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El. knyga: Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

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  • Formatas: EPUB+DRM
  • Išleidimo metai: 16-May-2017
  • Leidėjas: Springer International Publishing AG
  • Kalba: eng
  • ISBN-13: 9783319560878
Kitos knygos pagal šią temą:
Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN ExplorerDidesnis paveikslėlis
  • Formatas: EPUB+DRM
  • Išleidimo metai: 16-May-2017
  • Leidėjas: Springer International Publishing AG
  • Kalba: eng
  • ISBN-13: 9783319560878
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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 systems energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broadvariety 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 Explorers 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).
1 Introduction to Computational Meso-Bio-Nano (MBN) Science and MBN Explorer
1(42)
1.1 Meso-Bio-Nano Science: A Novel Field of Interdisciplinary Research
1(15)
1.1.1 Structure and Dynamics of MBN Systems
2(5)
1.1.2 Clustering, Self-organisation and Structure Formation in MBN Systems
7(3)
1.1.3 Novel Materials
10(2)
1.1.4 Novel Technologies
12(2)
1.1.5 Multiscale Nature of MBN Systems
14(2)
1.2 Computational Approaches in MBN Science
16(9)
1.2.1 Quantum Atomic and Nanoscales
16(1)
1.2.2 Classical Nano- and Mesoscales
17(4)
1.2.3 Monte Carlo Approach and Finite Element Method
21(3)
1.2.4 MBN Explorer---A Universal Multiscale Approach
24(1)
1.3 Basics of MBN Explorer and MBN Studio
25(18)
1.3.1 MBN Explorer Main Features
29(1)
1.3.2 Areas of Application of MBN Explorer
30(6)
1.3.3 MBN Studio Main Features
36(7)
2 Theoretical Approaches for Multiscale Computer Simulations
43(54)
2.1 Hierarchy of Theoretical Methods and Their Limitations: ab initio Methods and Model Approaches
43(3)
2.2 Methods for Studying Dynamical Molecular Processes and Related Phenomena
46(7)
2.2.1 Newtonian Dynamics
47(1)
2.2.2 Relativistic Dynamics
47(1)
2.2.3 Rigid Body Dynamics
48(1)
2.2.4 Temperature Control
49(4)
2.3 Modeling Interatomic Interactions
53(11)
2.3.1 Pairwise Potentials
53(6)
2.3.2 Many-Body Potentials
59(5)
2.4 Studying Biomolecules: The Force Field Concept and Beyond
64(8)
2.4.1 Molecular Mechanics Force Field
64(3)
2.4.2 Rupture of Covalent Bonds
67(2)
2.4.3 Rupture of Valence Angles
69(1)
2.4.4 Rupture of Dihedral Interactions
70(1)
2.4.5 Formation of New Bonds
71(1)
2.4.6 Partial Charges Redistribution
72(1)
2.5 Multiscale Methods
72(8)
2.5.1 Kinetic Monte Carlo Method
73(2)
2.5.2 Simplifications of the KMC Method
75(1)
2.5.3 Particle Dynamics Model
76(2)
2.5.4 Irradiation Driven Molecular Dynamics
78(2)
2.6 Computational Aspects of Multi-particle Simulations
80(17)
2.6.1 Basic Interaction Approach
80(1)
2.6.2 Linked Cell Interaction Approach
81(3)
2.6.3 Boundary Conditions
84(4)
2.6.4 Calculation of Coulomb Interactions
88(9)
3 Computational Modelling of MBN Systems
97(24)
3.1 Introduction
97(4)
3.2 MBN Studio Toolkit
101(7)
3.2.1 Basic Structure of MBN Studio
101(4)
3.2.2 Visualisation of the Results
105(1)
3.2.3 Modeling MBN Systems
106(2)
3.3 Modeling of Crystalline Structures
108(5)
3.3.1 Specific Features of Crystalline Structures
108(3)
3.3.2 Simulation of Crystalline Structures with MBN Studio
111(2)
3.4 Modelling of Liquids
113(3)
3.4.1 Liquids in MBN Studio
113(2)
3.4.2 Analysing Simulations with MBN Studio
115(1)
3.5 Modelling of Gases
116(3)
3.6 Modelling of Material Interphases
119(2)
4 Atomic Clusters and Nanoparticles
121(50)
4.1 Introduction
121(3)
4.2 The Problem of Global Minimum
124(3)
4.2.1 Cluster Fusion Process
125(1)
4.2.2 Scenarios for Cluster Fusion Process
126(1)
4.2.3 Selection Criteria for Cluster Fusion Process
127(1)
4.3 Noble Gas Clusters
127(17)
4.3.1 Mass Spectra and Sequence of Magic Numbers
128(1)
4.3.2 Fusion of Global Energy Minimum Clusters
129(7)
4.3.3 Cluster Binding Energies
136(3)
4.3.4 Cluster Magic Numbers
139(5)
4.4 Metal Clusters
144(9)
4.4.1 Structure and Properties of Small Metal Clusters
144(3)
4.4.2 Accounting for Many-Body Interactions
147(2)
4.4.3 Validation of Classical Description of Systems on the Atomic Scale
149(4)
4.5 Carbon Clusters: Fullerenes
153(12)
4.5.1 Classical Approach to Formation and Fragmentation of Fullerenes
155(5)
4.5.2 Electronic Structure Versus Geometry
160(5)
4.6 Deposited Clusters and Nanoparticles
165(6)
4.6.1 Liquid Drop Model Versus MD for a Cluster on a Surface
165(3)
4.6.2 Shell-Correction Approach to Semi-spheroidal Atomic Clusters
168(3)
5 Biomolecular Systems
171(28)
5.1 Introduction
171(1)
5.2 Phase and Structural Transitions in Polypeptide Chains
172(17)
5.2.1 Statistical Model for The α-Helix ↔ Random Coil Phase Transition
173(2)
5.2.2 Energetics of Alanine Polypeptide
175(10)
5.2.3 Correlation of Different Amino Acids in the Polypeptide
185(1)
5.2.4 Molecular Dynamics Simulations of π-Helix → Random Coil Phase Transition
186(3)
5.3 DNA Unzipping
189(10)
5.3.1 Methods of Simulations
191(2)
5.3.2 Modeling the DNA Duplex Unzipping
193(6)
6 Nanostructured Materials
199(56)
6.1 Introduction
199(2)
6.2 Modeling Carbon Nanostructures
201(13)
6.2.1 Carbon Allotropes
201(2)
6.2.2 Carbon Nanotubes and Their Basic Properties
203(7)
6.2.3 Molecular Dynamics of Carbon Nanotube Growth
210(4)
6.3 Stability and Fragmentation of Metal Nanowires
214(6)
6.3.1 Using KMC Method of MBN Explorer to Model Nanowire Fragmentation
215(1)
6.3.2 Results of Simulation
216(4)
6.4 Crystalline Superlattice of Nanoparticles
220(8)
6.4.1 C60 Crystals and Nanowires
220(1)
6.4.2 Modeling Cao-TMB Superlattice
220(3)
6.4.3 Asymmetric Growth of the C60-TMB Superlattice
223(5)
6.4.4 Outlook for Modeling Other Superlattices
228(1)
6.5 Self-assembly, Growth, Surface Pattern Formation
228(9)
6.5.1 Silver Nanoparticle Self-assembly on a Graphite Surface
229(3)
6.5.2 Comparison of 3D with 2D Morphologies on a Surface
232(5)
6.6 Nanofractals and Morphological Transitions
237(18)
6.6.1 Experimental Observation and Characterization of Morphological Transition
239(3)
6.6.2 Theoretical Description of Morphological Transition
242(13)
7 Composite Systems and Material Interfaces
255(22)
7.1 Introduction
255(1)
7.2 Nanoparticles in Biological Environments
256(6)
7.2.1 Radiosensitizing Nanoparticles
256(1)
7.2.2 Simulation of Coated Gold Nanoparticles in Water Environment
257(5)
7.3 Nanoalloys and Composite Metal Systems
262(3)
7.3.1 Many-Body Potentials for Nanoalloys and Composite Systems
262(2)
7.3.2 Modeling Titanium and Nickel-Titanium Samples
264(1)
7.4 Atomic, Molecular and NP Diffusion
265(6)
7.4.1 Basics of the Diffusion Process
266(2)
7.4.2 Diffusion at Ti-Ni Interfaces
268(1)
7.4.3 Diffusion of Nickel Cluster at the Interface of Titanium and Water
269(2)
7.5 Diffusion at Interfaces
271(6)
7.5.1 Theoretical and Computational Aspects
271(3)
7.5.2 Results of Numerical Simulations
274(3)
8 Thermo-Mechanical Properties of Materials
277(46)
8.1 Introduction
277(2)
8.2 Simulation of Thermo-Mechanical Properties Up to the Bulk Limit
279(7)
8.2.1 Modification of the EAM Potential
280(2)
8.2.2 Simulations of Metal Melting with the Modified EAM potential
282(4)
8.3 Nanoindentation
286(9)
8.3.1 Modeling the Crystals and the Indenter
288(1)
8.3.2 Simulation of the Nanoindentation Process
289(3)
8.3.3 Quantification of Mechanical Properties
292(3)
8.4 Nanoscale Phase Transitions
295(15)
8.4.1 Melting Phase Transitions on the Nanoscale
295(12)
8.4.2 Martensite-Austenite Phase Transition on the Nanoscale
307(3)
8.5 Thermodynamic Model for Protein Folding
310(13)
8.5.1 Theoretical Methods
312(5)
8.5.2 Verification of the Model Through Experiment
317(6)
9 Collisional Processes Involving MBN Systems
323(50)
9.1 Introduction
323(3)
9.2 Collision Processes Involving Atomic Clusters and NPs
326(9)
9.3 Collision Processes Involving Biomolecules
335(10)
9.3.1 Electrons and Biomolecular Interactions
337(2)
9.3.2 Ions and Biomolecular Interactions
339(6)
9.4 Particles Propagation Through Medium
345(7)
9.5 Collision Induced Fragmentation Processeses
352(7)
9.5.1 Water Splitting
353(3)
9.5.2 Fragmentation of Alanine Dipeptide
356(1)
9.5.3 Binding of Two Alanine Amino Acids
357(2)
9.6 Molecular Desorption Processes
359(3)
9.7 Thermo-Mechanical Effects in Collision Processes
362(11)
9.7.1 Hydrodynamic Expansion on the Nanometre Scale
363(1)
9.7.2 MD Simulations of Ion-induced Shock Waves in Biological Media
364(2)
9.7.3 Damaging Effects Due to Shock Waves
366(2)
9.7.4 Evaluation of the Shock Wave damaging effect
368(2)
9.7.5 Transport of Reactive Species by the Radial Collective Flow
370(3)
10 Novel and Emerging Technologies
373(30)
10.1 Introduction
373(1)
10.2 Crystalline Undulator as a Novel Light Source
374(10)
10.3 Fundamental Nanoscopic Processes in Ion Beam Cancer Therapy
384(6)
10.3.1 Basic Facts About Ion Beam Cancer Therapy
384(4)
10.3.2 Multiscale Scenario of Radiation Damage
388(2)
10.4 Surface Deposition Technologies: The Case of FEBID
390(13)
10.4.1 Surface Deposition Techniques and Irradiation Driven Chemistry
390(2)
10.4.2 Modeling of FEBID with IDMD
392(5)
10.4.3 Results of Simulations and Their Validation
397(6)
11 Future Outlook
403(8)
11.1 State-of-the-art and Outlook
403(1)
11.2 Further Development of MBN Explorer and MBN Studio
404(4)
11.3 How to Get MBN Explorer and MBN Studio?
408(3)
References 411(36)
Index 447
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