1 Introduction ................................................ 11
2 Computational methods ....................................... 15
2.1 Molecular dynamics method .............................. 15
2.1.1 Force fields .................................... 17
2.1.2 Data analysis ................................... 18
2.2 Energy optimization methods ............................ 19
2.3 Time/length scale problem .............................. 20
2.4 Classical nucleation theory ............................ 20
2.5 Diffusion controlled crystal aggregation ............... 22
3 Model development I: Aggregation from the vapour ............ 23
3.1 Motivation ............................................. 23
3.1.1 Method development .............................. 24
3.2 Test cases ............................................. 20
3.2.1 NaCl aggregation from the vapour ................ 26
3.2.2 CaF2 formation from the vapour .................. 30
3.3 Conclusions ............................................ 35
4 Model Development II: Crystallization from aqueous
solution .................................................... 37
4.1 Model expansion ........................................ 37
4.1.1 Details of the simulation model .................. 40
4.2 Crystal birth from aqueous solution .................... 42
4.2.1 Calcium fluoride aggregation .................... 42
4.2.2 Sodium chloride aggregation ..................... 40
1.3 Conclusions of the studies in water and discussion
of model deficiencies .................................. 47
5 Crystallization from non aqueous solution: ZnO nucleation
from Zn21 and OH ions ....................................... 49
5.1 Hydrogen bonds and proton transfer ..................... 49
5.1.1 Theoretical methods for studies of proton
transfer reactions .............................. 51
5.2 Model extension to proton transfer reactions ........... 51
5.3 The mechanism of the reaction "Zn2+ + 2OH- →
ZnO↓ + Н2O" ............................................ 54
5.4 Conclusions ............................................ 61
6 Growth controlling molecules: collagen ion interaction
analysis .................................................... 63
6.1 Hydroxyapatite and fluorapatite ........................ 63
6.1.1 Theoretical studies of apatites and apatite/
collagen composites ............................. 66
6.2 Collagen as a chemical entity and an organic matrix .... 69
6.2.1 Computational studies on collagen toward
collagen triple helix model ..................... 70
6.3 Force field details and simulation scheme .............. 73
6.4 Single ion association to a collagen helix ............. 70
6.5 Conclusions ............................................ 81
7 Towards biomineralization: fluorapatite-collagen
composites .................................................. 83
7.1 Growth control by collagen: Aggregation of calcium,
phosphate and fluoride ions on a protein matrix ........ 83
7.2 Conclusions ............................................ 93
8 Summary and outlook ......................................... 95
A Appendices I: Theory ..................................... 99
A.I Verlet algorithm ................................... 99
A.II Berendsen thermostat .............................. 100
A.III Berendsen barostat ................................ 101
A.IV Lorentz-Berthelot mixing rules .................... 102
В Appendices II: Details of computations .................. 103
B.I NaCl and CaF2 studies in vapour ................... 103
B.II NaCl and CaF2 aggregation in water ................ 105
B.III ZnO nucleation from ethanolic solution ............ 106
B.IV Ca2+, P43-, F- aggregation on collagen ............ 109
List of figures ............................................... 111
List of tables ................................................ 113
Bibliography .................................................. 115
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