A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water
The energy profile of self-assembly process of DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS in water was investigated by a coarse-grained molecular dynamics simulation using NAMD package. The self-assembly process was initiated from random configurations. The simulation was carried out for 160 ns. This...
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| Format: | Article |
| Language: | English |
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Wiley
2014-01-01
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| Series: | Journal of Chemistry |
| Online Access: | http://dx.doi.org/10.1155/2014/273084 |
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| author | Dwi Hudiyanti Muhammad Radifar Tri Joko Raharjo Narsito Narsito Sri Noegrohati |
| author_facet | Dwi Hudiyanti Muhammad Radifar Tri Joko Raharjo Narsito Narsito Sri Noegrohati |
| author_sort | Dwi Hudiyanti |
| collection | DOAJ |
| description | The energy profile of self-assembly process of DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS in water was investigated by a coarse-grained molecular dynamics simulation using NAMD package. The self-assembly process was initiated from random configurations. The simulation was carried out for 160 ns. This study presented proof that there were three major self-assembled arrangements which became visible for a certain duration when the simulation took place, that is, liposome, deformed liposome, and planar bilayer. The energy profile that shows plateau at the time of these structures emerge confirmed their stability therein. Our findings have highlighted the idea that liposomes and deformed liposomes are metastable phases which eventually will turn into planar bilayer, the stable one. |
| format | Article |
| id | doaj-art-12d5997d23d0499bbc82226dc10ac103 |
| institution | Kabale University |
| issn | 2090-9063 2090-9071 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Chemistry |
| spelling | doaj-art-12d5997d23d0499bbc82226dc10ac1032025-02-03T01:07:15ZengWileyJournal of Chemistry2090-90632090-90712014-01-01201410.1155/2014/273084273084A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in WaterDwi Hudiyanti0Muhammad Radifar1Tri Joko Raharjo2Narsito Narsito3Sri Noegrohati4Department of Chemistry, Diponegoro University, Jl. Prof. Sudharto, SH., Semarang 50257, IndonesiaGraduate School, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, IndonesiaDepartment of Chemistry, FMIPA, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, IndonesiaDepartment of Chemistry, FMIPA, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, IndonesiaFaculty of Pharmacy, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, IndonesiaThe energy profile of self-assembly process of DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS in water was investigated by a coarse-grained molecular dynamics simulation using NAMD package. The self-assembly process was initiated from random configurations. The simulation was carried out for 160 ns. This study presented proof that there were three major self-assembled arrangements which became visible for a certain duration when the simulation took place, that is, liposome, deformed liposome, and planar bilayer. The energy profile that shows plateau at the time of these structures emerge confirmed their stability therein. Our findings have highlighted the idea that liposomes and deformed liposomes are metastable phases which eventually will turn into planar bilayer, the stable one.http://dx.doi.org/10.1155/2014/273084 |
| spellingShingle | Dwi Hudiyanti Muhammad Radifar Tri Joko Raharjo Narsito Narsito Sri Noegrohati A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water Journal of Chemistry |
| title | A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water |
| title_full | A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water |
| title_fullStr | A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water |
| title_full_unstemmed | A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water |
| title_short | A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water |
| title_sort | coarse grained molecular dynamics simulation using namd package to reveal aggregation profile of phospholipids self assembly in water |
| url | http://dx.doi.org/10.1155/2014/273084 |
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