scholarly journals Molecular Dynamics Simulations and Empirical Observations on Soy Lecithin Liposome Preparation

2018 ◽  
Vol 16 (2) ◽  
pp. 222 ◽  
Author(s):  
Rini Dwiastuti ◽  
Muhammad Radifar ◽  
Marchaban Marchaban ◽  
Sri Noegrohati ◽  
Enade Perdana Istyastono

Soy lecithin is a phospholipid often used in liposome formulations. Determination of water and phospholipid composition is one of the problems in the liposome formulation. This study is using molecular dynamics simulation and empirical observation in producing liposome preparations. Phospholipids 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE) were objected in molecular dynamics simulations using Coarse Grained Molecular Dynamics (CGMD) approaches. The result showed that the molecular dynamic simulations could be employed to predict the liposome size. The molecular dynamic simulations resulted in liposome size of 71.22 ± 2.54 nm, which was located within the range of the liposome size resulted from the empirical observations (95.99 ± 43.02 nm). Moreover, similar liposome forms were observed on both results of molecular dynamics simulations and empirical approaches.

2017 ◽  
Vol 15 (31) ◽  
pp. 6541-6547 ◽  
Author(s):  
I. R. Sasselli ◽  
I. P. Moreira ◽  
R. V. Ulijn ◽  
T. Tuttle

Coarse grained molecular dynamic simulations demonstrate that interactions between species in dynamic peptide libraries can cause a disrupting self-assembly effect that affects the possible discovery of new materials.


2020 ◽  
Vol 22 (19) ◽  
pp. 10431-10437 ◽  
Author(s):  
Sung Sakong ◽  
Axel Groß

Water structures on a Pt(111) metal electrode critically depend on the electrochemical conditions, as shown by ab initio molecular dynamics simulations.


RSC Advances ◽  
2017 ◽  
Vol 7 (11) ◽  
pp. 6795-6799 ◽  
Author(s):  
Shuling Xiong ◽  
Shusen Chen ◽  
Shaohua Jin ◽  
Zhe Zhang ◽  
Yan Zhang ◽  
...  

TKX-50/HMX cocrystal model was established and calculated using PCFF force field by molecular dynamics simulations.


2020 ◽  
Author(s):  
Rajarshi Roy ◽  
Sayan Poddar ◽  
Parimal Kar

In the current study, we have investigated the conformational dynamics of a triantennary and a tetraantennary hybrid N-glycan associated with HIV glycoprotein using 20 micro-second long all-atom molecular dynamics simulations. <br>


2020 ◽  
Author(s):  
Rajarshi Roy ◽  
Sayan Poddar ◽  
Parimal Kar

In the current study, we have investigated the conformational dynamics of a triantennary and a tetraantennary hybrid N-glycan associated with HIV glycoprotein using 20 micro-second long all-atom molecular dynamics simulations. <br>


2016 ◽  
Vol 12 (1) ◽  
pp. 76-84 ◽  
Author(s):  
Wei-Kang Li ◽  
Qing-Chuan Zheng ◽  
Hong-Xing Zhang

Molecular dynamic simulations and MMPBSA calculations of tvMyb2-ap65-1 complex and its mutants, our work give important information to understand the interactions between tvMyb2-ap65-1.


F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 589 ◽  
Author(s):  
Andrew R. Dalby ◽  
Mohd Shahir Shamsir

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.


RSC Advances ◽  
2016 ◽  
Vol 6 (68) ◽  
pp. 63586-63596 ◽  
Author(s):  
Luying Wang ◽  
Randall S. Dumont ◽  
James M. Dickson

The amorphous aromatic polyamide membranes with different membrane densities were modeled to study the porous structure of free-volume pores and the pressure-driven water transport by using molecular dynamics simulations.


RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  

The formation mechanism of the bound rubber in elastomer nanocomposites using the coarse-grained molecular-dynamics simulations.


2017 ◽  
Author(s):  
Ronald D Hills, Jr

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.


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