Molecular Dynamics Simulation of Ultra-Fast Phase Transition in Water Nanofilms

2020 ◽  
Vol 142 (11) ◽  
Author(s):  
Malcolm Porterfield ◽  
Diana-Andra Borca-Tasciuc

Abstract Molecular dynamics simulations are used to explore explosive boiling of thin water films on a gold substrate. In particular, water films of 0.7, 1.6, and 2.5 nanometer thickness were examined. Three different surface wettabilities with contact angles of 11 deg, 47 deg, and 110 deg were simulated along with substrate temperatures of 400 K, 600 K, 800 K, and 1000 K. The 11 and 47 deg contact angles were obtained using a Morse interaction potential between the water film and gold substrate while the 47 and 110 deg contact angles were obtained via a Lennard-Jones potential. Evaporation was the first mode of phase change observed in all cases and explosive boiling did not occur until the substrate reached a temperature of 800 K. When explosive boiling was present for all three contact angles, it was consistently shown to occur first for the surface with a 47 deg contact angle and Lennard-Jones potential. These results suggest that explosive boiling onset is strongly dependent on the particularities of the interaction potential. For instance, the Morse potential is smoother when compared to the Lennard-Jones potential, but has more interaction sites per molecule—two hydrogen atoms and one oxygen atom versus one oxygen atom. Thus, even when the water film reaches a higher temperature with the Morse potential, explosive boiling onset is delayed as more interaction sites have to be disrupted. These results suggest that contact angle alone is insufficient and both the interaction strength and the number of atoms interacting at the interface must be considered when investigating trends of explosive boiling with surface wettability.

Author(s):  
Malcolm Porterfield ◽  
Diana Borca-Tasciuc

Abstract Molecular dynamics simulations are used to explore explosive boiling of thin water films on a gold substrate. In particular, water films of 2.5, 1.6 and 0.7 nanometer thickness were examined. Three different surface wettabilities with contact angles of 11, 47 and 110 degrees were simulated along with substrate temperatures of 400K, 600K, 800K and 1000K. The 11 degree contact angle was obtained using a Morse interaction potential between the water film and the gold substrate while the 47 and 110 degree contact angles were obtained via a Lennard-Jones potential. Evaporation was the first mode of phase change observed in all cases and explosive boiling did not occur until the substrate reached a temperature of 800K. When explosive boiling was present for all three contact angles, it was consistently shown to occur first for the surface with a 47 degree contact angle, contrary to the expectation that it would occur first on the substrate with an 11 degree contact angle. These results suggest that explosive boiling onset is strongly dependent on the particularities of the interaction potential. For instance, the Morse potential used to model the surface described by an 11 degree contact angle, is a softer potential as compared with Lennard-Jones, but has more interaction sites per molecule — two hydrogen atoms and one oxygen atom vs one oxygen atom. Thus, although the water film reaches a higher temperature with the Morse potential, explosive boiling onset is delayed as more interaction sites have to be disrupted. These results suggest that both the interaction strength and the number of atoms interacting at the interface must be considered when investigating trends of explosive boiling with surface wettability.


2021 ◽  
Vol 22 (11) ◽  
pp. 5914
Author(s):  
Mengsheng Zha ◽  
Nan Wang ◽  
Chaoyang Zhang ◽  
Zheng Wang

Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on the Lennard-Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single-cell Hi-C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis–Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D-FISH data.


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