Short-Range Order and Collective Dynamics of DMPC Bilayers: A Comparison between Molecular Dynamics Simulations, X-Ray, and Neutron Scattering Experiments

Abstract Neutron scattering results on Se1-xTex melts (x = 0.3, 0.6, 0.8) obtained at 460 °C are combined with earlier X-ray diffraction data. The behaviour of the number and distance of nearest neighbours is discussed with respect to chemical short-range order and transition from twofold to three-fold coordination. For Se70Te30 the radial concentration correlation function 4πr2 ρcc(r) has been evaluated. It shows clearly the preferred formation of unlike pairs (Se-Te) within the chains.

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Local structure of the Zr–Al metallic glasses studied by proposed n-body potential through molecular dynamics simulation

Journal of Materials Research ◽

10.1557/jmr.2010.0225 ◽

2010 ◽

Vol 25 (9) ◽

pp. 1679-1688 ◽

Cited By ~ 7

Author(s):

S.Z. Zhao ◽

J.H. Li ◽

B.X. Liu

Keyword(s):

Molecular Dynamics ◽

Metallic Glasses ◽

Short Range ◽

Short Range Order ◽

Range Order ◽

Dynamics Simulation ◽

Face Centered Cubic ◽

Dynamics Simulations ◽

Body Potential ◽

Pair Analysis

An n-body potential is first constructed for the Zr–Al system and proven to be realistic by reproducing a number of important properties of the system. Applying the constructed potential, molecular dynamics simulations, chemical short-range order (CSRO) calculation, and Honeycutt and Anderson (HA) pair analysis are carried out to study the Zr–Al metallic glasses. It is found that for the binary Zr–Al system, metallic glasses are energetically favored to be formed within composition range of 35–75 at.% Al. The calculation shows that the CSRO parameter is negative and could be up to −0.17, remarkably indicating that there exists a chemical short-range order in the Zr–Al metallic glasses. The HA pair analysis also reveals that there are diverse short-range packing units in the Zr–Al metallic glasses, in which icosahedra and icosahedra/face-centered cubic (fcc)-defect structures are predominant.

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Short-range order of undercooled melts of PdZr 2 intermetallic compound studied by X-ray and neutron scattering experiments

EPL (Europhysics Letters) ◽

10.1209/0295-5075/102/36001 ◽

2013 ◽

Vol 102 (3) ◽

pp. 36001 ◽

Cited By ~ 6

Author(s):

S. Klein ◽

D. Holland-Moritz ◽

D. M. Herlach ◽

N. A. Mauro ◽

K. F. Kelton

Keyword(s):

Intermetallic Compound ◽

Neutron Scattering ◽

Short Range ◽

Short Range Order ◽

Range Order ◽

X Ray ◽

Undercooled Melts

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Short-Range Order in Liquid Aluminum Chloride: Ab Initio Molecular Dynamics Simulations and Quantum-Chemical Calculations

The Journal of Physical Chemistry B ◽

10.1021/jp070517y ◽

2007 ◽

Vol 111 (19) ◽

pp. 5316-5321 ◽

Cited By ~ 9

Author(s):

A. L. L. East ◽

J. Hafner

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Aluminum Chloride ◽

Quantum Chemical ◽

Short Range ◽

Short Range Order ◽

Liquid Aluminum ◽

Ab Initio Molecular Dynamics ◽

Dynamics Simulations

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Assessment of molecular dynamics simulations for amorphous poly(3-hexylthiophene) using neutron and X-ray scattering experiments

Soft Matter ◽

10.1039/c9sm00807a ◽

2019 ◽

Vol 15 (25) ◽

pp. 5067-5083 ◽

Cited By ~ 5

Author(s):

Caitlyn M. Wolf ◽

Kiran H. Kanekal ◽

Yeneneh Y. Yimer ◽

Madhusudan Tyagi ◽

Souleymane Omar-Diallo ◽

...

Keyword(s):

Molecular Dynamics ◽

Neutron Scattering ◽

Molecular Dynamics Simulations ◽

Force Fields ◽

X Ray ◽

X Ray Scattering ◽

Dynamics Simulations ◽

Ray Scattering

An honest discussion on the strengths and limitations of molecular dynamics force fields for P3HT through neutron scattering.

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Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

10.1101/2019.12.26.888834 ◽

2019 ◽

Cited By ~ 2

Author(s):

Andreas Haahr Larsen ◽

Yong Wang ◽

Sandro Bottaro ◽

Sergei Grudinin ◽

Lise Arleth ◽

...

Keyword(s):

Molecular Dynamics ◽

Neutron Scattering ◽

Molecular Dynamics Simulations ◽

Small Angle ◽

Coarse Grained ◽

Scattering Data ◽

General Strategy ◽

X Ray ◽

Coarse Grained Simulations ◽

Dynamics Simulations

AbstractMany proteins contain multiple folded domains separated by flexible linkers, and the ability to describe the structure and conformational heterogeneity of such flexible systems pushes the limits of structural biology. Using the three-domain protein TIA-1 as an example, we here combine coarse-grained molecular dynamics simulations with previously measured small-angle scattering data to study the conformation of TIA-1 in solution. We show that while the coarse-grained potential (Martini) in itself leads to too compact conformations, increasing the strength of protein-water interactions results in ensembles that are in very good agreement with experiments. We show how these ensembles can be refined further using a Bayesian/Maximum Entropy approach, and examine the robustness to errors in the energy function. In particular we find that as long as the initial simulation is relatively good, reweighting against experiments is very robust. We also study the relative information in X-ray and neutron scattering experiments and find that refining against the SAXS experiments leads to improvement in the SANS data. Our results suggest a general strategy for studying the conformation of multi-domain proteins in solution that combines coarse-grained simulations with small-angle X-ray scattering data that are generally most easy to obtain. These results may in turn be used to design further small-angle neutron scattering experiments that exploit contrast variation through 1H/2H isotope substitutions.

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