Molecular dynamics simulation combined with small‐angle X‐ray/neutron scattering defining solution‐state protein structures

2020 ◽  
Author(s):  
Shang‐Wei Lin ◽  
Kuan‐Hsuan Su ◽  
Yi‐Qi Yeh ◽  
U‐Ser Jeng ◽  
Chun‐Ming Wu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Neutron Scattering ◽  
Small Angle ◽  
Protein Structures ◽  
Dynamics Simulation ◽  
X Ray ◽  
Solution State

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.

Investigation of atom distribution in Mg-9wt.%Al melt using small-angle X-ray scattering and molecular dynamics simulation

2017 ◽  
Vol 473 ◽  
pp. 47-53 ◽  
Author(s):  
Xiusong Huang ◽  
Xixi Dong ◽  
Chunming Yang ◽  
Feng Tian ◽  
Lehua Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Small Angle ◽  
Dynamics Simulation ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Structural Properties of Archaeal Lipid Bilayers: Small-Angle X-ray Scattering and Molecular Dynamics Simulation Study

Langmuir ◽  
2014 ◽  
Vol 30 (28) ◽  
pp. 8308-8315 ◽  
Author(s):  
Andraž Polak ◽  
Mounir Tarek ◽  
Matija Tomšič ◽  
Janez Valant ◽  
Nataša Poklar Ulrih ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structural Properties ◽  
Lipid Bilayers ◽  
Simulation Study ◽  
Small Angle ◽  
Dynamics Simulation ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray scattering

2006 ◽  
Vol 124 (20) ◽  
pp. 204719 ◽  
Author(s):  
Chandan Jana ◽  
G. Jayamurugan ◽  
Rajesh Ganapathy ◽  
Prabal K. Maiti ◽  
N. Jayaraman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Small Angle ◽  
Dynamics Simulation ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering
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