scholarly journals Structure and Dynamics of Curcumin Encapsulated Lecithin Micelles: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 6 (3) ◽  
pp. 113-120
Author(s):  
Lukman Hakim ◽  
Diah Mardiana ◽  
Urnik Rokhiyah ◽  
Maria Lucia Ardhani Dwi Lestari ◽  
Zubaidah Ningsih
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Local Density ◽  
Center Of Mass ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Spherical Micelle ◽  
Natural Surfactant ◽  
Dynamics Response ◽  
Nano Emulsion

Curcumin is a natural product with potential pharmaceutical applications that can be augmented by drug delivery technology such as nano emulsion. Our study focuses on microscopic structural and dynamics response of curcumin encapsulation in micellar system with lecithin as a natural surfactant under variations of composition and temperature using molecular dynamics (MD) simulations. The results highlight the self-assembly of lecithin micelle, with curcumin encapsulated inside, from initial random configurations in the absence of external field. The variation of composition shows that lecithin can aggregate into spherical and rod-like micelle with the second critical micelle concentration lies between 0.17-0.22 mol dm−3. The radial local density centering at the micelle center of mass shows that the effective radius of micelle is indeed defined by the hydrophilic groups of lecithin molecule and theencapsulated curcumin molecules are positioned closer to these hydrophilic groups than the innermost part of the micelle. The spherical micelle is shown to be thermally stable within the temperature range of 277-310 K without a perceivable change in the spherical eccentricity. The dynamics of micelle are enhanced by the temperature, but it is shown to be insensitive to the variation of lecithin-curcumin composition within the studied range. Simulation results are in agreement with the pattern obtained from experimental results based on particle size, polydispersity index, and encapsulation efficiency.

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

Sensors ◽  
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.

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

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.

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

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.

Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Kazushi Fujimoto ◽  
Tetsuro Nagai ◽  
Tsuyoshi Yamaguchi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mass Velocity ◽  
Center Of Mass ◽  
Heterogeneous Systems ◽  
Diffusion Constant ◽  
Dynamics Simulation ◽  
Coulombic Interaction ◽  
Ewald Method ◽  
Theoretical Predictions

<div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div>

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

2021 ◽  
Vol 12 ◽  
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.

scholarly journals Molecular Dynamics Simulation of Wetting Behavior: Contact Angle Dependency on Water Potential Models

2021 ◽  
Vol 1 (1) ◽  
pp. 10
Author(s):  
Lukman Hakim ◽  
Irsandi Dwi Oka Kurniawan ◽  
Ellya Indahyanti ◽  
Irwansyah Putra Pradana
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Liquid Droplet ◽  
Center Of Mass ◽  
Contact Angles ◽  
Surface Wettability ◽  
Dynamics Simulation ◽  
Potential Models ◽  
Surface Hydrophilicity ◽  
Dynamics Simulations

The underlying principle of surface wettability has obtained great attentions for the development of novel functional surfaces. Molecular dynamics simulations has been widely utilized to obtain molecular-level details of surface wettability that is commonly quantified in term of contact angle of a liquid droplet on the surface. In this work, the sensitivity of contact angle calculation at various degrees of surface hydrophilicity to the adopted potential models of water: SPC/E, TIP4P, and TIP5P, is investigated. The simulation cell consists of a water droplet on a structureless surface whose hydrophilicity is modified by introducing a scaling factor to the water-surface interaction parameter. The simulation shows that the differences in contact angle described by the potential models are systematic and become more visible with the increase of the surface hydrophilicity. An alternative method to compute a contact angle based on the height of center-of-mass of the droplet is also evaluated, and the resulting contact angles are generally larger than those determined from the liquid-gas interfacial line.

Molecular Dynamics Simulation of Neutron Damage in β-SIC

1998 ◽  
Vol 540 ◽  
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.

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

2015 ◽  
Vol 817 ◽  
pp. 797-802 ◽  
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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