Multiscale modeling of unfolding and bond dissociation of rubredoxin metalloprotein.

Mechanical properties of proteins that have a crucial effect on their operation. This study used a molecular dynamics simulation package to investigate rubredoxin unfolding on the atomic scale. Different simulation techniques were applied, and due to the dissociation of covalent/hydrogen bonds, this protein demonstrates several intermediate states in force-extension behavior. A conceptual model based on the cohesive finite element method was developed to consider the intermediate damages that occur during unfolding. This model is based on force-displacement curves derived from molecular dynamics results. The proposed conceptual model is designed to accurately identify bond rupture points and determine the associated forces. This is achieved by conducting a thorough comparison between molecular dynamics and cohesive finite element results. The utilization of a viscoelastic cohesive zone model allows for the consideration of loading rate effects. This rate-dependent model can be further developed and integrated into the multiscale modeling of large assemblies of metalloproteins, providing a comprehensive understanding of mechanical behavior while maintaining a reduced computational cost.

Fullerenes containing water molecules: a study of reactive molecular dynamics simulations.

A different technique was used to investigate fullerenes encapsulating a polar guest species. By reactive molecular dynamics simulations, three types of fullerenes were investigated on a gold surface: an empty C60, a single H2O molecule inside C60 (H2O@C60), and two water molecules inside C60 ((H2O)2@C60). Our findings revealed that despite the free movement of all fullerenes on gold surfaces, confined H2O molecules within the fullerenes result in a distinct pattern of motion in these systems. The (H2O)2@C60 complex had the highest displacement and average velocity, while C60 had the lowest displacement and average velocity. The symmetry of molecules and the polarity of water seem to be crucial in these cases. ReaxFF simulations showed that water molecules in an H2O molecule, H2O@C60, and (H2O)2@C60 have dipole moments of 1.76, 0.42, and 0.47 D, respectively. A combination of the non-polar C60 and polar water demonstrated a significant reduction in the dipole moment of H2O molecules due to encapsulation. The dipole moments of water molecules agreed with those in other studies, which can be useful in the development of biocompatible and high-efficiency nanocars.

Introducing Structures from Hexagonal Borophene to Nitrophene and Their Thermal Conductivity Investigation Using a Reactive Molecular Dynamics Simulation.

In the present work, the thermal conductivity (TC) of hexagonal structures of boron nitride and borophene was investigated by a reactive molecular dynamics (MD) simulation. Also, to figure out the effect of the boron and nitrogen in the hexagonal structure, five other hypothetical structures were created (in addition to the structure of boron nitride and borophene) and their structures were represented by the symbol BxNy, where x refers to the number of boron atoms and y refers to the number of nitrogen atoms. In this regard, B6N0 refers to borophene, B3N3 is boron nitride, and B0N6 is called nitrophene. The TC of B6N0 and B3N3 structures was calculated and compared with the literature values. Besides these two compounds, the five other structures have not been experimentally synthesized yet, so the TC of the five other hypothetical structures were predicted in the present work. The lowest TC belonged to B3N3, and the highest one was for B0N6. Based on the inherent potential of reactive MD simulation, during TC calculation, atoms' coordination and partial charges are changed and new bonds, rings, or even defects were automatically created on the surfaces. The coordination contour map showed that in B3N3, the atoms have collective movements like a large and single wave, while B0N6 and B6N0 have small group movements as vibrations. So, it became clear that the higher stability of structures caused more curved movements. In addition, the contour map of partial charges is calculated, and the results showed that the high differences in partial charge between atoms in the structure cause high TC, while small charge differences in the structure inhibit heat transfer and cause lower TC.

Effects of functionalization and silane modification of hexagonal boron nitride on thermal/mechanical/morphological properties of silicon rubber nanocomposite.

Hexagonal boron nitride (h-BN) nanoparticles could induce interesting properties to silicone rubber (SR) but, the weak filler-matrix interfacial interaction causes agglomeration of the nanoparticles and declines the performance of the nanocomposite. In this work, h-BN nanoparticles were surface modified using vinyltrimethoxysilane (VTMS) at different concentrations. Before silane modification, h-BN nanoparticles were hydroxylated using 5 molar sodium hydroxide. The nanoparticles were characterized to assess success of silane grafting. The pure and modified h-BN nanoparticles were applied at 1, 3 and 5 wt% to HTV silicon rubber (SR). The curing, thermal, mechanical and morphological properties and hydrophobicity of the nanocomposites were evaluated. The morphology of the SR nanocomposites was characterized using AFM and FE-SEM analysis. It was found that silane grafting on the h-BN nanoparticles improves crosslink density but declines curing rate index (CRI) of the SR nanocomposite (at 5 wt% loading content) by 0.7 (dN m) and 3.5%, respectively. It also increased water contact angle of the nanocomposites from 97.5° to 107°. The improved nanoparticle-rubber interfacial interactions caused better dispersion of h-BN nanoparticles in SR matrix (at 5 wt%) that enhanced the elongation at break, modulus at 300% and Tg of the SR nanocomposites.

Wettability of Tetrahexcarbon: MD, DFT, and AIMD Approaches.

Graphene and its allotropes have attracted attention due to their special electronic, mechanical, and thermal properties. Numerous studies investigate their wetting behavior. Tetrahexcarbon (THC) is a new carbon allotrope and is obtained from pentagraphene. This research, examines THC's wettability properties using reactive molecular dynamics (MD) and density functional theory (DFT) simulations. The results of molecular dynamics simulation reveal that THC is a hydrophobic substrate with a contact angle of 113.4° ± 2.8°. Using molecular dynamics, this research also evaluates quantities such as contact diameter, dipole moment, and density profile of water droplet. In addition, hydrogen and oxygen atoms' distribution functions, hydrogen bonds, path of the droplet's center of mass, and potential energy surface are presented. According to the simulation results, the droplet's structure on THC is slightly layered. Also, the water molecules' orientations in the interface are such that they do not allow the hydrogen bonds to form between water molecules and the THC substrate. The results of MD show that there are two different behavioral patterns for the hydrogen bonds between and within the water droplet's layers. Furthermore, this research utilizes DFT and AIMD in order to show how a water molecule interacts with THC. DFT exhibits that the water molecule's hydrogen atoms are toward the substrate. But an opposite configuration happens in the droplet-THC interface. The results of the atoms-in-molecules (AIM) theory indicate that there is a weak interaction between the water molecules and the THC substrate. The thermochemical results reveal that water molecules' adsorption is within the range of physical adsorption. Finally, NBO analysis shows that the THC's carbon atoms have a permanent partial charge. These results confirm that the THC is a hydrophobic material.

Controlled hydrophilization of black phosphorene: a reactive molecular dynamics simulation approach.

Following the exceptional electrical and optical properties of black phosphorene, its wetting behavior has attracted the attention of many researchers. In the present study, reactive molecular dynamics (MD) simulations have been used to investigate the controlled wetting behavior of black phosphorene surface. In the first step, the hydrophobic behavior of the pristine black phosphorene as well as the elliptical shape of the water droplet on this surface was investigated using MD simulations which are in agreement with the recently reported experimental data. In the next step, controlled hydrophilization of black phosphorene was performed through oxidation of the pristine black phosphorene in different sizes. The simulation results showed that oxidation of the black phosphorene surface turns it into a superhydrophilic surface by increasing the number of hydrogen bonds. It was observed that, by placing water droplets on the phosphorene oxide surfaces a wide range of wettability phenomena can be created so that a wide range of contact angles can be measured. The results indicated that the placement position of water molecules on the phosphorene oxide surface leads to two different wetting patterns. Also, in agreement with the results of the energy profile of the phosphorene surface, calculations of Helmholtz free energy showed that the energy barrier in the armchair direction of the phosphorene surface is higher than that in the zigzag direction. The results could lead to new applications of phosphorene to control wettability at the nanoscale.

Decisive structural elements in water and ion permeation through mechanosensitive channels of large conductance: insights from molecular dynamics simulation.

In this paper, a series of equilibrium molecular dynamics simulations (EMD), steered molecular dynamics (SMD), and computational electrophysiology methods are carried out to explore water and ion permeation through mechanosensitive channels of large conductance (MscL). This research aims to identify the pore-lining side chains of the channel in different conformations of MscL homologs by analyzing the pore size. The distribution of permeating water dipole angles through the pore domains enclosed by VAL21 and GLU104 demonstrated that water molecules are oriented toward the charged oxygen headgroups of GLU104 from their hydrogen atoms to retain this interaction in a stabilized fashion. Although, this behavior was not perceived for VAL21. Numerical assessments of the secondary structure clarified that, during the ion permeation, in addition to the secondary structure alterations, the structure of Tb-MscL would also undergo significant conformational changes. It was elucidated that VAL21, GLU104, and water molecules accomplish a fundamental task in ion permeation. The mentioned residues hinder ion permeation so that the pulling SMD force is increased remarkably when the ions permeate through the domains enclosed by VAL21 and GLU102. The hydration level and potassium diffusivity in the hydrophobic gate of the transmembrane domain were promoted by applying the external electric field. Furthermore, the implementation of an external electric field altered the distribution pattern for potassium ions in the system while intensifying the accumulation of Cl- in the vicinity of ARG11 and ARG98.

Unraveling Flow Separation at the Water-Carbon Nanotube Interface: An Atomic-Scale Overview by Molecular Dynamics Simulation.

Flow separation near the fluid-solid surface has attracted attention for decades. It is critical to understand the behavior of separated flow adjacent to the solid walls to broaden its range of potential applications. Therefore, we conducted molecular dynamics investigations to consider water flow separation at the water-carbon nanotube (CNT) interface for different diameters of CNTs between 13 and 50 Å and different pressures of 0.1-1.254 GPa. Density heat maps indicated that water flow separation is observed for all CNTs under high pressures, and an empty space of water molecules or evacuation is formed behind the CNTs. It is shown that in CNTs with small diameters, (10, 10) and (20, 20), the structure of the first layer (FL) of water molecules or hydrated layer adjacent to the CNT wall is completely preserved, indicating that evacuation occurs from behind the CNTs. In (30, 30) and (40, 40) CNTs, flow separation occurred from the FL of water molecules near the solid surface, and the layered structure of water around CNTs is completely destroyed. Our findings of fluid-solid and fluid-fluid interaction energies suggested that the flow separation can be due to an attraction between the FL of water molecules and CNT and a repulsion between the water molecules in the hydrated layer and the outer layers. Moreover, analyzing the relationship between the CNT size and flow separation revealed that in the case of small CNTs, there are extra water molecules that contribute to the structural stability of the hydrated layer by strengthening the repulsive interaction in the liquid-liquid surface.

High-Performance Biomimetic Water Channel: The Constructive Interplay of Interaction Parameters and Hydrophilic Doping Levels.

In this study, we introduce a superfast biomimetic water channel mimicking the hydrophobicity scales of the Aquaporin (AQP) pore lining. Molecular dynamics simulation is used to scrutinize the impact of hydrophilic doping level in the nanotube and the water-wall interaction strength on water permeability. In the designed biomimetic channel, the constructive interplay of Lennard-Jones (LJ) ε parameters and hydrophilic doping levels increased the possibility of ultrafast water transport. Moreover, a unique set of LJ parameters is discovered for each biomimetic channel with different hydrophilic doping levels, enhancing water permeation. Inside high-performance biomimetic channels, water distribution surprisingly implies a varying pore geometry that narrows down in the middle, mimicking the pattern obtained from GplF pore analysis, evoking the narrow pore induced by the aromatic/arginine selectivity filter. This exciting accordance occurred as a result of tailoring specific hydrophilic arrays within the hydrophobic channel backbone by mimicking the AQP pore interior. The main takeaway of hydrophilic doping arrays implanted within the hydrophobic nanotube is to break the large barrier in the water-wall vdW energy profile into multiple reduced ones to increase water conduction. Consequently, the "water jumping" phenomenon in the middle of the biomimetic channel occurs under specific circumstances. The biomimetic channel with the highest value of water permeability of about 13.67 ± 0.66 × 10-13 cm3·s-1 exhibits the best mechanism for artificial water channels (AWCs), serving superfast water transport considering the low entrance barrier and weak water-wall interaction.

A V(iii)-induced metallogel with solvent stimuli-responsive properties: structural proof-of-concept with MD simulations.

A new solvent stimuli-responsive metallogel (VGel) was synthesized through the introduction of vanadium ions into an adenine (Ade) and 1,3,5-benzene tricarboxylic acid (BTC) organogel, and its supramolecular self-assembly was investigated from a computational viewpoint. A relationship between the synthesized VGel integrity and the self-assembly of its components is demonstrated by a broad range of molecular dynamics (MD) simulations, an aspect that has not yet been explored for such a complex metallogel in particular. MD simulations and Voronoi tessellation assessments, both in agreement with experimental data, confirm the gel formation. Based on excellent water stability and the ethanol/methanol stimuli-responsive feature of the VGel an easy-to-use visualization assay for the detection of counterfeit liquor with a 6% (v/v) methanol limit of detection in 40% (v/v) ethanol is reported. These observations provide a cheap and technically simple method and are a step towards the immersible screening of similar molecules in methanol-spiked beverages.

Enhanced wettability of long narrow carbon nanotubes in a double-walled hetero-structure: unraveling the effects of a boron nitride nanotube as the exterior.

Studying the structure and dynamics of nano-confined water inside carbon nanotubes has consistently attracted the wide-spread interest of researchers. In the present work, molecular dynamics simulations indicated internal nonwetting behavior for the central region of the long and narrow single-wall carbon nanotube (5,5) (SWNT) and showed that continuous single-file water molecules are not formed through it. Unlike the SWNT, by adding boron nitride nanotubes (6,6) as an outer wall to the SWNT, a continuously long single-file water chain is formed through the double-walled carbon and boron nitride hetero-nanotube (DWHNT) and thorough internal wetting of the DWHNT is observed. The position and the number of water molecules, electrostatic potential heatmap of the nanotube's wall, free energy profile of nano-confined water, and number of hydrogen bonds between them confirmed the aforementioned results and complete internal wetting of the DWHNT. After using the boron nitride nanotube (6,6) as the outer wall, an homogeneous electrostatic potential distribution in the DWHNT and increase in the hydrophilic characteristics of the nano-channel wall are observed, bringing about gradual trapping of more water molecules through it. Finally, water molecules occupied the central region of the DWHNT and a thorough single-file water chain is formed inside the nano-channel. Water dipole orientation inside the DWHNT and their radial distribution function asserted the occurrence of the liquid-solid quasi-phase transition of single-file water molecules confined inside the long and narrow carbon nanotube (5,5) under ambient conditions.

Insights into interphase thickness characterization for graphene/epoxy nanocomposites: a molecular dynamics simulation.

This work presents a molecular dynamics simulation study on the interfacial characterization of graphene/epoxy nanocomposites. In polymeric nanocomposites, the thermo-mechanical properties of a system strongly depend on the characteristics of the interphase region between the matrix and the inclusions. The first step in the characterization of this interphase is to distinguish its border limit (i.e., the interphase thickness). Here, we present a methodology to systematically quantify the interphase thickness based on analyzing the variation of the local mass density profile. To this end, three functions (average accumulated mass density, accumulated standard deviation (ASD) and its first derivative) are successively applied on the local mass density profile. Using this procedure, the interphase limit can be easily detected regardless of the oscillatory nature of the local mass density. The effect of the epoxy crosslinking density and number of graphene layers on the interphase thickness is then investigated, and the results are analyzed by studying the interaction energies, polymer dynamics and distribution quality of reacted and unreacted components, as well as conformational changes of the polymer chains in the interphase region. The results reveal that the crosslinking density is the most influential parameter on the interphase thickness: the higher the crosslinking degree, the thicker the interphase region. To a lower extent, the interaction energy has also an effect on the interphase thickness since there is an inverse relationship between the interaction energy and the crosslinking density in our case study. Overall, the reported findings highlight useful insights into the detection and properties of the interphase region in thermoset composites.

Evaporation of Water on Suspended Graphene: Suppressing the Effect of Physically Heterogeneous Surfaces.

Evaporation of water nanodroplets on a hydrophilically adjusted graphene sheet was studied based on a molecular dynamics approach. Suspended graphene was used as a physically heterogeneous surface, and fixed graphene was considered as an ideally flat surface. State of the triple-phase contact line (TPCL) and shape evolution were addressed at four different temperatures on both substrates. Additionally, contact angle (CA) was studied during 3 and 22.5 ns simulations in both closed and opened conditions. The observed constant contact angle regime was predictable for the fixed graphene. However, it was not expected for the suspended system and was attributed to the oscillations of the substrate atoms. The size of the nanodroplet also affects the constant-contact-angle mode in both systems, when the number of water molecules decreases to less than 500. The oscillations created a surface on which physical heterogeneities were varying through time. Examination of the evaporation and condensation processes revealed higher rates for the fixed systems. Local mass fluxes were calculated to reveal the contribution of TPCL and meridian surface (MS) of the nanodroplet to evaporation and condensation. The obtained results indicate similar values for the mass flux ratio at the TPCL, which remains twice as large as the MS for both suspended and fixed graphene. The results confirm the assumption that a surface with varying heterogeneities can overwhelm the droplet and act as an ideally flat surface.

Formation and stability of water clusters at the molybdenum disulfide interface: a molecular dynamics simulation investigation.

In this work structural properties and dynamic behavior of a water nano droplet on the molybdenum disulfide were considered. The simulation results show that water molecules form polygon clusters on the interface, and most of which are hexagonal. Structures of water clusters at the interface are seen in two forms of curved and flattened polygons, which result in the formation of hydrogen bonds between and in the adjacent layers, respectively. Most of the clusters have circular flattened structures. Calculations of the lifetime of hydrogen bonds of water molecules at the interface also show that hydrogen bonds between water molecules at the interface have a low stability. This leads to the permanent formation and breaking down of hydrogen bonds of water molecules which can cause movement of water molecules and, consequently, the displacement of the center of mass and droplet motion. Considering the changes in the center of mass of a water droplet at the MoS2 interface display, the water droplet has a significant spontaneous motion.

Determinative factors in inhibition of aquaporin by different pharmaceuticals: Atomic scale overview by molecular dynamics simulation.

The inhibition of water permeation through aquaporins by ligands of pharmaceutical compounds is considered as a method to control the cell lifetime. The inhibition of aquaporin 1 (AQP1) by bacopaside-I and torsemide, was explored and its atomistic nature was elucidated by molecular docking and molecular dynamics (MD) simulation collectively along with Poisson-Boltzmann surface area (PBSA) method. Docking results revealed that torsemide has a lower level of docking energy in comparison with bacopaside-I at the cytoplasmic side. Furthermore, the effect of steric constraints on water permeation was accentuated. Bacopaside-I inhibits the channel properly due to the strong interaction with the channel and larger spatial volume, whereas torsemide blocks the cytoplasmic side of the channel imperfectly. The most probable active sites of AQP1 for the formation of hydrogen bonds between the inhibitor and the channel were identified by numerical analysis of the bonds. Eventually, free energy assessments indicate that binding of both inhibitors is favorable in complex with AQP1, and van der Waals interaction has an important contribution in stabilizing the complexes.

Molecular investigation of the wettability of rough surfaces using molecular dynamics simulation.

In the present study, a computational investigation on the effect of surface roughness on the wettability behavior of water nanodroplets has been performed via molecular dynamics simulation. To fabricate the roughness, several grooves with different depths and widths were considered on the top layer(s) of graphite. Free energy analysis indicates that surface roughness reduces the solid-liquid adhesion and the work done for the removal of the nanodroplet from the solid surface. This reduction increases with an increase in both the depth and width of the grooves. Furthermore, the adhesion in Wenzel state is greater than that in the Cassie-Baxter state. Results show that increasing the depth and decreasing the width of the grooves decrease the wettability and the nanodroplet locates in the Cassie-Baxter state. In addition, both the Cassie-Baxter and Wenzel models effectively predict the nanodroplet contact angle on the rough surfaces. Furthermore, the probability of successful interactions decreases in the solid-liquid interfaces due to the heterogeneity of the surface. Therefore, the density, the residence time and the hydrogen bond lifetime of the water molecules in the layer in the vicinity of the substrate decrease. In addition, surface roughness affects the orientation of the water molecules at the interface, the diffusion of water molecules as well as the movement of the water nanodroplet.

Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more accessible for use in microarrays to detect target single strands.

A review of the structure and dynamics of nanoconfined water and ionic liquids via molecular dynamics simulation.

During the past decade, the research on fluids in nanoconfined geometries has received considerable attention as a consequence of their wide applications in different fields. Several nanoconfined systems such as water and ionic liquids, together with an equally impressive array of nanoconfining media such as carbon nanotube, graphene and graphene oxide have received increasingly growing interest in the past years. Water is the first system that has been reviewed in this article, due to its important role in transport phenomena in environmental sciences. Water is often considered as a highly nanoconfined system, due to its reduction to a few layers of water molecules between the extended surface of large macromolecules. The second system discussed here is ionic liquids, which have been widely studied in the modern green chemistry movement. Considering the great importance of ionic liquids in industry, and also their oil/water counterpart, nanoconfined ionic liquid system has become an important area of research with many fascinating applications. Furthermore, the method of molecular dynamics simulation is one of the major tools in the theoretical study of water and ionic liquids in nanoconfinement, which increasingly has been joined with experimental procedures. In this way, the choice of water and ionic liquids in nanoconfinement is justified by applying molecular dynamics simulation approaches in this review article.

Structural and dynamical characterization of water on the Au (100) and graphene surfaces: A molecular dynamics simulation approach.

The positioning, adsorption, and movement of water on substrates is dependent upon the chemical nature and arrangement of the atoms of the surface. Therefore the behavior of water molecules on a substrate is a reflection of properties of the surface. Based on this premise, graphene and gold substrates were chosen to study this subject from a molecular perspective. In this work, the structural and dynamical behaviors of a water nanodroplet on Au (100) and the graphene interfaces have been studied by molecular dynamics simulation. The results have shown how the structural and dynamical behaviors of water molecules at the interface reflect the characteristics of these surfaces. The results have demonstrated that residence time and hydrogen bonds' lifetime at the water-Au (100) interface are bigger than at the water-graphene interface. Energy contour map analysis indicates a more uniform surface energy on graphene than on the gold surface. The obtained results illustrate that water clusters on gold and graphene form tetramer and hexamer structures, respectively. Furthermore, the water molecules are more ordered on the gold surface than on graphene. The study of hydrogen bonds showed that the order, stability, and the number of hydrogen bonds is higher on the gold surface. The positioning pattern of water molecules is also similar to the arrangement of gold atoms while no regularity was observed on graphene. The study of dynamical behavior of water molecules revealed that the movement of water on gold is much less than on graphene which is in agreement with the strong water-gold interaction in comparison to the water-graphene interaction.

Graphene confinement effects on melting/freezing point and structure and dynamics behavior of water.

In this work, the melting/freezing point of confined water between two graphene sheets was calculated from the direct coexistence of the solid-liquid interface. Also, molecular dynamics simulation of confined liquid water-ice between two graphene sheets was applied. The phase transition temperature of the confined ice-water mixture was calculated as 240K that was 29K less than the non-confined ice-water system. In order to study the behavior of water molecules at different distances from the graphene sheets, 5 regions were provided using some imaginary planes, located between two graphene sheets. The obtained simulation results showed that water molecules located in the region near each graphene sheet with the thickness of 2nm had a different behavior from other water molecules located in other regions. The results demonstrated that water molecules in the vicinity of graphene sheets had more mean square displacements than those in the middle regions.