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A Lattice Statistical Thermodynamic Study of Bilayer Amphiphile Molecules
Pak, Young-Shang,Pak, Hyung-Suk Korean Chemical Society 1990 Bulletin of the Korean Chemical Society Vol.11 No.5
In order to elucidate conformational properties of bilayer semiflexible amphiphile molecules, we derive a expression of free energy separation with respect to bilayer width, and segment density profiles on the basis of cubic lattice model. Our result shows that at the moderate surface coverage region (i.e., ${\sigma}$ < 0.35), bilayer system tends to have thermodynamically favorable bilayer width corresponding to free energy minimum condition resulting from the major contribution of attractive interaction between chain segments. However such a favorable bilayer width do not occur in the region of high surface converage (i.e., ${\sigma}$> 0.4) where repulsive interaction between chain segments is considered to be dominant.
A Statistical Theory of Conformational Properties of Amphiphile Molecules at the Air-Water Interface
Young Shang Pak,Hyungsuk Pak Korean Chemical Society 1991 Bulletin of the Korean Chemical Society Vol.12 No.2
A lattice mean field theory is developed to investigate the conformational properties of monolayer amphiphiles at the air-water interface. By generalizing Dill and Cantor's method and by extending Whittington's recurrence equation, we derive the supermatrix recurrence equation which is applied to calculation of various segment density profiles and order parameter, etc. In deriving the equation, we incorporated the chain stiffness effect and the chain connectivity which are distinguished features of linear chain molecule. Our result shows that, as the surface coverage $\sigma$ increases the chain ordering process with respect to vertical axis of the lattice system becomes dominant.
Computational Study of Human Calcitonin (hCT) Oligomer
Pak, Young-Shang,Shin, Jung-Ho,Jang, Soon-Min Korean Chemical Society 2009 Bulletin of the Korean Chemical Society Vol.30 No.12
We have performed long time REMD simulation on 15-19 residues of human calcitonin hormone (DFNKF) which is known to form highly ordered amyloid fibril. The simulation started from randomly oriented multiple DFNKF strand. Using all-atom level simulations with the generalized Born solvation (GB) model (param99MOD3), we observed spontaneous formation of ${\beta}$-sheet for tetramer. Interestingly, the current simulation gives anti-parallel sheet as a major conformation, consistent with experiments. The major interaction stabilizing the anti-parallel sheet seems to be the inter-strand hydrogen bond.
Yang, Chang-Won,Pak, Young-Shang Korean Chemical Society 2012 Bulletin of the Korean Chemical Society Vol.33 No.3
We performed replica exchange molecular dynamics (REMD) simulations of the tripzip2 peptide (betahairpin) using the GB implicit and TI3P explicit solvation models. By comparing the resulting free energy surfaces of these two solvation model, we found that the GB solvation model produced a distorted free energy map, but the explicit solvation model yielded a reasonable free energy landscape with a precise location of the native structure in its global free energy minimum state. Our result showed that in particular, the GB solvation model failed to describe the tryptophan packing of trpzip2, leading to a distorted free energy landscape. When the GB solvation model is replaced with the explicit solvation model, the distortion of free energy shape disappears with the native-like structure in the lowest free energy minimum state and the experimentally observed tryptophan packing is precisely recovered. This finding indicates that the main source of this problem is due to artifact of the GB solvation model. Therefore, further efforts to refine this model are needed for better predictions of various aromatic side chain packing forms in proteins.
Lee, Song-Hi,Pak, Young-Shang Korean Chemical Society 2004 Bulletin of the Korean Chemical Society Vol.25 No.4
Canonical sampling method has been presented to generate the initial conditions for reactive flux studies of organic reactions in water. Velocity Verlet version of Nose-Hoover chain dynamics algorithm has been employed to sample the initial conditions according to canonical distribution. The unstable normal mode of a transition state has been introduced to define a dividing plane separating reactant and product regions in reaction processes. This method has been implemented and tested for the case iels-Alder reaction of methyl vinyl ketone (MVK) and cyclopentadiene (CPD) in water, providing a reliable tool for further reactive flux molecular dynamics studies in condensed media.