scholarly journals Thermodynamic Scaling of the Shear Viscosity of Lennard-Jones Chains of Variable Rigidity

Liquids ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 96-108
Author(s):  
Stephanie Delage Santacreu ◽  
Hai Hoang ◽  
Samy Khennache ◽  
Guillaume Galliero
Keyword(s):  
Shear Viscosity ◽  
Force Fields ◽  
Coarse Grained ◽  
Molecular Models ◽  
Normal Alkanes ◽  
Lennard Jones ◽  
Simple Alternative ◽  
Points Of View ◽  
Dynamics Simulations ◽  
Real Fluids

In this work, the thermodynamic scaling framework has been used to emphasize the limitations of fully flexible coarse grained molecular models to yield shear viscosity of real liquids. In particular, extensive molecular dynamics simulations have confirmed that, while being reasonable to describe the viscosity of short normal alkanes, the fully flexible Lennard-Jones and Mie chains force fields are inadequate to capture the density dependence of shear viscosity of medium to long alkanes. In addition, it is shown that such a weakness in terms of coarse grained molecular models can be readily quantified by using the thermodynamic scaling framework. As a simple alternative to these force fields, it is demonstrated that the insertion of a variable intramolecular rigidity in the Lennard-Jones chains model exhibits promising results to model medium to long chain-like real fluids from both thermodynamic and viscosity points of view.

On the transport properties of simple liquids

1986 ◽  
Vol 64 (2) ◽  
pp. 211-214
Author(s):  
S. K. Datta
Keyword(s):  
Shear Viscosity ◽  
Pair Potential ◽  
Viscosity Coefficient ◽  
Simple Fluids ◽  
Jones Potential ◽  
Simple Liquids ◽  
Lennard Jones ◽  
Approximate Nature ◽  
Real Fluids ◽  
Analytical Expressions

Closed analytical expressions for the diffusion coefficient and shear-viscosity coefficient of dense, simple fluids characterized by the Lennard-Jones potential function have been obtained using the Weeks, Chandler, and Andersen criterion for the division of the pair potential. The expressions are then used to calculate these properties for some real fluids. The deviations between the estimated and measured values of the coefficients are attributed mostly to the approximate nature of the Kirkwood and Rice expressions for shear viscosity and the friction coefficient used to calculate those properties.

scholarly journals A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields

2021 ◽  
Author(s):  
Riccardo Capelli ◽  
Andrea Gardin ◽  
Charly Empereur-mot ◽  
Giovanni Doni ◽  
Giovanni M. Pavan
Keyword(s):  
Phase Transition ◽  
Force Fields ◽  
Coarse Grained ◽  
High Dimensional ◽  
Crucial Point ◽  
Structure And Dynamics ◽  
Intrinsic Resolution ◽  
Explicit Solvent ◽  
Gel Phase ◽  
Dynamics Simulations

<div><div><div><p>Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain insights useful for understanding the structural dynamics of these assemblies. In this context, one crucial point concerns the comparison of the performance and accuracy of classical force fields (FFs), which sometimes remains elusive. To date, the assessments performed on different classical potentials are mostly based on the comparison with experimental observables, which typically regard average properties. However, local differences of structure and dynamics, which are poorly captured by average measurements, can make a difference, but these are non-trivial to catch. Here we propose an agnostic way to compare different FFs at different resolutions (atomistic, united-atom, and coarse-grained), by means of a high-dimensional similarity metrics built on the framework of Smooth Overlap of Atomic Positions (SOAP). We compare and classify a set of 13 force fields, modeling 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Our SOAP kernels-based metrics allows us to compare, discriminate and correlate different force fields at different model resolutions in an unbiased, high-dimensional way. This also captures differences between FFs in modeling non-average events (originating from local transitions), such as for example the liquid-to-gel phase transition in dipalmitoylphosphatidylcholine (DPPC) bilayers, for which our metrics allows to identify nucleation centers for the phase transition, highlighting some intrinsic resolution limitations in implicit vs. explicit solvent force fields.</p></div></div></div>

Formation of Polyelectrolyte Brushes on Plate

2013 ◽  
Vol 749 ◽  
pp. 588-590
Author(s):  
Yang Yang ◽  
Chun Cheng Zuo ◽  
Yu Xin Zuo ◽  
Ying Yu
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Positive Charge ◽  
Coarse Grained ◽  
Lennard Jones Potential ◽  
Molecular Models ◽  
Jones Potential ◽  
Polyelectrolyte Brushes ◽  
Lennard Jones ◽  
Adsorption Density

The adsorption of polyelectrolyte chains on plate are studied using coarse-grained, bead-spring molecular models and Molecular dynamics computer simulation. It has been applied for studying the formation of polyelectrolyte brushes confined in the plates via the Lennard-Jones potential. The simulation result shows that the polyelectrolyte chains adsorption density is strongly affected by the length of the block carries the positive charge. Correspondingly, the counterions are added to the system. Upon changing the polyelectrolyte chain length N from 8 to 48, the profile of adsorption density decline between N=8 to N=18, and then rise. It has a minimum at N=18.These initial findings can be used as a guide for the preparation of actual polyelectrolyte brushes on plate by the adsorption approach.

scholarly journals Employing Hybrid Lennard-Jones and Axilrod-Teller Potentials to Parametrize Force Fields for the Simulation of Materials’ Properties

Materials ◽  
2021 ◽  
Vol 14 (21) ◽  
pp. 6352
Author(s):  
Danilo de Camargo Branco ◽  
Gary J. Cheng
Keyword(s):  
Molecular Dynamics ◽  
Material Properties ◽  
Force Fields ◽  
Ambient Conditions ◽  
Materials Properties ◽  
Materials Behaviors ◽  
Lennard Jones ◽  
Computational Materials ◽  
Dynamics Simulations ◽  
First Time

The development of novel materials has challenges besides their synthesis. Materials such as novel MXenes are difficult to probe experimentally due to their reduced size and low stability under ambient conditions. Quantum mechanics and molecular dynamics simulations have been valuable options for material properties determination. However, computational materials scientists may still have difficulty finding specific force field models for their simulations. Force fields are usually hard to parametrize, and their parameters’ determination is computationally expensive. We show the Lennard-Jones (2-body interactions) combined with the Axilrod-Teller (3-body interactions) parametrization process’ applicability for metals and new classes of materials (MXenes). Because this parametrization process is simple and computationally inexpensive, it allows users to predict materials’ behaviors under close-to-ambient conditions in molecular dynamics, independent of pre-existing potential files. Using the process described in this work, we have made the Ti2C parameters set available for the first time in a peer-reviewed work.

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