scholarly journals Diffusion of oxytocin in water: a molecular dynamics study

BIBECHANA ◽  
2021 ◽  
Vol 18 (1) ◽  
pp. 108-117
Author(s):  
Khimananda Acharya ◽  
Rajendra Prasad Koirala ◽  
Nurapati Pantha
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular System ◽  
Dynamics Simulation ◽  
Water Model ◽  
Binary Diffusion Coefficient ◽  
Self Diffusion ◽  
Different Temperatures ◽  
The Stability ◽  
Self Diffusion Coefficient

Classical molecular dynamics simulation is performed to estimate the diffusion coefficient of oxytocin in water at different temperatures, 288 K, 300 K, 313 K, 323 K, using GROningen Machine for Chemical Simulations (GROMOCS). The simulation is carried out using GROMOS43A1 force field and extended simple point charge (SPC/E) water model. The stability of the system is evaluated from energy profile of potential and kinetic energy, which assures well equilibrated molecular system. The self-diffusion coefficient of oxytocin and water is obtained from Einstein’s relation and binary diffusion coefficient is obtained from Darken’s relation. As temperature increases the diffusion coefficient also increases as per expectation. The diffusion coefficients of water from the present calculations agree well with the previously reported values, within the 10% of deviation. Furthermore, the activation energy has been studied using Arrhenius Plot. BIBECHANA 18 (2021) 108-117

scholarly journals Molecular dynamics study of diffusion of xenon in water at different temperatures

2018 ◽  
Vol 16 (2) ◽  
Author(s):  
Niraj Kumar ◽  
Narayan Prasad Adhikari
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Structural Properties ◽  
The Self ◽  
Dynamics Simulation ◽  
Velocity Autocorrelation Function ◽  
Arrhenius Behavior ◽  
Self Diffusion ◽  
Different Temperatures ◽  
Self Diffusion Coefficient

Molecular Dynamics simulation was performed using 2 xenon atoms as solute and 300 water molecules as solvent. We have studied the structural properties as well as transport property. As structural properties, we have determined the radial distribution function (RDF) of xenon-xenon, xenon-water, and water-water interactions. Study of RDF of xenon-xenon and oxygen-oxygen interactions of water shows that there is hydrophobic behavior of xenon in the presence of water. We have studied the self diffusion coefficient of xenon, water, and mutual diffusion coefficients of xenon in water. The self diffusion coefficient of xenon was estimated using both mean-squared displacement (MSD) and velocity autocorrelation function (VACF), while only MSD was used for water. The temperature dependence of the diffusion coefficient of xenon and water were found to follow the Arrhenius behavior. The activation energies obtained are 12.156 KJ/mole with MSD and 14.617 KJ/mole with VACF in the temperature range taken in this study.

Self Diffusion in Liquid Titanium: Quasielastic Neutron Scattering and Molecular Dynamics Simulation

2009 ◽  
Vol 289-292 ◽  
pp. 609-614 ◽  
Author(s):  
Andreas Meyer ◽  
Jürgen Horbach ◽  
O. Heinen ◽  
Dirk Holland-Moritz ◽  
T. Unruh
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Neutron Scattering ◽  
The Self ◽  
Dynamics Simulation ◽  
Self Diffusion ◽  
Quasielastic Neutron ◽  
Liquid Titanium ◽  
Quasielastic Neutron Scattering ◽  
Self Diffusion Coefficient

Self diffusion in liquid titanium was measured at 2000K by quasielastic neutron scattering (QNS) in combination with container less processing via electromagnetic levitation. At small wavenumbers q the quasielastic signal is dominated by incoherent scattering. Up to about 1.2 °A−1 the width of the quasielastic line exhibits a q2 dependence as expected for long range atomic transport, thus allowing to measure the self diffusion coefficient DTi. As a result the value DTi = (5.3± 0.2)× 10−9 m2s−1 was obtained.With a molecular dynamics (MD) computer simulation using an embedded atom model (EAM) for Ti, the self diffusion coefficient is determined from the mean square displacement as well as from the decay of the incoherent intermediate scattering function at different q. By comparing both methods, we show that the hydrodynamic prediction of a q2 dependence indeed extends up to about 1.2 °A−1. Since this result does not depend significantly on the details of the interatomic potential, our findings show that accurate values of self diffusion coefficients in liquid metals can be measured by QNS on an absolute scale.

scholarly journals Structural Analyses of [Li Salt+Triglyme)] and Ionic Transport in Li-Air Battery Using Molecular Dynamics Simulation

2020 ◽  
Vol 27 (1) ◽  
pp. 13-22
Author(s):  
Md Khorshed Alam ◽  
Wataru Yamamoto ◽  
Hiromitsu Takaba
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Force Fields ◽  
Ionic Transport ◽  
Dynamics Simulation ◽  
Self Diffusion ◽  
Air Battery ◽  
Self Diffusion Coefficient

In this work, molecular dynamics (MD) study of triglyme (G3) solution containing lithium bis (trifluoro methyl sulfonyl) amide (Li[TFSA]) were investigated using classical atomistic force fields. G3 is a typical solvent used in non-aqueous Li-air battery. It shows here coordination of Li+ with G3 and [TFSA]- does not significantly change with increasing the concentration of G3 but self-diffusion coefficient of all the ions increases with increasing G3 concentration. The density of [Li(G3)[TFSA] complex decreases with increasing G3 concentration which lead to accelerate diffusivity of ions. Bangladesh Journal of Physics, 27(1), 13-22, June 2020

Molecular dynamics study of diffusion of krypton in water at different temperatures

2016 ◽  
Vol 30 (11) ◽  
pp. 1650064 ◽  
Author(s):  
Dipendra Bhandari ◽  
N. P. Adhikari
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Diffusion Coefficients ◽  
Mean Square Displacement ◽  
Mutual Diffusion ◽  
Arrhenius Behavior ◽  
Self Diffusion ◽  
Velocity Autocorrelation ◽  
Different Temperatures ◽  
Self Diffusion Coefficient

Molecular dynamics study of diffusion of two krypton atoms in 300 SPC/E water molecules at temperatures 293, 303, 313, 323 and 333 K has been carried out. Self-diffusion coefficient of krypton and water along with their mutual diffusion coefficients are estimated. Self-diffusion coefficient for krypton is calculated by using Mean Square Displacement (MSD) method and Velocity Autocorrelation (VACF) method, while that for water is calculated by using MSD method only. The mutual diffusion coefficient is estimated by using the Darken’s relation. The diffusion coefficients are found to follow the Arrhenius behavior. The structural properties of the system have been estimated by the study of solute–solute, solvent–solvent, and solute–solvent Radial Distribution Function (RDF).

Molecular Dynamics Simulation of the Internal Mobilities in Molten (Dy1/3,K)Cl

2001 ◽  
Vol 56 (3-4) ◽  
pp. 273-278 ◽  
Author(s):  
Masahiko Matsumiya ◽  
Ryuzo Takagi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Self Diffusion ◽  
Electrical Conductivities ◽  
Internal Mobility ◽  
Dynamics Simulations ◽  
Self Diffusion Coefficient

Abstract Molecular dynamics simulations have been performed on molten (Dy1/3,K)Cl at 1093 K in order to compare the calculated self-exchange velocity (SEV), self-diffusion coefficient (D) and electrical con­ductivity with the corresponding experimental results. It was found that SEV, v, and D of potassium de­ crease with increasing concentration of dysprosium, as expected from the internal mobility, b. The decrease of bK, vK, and DK are ascribed to the tranquilization effect by Dy3+ which strongly inter­ acts with CP. On the contrary, bDy, vDy, and DDy increase with increasing concentration of Dy3+. This may be attributed to the stronger association of Dy3+ with Cl- due to the enhanced charge asym­ metry of the two cations neighboring to the Cl-. In addition, the sequence of the calculated SEV's, D's and electrical conductivities for the various compositions were consistent with those of the referred ex­ perimental results.

Temperature dependence of diffusion coefficient of nitrogen gas in water: A molecular dynamics study

2014 ◽  
Vol 28 (14) ◽  
pp. 1450084 ◽  
Author(s):  
Keshav Sharma ◽  
Narayan P. Adhikari
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Structural Properties ◽  
Diffusion Coefficients ◽  
Molecular Nitrogen ◽  
Velocity Autocorrelation Function ◽  
Self Diffusion ◽  
Water Solvent ◽  
Different Temperatures ◽  
Self Diffusion Coefficient

We have carried out the molecular dynamics (MD) simulation to study the structural properties and to estimate the diffusivity of molecular nitrogen ( N 2) gas (solute) in extended simple point charge model (SPC/E) water (solvent) with N 2 mole fraction of 0.018 at different temperatures. For the structural properties of the system, we have determined radial distribution function (RDF). The solute–solute, solute–solvent and solvent–solvent RDF have been evaluated. Self-diffusion coefficient of N 2 was estimated by evaluating mean-squared displacement (MSD) and velocity autocorrelation function (VACF) separately. The diffusion coefficients obtained from the two methods agree within 3%. The results are in agreement with the experimentally determined values within 10%. The self-diffusion coefficient of water ( H 2 O ) was also estimated by evaluating MSD. Mutual diffusion coefficient of the system have also been estimated invoking Darken's relation. The temperature dependance of the diffusion coefficients were found to follow Arrhenius relation.

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