Analysis of the solution structure of Thermosynechococcus elongatus photosystem I in n-dodecyl-β-d-maltoside using small-angle neutron scattering and molecular dynamics simulation

2014 ◽  
Vol 550-551 ◽  
pp. 50-57 ◽  
Author(s):  
Rosemary K. Le ◽  
Bradley J. Harris ◽  
Ifeyinwa J. Iwuchukwu ◽  
Barry D. Bruce ◽  
Xiaolin Cheng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Neutron Scattering ◽  
Photosystem I ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Solution Structure ◽  
Dynamics Simulation

Effect of the solute–solvent interface on small-angle neutron scattering from organic solutions of short alkyl chain molecules as revealed by molecular dynamics simulation

2013 ◽  
Vol 46 (2) ◽  
pp. 372-378 ◽  
Author(s):  
Roman A. Eremin ◽  
Kholmirzo Kholmurodov ◽  
Viktor I. Petrenko ◽  
László Rosta ◽  
Mikhail V. Avdeev
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Scattering Length ◽  
Solvent Molecule ◽  
Dynamics Simulation ◽  
Time Averaging ◽  
Acid Molecule

The problem of describing the experimental small-angle neutron scattering (SANS) from diluted solutions of saturated monocarboxylic acids with short chain lengths (myristic and stearic acids) in deuterated decalin is considered. The method of classical molecular dynamics simulation (MDS) is used to obtain the atomic number density distributions, and, as a consequence, the scattering length density (SLD) distribution in the solute–solvent interface area (about 1 nm around the acid molecules), assuming the acid molecules to be rigid and non-associated in the solutions. MDS is performed for solutions in a parallelepiped cell of 5.5 × 5.3 × 5.3 nm (one acid molecule per cell) under normal conditions. The time averaging of the obtained distributions is done over 2 ns (after the system thermalization). It is shown that a specific short-range ordering organization of the solvent molecules in the vicinity of the acid molecules has a significant effect on the scattering, which is mainly determined by a relatively large ratio between the effective size of the solvent molecule and the cross-section diameter of the acid molecule. Various approximations to the simulated SLD distributions, based on the cylinder-type symmetry of the acid molecules, are probed to achieve the best consistency with the experimental SANS curves by varying the residual incoherent background.

scholarly journals Aggregation of cyclic polypeptoids bearing zwitterionic end-groups with attractive dipole–dipole and solvophobic interactions: a study by small-angle neutron scattering and molecular dynamics simulation

2017 ◽  
Vol 19 (22) ◽  
pp. 14388-14400 ◽  
Author(s):  
Pu Du ◽  
Ang Li ◽  
Xin Li ◽  
Yueheng Zhang ◽  
Changwoo Do ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Aggregation Behavior ◽  
Dynamics Simulation ◽  
End Groups ◽  
Solvophobic Interactions

The aggregation behavior of cyclic polypeptoids has been studied using experiments and simulations.

scholarly journals Solution structure of macromolecules using small angle neutron scattering and molecular simulations

2020 ◽  
Vol 236 ◽  
pp. 03003
Author(s):  
Jayesh S. Bhatt
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Solution Structure ◽  
Molecular Simulations ◽  
Liquid Solution ◽  
Scattering Data ◽  
Monte Carlo Techniques

An introductory account of using molecular simulations to deduce solution structure of macromolecules using small angle neutron scattering data is presented for biologists. The presence of a liquid solution provides mobility to the molecules, making it difficult to pin down their structure. Here a simple introduction to molecular dynamics and Monte Carlo techniques is followed by a recipe to use the output of the simulations along with the scattering data in order to infer the structure of macromolecules when they are placed in a liquid solution. Some practical issues to be watched for are also highlighted.

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