Predicting Methane Diffusivity in Polymeric Membranes by Molecular Dynamics

2015 ◽  
Vol 1119 ◽  
pp. 461-465
Author(s):  
M.K. Hadj-Kali ◽  
A. Bessadok-Jemai ◽  
S. Haider ◽  
Y. Alzeghayer
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Polymeric Membranes ◽  
Transport Mechanisms ◽  
Fluid Equation ◽  
Cell Modules ◽  
Dynamics Simulations ◽  
Materials Studio

Diffusion coefficients of methane (CH4) have been obtained by Molecular Dynamics (MD) simulations combined with Einstein fluid equation. Three polymers were considered, namely polyethylene, polypropylene and poly (cis-1,4-butadiene). All calculations were performed by means of Polymer Builder and Amorphous Cell modules within Materials Studio (Accelrys). The obtained diffusivity results are within the range of published results for similar small molecules. Molecular dynamics simulations proved to be a useful tool for understanding the detailed descriptions and transport mechanisms occurring within the material.

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

Molecular Dynamics Simulations of Atoms Diffusion in Solid

2018 ◽  
Vol 15 ◽  
pp. 51-64
Author(s):  
Yu Lu Zhou ◽  
Xiao Ma Tao ◽  
Qing Hou ◽  
Yi Fang Ouyang
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Einstein Relation ◽  
Interatomic Potentials ◽  
Body System ◽  
Many Body ◽  
Point Particles ◽  
Bulk Surface ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations, which treat atoms as point particles and trace their individual trajectories, are always employed to investigate the transport properties of a many-body system. The diffusion coefficients of atoms in solid can be obtained by the Einstein relation and the Green-Kubo relation. An overview of the MD simulations of atoms diffusion in the bulk, surface and grain boundary is provided. We also give an example of the diffusion of helium in tungsten to illustrate the procedure, as well as the importance of the choice of interatomic potentials. MD simulations can provide intuitive insights into the atomic mechanisms of diffusion.

Lanthanoids(III) and actinoids(III) in water: Diffusion coefficients and hydration enthalpies from polarizable molecular dynamics simulations

2012 ◽  
Vol 85 (1) ◽  
pp. 237-246 ◽  
Author(s):  
Fausto Martelli ◽  
Sacha Abadie ◽  
Jean-Pierre Simonin ◽  
Rodolphe Vuilleumier ◽  
Riccardo Spezia
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Heavy Ions ◽  
Md Simulations ◽  
Contradictory Result ◽  
Dielectric Friction ◽  
Water Interaction ◽  
Diffusive Regime ◽  
Dynamics Simulations ◽  
Good Agreement

By using polarizable molecular dynamics (MD) simulations of lanthanoid(III) and actinoid(III) ions in water, we obtained ionic diffusion coefficients and hydration enthalpies for both series. These values are in good agreement with experiments. Simulations thus allow us to relate them to microscopic structure. In particular, across the series the diffusion coefficients decrease, reflecting the increase of ion–water interaction. Hydration enthalpies also show that interactions increase from light to heavy ions in agreement with experiment. The apparent contradictory result of the decrease of the diffusion coefficient with decreasing ionic radius is tentatively explained in terms of dielectric friction predominance on Stokes’ diffusive regime.

Molecular Modelling of Small Molecule Diffusion in Biopolymer Blends Membranes for Biomedical Applications

2006 ◽  
Author(s):  
Mariana Ionita ◽  
Davide Silvestri ◽  
Alfonso Gautieri ◽  
Emiliano Votta ◽  
Gianluca Ciardelli ◽  
...  
Keyword(s):  
Small Molecules ◽  
Diffusion Coefficients ◽  
Diffusion Constant ◽  
Polymeric Materials ◽  
Md Simulations ◽  
Synthetic Polymers ◽  
Computational Method ◽  
Poly Vinyl Alcohol ◽  
Dynamics Simulations ◽  
Biological Performance

In order to improve the biological performance of synthetic polymers and to enhance the mechanical characteristics by tailoring the permeability properties of biopolymers, a new class of specifically designed materials (bioartificial polymeric materials), consisting of blends of synthetic polymers and biopolymers, has been recently introduced. In this work we present a computational method based on molecular mechanics (MM) and dynamics (MD) techniques, to investigate their permeability to small molecules. The permeability properties was assessed of poly(vinyl alcohol)-(PVA)- dextran-(Dex) and poly(acrylic acid)-(PAA)-Dex membranes with different blend composition. Amorphous bulk models of PVA–Dex and PAA–Dex mixtures with 80:20, 60:40, 40:60 (w/w) ratios were generated. Two steps have been performed iteratively, the former using a MM simulation for equilibration and the latter using MD simulations for model refinement. Virtual uniaxial traction tests were performed, adopting the Second Derivative (SD) procedure, in order to assess the mechanical behavior of the bulk models. The diffusion coefficients for H2O were determined via NVT molecular dynamics simulations. Using the data of the motion of water inside the bulk models, the diffusivity constant was calculated applying the Einstein equation. Correlation of diffusion coefficients with free volume, was found. The results of the simulations agree with theoretical considerations: as the content of dextran increases from 80:20 to 40:60 a 86 % decrease of the diffusion constant is obtained and the values (range 0.14–56.5 10−6 cm2s−1) have the order of magnitude expected, and similar on the diffusion of small molecules in amorphous polymeric membranes.

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

Mechanism of stacking fault annihilation in 3C-SiC epitaxially grown on Si(001) by molecular dynamics simulations

CrystEngComm ◽  
2021 ◽  
Author(s):  
Andrey Sarikov ◽  
Anna Marzegalli ◽  
Luca Barbisan ◽  
Massimo Zimbone ◽  
Corrado Bongiorno ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Stacking Faults ◽  
Md Simulations ◽  
Stacking Fault ◽  
Dynamics Simulations

In this work, annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in...

scholarly journals Molecular Dynamics Simulations of Crystal Nucleation near Interfaces in Incompatible Polymer Blends

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 347
Author(s):  
Wenlin Zhang ◽  
Lingyi Zou
Keyword(s):  
Molecular Dynamics ◽  
Polymer Blends ◽  
Md Simulations ◽  
Nucleation And Growth ◽  
Crystal Nucleation ◽  
Crystalline Order ◽  
Mobile Species ◽  
Deep Supercooling ◽  
Crystallizable Polymer ◽  
Dynamics Simulations

We apply molecular dynamics (MD) simulations to investigate crystal nucleation in incompatible polymer blends under deep supercooling conditions. Simulations of isothermal nucleation are performed for phase-separated blends with different degrees of incompatibility. In weakly segregated blends, slow and incompatible chains in crystallizable polymer domains can significantly hinder the crystal nucleation and growth. When a crystallizable polymer is blended with a more mobile species in interfacial regions, enhanced molecular mobility leads to the fast growth of crystalline order. However, the incubation time remains the same as that in pure samples. By inducing anisotropic alignment near the interfaces of strongly segregated blends, phase separation also promotes crystalline order to grow near interfaces between different polymer domains.

scholarly journals Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

scholarly journals Simulated Breathing: Application of Molecular Dynamics Simulations to Pulmonary Lung Surfactant

Symmetry ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1259
Author(s):  
Maksymilian Dziura ◽  
Basel Mansour ◽  
Mitchell DiPasquale ◽  
P. Charukeshi Chandrasekera ◽  
James W. Gauld ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Pulmonary Surfactant ◽  
Lung Surfactant ◽  
Protein Composition ◽  
Md Simulations ◽  
Building Blocks ◽  
Future Research ◽  
Total Composition ◽  
Protein Components ◽  
Dynamics Simulations

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to the system as a whole. Moreover, a couple of theories/models that are associated with the functions of PS have been addressed. Finally, molecular dynamic (MD) simulations of pulmonary surfactant have been emphasized to not only showcase various group’s findings, but also to demonstrate the validity and importance that MD simulations can have in future research exploring the PS monolayer system.

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