| 5 |
|
condensed matters. As the underlying physical law behind molecular |
| 6 |
|
modeling of soft condensed matter, statistical mechanical principles |
| 7 |
|
used in this dissertation are briefly reviewed in |
| 8 |
< |
Chapt.~\ref{chapt:introduction}. Following that, an introduction to |
| 8 |
> |
Chapter.~\ref{chapt:introduction}. Following that, an introduction to |
| 9 |
|
molecular simulation techniques including newtonian dynamics and |
| 10 |
|
Langevin dynamics was provided. Even though the motions of soft |
| 11 |
|
condensed systems are characterized by different ODEs between |
| 15 |
|
performance and stability, especially during long simulations. Thus, |
| 16 |
|
the theory of geometric integration and the methods to construct |
| 17 |
|
symplectic integrators are also covered in |
| 18 |
< |
Chapt.~\ref{chapt:introduction}, as well as the mathematics behind |
| 18 |
> |
~\ref{chapt:introduction}, as well as the mathematics behind |
| 19 |
|
the elegant symplectic integration scheme involving rigid body |
| 20 |
|
dynamics. |
| 21 |
|
|
| 22 |
< |
In Chapt.~\ref{chapt:methodology}, the basic methods used in this |
| 22 |
> |
In Chapter.~\ref{chapt:methodology}, the basic methods used in this |
| 23 |
|
work were discussed. An overview of the DLM method was given showing |
| 24 |
|
that DLM distinguished itself by its accuracy and efficiency during |
| 25 |
|
long time simulation. Following this, the DLM method was extended to |
| 30 |
|
to study diffusion by measuring the constraint force was proposed |
| 31 |
|
and verified. |
| 32 |
|
|
| 33 |
< |
Chapt.~\ref{chapt:lipid} provided a general background to transport |
| 33 |
> |
Chapter.~\ref{chapt:lipid} provided a general background to transport |
| 34 |
|
phenomena in biological membranes. Atomistic simulations were |
| 35 |
|
applied to study the headgroup solvation for different |
| 36 |
|
phospholipids. A simple but relatively accurate and efficient |
| 43 |
|
|
| 44 |
|
The current status of experimental and theoretical approaches to |
| 45 |
|
study phase transition in banana-shaped liquid crystal system was |
| 46 |
< |
first reviewed in Chapt.~\ref{chapt:liquidcrystal}. A new rigid body |
| 46 |
> |
first reviewed in Chapter.~\ref{chapt:liquidcrystal}. A new rigid body |
| 47 |
|
model consisting of three identical Gay-Berne particles was then |
| 48 |
|
proposed to represent the banana shaped liquid crystal. Starting |
| 49 |
|
from an isotropic configuration, we successfully explored an unique |
| 50 |
|
chevron structure. Calculations from various order parameters and |
| 51 |
|
correlation functions also confirmed this discovery. |
| 52 |
|
|
| 53 |
< |
Lastly, Chapt.~\ref{chapt:langevin} summarized the applications of |
| 53 |
> |
Lastly, Chapter.~\ref{chapt:langevin} summarized the applications of |
| 54 |
|
Langevin dynamics and the development of Brownian dynamics. By |
| 55 |
|
embedding hydrodynamic properties into the sophisticated rigid body |
| 56 |
|
dynamics algorithms, we developed a new Langevin dynamics for |
