scholarly journals Achilles: A Tool for Contact Angle Estimation from Molecular Dynamics Simulations

Author(s):  
Sumith Yesudasan

In this work, a tool for estimating the contact angle from the molecular dynamics simulations is developed and presented. The tool (Achilles) can detect water droplet on hydrophobic and hydrophilic surfaces. The tool can reconstruct the droplets broken across the periodic boundaries. Further a neighbor density based accurate filter is used to find the droplet liquid vapor interface and a circle is fitted using it after removing the dense layers of water next to solid surface. This fitted circle is solved for contact angle and results are outputted in the form of graphical images and text. The entire content of the internal computations of the tool is broken down into 4 phases and users can monitor the outcomes at every phase through output images. The tool is tested using sample molecular dynamics results of water droplet on hydrophobic and hydrophilic surfaces. We believe this tool can be a good addition to the molecular dynamics simulation community who work on the interfacial physics, droplet evaporation, super hydrophobic surfaces, and wettability etc.

2021 ◽  
Vol 21 (1) ◽  
pp. 85-97
Author(s):  
Zhentao Dong ◽  
Haitao Xue ◽  
Bohong Li ◽  
Shansi Tian ◽  
Shuangfang Lu ◽  
...  

Wettability is an important physical property of shale. This parameter is related to the shale material composition and the fluid properties in the shale pores and plays an important role in the exploration and development of shale oil. Wettability is affected by the scale and roughness. The contact angle at the nanoscale on a smooth surface can better reflect the wettability of shale than the contact angle at higher scales. Molecular dynamics simulations can be used to measure the contact angle on a smooth surface at the nanoscale. This paper focuses on the effects of organic matter and minerals in shale and different components of shale oil on shale wettability. Wetting models of “organic matter-oil component-water,” “quartz-oil component-water” and “kaolinite-oil component-water” at the nanoscale were constructed. Molecular dynamics simulation was used to study the morphological changes of different oil components and water on different surfaces. Studies have shown that organic matter is strongly oleophilic and hydrophobic. Polar components in shale oil can make organic matter slightly hydrophilic. It was recognized by quartz wettability experiments and simulation methods at the nanoscale that the cohesive energy of a liquid has a significant influence on the degree of spreading of the liquid on the surface. The “liquid–liquid–solid” wettability experiment is an effective method for determining mineral oleophilic or hydrophilic properties. The nanoquartz in the shale is strongly hydrophilic. The water wetting angle is related to the crude oil component. Nanokaolinite can have a tetrahedral or an octahedral surface; the tetrahedral surface is oleophilic and hydrophobic, and the octahedral surface exhibits strong hydrophilicity. The wettabilities of both surfaces are related to the crude oil component.


2021 ◽  
Author(s):  
Isa Silveira de Araujo ◽  
◽  
Archana Jagadisan ◽  
Zoya Heidari ◽  
◽  
...  

Reliable quantification of wettability is critical in assessment of fluid distribution, capillary pressure, relative permeability, and flow properties of fluids in reservoirs. Wettability of reservoirs can be affected by chemical composition of rock-fluid system, salinity, and reservoir temperature. Experimental assessment of wettability under reservoir conditions, while gaining control on the aforementioned parameters, may be tedious and challenging. Several published researches have used experimental studies to focus on determining the impact of individual factors on wettability of rock. However, studies on the combined effects of these factors are limited, although critical, for better understanding of wettability of hydrocarbon reservoirs. In this paper we introduce a workflow for assessment of wettability of rocks at reservoir condition using molecular dynamics (MD) simulations. The outcomes include (i) quantifying the wettability of pure minerals, (ii) quantifying the impact of reservoir temperature on wettability of pure mineral. The inputs to the simulation include molecules of pure minerals (quartz, calcite, albite) packed in a cubical simulation box. The molecules are condensed to form a flat surface. Subsequently, water and oil (hexane) molecules are placed on the surface of the mineral. We then perform simulations with constant number of particles, temperature and volume (NVT) on the system till equilibrium is reached. At equilibrium, the contact angle formed by the water droplet is measured. Contact angle is simulated for temperature conditions in the range of 300 to 380 K. The results showed that the contact angle between water-mineral for quartz, calcite, and albite at room temperature (300 K) ranges from 30º to 45º, indicating that the surface of these minerals is hydrophilic, with different degrees of hydrophilicity. This information is essential for reliable fluid flow simulations, which are often overlooked in conventional approaches. We also found that the temperature has a measurable impact on the contact angles formed by water droplet. We found that increase in temperature from 300 to 380 K decreases the contact angles by approximately 30% on quartz surfaces, 20% on albite surfaces, and 24% on calcite surfaces. The results for the hexane-mineral system show that the hexane behaved similarly in the three minerals surface. A thin film of hexane is formed at the surface corresponding to a contact angle of 0º. The method introduced in this paper has application for reliable evaluation of wettability at any reservoir of interest by knowing the molecular structure of clay and non-clay minerals as well as fluid content. Moreover, the challenges of wettability determination under high temperature and pressure conditions can also be efficiently addressed by using molecular dynamics simulations.


RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.


2021 ◽  
Vol 1 (1) ◽  
pp. 10
Author(s):  
Lukman Hakim ◽  
Irsandi Dwi Oka Kurniawan ◽  
Ellya Indahyanti ◽  
Irwansyah Putra Pradana

The underlying principle of surface wettability has obtained great attentions for the development of novel functional surfaces. Molecular dynamics simulations has been widely utilized to obtain molecular-level details of surface wettability that is commonly quantified in term of contact angle of a liquid droplet on the surface. In this work, the sensitivity of contact angle calculation at various degrees of surface hydrophilicity to the adopted potential models of water: SPC/E, TIP4P, and TIP5P, is investigated. The simulation cell consists of a water droplet on a structureless surface whose hydrophilicity is modified by introducing a scaling factor to the water-surface interaction parameter. The simulation shows that the differences in contact angle described by the potential models are systematic and become more visible with the increase of the surface hydrophilicity. An alternative method to compute a contact angle based on the height of center-of-mass of the droplet is also evaluated, and the resulting contact angles are generally larger than those determined from the liquid-gas interfacial line.


2015 ◽  
Vol 17 (45) ◽  
pp. 30307-30317 ◽  
Author(s):  
Sathish Kumar Mudedla ◽  
Ettayapuram Ramaprasad Azhagiya Singam ◽  
Kanagasabai Balamurugan ◽  
Venkatesan Subramanian

The complexation of siRNA with positively charged gold nanoclusters has been studied using classical molecular dynamics simulations.


CrystEngComm ◽  
2018 ◽  
Vol 20 (25) ◽  
pp. 3569-3580 ◽  
Author(s):  
Xiaoxiao Sui ◽  
Yongjian Cheng ◽  
Naigen Zhou ◽  
Binbing Tang ◽  
Lang Zhou

Based on the Stillinger–Weber potential, molecular dynamics simulations of the solidification processes of multicrystalline silicon were carried out.


RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  

The formation mechanism of the bound rubber in elastomer nanocomposites using the coarse-grained molecular-dynamics simulations.


2020 ◽  
Vol 22 (3) ◽  
pp. 1154-1167 ◽  
Author(s):  
Khair Bux ◽  
Syed Tarique Moin

Molecular dynamics simulations were applied to an isolated cholesterol immersed in four different solvents of varying polarity, such as water, methanol, dimethyl sulfoxide and benzene, to gain insights into the structural and dynamical properties.


2018 ◽  
Vol 18 (20) ◽  
pp. 1755-1768 ◽  
Author(s):  
Ahmad Abu Turab Naqvi ◽  
Taj Mohammad ◽  
Gulam Mustafa Hasan ◽  
Md. Imtaiyaz Hassan

Protein-ligand interaction is an imperative subject in structure-based drug design and protein function prediction process. Molecular docking is a computational method which predicts the binding of a ligand molecule to the particular receptor. It predicts the binding pose, strength and binding affinity of the molecules using various scoring functions. Molecular docking and molecular dynamics simulations are widely used in combination to predict the binding modes, binding affinities and stability of different protein-ligand systems. With advancements in algorithms and computational power, molecular dynamics simulation is now a fundamental tool to investigative bio-molecular assemblies at atomic level. These methods in association with experimental support have been of great value in modern drug discovery and development. Nowadays, it has become an increasingly significant method in drug discovery process. In this review, we focus on protein-ligand interactions using molecular docking, virtual screening and molecular dynamics simulations. Here, we cover an overview of the available methods for molecular docking and molecular dynamics simulations, and their advancement and applications in the area of modern drug discovery. The available docking software and their advancement including application examples of different approaches for drug discovery are also discussed. We have also introduced the physicochemical foundations of molecular docking and simulations, mainly from the perception of bio-molecular interactions.


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