scholarly journals Coarse-Grained Simulations of the Effects of Chain Length, Solvent Quality, and Chemical Defects on the Solution-Phase Morphology of MEH-PPV Conjugated Polymers

2012 ◽  
Vol 65 (5) ◽  
pp. 463 ◽  
Author(s):  
Ming Chiu ◽  
Tak W. Kee ◽  
David M. Huang
Keyword(s):  
Polymer Chains ◽  
Coarse Grained ◽  
Radius Of Gyration ◽  
Implicit Solvent ◽  
Coarse Grained Model ◽  
Solvent Quality ◽  
Defect Content ◽  
Coarse Grained Simulations ◽  
Chain Lengths ◽  
Poor Solvent

A mesoscale coarse-grained model of the conjugated polymer poly(2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV) in implicit solvent is developed. The model is parametrized to reproduce the local structure and dynamics of an atomistic simulation model and accounts for the effects of solvent quality and saturation chemical defects on the polymer structure. Polymers with defect concentrations of 0 to 10 % are simulated using Langevin dynamics in tetrahydrofuran (THF) and in a model poor solvent for chain lengths and solution concentrations used experimentally. The polymer chains are extended in THF and collapse into compact structures in the poor solvent. The radius of gyration decreases with defect content in THF and agrees quantitatively with experiment. The structures formed in poor solvent by chains with 300 monomer units change from toroidal to cylindrical with increasing defect content, while chains containing 1000 monomers form cylinders regardless of defect content. These results have implications for energy transfer in MEH-PPV.

Corrigendum to: Coarse-Grained Simulations of the Effects of Chain Length, Solvent Quality, and Chemical Defects on the Solution-Phase Morphology of MEH-PPV Conjugated Polymers

2013 ◽  
Vol 66 (4) ◽  
pp. 505
Author(s):  
Ming Chiu ◽  
Tak W. Kee ◽  
David M. Huang
Keyword(s):  
Polymer Chains ◽  
Coarse Grained ◽  
Radius Of Gyration ◽  
Implicit Solvent ◽  
Coarse Grained Model ◽  
Solvent Quality ◽  
Defect Content ◽  
Coarse Grained Simulations ◽  
Chain Lengths ◽  
Poor Solvent

A mesoscale coarse-grained model of the conjugated polymer poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV) in implicit solvent is developed. The model is parametrized to reproduce the local structure and dynamics of an atomistic simulation model and accounts for the effects of solvent quality and saturation chemical defects on the polymer structure. Polymers with defect concentrations of 0 to 10 % are simulated using Langevin dynamics in tetrahydrofuran (THF) and in a model poor solvent for chain lengths and solution concentrations used experimentally. The polymer chains are extended in THF and collapse into compact structures in the poor solvent. The radius of gyration decreases with defect content in THF and agrees quantitatively with experiment. The structures formed in poor solvent by chains with 300 monomer units change from toroidal to cylindrical with increasing defect content, while chains containing 1000 monomers form cylinders regardless of defect content. These results have implications for energy transfer in MEH-PPV.

A Finite Element-Based Coarse-Grained Model for Cell–Nanomaterial Interactions by Combining Absolute Nodal Coordinate Formula and Brownian Dynamics

2020 ◽  
Vol 88 (4) ◽  
Author(s):  
Teng Ma ◽  
Yuanpeng Liu ◽  
Guochang Lin ◽  
Changguo Wang ◽  
Huifeng Tan
Keyword(s):  
Finite Element ◽  
Brownian Dynamics ◽  
Lipid Membrane ◽  
Contact Region ◽  
Detection Algorithm ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Absolute Nodal Coordinate ◽  
Coarse Grained Model ◽  
Dynamics Simulations

Abstract A fundamental understanding of the interactions between one-dimensional nanomaterials and the cell membrane is of great importance for assessing the hazardous effects of viruses and improving the performance of drug delivery. Here, we propose a finite element-based coarse-grained model to describe the cell entry of nanomaterials based on an absolute nodal coordinate formula and Brownian dynamics. The interactions between nanoparticles and lipid membrane are described by the Lennard–Jones potential, and a contact detection algorithm is used to determine the contact region. Compared with the theoretical and published experimental results, the correctness of the model has been verified. We take two examples to test the robustness of the model: the endocytosis of nanorods grafted with polymer chains and simultaneous entry of multiple nanorods into a lipid membrane. It shows that the model can not only capture the effect of ligand–receptor binding on the penetration but also accurately characterize the cooperative or separate entry of multiple nanorods. This coarse-grained model is computationally highly efficient and will be powerful in combination with molecular dynamics simulations to provide an understanding of cell–nanomaterial interactions.

scholarly journals Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Astrid F. Brandner ◽  
Stepan Timr ◽  
Simone Melchionna ◽  
Philippe Derreumaux ◽  
Marc Baaden ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lattice Boltzmann ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Mesoscopic Scale ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Cellular Compartments ◽  
Biological Entities

Abstract In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments.

scholarly journals The influence of arm composition on the self-assembly of low-functionality telechelic star polymers in dilute solutions

2020 ◽  
Author(s):  
Esmaeel Moghimi ◽  
Iurii Chubak ◽  
Dimitra Founta ◽  
Konstantinos Ntetsikas ◽  
George Polymeropoulos ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dynamic Properties ◽  
Star Polymers ◽  
Coarse Grained ◽  
Dilute Solutions ◽  
Solvent Quality ◽  
Physical Experiments ◽  
Coarse Grained Simulations ◽  
Two Populations

Abstract We combine synthesis, physical experiments, and computer simulations to investigate self-assembly patterns of low-functionality telechelic star polymers (TSPs) in dilute solutions. In particular, in this work, we focus on the effect of the arm composition and length on the static and dynamic properties of TSPs, whose terminal blocks are subject to worsening solvent quality upon reducing the temperature. We find two populations, single stars and clusters, that emerge upon worsening the solvent quality of the outer block. For both types of populations, their spatial extent decreases with temperature, with the specific details (such as temperature at which the minimal size is reached) depending on the coupling between inter- and intra-molecular associations as well as their strength. The experimental results are in very good qualitative agreement with coarse-grained simulations, which offer insights into the mechanism of thermoresponsive behavior of this class of materials.

scholarly journals Coarse-Grained Model DNA with Explicit H-Bonding and Implicit Solvent

2013 ◽  
Vol 104 (2) ◽  
pp. 423a
Author(s):  
Lance E. Edens ◽  
James A. Brozik ◽  
David J. Keller
Keyword(s):  
Coarse Grained ◽  
Implicit Solvent ◽  
Coarse Grained Model

scholarly journals Fat SIRAH: Coarse-grained phospholipids to explore membrane-protein dynamics

2019 ◽  
Author(s):  
Exequiel E. Barrera ◽  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Membrane Protein ◽  
Effective Interaction ◽  
Coarse Grained ◽  
Single Amino Acid ◽  
Head Groups ◽  
Lipid Species ◽  
Good Reproduction ◽  
Consistent Manner ◽  
Coarse Grained Simulations ◽  
Chain Lengths

ABSTRACTTne capability to handle highly heterogeneous molecular assemblies in a consistent manner is among the greatest challenges faced when deriving simulation parameters. This is particularly the case for coarse-grained simulations in which chemical functional groups are lumped into effective interaction centers for which transferability between different chemical environments is not guaranteed. Here we introduce the parameterization of a set of CG phospholipids compatible with the latest version of the SIRAH force field for proteins. The newly introduced lipid species include different acylic chain lengths, partial unsaturation, as well as polar and acidic head groups that show a very good reproduction of structural membrane determinants, as areas per lipid, thickness, order parameter, etc., and their dependence with temperature. Simulation of membrane proteins showed unprecedented accuracy in the unbiased description of the thickness-dependent membrane-protein orientation in systems where this information is experimentally available (namely, the SarcoEndoplasmic Reticulum Calcium –SERCA-pump and its regulator Phospholamban). The interactions that lead to this faithful reproduction can be traced down to single amino acid-lipid interaction level and show full agreement with biochemical data present in the literature. Finally, the present parameterization is implemented in the GROMACS and AMBER simulation packages facilitating its use to a wide portion of the Biocomputing community.

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