Molecular Dynamics Simulations of Oil-Water Wetting Models of Organic Matter and Minerals in Shale at the Nanometer Scale

2021 ◽  
Vol 21 (1) ◽  
pp. 85-97
Author(s):  
Zhentao Dong ◽  
Haitao Xue ◽  
Bohong Li ◽  
Shansi Tian ◽  
Shuangfang Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Organic Matter ◽  
Crude Oil ◽  
Molecular Dynamics Simulations ◽  
Smooth Surface ◽  
Dynamics Simulation ◽  
Shale Oil ◽  
Water Wetting ◽  
Dynamics Simulations

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.

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

2021 ◽  
Author(s):  
Sumith Yesudasan
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Molecular Dynamics Simulations ◽  
Water Droplet ◽  
Dynamics Simulation ◽  
Hydrophilic Surfaces ◽  
Interfacial Physics ◽  
Droplet Liquid ◽  
Dynamics Simulations ◽  
Molecular Dynamics Results

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.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

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

scholarly journals Molecular Dynamics Simulation of Wetting Behavior: Contact Angle Dependency on Water Potential Models

2021 ◽  
Vol 1 (1) ◽  
pp. 10
Author(s):  
Lukman Hakim ◽  
Irsandi Dwi Oka Kurniawan ◽  
Ellya Indahyanti ◽  
Irwansyah Putra Pradana
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Liquid Droplet ◽  
Center Of Mass ◽  
Contact Angles ◽  
Surface Wettability ◽  
Dynamics Simulation ◽  
Potential Models ◽  
Surface Hydrophilicity ◽  
Dynamics Simulations

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.

Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study

2015 ◽  
Vol 17 (45) ◽  
pp. 30307-30317 ◽  
Author(s):  
Sathish Kumar Mudedla ◽  
Ettayapuram Ramaprasad Azhagiya Singam ◽  
Kanagasabai Balamurugan ◽  
Venkatesan Subramanian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Simulation Study ◽  
Gold Nanoclusters ◽  
Dynamics Simulation ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
Positively Charged

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

Molecular dynamics simulation of the solidification process of multicrystalline silicon from homogeneous nucleation to grain coarsening

CrystEngComm ◽  
2018 ◽  
Vol 20 (25) ◽  
pp. 3569-3580 ◽  
Author(s):  
Xiaoxiao Sui ◽  
Yongjian Cheng ◽  
Naigen Zhou ◽  
Binbing Tang ◽  
Lang Zhou
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Homogeneous Nucleation ◽  
Solidification Process ◽  
Dynamics Simulation ◽  
Multicrystalline Silicon ◽  
Solidification Processes ◽  
Dynamics Simulations ◽  
Weber Potential

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

scholarly journals Formation mechanism of bound rubber in elastomer nanocomposites: a molecular dynamics simulation study

RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Bound Rubber ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

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

Solvation of cholesterol in different solvents: a molecular dynamics simulation study

2020 ◽  
Vol 22 (3) ◽  
pp. 1154-1167 ◽  
Author(s):  
Khair Bux ◽  
Syed Tarique Moin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dimethyl Sulfoxide ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Dynamical Properties ◽  
Dynamics Simulations

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.

Advancements in Docking and Molecular Dynamics Simulations Towards Ligand-receptor Interactions and Structure-function Relationships

2018 ◽  
Vol 18 (20) ◽  
pp. 1755-1768 ◽  
Author(s):  
Ahmad Abu Turab Naqvi ◽  
Taj Mohammad ◽  
Gulam Mustafa Hasan ◽  
Md. Imtaiyaz Hassan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Drug Discovery ◽  
Molecular Dynamics Simulations ◽  
Computational Method ◽  
Dynamics Simulation ◽  
Ligand Molecule ◽  
Ligand Interaction ◽  
Modern Drug ◽  
Dynamics Simulations

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.

Estimation of the Chemical Potential and the Activity of NaCl in Molten DyCl3-NaCl by Molecular Dynamics Simulation

1998 ◽  
Vol 53 (8) ◽  
pp. 655-658
Author(s):  
Masanori Sakurai ◽  
Ryuzo Takagi ◽  
Ashok K. Adyaa ◽  
Marcelle Gaune-Escard
Keyword(s):  
Molecular Dynamics ◽  
Phase Diagram ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Chemical Potential ◽  
Dynamics Simulation ◽  
Dynamics Simulations ◽  
Positional Data ◽  
Liquidus Temperatures

Abstract Molecular dynamics simulations of molten DyCl3-NaCl were carried out at liquidus temperatures of the phase diagram. The chemical potential and the activity of NaCl was successfully estimated with the method proposed by Powles et al., which requires only positional data of the ions at the temperatures in question.

‘Piperazining’ the catalytic gatekeepers: unraveling the pan-inhibition of SRC kinases; LYN, FYN and BLK by masitinib

2019 ◽  
Vol 11 (18) ◽  
pp. 2365-2380
Author(s):  
Aimen K Aljoundi ◽  
Clement Agoni ◽  
Fisayo A Olotu ◽  
Mahmoud ES Soliman
Keyword(s):  
Molecular Dynamics ◽  
B Cell ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanisms ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Dynamics Simulation ◽  
Large B Cell Lymphoma ◽  
Dynamics Simulations ◽  
Large B Cell

Aim: Blocking oncogenic signaling of B-cell receptor (BCR) has been explored as a viable strategy in the treatment of diffuse large B-cell lymphoma. Masitinib is shown to multitarget LYN, FYN and BLK kinases that propagate BCR signals to downstream effectors. However, the molecular mechanisms of its selectivity and pan-inhibition remain elusive. Materials & methods: This study therefore employed molecular dynamics simulations coupled with advanced post-molecular dynamics simulation techniques to unravel the structural mechanisms that inform the reported multitargeting ability of masitinib. Results: Molecular dynamics simulations revealed initial selective targeting of catalytic residues (Asp334/Glu335 – LYN; Asp130/Asp148/Glu54 – FYN; Asp89 – BLK) by masitinib, with high-affinity interactions via its piperazine ring at the entrance of the ATP-binding pockets, before systematic access into the hydrophobic deep pocket grooves. Conclusion: Identification of these ‘gatekeeper’ residues could open up a novel paradigm of structure-based design of highly selective pan-inhibitors of BCR signaling in the treatment of diffuse large B-cell lymphoma.

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