A molecular dynamics study of ices III and V using TIP4P and TIP5P water models

2003 ◽  
Vol 81 (1-2) ◽  
pp. 11-16 ◽  
Author(s):  
R B Ayala ◽  
V Tchijov
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Molecular Interactions ◽  
Specific Volume ◽  
Molecular Dynamics Calculations ◽  
Water Models ◽  
Good Agreement

Simulations of ices III and V are performed using molecular dynamics calculations in the NPT ensemble. To represent molecular interactions in both ices, two potentials, TIP4P and TIP5P, are used. The specific volume of ice III is calculated as a function of temperature at pressure P = 250 MPa, as well as a function of pressure at temperature T = 246 K. For ice V, the specific volume is calculated as a function of temperature at P = 500 MPa and as a function of pressure at T = 238 K. In both cases, both TIP4P and TIP5P models are used. The results of the calculations are in good agreement with the experimental data of other researchers. PACS No.: 31.15Qg

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

THE CORRELATION BETWEEN BOND ANGLE DISTRIBUTION AND THE COORDINATION OF SILICA LIQUID UNDER PRESSURE

2012 ◽  
Vol 26 (20) ◽  
pp. 1250117 ◽  
Author(s):  
L. T. VINH ◽  
N. V. HUY ◽  
P. K. HUNG
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Bond Angle ◽  
Simple Expression ◽  
Dynamics Simulation ◽  
Angle Distribution ◽  
Bond Angle Distribution ◽  
Simulation Results ◽  
Substantial Change ◽  
Good Agreement

Molecular dynamics simulation is carried out for liquid SiO 2 at pressure ranged from zero to 30 GPa and by using BKS, Born–Mayer type and Morse–Stretch potentials. The constructed models reproduce well the experimental data in terms of mean coordination number, bond angle and pair radial distribution function. Furthermore, the density of all samples can be expressed by a linear function of fractions SiO x. It is found that the topology of units SiO x and linkages OSi y is unchanged upon compression although the liquid undergoes substantial change in its network structure. Consequently, the partial bond angle distribution for SiO x and OSi y is identical for all samples constructed by the same potential. This result allows to establishing a simple expression between total bond angle distribution (BAD) and fraction of SiO x and OSi y. The simulation shows a good agreement between the calculation and simulation results for both total O–Si–O and Si–O–Si BADs. This supports a technique to estimate amount of units SiO x and linkages OSi y on base of total Si–O–Si and O–Si–O BADs measured experimentally.

A Theoretical Study Of The Energetics And Vibrational Spectra Of Oxygenated (100) Diamond Surfaces

1995 ◽  
Vol 416 ◽  
Author(s):  
S. Skokov ◽  
B. Weiner ◽  
M. Frenklach
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Vibrational Spectra ◽  
Theoretical Study ◽  
Local Environment ◽  
Hydroxyl Groups ◽  
Vibrational Modes ◽  
Diamond Surfaces ◽  
Molecular Dynamics Calculations

ABSTRACTStatic quantum ab initio and quantum semiempirical molecular dynamics calculations were employed to study reconstructions of (100) diamond surfaces in presence of hydrogen and oxygen. The results indicate that the energetically most favorable structures of oxygenated surfaces are those with chemisorbed hydroxyl groups. It was found that hydrogen bonds are formed among chemisorbed oxygenated species. The formation of these hydrogen bonds is shown to be an important factor in stabilization of adlayers. A number of important vibrational modes characteristic of oxygenated diamond surfaces were identified. The analysis of surface vibrational spectra demonstrates the influence of the local environment on the position of vibrational modes and can be useful for interpretation of experimental data.

Molecular dynamics study of solid argon with N2, O2, and CO impurities

1982 ◽  
Vol 60 (9) ◽  
pp. 1365-1370 ◽  
Author(s):  
Shūichi Nosé ◽  
Michael L. Klein
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Melting Point ◽  
Diatomic Molecules ◽  
Power Spectra ◽  
Preferred Orientation ◽  
Molecular Dynamics Calculations ◽  
Solid Argon

Molecular dynamics calculations employing atom–atom (exp-6) potentials are reported for solid argon in which 5% of the lattice sites are occupied by diatomic molecules. At temperatures close to the melting point (T ~ 80 K) the molecules are reorienting rapidly with no preferred orientation. Upon cooling, however, a distinct preference is observed for the crystallographic [Formula: see text] direction. Power spectra that characterize the translational and reorientational motions in the system have been evaluated. The results are discussed in light of available experimental data.

Molecular Dynamics Calculations of InSb Thermal Conductivity

2010 ◽  
Vol 297-301 ◽  
pp. 1400-1407
Author(s):  
Giovano de Oliveira Cardozo ◽  
José Pedro Rino
Keyword(s):  
Experimental Data ◽  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Infinite System ◽  
Thermal Conductivity Coefficient ◽  
Direct Method ◽  
Molecular Dynamics Calculations ◽  
Non Equilibrium Molecular Dynamics ◽  
Three Body ◽  
Non Equilibrium

Equilibrium and non-equilibrium molecular dynamics calculations of thermal conductivity coefficient are presented for bulk systems of InSb, using an effective two- and three-body inter atomic potential which demonstrated to be very transferable. In the calculations, the obtained coefficients were comparable to the experimental data. In the case of equilibrium simulations a Green-Kubo approach was used and the thermal conductivity was calculated for five temperatures between 300 K and 900 K. For the non equilibrium, or direct method, which is based on the Fourier’s law, the thermal conductivity coefficient was determined at a mean temperature of 300K. In this case it was used a pair of reservoirs, placed at a distance L from each other, and with internal temperatures fixed in 250 K, for the cold reservoir, and 350 K for the hot one. In order to obtain an approach to an infinite system coefficient, four different values of L were used, and the data was extrapolated to L→∞.

Proton-transfer dynamics in the (HCO3 −)2 dimer of KHCO3 from Car–Parrinello and path-integrals molecular dynamics calculations

2010 ◽  
Vol 66 (2) ◽  
pp. 222-228 ◽  
Author(s):  
Przemyslaw D. Dopieralski ◽  
Zdzislaw Latajka ◽  
Ivar Olovsson
Keyword(s):  
Molecular Dynamics ◽  
Neutron Diffraction ◽  
Proton Transfer ◽  
Close Agreement ◽  
Path Integrals ◽  
Experimental Ir ◽  
Molecular Dynamics Calculations ◽  
Time Gap ◽  
Highly Correlated ◽  
Good Agreement

The proton motion in the (HCO_3^-)2 dimer of KHCO3 at 298 K has been studied with Car–Parrinello molecular dynamics (CPMD) and path-integrals molecular dynamics (PIMD) simulations. According to earlier neutron diffraction studies at 298 K hydrogen is disordered and occupies two positions with an occupancy ratio of 0.804/0.196. A simulation with only one unit cell is not sufficient to reproduce the disorder of the protons found in the experiments. The CPMD results with four cells, 0.783/0.217, are in close agreement with experiment. The motion of the two protons along the O...O bridge is highly correlated inside one dimer, but strongly uncoupled between different dimers. The present results support a mechanism for the disorder which involves proton transfer from donor to acceptor and not orientational disordering of the entire dimer. The question of simultaneous or successive proton transfer in the two hydrogen bonds in the dimer remains unanswered. During the simulation situations with almost simultaneous proton transfer with a time gap of around 1 fs were observed, as well as successive processes where first one proton is transferred and then the second one with a time gap of around 20 fs. The calculated vibrational spectrum is in good agreement with the experimental IR spectrum, but a slightly different assignment of the bands is indicated by the present simulations.

scholarly journals Nitrogen Dissolution in Liquid Ga and Fe: Comprehensive Ab Initio Analysis, Relevance for Crystallization of GaN

Materials ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 1306
Author(s):  
Jacek Piechota ◽  
Stanislaw Krukowski ◽  
Petro Sadovyi ◽  
Bohdan Sadovyi ◽  
Sylwester Porowski ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Chemical Potential ◽  
Nitrogen Solubility ◽  
Molecular Nitrogen ◽  
Ideal Gas ◽  
The Difference ◽  
Good Agreement

The dissolution of molecular nitrogen in Ga and Fe was investigated by ab initio calculations and some complementary experiments. It was found that the N bonding inside these solvents is fundamentally different. For Ga, it is between Ga4s and Ga4p and N2p states whereas for Fe this is by N2p to Fe4s, Fe4p and Fe3d states. Accordingly, the energy of dissolution of N2 for arbitrarily chosen starting atomic configurations was 0.535 eV/mol and −0.299 eV/mol for Ga and Fe, respectively. For configurations optimized with molecular dynamics, the difference between the corresponding energy values, 1.107 eV/mol and 0.003 eV/mol, was similarly large. Full thermodynamic analysis of chemical potential was made employing entropy-derived terms in a Debye picture. The entropy-dependent terms were obtained via a normal conditions path to avoid singularity of ideal gas entropy at zero K. Nitrogen solubility as a function of temperature and N2 pressure was evaluated, being much higher for Fe than for Ga. For T=1800 K and p=104 bar, the N concentration in Ga was 3×10−3 at. fr. whereas for Fe, it was 9×10−2 at. fr. in very good agreement with experimental data. It indicates that liquid Fe could be a prospective solvent for GaN crystallization from metallic solutions.

Effects of Chlorine on Aluminum Refining: A Review and an Ab Initio Molecular Dynamics Study

2011 ◽  
Vol 467-469 ◽  
pp. 1404-1409 ◽  
Author(s):  
Yan Liu ◽  
Bao De Sun ◽  
Jun Wang ◽  
Yong Bing Dai
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Ab Initio ◽  
Hydrogen Diffusion ◽  
Liquid Aluminum ◽  
Refining Process ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Dynamics Calculations ◽  
Comprehensive Introduction ◽  
Diffusion Of Hydrogen

A comprehensive introduction of current aluminum refining technology is reviewed in this work especially the effects of chlorine on refining process is discussed. The mechanism of chlorine on improving hydrogen diffusion has been studied by ab initio molecular dynamics calculations and we obtain the diffusivity of hydrogen in liquid aluminum which is in agreement with the experimental data. It can be concluded that the diffusion of hydrogen in aluminum melts can be enhanced on the presence of chlorine.

Melting curves of Cu, Pt, Pd and Au under high pressures

2016 ◽  
Vol 30 (05) ◽  
pp. 1650013 ◽  
Author(s):  
Baoling Zhang ◽  
Baowen Wang ◽  
Qingxin Liu
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
High Pressures ◽  
Melting Curve ◽  
Interaction Forces ◽  
Metal Atoms ◽  
Melting Curves ◽  
Simulation Results ◽  
Dynamics Method ◽  
Good Agreement

Melting curves of Cu, Pt, Pd and Au were calculated via the molecular dynamics method in the temperature range of [Formula: see text]1000–5000 K. The simulation results were compared with the recent high pressure experimental data reported by Errandonea, and the obtained melting curves of Cu, Pt and Au were all in good agreement with his results. For Pd, there were some differences between the obtained melting curve and the experimental data and these differences increased with decreasing temperature to about 7 GPa at 2000 K. The effects of the interaction forces between metal atoms at high atomic densities on the pressure of the system were analyzed. It was found that the pressure in metals predominantly depends on the interaction forces between atoms at high atomic densities. In addition, expressions for melting pressure as a function of temperature have been obtained by fitting the simulation results.

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