• Bulletin of the Korean Chemical Society
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• v.24 no.11
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• pp.1590-1598
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• 2003

In this paper we have presented the results for viscosity and self-diffusion constants of model systems for four liquid n-alkanes ($C_{12}, C_{20}, C_{32}, and C_{44}$) in a canonical ensemble at several temperatures using molecular dynamics (MD) simulations. The small chains of these n-alkanes are clearly $<{R_{ee}}^2>/6<{R_g}^2>>1$, which leads to the conclusion that the liquid n-alkanes over the whole temperatures considered are far away from the Rouse regime. Calculated viscosity ${\eta}$ and self-diffusion constants D are comparable with experimental results and the temperature dependence of both ${\eta}$ and D is suitably described by the Arrhenius plot. The behavior of both activation energies, $E_{\eta}$ and $E_D$, with increasing chain length indicates that the activation energies approach asymptotic values as n increases to the higher value, which is experimentally observed. Two calculated monomeric friction constants ${\zeta}$ and ${\zeta}_D$ give a correct qualitative trend: decrease with increasing temperature and increase with increasing chain length n. Comparison of the time auto-correlation functions of the end-to-end vector calculated from the Rouse model for n-dodecane ($C_{12}$) at 273 K and for n-tetratetracontane ($C_{44}$) at 473 K with those extracted directly from our MD simulations confirms that the short chain n-alkanes considered in this study are far away from the Rouse regime.

• Macromolecular Research
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• v.10 no.6
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• pp.297-303
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• 2002

We have investigated the microstructural properties of a weakly charged polyelectrolyte modeled with both Hookean spring and Debye-Huckel potential, by employing a novel hybrid scheme of molecular dynamics (MD) and Monte Carlo (MC) simulations. Although the off-lattice pivot step facilitates the earlier computations stage, it gives rise to oscillations and hinders the stable equilibrium state. In order to overcome this problem, we adopt the MC off-lattice pivot step in early stage only, and then switch the computation to a pure MD step. The result shows that the computational speed-up compared to the previous method is entirely above 10 to 50, without loss of the accuracy. We examined the conformations of polyelectrolyte in solvents in terms of the end-to-end distance, radius of gyration, and structure factor with variations of the screening effects of solvent and the monomer charges. The emphasis can favorably be given on the elongation behavior of a polyelectrolyte chain, with observing the simultaneous snapshots.

• Journal of Environmental Science International
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• v.25 no.7
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• pp.927-935
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• 2016

Dissolved oxygen is necessary for many biological processes as well as many industrial practices. Dissolved oxygen released from water in dissolved air flotation (DAF) systems can be have many different applications. However, DAF systems are very costly to operate. To develop more efficient DAF systems, a deeper understanding of the process of oxygen being released from water is required. In this study, molecular dynamics (MD) simulations were used to simulate 100 oxygen molecules surrounded by 31002 water molecules at temperatures ranging from $0^{\circ}C$ to $100^{\circ}C$. Simulations were carried out for 10 ns, during which, in most cases, all the oxygen molecules were released from the water droplet. With MD simulations, visualization of the molecules escaping the water droplet was possible, which aided the understanding of the interactions between molecules at the nano-scale. The results showed that as the oxygen molecules moved near the edge of the water droplet that the oxygen molecules hesitated before escaping the water droplet or returned to the interior of the water droplet. This was because of the attractive forces between the water and oxygen molecules. Moreover, after most of the oxygen molecules were released from the droplet, some were found to return to the droplet's edge or even the interior of the droplet. It was also confirmed that oxygen molecules were released at a faster rate at higher temperatures.

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.783-792
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• 2014

The binding interaction between a hemolytic peptide ${\delta}$-lysin and a zwitterionic lipid bilayer POPC was investigated through a series of molecular dynamics (MD) simulations. ${\delta}$-Lysin is a 26-residue, amphipathic, ${\alpha}$-helical peptide toxin secreted by Staphylococcus aureus. Unlike typical antimicrobial peptides, ${\delta}$-lysin has no net charge and it is often found in aggregated forms in solution even at low concentration. Our study showed that only the monomer, not dimer, inserts into the bilayer interior. The monomer is preferentially attracted toward the membrane with its hydrophilic side facing the bilayer surface. However, peptide insertion requires the opposite orientation where the hydrophobic side of peptide points toward the membrane interior. Such orientation allows the charged residues, Lys and Asp, to have stable salt bridges with the lipid head-group while the hydrophobic residues are buried deeper in the hydrophobic lipid interior. Our simulations suggest that breaking these salt bridges is the key step for the monomer to be fully inserted into the center of lipid bilayer and, possibly, to translocate across the membrane.

• Proceedings of the Korean Society for Technology of Plasticity Conference
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• 2007.10a
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• pp.348-351
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• 2007

Simulations of the buckling behavior of a single wall carbon nanotube(SWCNT) was carried out using molecular dynamics simulation. Molecular dynamics simulations were done with 1fs of time step. Tersoff's potential function was used as the interatomic potential function since it has been proved to be reliable to describe the C-C bonds in carbon nanotubes. Compressive force was applied by moving the top end of the nanotube at a constant velocity. Buckling behavior under compressive load was observed for (15,15) armchair SWCNTs with 2nm of diameter and 24.9nm of length. Buckling load and critical strain is obtained from the MD simulation. Deformation occurred on the top region of the CNT because of fast downward velocity.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.169-182
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• 2014

이 연구에서는 Lennard-Jones (LJ) particle을 이용하여 상분리 현상을 이해하기 위한 컴퓨터 시뮬레이션 연구를 수행하였다. 초기에 균일하게 분포되어 있는 LJ 입자들을 시뮬레이션 하면 상대적으로 dense phase와 dilute phase로 상분리 현상이 일어나게 된다. 상분리 현상의 첫 번째 단계를 핵 생성 (nucleation) 이라고 한다. 본 연구에서는 Brownian Dynamics (BD) Simulation과 Molecular Dynamics (MD) Simulation을 이용하여 상평형 그림을 구하고 초기에 일어나는 LJ 입자들의 nucleation rates를 구하였다.

• Journal of the Mineralogical Society of Korea
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• v.30 no.4
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• pp.161-172
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• 2017

Clay minerals play a major role in the geochemical cycles of metals in the Critical Zone, the Earth surface-layer ranging from the groundwater bottom to the tree tops. Atomistic scale research of the very fine particles can help understand the fundamental mechanisms of the important geochemical processes and possibly apply to development of hybrid nanomaterials. Molecular dynamics (MD) simulations can provide atomistic level insights into the crystal structures of clay minerals and the chemical reactivity. Classical MD simulations use a force field which is a parameter set of interatomic pair potentials. The ClayFF force field has been widely used in the MD simulations of dioctahedral clay minerals as the force field was developed mainly based on dioctahedral phyllosilicates. The ClayFF is often used also for trioctahedral mineral simulations, but disagreement exits in selection of the interatomic potential parameters, particularly for Mg atom-types of the octahedral sheet. In this study, MD simulations were performed for trioctahedral clay minerals such as brucite, lizardite, and talc, to test how the two different Mg atom types (i.e., 'mgo' or 'mgh') affect the simulation results. The structural parameters such as lattice parameters and interatomic distances were relatively insensitive to the choice of the parameter, but the vibrational power spectra of hydroxyls were more sensitive to the choice of the parameter particularly for lizardite.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 2002.10b
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• pp.59-60
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• 2002

In this digest, we briefly review our current molecular dynamics (MD) simulations that utilize both the reactive empirical bond order potential (REBO) and the adaptive intermolecular REBO (AIREBO) potential energy functions. The AIREBO potential includes intermolecular interactions, so that self·assembled monolayers, and liquids, can be modeled. We have examined the mechanical and tribological properties of model self assembled monolayers and amorphous carbon films. Self-assembled monolayers are modeled by covalently bonding hydrocarbon chains to diamond substrates. Because the REBO potentials can model chemical reactions, specific compression and sliding induced chemical reactions were identified.

• Bulletin of the Korean Chemical Society
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• v.30 no.5
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• pp.1139-1142
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• 2009

Refinement of NMR structures by molecular dynamics (MD) simulations with a solvent model has improved the structural quality. In this study, we applied MD refinement with the generalized Born (GB) implicit solvent model to protein structure determined under membrane-like environments. Despite popularity of the GB model, its applications to the refinement of NMR structures of hydrophobic proteins, in which detergents or organic solvents enclose proteins, are limited, and there is little information on the use of another GB parameter for these cases. We carried out MD refinement of crambin NMR structure in dodecylphosphocholine (DPC) micelles (Ahn et al., J. Am. Chem. Soc. 2006, 128, 4398-4404) with GB/Surface area model and two different surface tension coefficients, one for aquatic and the other for hydrophobic conditions. Our data show that, of two structures by MD refinement with GB model, the one refined with the parameter to consider hydrophobic condition had the better qualities in terms of precision and solvent accessibility.

• Korean Journal of Mineralogy and Petrology
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• v.33 no.1
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• pp.19-28
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• 2020

Ranciéte is a hexagonal phyllomanganate mineral containing random Mn(IV) vacancies with hydrated Ca²⁺ cations charged balanced as interlayer cations. Its Mn²⁺ analogue is called takanelite, and ranciéite and takanelite are regarded as end-members of a solid solution series of (Ca²⁺,Mn²⁺)Mn₄O₉·nH₂O. Because the minerals are found as very small particles associated with other minerals, the crystal structures of the solid solution series have yet to be defined. In this research, we conducted classical molecular dynamics (MD) simulations of ranciéite and takanelite by varying the Mn²⁺/Ca²⁺ interlayer cation ratio to find relations between the interlayer cations and mineral structures. MD simulation results of chalcophanite group minerals are compared with experimental results to verify our method applied. Then, lattice parameters of ranciéite and takanelite models are presented along with detailed interlayer structures as to the distribution and coordination of cations and water molecules. This study shows the potentials of MD simulations in entangling complicated phyllomanganates structures.