Kim Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems

1. Auflage 2010
ISBN: 978-1-4419-7601-7
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 170 Seiten

Reihe: Springer Theses

This volume develops multiscale and multiphysics simulation methods to understand nano- and bio-systems by overcoming the limitations of time- and length-scales. Here the key issue is to extend current computational simulation methods to be useful for providing microscopic understanding of complex experimental systems. This thesis discusses the multiscale simulation approaches in nanoscale metal-insulator-metal junction, molecular memory, ionic transport in zeolite systems, dynamics of biomolecules such as lipids, and model lung system. Based on the cases discussed here, the author suggests various systematic strategies to overcome the limitations in time- and length-scales of the traditional monoscale approaches.

Autoren/Hrsg.

Kim, Hyungjun

Inhaltsverzeichnis

1;Foreword;7
2;Acknowledgments;9
3;Contents;11
4;List of Figures;15
5;List of Tables;27
6;1 Introduction ;29
7;2 Negative Differential Resistance of Oligo (Phenylene Ethynylene) Self-Assembled Monolayer Systems: The Electric Field Induced Conformational Change Mechanism ;36
7.1;2.1 Introduction;36
7.2;2.2 Simulation Details;37
7.2.1;2.2.1 Computational Details of QM Calculations;37
7.2.2;2.2.2 Conductivities of P and T Conformations (NEGF Calculations);38
7.2.3;2.2.3 Coarse-Grained NN Interacting Hamiltonian;38
7.2.4;2.2.4 Extracting NN Model Parameters from QM/FF Energies;38
7.2.5;2.2.5 Coarse-Grained MC Simulations;40
7.3;2.3 Results and Discussion;41
7.3.1;2.3.1 Two Conformations of AN-OPE;41
7.3.2;2.3.2 Electrical Conductivities of P and T;43
7.3.3;2.3.3 Response to Constant External Field;45
7.3.4;2.3.4 NDR for Time Dependent Electric Field;50
7.4;2.4 Conclusions;52
7.5;Bibliography;52
8;3 Free Energy Barrier for Molecular Motions in Bistable [2]Rotaxane Molecular Electronic Devices ;54
8.1;3.1 Introduction;54
8.2;3.2 Simulation Details;56
8.2.1;3.2.1 Potential of Mean Force from Constrained Molecular Dynamics Simulation;56
8.2.2;3.2.2 Constrained Molecular Dynamics Simulation;58
8.2.3;3.2.3 Force Field and MD Parameters;59
8.3;3.3 Results and Discussion;62
8.3.1;3.3.1 Charge Scheme: Adiabatic Approximation;62
8.3.2;3.3.2 Free Energy Profiles from PMF Calculations;63
8.4;3.4 Conclusions;69
8.5;Bibliography;69
9;4 Sodium Diffusion Through Aluminum-Doped Zeolite BEA System: Effect of Water Solvation ;73
9.1;4.1 Introduction;73
9.2;4.2 Simulation Details;74
9.2.1;4.2.1 Force Field;74
9.2.2;4.2.2 Grand Canonical Monte Carlo (GCMC) Method and Molecular Dynamics (MD) Simulation;76
9.2.3;4.2.3 Construction of Models and Calculation of Properties;76
9.3;4.3 Results and Discussion;77
9.3.1;4.3.1 Water Absorption;77
9.3.2;4.3.2 Structure of Water in Zeolite;79
9.3.3;4.3.3 Effect of Water Contents on Sodium Diffusion;80
9.3.4;4.3.4 Effect of Temperature on Sodium Diffusion;83
9.4;4.4 Conclusions;87
9.5;Bibliography;88
10;5 Experimental and Theoretical Investigationinto the Correlation Between Mass and Ion Mobility for Choline and Other Ammonium Cations in N2 ;90
10.1;5.1 Introduction;90
10.2;5.2 Experimental Section;93
10.2.1;5.2.1 Chemicals and Reagents;93
10.2.2;5.2.2 Electrospray Ionization Ion Mobility Spectrometer;93
10.2.3;5.2.3 Computational Modeling;94
10.3;5.3 Results;95
10.3.1;5.3.1 Mass-Mobility Correlation of Ammonium Cations;95
10.3.2;5.3.2 Tertiary and Quaternary Ammonium Cations with Similar Molecular Weights;97
10.3.3;5.3.3 Functional Group Isomers of Ammonium Cations;98
10.3.4;5.3.4 Collision Cross-Sections of Ions in N2 via the TrajectoryMethod;99
10.4;5.4 Discussion;100
10.4.1;5.4.1 Classical Ion-Neutral Collision Model;100
10.4.2;5.4.2 Computational Trajectory Method;101
10.4.3;5.4.3 Ion-Quadrupole Potential;101
10.4.4;5.4.4 Ion-Induced Dipole Potential;103
10.4.5;5.4.5 Van der Waals Potential;104
10.4.6;5.4.6 Mass-Mobility Correlation;104
10.5;5.5 Conclusions;107
10.6;Bibliography;107
11;6 Structural Characterization of Unsaturated Phospholipids Using Traveling Wave Ion Mobility Spectrometry ;109
11.1;6.1 Introduction;109
11.2;6.2 Experimental Section;111
11.2.1;6.2.1 Chemicals and Reagents;111
11.2.2;6.2.2 Electrospray Ionization Traveling Wave Ion Mobility Mass Spectrometer;112
11.2.3;6.2.3 Collision Cross-Section Calibration;113
11.2.4;6.2.4 Computational Modeling;113
11.3;6.3 Results;114
11.3.1;6.3.1 Saturated Phosphatidylcholine Cations;114
11.3.2;6.3.2 Unsaturated Phosphatidylcholine Cations;115
11.3.3;6.3.3 Sodiated Phosphatidylcholine Cations;115
11.3.4;6.3.4 Estimated Collision Cross-Sections of Ions Using T-Wave Calibration;117
11.3.5;6.3.5 Determination of Collision Cross-Sections of Ions;117
11.3.6;6.3.6 Calculated Collision Cross-Sections of Ions Using the Trajectory Method;120
11.4;6.4 Discussion;121
11.4.1;6.4.1 Effect of Drift Gas on Ion Mobility;121
11.4.2;6.4.2 Geometrical Effect on the Collision Cross-Sections of Phosphatidyl- choline Cations;122
11.4.3;6.4.3 Mass-Mobility Correlations of PhophatidylcholineCations;124
11.4.4;6.4.4 Characterizing Unsaturated Phosphatidylcholines from Mass-Mobility Correlation;126
11.5;6.5 Conclusions;127
11.6;Bibliography;128
12;7 Interfacial Reactions of Ozone with Lipidsand Proteins in a Model Lung Surfactant System ;130
12.1;7.1 Introduction;131
12.2;7.2 Methods;134
12.2.1;7.2.1 Chemicals and Reagents;134
12.2.2;7.2.2 Online FIDI-MS Technique and Heterogeneous Oxidationby O3;134
12.2.3;7.2.3 Molecular Dynamic Simulations;134
12.3;7.3 Results and Discussion;135
12.3.1;7.3.1 Interfacial Reaction of POPG with O3;135
12.3.2;7.3.2 Interfacial Oxidation of SP-B1-25;137
12.3.3;7.3.3 Oxidation of SP-B1-25 in POG Monolayer by O3;139
12.3.4;7.3.4 Interactions of SP-B1-25 in a Lipid Monolayer;139
12.4;7.4 Conclusions;142
12.5;Bibliography;145
13;8 Appendices ;147
13.1;8.1 Appendix A: Discussions on Coarse-Graining of Time- and Length-Scale in Monte Carlo Simulations for AN-OPE SAM;147
13.1.1;8.1.1 Time-Scale;147
13.1.2;8.1.2 Length-Scale;147
13.2;8.2 Appendix B: Effect of Molecular Fluctuations on the Electrical Conductivity of AN-OPE SAM;148
13.3;8.3 Appendix C: NDR in Other OPE-derivative Systems;151
13.3.1;8.3.1 Bare OPE;151
13.3.2;8.3.2 Nitro OPE;151
13.4;8.4 Appendix D: Conversion Factor Between External Electric Field and Bias Voltage;153
13.5;8.5 Appendix E: Mulliken Charge Distributions of Bistable [2]Rotaxane Molecular Switch Depending on CBPQT4+ Ring's Position;153
13.6;8.6 Appendix F: Consideration of Metric Effect on the Bistable [2]Rotaxane Molecule During the Constant MD Simulations Using Fixman's Theorem;182
13.7;8.7 Appendix G: Time for Consumption of POPG;182
13.8;8.8 Appendix H: Bulk-Phase Ozonolysis;183
13.8.1;8.8.1 Methods;183
13.8.2;8.8.2 Results and Discussion;184
13.9;Bibliography;188
14;Index;190