Siddiki -- 9.1.Introduction -- 9.2.Electrostatic Modeling of Semiconductor Crystals: Solving Differential Equations -- 9.2.1.Solving the Poisson Equation in 1D -- 9.2.2.Generalization to 3D -- 9.2.2.1.Chemical Etching or Surface Oxidation -- 9.2.2.2.Gating -- 9.2.3.Solving the Poisson and Schrodinger Equations in 1D -- 9.2.4.Solving the Poisson and Schrodinger Equations in 2D with a Magnetic Field -- 9.3.Quantized Hall Effects and Related Phenomena -- 9.3.1.Bulk Theories -- 9.3.1.1.Impurity Potential -- 9.3.1.2.Coulomb vs. Gaussian -- 9.3.1.3.Effects of Spacer Thickness -- 9.3.2.Edge Theories -- 9.3.3.Interactions -- 9.3.3.1.Screening -- 9.3.3.2.Linear Screening of the Disorder Potential -- 9.3.3.3.Direct Coulomb -- 9.3.3.4.Zeeman Effect -- 9.3.3.5.Indirect Coulomb Interactions and Spin-Orbit Coupling -- 9.3.3.6.Calculating the Resistances -- 9.3.3.7.Summary -- 9.4.Recent Experimental Systems and Their Microscopic Modeling -- 9.4.1.Corbino Geometry -- 9.4.2.Quantum-Point Contacts -- 9.4.3.Double-Layer Systems Subject to T B-Direct Coulomb Interaction -- 9.4.4.Interferometers -- 9.4.5.Cleaved-Edge Overgrown Samples -- 9.4.6.Curved Crystals -- 9.5.Related Interesting Systems -- 9.5.1.Fractional Quantum Hall Effect -- 9.5.2.Excitonic Bose-Einstein Condensation -- 9.5.3.Rotating Ultracold Atoms -- 9.5.4.Graphene -- 9.6.Conclusion -- Acknowledgments -- References.
- Subject(s):
- ISBN:
- 9781439810392 (alk. paper)
1439810397 (alk. paper) - Bibliography Note:
- Includes bibliographical references and index.
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