Coarse-Grained Computer Simulation of Nanoconfined Polyamide-6,6

2011 ◽  
Vol 44 (8) ◽  
pp. 3117-3128 ◽  
Author(s):  
Hossein Eslami ◽  
Hossein Ali Karimi-Varzaneh ◽  
Florian Müller-Plathe
Keyword(s):  
Computer Simulation ◽  
Coarse Grained

The structure of polymer brushes near the transition from dilute to dense systems. A computer simulation study

Soft Matter ◽  
2021 ◽  
Author(s):  
Piotr Polanowski ◽  
Andrzej Sikorski
Keyword(s):  
Computer Simulation ◽  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Simulation Study ◽  
Polymer Brushes ◽  
Polymer Brush ◽  
Coarse Grained ◽  
Computer Simulation Study ◽  
Coarse Grained Model ◽  
Cooperative Motion

Monodisperse polymer brushes were studied by means of Monte Carlo simulations. A coarse-grained model of a polymer brush was designed in order and the Cooperative Motion Algorithm was employed to...

Computer Simulation of Polymer Chains in Confinement

2008 ◽  
Vol 138 ◽  
pp. 451-475 ◽  
Author(s):  
Andrzej Sikorski
Keyword(s):  
Computer Simulation ◽  
Brownian Dynamics ◽  
Dynamic Properties ◽  
Practical Importance ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Theoretical Treatment ◽  
Narrow Slit ◽  
Exchange Method ◽  
Confined Polymers

Properties of macromolecules confined in a narrow slit, pore or capillary are important due to of their practical importance. Theoretical treatment of such systems is also interesting because the introduction of confinement has an impact on most properties of polymer chains and it gained a longstanding attention. In order to determine the properties of such systems coarse-grained models of confined polymers were designed where macromolecules were represented by united atoms. Lattice approximation was also often introduced. Different macromolecular architectures were studied: linear, cyclic and star-branched chains. Computer simulation techniques (the variants of the Monet Carlo method like the Metropolis algorithm and the Replica Exchange method as well as Molecular Dynamics and Brownian Dynamics methods) applied for studies of such models were reviewed and evaluated. The structure of the polymer film and the dynamic properties were mainly presented and discussed. The influence of the width of the slit, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that a moderate confinement stabilizes folded chains while a strong confinement does not.

scholarly journals Computer simulation of knotted proteins unfold and translocation through nano-pores

2018 ◽  
Author(s):  
M. A. Shahzad
Keyword(s):  
Computer Simulation ◽  
Computational Model ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Constant Force ◽  
Translocation Mechanism ◽  
Translocation Time ◽  
Knotted Protein ◽  
Knotted Proteins ◽  
Pulling Force

We study the unfold and translocation of knotted protein, YibK and YbeA, through α-hemolysin nano-pore via a coarse grained computational model. We observe that knot of protein unfold in advance before the translocation take place. We also characterized the translocation mechanism by studying the thermodynamical and kinetic properties of the process. In particular, we study the average of translocation time, and the translocation probability as a function of pulling force F acting in the channel. In limit of low pulling inward constant force acting along the axis of the pore, the YibK knotted protein takes longer average translocation time as compare to YbeA knotted protein.

Gelation of patchy ligand shell nanoparticles decorated by liquid-crystalline ligands: computer simulation study

Soft Matter ◽  
2018 ◽  
Vol 14 (19) ◽  
pp. 3799-3810 ◽  
Author(s):  
Jaroslav M. Ilnytskyi ◽  
Arsen Slyusarchuk ◽  
Stefan Sokołowski
Keyword(s):  
Computer Simulation ◽  
Simulation Study ◽  
Liquid Crystalline ◽  
Coarse Grained ◽  
Computer Simulation Study ◽  
Shell Nanoparticles ◽  
Ligand Shell

We consider the coarse-grained modelling of patchy ligand shell nanoparticles with liquid crystalline ligands.

COMPUTER MODEL OF A LYSOZYME CRYSTAL GROWTH WITH/WITHOUT NANOTEMPLATE — A COMPARISON

2006 ◽  
Vol 17 (09) ◽  
pp. 1359-1366 ◽  
Author(s):  
J. SIÓDMIAK ◽  
A. GADOMSKI ◽  
E. PECHKOVA ◽  
C. NICOLINI
Keyword(s):  
Computer Simulation ◽  
Monte Carlo ◽  
Crystal Growth ◽  
Computer Model ◽  
Monte Carlo Technique ◽  
Coarse Grained ◽  
Langmuir Blodgett ◽  
Lattice Monte Carlo ◽  
Experimental Findings ◽  
Lysozyme Crystal

The results of a computer simulation of the lysozyme crystal growth influenced by monomer and tetramer (aggregate) units are discussed. A very recently introduced computer model of biopolymer crystal growth and aggregation is based on the 2D lattice Monte Carlo technique and the coarse-grained HP approximation of the lysozyme monomeric unit. Acceleration of the lysozyme crystal growth by a factor of 4/3, based on the 2AUB (PDB ID) lysozyme unit, obtained from the Langmuir–Blodgett nanotemplate method, has clearly been confirmed by means of the proposed computer simulation. It is concluded that the aggregates (tetramers) involving 2AUB lysozyme crystal growth can be expected to be slightly accelerated when compared to its monomer-based (PDB ID: 193L) counterpart, which is in excellent accord with very recent experimental findings of the emerging applied science called protein nanocrystallography.

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