Substrate induced freezing, melting and depinning transitions in two-dimensional liquid crystalline systems

2022 ◽  
Author(s):  
Bharti bharti ◽  
Debabrata Deb
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystals ◽  
Molecular Dynamics Simulations ◽  
Liquid Crystalline ◽  
Two Dimensional ◽  
One Dimensional ◽  
The One ◽  
Dynamics Simulations

We use molecular dynamics simulations to investigate the ordering phenomena in two-dimensional (2D) liquid crystals over the one-dimensional periodic substrate (1DPS). We have used Gay-Berne (GB) potential to model the...

scholarly journals Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results

2019 ◽  
Author(s):  
Bradley W. Treece ◽  
Frank Heinrich ◽  
Arvind Ramanathan ◽  
Mathias Lösche
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Real Space ◽  
Time Averaging ◽  
One Dimensional ◽  
Neutron Reflection ◽  
Interfacial Structures ◽  
Associated Proteins ◽  
The One ◽  
Dynamics Simulations

AbstractWe present a method to incorporate structural results from neutron reflectometry, a technique that determines interfacial structures such as protein-membrane complexes at a solid surface, into molecular dynamics simulations. By analyzing component volume occupancy profiles, which describe the one-dimensional distribution of a particular molecular component within an interfacial architecture, we construct a real-space constraint in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown for an earlier investigation where an NR-derived structure was well captured by an independent MD simulation, and may lead to faster equilibration of ensemble structures. We further show that time averaging of the observable when biasing with this approach permits fluctuations about the average, which are necessary for conformational exploration of the protein. The method described here also provides insights into systems that are characterized by NR and MD when the two show slight differences in their profiles. This is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and take prohibitively long to equilibrate in simulations.

Molecular dynamics simulations of bottlebrush macromolecules in two dimensional polymeric melts under flow conditions

Soft Matter ◽  
2011 ◽  
Vol 7 (6) ◽  
pp. 2805 ◽  
Author(s):  
Jan-Michael Y. Carrillo ◽  
Sergei S. Sheiko ◽  
Andrey V. Dobrynin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Two Dimensional ◽  
Flow Conditions ◽  
Dynamics Simulations

The EcCLC antiporter embedded in the lipidic liquid crystalline films – molecular dynamics simulations and electrochemistry

2021 ◽  
Author(s):  
Przemysław Miszta ◽  
Ewa Nazaruk ◽  
Dorota Nieciecka ◽  
Mariusz Możajew ◽  
Pawel Krysinski ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Transport Properties ◽  
Liquid Crystalline ◽  
Cubic Phases ◽  
Crystalline Films ◽  
Dynamics Simulations

Lipidic-liquid crystalline nanostructures (lipidic cubic phases), which are biomimetic and stable in excess of water, were used as a convenient environment to investigate the transport properties of the membrane antiporter...

Molecular dynamics simulations on the dynamics of two-dimensional rounded squares

2018 ◽  
Vol 27 (8) ◽  
pp. 088203 ◽  
Author(s):  
Zhang-lin Hou ◽  
Ying Ju ◽  
Yi-wu Zong ◽  
Fang-fu Ye ◽  
Kun Zhao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Two Dimensional ◽  
Dynamics Simulations

Scattering patterns and stress–strain relations on phase-separated ABA block copolymers under uniaxial elongating simulations

Soft Matter ◽  
2019 ◽  
Vol 15 (5) ◽  
pp. 926-936 ◽  
Author(s):  
Katsumi Hagita ◽  
Keizo Akutagawa ◽  
Tetsuo Tominaga ◽  
Hiroshi Jinnai
Keyword(s):  
Molecular Dynamics ◽  
Block Copolymers ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Two Dimensional ◽  
Stress Strain ◽  
Uniaxial Stretching ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

To develop molecularly based interpretations of the two-dimensional scattering patterns (2DSPs) of phase-separated block copolymers (BCPs), we performed coarse-grained molecular dynamics simulations of ABA tri-BCPs under uniaxial stretching for block-fractions where the A-segment (glassy domain) is smaller than the B-segment (rubbery domain), and estimated the behaviour of their 2DSPs.

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