Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

Silicalite is an important nanoporous material that finds applications in several industries, including gas separation and catalysis. While the sorption, structure, and dynamics of several molecules confined in the pores of silicalite have been reported, most of these studies have been restricted to low pressures. Here we report a comparative study of sorption, structure, and dynamics of CO2 and ethane in silicalite at high pressures (up to 100 bar) using a combination of Monte Carlo (MC) and molecular dynamics (MD) simulations. The behavior of the two fluids is studied in terms of the simulated sorption isotherms, the positional and orientational distribution of sorbed molecules in silicalite, and their translational diffusion, vibrational spectra, and rotational motion. Both CO2 and ethane are found to exhibit orientational ordering in silicalite pores; however, at high pressures, while CO2 prefers to reside in the channel intersections, ethane molecules reside mostly in the sinusoidal channels. While CO2 exhibits a higher self-diffusion coefficient than ethane at low pressures, at high pressures, it becomes slower than ethane. Both CO2 and ethane exhibit rotational motion at two time scales. At both time scales, the rotational motion of ethane is faster. The differences observed here in the behavior of CO2 and ethane in silicalite pores can be seen as a consequence of an interplay of the kinetic diameter of the two molecules and the quadrupole moment of CO2.

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Understanding Covalent Grafting of Nanotubes onto Polymer Nanocomposites: Molecular Dynamics Simulation Study

Sensors ◽

10.3390/s21082621 ◽

2021 ◽

Vol 21 (8) ◽

pp. 2621

Author(s):

Seunghwa Yang

Keyword(s):

Molecular Dynamics ◽

Load Transfer ◽

Cell Model ◽

Md Simulations ◽

Dynamics Simulation ◽

Covalent Grafting ◽

Modelling Strategies ◽

Multi Walled Carbon Nanotubes ◽

Walled Carbon Nanotubes ◽

External Loads

Here, we systematically interrogate the effects of grafting single-walled (SWNT) and multi-walled carbon nanotubes (MWNT) to polymer matrices by using molecular dynamics (MD) simulations. We specifically investigate key material properties that include interfacial load transfer, alteration of nanotube properties, and dispersion of nanotubes in the polymer matrix. Simulations are conducted on a periodic unit cell model of the nanocomposite with a straight carbon nanotube and an amorphous polyethylene terephthalate (PET) matrix. For each type of nanotube, either 0%, 1.55%, or 3.1% of the carbon atoms in the outermost nanotubes are covalently grafted onto the carbon atoms of the PET matrix. Stress-strain curves and the elastic moduli of nanotubes and nanocomposites are determined based on the density of covalent grafting. Covalent grafting promotes two rivalling effects with respect to altering nanotube properties, and improvements in interfacial load transfer in the nanocomposites are clearly observed. The enhanced interface enables external loads applied to the nanocomposites to be efficiently transferred to the grafted nanotubes. Covalent functionalization of the nanotube surface with PET molecules can alter the solubility of nanotubes and improve dispersibility. Finally, we discuss the current limitations and challenges in using molecular modelling strategies to accurately predict properties on the nanotube and polymers systems studied here.

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A Study on the Uniaxial Tension of FCC Metals at Nano Level Using MD

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.32.255 ◽

2008 ◽

Vol 32 ◽

pp. 255-258

Author(s):

Bohayra Mortazavi ◽

Akbar Afaghi Khatibi

Keyword(s):

Molecular Dynamics ◽

Uniaxial Tension ◽

Md Simulations ◽

Dynamics Simulation ◽

Face Centered Cubic ◽

Engineering Strain ◽

Fcc Metals ◽

Engineering Stress ◽

Nano Science ◽

Face Centered

Molecular Dynamics (MD) are now having orthodox means for simulation of matter in nano-scale. It can be regarded as an accurate alternative for experimental work in nano-science. In this paper, Molecular Dynamics simulation of uniaxial tension of some face centered cubic (FCC) metals (namely Au, Ag, Cu and Ni) at nano-level have been carried out. Sutton-Chen potential functions and velocity Verlet formulation of Noise-Hoover dynamic as well as periodic boundary conditions were applied. MD simulations at different loading rates and temperatures were conducted, and it was concluded that by increasing the temperature, maximum engineering stress decreases while engineering strain at failure is increasing. On the other hand, by increasing the loading rate both maximum engineering stress and strain at failure are increasing.

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Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

MRS Proceedings ◽

10.1557/opl.2014.715 ◽

2014 ◽

Vol 1700 ◽

pp. 61-66

Author(s):

Guttormur Arnar Ingvason ◽

Virginie Rollin

Keyword(s):

Molecular Dynamics ◽

Polymer Matrix ◽

Large Scale ◽

Md Simulations ◽

Dynamics Simulation ◽

Atomistic Simulations ◽

Polymer Molecules ◽

Molecular Potential ◽

Pull Out ◽

Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

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Molecular Dynamics Simulation of Cis-Trans N-Methylformamide (NMF) Liquid Mixture. Structure and Dynamics

International Conference of Computational Methods in Sciences and Engineering 2004 (ICCMSE 2004) ◽

10.1201/9780429081385-117 ◽

2019 ◽

pp. 479-482

Author(s):

Ioannis Skarmoutsos ◽

Jannis Samios

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Liquid Mixture ◽

Dynamics Simulation ◽

Structure And Dynamics

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An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

Frontiers in Pharmacology ◽

10.3389/fphar.2021.717757 ◽

2021 ◽

Vol 12 ◽

Cited By ~ 1

Author(s):

Trina Ekawati Tallei ◽

Fatimawali ◽

Afriza Yelnetty ◽

Rinaldi Idroes ◽

Diah Kusumawaty ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Three Dimensional ◽

Md Simulations ◽

Inhibitory Effect ◽

Dynamics Simulation ◽

Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

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Computational Prediction of Heteromeric Protein Complex Disassembly Order with Hybrid Monte Carlo/Molecular Dynamics Simulation

10.1101/2022.01.12.476000 ◽

2022 ◽

Author(s):

Ikuo Kurisaki ◽

Shigenori Tanaka

Keyword(s):

Molecular Dynamics ◽

Monte Carlo ◽

Protein Complex ◽

Protein Complexes ◽

Structural Bioinformatics ◽

Dynamics Simulation ◽

Tryptophan Synthase ◽

Selection Scheme ◽

Hybrid Monte Carlo ◽

Multimeric Protein

The physicochemical entity of biological phenomenon in the cell is a network of biochemical reactions and the activity of such a network is regulated by multimeric protein complexes. Mass spectroscopy (MS) experiments and multimeric protein docking simulations based on structural bioinformatics techniques have revealed the molecular-level stoichiometry and static configuration of subcomplexes in their bound forms, then revealing the subcomplex populations and formation orders. Meanwhile, these methodologies are not designed to straightforwardly examine temporal dynamics of multimeric protein assembly and disassembly, essential physicochemical properties to understand functional expression mechanisms of proteins in the biological environment. To address the problem, we had developed an atomistic simulation in the framework of the hybrid Monte Carlo/Molecular Dynamics (hMC/MD) method and succeeded in observing disassembly of homomeric pentamer of the serum amyloid P component protein in experimentally consistent order. In this study, we improved the hMC/MD method to examine disassembly processes of the tryptophan synthase tetramer, a paradigmatic heteromeric protein complex in MS studies. We employed the likelihood-based selection scheme to determine a dissociation-prone subunit pair at each hMC/MD simulation cycle and achieved highly reliable predictions of the disassembly orders with the success rate over 0.9 without a priori knowledge of the MS experiments and structural bioinformatics simulations. We similarly succeeded in reliable predictions for the other three tetrameric protein complexes. These achievements indicate the potential availability of our hMC/MD approach as the general purpose methodology to obtain microscopic and physicochemical insights into multimeric protein complex formation.

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Local intermolecular structure and dynamics in binary supercritical solutions. A molecular dynamics simulation study of methane in carbon dioxide

Journal of Molecular Liquids ◽

10.1016/j.molliq.2005.11.023 ◽

2006 ◽

Vol 125 (2-3) ◽

pp. 181-186 ◽

Cited By ~ 15

Author(s):

Ioannis Skarmoutsos ◽

Jannis Samios

Keyword(s):

Carbon Dioxide ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Structure And Dynamics ◽

Supercritical Solutions

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Molecular Dynamics Simulation of Neutron Damage in β-SIC

MRS Proceedings ◽

10.1557/proc-540-171 ◽

1998 ◽

Vol 540 ◽

Cited By ~ 8

Author(s):

J.M. Perlado ◽

L. Malerba ◽

T. Diaz De La Rubia

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Point Defects ◽

Damage Accumulation ◽

Md Simulations ◽

Dynamics Simulation ◽

Temperature Sensitive ◽

Neutron Damage ◽

Preliminary Study ◽

Threshold Displacement

AbstractMolecular Dynamics (MD) simulations of neutron damage in β-SiC have been performed using a modified version of the Tersoff potential. The Threshold Displacement Energy (TDE) for Si and C atoms at 300 K has been determined along directions [001], [110], [111] and [ 1 1 1 ]. The existence of recombination barriers, which allow the formation of metastable, temperature-sensitive defects even below the threshold, has been observed. Displacement cascades produced by both C- and Si-recoils of energies spanning from 0.5 keV up to, respectively, 5 keV and 8 keV have also been simulated at 300 K and 1300 K. Their analysis, together with the analysis of damage accumulation (∼3.4×10-3 DPA) at 1300 K, reveals that the two sub-lattices exhibit opposite responses to irradiation: whereas only a little damage is produced on the “ductile” Si sub-lattice, many point-defects accumulate on the much more “fragile” C sub-lattice. A preliminary study of the nature and clustering tendency of these defects is performed. The possibility of disorder-induced amorphization is considered and the preliminary result is that no amorphization takes place at the dose and temperature simulated.

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Influence of Carbon Nanotube Aspect Ratio on Glass Transition Temperature of Polymers: A Molecular Dynamics Simulation Study

Materials Science Forum ◽

10.4028/www.scientific.net/msf.817.797 ◽

2015 ◽

Vol 817 ◽

pp. 797-802 ◽

Cited By ~ 2

Author(s):

Cai Jiang ◽

Jian Wei Zhang ◽

Shao Feng Lin ◽

Su Ju ◽

Da Zhi Jiang

Keyword(s):

Molecular Dynamics ◽

Glass Transition ◽

Carbon Nanotube ◽

Transition Temperature ◽

Glass Transition Temperature ◽

Aspect Ratio ◽

Epoxy Resin ◽

Md Simulations ◽

Diglycidyl Ether ◽

Dynamics Simulation

Molecular dynamics (MD) simulations on three single walled carbon nanotube (SWCNT) reinforced epoxy resin composites were conducted to study the influence of SWCNT type on the glass transition temperature (Tg) of the composites. The composite matrix is cross-linked epoxy resin based on the epoxy monomers bisphenol A diglycidyl ether (DGEBA) cured by diaminodiphenylmethane (DDM). MD simulations of NPT (constant number of particles, constant pressure and constant temperature) dynamics were carried out to obtain density as a function of temperature for each composite system. The Tg was determined as the temperature corresponding to the discontinuity of plot slopes of the densityvsthe temperature. In order to understand the motion of polymer chain segments above and below the Tg, various energy components and the MSD at various temperatures of the composites were investigated and their roles played in the glass transition process were analyzed. The results show that the Tg of the composites increases with increasing aspect ratio of the embedded SWCNT

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