Molecular Dynamics Simulation of the Glass Transition of Ortho-Terphenyl in Bulk and Thin Films

2006 ◽  
Vol 924 ◽  
Author(s):  
Jayeeta Ghosh ◽  
Roland Faller
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
A Priori ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Technological Advancement ◽  
Atomistic Model ◽  
Reorientation Dynamics ◽  
Bulk Model ◽  
Dynamics Simulations

ABSTRACTThe glass transition temperature in thin film depends strongly on film thickness and interaction with the substrate and it is normally a priori not clear which way it deviates from the bulk value. This causes new challenge in the technological advancement of smaller and smaller electronic devices. In this study molecular dynamics simulations of a low-molecular weight organic glass former, ortho-terphenyl, are carried out in bulk and freestanding films. The main motivation is to provide insight into the confinement effect without interface interactions. Based on earlier models of ortho-terphenyl we developed an atomistic model for bulk simulations. The model reproduces the literature data from simulations as well as experiments. After characterizing the bulk model we form a freestanding film. This film gives us the opportunity to study the dynamical heterogeneity near the glass transition by in-plane mobility and reorientation dynamics. We also develop a structurally coarse-grained model for this glass former based on our atomistic model to study bigger system for a longer period of time.

A COARSE-GRAINED MODEL OF MONOOLEIN: COMPARISON WITH THE ATOMISTIC MODEL

2009 ◽  
Vol 08 (01n02) ◽  
pp. 169-173
Author(s):  
J. H. KIM ◽  
S. H. CHOI ◽  
D. H. JUNG ◽  
C. S. CHO ◽  
Y. J. CHOI
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayer ◽  
Dissipative Particle Dynamics ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Atomistic Model ◽  
Coarse Grained Model ◽  
Cosmetic Industry ◽  
Dynamics Simulations ◽  
Potential Parameters

Monoolein (2,3-dihydroxypropyl (Z)-octadec-9-enoate) is one of the monoacylglycerol and has been studied for various applications in food, pharmaceutical, and cosmetic industry. Those applications make use of the phase behavior of monoolein. In order to understand the lipid bilayer phase of monoolein in mesoscale, a coarse-grained model has been built and tested in this work. The monoolein molecule was represented by two hydrophilic heads and six hydrophobic tails. The three water molecules were also represented as one bead. For comparison, the atomistic model has also been used for molecular dynamics simulation on the lipid bilayer phase in isothermal-isobaric (NPT) ensemble. The interaction and bond bending potential parameters for dissipative particle dynamics (DPD) were obtained with molecular dynamics simulations on lipid bilayer in water. And we also obtained the interaction parameters of the coarse-grained model, which agree well with the atomistic model. We compared the simulated phases using the coarse-grained model with using the atomistic model. With these parameters, we successfully reproduced the lamella phase of monoolein in DPD simulations.

scholarly journals Formation mechanism of bound rubber in elastomer nanocomposites: a molecular dynamics simulation study

RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Bound Rubber ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

The formation mechanism of the bound rubber in elastomer nanocomposites using the coarse-grained molecular-dynamics simulations.

scholarly journals Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

2017 ◽  
Author(s):  
Ronald D Hills, Jr
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Interfacial Behavior ◽  
Potentials Of Mean Force ◽  
Arginine Residues ◽  
Dynamics Simulations

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.

scholarly journals Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins

2016 ◽  
Author(s):  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
A Priori ◽  
Model Systems ◽  
Dynamics Simulation ◽  
High Mass ◽  
Mean Square ◽  
Dynamics Simulations

ABSTRACTPredicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2–9 ± 1 Å2for Cα and 7.3 ± 0.9–9.6 ± 0.2 Å2for Cγ, when the sampling was done, for each of these proteins, over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations using AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive toa prioriprediction of crystallographic B-factors of a folded globular protein.

Molecular dynamics simulation study of linear, bottlebrush, and star-like amphiphilic block polymer assembly in solution

Soft Matter ◽  
2019 ◽  
Vol 15 (19) ◽  
pp. 3987-3998 ◽  
Author(s):  
Michiel G. Wessels ◽  
Arthi Jayaraman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Block Polymers ◽  
Block Polymer ◽  
Polymer Architectures ◽  
Amphiphilic Block Polymers ◽  
Dynamics Simulations

In this study we investigate the effect of varying branched polymer architectures on the assembly of amphiphilic block polymers in solution using coarse-grained molecular dynamics simulations.

Study of the conformation of polyelectrolyte aggregates using coarse-grained molecular dynamics simulations

Soft Matter ◽  
2017 ◽  
Vol 13 (35) ◽  
pp. 5991-5999 ◽  
Author(s):  
Toshiki Mima ◽  
Tomoyuki Kinjo ◽  
Shunsuke Yamakawa ◽  
Ryoji Asahi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

The conformation of polyelectrolyte aggregates as a function of the backbone rigidity is investigated by coarse-grained molecular dynamics simulation.

Molecular dynamics simulation of thermo-mechanical behaviour of elastomer cross-linked via multifunctional zwitterions

2019 ◽  
Vol 21 (38) ◽  
pp. 21615-21625 ◽  
Author(s):  
Naveed Athir ◽  
Ling Shi ◽  
Sayyed Asim Ali Shah ◽  
Zhiyu Zhang ◽  
Jue Cheng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Mechanical Behaviour ◽  
Mechanical Response ◽  
Polymer Chains ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Dynamics Simulations

Coarse-grained (CG) molecular dynamics simulations have been employed to study the thermo-mechanical response of a physically cross-linked network composed of zwitterionic moieties and fully flexible elastomeric polymer chains.

Molecular Dynamics Simulations of Supercooled Liquid Metals and Glasses

2000 ◽  
Vol 644 ◽  
Author(s):  
Hyon-Jee Lee ◽  
Yue Qi ◽  
Alejandro Strachan ◽  
Tahir Cagin ◽  
William A. Goddard ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
Liquid State ◽  
Liquid Metals ◽  
Alloy System ◽  
Supercooled Liquid ◽  
Packing Fraction ◽  
Solute Concentration ◽  
Dynamics Simulation ◽  
Dynamics Simulations

AbstractThe thermodynamic, transport and structural properties of a binary metallic glass former in solid, liquid, and glass phases were studied using molecular dynamics simulation. We used a model binary alloy system with a sufficient atomic size mismatch and observed a glass transition in a quenching process. The diffusivity and viscosity were calculated in the liquid state and the super-cooled liquid state. The smaller atom showed higher diffusivity and more configurational randomness compared to the larger atom. The viscosity increased abruptly around the glass transition temperature. The solvent/solute concentration effect on the glass transition was examined in terms of a packing fraction. We find that the glass forming ability increases with the packing fraction in the liquid state because the densely-packed material requires more time to rearrange and crystallize.

scholarly journals Structural and Dynamic Properties of Hydrophobic Eutectic Solvents Based on Menthol and Fatty Acids: a Molecular Dynamics Simulation Study

2021 ◽  
Author(s):  
Samaneh Barani Pour ◽  
Jaber Jahanbin Sardroodi ◽  
Alireza Rastkar Ebrahimzadeh
Keyword(s):  
Molecular Dynamics ◽  
Fatty Acids ◽  
Dynamic Properties ◽  
Mean Square Displacement ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Eutectic Mixtures ◽  
Dynamical Properties ◽  
Reorientation Dynamics ◽  
Dynamics Simulations

Abstract The structural and dynamical properties of the binary mixture of Menthol (MEN) and Fatty acids (FAs) were investigated using molecular dynamics simulations. We focused on the relationship between the structural and dynamical properties of the eutectic mixtures of MEN and FAs with different molar percentages of FAs. Structural properties of the eutectic mixtures were characterized by calculating the combined distribution functions(CDFs), the radial distribution functions (RDFs), and the angular distribution functions (ADFs), and the Hydrogen bonding network between species and Spatial distribution functions (SDF). Further interaction between menthol and Caprylic acid molecules was confirmed by the results of these analyzes. Also, the transport properties of the mixtures were investigated by using the mean square displacement (MSD) of the centers of mass of the species, self-diffusion coefficients and vector reorientation dynamics (VRD) of bonds. The simulation results indicated that intermolecular interactions have a significant effect on the dynamic properties of species.

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