The Role of Graphene Monolayers in Enhancing the Yield of Bacteriorhodopsin Photostates for Optical Memory Applications

Bacteriorhodopsin (bR) is a photoactive protein that has gained increasing importance as a tool for optical memory storage due to its remarkable photochemical and thermal stability. The two stable photostates (bR and Q) obtained during the bR photocycle are appropriate to designate the binary bit 0 and 1, respectively. Such devices, however, have limited success due to a low quantum yield of the Q state. Many studies have used genetic and chemical modification as optimization strategies to increase the yield of the Q state. Nonetheless, this compromises the overall photochemical stability of bR. This paper introduces a unique way of stabilizing the conformations of bacteriorhodopsin and, thereby, the bR and Q photostates through adsorption onto graphene. All-atom molecular dynamics (MD) simulations with NAMD and CHARMM force fields have been used here to understand the interactive events at the interface of the retinal chromophore within bR and a single-layer graphene sheet. Based on the stable RMSD (~4.5 Å), secondary structure, interactive van der Waals energies (~3000 kcal/mol) and electrostatic energies (~2000 kcal/mol), it is found that the adsorption of bR onto graphene can stabilize its photochemical behavior. Furthermore, the optimal adsorption distance for bR is found to be ~4.25 Å from the surface of graphene, which is regulated by a number of interfacial water molecules and their hydrogen bonds. The conformations of the key amino acids around the retinal chromophore that are responsible for the proton transport are also found to be dependent on the adsorption of bR onto graphene. The quantity and lifetime of the salt bridges also indicate that more salt bridges were formed in the absence of graphene, whereas more were broken in the presence of it due to conformational changes. Finally, the analysis on the retinal dihedrals (C11 = C12-C13 = C14, C12-C13 = C14-C15, C13 = C14-C15 = NZ and C14-C15 = NZ-CE) show that bacteriorhodopsin in the presence of graphene exhibits increased stability and larger dihedral energy values.

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Polymeric Thin Films for Electro-Optic Modulator and High Density Optical Memory Applications

MRS Proceedings ◽

10.1557/proc-392-43 ◽

1995 ◽

Vol 392 ◽

Author(s):

Larry R. Dalton ◽

Aaron W. Harper ◽

Zhiyong Liang ◽

Jingsong Zhu ◽

Uzi Efron ◽

...

Keyword(s):

Conformational Changes ◽

Optical Waveguides ◽

Optical Memory ◽

High Density ◽

Hole Burning ◽

Spectral Hole Burning ◽

Polymeric Thin Films ◽

Buried Channel ◽

Electro Optic ◽

Memory Applications

AbstractChromophores capable of undergoing conformational changes when exposed to ultraviolet or visible light have been synthesized with functional groups permitting attachment to polymer matrices. One class of such chromophores, containing reactive functionalities at both ends of the chromophore, are referred to as double-end crosslinkable (DEC) chromophores. These chromophores are used in the synthesis of hardened nonlinear optically active lattices and in the fabrication of buried channel nonlinear optical waveguides by photoprocessing; development of such waveguides represents a critical step in the production of polymeric electro-optic modulators. Such chromophores are also crucial to the phenomena of laser-assisted poling (also known as photochemically-induced poling). Finally, these chromophores are attached to the surface of polystyrene beads permitting the realization of room temperature spectral hole burning exploiting morphology-dependent resonances. Such resonances provide the basis of wavelength coding for the development of high density optical memories.

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Wrinkling in Graphene Subjected to Gradient Tension

NANO ◽

10.1142/s179329201550037x ◽

2015 ◽

Vol 10 (03) ◽

pp. 1550037 ◽

Cited By ~ 2

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.

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pH-driven physicochemical conformational changes of single-layer graphene oxide

Chemical Communications ◽

10.1039/c1cc13725e ◽

2011 ◽

Vol 47 (34) ◽

pp. 9645 ◽

Cited By ~ 67

Author(s):

Raymond L. D. Whitby ◽

Alina Korobeinyk ◽

Vladimir M. Gun'ko ◽

Rosa Busquets ◽

Andrew B. Cundy ◽

...

Keyword(s):

Graphene Oxide ◽

Conformational Changes ◽

Single Layer ◽

Single Layer Graphene ◽

Layer Graphene

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

International Journal of Applied Mechanics ◽

10.1142/s1758825116500216 ◽

2016 ◽

Vol 08 (02) ◽

pp. 1650021 ◽

Cited By ~ 6

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.

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Molecular Dynamics Simulations of HLA-CW4-Β2M-KIR2DL1 Protein and Homology Modeling of a Complex Associated with Psoriasis Disease (HLA-CW6-Β 2M-KIR2DS1)

10.1101/2021.12.20.473468 ◽

2021 ◽

Author(s):

Mansour H Almatarneh ◽

Ahmad M Alqaisi ◽

Enas K Ibrahim ◽

Ghada G Kayed ◽

Joshua W Hollett

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Complex Structure ◽

3D Structure ◽

Md Simulations ◽

Salt Bridges ◽

Small Peptide ◽

Β2 Microglobulin ◽

Dynamics Simulations ◽

The Right

Molecular dynamics (MD) simulation was used to study the interactions of two immune proteins of HLA-Cw4-β2m-KIR2DL1 complex with small peptide QYDDAVYKL (nine amino acids) in an aqueous solution. This study aims to gain a detailed information about the conformational changes and the dynamics of the complex. The right parameters and force field for performing the MD simulations that was needed to calibrate the complex structure were determined. The non-bonded interactions (Electrostatic and van der Waals contributions), H-bond formation, and salt bridges between the ligand HLA-Cw4 and the receptor KIR2DL1 were estimated using the obtained MD trajectories. The buried surface area due to binding was calculated to get insight into the causes of specificity of receptor to ligand and explains mutations experiment. The study concluded that β2-microglobulin, one part of the complex, is not directly interacting with the peptide at the groove; therefore, it could be neglected from simulation. Our results showed that β2-microglobulin does not have any significant effect on the dynamics of the 3D-structure of the complex. This project will help in understanding to optimize candidate drug design, a small peptide that disrupts the interaction, for the optimal biological effect.

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The Crack Angle of 60° Is the Most Vulnerable Crack Front in Graphene According to MD Simulations

Crystals ◽

10.3390/cryst11111355 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1355

Author(s):

Ishaq I. Alahmed ◽

Sameh M. Altanany ◽

Ismail Abdulazeez ◽

Hassan Shoaib ◽

Abduljabar Q. Alsayoud ◽

...

Keyword(s):

Mechanical Properties ◽

Fracture Toughness ◽

Tensile Strength ◽

Strain Rate ◽

Crack Front ◽

Single Layer ◽

Md Simulations ◽

Crack Size ◽

Single Layer Graphene ◽

Crack Angle

Graphene is a type of 2D material with unique properties and promising applications. Fracture toughness and the tensile strength of a material with cracks are the most important parameters, as micro-cracks are inevitable in the real world. In this paper, we investigated the mechanical properties of triangular-cracked single-layer graphene via molecular dynamics (MD) simulations. The effect of the crack angle, size, temperature, and strain rate on the Young’s modulus, tensile strength, fracture toughness, and fracture strain were examined. We demonstrated that the most vulnerable triangle crack front angle is about 60°. A monitored increase in the crack angle under constant simulation conditions resulted in an enhancement of the mechanical properties. Minor effects on the mechanical properties were obtained under a constant crack shape, constant crack size, and various system sizes. Moreover, the linear elastic characteristics, including fracture toughness, were found to be remarkably influenced by the strain rate variations.

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An ordinary state-based peridynamic model for the fracture of zigzag graphene sheets

Proceedings of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rspa.2018.0019 ◽

2018 ◽

Vol 474 (2217) ◽

pp. 20180019 ◽

Cited By ~ 3

Author(s):

Xuefeng Liu ◽

Xiaoqiao He ◽

Jinbao Wang ◽

Ligang Sun ◽

Erkan Oterkus

Keyword(s):

Crack Propagation ◽

Single Layer ◽

Coarse Graining ◽

Md Simulations ◽

Single Layer Graphene ◽

Graphene Sheets ◽

Nanoscale Systems ◽

Fracture Failure ◽

Peridynamic Model ◽

Average Crack

This study develops an ordinary state-based peridynamic coarse-graining (OSPD-CG) model for the investigation of fracture in single-layer graphene sheets (SLGS), in which the peridynamic (PD) parameters are derived through combining the PD model and molecular dynamics (MD) simulations from the fully atomistic system via energy conservation. The fracture failure of pre-cracked SLGS under uniaxial tension is studied using the proposed PD model. And the PD simulation results agree well with those from MD simulations, including the stress–strain relations, the crack propagation patterns and the average crack propagation velocities. The interaction effect between cracks located at the centre and the edge on the crack propagation of the pre-cracked SLGS is discussed in detail. This work shows that the proposed PD model is much more efficient than the MD simulations and, thus, indicates that the PD-based method is applicable to study larger nanoscale systems.

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Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling

International Journal of Molecular Sciences ◽

10.3390/ijms22010270 ◽

2020 ◽

Vol 22 (1) ◽

pp. 270

Author(s):

Hisham M. Dokainish ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Md Simulations ◽

Conformational Sampling ◽

Salt Bridges ◽

Multidomain Proteins ◽

Charged Residues ◽

Ligand Interactions ◽

Moving Domains ◽

Domain Motions

Conformational transitions in multidomain proteins are essential for biological functions. The Apo conformations are typically open and flexible, while the Holo states form more compact conformations stabilized by protein-ligand interactions. Unfortunately, the atomically detailed mechanisms for such open-closed conformational changes are difficult to be accessed experimentally as well as computationally. To simulate the transitions using atomistic molecular dynamics (MD) simulations, efficient conformational sampling algorithms are required. In this work, we propose a new approach based on generalized replica-exchange with solute tempering (gREST) for exploring the open-closed conformational changes in multidomain proteins. Wherein, selected surface charged residues in a target protein are defined as the solute region in gREST simulation and the solute temperatures are different in replicas and exchanged between them to enhance the domain motions. This approach is called gREST selected surface charged residues (gREST_SSCR) and is applied to the Apo and Holo states of ribose binding protein (RBP) in solution. The conformational spaces sampled with gREST_SSCR are much wider than those with the conventional MD, sampling open-closed conformational changes while maintaining RBP domains’ stability. The free-energy landscapes of RBP in the Apo and Holo states are drawn along with twist and hinge angles of the two moving domains. The inter-domain salt-bridges that are not observed in the experimental structures are also important in the intermediate states during the conformational changes.

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

Molecules ◽

10.3390/molecules24071336 ◽

2019 ◽

Vol 24 (7) ◽

pp. 1336 ◽

Cited By ~ 8

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.

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