Molecular Modeling at the Atomic Scale

Molecular Modeling at the Atomic Scale

by Ruhong Zhou
Released August 2014
Publisher(s): CRC Press
ISBN: 9781466562967

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Book description

Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts.

The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage.

This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.

Table of contents

  1. Front Cover (1/2)
  2. Front Cover (2/2)
  3. Contents
  4. Series Preface
  5. Preface
  6. Editor
  7. Contributors (1/2)
  8. Contributors (2/2)
  9. Chapter 1: Introduction to Molecular Dynamics and Enhanced Sampling Algorithms (1/6)
  10. Chapter 1: Introduction to Molecular Dynamics and Enhanced Sampling Algorithms (2/6)
  11. Chapter 1: Introduction to Molecular Dynamics and Enhanced Sampling Algorithms (3/6)
  12. Chapter 1: Introduction to Molecular Dynamics and Enhanced Sampling Algorithms (4/6)
  13. Chapter 1: Introduction to Molecular Dynamics and Enhanced Sampling Algorithms (5/6)
  14. Chapter 1: Introduction to Molecular Dynamics and Enhanced Sampling Algorithms (6/6)
  15. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (1/10)
  16. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (2/10)
  17. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (3/10)
  18. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (4/10)
  19. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (5/10)
  20. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (6/10)
  21. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (7/10)
  22. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (8/10)
  23. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (9/10)
  24. Chapter 2: Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods : Challenges, Methods, and Recent Applications (10/10)
  25. Chapter 3: Development of AMOEBA Force Field with Advanced Electrostatics (1/6)
  26. Chapter 3: Development of AMOEBA Force Field with Advanced Electrostatics (2/6)
  27. Chapter 3: Development of AMOEBA Force Field with Advanced Electrostatics (3/6)
  28. Chapter 3: Development of AMOEBA Force Field with Advanced Electrostatics (4/6)
  29. Chapter 3: Development of AMOEBA Force Field with Advanced Electrostatics (5/6)
  30. Chapter 3: Development of AMOEBA Force Field with Advanced Electrostatics (6/6)
  31. Chapter 4: Molecular Simulations of Protein Folding Dynamics and Thermodynamics (1/6)
  32. Chapter 4: Molecular Simulations of Protein Folding Dynamics and Thermodynamics (2/6)
  33. Chapter 4: Molecular Simulations of Protein Folding Dynamics and Thermodynamics (3/6)
  34. Chapter 4: Molecular Simulations of Protein Folding Dynamics and Thermodynamics (4/6)
  35. Chapter 4: Molecular Simulations of Protein Folding Dynamics and Thermodynamics (5/6)
  36. Chapter 4: Molecular Simulations of Protein Folding Dynamics and Thermodynamics (6/6)
  37. Chapter 5: Minimal Models for the Structure and Dynamics of Nucleic Acids (1/5)
  38. Chapter 5: Minimal Models for the Structure and Dynamics of Nucleic Acids (2/5)
  39. Chapter 5: Minimal Models for the Structure and Dynamics of Nucleic Acids (3/5)
  40. Chapter 5: Minimal Models for the Structure and Dynamics of Nucleic Acids (4/5)
  41. Chapter 5: Minimal Models for the Structure and Dynamics of Nucleic Acids (5/5)
  42. Chapter 6: Amyloid Peptide Aggregation : Computational Techniques to Deal with Multiple Time and Length Scales (1/6)
  43. Chapter 6: Amyloid Peptide Aggregation : Computational Techniques to Deal with Multiple Time and Length Scales (2/6)
  44. Chapter 6: Amyloid Peptide Aggregation : Computational Techniques to Deal with Multiple Time and Length Scales (3/6)
  45. Chapter 6: Amyloid Peptide Aggregation : Computational Techniques to Deal with Multiple Time and Length Scales (4/6)
  46. Chapter 6: Amyloid Peptide Aggregation : Computational Techniques to Deal with Multiple Time and Length Scales (5/6)
  47. Chapter 6: Amyloid Peptide Aggregation : Computational Techniques to Deal with Multiple Time and Length Scales (6/6)
  48. Chapter 7: Lipid Bilayers : Structure, Dynamics, and Interactions with Antimicrobial Peptides (1/6)
  49. Chapter 7: Lipid Bilayers : Structure, Dynamics, and Interactions with Antimicrobial Peptides (2/6)
  50. Chapter 7: Lipid Bilayers : Structure, Dynamics, and Interactions with Antimicrobial Peptides (3/6)
  51. Chapter 7: Lipid Bilayers : Structure, Dynamics, and Interactions with Antimicrobial Peptides (4/6)
  52. Chapter 7: Lipid Bilayers : Structure, Dynamics, and Interactions with Antimicrobial Peptides (5/6)
  53. Chapter 7: Lipid Bilayers : Structure, Dynamics, and Interactions with Antimicrobial Peptides (6/6)
  54. Chapter 8: Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations (1/6)
  55. Chapter 8: Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations (2/6)
  56. Chapter 8: Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations (3/6)
  57. Chapter 8: Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations (4/6)
  58. Chapter 8: Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations (5/6)
  59. Chapter 8: Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations (6/6)
  60. Chapter 9: Simulating Membranes and Membrane Proteins (1/7)
  61. Chapter 9: Simulating Membranes and Membrane Proteins (2/7)
  62. Chapter 9: Simulating Membranes and Membrane Proteins (3/7)
  63. Chapter 9: Simulating Membranes and Membrane Proteins (4/7)
  64. Chapter 9: Simulating Membranes and Membrane Proteins (5/7)
  65. Chapter 9: Simulating Membranes and Membrane Proteins (6/7)
  66. Chapter 9: Simulating Membranes and Membrane Proteins (7/7)
  67. Chapter 10: Protein and Nanoparticle Interactions : Perspectives of Nanomedicine and Nanotoxicity (1/7)
  68. Chapter 10: Protein and Nanoparticle Interactions : Perspectives of Nanomedicine and Nanotoxicity (2/7)
  69. Chapter 10: Protein and Nanoparticle Interactions : Perspectives of Nanomedicine and Nanotoxicity (3/7)
  70. Chapter 10: Protein and Nanoparticle Interactions : Perspectives of Nanomedicine and Nanotoxicity (4/7)
  71. Chapter 10: Protein and Nanoparticle Interactions : Perspectives of Nanomedicine and Nanotoxicity (5/7)
  72. Chapter 10: Protein and Nanoparticle Interactions : Perspectives of Nanomedicine and Nanotoxicity (6/7)
  73. Chapter 10: Protein and Nanoparticle Interactions : Perspectives of Nanomedicine and Nanotoxicity (7/7)
  74. Chapter 11: Modeling of DNA Sequencing with Solid-State Nanopores (1/4)
  75. Chapter 11: Modeling of DNA Sequencing with Solid-State Nanopores (2/4)
  76. Chapter 11: Modeling of DNA Sequencing with Solid-State Nanopores (3/4)
  77. Chapter 11: Modeling of DNA Sequencing with Solid-State Nanopores (4/4)
  78. Chapter 12: Biological Water under Confinement : Nanoscale Dewetting (1/7)
  79. Chapter 12: Biological Water under Confinement : Nanoscale Dewetting (2/7)
  80. Chapter 12: Biological Water under Confinement : Nanoscale Dewetting (3/7)
  81. Chapter 12: Biological Water under Confinement : Nanoscale Dewetting (4/7)
  82. Chapter 12: Biological Water under Confinement : Nanoscale Dewetting (5/7)
  83. Chapter 12: Biological Water under Confinement : Nanoscale Dewetting (6/7)
  84. Chapter 12: Biological Water under Confinement : Nanoscale Dewetting (7/7)
  85. Back Cover

Product information

  • Title: Molecular Modeling at the Atomic Scale
  • Author(s): Ruhong Zhou
  • Release date: August 2014
  • Publisher(s): CRC Press
  • ISBN: 9781466562967