Dynamical behavior of one-dimensional water molecule chains in zeolites: Nanosecond time-scale molecular dynamics simulations of bikitaite

2004 ◽  
Vol 120 (19) ◽  
pp. 9233-9244 ◽  
Author(s):  
Pierfranco Demontis ◽  
Giovanna Stara ◽  
Giuseppe B. Suffritti
Keyword(s):  
Molecular Dynamics ◽  
Water Molecule ◽  
Molecular Dynamics Simulations ◽  
Time Scale ◽  
Dynamical Behavior ◽  
One Dimensional ◽  
Nanosecond Time Scale ◽  
Dynamics Simulations

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 Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pablo Herrera-Nieto ◽  
Adrià Pérez ◽  
Gianni De Fabritiis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Intrinsically Disordered Proteins ◽  
Dynamical Behavior ◽  
Disordered Proteins ◽  
Partially Ordered ◽  
Intrinsically Disordered ◽  
State Models ◽  
Dynamics Simulations

Abstract The exploration of intrinsically disordered proteins in isolation is a crucial step to understand their complex dynamical behavior. In particular, the emergence of partially ordered states has not been explored in depth. The experimental characterization of such partially ordered states remains elusive due to their transient nature. Molecular dynamics mitigates this limitation thanks to its capability to explore biologically relevant timescales while retaining atomistic resolution. Here, millisecond unbiased molecular dynamics simulations were performed in the exemplar N-terminal region of p53. In combination with state-of-the-art Markov state models, simulations revealed the existence of several partially ordered states accounting for $$\sim $$ ∼ 40% of the equilibrium population. Some of the most relevant states feature helical conformations similar to the bound structure of p53 to Mdm2, as well as novel $$\beta $$ β -sheet elements. This highlights the potential complexity underlying the energy surface of intrinsically disordered proteins.

Phase transition-like behavior of the water monolayer close to the polarized surface of a nanotube

2018 ◽  
Vol 20 (31) ◽  
pp. 20391-20397 ◽  
Author(s):  
Li Zeng ◽  
Xiaoyan Zhou ◽  
Xiao Huang ◽  
Hangjun Lu
Keyword(s):  
Phase Transition ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamical Behavior ◽  
Charged Surface ◽  
Water Layers ◽  
Effects Of Temperature ◽  
Polarized Surface ◽  
Dynamics Simulations

By molecular dynamics simulations, we have investigated effects of temperature on the dynamical behavior of water layers at the charged surface of a nanotube.

Molecular Dynamics Simulations of Water Molecule-Bridges in Polar Domains of Humic Acids

2011 ◽  
Vol 45 (19) ◽  
pp. 8411-8419 ◽  
Author(s):  
Adelia J. A. Aquino ◽  
Daniel Tunega ◽  
Hasan Pašalić ◽  
Gabriele E. Schaumann ◽  
Georg Haberhauer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water Molecule ◽  
Molecular Dynamics Simulations ◽  
Humic Acids ◽  
Dynamics Simulations

Heterogeneous dynamics of ionic liquids in confined films with varied film thickness

2014 ◽  
Vol 16 (38) ◽  
pp. 20731-20740 ◽  
Author(s):  
Yong-Lei Wang ◽  
Zhong-Yuan Lu ◽  
Aatto Laaksonen
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Ionic Liquids ◽  
Film Thickness ◽  
Molecular Dynamics Simulations ◽  
Dynamical Behavior ◽  
Heterogeneous Dynamics ◽  
Dynamics Simulations

Dynamical behavior and characteristics of 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) in confined films with varied film thickness have been investigated using atomistic molecular dynamics simulations.

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