• Proceedings of the Korean Vacuum Society Conference
• /
• 2010.08a
• /
• pp.54-55
• /
• 2010

Vacancy defects in graphene can be created by electron or ion irradiation and those induce ripples which can change the electronic properties of graphene. Recently, the formation of defect structures such as vacancy defects and non-hexagonal rings has been reported in the high resolution transmission electron microscope (HR-TEM) of reduced graphene oxide [1]. In those HR-TEM images, it is noticed that the dislocations with pentagon-heptagon (5-7) pairs are formed and diffuses. Interestingly, it is also observed that two 5-7 pairs are separated and diffuse far away from each other. The separation of 5-7 pairs has been known to be due to their self-diffusion. However, from our tight-binding molecular dynamics simulation, it is found that the separation of 5-7 pairs is due to the diffusion of single vacancy defects and coalescence with 5-7 pairs. The diffusion and coalescence of single vacancy defects is too fast to be observed even in HR-TEM. We also implemented Van der Waals interaction in our tight-binding carbon model to describe correctly bi-layer and multi-layer graphene. The compressibility of graphite along c-axis in our tight-binding calculation is found to be in excellent agreement with experiment. We also discuss the difference between single layer and bi-layer graphene about vacancy diffusion and reconstruction.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.11
• /
• pp.3195-3200
• /
• 2010

We have performed molecular dynamics simulations of atomistic models of $C_{60}$ molecules and DMPC bilayer membranes to study the static and dynamic effects of carbon nanoparticles on biological membranes. All four $C_{60}$-membrane systems were investigated representing dilute and concentrated solutions of $C_{60}$ residing either inside or outside the membrane. The concentrated $C_{60}$ molecules in water phase start forming an aggregated cluster. Due to its heavy mass, the cluster tends to adhere on the surface of the bilayer membrane, hindering both translational and rotational diffusion of individual $C_{60}$. On the other hand, once $C_{60}$ molecules accumulate inside the membrane, they are well dispersed in the central region of the bilayer membrane. Because of the homogeneous dispersion of $C_{60}$ inside the membrane, each leaflet is pushed away from the center, making the bilayer membrane thicker. This thickening of the membrane provides more room for both translational and rotational motions of $C_{60}$ inside the membrane compared to that in the water region. As a result, the dynamics of $C_{60}$ inside the membrane becomes faster with increasing its concentration.

• International Journal of Control, Automation, and Systems
• /
• v.4 no.3
• /
• pp.382-393
• /
• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.

• Proceeding of EDISON Challenge
• /
• 2016.03a
• /
• pp.32-36
• /
• 2016

단일금속 나노입자에 비해 나노합금입자는 발광이나 촉매력과 같은 여러 특징들이 더 뛰어나게 나타난다고 잘 알려져 있다. 이에 따라 실험적인 연구뿐 아니라 이론적으로도 나노합금입자의 특성과 구조를 밝히려는 노력이 이루어지고 있다. 그러나 대부분의 연구는 자유공간을 상정하여 진행되고 있어, 갇힌 공간 속의 입자에 대한 연구는 부족한 실정이다. 이러한 배경으로 본 연구에서는 Sutton-Chen (SC) 포텐셜을 주요 이론으로 하여, 복제교환분자동력학(replica exchange molecular dynamics, REMD) 모의실험을 통해 가두는 공간의 크기에 따라 금-팔라듐 나노합금입자(Au17Pd17)의 구조와 특성이 어떻게 달라지는지 EDISON에 등록된 metal_alloy 프로그램(molecular dynamics simulation of metal alloy nano-cluster)을 사용해 살펴보았다. 결과적으로 입자가 상전이 이전의 낮은 온도에서 존재하면, 둘러싼 공간의 크기와 무관하게 안정한 구조의 중심에 항상 팔라듐 원자가 위치한다는 것이 확인되었다. 또, 가두는 공간의 크기마다 상전이가 일어나는 온도 구간의 차이가 나타났으며, 작은 공간에 갇힌 입자일수록 입자의 최대 직경이 작아지면서 상대적으로 높은 에너지를 가지는 구조를 형성하였다. 이는 입자가 존재하는 공간이 좁을수록 에너지의 증가를 통하면서 최대한 공간을 활용할 수 있는 구조를 선택하는 것으로 보인다.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2010.02a
• /
• pp.340-340
• /
• 2010

Various structures of vacancy defects in graphene layers and carbon nanotubes have been reported by high resolution transmission electron microscope (HR-TEM) and those arouse an interest of reconstruction processes of vacancy defects. In this talk, we present reconstruction processes of vacancy defects in a graphene and a carbon nanotube by tight-binding molecular dynamics (TBMD) simulations and by first principles total energy calculations. We found that a structure of a dislocation defect with two pentagon-heptagon (5-7) pairs in graphene becomes more stable than other structures when the number of vacancy units is ten and over. The simulation study of scanning tunneling microscopy reveals that the pentagon-heptagon pair defects perturb the wavefunction of electrons near Fermi level to produce the $\sqrt{3}\;{\times}\;\sqrt{3}$ superlattice pattern, which is in excellent agreement with experiment. It is also observed in our tight-binding molecular dynamics simulation that 5-7 pair defects play a very important role in vacancy reconstruction in a graphene layer and carbon nanotubes.

• Multiscale and Multiphysics Mechanics
• /
• v.1 no.1
• /
• pp.53-64
• /
• 2016

Amyloid fibrils have recently been considered as an interesting material, since they exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is larger than that of other protein materials. Despite recent findings of these excellent mechanical properties for amyloid fibrils, it has not been fully understood how these excellent mechanical properties are achieved. In this work, we have studied the nanomechanical deformation behaviors and properties of amyloid fibrils such as their elastic modulus as well as fracture strength, by using atomistic simulations, particularly steered molecular dynamics simulations. Our simulation results suggest the important role of the length of amyloid fibrils in their mechanical properties such that the fracture force of amyloid fibril is increased when the fibril length decreases. This length scale effect is attributed to the rupture mechanisms of hydrogen bonds that sustain the fibril structure. Moreover, we have investigated the effect of boundary condition on the nanomechanical deformation mechanisms of amyloid fibrils. It is found that the fracture force is critically affected by boundary condition. Our study highlights the crucial role of both fibril length and boundary condition in the nanomechanical properties of amyloid fibrils.

• Bulletin of the Korean Chemical Society
• /
• v.20 no.3
• /
• pp.285-290
• /
• 1999

In the present paper, we report a molecular dynamics (MD) simulation study for the structure and dynamics of H+ ions in non-rigid dehydrated H12-A zeolite framework at 298.15 K, using the same method we used in our previous studies of rigid and non-rigid zeolite-A frameworks. It is found that two different structures appear, depending on the choice of the Lennard-Jones parameter (σ) for the H+ ion, as is also observed in the study of rigid dehydrated H12-A zeolite framework, but the ranges of σ are different for the two structures. It is also found that some of the H+ ions exchanged their sites without changing the number of H+ ions at each site. The agreement between experimental and calculated structural parameters for non-rigid dehydrated H12-A zeolite is generally quite good. The calculated IR spectrum by Fourier transform of the total dipole moment auto-correlation function shows two major peaks, one around 2700 cm-1 and the other around 7000 cm-1. The former appears in the calculated IR spectra of non-rigid zeolite-A framework only system and the latter remains unexplained except, perhaps, as an indication of a new formation of a vibrational mode of the framework due to the adsorption of the H+ ions.

• Bulletin of the Korean Chemical Society
• /
• v.13 no.3
• /
• pp.317-324
• /
• 1992

Structure and dynamics of $Na^+$ ions are investigated by molecular dynamics simulations of rigid dehydrated zeolite-A at several temperatures using a simple Lennard-Jones potential plus Coulomb potential. A best-fitted set of electrostatic charges is chosen from the results of simulation at 298.15 K and Ewald summation technique is used for the long-ranged character of Coulomb interaction. The calculated x, y, and z coordinates of $Na^+$ ions are in good agreement with the positions determined by X-ray crystallography within statistical errors, their random movings in different types of closed cages are well described by time-correlation functions, and $Na_Ⅰ$ type ions are found to be less diffusive than $Na_Ⅱ$ and $Na_{III}$. At 600.0 K, the unstable $Na_{III}$ type ion pushes down one of nearest $Na_{I}$ ions into the $\beta-cage$ and sits on the stable site Ⅰ, and the captured ion in the $\beta-cage$ wanders over and attacks one of 8 $Na_{I}$ type ions.

• Journal of Microbiology and Biotechnology
• /
• v.31 no.11
• /
• pp.1576-1582
• /
• 2021

Bacterial β-glucuronidase in the intestine is involved in the conversion of 7-ethyl-10-hydroxycamptochecin glucuronide (derived from irinotecan) to 7-ethyl-10-hydroxycamptothecin, which causes intestinal bleeding and diarrhea (side effects of anti-cancer drugs). Twelve compounds (1-12) from Polygala tenuifolia were evaluated in terms of β-glucuronidase inhibition in vitro. 4-O-Benzoyl-3'-O-(O-methylsinapoyl) sucrose (C3) was highly inhibitory at low concentrations. C3 (an uncompetitive inhibitor) exhibited a k_i value of 13.4 μM; inhibitory activity increased as the substrate concentration rose. Molecular simulation revealed that C3 bound principally to the Gln158-Tyr160 enzyme loop. Thus, C3 will serve as a lead compound for development of new β-glucuronidase inhibitors.

• Proceedings of the Korean Society for Technology of Plasticity Conference
• /
• 1999.03b
• /
• pp.173-178
• /
• 1999

In this study MD simulations have been performed to observe the behavior of a grain boundary in an a-Fe plate under 2-dimensional loading. In MD simulation the acceleration of every molecule can be achieved from the potential energy and the force interacting between each molecule and the integration of the motion equation by using Verlet method gives the displacement of each molecule. Initially four a-Fe rectangular plates having different misorientation angles of grain boundary were modeled by using the Johnson potential and Morse potential We compared the potential energy of the grain boundary system with that of the perfect structure model. Also we could obtain the width of the grain boundary by investigating the local potential energy distribution. The tensile loading for each grain boundary models was applied and the behavior of grin boundary was studied. From this study it was clarified that in the case using Johnson potential the obvious fracture mechanism occurs along the grain boundary in the case of Morse potential the diffusion of the grain boundary appears instead of the grain boundary fracture.