scholarly journals Study of the Lamellar and Micellar Phases of Pluronic F127: A Molecular Dynamics Approach

Processes ◽  
2019 ◽  
Vol 7 (9) ◽  
pp. 606 ◽  
Author(s):  
Juan Albano ◽  
Damian Grillo ◽  
Julio Facelli ◽  
Marta Ferraro ◽  
Mónica Pickholz
Keyword(s):  
Molecular Dynamics ◽  
Amorphous Structure ◽  
Pluronic F127 ◽  
Coarse Grain ◽  
Lamellar Thickness ◽  
Initial Polymer ◽  
Lamellar Phases ◽  
New Information ◽  
Order Of Magnitude ◽  
Dynamics Simulations

In this work, we analyzed the behavior of Pluronic F127 through molecular dynamics simulations at the coarse-grain level, focusing on the micellar and lamellar phases. To this aim, two initial polymer conformations were considered, S-shape and U-shape, for both simulated phases. Through the simulations, we were able to examine the structural and mechanical properties that are difficult to access through experiments. Since no transition between S and U shapes was observed in our simulations, we inferred that all single co-polymers had memory of their initial configuration. Nevertheless, most copolymers had a more complex amorphous structure, where hydrophilic beads were part of the lamellar-like core. Finally, an overall comparison of the micellar a lamellar phases showed that the lamellar thickness was in the same order of magnitude as the micelle diameter (approx. 30 nm). Therefore, high micelle concentration could lead to lamellar formation. With this new information, we could understand lamellae as orderly packed micelles.

Oxygen Anion Diffusion in Doped Ceria MxCe1-xO2-0.5x (M=Gd, Sm and Pr): A Molecular Dynamics Simulation Study

MRS Advances ◽  
2019 ◽  
Vol 4 (13) ◽  
pp. 783-792 ◽  
Author(s):  
Neetu Kumari ◽  
Uzma Anjum ◽  
M. Ali Haider ◽  
Suddhastawa Basu
Keyword(s):  
Molecular Dynamics ◽  
Dopant Concentration ◽  
Optimum Concentration ◽  
Dynamics Simulation ◽  
Doped Ceria ◽  
Oxygen Anion ◽  
Anion Diffusion ◽  
Order Of Magnitude ◽  
Pure Ceria ◽  
Dynamics Simulations

ABSTRACTMolecular dynamics simulations were utilized to determine the oxygen anion diffusivity in pure ceria (CeO2) and doped ceria MxCe1-xO2-0.5x(M=Gd, Sm and Pr) with varying level of dopant concentration from 5-30% (x = 0.05-0.3). Doping with Gd showed an improvement in oxygen anion diffusivity value by two order of magnitude (D = 4.67x10-8cm2/s at 1173 K) as compared to the undoped ceria (D = 1.33x10-10cm2/s at 1173 K). 10% of doping level was estimated as the optimum concentration of all the dopants at which all of the doped ceria materials showed maximum diffusivity of oxygen anion. Among the three dopants studied, Pr was observed to show maximum diffusivity of oxygen anion in the temperature range of 773-1173 K of simulations.

Molecular Dynamics Simulation of Structural Changes of Ag965 Clusters during Freezing

2013 ◽  
Vol 683 ◽  
pp. 348-352
Author(s):  
J.H. Xia ◽  
Zheng Fu Cheng ◽  
Xu Yang Xiao
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Pair Correlation ◽  
Orientational Order ◽  
Amorphous Structure ◽  
Rapid Quenching ◽  
Dynamics Simulation ◽  
Angle Distribution ◽  
Quenching Condition ◽  
Dynamics Simulations

The structural transitions of Ag965clusters during two different quenching processes (Q1:1.0×1014K/s, Q2: 1.0×1012K/s) were studied using molecular dynamics simulations. This work gives the structure properties including the variations with temperature of pair-correlation function, bond-angle distribution function, bond pairs and bond orientational order parameters in both rapid quenching processes. Our results indicated that the liquid Ag965 was frozen into amorphous structure at 100 K under the quenching condition Q1. While the liquid Ag965transformed to hexagonal close-packed (hcp) phase at the temperature 100 K under the quenching condition Q2.These instructions give you basic guidelines for preparing papers for conference proceedings.

Mechanisms of Molecular Beam Epitaxial Growth on Reconstructed Si{100}: Thermal and Energized Beams

1988 ◽  
Vol 141 ◽  
Author(s):  
B. J. Garrison ◽  
M. T. Miller ◽  
D.W. Brenner
Keyword(s):  
Molecular Dynamics ◽  
Low Temperature ◽  
Epitaxial Growth ◽  
Gas Phase ◽  
Molecular Beam ◽  
Energy Deposition ◽  
Amorphous Structure ◽  
Molecular Beam Epitaxial ◽  
Dynamics Simulations ◽  
Molecular Beam Epitaxial Growth

Summary:Molecular dynamics simulations have been performed that examine the microscopic mechanisms of rearrangements of atoms on the Si{ 1001 surface due to deposition of gas phase atoms. For thermal energy deposition we find that the gas atoms initially attach to dangling bonds of the surface dimer atoms. The dimer ’unreconstruction’ is due to a diffusion event on the surface, thus is temperature activated. We also find that dimers may open in regions of the surface where there are several atoms not at lattice sites, thus a low temperature amorphous structure. For 5-10 eV deposition there are direct mechanisms of dimer opening that occur on the 50-100 fs timescale. For energies greater than 15-20 eV there is implantation of the silicon atoms which leads to subsurface damage.

Dissolution Dynamics of Sub-Critical Clusters in Liquid Silicon

1990 ◽  
Vol 205 ◽  
Author(s):  
Michael J. Uttormark ◽  
Stephen J. Cook ◽  
Michael O. Thompson ◽  
Paulette Clancy
Keyword(s):  
Molecular Dynamics ◽  
System Size ◽  
Atomic Processes ◽  
Spontaneous Nucleation ◽  
New Information ◽  
Different Temperatures ◽  
Transient Nucleation ◽  
Dynamics Simulations ◽  
Small Clusters ◽  
Kinetics Of

AbstractPrevious attempts to simulate by Molecular Dynamics the spontaneous nucleation and growth of a crystalline Stillinger-Weber ‘silicon’ from the liquid have been essentially impossible because of constraints on system size and time scales. We have overcome these limitations by studying the related problem of the disintegration of crystalline ‘embryos’ into the liquid phase at temperatures slightly above the melting point. Molecular Dynamics simulations using the Stillinger-Weber potential were performed by embedding crystallites of 400 atoms in a liquid consisting of approximately 3600 atoms. During each simulation, the time-evolution of the size and shape of the embryo was followed until it became indistinguishable from the liquid. These simulations provide intriguing new information on the atomic processes involved in dissolution and on the macroscopic kinetics of small clusters. Comparisons of results at different temperatures, system sizes and initial configurations are shown and the implications of these cluster dynamics for crystal growth in supercooled liquids, homogeneous nucleation, and transient nucleation are discussed.

scholarly journals Comment on ‘Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size’

2019 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L. de Groot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
Conformational Transitions ◽  
Human Hemoglobin ◽  
Order Of Magnitude ◽  
The Stability ◽  
Dynamics Simulations ◽  
T State

AbstractA recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed. Here, we express three main concerns about that study. In addition, we show that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

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

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L de Groot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Size Dependence ◽  
Conformational Transitions ◽  
Human Hemoglobin ◽  
Order Of Magnitude ◽  
The Stability ◽  
Dynamics Simulations ◽  
T State

A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

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