scholarly journals Interaction between Graphene-Based Materials and Small Ag, Cu, and CuO Clusters: A Molecular Dynamics Study

Nanomaterials ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1378
Author(s):  
Isabel Lado-Touriño ◽  
Alicia Páez-Pavón
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Mean Square Displacement ◽  
Md Simulations ◽  
Great Promise ◽  
Resistant Bacteria ◽  
Pristine Graphene ◽  
Metallic Oxide ◽  
Antibacterial Compounds ◽  
Adsorption Energies

The excessive use of antibiotics has contributed to the rise in antibiotic-resistant bacteria, and thus, new antibacterial compounds must be developed. Composite materials based on graphene and its derivatives doped with metallic and metallic oxide nanoparticles, particularly Ag, Cu, and Cu oxides, hold great promise. These materials are often modified with polyethylene glycol (PEG) to improve their pharmacokinetic behavior and their solubility in biological media. In this work, we performed molecular dynamics (MD) simulations to study the interaction between small Ag, Cu, and CuO clusters and several graphene-based materials. These materials include pristine graphene (PG) and pristine graphene nanoplatelets (PGN) as well as PEGylated graphene oxide (GO_PEG) and PEGylated graphene oxide nanoplatelets (GO-PEG_N). We calculated the adsorption energies, mean equilibrium distances between the nanoparticles and graphene surfaces, and mean square displacement (MSD) of the nanoclusters. The results show that PEGylation favors the adsorption of the clusters on the graphene surfaces, causing an increase in adsorption energies and a decrease in both distances and MSD values. The strengthening of the interaction could be crucial to obtain effective antibacterial compounds.

Effect of an ionic environment on membrane fouling: a molecular dynamics study

2021 ◽  
Author(s):  
Shivam Tiwari ◽  
Abhijit Gogoi ◽  
K. Anki Reddy
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Membrane Fouling ◽  
Md Simulations ◽  
Ionic Environment

The effect of the ionic environment on membrane fouling was investigated for polyamide (PA) and graphene oxide (GO) membranes using equilibrium molecular dynamics (MD) simulations.

scholarly journals A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations

2021 ◽  
Vol 22 (19) ◽  
pp. 10813
Author(s):  
Congcong Li ◽  
Zhongkui Lu ◽  
Min Wang ◽  
Siao Chen ◽  
Lu Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Graphene Oxide ◽  
Md Simulations ◽  
Strong Interactions ◽  
Limiting Factor ◽  
Active Site Residues ◽  
Detailed Mechanism ◽  
Dynamics Simulations ◽  
Thermal Stability Of

Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface.

scholarly journals Thermal Transport in Graphene Oxide Films: Theoretical Analysis and Molecular Dynamics Simulation

Nanomaterials ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 285 ◽  
Author(s):  
Yi Yang ◽  
Dan Zhong ◽  
Yilun Liu ◽  
Donghui Meng ◽  
Lina Wang ◽  
...  
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Molecular Dynamics Simulation ◽  
Thermal Transport ◽  
Oxide Films ◽  
Vacancy Defect ◽  
Transport Processes ◽  
Dynamics Simulation ◽  
Great Promise

As a derivative material of graphene, graphene oxide films hold great promise in thermal management devices. Based on the theory of Fourier formula, we deduce the analytical formula of the thermal conductivity of graphene oxide films. The interlaminar thermal property of graphene oxide films is studied using molecular dynamics simulation. The effect of vacancy defect on the thermal conductance of the interface is considered. The interfacial heat transfer efficiency of graphene oxide films strengthens with the increasing ratio of the vacancy defect. Based on the theoretical model and simulation results, we put forward an optimization model of the graphene oxide film. The optimal structure has the minimum overlap length and the maximum thermal conductivity. An estimated optimal overlap length for the GO (graphene-oxide) films with degree of oxidation 10% and density of vacancy defect 2% is 0.33 μm. Our results can provide effective guidance to the rationally designed defective microstructures on engineering thermal transport processes.

scholarly journals A molecular dynamics study on the diffusion and imprint ability of spectinomycin under different sizes of aniline oligomers

2022 ◽  
Author(s):  
Chanadan Douykhumklaw ◽  
Thana Sutthibutpong
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mean Square Displacement ◽  
Md Simulations ◽  
Template Molecule ◽  
Aniline Oligomers ◽  
The Mean ◽  
The Stability ◽  
Further Development ◽  
Aniline Oligomer

Abstract Molecularly imprinted polymers (MIP) are the polymers created by molecular imprinting techniques that leave cavities for the specific interactions with a template molecule, and have been applied in molecular selectivity tasks. In this study, the molecular dynamics (MD) simulation technique was used to demonstrate that aniline oligomer could be developed as a potential MIP for detection and separation of the spectinomycin drug molecule for gonorrhoea treatment. MD simulations were performed for the systems of a spectinomycin within aniline oligomers of different sizes. The mean square displacement (MSD) and the diffusivity calculated from MD simulations showed that the diffusion coefficient was significantly dropped when the length of aniline oligomer was greater than two. The diffusion coefficient of spectinomycin became the lowest within aniline trimers, corresponded to the highest atomic distribution of MIP around the template. Then, the specific cavity in MIP systems with and without spectinomycin were calculated to assess the stability of the cavity created by the template. The volume of a cavity created within the trimer system was closest to the spectinomycin volume, and therefore became the optimal oligomer size for further development of MIP.

Molecular dynamics simulations reveal how graphene oxide stabilizes and activates lipase in an anhydrous gas

2019 ◽  
Vol 21 (45) ◽  
pp. 25425-25430 ◽  
Author(s):  
Zhongwang Fu ◽  
Weina Xu ◽  
Gong Chen ◽  
Zheyu Wang ◽  
Diannan Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Simulated Annealing ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Candida Antarctica ◽  
Lipase B ◽  
Annealing Procedure ◽  
Dynamics Simulations ◽  
Simulated Annealing Procedure

The interaction between Candida antarctica lipase B (CALB) and graphene oxide (GO) in an anhydrous gas was studied using molecular dynamics (MD) simulations augmented with a simulated annealing procedure to accelerate relaxation towards equilibrium.

scholarly journals Intrinsic high water/ion selectivity of graphene oxide lamellar membranes in concentration gradient-driven diffusion

2016 ◽  
Vol 7 (12) ◽  
pp. 6988-6994 ◽  
Author(s):  
Pengzhan Sun ◽  
Renzhi Ma ◽  
Hui Deng ◽  
Zhigong Song ◽  
Zhen Zhen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Concentration Gradient ◽  
Ion Selectivity ◽  
High Water ◽  
Water Desalination ◽  
Dynamics Simulation ◽  
Great Promise

A combined experimental and molecular dynamics simulation study shows that intrinsic high water/ion selectivity of graphene oxide lamellar membrane was achieved in concentration gradient-driven diffusion, showing great promise in water desalination.

scholarly journals Water/Alcohol Separation in Graphene Oxide Membranes: Insights from Molecular Dynamics and Monte Carlo Simulations

MRS Advances ◽  
2018 ◽  
Vol 3 (1-2) ◽  
pp. 109-114 ◽  
Author(s):  
Daiane Damasceno Borges ◽  
Cristiano F. Woellner ◽  
Pedro A. S. Autreto ◽  
Douglas S. Galvao
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Functional Groups ◽  
Water Molecules ◽  
Pristine Graphene ◽  
Strong Impact ◽  
Water Permeation ◽  
Oxide Membranes ◽  
Graphene Oxide Membranes ◽  
Water Alcohol

ABSTRACTGraphene-based membranes have been investigated as promising candidates for water filtration and gas separation applications. Experimental evidences have shown that graphene oxide can be impermeable to liquids, vapors and gases, while allowing a fast permeation of water molecules. This phenomenon has been attributed to the formation of a network of nano capillaries that allow nearly frictionless water flow while blocking other molecules by steric hindrance effects. It is supposed that water molecules are transported through the percolated two-dimensional channels formed between graphene-based sheets. Although these channels allow fast water permeation in such materials, the flow rates are strongly dependent on how the membranes are fabricated. Also, some fundamental issues regarding the nanoscale mechanisms of water permeation are still not fully understood and their interpretation remains controversial. In this work, we have investigated the dynamics of water permeation through pristine graphene and graphene oxide model membranes that have strong impact on water/alcohol separation. We have carried out fully atomistic classical molecular dynamics simulations of systems composed of multiple layered graphene-based sheets into contact with a pure water reservoir under controlled thermodynamics conditions (e. g., by varying temperature and pressure values). We have systematically analysed how the transport dynamics of the confined nanofluids depend on the interlayer distances and the role of the oxide functional groups. Our results show the water flux is much more effective for graphene than for graphene oxide membranes. These results can be attributed to the H-bonds formation between oxide functional groups and water, which traps the water molecules and precludes ultrafast water transport through the nanochannels.

scholarly journals Effects of Graphene Oxidation on Interaction Energy and Interfacial Thermal Conductivity of Polymer Nanocomposite: A Molecular Dynamics Approach

Nanomaterials ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1709
Author(s):  
Francesco Maria Bellussi ◽  
Carlos Sáenz Ezquerro ◽  
Manuel Laspalas ◽  
Agustín Chiminelli
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Interaction Energy ◽  
Polymer Nanocomposites ◽  
Polymer Nanocomposite ◽  
Nonequilibrium Molecular Dynamics ◽  
Interfacial Thermal Resistance ◽  
Interfacial Region ◽  
Pristine Graphene ◽  
Kapitza Resistance

Interfacial characteristics of polymer nanocomposites represent a crucial aspect to understand their global properties and to evaluate the interaction between nanofillers and matrix. In this work we used a molecular dynamics (MD) approach to characterize the interfacial region at the atomistic scale of graphene-based polymer nanocomposites. Three different polymer matrixes were considered, polylactic acid (PLA), polypropylene (PP) and epoxy resin (EPO), which were reinforced with three types of graphene fillers: pristine graphene (G), graphene oxide (GO) and reduced graphene oxide (rGO). In particular, the compatibility of the nanofillers in polymer matrixes were evaluated in terms of the interaction energy, while the interfacial thermal resistance (Kapitza resistance) between matrices and fillers was calculated with a nonequilibrium molecular dynamics (NEMD) method. Results showed that the oxidation degree plays an important role on the studied properties of the interfacial region. In particular, it was observed that the Kapitza resistance is decreased in the oxidized graphene (GO and rGO), while interaction energy depended on the polarity of the polymer matrix molecules and the contribution of the Coulombic component.

The Influence of Graphene Sheet on the Dynamics of Cholesterol Molecules in the Lodgment Located near a Transmembrane Protein – MD Study

2008 ◽  
Vol 140 ◽  
pp. 141-146
Author(s):  
P. Raczynski ◽  
A. Dawid ◽  
Z. Gburski
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Graphene Sheet ◽  
Transmembrane Protein ◽  
Mean Square Displacement ◽  
Md Simulations ◽  
Mean Square ◽  
Velocity Autocorrelation ◽  
The Mean ◽  
Velocity Autocorrelation Functions

Molecular dynamics (MD) simulations have been made for a cluster of cholesterols localized near the transmembrane protein at the physiological temperature of 310 K. It was observed that the cholesterol molecules form a lodgment on the surface of protein. Additional studies were made of the influence of graphene sheet on several physical observables of cholesterol molecules including: the radial distribution function, the mean square displacement, diffusion coefficient and the linear and angular velocity autocorrelation functions.

scholarly journals Large scale relative protein ligand binding affinities using non-equilibrium alchemy

2020 ◽  
Vol 11 (4) ◽  
pp. 1140-1152 ◽  
Author(s):  
Vytautas Gapsys ◽  
Laura Pérez-Benito ◽  
Matteo Aldeghi ◽  
Daniel Seeliger ◽  
Herman van Vlijmen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Ligand Binding ◽  
Large Scale ◽  
Md Simulations ◽  
Great Promise ◽  
Binding Affinities ◽  
Structure Based Drug Design ◽  
Thermodynamic Cycles ◽  
Binding Affinity Calculations

Relative ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-physical (alchemical) thermodynamic cycles have shown great promise for structure-based drug design.

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