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

By: Hyungjun Kim

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Hardcover | 19 November 2010

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200 Pages

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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.

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Published: 27th December 2012

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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-B_1-25 in POG Monolayer by O₃	p. 116
Interactions of SP-B_1-25 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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Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems

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Hardcover

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