Types of polypeptide self-organization: molecular dynamics simulations

2001 ◽  
Author(s):  
Alexander I. Melker ◽  
Zakhar M. Frenkel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Organization ◽  
Dynamics Simulations

scholarly journals Molecular dynamics simulations of the self-organization of side-chain decorated polyaromatic conjugation molecules: phase separated lamellar and columnar structures and dispersion behaviors in toluene solvent

RSC Advances ◽  
2018 ◽  
Vol 8 (20) ◽  
pp. 11134-11144 ◽  
Author(s):  
Lanyan He ◽  
Pingmei Wang ◽  
Lipeng He ◽  
Zhou Qu ◽  
Jianhui Luo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Md Simulations ◽  
The Self ◽  
Self Organization ◽  
Side Chain ◽  
Dynamics Simulations

The self-organization of five model side-chain decorated polyaromatic asphaltene molecules with or without toluene solvent was investigated by means of molecular dynamic (MD) simulations.

scholarly journals From nanoaggregates to mesoscale ribbons: the multistep self-organization of amphiphilic peptides

2021 ◽  
Author(s):  
Grazia Maria Laura Messina ◽  
Claudia Mazzuca ◽  
Monica Dettin ◽  
Annj Zamuner ◽  
Benedetta Di Napoli ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscopy ◽  
Molecular Dynamics Simulations ◽  
Organization Structure ◽  
Self Organization ◽  
Force Microscopy ◽  
Amphiphilic Peptides ◽  
Atomic Force ◽  
Dynamics Simulations

The paper reports Atomic Force Microscopy results and Molecular Dynamics simulations on the striking differences of long-term self-organization structure for the negatively charged (AcA4)2KD (“double tail”) and AcA4D (“single tail”)...

Molecular dynamics study of coagulation in silica-nanocolloid–water–NaCl systems based on the atomistic model

2014 ◽  
Vol 16 (43) ◽  
pp. 24000-24017 ◽  
Author(s):  
Junko Habasaki ◽  
Masamichi Ishikawa
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
The Self ◽  
Self Organization ◽  
Atomistic Model ◽  
Dynamics Simulations

Structures obtained by coagulation of nanocolloidal silica in water with NaCl are examined by large scale atomistic molecular dynamics simulations for better understanding of the self-organization in aggregates and the gel.

scholarly journals Confinement-induced self-organization in growing bacterial colonies

2021 ◽  
Vol 7 (4) ◽  
pp. eabc8685
Author(s):  
Zhihong You ◽  
Daniel J. G. Pearce ◽  
Luca Giomi
Keyword(s):  
Molecular Dynamics ◽  
Stress Relaxation ◽  
Molecular Dynamics Simulations ◽  
Mechanical Response ◽  
Self Organization ◽  
Global Alignment ◽  
Normal Stresses ◽  
Continuous Modeling ◽  
Dynamics Simulations ◽  
Short Time

We investigate the emergence of global alignment in colonies of dividing rod-shaped cells under confinement. Using molecular dynamics simulations and continuous modeling, we demonstrate that geometrical anisotropies in the confining environment give rise to an imbalance in the normal stresses, which, in turn, drives a collective rearrangement of the cells. This behavior crucially relies on the colony’s solid-like mechanical response at short time scales and can be recovered within the framework of active hydrodynamics upon modeling bacterial colonies as growing viscoelastic gels characterized by Maxwell-like stress relaxation.

scholarly journals Impact of Doxorubicin on Self-Organization of Congo Red: Quantum Chemical Calculations and Molecular Dynamics Simulations

ACS Omega ◽  
2020 ◽  
Vol 5 (31) ◽  
pp. 19377-19384
Author(s):  
Klaudia Kwiecińska ◽  
Anna Stachowicz-Kuśnierz ◽  
Anna Jagusiak ◽  
Irena Roterman ◽  
Jacek Korchowiec
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical Calculations ◽  
Congo Red ◽  
Quantum Chemical ◽  
Self Organization ◽  
Dynamics Simulations
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