| Introduction | p. 1 |
| Negative Differential Resistance of Oligo (Phenylene Ethynylene) Self-Assembled Monolayer Systems: The Electric Field Induced Conformational Change Mechanism | p. 9 |
| Introduction | p. 9 |
| Simulation Details | p. 10 |
| Computational Details of QM Calculations | p. 10 |
| Conductivities of P and T Conformations (NEGF Calculations) | p. 11 |
| Coarse-Grained NN Interacting Hamiltonian | p. 11 |
| Extracting NN Model Parameters from QM/FF Energies | p. 11 |
| Coarse-Grained MC Simulations | p. 13 |
| Results and Discussion | p. 14 |
| Two Conformations of AN-OPE | p. 14 |
| Electrical Conductivities of P and T | p. 16 |
| Response to Constant External Field | p. 18 |
| NDR for Time Dependent Electric Field | p. 23 |
| Conclusions | p. 25 |
| Bibliography | p. 25 |
| Free Energy Barrier for Molecular Motions in Bistable[2]Rotaxane Molecular Electronic Devices | p. 27 |
| Introduction | p. 27 |
| Simulation Details | p. 29 |
| Potential of Mean Force from Constrained Molecular Dynamics Simulation | p. 29 |
| Constrained Molecular Dynamics Simulation | p. 31 |
| Force Field and MD Parameters | p. 32 |
| Results and Discussion | p. 35 |
| Charge Scheme: Adiabatic Approximation | p. 35 |
| Free Energy Profiles from PMF Calculations | p. 36 |
| Conclusions | p. 42 |
| Bibliography | p. 42 |
| Sodium Diffusion Through Aluminum-Doped Zeolite BEA System: Effect of Water Solvation | p. 47 |
| Introduction | p. 47 |
| Simulation Details | p. 48 |
| Force Field | p. 48 |
| Grand Canonical Monte Carlo (GCMC) Method and Molecular Dynamics (MD) Simulation | p. 50 |
| Construction of Models and Calculation of Properties | p. 50 |
| Results and Discussion | p. 51 |
| Water Absorption | p. 51 |
| Structure of Water in Zeolite | p. 53 |
| Effect of Water Contents on Sodium Diffusion | p. 54 |
| Effect of Temperature on Sodium Diffusion | p. 57 |
| Conclusions | p. 61 |
| Bibliography | p. 62 |
| Experimental and Theoretical Investigation into the Correlation Between Mass and Ion Mobility for Choline and Other Ammonium Cations in N2 | p. 65 |
| Introduction | p. 65 |
| Experimental Section | p. 68 |
| Chemicals and Reagents | p. 68 |
| Electrospray Ionization Ion Mobility Spectrometer | p. 68 |
| Computational Modeling | p. 69 |
| Results | p. 70 |
| Mass-Mobility Correlation of Ammonium Cations | p. 70 |
| Tertiary and Quaternary Ammonium Cations with Similar Molecular Weights | p. 72 |
| Functional Group Isomers of Ammonium Cations | p. 73 |
| Collision Cross-Sections of Ions in N2 via the Trajectory Method | p. 74 |
| Discussion | p. 75 |
| Classical Ion-Neutral Collision Model | p. 75 |
| Computational-Trajectory Method | p. 76 |
| Ion-Quadrupole Potential | p. 76 |
| Ion-Induced Dipole Potential | p. 78 |
| Van der Waals Potential | p. 79 |
| Mass-Mobility Correlation | p. 79 |
| Conclusions | p. 82 |
| Bibliography | p. 82 |
| Structural Characterization of Unsaturated Phospholipids Using Traveling Wave Ion Mobility Spectrometry | p. 85 |
| Introduction | p. 85 |
| Experimental Section | p. 87 |
| Chemicals and Reagents | p. 87 |
| Electrospray Ionization Traveling Wave Ion Mobility Mass Spectrometer | p. 88 |
| Collision Cross-Section Calibration | p. 89 |
| Computational Modeling | p. 89 |
| Results | p. 90 |
| Saturated Phosphatidylcholine Cations | p. 90 |
| Unsaturated Phosphatidylcholine Cations | p. 91 |
| Sodiated Phosphatidylcholine Cations | p. 91 |
| Estimated Collision Cross-Sections of Ions Using T-Wave Calibration | p. 93 |
| Determination of Collision Cross-Sections of Ions | p. 93 |
| Calculated Collision Cross-Sections of Ions Using the Trajectory Method | p. 96 |
| Discussion | p. 97 |
| Effect of Drift Gas on Ion Mobility | p. 97 |
| Geometrical Effect on the Collision Cross-Sections of Phosphatidyl-choline Cations | p. 98 |
| Mass-Mobility Correlations of Phophatidylcholine Cations | p. 100 |
| Characterizing Unsaturated Phosphatidylcholines from Mass-Mobility Correlation | p. 102 |
| Conclusions | p. 103 |
| Bibliography | p. 104 |
| Interfacial Reactions of Ozone with Lipids and Proteins in a Model Lung Surfactant System | p. 107 |
| Introduction | p. 108 |
| Methods | p. 111 |
| Chemicals and Reagents | p. 111 |
| Online FIDI-MS Technique and Heterogeneous Oxidation by O3 | p. 111 |
| Molecular Dynamic Simulations | p. 111 |
| Results and Discussion | p. 112 |
| Interfacial Reaction of POPG with 03 | p. 112 |
| Interfacial Oxidation of SP-B1-25 | p. 114 |
| Oxidation of SP-B1-25 in POG Monolayer by O3 | p. 116 |
| Interactions of SP-B1-25 in a Lipid Monolayer | p. 116 |
| Conclusions | p. 119 |
| Bibliography | p. 122 |
| Appendices | p. 125 |
| Discussions on Coarse-Graining of Time- and Length-Scale in Monte Carlo Simulations for AN-OPE SAM | p. 125 |
| Time-Scale | p. 125 |
| Length-Scale | p. 125 |
| Effect of Molecular Fluctuations on the Electrical Conductivity of AN-OPE SAM | p. 126 |
| NDR in Other OPE-derivative Systems | p. 129 |
| Bare OPE | p. 129 |
| Nitro OPE | p. 129 |
| Conversion Factor Between External Electric Field and Bias Voltage | p. 131 |
| Mulliken Charge Distributions of Bistable [2]Rotaxane Molecular Switch Depending on CBPQT4+ Ring's Position | p. 131 |
| Consideration of Metric Effect on the Bistable [2]Rotaxane Molecule During the Constant MD Simulations Using Fixman's Theorem | p. 160 |
| Time for Consumption of POPG | p. 160 |
| Bulk-Phase Ozonolysis | p. 161 |
| Methods | p. 161 |
| Results and Discussion | p. 162 |
| Bibliography | p. 166 |
| Index | p. 169 |
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