2.3 Modeling Interatomic Interactions Pairwise Potentials Many-Body Potentials Studying Biomolecules: The Force

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1 Contents 1 Introduction to Computational Meso-Bio-Nano (MBN) Science and MBN EXPLORER Meso-Bio-Nano Science: A Novel Field of Interdisciplinary Research Structure and Dynamics of MBN Systems Clustering, Self-organisation and Structure Formation in MBN Systems Novel Materials Novel Technologies Multiscale Nature of MBN Systems Computational Approaches in MBN Science Quantum Atomic and Nanoscales Classical Nano- and Mesoscales Monte Carlo Approach and Finite Element Method MBN EXPLORER A Universal Multiscale Approach Basics of MBN EXPLORER and MBN STUDIO MBN EXPLORER Main Features Areas of Application of MBN EXPLORER MBN STUDIO Main Features Theoretical Approaches for Multiscale Computer Simulations Hierarchy of Theoretical Methods and Their Limitations: ab initio Methods and Model Approaches Methods for Studying Dynamical Molecular Processes and Related Phenomena Newtonian Dynamics Relativistic Dynamics Rigid Body Dynamics Temperature Control vii

2 viii Contents 2.3 Modeling Interatomic Interactions Pairwise Potentials Many-Body Potentials Studying Biomolecules: The Force Field Concept and Beyond Molecular Mechanics Force Field Rupture of Covalent Bonds Rupture of Valence Angles Rupture of Dihedral Interactions Formation of New Bonds Partial Charges Redistribution Multiscale Methods Kinetic Monte Carlo Method Simplifications of the KMC Method Particle Dynamics Model Irradiation Driven Molecular Dynamics Computational Aspects of Multi-particle Simulations Basic Interaction Approach Linked Cell Interaction Approach Boundary Conditions Calculation of Coulomb Interactions Computational Modelling of MBN Systems Introduction MBN STUDIO Toolkit Basic Structure of MBN STUDIO Visualisation of the Results Modeling MBN Systems Modeling of Crystalline Structures Specific Features of Crystalline Structures Simulation of Crystalline Structures with MBN STUDIO Modelling of Liquids Liquids in MBN STUDIO Analysing Simulations with MBN STUDIO Modelling of Gases Modelling of Material Interphases Atomic Clusters and Nanoparticles Introduction The Problem of Global Minimum Cluster Fusion Process Scenarios for Cluster Fusion Process Selection Criteria for Cluster Fusion Process

3 Contents ix 4.3 Noble Gas Clusters Mass Spectra and Sequence of Magic Numbers Fusion of Global Energy Minimum Clusters Cluster Binding Energies Cluster Magic Numbers Metal Clusters Structure and Properties of Small Metal Clusters Accounting for Many-Body Interactions Validation of Classical Description of Systems on the Atomic Scale Carbon Clusters: Fullerenes Classical Approach to Formation and Fragmentation of Fullerenes Electronic Structure Versus Geometry Deposited Clusters and Nanoparticles Liquid Drop Model Versus MD for a Cluster on a Surface Shell-Correction Approach to Semi-spheroidal Atomic Clusters Biomolecular Systems Introduction Phase and Structural Transitions in Polypeptide Chains Statistical Model for The a-helix $ Random Coil Phase Transition Energetics of Alanine Polypeptide Correlation of Different Amino Acids in the Polypeptide Molecular Dynamics Simulations of p-helix $ Random Coil Phase Transition DNA Unzipping Methods of Simulations Modeling the DNA Duplex Unzipping Nanostructured Materials Introduction Modeling Carbon Nanostructures Carbon Allotropes Carbon Nanotubes and Their Basic Properties Molecular Dynamics of Carbon Nanotube Growth Stability and Fragmentation of Metal Nanowires Using KMC Method of MBN EXPLORER to Model Nanowire Fragmentation Results of Simulation

4 x Contents 6.4 Crystalline Superlattice of Nanoparticles C 60 Crystals and Nanowires Modeling C 60 -TMB Superlattice Asymmetric Growth of the C 60 -TMB Superlattice Outlook for Modeling Other Superlattices Self-assembly, Growth, Surface Pattern Formation Silver Nanoparticle Self-assembly on a Graphite Surface Comparison of 3D with 2D Morphologies on a Surface Nanofractals and Morphological Transitions Experimental Observation and Characterization of Morphological Transition Theoretical Description of Morphological Transition Composite Systems and Material Interfaces Introduction Nanoparticles in Biological Environments Radiosensitizing Nanoparticles Simulation of Coated Gold Nanoparticles in Water Environment Nanoalloys and Composite Metal Systems Many-Body Potentials for Nanoalloys and Composite Systems Modeling Titanium and Nickel-Titanium Samples Atomic, Molecular and NP Diffusion Basics of the Diffusion Process Diffusion at Ti-Ni Interfaces Diffusion of Nickel Cluster at the Interface of Titanium and Water Diffusion at Interfaces Theoretical and Computational Aspects Results of Numerical Simulations Thermo-Mechanical Properties of Materials Introduction Simulation of Thermo-Mechanical Properties Up to the Bulk Limit Modification of the EAM Potential Simulations of Metal Melting with the Modified EAM potential

5 Contents xi 8.3 Nanoindentation Modeling the Crystals and the Indenter Simulation of the Nanoindentation Process Quantification of Mechanical Properties Nanoscale Phase Transitions Melting Phase Transitions on the Nanoscale Martensite-Austenite Phase Transition on the Nanoscale Thermodynamic Model for Protein Folding Theoretical Methods Verification of the Model Through Experiment Collisional Processes Involving MBN Systems Introduction Collision Processes Involving Atomic Clusters and NPs Collision Processes Involving Biomolecules Electrons and Biomolecular Interactions Ions and Biomolecular Interactions Particles Propagation Through Medium Collision Induced Fragmentation Processeses Water Splitting Fragmentation of Alanine Dipeptide Binding of Two Alanine Amino Acids Molecular Desorption Processes Thermo-Mechanical Effects in Collision Processes Hydrodynamic Expansion on the Nanometre Scale MD Simulations of Ion-induced Shock Waves in Biological Media Damaging Effects Due to Shock Waves Evaluation of the Shock Wave damaging effect Transport of Reactive Species by the Radial Collective Flow Novel and Emerging Technologies Introduction Crystalline Undulator as a Novel Light Source Fundamental Nanoscopic Processes in Ion Beam Cancer Therapy Basic Facts About Ion Beam Cancer Therapy Multiscale Scenario of Radiation Damage

6 xii Contents 10.4 Surface Deposition Technologies: The Case of FEBID Surface Deposition Techniques and Irradiation Driven Chemistry Modeling of FEBID with IDMD Results of Simulations and Their Validation Future Outlook State-of-the-art and Outlook Further Development of MBN EXPLORER and MBN STUDIO How to Get MBN EXPLORER and MBN STUDIO? References Index

Contents. Preface to the first edition

Contents. Preface to the first edition Contents List of authors Preface to the first edition Introduction x xi xiii 1 The nanotechnology revolution 1 1.1 From micro- to nanoelectronics 2 1.2 From the macroscopic to the nanoscopic world 4 1.3