• Title/Summary/Keyword: MD simulations

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Design of Modified CGA for Address Autoconfiguration and Digital Signature in Hierarchical Ad Hoc Network (개선된 CGA(Modified CGA)를 이용한 계층적 애드 혹 네트워크에서의 주소 자동 설정 및 전자 서명 제공 방안)

  • Lee, Hye-Won;Kim, Guk-Boh;Mun, Young-Song
    • Journal of KIISE:Information Networking
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    • v.33 no.2
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    • pp.175-182
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    • 2006
  • The CGA proposed by IETF working group prevents address spoofing and stealing and provides digital signature to users, but key collision problem arises. To solve this critical problem, the CGA defines the SEC field within address format, which is set to high value when high security is required and vice versa, but the CGA faces a dilemma between security and the processing time. As SEC value increases, the processing time to generate the CGA grows dramatically while key collision ratio increases if low SEC value is applied to the CGA. We propose modified CGA (MCGA) that has shorter processing time than the CGA and offers digital signature with small overheads. To solve key collision problem, we employ hierarchical ad hoc network. The MCGA is applicable to IPv6 networks as well public networks. In this paper, we design a mathematical model to analyze the processing time for MCGA and CGA first and evaluate the processing time via simulations, where the processing time for MCGA is reduced down 3.3 times when SEC value is set to 0 and 68,000 times when SEC value is set to 1. Further, we have proved that the CGA is inappropriate for both ad hoc networks and IPv6 networks when the SEC field is set to more than 3.

Molecular Dynamics Simulation Study for Ionic Strength Dependence of RNA-host factor Interaction in Staphylococcus aureus Hfq

  • Lazar, Prettina;Lee, Yun-O;Kim, Song-Mi;Chandrasekaran, Meganathan;Lee, Keun-Woo
    • Bulletin of the Korean Chemical Society
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    • v.31 no.6
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    • pp.1519-1526
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    • 2010
  • The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.