Jeffrey R. Reimers

Computational Methods for Large Systems

Electronic Structure Approaches for Biotechnology and Nanotechnology

• Gebundenes Buch

Produktbeschreibung

While its results normally complement the information obtained by chemical experiments, computer computations can in some cases predict unobserved chemical phenomena Electronic-Structure Computational Methods for Large Systems gives readers a simple description of modern electronic-structure techniques. It shows what techniques are pertinent for particular problems in biotechnology and nanotechnology and provides a balanced treatment of topics that teach strengths and weaknesses, appropriate and inappropriate methods. It's a book that will enhance the your calculating confidence and improve your ability to predict new effects and solve new problems.

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Learn how to choose and apply the best electronic structure methods to solve real-world problems in nanotechnology and biotechnology
There are a variety of computational methods to choose from to solve almost any electronic structure problem in nanotechnology and biotechnology, including problems involving complex systems with hundreds of thousands of atoms. This book presents the best and most useful of these computational methods, carefully explaining each one's strengths and weaknesses. Moreover, a broad range of practical applications are developed and then demonstrated with the use of detailed examples, helping you choose the best method for your particular needs.
Each chapter of Computational Methods for Large Systems has been written by one or more leading experts in the development and application of computational methods. Chapters are logically organized into four parts:
Part A, DFT: The Basic Workhorse, explores the use of density-functional theory (DFT) for performing electronic structure computations on ground and excited states of large biological, chemical, and physical systems.
Part B, Higher Accuracy Methods, presents methods that can be used when modern DFT approaches don't work, including quantum Monte Carlo, coupled cluster calculations, and renormalized band-structure theory.
Part C, More Economical Methods, examines methods such as semi-empirical DFT and Hartree-Fock-based approaches as well as empirical Hubbard models that enable researchers to work with larger systems at more approximate levels.
Part D, Advanced Applications, applies electronic structure methods to nanoparticle and graphene structure, photobiology, control of polymerization processes, non-linear optics, nanoparticle optics, heterogeneous catalysis, spintronics, and molecular electronics.
With extensive references to the primary literature, Computational Methods for Large Systems is an ideal reference for computational scientists as well as a text for graduate students in computational chemistry, physics, biochemistry, biotechnology, materials science, and nanoscience.

Produktdetails

• Verlag: Wiley & Sons
• 1. Auflage
• Seitenzahl: 688
• Erscheinungstermin: 11. Oktober 2011
• Englisch
• Abmessung: 236mm x 160mm x 38mm
• Gewicht: 1139g
• ISBN-13: 9780470487884
• ISBN-10: 0470487887
• Artikelnr.: 28242839

Autorenporträt

JEFFREY R. REIMERS, PhD, is an Australian Research Council Professorial Research Fellow and works in the fields of molecular electronics and photosynthesis at The University of Sydney. Recently, he has been involved in the design and construction of single-molecule devices and has instituted a scanning-tunneling microscopy laboratory. Dr. Reimers has developed computational methods to solve problems involving strong electron-vibration coupling in biological photosynthesis, electron transport, and metal-organic chemistry.

Inhaltsangabe

Contributors xiii Preface: Choosing the Right Method for Your Problem xvii
A. DFT: The Basic Workforce 1 1. Principles of Density Functional Theory:
Equilibrium and Nonequilibrium Applications 3 Ferdinand Evers 1.1
Equilibrium Theories 3 1.2 Local Approximations 8 1.3 Kohn-Sham Formulation
11 1.4 Why DFT Is So successful 13 1.5 Exact Properties of DFTs 14 1.6
Time-Dependent DFT 19 1.7 TDDFT and Transport Calculations 28 1.8 Modeling
Reservoirs In and Out of Equilibrium 34 2. SIESTA: A Linear-Scaling Method
for Density Functional Calculations 45 Julian D. Gale 2.1 Introduction 45
2.2 Methodology 48 2.3 Future Perspectives 73 3. Large-Scale
Plane-Wave-Based Density Functional Theory: Formalism, Parallelization, and
Applications 77 Eric Bylaska, Kiril Tsemekhman, Niranjan Govind, and Marat
Valiev 3.1 Introduction 78 3.2 Plane-Wave Basis Set 79 3.3 Pseudopotential
Plane-Wave Method 81 3.4 Charged Systems 89 3.5 Exact Exchange 92 3.6
Wavefunction Optimization for Plane-Wave Methods 95 3.7 Car - Parrinello
Molecular Dynamics 98 3.8 Parallelization 101 3.9 AIMD Simulations of
Highly Charged Ions in Solution 106 3.10 Conclusions 110 B. Higher-Accuracy
Methods 117 4. Quantum Monte Carlo, Or, Solving the Many-Particle
Schrödinger Equation Accurately While Retaining Favorable Scaling with
System Size 119 Michael D. Towler 4.1 Introduction 119 4.2 Variational
Monte Carlo 124 4.3 Wavefunctions and Their Optimization 127 4.4 Diffusion
Monte Carlo 137 4.5 Bits and Pieces 146 4.6 Applications 157 4.7
Conclusions 160 5. Coupled-Cluster Calculations for Large Molecular and
Extended Systems 167 Karol Kowalski, Jeff R. Hammond, Wibe A. de Jong,
Peng-Dong Fan, Marat Valiev Dunyou Wang, and Niranjan Govind 5.1
Introduction 168 5.2 Theory 168 5.3 General Structure of Parallel
Coupled-Cluster Codes 174 5.4 Large-Scale Coupled-Cluster Calculations 179
5.5 Conclusions 194 6. Strong-Correlated Electrons: Renormalized Band
Structure Theory and Quantum Chemical Methods 201 Liviu Hozoi and Peter
Fulde 6.1 Introduction 201 6.2 Measure of the Strength of Electron
Correlations 204 6.3 Renormalized Band Structure Theory 206 6.4 Quantum
Chemical Methods 208 6.5 Conclusions 221 C. More-Economical Methods 225 7.
The Energy-Based Fragmentation Approach for Ab Initio Calculations of Large
Systems 227 Wei Li, Weijie Hua, Tao Fang, and Shuhua Li 7.1 Introduction
227 7.2 The Energy-Based Fragmentation Approach and Its Generalized Version
230 7.3 Results and Discussion 238 7.4 Conclusions 251 7.5 Appendix:
Illustrative Example of the GEBF Procedure 252 8. MNDO-like Semiempirical
Molecular Orbital Theory and Its Application to Large Systems 259 Timothy
Clark and James J. P. Stewart 8.1 Basic Theory 259 8.2 Parameterization 271
8.3 Natural History or Evolution of MNDO-like Methods 278 8.4 Large Systems
281 9. Self-Consistent-Charge Density Functional Tight-Binding Method: An
Efficient Approximation of Density Functional Theory 287 Marcus Elstner and
Michael Cous 9.1 Introduction 287 9.2 Theory 289 9.3 Performance of
Standard SCC-DFTB 300 9.4 Extensions of Standard SCC-DFTB 302 9.5
Conclusions 304 10. Introduction to Effective Low-Energy Hamiltonians in
Condensed Matter Physics and Chemistry 309 Sen J. Powell 10.1 Brief
Introduction to Second Quantization Notation 310 10.2 Hückel or
Tight-Binding Model 314 10.3 Hubbard Model 326 10.4 Heisenberg Model 339
10.5 Other Effective Low-Energy Hamiltonians for Correlated Electrons 349
10.6 Holstein Model 353 10.7 Effective Hamiltonian or Semiempirical Model?
358 D. Advanced Applications 367 11. SIESTA: Properties and Applications
369 Michael J. Ford 11.1 Ethynylbenzene Adsorption on Au(111) 370 11.2
Dimerization of Thiols on Au(111) 377 11.3 Molecular Dynamics of
Nanoparticles 384 11.4 Applications to Large Numbers of Atoms 387 12.
Modeling Photobiology Using Quantum Mechanics and Quantum
Mechanics/Molecular Mechanics Calculations 397 Xin Li, Lung Wa Chung, and
Keiji Morokuma 12.1 Introduction 397 12.2 Computational Strategies: Methods
and Models 400 12.3 Applications 410 12.4 Conclusions 425 13. Computational
Methods for Modeling Free-Radical Polymerization 435 Michelle L. Coote and
Chung Lin 13.1 Introduction 435 13.2 Model Reactions for Free-Radical
Polymerization Kinetics 441 13.3 Electronic Structure Methods 444 13.4
Calculation of Kinetics and Thermodynamics 457 13.5 Conclusion 468 14.
Evaluation of Nonlinear Optical Properties of Large Conjugated Molecular
Systems by Long-Range-Corrected Density Functional Theory 475 Hideo Sekino,
Akihide Miyazaki, Jong-Won Song, and Kimihiko Hirao 14.1 Introduction 476
14.2 Nonlinear Optical Response Theory 478 14.3 Long-Range-Corrected
Density Functional Theory 480 14.4 Evaluation of Hyperpolarizability for
Long Conjugated Systems 482 14.5 Conclusions 488 15. Calculating the Raman
and HyperRaman Spectra of Large Molecules and Molecules Interacting with
Nanoparticles 493 Nicholas Valley, Lasse Jensen, Jochen Autschbach, and
George C. Schatz 15.1 Introduction 494 15.2 Displacement of Coordinates
Along Normal Modes 496 15.3 Calculation of Polarizabilities Using TDDFT 496
15.4 Derivatives of the Polarizabilities with Respect to Normal Modes 500
15.5 Orientation Averaging 501 15.6 Differential Cross Sections 502 15.7
Surface-Enhanced Raman and HyperRaman Spectra 506 15.8 Application of
Tensor Rotations to Raman Spectra for Specific Surface Orientations 507
15.9 Resonance Raman 508 15.10 Determination of Resonant Wavelength 509
15.11 Summary 511 16. Metal Surfaces and Interfaces: Properties from
Density Functional Theory 515 Irene Yarovsky, Michelle J. S. Spencer, and
Ian K. Snook 16.1 Background, Goals, and Outline 515 16.2 Methodology 517
16.3 Structure and Properties of Iron Surfaces 521 16.4 Structure and
Properties of Iron Interfaces 538 16.5 Summary, Conclusions, and Future
Work 553 17. Surface Chemistry and Catalysis from Ab Initio-Based
Multiscale Approaches 561 Catherin Samofl and Simone Piccinin 17.1
Introduction 561 17.2 Predicting Surface Structures and Phase Transitions
563 17.3 Surface Phase Diagrams from Ab Initio Atomistic Thermodynamics 568
17.4 Catalysis and Diffusion from Ab Initio Kinetic Monte Carlo Simulations
576 17.5 Summary 584 18. Molecular Spintronics 589 Woo Youn Kim and Kwang
S. Kim 18.1 Introduction 589 18.2 Theoretical Background 591 18.3 Numerical
Implementation 600 18.4 Examples 604 18.5 Conclusions 612 19. Calculating
Molecular Conductance 645 Gemma C. Solomon and Mark A. Ratner 19.1
Introduction 615 19.2 Outline of the MEGF Approach 617 19.3 Electronic
Structure Challenges 623 19.4 Chemical Trends 625 19.5 Features of
Electronic Transport 630 19.6 Applications 634 19.7 Conclusions 639 Index
649