scholarly journals Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

2013 ◽  
Vol 4 ◽  
pp. 567-587 ◽  
Author(s):  
Pavel V Komarov ◽  
Pavel G Khalatur ◽  
Alexei R Khokhlov
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Large Scale ◽  
Water Channel ◽  
Ion Association ◽  
Characteristic Size ◽  
Potential Of Mean Force ◽  
Nafion Membrane ◽  
Quantum Molecular Dynamics ◽  
Ion Conducting

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

scholarly journals Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

2021 ◽  
Vol 22 (10) ◽  
pp. 5220
Author(s):  
Jarosław J. Panek ◽  
Joanna Zasada ◽  
Bartłomiej M. Szyja ◽  
Beata Kizior ◽  
Aneta Jezierska
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Quantum Effects ◽  
Potential Of Mean Force ◽  
Probability Density Distribution ◽  
Donor And Acceptor ◽  
Nuclear Quantum Effects ◽  
Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

Bayesian active learning of interatomic force field for molecular dynamics simulation of Pt/Ag(111)

2021 ◽  
Author(s):  
Kai Xu ◽  
Lei Yan ◽  
Bingran You
Keyword(s):  
Molecular Dynamics ◽  
Active Learning ◽  
Force Field ◽  
Density Functional ◽  
Process Model ◽  
Large Scale ◽  
Computational Cost ◽  
Dynamics Simulation ◽  
Potential Energy Landscape ◽  
Three Body

Force field is a central requirement in molecular dynamics (MD) simulation for accurate description of the potential energy landscape and the time evolution of individual atomic motions. Most energy models are limited by a fundamental tradeoff between accuracy and speed. Although ab initio MD based on density functional theory (DFT) has high accuracy, its high computational cost prevents its use for large-scale and long-timescale simulations. Here, we use Bayesian active learning to construct a Gaussian process model of interatomic forces to describe Pt deposited on Ag(111). An accurate model is obtained within one day of wall time after selecting only 126 atomic environments based on two- and three-body interactions, providing mean absolute errors of 52 and 142 meV/Å for Ag and Pt, respectively. Our work highlights automated and minimalistic training of machine-learning force fields with high fidelity to DFT, which would enable large-scale and long-timescale simulations of alloy surfaces at first-principles accuracy.

MD Analysis of Effect of Relative Humidity on Molecular Chain’s Network Structure of PEM

2016 ◽  
Vol 725 ◽  
pp. 238-242
Author(s):  
Isamu Riku ◽  
Keisuke Kawanishi ◽  
Koji Mimura
Keyword(s):  
Molecular Dynamics ◽  
Relative Humidity ◽  
Computational Model ◽  
Network Structure ◽  
Water Channel ◽  
High Density ◽  
Nafion Membrane ◽  
Water Molecules ◽  
Low Density ◽  
Density Of Water

To clarify the effect of relative humidity on molecular chain’s network structure, we at first employ Molecular Dynamics (MD) method to constitute the computational model for Nafion membrane, in which the water channel is artificially reproduced with an aggregation of water molecules. And then, relaxation calculation is performed and a relatively stable microstructure of Nafion membrane is derived. It is found that the regions of relatively low density of molecular chain’s network appear interchangeably together with those of relatively high density of water molecules.

Polyaniline and CN-functionalized polyaniline as organic cathodes for lithium and sodium ion batteries: a combined molecular dynamics and density functional tight binding study in solid state

2018 ◽  
Vol 20 (1) ◽  
pp. 232-237 ◽  
Author(s):  
Yingqian Chen ◽  
Johann Lüder ◽  
Man-Fai Ng ◽  
Michael Sullivan ◽  
Sergei Manzhos
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Ab Initio ◽  
Cathode Materials ◽  
Density Functional ◽  
Large Scale ◽  
Tight Binding ◽  
Sodium Ion ◽  
Discharge Process ◽  
Sodium Ion Batteries

We present the first large-scale ab initio simulation of the discharge process of polymeric cathode materials for electrochemical batteries in solid state.

scholarly journals Bayesian active learning of interatomic force field for molecular dynamics simulation of Pt/Ag(111)

2021 ◽  
Author(s):  
Kai Xu ◽  
Lei Yan ◽  
Bingran You
Keyword(s):  
Molecular Dynamics ◽  
Active Learning ◽  
Force Field ◽  
Density Functional ◽  
Process Model ◽  
Large Scale ◽  
Computational Cost ◽  
Dynamics Simulation ◽  
Potential Energy Landscape ◽  
Three Body

Force field is a central requirement in molecular dynamics (MD) simulation for accurate description of the potential energy landscape and the time evolution of individual atomic motions. Most energy models are limited by a fundamental tradeoff between accuracy and speed. Although ab initio MD based on density functional theory (DFT) has high accuracy, its high computational cost prevents its use for large-scale and long-timescale simulations. Here, we use Bayesian active learning to construct a Gaussian process model of interatomic forces to describe Pt deposited on Ag(111). An accurate model is obtained within one day of wall time after selecting only 126 atomic environments based on two- and three-body interactions, providing mean absolute errors of 52 and 142 meV/Å for Ag and Pt, respectively. Our work highlights automated and minimalistic training of machine-learning force fields with high fidelity to DFT, which would enable large-scale and long-timescale simulations of alloy surfaces at first-principles accuracy.

Quantum molecular dynamics simulation of Σ13 grain boundary in Si

1992 ◽  
Vol 50 (1) ◽  
pp. 212-213
Author(s):  
M.J. Kim ◽  
H. Ma ◽  
R.W. Carpenter ◽  
S.H. Lin ◽  
O.F. Sankey
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundary ◽  
Density Functional ◽  
Local Density ◽  
Tight Binding ◽  
Equilibrium Structure ◽  
Dynamics Simulation ◽  
Boundary Structure ◽  
Quantum Molecular Dynamics ◽  
Binding Model

Grain boundary (GB) structure determination at an atomic level by HREM had received increasing attention in recent years. However, models of grain boundary structure deduced from the experiment results are usually not unique, and they do not necessarily represent the equilibrium structure. A newly developed quantum-molecular-dynamics (QMD) method, which does not depend on any empirical potentials, can be used to test these models and find the equilibrium atomic structure through simulated quenching. The method employs an electronic structure tight-binding model based on density functional theory within the local density approximation and the nonlocal pseudopotential scheme, and is used to compute the total energy and atomic forces for a variety of covalent materials. In the present study, this QMD method, coupled with image simulation, was used to predict the relaxed atomic configuration for the Σ=13 (510), [001] tilt grain boundary in Si.

Mesoscale Electrostatics Driving Particle Dynamics in Non-Homogeneous Dielectrics

2018 ◽  
Author(s):  
sigbjoern Loeland Bore ◽  
Hima Bindu Kolli ◽  
Toshihiro Kawakatsu ◽  
Giuseppe Milano ◽  
Michele Cascella
Keyword(s):  
Lipid Bilayers ◽  
Poisson Equation ◽  
Soft Matter ◽  
Density Functional ◽  
Large Scale ◽  
Numerical Solutions ◽  
Potential Of Mean Force ◽  
Electrostatic Energy ◽  
Generalized Poisson ◽  
Oil Mixtures

<div>We introduce a density functional-based formalism to compute the electrostatic energy and forces for a mesoscopic system in the condensed phase, described with molecular resolution. The dielectric permittivity is variable in space, and it is dependent on the density fields of the individual particles present in the system. The electrostatic potential is obtained from standard numerical solutions of the generalized Poisson equation. The presence of a particle-dependent varying dielectrics produces the appearance of mesoscopic polarization forces, which are dependent on the local fluctuations of the permittivity, as well as of the electrostatic field. The proposed implementation is numerically robust, with an error on the Coulomb forces that can be systematically controlled by the mesh of spatial grid used for solving the generalized Poisson equation. We show that the method presented here is able to reproduce the concentration-dependent partitioning of an ideal salt in water/oil mixtures, in particular, reproducing the ∝ 1/epsilon dependency of the partition coefficient for the free ions predicted by Born theory. Moreover, this approach reproduces the correct electrostatic features of both dipolar and charged lipid bilayers, with positive membrane and dipole potentials. The sum of both Coulomb and polarization interactions inside the membrane yields a globally repulsive potential of mean force for the ions, independently on their charge. The computational efficiency of the method makes it particularly suitable for the description of large scale polyelectrolyte soft-matter systems.</div>

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