scholarly journals Structure and dynamics of water confined in cylindrical nanopores with varying hydrophobicity

2021 ◽  
Vol 379 (2208) ◽  
pp. 20200403 ◽  
Author(s):  
Antonio Tinti ◽  
Gaia Camisasca ◽  
Alberto Giacomello
Keyword(s):  
Structural Features ◽  
Nanoporous Materials ◽  
Dynamics Simulation ◽  
Generic Model ◽  
Confined Water ◽  
Core Domain ◽  
Biologically Relevant ◽  
Lennard Jones ◽  
Structure And Dynamics ◽  
Dynamical Features

We report a detailed study of the main structural and dynamical features of water confined in model Lennard–Jones nanopores with tunable hydrophobicity and finite length ( L = 26 Å). The generic model of cylindrical confinement used is able to reproduce the wetting features of a large class of technologically and biologically relevant systems spanning from crystalline nanoporous materials, to mesoporous silica and ion channels. The aim of this work is to discuss the influence of parameters such as wall hydrophobicity, temperature, and pore size on the structural and dynamical features of confined water. Our simulation campaign confirmed the existence of a core domain in which water displays bulk-like structural features even in extreme ( R = 7.0  Å) confinement, while dynamical properties were shown to depend non-trivially on the size and hydrophobicity of the pores. This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.

scholarly journals Insight into the Structure and Dynamics of Polymers by Neutron Scattering Combined with Atomistic Molecular Dynamics Simulations

Polymers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3067
Author(s):  
Arantxa Arbe ◽  
Fernando Alvarez ◽  
Juan Colmenero
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Structural Features ◽  
Length Scales ◽  
Polymeric Systems ◽  
Structure And Dynamics ◽  
Dynamical Features ◽  
Dynamics Simulations ◽  
Insight Into

Combining neutron scattering and fully atomistic molecular dynamics simulations allows unraveling structural and dynamical features of polymer melts at different length scales, mainly in the intermolecular and monomeric range. Here we present the methodology developed by us and the results of its application during the last years in a variety of polymers. This methodology is based on two pillars: (i) both techniques cover approximately the same length and time scales and (ii) the classical van Hove formalism allows easily calculating the magnitudes measured by neutron scattering from the simulated atomic trajectories. By direct comparison with experimental results, the simulated cell is validated. Thereafter, the information of the simulations can be exploited, calculating magnitudes that are experimentally inaccessible or extending the parameters range beyond the experimental capabilities. We show how detailed microscopic insight on structural features and dynamical processes of various kinds has been gained in polymeric systems with different degrees of complexity, and how intriguing questions as the collective behavior at intermediate length scales have been faced.

STRUCTURE AND DYNAMICS: THE TRANSITION FROM NONEQUILIBRIUM TO EQUILIBRIUM IN INTEGRATE-AND-FIRE DYNAMICS

2012 ◽  
Vol 22 (07) ◽  
pp. 1250174 ◽  
Author(s):  
CESAR H. COMIN ◽  
JOÃO L. B. BATISTA ◽  
MATHEUS P. VIANA ◽  
LUCIANO DA F. COSTA ◽  
BRUNO A. N. TRAVENÇOLO ◽  
...  
Keyword(s):  
Systematic Approach ◽  
Local Level ◽  
Small World ◽  
Structural Features ◽  
Fire Dynamics ◽  
Integrate And Fire ◽  
Structure And Dynamics ◽  
Topological Features ◽  
Dynamical Features ◽  
Local Topology

The transient and equilibrium properties of dynamics unfolding in complex systems can depend critically on specific topological features of the underlying interconnections. In this work, we investigate such a relationship with respect to the integrate-and-fire dynamics emanating from a source node and an extended network model that allows control of the small-world feature as well as the length of the long-range connections. A systematic approach to investigate the local and global correlations between structural and dynamical features of the networks was adopted that involved extensive simulations (one and a half million cases) so as to obtain two-dimensional correlation maps. Smooth, but diverse surfaces of correlation values were obtained in all cases. Regarding the global cases, it has been verified that the onset avalanche time (but not its intensity) can be accurately predicted from the structural features within specific regions of the map (i.e. networks with specific structural properties). The analysis at local level revealed that the dynamical features before the avalanches can also be accurately predicted from structural features. This is not possible for the dynamical features after the avalanches take place. This is so because the overall topology of the network predominates over the local topology around the source at the stationary state.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

The Effect of Magnetic Field on the Hydration of Nanoscopic Hydrophobic N-Alkane Plates

2011 ◽  
Vol 228-229 ◽  
pp. 1007-1011
Author(s):  
Wei Wei Zhang ◽  
Long Qiu Li ◽  
Guang Yu Zhang ◽  
Hui Juan Dong
Keyword(s):  
Magnetic Field ◽  
External Magnetic Field ◽  
Dynamics Simulation ◽  
Free Energy Barrier ◽  
Confined Water ◽  
Magnetic Exposure ◽  
Hydrophobic Solutes ◽  
The Magnetic Field ◽  
Density Of Water ◽  
Induced Adsorption

The effect of an external magnetic field on the hydration behavior of nanoscopic n-octane plates has been extensively investigated using molecular dynamics simulation in an isothermal-isobaric ensemble. The solute plates with different intermolecular spacing have also been considered to examine the effect of the topology of hydrophobic plates on the adsorption behavior of confined water in the presence of an external magnetic field with an intensity ranging from 0.1T to 1 T. The results demonstrate that magnetic exposure decreases the density of water for the plates with intermolecular spacing of a0 = 4 and 5 Å. This suggests that the free energy barrier for evaporation can be lowered by the applied field, and the hydrophobic solutes consisting of condensed n-octane molecules are apt to aggregate in the aqueous solution. In contrast, the magnetic field improves the dissolution or wetting of solutes comprised of loosely packed n-octane plates of a0=7Å. A magnetic-field-induced adsorption-to-desorption translation, which is in agreement with the experimental results provided by Ozeki, has also been observed for the plates with intermolecular spacing of a0 = 6 Å.

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