• Genomics & Informatics
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• v.15 no.4
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• pp.142-146
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• 2017

More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin. To analyze how the leader peptide affects the maturation of insulin structurally, we adapted several in silico simulations using 13 artificial proinsulin sequences. Three-dimensional structures of models were predicted and compared. Although their sequences had few differences, the predicted structures were somewhat different. The structures were refined by molecular dynamics simulation, and the energy of each model was estimated. Then, protein-protein docking between the models and trypsin was carried out to compare how efficiently the protease could access the cleavage sites of the proinsulin models. The results showed some concordance with experimental results that have been reported; so, we expect our analysis will be used to predict the optimized sequence of artificial proinsulin for more effective production.

• Genomics & Informatics
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• v.15 no.4
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• pp.147-155
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• 2017

Apurinic/apyrimidinic endonuclease 1 (APE1) is an enzyme responsible for the initial step in the base excision repair pathway and is known to be a potential drug target for treating cancers, because its expression is associated with resistance to DNA-damaging anticancer agents. Although several inhibitors already have been identified, the identification of novel kinds of potential inhibitors of APE1 could provide a seed for the development of improved anticancer drugs. For this purpose, we first classified known inhibitors of APE1. According to the classification, we constructed two distinct pharmacophore models. We screened more than 3 million lead-like compounds using the pharmacophores. Hits that fulfilled the features of the pharmacophore models were identified. In addition to the pharmacophore screen, we carried out molecular docking to prioritize hits. Based on these processes, we ultimately identified 1,338 potential inhibitors of APE1 with predicted binding affinities to the enzyme.

• Journal of Electrical Engineering and Technology
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• v.10 no.2
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• pp.625-633
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• 2015

The effect of altitude on thermal conduction, surface temperature, and thermal radiation of partial arc was investigated on the basis of molecular gas dynamics to facilitate a deep understanding of the pollution surface discharge mechanism. The DC flashover model was consequently modified at high altitude. The validity of the modified DC flashover model proposed in this paper was proven through a comparison with the results of high-altitude simulation experiments and earlier models. Moreover, the modified model was found to be better than the earlier modified models in terms of forecasting the flashover voltage. Findings indicated that both the thermal conduction coefficient and the surface thermodynamics temperature of partial arc had a linear decrease tendency with the altitude increasing from 0 m to 3000 m, both of which dropped by approximately 30% and 3.6%, respectively. Meanwhile, the heat conduction and the heat radiation of partial arc both had a similar linear decrease of approximately 15%. The maximum error of DC pollution flashover voltage between the calculation value according to the modified model and the experimental value was within 6.6%, and the pollution flashover voltage exhibited a parabola downtrend with increasing of pollution.

• Advances in nano research
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• v.3 no.3
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• pp.143-168
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• 2015

Initiation of crack and its growth simulation requires accurate model of traction - separation law. Accurate modeling of traction-separation law remains always a great challenge. Atomistic simulations based prediction has great potential in arriving at accurate traction-separation law. The present paper is aimed at establishing a method to address the above problem. A method for traction-separation law prediction via utilizing atomistic simulations data has been proposed. In this direction, firstly, a simpler approach of common neighbor analysis (CNA) for the prediction of crack growth has been proposed and results have been compared with previously used approach of threshold potential energy. Next, a scheme for prediction of crack speed has been demonstrated based on the stable crack growth criteria. Also, an algorithm has been proposed that utilizes a variable relaxation time period for the computation of crack growth, accurate stress behavior, and traction-separation atomistic law. An understanding has been established for the generation of smoother traction-separation law (including the effect of free surface) from a huge amount of raw atomistic data. A new curve fit has also been proposed for predicting traction-separation data generated from the molecular dynamics simulations. The proposed traction-separation law has also been compared with the polynomial and exponential model used earlier for the prediction of traction-separation law for the bulk materials.

• Journal of the Korean Society of Manufacturing Technology Engineers
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• v.24 no.4
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• pp.421-427
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• 2015

In this paper, a description is given of finite element method (FEM) simulations of the elastic bending modulus of multi-layered graphene sheets that were carried out to investigate the mechanical behavior of graphene sheets with different gap thicknesses through molecular mechanics theory. The interaction forces between layers with various gap thicknesses were considered based on the van der Waals interaction. A finite element (FE) model of a multi-layered rectangular graphene sheet was proposed with beam elements representing bonded interactions and spring elements representing non-bonded interactions between layers and between diagonally adjacent atoms. As a result, the average elastic bending modulus was predicted to be 1.13 TPa in the armchair direction and 1.18 TPa in the zigzag direction. The simulation results from this work are comparable to both experimental tests and numerical studies from the literature.

• Composites Research
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• v.30 no.3
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• pp.193-201
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• 2017

Molecular dynamics simulation and the Mori-Tanaka micromechanics study are performed to investigate the effect of the covalent grafting between CNT and polyester on the mechanical behavior and load transfer of nanocomposites. The transversely isotropic stress-strain curves are determined through the tension and shear simulations according to the covalent grafting. Also, isotropic properties of randomly dispersed nanocomposites are obtained by orientation averaging the transversely isotropic stiffness matrix. By addressing the grafting, the transverse Young's modulus and shear moduli of the nanocomposites are improved, while the longitudinal Young's modulus decreases due to the degradation of the grafted CNT.

• Advances in materials Research
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• v.1 no.4
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• pp.245-268
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• 2012

Results of isothermal torsional oscillation tests are reported on melts of linear low density polyethylene and isotactic polypropylene. Prior to rheological tests, specimens were annealed at various temperatures ranging from $T_a$ = 180 to $310^{\circ}C$ for various amounts of time (from 30 to 120 min). Thermal treatment induced degradation of the melts and caused pronounced decreases in their molecular weights. With reference to the concept of transient networks, constitutive equations are developed for the viscoelastic response of polymer melts. A melt is treated as an equivalent network of strands bridged by junctions (entanglements and physical cross-links). The time-dependent response of the network is modelled as separation of active strands from and merging of dangling strands with temporary nodes. The stress-strain relations involve three adjustable parameters (the instantaneous shear modulus, the average activation energy for detachment of active strands, and the standard deviation of activation energies) that are determined by matching the dependencies of storage and loss moduli on frequency of oscillations. Good agreement is demonstrated between the experimental data and the results of numerical simulation. The study focuses on the effect of molecular weight of polymer melts on the material constants in the constitutive equations.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.310-310
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• 2011

Morphological evolution of amorphous carbon film is investigated by molecular dynamics simulation. Here, energetic carbon atoms (75 eV) are deposited on the diamond (001) substrate to find effect of incidence angles. At normal and near-normal incidences ($0^{\circ}{\sim}30^{\circ}$) atomically smooth surfaces are observed during their growth. However, rough surfaces emerge and develop into a ripple structure at grazing incidences ($60^{\circ}{\sim}70^{\circ}$). The different growth modes according to the incidence angles can be described by impact-induced displacements of atoms. Downhill transport along any sloped surfaces is predominant for the case of normal incidence. As the incidence angles become grazing, uphill transport is allowed along the surfaces, which have smaller slopes than incidence angle, so the surface features can be amplified. Impact-induced transport and self-shadowing effect can be responsible to the initial growth of seeding structures at a grazing incidence, which would be grown up as tilted columnar structures in further depositions.

• Korean Journal of Materials Research
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• v.16 no.2
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• pp.92-98
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• 2006

Molecular dynamics simulations were performed to study interface structures between an $Al_2O_3$ crystalline phase and a interface phase of $CaAl_2Si_2O_8$. We calculated atomic structures and excess interface energies in systems with different thicknesses of the interface film. It was found that excess interface energies at first readily decreased with increasing film thickness, but increased for larger thicknesses of more than 2 nm. The excess energies of $Al_2O_3/CaAl_2Si_2O_8$ interfaces exhibit a minimum at a thickness around 1 nm. In this range of film thicknesses, the atoms in the interface film show a short-range ordered structure and slow diffusion rather than the random structure and rapid diffusion expected to an observation of an equilibrium thickness for interface films in ceramics.

• Journal of the Korean Society for Heat Treatment
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• v.13 no.4
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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.