scholarly journals Determination of Reference Chemical Potential Using Molecular Dynamics Simulations

2010 ◽  
Vol 2010 ◽  
pp. 1-5 ◽  
Author(s):  
Krishnadeo Jatkar ◽  
Jae W. Lee ◽  
Sangyong Lee
Keyword(s):  
Molecular Dynamics ◽  
Gas Hydrates ◽  
Chemical Potential ◽  
Md Simulations ◽  
Water Molecules ◽  
Chemical Potential Difference ◽  
Guest Molecules ◽  
Experimental Values ◽  
Dynamics Simulations

A new method implementing molecular dynamics (MD) simulations for calculating the reference properties of simple gas hydrates has been proposed. The guest molecules affect interaction between adjacent water molecules distorting the hydrate lattice, which requires diverse values of reference properties for different gas hydrates. We performed simulations to validate the experimental data for determining , the chemical potential difference between water and theoretical empty cavity at the reference state, for structure II type gas hydrates. Simulations have also been used to observe the variation of the hydrate unit cell volume with temperature. All simulations were performed using TIP4P water molecules at the reference temperature and pressure conditions. The values were close to the experimental values obtained by the Lee-Holder model, considering lattice distortion.

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.

scholarly journals HP-induced supra-molecular organization of guest molecules in FER-type zeolites

2014 ◽  
Vol 70 (a1) ◽  
pp. C1469-C1469
Author(s):  
Rossella Arletti ◽  
Simona Quartieri ◽  
Giovanna Vezzalini ◽  
Ettore Fois ◽  
Gloria Tabacchi
Keyword(s):  
Silicone Oil ◽  
Md Simulations ◽  
Membered Ring ◽  
Molecular Organization ◽  
Water Molecules ◽  
Structural Refinement ◽  
Guest Molecules ◽  
Guest Species ◽  
Dynamics Simulations ◽  
Stiffening Effect

The response to pressure of a synthetic all-silica ferrierite (Si-FER) and of a natural ferrierite from Monastir (Sardinia, Italy) (Mon-FER, Na0.56 K1.19 Mg2.02 Ca0.52 Sr0.14)(Al6.89Si29.04)O72 ·17.86 H2O) is here investigated combining HP synchrotron XRPD experiments and molecular dynamics simulations. The experiments were carried out by using penetrating (methanol:ethanol:water 16:3:1, m.e.w.; ethanol:water 1:3, e.w.) and non-penetrating (silicone oil, s.o.) pressure transmitting media (PTM). In Si-FER compressed in e.w., both water (w.) and ethanol molecules (e.) enter the pore system even at 0.2 GPa. The structural refinement of the data collected at 0.8 GPa reveals 8 w. and 4 e. molecules in the 10- and 6-membered ring channels, in tight agreement with the results of MD simulations. In Si-FER compressed at 0.2 GPa in m.e.w., only water molecules penetrate the 10-membered ring channels (15 per u.c.), organized in chains running along the channel axis. The interactions among the guest species and the framework oxygen atoms are very weak, due to the hydrophobicity of the framework. Upon decompression, the intruded extra-molecules are not completely released, so giving rise to new materials with different extra-framework contents. The results obtained for Si-FER compressed in m.e.w. and s.o. were compared to those obtained for Mon-FER, demonstrating that the zeolite composition and the PTM strongly influence the overall elastic parameters of the investigated samples. Specifically, Mon-FER shows a much higher rigidy than Si-FER in both media, due to the stiffening effect of the numerous extraframework species present in the natural sample. The higher rigidity of Si-FER in m.e.w. with respect to s.o. can be explained by the penetration, in the former case, of the PTM molecules, which contribute to stiffen the framework.

scholarly journals Molecular dynamics simulations of potassium channels

2007 ◽  
Vol 5 (3) ◽  
pp. 635-671 ◽  
Author(s):  
Carmen Domene
Keyword(s):  
Molecular Dynamics ◽  
Potassium Channels ◽  
Molecular Dynamics Simulations ◽  
Experimental Work ◽  
Three Dimensional ◽  
Md Simulations ◽  
Structure And Dynamics ◽  
Dynamics Simulations ◽  
New Algorithms

AbstractDespite the complexity of ion-channels, MD simulations based on realistic all-atom models have become a powerful technique for providing accurate descriptions of the structure and dynamics of these systems, complementing and reinforcing experimental work. Successful multidisciplinary collaborations, progress in the experimental determination of three-dimensional structures of membrane proteins together with new algorithms for molecular simulations and the increasing speed and availability of supercomputers, have made possible a considerable progress in this area of biophysics. This review aims at highlighting some of the work in the area of potassium channels and molecular dynamics simulations where numerous fundamental questions about the structure, function, folding and dynamics of these systems remain as yet unresolved challenges.

Molecular dynamics simulations of some amorphous and crystalline photonic materials

1990 ◽  
Vol 5 (5) ◽  
pp. 1104-1109 ◽  
Author(s):  
Pradeep P. Phule ◽  
Pierre A. Deymier ◽  
Subhash H. Risbud
Keyword(s):  
Molecular Dynamics ◽  
Optical Switching ◽  
Bond Distance ◽  
Md Simulations ◽  
Dielectric Constants ◽  
Nonlinear Susceptibility ◽  
Naci Crystal ◽  
Doped Glasses ◽  
Experimental Values ◽  
Dynamics Simulations

Constant pressure molecular dynamics (MD) simulations have been used to simulate amorphous and crystalline forms of BaTiO3 and TiO2. Simulation results for pure RaTiO3 and TiO2 glasses show fourfold titanium coordination with a Ti–O bond distance of 1.8 Å, consistent with experimental evidence for the structure of titania doped glasses for all optical switching and ultra low expansivity (ULE) TiO2–SiO2 glasses. Radial distribution function data for crystalline, liquid, and amorphous forms of BaTiO3 were also obtained. The displacement polarization and its contribution to susceptibilities have been calculated by application of an electric field to the simulation cell. The calculated ionic dielectric constants (Ki) for simulated NaCI (crystal), TiO2 glass, and TiO2 (crystal) were 3.34, 5.96, and 19.4 as compared to the experimental values of ≍3.34, 3–10, and 78, respectively. The calculated cubic nonlinear susceptibility (ξ3) values for NaCI (crystal), TiO2 (glass), and TiO2 (crystal) were, respectively, 0.194, 2.175, and 4.68 (x 10−18m2V−2). The increase in ξ3 values is consistent with experimentally observed trends of the linear refractive indices. Improved agreement between experimental and calculated values of susceptibilities and dielectric constant was obtained for materials with higher ionicity.

Excess Properties of Water-Methanol Mixtures as Studied by MD Simulations

1991 ◽  
Vol 46 (1-2) ◽  
pp. 95-99 ◽  
Author(s):  
G. Pálinkás ◽  
I. Bakó
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Mole Fraction ◽  
Extreme Values ◽  
Md Simulations ◽  
Excess Properties ◽  
Water Molecules ◽  
Methanol Mixture ◽  
Dynamics Simulations ◽  
Pair Interactions

AbstractMolecular dynamics simulations with pair interactions reproduce experimental excess properties of methanol-water mixtures. Water molecules lose, and methanol molecules gain neighbours in the mixtures as compared to the solvents. The water-methanol mixture with 0.25 mole fraction of methanol, resulting in extreme values for different excess properties, is characterized by the highest number of molecules with maximal number of H-bonded neighbours.

scholarly journals Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Krystel El Hage ◽  
Florent Hédin ◽  
Prashant K Gupta ◽  
Markus Meuwly ◽  
Martin Karplus
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Effect ◽  
Md Simulations ◽  
Water Molecules ◽  
Human Hemoglobin ◽  
Standard Size ◽  
Wide Range ◽  
Dynamics Simulations

Recent molecular dynamics (MD) simulations of human hemoglobin (Hb) give results in disagreement with experiment. Although it is known that the unliganded (T0) and liganded (R4) tetramers are stable in solution, the published MD simulations of T0 undergo a rapid quaternary transition to an R-like structure. We show that T0 is stable only when the periodic solvent box contains ten times more water molecules than the standard size for such simulations. The results suggest that such a large box is required for the hydrophobic effect, which stabilizes the T0 tetramer, to be manifested. Even in the largest box, T0 is not stable unless His146 is protonated, providing an atomistic validation of the Perutz model. The possibility that extra large boxes are required to obtain meaningful results will have to be considered in evaluating existing and future simulations of a wide range of systems.

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