Adsorption and Conformational Evolution of Alpha-Helical BSA Segments on Graphene: A Molecular Dynamics Study

2016 ◽  
Vol 08 (02) ◽  
pp. 1650021 ◽  
Author(s):  
Jingjie Yeo ◽  
Yuan Cheng ◽  
You Ting Han ◽  
Yingyan Zhang ◽  
Guijian Guan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Conformational Dynamics ◽  
Single Layer ◽  
Md Simulations ◽  
Single Layer Graphene ◽  
Strong Interactions ◽  
Helical Structures ◽  
Single Segment ◽  
Helical Content ◽  
The Individual

Molecular dynamics (MD) simulations are performed to investigate the adsorption mechanics and conformational dynamics of single and multiple bovine serum albumin (BSA) peptide segments on single-layer graphene through analysis of parameters such as the root-mean-square displacements, number of hydrogen bonds, helical content, interaction energies, and motions of mass center of the peptides. It is found that for the single segment system, destabilization of the helical structures in the form of the reduction in hydrogen bond numbers and [Formula: see text]-helical content of the peptides occurred due to the strong interactions between BSA peptides and graphene. Similar destabilizations of the individual segments in the multi-segment system can occur as well, albeit with greater complexity and in a lesser degree due to the inter-segment interactions. Alleviation of decreases in the total helical content in the multi-segment system indicates protective capabilities of segment–segment interactions, which weaken their interactions with graphene. Diffusive motion upon adsorption of the segment(s) onto graphene is found to be highly confined, and the distance traversed by each segment in the multi-segment system was more significant than that in the single segment system, similarly attributable to reductions in their interactions with graphene due to inter-segment interactions.

scholarly journals Nanoindentation of Graphene-Reinforced Silica Aerogel: A Molecular Dynamics Study

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1336 ◽  
Author(s):  
Sandeep Patil
Keyword(s):  
Molecular Dynamics ◽  
Silica Aerogel ◽  
Single Layer ◽  
Md Simulations ◽  
Silica Aerogels ◽  
Single Layer Graphene ◽  
Combined System ◽  
Indentation Force ◽  
Indentation Tests ◽  
The Individual

In the present work, we performed nanoindentation tests using molecular dynamics (MD) simulations on graphene, native silica aerogels, and single- and multi-layered graphene-reinforced silica aerogel nanocomposites. This work mainly focused on the two aspects of nanoindentation simulations: first, the resultant indentation force–depth curves, and second, the associated mechanical deformation behavior. We found that in the single-layer graphene-reinforced silica aerogel nanocomposite, the indentation resistance was four-fold that of native silica aerogels. Moreover, the combined system proved to be higher in stiffness compared to the individual material. Furthermore, the indentation resistance was increased significantly as we proceeded from single- to two-layered graphene-reinforced silica aerogel nanocomposites. The results of the study provide a detailed understanding of the mechanical behavior during the indentation tests of nanocomposites, which helps to design advanced nanoscale multi-layered materials.

Wrinkling in Graphene Subjected to Gradient Tension

NANO ◽  
2015 ◽  
Vol 10 (03) ◽  
pp. 1550037 ◽  
Author(s):  
Jianzhang Huang ◽  
Qiang Han
Keyword(s):  
Molecular Dynamics ◽  
Single Layer ◽  
Md Simulations ◽  
Area Ratio ◽  
Single Layer Graphene ◽  
Layer Graphene ◽  
Out Of Plane ◽  
Displacement Direction ◽  
Effects Of Temperature ◽  
Plane Displacement

In the present study, the initiation and evolution mechanisms of wrinkles in a square single layer graphene sheet (SLGS) under gradient tensile displacements are investigated based on molecular dynamics (MD) simulations. The mechanism of wrinkling process is elucidated by studying the atomic out-of-plane displacements development of the key atoms in SLGS. It reveals that the loading and boundary conditions play dominant roles in the wrinkling deformation of graphene. The dependences of the wrinkling amplitude, wavelength, out-of-plane displacement, direction angle and wrinkling area ratio on the applied gradient tensile displacements are obtained. The effects of temperature, size of graphene and loading grads on graphene wrinkling are investigated.

The effect of Nanopores Geometry on Desalination of Single-layer Graphene-based Membranes: A Molecular Dynamics Study

2021 ◽  
pp. 116749
Author(s):  
Amirhossein Bagheri Sarvestani ◽  
Alireza Chogani ◽  
Maryam Shariat ◽  
Ali Moosavi ◽  
Hamid Kariminasab
Keyword(s):  
Molecular Dynamics ◽  
Single Layer ◽  
Single Layer Graphene ◽  
Layer Graphene

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.

Interactions of a DNA G-quadruplex with TMAO and urea: a molecular dynamics study on co-solute compensation mechanisms

2021 ◽  
Author(s):  
Ewa Anna Oprzeska-Zingrebe ◽  
Jens Smiatek
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Compensation Mechanisms ◽  
G Quadruplex ◽  
The Individual

We study the individual and combined influence of TMAO and urea on a basket-type DNA G-quadruplex by means of atomistic molecular dynamics (MD) simulations.

scholarly journals Conservation of the conformational dynamics and ligand binding within M49 enzyme family

RSC Advances ◽  
2018 ◽  
Vol 8 (24) ◽  
pp. 13310-13322 ◽  
Author(s):  
Saša Kazazić ◽  
Zrinka Karačić ◽  
Igor Sabljić ◽  
Dejan Agić ◽  
Marko Tomin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Dynamics ◽  
Ligand Binding ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Dipeptidyl Peptidase ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Enzyme Family ◽  
Hydrogen Deuterium

The hydrogen deuterium exchange (HDX) mass spectrometry combined with molecular dynamics (MD) simulations was employed to investigate conformational dynamics and ligand binding within the M49 family (dipeptidyl peptidase III family).

scholarly journals A Molecular Dynamics Study on Wrinkles in Graphene with Simply Supported Boundary under In-Plane Shear

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Jianzhang Huang ◽  
Qiang Han
Keyword(s):  
Molecular Dynamics ◽  
Single Layer ◽  
Single Layer Graphene ◽  
Propagation Process ◽  
Plane Shear ◽  
Simply Supported ◽  
Layer Graphene ◽  
Out Of Plane ◽  
Formation And Evolution ◽  
Dynamics Simulations

The formation and evolution mechanisms of wrinkling in a rectangular single layer graphene sheet (SLGS) with simply supported boundary subjected to in-plane shear displacements are investigated using molecular dynamics simulations. Through investigating the out-of-plane displacements of the key point atom, we clarify the wrinkling growth and propagation process. Our results show that the boundary condition plays important roles in the wrinkling deformation. And the dependence of wrinkling parameters on the applied shear displacements is captured. Based on the elasticity theory, the formation mechanism of graphene wrinkling is revealed from the viewpoint of elastic energy. The effects of aspect ratio of graphene, temperature, and loading velocity on graphene wrinkling parameters and patterns are also investigated.

Synthesis of Polyacetylene-like Modified Graphene Oxide Aerogel and Its Enhanced Electrical Properties

2019 ◽  
Author(s):  
Enrico Greco ◽  
Jing Shang ◽  
jiali zhu ◽  
Tong Zhu
Keyword(s):  
Graphene Oxide ◽  
Three Dimensional ◽  
Single Layer ◽  
Internal Surface ◽  
Solid Material ◽  
Single Layer Graphene ◽  
Covalent Bonds ◽  
Surface Areas ◽  
Modified Graphene Oxide ◽  
The Individual

<p>A graphene-based or carbon-based aerogel is a three-dimensional (3D) solid material in which the carbon atoms are arranged in a sheet-like nanostructure. In this study, we report the synthesis of low-density polymer-modified aerogel monoliths by 3D macro-assemblies of graphene oxide sheets that exhibit significant internal surface areas (982 m<sup>2</sup>/g) and high electrical conductivity (∼0.1 to 1 × 10<sup>2</sup> S/cm). Different types of materials were prepared to obtain a single monolithic solid starting from a suspension of single-layer graphene oxide (GO) sheets, and a polymer, made from the precursors 4-carboxybenzaldehyde and polyvinyl alcohol. These materials were used to cross-link the individual sheets by covalent bonds, resulting in wet-gels that were supercritically dried and then, in some cases, thermally reduced to yield graphene aerogel composites. The average densities were approaching 15-20 mg/cm<sup>3</sup>. This approach allowed for the modulation of distance between the sheets, pore dimension, surface area, and related properties. This specific GO/Polymer ratio has suitable malleability making it a viable candidate for use in conductivity 3D printing; it also has other properties suitable for energy storage, catalysis, sensing and biosensing applications, bioelectronics, and superconductors.</p>

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