MOLECULAR DYNAMICS SIMULATIONS OF DMPC/DPPC MIXED BILAYERS

2007 ◽  
Vol 18 (01) ◽  
pp. 73-89 ◽  
Author(s):  
ARMEN H. POGHOSYAN ◽  
HRANT H. GHARABEKYAN ◽  
ARAM A. SHAHINYAN
Keyword(s):  
Md Simulation ◽  
Orientational Order ◽  
Hydrocarbon Chain ◽  
Water Molecules ◽  
Hydrocarbon Chains ◽  
Racemic Mixtures ◽  
Area Per Lipid ◽  
Dynamics Simulations ◽  
Experimental Findings ◽  
Good Agreement

We have performed the atomistic MD simulation of dimyristoylphosphatidylcholine(DMPC)/dipalmitoylphosphatidylcholine(DPPC) mixed bilayers, consisting of various fraction of lipids, i.e., with fraction 0.25, 0.5 and 0.75 and hydration level 33 water molecules per lipid. The simulations were performed using NAMD code.The area per lipid, densities, orientational order parameters and tilt angle of hydrocarbon chain and also the interdigitation of chains were calculated. It has been established that the interdigitation degree of hydrocarbon chains is increased as the DPPC fraction is decreased. It has been also stated that the area per lipid value in case of racemic mixtures is about 0.72 nm2, which is in good agreement with experimental estimations. The hydrocarbon thickness is increased as the DPPC fraction increased. The DMPC/DPPC mixtures behave as almost ideally mixtures.The diffusion coefficients were also calculated and the results are in agreement with experimental findings.All the calculated parameters were compared with values obtained either from experimental data of DPPC or DMPC depending on the fraction of compound. The reason is that there are no experimental findings on DMPC/DPPC mixtures.

scholarly journals Entropy Rules: Molecular Dynamics Simulations of Model Oligomers for Thermoresponsive Polymers

Entropy ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. 1187
Author(s):  
Alexander Kantardjiev ◽  
Petko M. Ivanov
Keyword(s):  
Entropy Change ◽  
Atomic Scale ◽  
Solution Temperature ◽  
Water Molecules ◽  
Thermoresponsive Polymers ◽  
Simulation Data ◽  
Critical Solution Temperature ◽  
Extended Conformation ◽  
Dynamics Simulations ◽  
Experimental Findings

We attempted to attain atomic-scale insights into the mechanism of the heat-induced phase transition of two thermoresponsive polymers containing amide groups, poly(N-isopropylacrylamide) (PNIPAM) and poly(2-isopropyl-2-oxazoline) (PIPOZ), and we succeeded in reproducing the existence of lower critical solution temperature (LCST). The simulation data are in accord with experimental findings. We found out that the entropy has an important contribution to the thermodynamics of the phase separation transition. Moreover, after decomposing further the entropy change to contributions from the solutes and from the solvent, it appeared out that the entropy of the solvent has the decisive share for the lowering of the free energy of the system when increasing the temperature above the LCST. Our conclusion is that the thermoresponsive behavior is driven by the entropy of the solvent. The water molecules structured around the functional groups of the polymer that are exposed to contact with the solvent in the extended conformation lower the enthalpy of the system, but at certain temperature the extended conformation of the polymer collapses as a result of dominating entropy gain from “released” water molecules. We stress also on the importance of using more than one reference molecule in the simulation box at the setup of the simulation.

Structural and Dynamical Properties of an LiCl · 3H2O Solution

1988 ◽  
Vol 43 (12) ◽  
pp. 1103-1110 ◽  
Author(s):  
Y. Tamura ◽  
K. Tanaka ◽  
E. Spohr ◽  
K. Heinzinger
Keyword(s):  
Md Simulation ◽  
Distribution Functions ◽  
Water Molecules ◽  
Self Diffusion ◽  
Lennard Jones ◽  
Pair Potentials ◽  
Velocity Autocorrelation ◽  
Ion Interactions ◽  
Order Of Magnitude ◽  
Good Agreement

An MD simulation of an 18.5 molal LiCl aqueous solution was performed with the flexible Bopp-Jancso-Heinzinger model for water, ion-water pair potentials derived from ab initio calcula­tions and the ion-ion interactions described by a potential of Born-Mayer-Huggins (BMH) type. The comparison with a simulation of the same system, where the ion-ion interactions were described by a (12-6) Lennard-Jones + Coulomb potential, demonstrates that such a change affects not only the ion-ion but also the ion-water radial distribution functions significantly, and that the results with the BMH potential conform better to X-ray results. The self-diffusion coefficients for water and the ions are found to be lower by almost one order of magnitude compared with dilute solutions, in good agreement with experimental results. The spectral densities of the hindered translational motions as well as those of the librations and the internal vibrations of the water molecules have been calculated from the simulations through the corresponding velocity autocorrelation functions.

scholarly journals Water Infiltration in ZSM-5 Zeolites: Effect of Pore Volume and Water Structure

2012 ◽  
Author(s):  
Shalabh C. Maroo ◽  
Tom Humplik ◽  
Tahar Laoui ◽  
Evelyn N. Wang
Keyword(s):  
Water Structure ◽  
Water Desalination ◽  
Water Infiltration ◽  
Water Molecules ◽  
Geometric Approximation ◽  
Dynamics Simulations ◽  
Experimental Findings ◽  
Nano Crystal ◽  
Infiltration Behavior ◽  
Zeolite Crystals

This study investigates the infiltration of water in ZSM-5 zeolite crystals via molecular dynamics simulations and experiments. A zeolite nano-crystal is constructed in the simulations and is surrounded by water molecules which enter and saturate the pores. The average number of water molecules per unit cell of the zeolite is determined along with the radial distribution function of water inside the zeolites. A geometric approximation of the zeolite pores and intersections is proposed and verified. Partial charge on the zeolite atoms is found to be a crucial parameter which governs the water infiltration behavior. ZSM-5 zeolite crystals were also synthesized and water infiltration experiments were conducted using an Instron. The simulation and experimental findings are compared and discussed. The understanding gained from these studies will be important for the development of zeolite based reverse osmosis membranes for water desalination.

Some Properties of Molten KCl at High Density Studied by MD Simulation

1981 ◽  
Vol 36 (10) ◽  
pp. 1106-1111 ◽  
Author(s):  
Ryuzo Takagi ◽  
Isao Okada ◽  
Kazutaka Kawamura
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Thermodynamic Properties ◽  
Diffusion Coefficients ◽  
Md Simulation ◽  
Ambient Pressure ◽  
The Self ◽  
Self Diffusion ◽  
Dynamics Simulations ◽  
Good Agreement

Molecular dynamics simulations of molten KCl have been performed at 1173 K with the molar volumes of 52.0 (the value under ambient pressure), 50.0, 48.0 and 45.0 cm3 mol-1 . Some thermodynamic properties at higher densities have been evaluated, which are generally in good agreement with the experimentally obtained ones and Monte Carlo results. Both at normal and higher densities, the self-exchange velocities of neighbouring unlike ions (SEV) are found to be proportional to the internal mobilities with nearly the same constant as derived previously for molten LiCl, RbCl and their 1 : 1 mixture. Calculated transport properties such as the SEV and the self-diffusion coefficients considerably decrease with increasing density, while the configuration does not change much.

HOMOLOGY MODELING AND SUBSTRATE BINDING STUDY OF HUMAN KYNURENINE AMINOTRANSFERASE III

2012 ◽  
Vol 11 (04) ◽  
pp. 855-870 ◽  
Author(s):  
YU XU ◽  
QING-CHUAN ZHENG ◽  
HONG-XING ZHANG ◽  
CHIA-CHUNG SUN
Keyword(s):  
Homology Modeling ◽  
Active Sites ◽  
Md Simulation ◽  
3D Structure ◽  
Strong Interactions ◽  
Binding Modes ◽  
Kynurenine Aminotransferase ◽  
Dynamics Simulations ◽  
Key Residues ◽  
Good Agreement

Kynurenine aminotransferase III (KAT III) is a novel member of the kynurenine aminotransferase enzyme family. Its active site topology and structure characteristics have not been established. In this study, with extensive computational simulations, including homology modeling and molecular dynamics simulations, a 3D structure model of human KAT III dimer was created and refined. Furthermore, CDOCKER approach was employed to dock two ligands (L-methionine and L-tryptophan) into the active sites of human KAT III dimer and uncover the ligand-binding modes. The complexes were subjected to 5 ns MD simulation, and the results indicate that TYR119 and TRP13 might be the key residues as they have the large contributions to the binding affinity, which is in good agreement with the experimental results. Moreover, another two residues (ASP120 and TYR57) are also found that their strong interactions stabilize the whole system. The structural and biochemical insights obtained from the present study will be helpful for designing the specific inhibitors of human KAT III.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Numerical Study and Experimental Validation of Deformation of FCC CuAl Single Crystal Obtained by Additive Manufacturing

Metals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 582
Author(s):  
Anton Y. Nikonov ◽  
Andrey I. Dmitriev ◽  
Dmitry V. Lychagin ◽  
Lilia L. Lychagina ◽  
Artem A. Bibko ◽  
...  
Keyword(s):  
Single Crystal ◽  
Numerical Study ◽  
Strain Curve ◽  
Aluminum Bronze ◽  
Partial Dislocations ◽  
Slip Planes ◽  
Loaded Material ◽  
Dislocation Movement ◽  
Dynamics Simulations ◽  
Experimental Findings

The importance of taking into account directional solidification of grains formed during 3D printing is determined by a substantial influence of their crystallographic orientation on the mechanical properties of a loaded material. This issue is studied in the present study using molecular dynamics simulations. The compression of an FCC single crystal of aluminum bronze was performed along the <111> axis. A Ni single crystal, which is characterized by higher stacking fault energy (SFE) than aluminum bronze, was also considered. It was found that the first dislocations started to move earlier in the material with lower SFE, in which the slip of two Shockley partials was observed. In the case of the material with higher SFE, the slip of a full dislocation occurred via successive splitting of its segments into partial dislocations. Regardless of the SFE value, the deformation was primarily occurred by means of the formation of dislocation complexes involved stair-rod dislocations and partial dislocations on adjacent slip planes. Hardening and softening segments of the calculated stress–strain curve were shown to correspond to the periods of hindering of dislocations at dislocation pileups and dislocation movement between them. The simulation results well agree with the experimental findings.

scholarly journals Electrical Breakdown Mechanism of Transformer Oil with Water Impurity: Molecular Dynamics Simulations and First-Principles Calculations

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 123
Author(s):  
Bin Cao ◽  
Ji-Wei Dong ◽  
Ming-He Chi
Keyword(s):  
Molecular Dynamics ◽  
Thermal Diffusion ◽  
First Principles ◽  
Electrical Breakdown ◽  
Transformer Oil ◽  
Water Molecules ◽  
Conducting Channel ◽  
Breakdown Mechanism ◽  
Water Impurity ◽  
Dynamics Simulations

Water impurity is the essential factor of reducing the insulation performance of transformer oil, which directly determines the operating safety and life of a transformer. Molecular dynamics simulations and first-principles electronic-structure calculations are employed to study the diffusion behavior of water molecules and the electrical breakdown mechanism of transformer oil containing water impurities. The molecular dynamics of an oil-water micro-system model demonstrates that the increase of aging acid concentration will exponentially expedite thermal diffusion of water molecules. Density of states (DOS) for a local region model of transformer oil containing water molecules indicates that water molecules can introduce unoccupied localized electron-states with energy levels close to the conduction band minimum of transformer oil, which makes water molecules capable of capturing electrons and transforming them into water ions during thermal diffusion. Subsequently, under a high electric field, water ions collide and impact on oil molecules to break the molecular chain of transformer oil, engendering carbonized components that introduce a conduction electronic-band in the band-gap of oil molecules as a manifestation of forming a conductive region in transformer oil. The conduction channel composed of carbonized components will be eventually formed, connecting two electrodes, with the carbonized components developing rapidly under the impact of water ions, based on which a large number of electron carriers will be produced similar to “avalanche” discharge, leading to an electrical breakdown of transformer oil insulation. The water impurity in oil, as the key factor for forming the carbonized conducting channel, initiates the electric breakdown process of transformer oil, which is dominated by thermal diffusion of water molecules. The increase of aging acid concentration will significantly promote the thermal diffusion of water impurities and the formation of an initial conducting channel, accounting for the degradation in dielectric strength of insulating oil containing water impurities after long-term operation of the transformer.

scholarly journals Structure and Interdigitation of Chain-Asymmetric Phosphatidylcholines and Milk Sphingomyelin in the Fluid Phase

Symmetry ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1441
Author(s):  
Moritz P. K. Frewein ◽  
Milka Doktorova ◽  
Frederick A. Heberle ◽  
Haden L. Scott ◽  
Enrico F. Semeraro ◽  
...  
Keyword(s):  
Chain Length ◽  
Hydration Shell ◽  
Fluid Phase ◽  
Hydrocarbon Chain ◽  
Specific Model ◽  
Glycerol Backbone ◽  
Membrane Composition ◽  
Membrane Structures ◽  
Hydrocarbon Chain Length ◽  
Dynamics Simulations

We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center, we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, previously reported for gel phase structures, also extend to the more relevant physiological fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementarily performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. The extent of this back-bending was similar to that in chain symmetric bilayers. For both cases of adaptation to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.

scholarly journals Origin and control of ionic hydration patterns in nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Water Molecules ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

Sign in / Sign up

Export Citation Format

Share Document