Analysis of the network topology in liquid water and hydrogen sulphide by computer simulation

Ruocco, G.; Sampoli, M.; Vallauri, R.

doi:10.1063/1.462889

Cited by 87 publications

(84 citation statements)

References 34 publications

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“…The area per lipid molecule for each molecule type was calculated using a home-developed code on the basis of Voronoi tessellation method (http://www.cs.cmu.edu/~quake/triangle.html) 31 . The detailed calculation procedure was similar to that reported previously for lipid mixtures [32][33][34][35] .…”

Section: Discussionmentioning

confidence: 99%

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Molecular Dynamics Simulations of Ternary Membrane Mixture: Phosphatidylcholine, Phosphatidic Acid, and Cholesterol

et al. 2007

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A ternary mixture of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl phosphatidic acid (POPA), and cholesterol (CHOL) works effectively for a functional conformation of nicotinic acetylcholine receptor (nAChR) that can undergo agonist-induced conformation changes, but POPC alone can stabilize only a desensitized state of nAChR. To gain insights into the lipid mixture that have strong impact to nAChR functions, we performed more than 50-ns all atom molecular dynamic (MD) simulations at 303 K on a fully hydrated bilayer consisting of 240 POPC, 80 POPA, and 80 CHOL (3:1:1). The MD simulation revealed various interactions between different types of molecular pairs that ultimately regulated lipid organization. The heterogeneous interactions among three different constituents resulted in a broad spectrum of lipid properties, including extensive distribution of average area per lipids and varied lipid ordering as a function of lipid closeness to CHOL. Higher percentage of POPA than POPC had close association with CHOL, which coincided with relatively higher ordering of POPA molecules in their acyl chains near lipid head groups. Lower fraction of gauche dihedrals was also found in the same region of POPA. Although the CHOL molecules had the effects on the enhancement of surrounding lipid order, relatively low lipid order parameters and high fraction of gauche bonds were observed in the ternary mixture. Collectively, these results suggest that the dynamical structure of the ternary system could be determinant for a functional nAChR.

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Section: Discussionmentioning

confidence: 99%

“…For our simulated POPC-POPA-CHOL system, the area per molecule for each constituent in the ternary mixture was calculated using aforementioned Voronoi method 31 and summarized in the histograms depicted in Fig. 5.…”

Section: Average Area Per Moleculementioning

confidence: 99%

Molecular Dynamics Simulations of Ternary Membrane Mixture: Phosphatidylcholine, Phosphatidic Acid, and Cholesterol

et al. 2007

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“…Alternatives are reported [13]. Asphericity has been considered in polymers [13,21,[72][73][74], water [21,[75][76][77][78][79] , silica [21], small molecules [75], packed beds of particles [80], hard [81] and soft [82] spheres and its better ability to discriminate different local structures with respect to other features of the Voronoi polyhedron has been noted [80,82].…”

Section: Introductionmentioning

confidence: 99%

Weak links between fast mobility and local structure in molecular and atomic liquids

Bernini

Puosi

Leporini

2015

The Journal of Chemical Physics

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We investigate by Molecular-Dynamics simulations the fast mobility -the rattling amplitude of the particles temporarily trapped by the cage of the neighbors -in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

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“…the volume and the asphericity of the Voronoi polyhedron (VP) surrounding a tagged particle. VP asphericity has been analyzed also in water [74][75][76], small molecules [77], hard spheres [78] and polymers [41,45,79,80]. For a VP with V v volume and A v surface the asphericity is defined as:…”

Section: Introductionmentioning

confidence: 99%

Cage rattling does not correlate with the local geometry in molecular liquids

Bernini

Puosi

Leporini

2015

Journal of Non-Crystalline Solids

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Molecular-dynamics simulations of a liquid of short linear molecules have been performed to investigate the correlation between the particle dynamics in the cage of the neighbors and the local geometry. The latter is characterized in terms of the size and the asphericity of the Voronoi polyhedra. The correlation is found to be poor. In particular, in spite of the different Voronoi volume around the end and the inner monomers of a molecule, all the monomers exhibit coinciding displacement distribution when they are caged (as well as at longer times during the structural relaxation). It is concluded that the fast dynamics during the cage trapping is a non-local collective process involving monomers beyond the nearest neighbours.PACS numbers:

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Analysis of the network topology in liquid water and hydrogen sulphide by computer simulation

Abstract: Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water

Cited by 87 publications

References 34 publications

Molecular Dynamics Simulations of Ternary Membrane Mixture: Phosphatidylcholine, Phosphatidic Acid, and Cholesterol

Molecular Dynamics Simulations of Ternary Membrane Mixture: Phosphatidylcholine, Phosphatidic Acid, and Cholesterol

Weak links between fast mobility and local structure in molecular and atomic liquids

Cage rattling does not correlate with the local geometry in molecular liquids

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