• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.49 no.6
• /
• pp.815-822
• /
• 2016

The cationic biopolymer chitosan has several applications in medicine. Chitosan is the deacetylated derivative of chitin, the second most abundant naturally occurring polymer. Recent studies have investigated the relationship between chitosan and antibacterial activity. However, the molecular interactions and mechanisms have not been detailed. This study used molecular dynamics simulations to study interactions between chitosan and anionic bacterial membranes (POPE-POPG) and electrically neutral non-bacterial membranes (POPC). We calculated the free energy using umbrella sampling to compare the interactions between membranes and chitosan in different protonation states. Fully protonated chitosan interacted most strongly with the bacterial membranes, but weakly with non-bacterial membranes. These results suggest that electrostatic interactions are the main mechanism of the antibacterial activity of chitosan, and they provide insights into the design of novel antibacterial and antimicrobial agents.

• Macromolecular Research
• /
• v.8 no.2
• /
• pp.59-65
• /
• 2000

We simulated the conformational changes of polymethacrylates which have side chains with different lengths (methyl and butyl) by molecular dynamics simulation technique. Bulk states of atactic amorphous polymers relaxed at a higher temperature were generated. The chain behaviors of polymethacrylates were investigated upon varying temperatures. Molecular structural information was then obtained by characterizing radial distribution function(RDF), mean square displacement, self diffusion constant, and Connolly surfaces, among others. The estimated self diffusion constants and RDF values of PMMA and PBMA were found to be in good agreement with our expectation in view of the chain flexibility.

• Bulletin of the Korean Chemical Society
• /
• v.18 no.4
• /
• pp.415-424
• /
• 1997

Conformational flexibilities of the GlcNAc(β1,3)Gal(β)OMe are investigated through NMR spectroscopy and molecular modeling. Adiabatic energy map generated with a dielectric constant of 50 contains three local minima. All of the molecular dynamics simulations on three local minimum energy structures show fluctuations between two low energy structures, N2 at φ=80° and ψ=60° and N3 at φ=60° and ψ=-40°. We have presented adequate evidences to state that GlcNAc(β1,3)Gal(β)OMe exists in two conformationally discrete forms. Two state model of N2 and N3 conformers with a population ratio of 40:60 is used to calculate the effective cross relaxation rate and reproduces the experimental NOEs very well. Molecular dynamics simulation in conjunction with two state model proves successfully the dynamic equilibrium existed in GlcNAc(β1,3)Gal(β)OMe and can be considered as a powerful method to analyze the motional properties in the structure of carbohydrate. This observation also cautions against the indiscriminate use of a rigid model to analyze NMR data.

• Bulletin of the Korean Chemical Society
• /
• v.16 no.12
• /
• pp.1153-1162
• /
• 1995

The conformational details of β-lactose are investigated through molecular dynamics simulations in conjunction with the adiabatic potential energy map. The adiabatic energy map generated in vacuo contains five local minima. The lowest energy structure on the map does not correspond to the structure determined experimentally by NMR and the X-ray crystallography. When aqueous solvent effect is incorporated into the energy map calculation by increasing the dielectric constant, one of the local minima in the vacuum energy map becomes the global minimum in the resultant energy map. The lowest energy structure of the energy map generated in aquo is consistent with the one experimentally determined. Molecular dynamics simulations starting from those fivelocal minima on the vacuum energy map reveal that conformational transitions can take place among various conformations. Molecular dynamics simulations of the lactose and ricin B chain complex system in a stochastic boundary indicate that the most stable conformation in solution phase is bound to the binding site and that there are conformational changes in the exocyclic region of the lactose molecule upon binding.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
• /
• 2002.10b
• /
• pp.73-75
• /
• 2002

Recently, remarkable agreement has been reported between nonequilibrium molecular dynamics simulation and high-pressure Couette rheometry on squalane. We utilized the parameters obtained from this unique collaboration along with high-pressure viscometer measurements to calculate the elastohydrodynamic traction curve. A comparison with measured traction at 1.29 GPa shows excellent agreement, confirming the validity of the measurements and simulations. It should no longer be necessary to invoke a different rheological response to explain film thickness and traction.

• Journal of the Korean Chemical Society
• /
• v.56 no.6
• /
• pp.669-672
• /
• 2012

Classical molecular dynamics (MD) simulations using a scaled OSS2 potential originally derived from ab initio calculations are used to study the radial distribution functions of water. The original OSS2 water potential is shown to represent a glassy or an ice at ambient temperature, but the diffusion coefficient increases on increasing the temperature of the system or decreasing the density. This suggests scaling the OSS2 potential. The O-O, O-H, and H-H radial distribution functions and the corresponding coordination numbers for the scaled OSS2 potential, obtained by MD simulation, are in good agreement with the experiment results and calculations for the SPC/E water potential over a range of temperatures.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.11
• /
• pp.3909-3913
• /
• 2011

In this paper we have carried out molecular dynamics simulations (MD) for model systems of liquid n-alkane oligomers ($C_{12}{\sim}C_{80}$) at high temperatures (~2300 K) in a canonical ensemble to calculate viscosity ${\eta}$, self-diffusion constants D, and monomeric friction constant ${\zeta}$. We found that the long chains of these n-alkanes at high temperatures show an abnormality in density and in monomeric friction constant. The behavior of both activation energies, $E_{\eta}$ and $E_D$, and the mass and temperature dependence of ${\eta}$, D, and ${\zeta}$ are discussed.

• Journal of the Korean Magnetic Resonance Society
• /
• v.1 no.2
• /
• pp.79-94
• /
• 1997

The solution structure of bovine pancreatic trypsin inhibitor(BPTI) has been refined by NMR chemical shift data of C${\alpha}$H using classical molecular dynamics simulation. The structure dependent part of the observable chemical shift was modeled by ring current effect, magnetic anisotropy effect from the nearby groups, whereas the structure independent part was replaced with the random coil shift. A new harmonic function derived from the differences between the observed and calculated chemical shifts was added into physical force field as an pseudo potential energy term with force constant of 250 kJmol-1 ppm-2. During the 1.5 ns molecular dynamics simulation with chemical shift restraints BPTI has accessed different conformation space compared to crystal and NOE driven structure.

• Transactions of the Korean Society of Mechanical Engineers A
• /
• v.30 no.7 s.250
• /
• pp.809-815
• /
• 2006

The temperature and loading-rate dependence on the mechanical behavior of single-walled carbon nanotubes under axial compression and torsion is examined with classical molecular dynamics simulation. The critical buckling is found to depend on the temperature and loading-rate. The yielding under torsion is also found to depend on the temperature and loading-rate. But it is shown that the compression and torsional stiffness are independent of the varied temperatures and loading-rates.

• Proceedings of the Korean Society of Precision Engineering Conference
• /
• 1993.10a
• /
• pp.83-88
• /
• 1993

Recently, the analysis of microcutting with submicrometer depth of cut is tried to get a more high quality surface product, but to get a valuable result another method instead of conventional finite element method must be considered because finite elment method is impossible for a very small focused region and mesh size. As the altermative method, Molecular Dynamics or Statics is suggested and acceoted in the field of microcutting, indentation and crack propagation. In this paper using Molecuar Dynamics simulation, the phenomena of microcutting with subnanometer chip thickness is studied and the cutting mechanism for tool edge configuration is evaluated. As the result of simulation the atomistic chip formation is achieved.