Molecular Dynamics Simulation of Quasi-Two-Dimensional Water Network on Ice Nucleation Protein

2011 ◽  
Author(s):  
Daisuke Murakami ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Water Clusters ◽  
Ice Nucleation ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Two Dimensional ◽  
Threshold Density ◽  
Ice Nucleation Protein ◽  
Network Of Hydrogen Bonds ◽  
Dynamics Simulations

An ice nucleation protein induces a phase transition from liquid water to ice in air. A specific hydrophilic surface of the protein may have an influence on the network of hydrogen bonds touching on the protein. However, microscopic characteristics of the ice nucleation protein and behavior of water molecules on it have not been clarified. So we carried out molecular dynamics simulations in various quasi-two-dimensional densities of water molecules on the ice nucleation protein. The percolation threshold of water clusters was confirmed. Comparing another hydrophilic protein, the threshold density in both cases had nearly the same value. But percolation probabilities and mean cluster sizes near the threshold were different between both cases. Those results implied that the threshold density was consistent with the conventional theory, but the forming of water clusters near the threshold was influenced by the hydrophilicity on the ice nucleation protein.

scholarly journals Icephobicity of Functionalized Graphene Surfaces

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Xiang-Xiong Zhang ◽  
Min Chen
Keyword(s):  
Molecular Dynamics ◽  
Freezing Temperature ◽  
Ice Nucleation ◽  
Chloride Ions ◽  
Water Molecules ◽  
Sodium Ions ◽  
Functionalized Graphene ◽  
Functionalized Surfaces ◽  
The Difference ◽  
Dynamics Simulations

Manipulating the ice nucleation ability of liquid water by solid surface is of fundamental importance, especially in the design of icephobic surfaces. In this paper, the icephobicity of graphene surfaces functionalized by sodium ions, chloride ions, or methane molecules is investigated using molecular dynamics simulations. The icephobicity of the surface is evaluated by the freezing temperature. The freezing temperature on surface functionalized by methane molecules decreases at first and then increases as a function of the number groups, while the freezing temperature increases monotonically as a function of the number groups upon surfaces functionalized by sodium ions or chloride ions. The difference can be partially explained by the potential morphologies near the surfaces. Additionally, the validity of indicating the ice nucleation ability of water molecules using the number of six rings in the system is examined. Current study shows that the ice nucleation upon functionalized surfaces is inhibited when compared with smooth graphene substrate, which proves the feasibility of changing the icephobicity of the surfaces by functionalizing with certain ions or molecules.

Molecular Dynamics Simulation of Water-Based Nano-Lubrication

2013 ◽  
Vol 773 ◽  
pp. 585-588
Author(s):  
Su Mei Zhang ◽  
Pei Hong Guo ◽  
Jia Nan Zhu ◽  
Xiao Ping Wen
Keyword(s):  
Molecular Dynamics ◽  
Reduction Rate ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Stabilization Time ◽  
Shear Rates ◽  
Water Based ◽  
Dynamics Simulations ◽  
Metal Wall ◽  
Number Of Particles

Molecular dynamics simulations of water-based nanolubrication in Couette flow are carried out. The water molecules are simulated by the TIP3P model. Three different shear rates are 20 m/s and 40 m/s and 60 m/s, and the vertical pressure acted on the metal wall are 10GPa, 20 GPa, 30 GPa and 40 GPa respectively. The simulated results show that the greater pressure, the smaller the stable value of friction spacing, while the reduction rate of the stable value becomes small. Meanwhile, as pressure increases, the stabilization time is longer. However, under the same pressure, shear rate of influence on the friction spacing is not obvious. The friction spacing increases with the number of particles, showing that the presence of nanoparticles can enhance the bearing capacity.

Water Structure on Mica Surfaces: Investigating the Effect of Cations

2019 ◽  
Author(s):  
Jiarun Zhou ◽  
Nurun Nahar Lata ◽  
Sapna Sarupria ◽  
will cantrell
Keyword(s):  
Divalent Cations ◽  
Water Structure ◽  
Ice Nucleation ◽  
Water Molecules ◽  
Interfacial Water ◽  
Ice Nucleation Protein ◽  
Naturally Occurring ◽  
Air Interface ◽  
Bulk Structure ◽  
Dynamics Simulations

We studied thin films of water at the mica-air interface using infrared spectroscopy and molecular dynamics simulations. We investigate the influence of ions on interfacial water by exchanging the naturally occurring K<sup>+</sup> ion with H<sup>+</sup>/Na<sup>+</sup>, Ca<sup>2+</sup>, and Mg<sup>2+</sup>. The experiments do not show a difference in the bulk structure (<i>i. e.</i> in the infrared spectra), but indicate that water is more strongly attracted to the Mg<sup>2+</sup> mica. The simulations reveal that the cation-water interactions significantly influence the microscopic arrangement of water on mica. Our results indicate that the divalent cations result in strong water-mica interactions, which leads to longer hydrogen bond lifetimes and larger hydrogen bonded clusters of interfacial water molecules. These results have implications for surface-mediated processes such as heterogeneous ice nucleation, protein assembly and catalysis.

Molecular Dynamics Simulation of the Thermal Conductivity of Silicon-Germanene Nanoribbon (SiGeNR): A Comparison with Silicene Nanoribbon (SiNR) and Germanene Nanoribbon (GeNR)

2015 ◽  
Vol 1105 ◽  
pp. 285-289 ◽  
Author(s):  
Jessa Mae P. Tagalog ◽  
Cachey Girly Alipala ◽  
Giovanni J. Paylaga ◽  
Naomi T. Paylaga ◽  
Rolando V. Bantaculo
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Silicon Germanium ◽  
Large Scale ◽  
Room Temperature ◽  
Single Layer ◽  
Dynamics Simulation ◽  
Two Dimensional ◽  
Silicon And Germanium ◽  
Dynamics Simulations

This study examines the nature of thermal transport properties of single layer two-dimensional honeycomb structures of silicon-germanene nanoribbon (SiGeNR), silicene nanoribbon (SiNR) and germanene nanoribbon (GeNR) which have not yet been characterized experimentally. SiGeNR, SiNR and GeNR are the allotropes of silicon-germanium, silicon and germanium, respectively, withsp2hybridization. The thermal conductivity of the materials has been investigated using Tersoff potential through LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) by performing the molecular-dynamics simulations. The temperature is varied (50 K, 77 K, 150 K, 300 K, 500 K, 700 K, 1000 K, and 1200 K) with fixed nanoribbon dimension of 50 nm × 10 nm. The length is also varied (10 nm, 20 nm, 30 nm, 40 nm, and 50 nm) while the temperature is fixed at room temperature and the width is also fixed at 10 nm. The obtained results showed that the thermal conductivity of SiGeNR at room temperature is approximately 10 times higher than GeNR and approximately 6 times higher compared to SiNR. The thermal conductivity increases as the temperature is increased from 50 K – 300 K, and as the temperature is further increased, the thermal conductivity decreases with temperature. Moreover, the thermal conductivity in SiGeNR, SiNR, and GeNR increases as the length is being increased. Predicting new features of SiGeNR, SiNR and GeNR open new possibilities for nanoelectronic device applications of group IV two-dimensional materials.

Acceleration of molecular dynamics simulation of multiphase systems on GPU

2012 ◽  
Vol 9 (2) ◽  
pp. 76-79
Author(s):  
D.F. Marin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Intermolecular Interaction ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Lennard Jones ◽  
Multiphase Systems ◽  
And Performance ◽  
Dynamics Simulations

The paper presents results on acceleration of molecular dynamics simulations with the usage of GPUs. A system of water molecules is considered as an example of polar liquid. The intermolecular interaction is modeled with the usage of Coulomb and truncated Lennard-Jones potentials. Results of computational experiments on acceleration and performance of the developed code are presented.

scholarly journals Effects of Hydration and Temperature on the Microstructure and Transport Properties of Nafion Polyelectrolyte Membrane: A Molecular Dynamics Simulation

Membranes ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 695
Author(s):  
Guoling Zhang ◽  
Guogang Yang ◽  
Shian Li ◽  
Qiuwan Shen ◽  
Hao Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Water Content ◽  
Water Clusters ◽  
Polymer Electrolyte Membrane ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydration Level ◽  
Hydronium Ions

To investigate the effects of temperature and hydration on the microstructure of polymer electrolyte membrane and the transport of water molecules and hydronium ions, molecular dynamics simulations are performed on Nafion 117 for a series of water contents at different temperatures. The interactions among the sulfonate groups, hydronium ions, and water molecules are studied according to the analysis of radial distribution functions and coordination numbers. The sizes and connectivity of water clusters are also discussed, and it is found that the hydration level plays a key role in the phase separation of the membrane. However, the effect of the temperature is slight. When the water content increases from 3.5 to 16, the size of water clusters in the membrane increases, and the clusters connect to each other to form continuous channels for diffusion of water molecules and hydronium ions. The diffusion coefficients are estimated by studying the mean square displacements. The results show that the diffusion of water molecules and hydronium ions are both enhanced by the increase of the temperature and hydration level. Furthermore, the diffusion coefficient of water molecules is always much larger than that of hydronium ions. However, the ratio of the diffusion coefficient of water molecules to that of hydronium ions decreases with the increase of water content.

scholarly journals Transport mechanisms of water molecules and ions in sub-nano channels of nanostructured water treatment liquid-crystalline membranes: a molecular dynamics simulation study

2020 ◽  
Vol 6 (3) ◽  
pp. 604-611 ◽  
Author(s):  
Hiroki Nada ◽  
Takeshi Sakamoto ◽  
Masahiro Henmi ◽  
Takafumi Ogawa ◽  
Masahiro Kimura ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water Treatment ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Liquid Crystalline ◽  
Dynamics Simulation ◽  
Self Organization ◽  
Water Molecules ◽  
Transport Mechanisms ◽  
Dynamics Simulations

Transport mechanisms of water molecules and ions in the liquid crystalline (LC) membranes with sub-nano channels formed by self-organization of thermotropic ionic LC compounds were elucidated by molecular dynamics simulations.

scholarly journals A method for detection of permeation events in Molecular Dynamics simulations of lipid bilayers

2021 ◽  
Author(s):  
Carlos R. S. Camilo ◽  
J. Roberto Ruggiero ◽  
Alexandre S. de Araujo
Keyword(s):  
Molecular Dynamics ◽  
Cell Membrane ◽  
Lipid Bilayers ◽  
Complex Structure ◽  
Phospholipid Bilayer ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Human Knowledge ◽  
Crossing Time ◽  
Dynamics Simulations

The cell membrane is one of the most important structures of life. Understanding its functioning is essential for several human knowledge areas, mainly how it controls the efflux of substances between the cytoplasm and the environment. Being a complex structure, composed of several classes of compounds such as lipids, proteins, sugars, etc., a convenient way to mimic it is through a phospholipid bilayer. The Molecular Dynamics simulation of lipid bilayers in solution is the main computational approach to model the cell membrane. In this work, we present a method to detect permeation events of molecules through the lipid bilayer, characterizing its crossing time and trajectory. By splitting the simulation box into well-defined regions, the method distinguishes the passage of molecules through the bilayer from artifacts produced by crossing molecules through the simulation box edges when using periodic boundary conditions. We apply the method to study the spontaneous permeation of water molecules through bilayers with different lipid compositions and modeled with different force fields. Our method successfully characterizes the permeation events, and the results obtained show that the frequency and time of permeation are independent of the force field used to model the phospholipids. Besides, it is observed that the increase in the concentration of cholesterol molecules in lipid bilayers induces the reduction of permeation events due to its compacting action on the bilayer, making it denser and, therefore, hindering the diffusion of water molecules inside it. The computational tool to perform the method discussed here is available on https://github.com/crobertocamilo/MD-permeation.

Water Structure on Mica Surfaces: Investigating the Effect of Cations

2019 ◽  
Author(s):  
Jiarun Zhou ◽  
Nurun Nahar Lata ◽  
Sapna Sarupria ◽  
will cantrell
Keyword(s):  
Divalent Cations ◽  
Water Structure ◽  
Ice Nucleation ◽  
Water Molecules ◽  
Interfacial Water ◽  
Ice Nucleation Protein ◽  
Naturally Occurring ◽  
Air Interface ◽  
Bulk Structure ◽  
Dynamics Simulations

We studied thin films of water at the mica-air interface using infrared spectroscopy and molecular dynamics simulations. We investigate the influence of ions on interfacial water by exchanging the naturally occurring K<sup>+</sup> ion with H<sup>+</sup>/Na<sup>+</sup>, Ca<sup>2+</sup>, and Mg<sup>2+</sup>. The experiments do not show a difference in the bulk structure (<i>i. e.</i> in the infrared spectra), but indicate that water is more strongly attracted to the Mg<sup>2+</sup> mica. The simulations reveal that the cation-water interactions significantly influence the microscopic arrangement of water on mica. Our results indicate that the divalent cations result in strong water-mica interactions, which leads to longer hydrogen bond lifetimes and larger hydrogen bonded clusters of interfacial water molecules. These results have implications for surface-mediated processes such as heterogeneous ice nucleation, protein assembly and catalysis.

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