• Genomics & Informatics
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• 제4권2호
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• pp.71-76
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• 2006

We have investigated biological responses to radiofrequency (RF) radiation in in vitro and in vivo models. By measuring the levels of heat shock proteins as well as the activation of mitogen activated protein kinases (MAPKs), we could not detect any differences upon RF exposure. In this study, we used more sensitive method to find the molecular responses to RF radiation. Jurkat, human T-Iymphocyte cells were exposed to 1763 MHz RF radiation at an average specific absorption rate (SAR) of 10 W/kg for one hour and harvested immediately (R0) or after five hours (R5). From the profiles of 30,000 genes, we selected 68 differentially expressed genes among sham (S), R0 and R5 groups using a random-variance F-test. Especially 45 annotated genes were related to metabolism, apoptosis or transcription regulation. Based on support vector machine (SVM) algorithm, we designed prediction model using 68 genes to discriminate three groups. Our prediction model could predict the target class of 19 among 20 examples exactly (95% accuracy). From these data, we could select the 68 biomarkers to predict the RF radiation exposure with high accuracy, which might need to be validated in in vivo models.

• 한국컴퓨터그래픽스학회논문지
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• 제18권3호
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• pp.1-7
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• 2012

본 논문에서는 단백질 분자 간의 인터페이스를 계산하는 알고리즘을 제안한다. 분자가 반데르바스 (van der Waals) 반경을 갖는 구의 집합으로 표현될 때, 공간 상의 한 점 p로부터 분자까지의 거리는 p로부터 가장 가까운 구까지의 거리에 대응한다. 분자 인터페이스는 두 개의 분자에 대해 같은 거리에 있는 점들로 구성된다. 제안된 알고리즘은 공간을 복셀의 집합로 분할한뒤, 각 복셀을 지나는 구의 위치 정보를 저장하여 복셀맵 (voxel map)을 구성하였다. 복셀맵을 이용하여 한 점으로부터 분자까지의 거리를 계산하며, GPU (graphic processor unit)를 이용하여 병렬처리를 수행함으로써 효율적으로 인터페이스를 근사한다.

• 열처리공학회지
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• 제13권4호
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• pp.259-264
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• 2000

In this study, we quantitatively measure the ion ranges of arsenic with energies ranging from 10 KeV to 100 KeV, implanted at $3^{\circ}$, $9^{\circ}$ $15^{\circ}$ the (100) plane, and the damage created during ion implantation. To obtain detailed information of ion range and damage distributions in low energy region where elastic collisions dominate the slowing down process, molecular dynamics computer simulation was performed and compared to the existing results. The effects of implant energy and degree on damage generation are present. The number of vacancy were calculated from the deposited energy using Kinchin-Pease equation. In the energy range 10 keV-100 keV, simulations show that the number of Frenckel pairs produced by As-ion bimbardment is 9 and incident angle dependence of the vacancy was the same but defects were distributed at different depth.

• Bulletin of the Korean Chemical Society
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• 제23권1호
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• pp.48-52
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• 2002

Using several molecular modeling programs we have performed computer simulations to investigate the complexation behaviors of an ester derivative of p-tert-butylcalix[5]arene (1e) toward a variety of butylammonium ions. Semi-empirical AM1 method was used for calculating the binding energies and the formation enthalpies. MM and CVFF forcefields for molecular mechanics calculations were adapted to express the complexation energies of the host. Molecular dynamics were performed to the calculated complex systems to simulate the ionophoric behavior of the host-guest complexes. The absolute Gibbs free energies of the host (1e) complexed with four kinds of butylammonium ions have been calculated using the Finite Difference Thermodynamic Integration (FDTI) method in Discover. Calculation results show that the trend in complex formation is n-$BuNH_3^+$ > iso-$BuNH_3^+$ >> sec-$BuNH_3^+$ > tert-$BuNH_3^+$, which is in good agreement with the experimental results.

• Journal of Advanced Marine Engineering and Technology
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• 제29권1호
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• pp.34-41
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• 2005

An experimental study of molecular motions on a liquid-vapor interface is limited due to micro-scale characteristics of a system with an angstrom or a nanometer size Therefore, in recent, many studies for micro-scale systems have been conducted by a computer simulation because it is free from experimental limitations. In this study, through the molecular dynamic (MD) method. molecular behavior was clarified on a liquid-vapor interface and a criterion to distinguish between liquid and vapor was suggested by a potential energy and the number of neighboring molecules. At an interface. the potential energy of a molecule was increased but the number of neighboring molecules was decreased when the molecule moved into a vapor region from a liquid region, and vice versa.

• 반도체디스플레이기술학회지
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• 제10권4호
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• pp.47-51
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• 2011

We investigated the substrate surface polishing by the spherical rigid abrasive under the compression using classical molecular dynamics modeling. We performed three-dimensional molecular dynamic simulations using the Morse potential functions for the various slide-to-roll ratios, from 0 to 1, and then, the compressive forces acting on the spherical rigid abrasive were calculated as functions of the time and the slide-to-roll ratio. The friction coefficients obtained from the classical molecular dynamics simulations were compared to those obtained from the experiments; and found that the molecular dynamic simulation results with the slide-to-roll ratio of 0 value were in good agreement with the experimental results.

• 통합자연과학논문집
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• 제7권2호
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• pp.75-78
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• 2014

Computer-aided drug design uses computational chemistry to discover, enhance, or study drugs and related biologically active molecules. It is now proved to be effective in reducing costs and speeding up drug discovery. In this short review, we discussed on the importance of combining molecular docking and molecular dynamics simulation methodologies. We also reviewed the importance of protein flexibility, refinement of docked complexes using molecular dynamics and the use of free energy calculations for the calculation of accurate binding energies has been reviewed.

• 대한전자공학회:학술대회논문집
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• 대한전자공학회 2004년도 하계종합학술대회 논문집(2)
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• pp.501-504
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• 2004

High quality GaN layer was obtained on 0001 sapphire substrate using ammonia($NH_3$) as a nitrogen source by gas source molecular beam epitaxy. As a result, RHEED is used to investigate the relaxation processes which take place during the growth of GaN. In-situ RHEED(reflection high electron energy diffraction) appeared streaky-like pattern. The full Width at half maximum of the x-ray diffraction(FWHM) rocking curve measured from plane of GaN has exhibited as narrow as 8arcmin and surface roughness was 7.83nm. Photoluminescence measurement of GaN was investigated at room temperature, where the intensity of the band edge emission is much stronger than that of deep level emission. The GaN epitaxy layer according to various growth condition was investigated.

• Bulletin of the Korean Chemical Society
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• 제24권6호
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• pp.757-762
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• 2003

Since theoretical investigations of gas phase clusters enable the evaluation of intrinsic molecular properties and intermolecular interactions, one can predict the macroscopic properties of bulk matter, from a microscopic determination of the properties of individual atoms, molecules, or clusters. Based on the insights obtained from theoretical investigations of the properties of a large number of cluster systems (ranging from simple water clusters to large π-systems), we have investigated the properties of various novel molecular systems including endo/exohedral fullerenes, nanotori, nonlinear optical materials, ionophores/receptors, polypeptides, enzymes, organic nanotubes, nanowires, and electronic and nano-mechanical molecular devices. The present minireview highlights some of the interesting results obtained in the course of our extensive theoretical investigations of clusters and nanomaterials.

• 한국전기전자재료학회논문지
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• 제25권7호
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• pp.569-573
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• 2012

We investigated the speed change of the diamond spherical abrasive during the substrate surface polishing under the pad compression by using classical molecular dynamics modeling. We performed three-dimensional molecular dynamics simulations using the Morse potential functions for the copper substrate and the Tersoff potential function for the diamond abrasive. As the compressive pressure increased, the indented depth of the diamond abrasive increased and then, the speed of the diamond abrasive along the direction of the pad moving was decreased. Molecular simulation result such as the abrasive speed decreasing due to the pad pressure increasing gave important information for the chemical mechanical polishing including the mechanical removal rate with both the pad speed and the pad compressive pressure.