The longitudinal optic-like mode in molten alkali halides: A molecular dynamics approximation to inelastic x-ray scattering experiments

2010 ◽  
Vol 132 (5) ◽  
pp. 054503 ◽  
Author(s):  
O. Alcaraz ◽  
J. Trullàs
Keyword(s):  
Molecular Dynamics ◽  
Alkali Halides ◽  
X Ray ◽  
X Ray Scattering ◽  
Longitudinal Optic ◽  
Dynamics Approximation ◽  
Ray Scattering

Liquid Structure of 1-Ethyl-3-methylimidazolium Alkyl Sulfates by X-ray Scattering and Molecular Dynamics

2012 ◽  
Vol 116 (45) ◽  
pp. 13448-13458 ◽  
Author(s):  
Marina Macchiagodena ◽  
Fabio Ramondo ◽  
Alessandro Triolo ◽  
Lorenzo Gontrani ◽  
Ruggero Caminiti
Keyword(s):  
Molecular Dynamics ◽  
Liquid Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Alkyl Sulfates ◽  
Ray Scattering

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

Liquid Structure of 1-Propanol by Molecular Dynamics Simulations and X-Ray Scattering

2004 ◽  
Vol 33 (6/7) ◽  
pp. 797-809 ◽  
Author(s):  
Isao Akiyama ◽  
Masaya Ogawa ◽  
Keiichi Takase ◽  
Toshiyuki Takamuku ◽  
Toshio Yamaguchi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Liquid Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Dynamics Simulations ◽  
Ray Scattering

scholarly journals Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

2014 ◽  
Vol 111 (50) ◽  
pp. 17887-17892 ◽  
Author(s):  
Michael E. Wall ◽  
Andrew H. Van Benschoten ◽  
Nicholas K. Sauter ◽  
Paul D. Adams ◽  
James S. Fraser ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Dynamics ◽  
X Ray ◽  
X Ray Scattering ◽  
Dynamics Simulations ◽  
Ray Scattering

Elucidation of the Structure of Organic Solutions in Solvent Extraction by Combining Molecular Dynamics and X-ray Scattering

2014 ◽  
Vol 53 (21) ◽  
pp. 5346-5350 ◽  
Author(s):  
Geoffroy Ferru ◽  
Donatien Gomes Rodrigues ◽  
Laurence Berthon ◽  
Olivier Diat ◽  
Pierre Bauduin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solvent Extraction ◽  
X Ray ◽  
X Ray Scattering ◽  
Organic Solutions ◽  
Ray Scattering

Choline salicylate ionic liquid by X-ray scattering, vibrational spectroscopy and molecular dynamics

2016 ◽  
Vol 218 ◽  
pp. 39-49 ◽  
Author(s):  
Luana Tanzi ◽  
Michele Nardone ◽  
Paola Benassi ◽  
Fabio Ramondo ◽  
Ruggero Caminiti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Vibrational Spectroscopy ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering
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