## Abstract SL1 is a stemβloop RNA sequence from the genome of HIVβ1 thought to be the initiation site for the dimerization of the retroviral genomic RNA. The aim of this study is to check the stability in solution of different experimental dimeric structures available in the literature. Two kinds
Configurations of solute molecules from homogeneous binary solution during crystallization on molecular dynamics simulations
β Scribed by Kouji Maeda; Yusuke Asakuma; Keisuke Fukui
- Publisher
- Elsevier Science
- Year
- 2005
- Tongue
- English
- Weight
- 820 KB
- Volume
- 122
- Category
- Article
- ISSN
- 0167-7322
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β¦ Synopsis
Crystallization of solute molecules from homogeneous binary Lennard-Jones solutions was simulated by molecular dynamics of an NPT ensemble. Isothermal (equilibrium) and cooling (non-equilibrium) conditions were examined to observe the configuration of solute molecules for the crystallization process. The isothermal simulations could clearly determine the temperature of crystallization or nucleation of solute molecules by the change of density. The cooling simulations could describe the effect of cooling rate on the temperature of crystallization or nucleation. The configurations of solute molecules in the solution during crystallization were discussed from the radial distribution function (RDF) and the local composition of solute (LC) in the solution. The nuclei that have a crystalline structure could be distinguished from clusters that have a liquid structure. It was found that the liquid clusters were not stable, but the crystal nuclei have very rigid structure and were stable. LC was used to image how many solute molecules gathered in the solution with relation to the clusters and nuclei. It was found that LC fluctuated dramatically when the solute molecules crystallized. The cooling simulations showed that the configuration of solute molecules obtained at a slower cooling rate showed the crystalline structure, but the faster cooling rate caused the liquid structure of clusters in the solutions even at low temperature.
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