Surface Ligand Rigidity Modulates Lipid Raft Affinity of Ultra-small Hydrophobic Nanoparticles: Insights from Molecular Dynamics Simulations

Nanoscale ◽  
2021 ◽  
Author(s):  
Xiaoqian Lin ◽  
Xubo Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Rafts ◽  
Lipid Raft ◽  
The Other ◽  
Membrane Domains ◽  
Surface Ligand ◽  
Proper Functions ◽  
Dynamics Simulations ◽  
Small Hydrophobic

Differential preferences between lipids and proteins drive the formation of dynamical nanoscale membrane domains (lipid rafts), which play key roles in proper functions of the cell. On the other hand,...

Optimization of hydrophobic nanoparticles to better target lipid rafts with molecular dynamics simulations

Nanoscale ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 4101-4109 ◽  
Author(s):  
Xiaoqian Lin ◽  
Xubo Lin ◽  
Ning Gu
Keyword(s):  
Molecular Dynamics ◽  
Plasma Membrane ◽  
Molecular Dynamics Simulations ◽  
Lipid Rafts ◽  
Membrane Domains ◽  
Dynamics Simulations

Due to different interactions between lipids and proteins, a plasma membrane can segregate into different membrane domains.

scholarly journals Local Structuring of Diketopyrrolopyrrole (DPP)-Based Semiconducting Polymers Using Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Maryam Reisjalali ◽  
Jose Javier Burgos Marmol ◽  
Alessandro Troisi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electronic Devices ◽  
Atomic Level ◽  
Semiconducting Polymers ◽  
The Other ◽  
Charge Mobility ◽  
High Charge ◽  
High Performing ◽  
Dynamics Simulations

High performing organic semiconducting polymers show great potentials for use in electronic devices which is greatly dependent on the material crystallinity and packing. A series of short oligomers of the diketopyrrolopyrrole (DPP)-based materials that have shown to have high charge mobility are studied to understand the local structuring at atomic level for these materials. The simulations show that the tendency for this material class to form aggregates is driven by the interaction between DPP fragments, but this is modulated by the other conjugated fragments of the materials which afect the rigidity of the polymer and the ability to form aggregates of larger size.<br>

scholarly journals Catalytic Effect of Ti or Pt in a Hexagonal Boron Nitride Surface for Capturing CO2

Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 662
Author(s):  
J. M. Ramirez-de-Arellano ◽  
A. Fransuani Jiménez G. ◽  
L. F. Magaña
Keyword(s):  
Molecular Dynamics ◽  
Boron Nitride ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Atmospheric Pressure ◽  
Catalytic Effect ◽  
Hexagonal Boron Nitride ◽  
The Other ◽  
Adsorption Of Co2 ◽  
Dynamics Simulations

We investigated the effect of doping a hexagonal boron nitride surface (hBN) with Ti or Pt on the adsorption of CO2. We performed first-principles molecular dynamics simulations (FPMD) at atmospheric pressure, and 300 K. Pristine hBN shows no interaction with the CO2 molecule. We allowed the Ti and Pt atoms to interact separately, with either a B-vacancy or an N-vacancy. Both Ti and Pt ended chemisorbed on the surface. The system hBN + Ti always chemisorbed the CO2 molecule. This chemisorption happens in two possible ways. One is without dissociation, and in the other, the molecule breaks in CO and O. However, in the case of the Pt atom as dopant, the resulting system repels the CO2 molecule.

MOLECULAR DYNAMICS SIMULATIONS OF LIQUID CRYSTAL ANCHORING AT AN AMORPHOUS POLYMER SURFACE

1999 ◽  
Vol 10 (02n03) ◽  
pp. 415-429 ◽  
Author(s):  
T. P. DOERR ◽  
P. L. TAYLOR
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystal ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amorphous Polymer ◽  
Polymer Surface ◽  
The Other ◽  
Substantial Fraction ◽  
Dynamics Simulations ◽  
First Time

Atomistic molecular dynamics simulations have been used, apparently for the first time, to investigate the anchoring behavior of a liquid crystal at the interface with an amorphous polymer. The simulations studied a system consisting of the nematogen 5CB at the surface of amorphous polyethylene, and used the simple Dreiding II force field. The simulations indicate a preference for nonplanar anchoring. Two distinct microscopic paths have been identified by which the liquid crystal changes orientation at the surface. In one case, only one or a few of the 5CB molecules are rotating at any particular time. In the other case, a substantial fraction of the molecules rotate simultaneously.

scholarly journals Computational screening of nanoparticles coupling to Aβ40 peptides and fibrils

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Soumyo Sen ◽  
Lela Vuković ◽  
Petr Král
Keyword(s):  
Molecular Dynamics ◽  
Neurodegenerative Diseases ◽  
Molecular Dynamics Simulations ◽  
Amyloid Fibrils ◽  
The Other ◽  
Beta Sheet ◽  
Computational Screening ◽  
Synthetic Inhibitor ◽  
Other Hand ◽  
Dynamics Simulations

AbstractBlocking the formation, growth, and breaking of amyloid fibrils by synthetic nanosystems could provide a treatment of neurodegenerative diseases. With this in mind, here atomistic molecular dynamics simulations are used to screen for nanoparticles (NPs), covered with different mixtures of ligands, including positively and negatively charged ligands, Aβ40-cut-peptide, and synthetic inhibitor ligands, in their selective coupling to Aβ40 peptides and their fibrils. The simulations reveal that only Aβ40-cut-peptide-covered NPs have strong and selective coupling to Aβ40 monomers. On the other hand, positive, positive-neutral, Janus, and peptide NPs couple to the beta sheet surfaces of Aβ40 fibrils and only the negative-neutral NPs couple to the fibril tips.

scholarly journals Permeabilities of CO2, H2S and CH4 through Choline-Based Ionic Liquids: Atomistic-Scale Simulations

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 2014 ◽  
Author(s):  
Abdukarem Amhamed ◽  
Mert Atilhan ◽  
Golibjon Berdiyorov
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Diffusion Rate ◽  
The Other ◽  
Permeability Coefficients ◽  
Gas Molecules ◽  
Dynamics Simulations ◽  
And Diffusion

Molecular dynamics simulations are used to study the transport of CO 2 , H 2 S and CH 4 molecules across environmentally friendly choline-benzoate and choline-lactate ionic liquids (ILs). The permeability coefficients of the considered molecules are calculated using the free energy and diffusion rate profiles. Both systems show the largest resistance to CH 4 , whereas more than 5 orders of magnitude larger permeability coefficients are obtained for the other two gas molecules. The CO 2 /CH 4 and H 2 S/CH 4 selectivity was estimated to be more than 10 4 and 10 5 , respectively. These results indicate the great potential of the considered ILs for greenhouse gas control.

scholarly journals Local Structuring of Diketopyrrolopyrrole (DPP)-Based Semiconducting Polymers Using Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Maryam Reisjalali ◽  
Jose Javier Burgos Marmol ◽  
Alessandro Troisi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electronic Devices ◽  
Atomic Level ◽  
Semiconducting Polymers ◽  
The Other ◽  
Charge Mobility ◽  
High Charge ◽  
High Performing ◽  
Dynamics Simulations

High performing organic semiconducting polymers show great potentials for use in electronic devices which is greatly dependent on the material crystallinity and packing. A series of short oligomers of the diketopyrrolopyrrole (DPP)-based materials that have shown to have high charge mobility are studied to understand the local structuring at atomic level for these materials. The simulations show that the tendency for this material class to form aggregates is driven by the interaction between DPP fragments, but this is modulated by the other conjugated fragments of the materials which afect the rigidity of the polymer and the ability to form aggregates of larger size.<br>

scholarly journals Can small hydrophobic gold nanoparticles inhibit β2-microglobulin fibrillation?

Nanoscale ◽  
2014 ◽  
Vol 6 (14) ◽  
pp. 7903-7911 ◽  
Author(s):  
Giorgia Brancolini ◽  
Dimitrios Toroz ◽  
Stefano Corni
Keyword(s):  
Molecular Dynamics ◽  
Gold Nanoparticles ◽  
Molecular Dynamics Simulations ◽  
Β2 Microglobulin ◽  
Dynamics Simulations ◽  
Small Hydrophobic

Molecular dynamics simulations suggest that small hydrophobic gold nanoparticles can stabilize the native folding of the β2-microglobulin protein.

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