• BMB Reports
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• v.49 no.8
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• pp.431-436
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• 2016

Human papillomavirus (HPV) is the major cause of cervical cancer, a deadly threat to millions of females. The early oncogene product (E7) of the high-risk HPV16 is the primary agent associated with HPV-related cervical cancers. In order to understand how E7 contributes to the transforming activity, we investigated the structural features of the flexible N-terminal region (46 residues) of E7 by carrying out N-15 heteronuclear NMR experiments and replica exchange molecular dynamics simulations. Several NMR parameters as well as simulation ensemble structures indicate that this intrinsically disordered region of E7 contains two transient (10-20% populated) helical pre-structured motifs that overlap with important target binding moieties such as an E2F-mimic motif and a pRb-binding LXCXE segment. Presence of such target-binding motifs in HPV16 E7 provides a reasonable explanation for its promiscuous target-binding behavior associated with its transforming activity.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.27 no.10
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• pp.1754-1761
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• 2003

The atomic force microscopy (AFM) based lithographic technique has been used directly to machine material surface and fabricate nano components in MEMS (micro electro mechanical system). In this paper, three-dimensional molecular dynamics (MD) simulations have been conducted to evaluate the characteristic of deformation process at atomistic scale for nano-lithography process. Effects of specific combinations of crystal orientations and cutting directions on the nature of atomistic deformation were investigated. The interatomic force between diamond tool and workpiece of copper material was assumed to be derived from the Morse potential function. The variation of tool geometry and cutting depth was also evaluated and the effect on machinability was investigated. The result of the simulation shows that crystal plane and cutting direction significantly influenced the variation of the cutting forces and the nature of deformation ahead of the tool as well as the surface deformation of the machined surface.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.31 no.5
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• pp.435-447
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• 2007

Recently, as MEMS and NEMS devices have been widely used in the various engineering applications, the characteristics of nanoscale systems are investigated in the limelight. However, as opposed to a macroscale system, the identification of the state of nanoscale systems is extremely hard because they can include only the order of $10^3{\sim}10^5$ molecules, which requires highly expensive and accurate experimental apparatus for an investigation. This limitations make the study on nanoscale system use computer simulations. Therefore, it is strongly required to identify the state of nanoscale system simulated in computer simulation. In this molecular dynamics(MD) study, we suggest that the potential energy of individual molecule can be used as criterion for defining the state of clusters or nanoscale systems. In addition, we compared the phase state from the potential energy with one from the radial distribution function(RDF) for verification. The comparison showed that the intermolecular potential energy can be used as a criteria distinguishing the phase state of nanoscale systems.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.160.2-160.2
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• 2014

Recently silicon has attracted intense interest as a promising anode material of lithium-ion batteries due to its extremely high capacity of 4200 mA/g (for Li4.2Si) that is much higher than 372 mAh/g (for LiC6) of graphite. However, it seriously suffers from large volume change (even up to 300%) of the electrode upon lithiation, leading to its pulverization or mechanical failure during lithiation/delithiation processes and the rapid capacity fading. To overcome this problem, Si nanowires have been considered. Use of such Si nanowires provides their facile relaxation during lithiation/delithiation without mechanical breaking. To design better Si electrodes, a study to unveil atomic-scale mechanisms involving the volume expansion and the phase transformation upon lithiation is critical. In order to investigate the lithiation mechanism in Si nanowires, we have developed a reactive force field (ReaxFF) for Si-Li systems based on density functional theory calculations. The ReaxFF method provides a highly transferable simulation method for atomistic scale simulation on chemical reactions at the nanosecond and nanometer scale. Molecular dynamics (MD) simulations with the ReaxFF reproduces well experimental anisotropic volume expansion of Si nanowires during lithiation and diffusion behaviors of lithium atoms, indicating that it would be definitely helpful to investigate lithiation mechanism of Si electrodes and then design new Si electrodes.

• Mass Spectrometry Letters
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• v.6 no.3
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• pp.59-64
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• 2015

Quadrupole ion trap mass analyzer with a simplified geometry, namely, the cylindrical ion trap (CIT), has been shown to be well-suited using in miniature mass spectrometry and even in mass spectrometer arrays. Computation of stability regions is of particular importance in designing and assembling an ion trap. However, solving CIT equations are rather more difficult and complex than QIT equations, so, analytical and matrix methods have been widely used to calculate the stability regions. In this article we present the results of numerical simulations of the physical properties and the fractional mass resolutions m/Δm of the confined ions in the first stability region was analyzed by the fifth order Runge-Kutta method (RKM5) at the optimum radius size for both ion traps. Because of similarity the both results, having determining the optimum radius, we can make much easier to design CIT. Also, the simulated results has been performed a high precision in the resolution of trapped ions at the optimum radius size.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.6 no.9
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• pp.2037-2051
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• 2012

Cognitive radio (CR) is envisioned as a promising paradigm of exploiting intelligence for enhancing efficiency of underutilized spectrum bands. In CR, the main concern is to reliably sense the presence of primary users (PUs) to attain protection against harmful interference caused by potential spectrum access of secondary users (SUs). In this paper, evolutionary algorithms, namely, particle swarm optimization (PSO) and genetic algorithm (GA) are proposed to minimize the total sensing decision error at the common soft data fusion (SDF) centre of a structurally-centralized cognitive radio network (CRN). Using these techniques, evolutionary operations are invoked to optimize the weighting coefficients applied on the sensing measurement components received from multiple cooperative SUs. The proposed methods are compared with each other as well as with other conventional deterministic algorithms such as maximal ratio combining (MRC) and equal gain combining (EGC). Computer simulations confirm the superiority of the PSO-based scheme over the GA-based and other conventional MRC and EGC schemes in terms of detection performance. In addition, the PSO-based scheme also shows promising convergence performance as compared to the GA-based scheme. This makes PSO an adequate solution to meet real-time requirements.

• Journal of Communications and Networks
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• v.13 no.6
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• pp.639-654
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• 2011

In this paper, we present a channel access mechanism, referred to as the enhanced mesh coordinated channel access (eMCCA) mechanism, for IEEE 802.11s-based wireless mesh networks. The current draft of IEEE 802.11s includes an optional medium access control (MAC), denoted as MCCA, which is designed to provide collision-free and guaranteed channel access during reserved periods. However, the MCCA mechanism fails to achieve the desired goal in the presence of contending non-MCCA nodes; this is because non-MCCA nodes are not aware of MCCA reservations and have equal access opportunities during reserved periods. We first present a probabilistic analysis that reveals the extent to which the performance of MCCA may be affected by contending non-MCCA nodes. We then propose eMCCA, which allows MCCA-enabled nodes to enjoy collision-free and guaranteed channel access during reserved periods by means of prioritized and preemptive access mechanisms. Finally, we evaluate the performance of eMCCA through extensive simulations under different network scenarios. The simulation results indicate that eMCCA outperforms other mechanisms in terms of success rate, network throughput, end-to-end delay, packet-loss rate, and mesh coordinated channel access opportunity-utilization.

• Journal of the Korean Ceramic Society
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• v.44 no.6 s.301
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• pp.319-324
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• 2007

The structural properties of $SiO_2$ liquid at finite temperatures have been investigated by molecular dynamics (MD) simulations utilizing the Tersoff interatomic potential. During cooling process, the $SiO_2$ liquid structure quenched with a cooling rate of $1.0{\times}10^{11}K/sec$ shows the traditional properties observed in the experiments. The coordination defects of system decrease with decreasing temperature up to 17%. The $SiO_2$ glass quenched up to 1600 K contains defects consisting of the fivefold coordination of Si, and the threefold coordination of O atoms. The calculated diffusion coefficients which are calculated by monitoring. the mean-square displacement of atoms drop to almost zero below 3000 K ($<10^{-6}\;cm^2/sec$) but has a fluctuations at low temperature. The structure properties of $SiO_2$ liquid shows a significant dependence on the temperature during cooling process. Bond-angle distribution at around $120^{\circ}$ originate from the O and Si atoms consisting of the over-coordinated O atoms.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2008.06a
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• pp.379-380
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• 2008

Molecular Dynamics (MD) simulations have been used to model the dynamics of the charge-compensating sodium ions in the non-stoichiometric hollandite Nax$(Ti_{8-x}Cr_x)O_{16}$. These interstitial ions reside in 'tunnels' in the crystal structure and move under the forces of both the ions making up the cage structure and the many body interactions of the other sodium ions in the tunnel. The Velocity Autocorrelation Function (VAF) of the sodium ions is calculated for a range of temperature from 250K to 1000K and converted into the linear ac-conductivity and ac-susceptibility response via Fourier transformation. A peak is found in the conductivity around $6\times10^{12}$ Hz that has some of the character of a Poley absorption. Here it is shown to be due to an harmonically coupled site vibrations of the sodium atoms, which extend only over a limited range. At frequencies below the peak the conductivity tends towards a constant i.e. dc value corresponding to a constant flow of ions through the simulation cell. At high temperatures the conductivity due to this ion transport process behaves like a metal with an insulator to metal transition occurring around a specific temperature.

• Proceedings of the KSME Conference
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• 2004.04a
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• pp.1382-1387
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• 2004

From the viewpoint of a macro state, there is no thermal boundary resistance (TBR) at an interface if both surfaces at an interface are perfectly contacted. However, recent molecular dynamics (MD) studies reported that there still exists the TDR at the interface in an ideal epitaxial superlttice. Our previous studies suggested the model to predict the TBR not only quantitatively also qualitatively in superlattices. The suggested model was based on the classical theory of a wave reflection, and provided highly satisfactory results for an engineering purpose. However, it was not the complete model because our previous model was derived by considering only the effects from a mass ratio and a potential ratio of two species. The interaction of two species presented by the Lennard-Jones (L-J) potential is governed by the mutual ratio of the masses, the potential well depths, and the diameters. In this study, we performed the preliminary simulations to investigate the effect resulting from the diameter ratio of two species for the completion of our model and confirmed that it was also a ruling factor to the TBR at an interface in superlattices.