Molecular Dynamics Simulations of Bubble Formation in Nanochannels

Author(s):  
Manoj Sridhar ◽  
Anthony B. Hmelo ◽  
Leonard C. Feldman ◽  
Dongyan Xu ◽  
Deyu Li

The behavior of confined fluids is of great interest due to the proliferation and applications of micro- and nanofluidic devices. Recent computational and experimental results have shown that fluids exhibit unusual phase change behavior when confined to very small length scales where the fluid physics is dominated by interactions with the confining channel walls. In particular, understanding the liquid-vapor phase transition and bubble nucleation process in confined spaces presents opportunities for making valves and pumps in nanofluidic networks. In this paper, we present molecular dynamics simulations of thermal bubble nucleation in fluids confined in nanochannels. To verify the computational models, bulk argon and bulk water were first modeled under conditions similar to those reported in the literature. The results were similar to those presented in the literature, indicating that our computational models could reproduce published data. We then modeled argon and water systems confined between two parallel silicon plates with nanometer separation. To simulate cases more extensively encountered in reality, we performed Molecular Dynamics (MD) simulations in the isothermal-isobaric (NPT) ensemble by allowing the top silicon plate to move up and down under a constant external pressure during the simulation. For either the nano-confined argon or the nano-confined water system, results indicated no bubble generation under an external pressure of 0.1 MPa, even for temperatures much higher than the boiling temperature of the respective fluids at 0.1 MPa. We also observed that there was no bubble generation in either the argon or water NPT system when the external pressure was reduced to as low as 0.01 MPa. The density of the nano-confined fluids at constant temperature was observed to be independent of external pressure on the system. This suggests that the nanoconfined fluids behave like liquids with low compressibility even at temperatures close to their superheat limit.

2014 ◽  
Vol 26 (3) ◽  
pp. 032003 ◽  
Author(s):  
Takahiro Ito ◽  
Henri Lhuissier ◽  
Sander Wildeman ◽  
Detlef Lohse

2018 ◽  
Vol 42 (19) ◽  
pp. 16258-16272 ◽  
Author(s):  
Elham Jalalitalab ◽  
Mohsen Abbaspour ◽  
Hamed Akbarzadeh

Different morphologies of water molecules are confined between two parallel graphene surfaces.


Antioxidants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1039
Author(s):  
Andreia Mónico ◽  
Joan Guzmán-Caldentey ◽  
María A. Pajares ◽  
Sonsoles Martín-Santamaría ◽  
Dolores Pérez-Sala

The intermediate filament protein vimentin is involved in essential cellular processes, including cell division and stress responses, as well as in the pathophysiology of cancer, pathogen infection, and autoimmunity. The vimentin network undergoes marked reorganizations in response to oxidative stress, in which modifications of vimentin single cysteine residue, Cys328, play an important role, and is modulated by zinc availability. However, the molecular basis for this regulation is not fully understood. Here, we show that Cys328 displays a low pKa, supporting its reactivity, and is readily alkylated and oxidized in vitro. Moreover, combined oxidation and crosslinking assays and molecular dynamics simulations support that zinc ions interact with Cys328 in its thiolate form, whereas Glu329 and Asp331 stabilize zinc coordination. Vimentin oxidation can induce disulfide crosslinking, implying the close proximity of Cys328 from neighboring dimers in certain vimentin conformations, supported by our computational models. Notably, micromolar zinc concentrations prevent Cys328 alkylation, lipoxidation, and disulfide formation. Moreover, zinc selectively protects vimentin from crosslinking using short-spacer cysteine-reactive but not amine-reactive agents. These effects are not mimicked by magnesium, consistent with a lower number of magnesium ions hosted at the cysteine region, according to molecular dynamics simulations. Importantly, the region surrounding Cys328 is involved in interaction with several drugs targeting vimentin and is conserved in type III intermediate filaments, which include glial fibrillary acidic protein and desmin. Altogether, our results identify this region as a hot spot for zinc binding, which modulates Cys328 reactivity. Moreover, they provide a molecular standpoint for vimentin regulation through the interplay between cysteine modifications and zinc availability.


Materials ◽  
2019 ◽  
Vol 12 (15) ◽  
pp. 2354 ◽  
Author(s):  
Zhang ◽  
Yun ◽  
Liu

The behaviors of xenon in molybdenum were studied using molecular statics andmolecular dynamics simulations. The diffusion mechanism of xenon atoms was studied combiningmolecular dynamics, nudged elastic band, and temperature-accelerated dynamics methods. Thevacancy-assisted diffusion mechanism was analyzed and the corresponding energy barriers werecalculated. The clustering process of scattered xenon atoms was studied at an elevated temperature.Xenon bubbles were observed to form when the concentration of xenon atoms exceeded a thresholdconcentration value. Meanwhile, the interaction of xenon bubble and vacancies was investigated viathe nudged elastic band method. The results showed that there exists a region around the xenonbubble where the migration energy of vacancy is significantly influenced. This work provides usefulinsights towards a better understanding of the behaviors of xenon in molybdenum.


2018 ◽  
Vol 20 (3) ◽  
pp. 1707-1715 ◽  
Author(s):  
Luca Sementa ◽  
Giovanni Barcaro ◽  
Susanna Monti ◽  
Vincenzo Carravetta

Melting and sintering of silicon nanoparticles are investigated by means of classical molecular dynamics simulations to disclose the dependence of modelling on the system type, the simulation procedure and interaction potential.


2001 ◽  
Vol 114 (15) ◽  
pp. 6869-6877 ◽  
Author(s):  
Luzheng Zhang ◽  
Ramkumar Balasundaram ◽  
Stevin H. Gehrke ◽  
Shaoyi Jiang

Sign in / Sign up

Export Citation Format

Share Document