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.

Mechanism of stacking fault annihilation in 3C-SiC epitaxially grown on Si(001) by molecular dynamics simulations

CrystEngComm ◽  
2021 ◽  
Author(s):  
Andrey Sarikov ◽  
Anna Marzegalli ◽  
Luca Barbisan ◽  
Massimo Zimbone ◽  
Corrado Bongiorno ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Stacking Faults ◽  
Md Simulations ◽  
Stacking Fault ◽  
Dynamics Simulations

In this work, annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in...

scholarly journals Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

Structural stability of CmTin microclusters and nanoparticles: Molecular–dynamics simulations

2005 ◽  
Vol 1 (4) ◽  
pp. 204-209
Author(s):  
O.B. Malcıoğlu ◽  
Ş. Erkoç
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binary Systems ◽  
Minimum Energy ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Atomic Interactions ◽  
Dynamics Simulations ◽  
Three Body ◽  
Initial Geometry

The minimum energy structures of CmTin microclusters and nanoparticles have been investigated theoretically by performing molecular–dynamics (MD) simulations. Selected crystalline and completely random initial geometries are considered. The potential energy function (PEF) used in the calculations includes two– and three–body atomic interactions for C-Ti binary systems. Molecular–dynamics simulations have been performed at 1 K and 300 K. It has been found that initial geometry has a very strong influence on relaxed geometry

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.

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

scholarly journals Evaluation of the effect of nickel clusters on the formation of incipient soot particles from polycyclic aromatic hydrocarbons via ReaxFF molecular dynamics simulations

2019 ◽  
Vol 21 (19) ◽  
pp. 9865-9875 ◽  
Author(s):  
Sharmin Shabnam ◽  
Qian Mao ◽  
Adri C. T. van Duin ◽  
K. H. Luo
Keyword(s):  
Molecular Dynamics ◽  
Polycyclic Aromatic Hydrocarbons ◽  
Molecular Dynamics Simulations ◽  
Aromatic Hydrocarbons ◽  
Md Simulations ◽  
Soot Particles ◽  
Nickel Clusters ◽  
Polycyclic Aromatic ◽  
Dynamics Simulations

Effect of nickel clusters on the formation of incipient soot from PAH precursors via ReaxFF-MD simulations.

scholarly journals Molecular dynamics simulations of the self-organization of side-chain decorated polyaromatic conjugation molecules: phase separated lamellar and columnar structures and dispersion behaviors in toluene solvent

RSC Advances ◽  
2018 ◽  
Vol 8 (20) ◽  
pp. 11134-11144 ◽  
Author(s):  
Lanyan He ◽  
Pingmei Wang ◽  
Lipeng He ◽  
Zhou Qu ◽  
Jianhui Luo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Md Simulations ◽  
The Self ◽  
Self Organization ◽  
Side Chain ◽  
Dynamics Simulations

The self-organization of five model side-chain decorated polyaromatic asphaltene molecules with or without toluene solvent was investigated by means of molecular dynamic (MD) simulations.

Enhanced self-healing performance of graphene oxide/vitrimer nanocomposites: A molecular dynamics simulations study

Polymer ◽  
2020 ◽  
Vol 206 ◽  
pp. 122862
Author(s):  
Chanwook Park ◽  
Geonwoo Kim ◽  
Jiwon Jung ◽  
Balaji Krishnakumar ◽  
Sravendra Rana ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Molecular Dynamics Simulations ◽  
Self Healing ◽  
Dynamics Simulations

Surface structure of organoclays as examined by X-ray photoelectron spectroscopy and molecular dynamics simulations

Clay Minerals ◽  
2015 ◽  
Vol 50 (3) ◽  
pp. 353-367 ◽  
Author(s):  
B. Schampera ◽  
R. Solc ◽  
S.K. Woche ◽  
R. Mikutta ◽  
S. Dultz ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Photoelectron Spectroscopy ◽  
Md Simulations ◽  
Organic Cations ◽  
Conformational Structure ◽  
Xps Spectra ◽  
X Ray ◽  
Dynamics Simulations ◽  
External Interface

AbstractOrganoclays are sorbent materials prepared from clays by exchanging inorganic with organic cations. Their properties depend on the loading and conformational structure of the organic cations, but little information is available about the surface structures of organoclays. In this work, X-ray photoelectron spectroscopy (XPS) and classical molecular dynamics (MD) simulations are combined to characterize the external interface of an organoclay prepared from hexadecylpyridinium (HDPy+) and bentonite. The XPS survey spectra show well the varying elemental composition of the surface with increasing amount of surfactant, showing a decreasing contribution of clay-derived elements with increasing organic coverage. The high-resolution C 1s XPS spectra depict sensitively the surface arrangement of the surfactant. In combination with MD simulations, the results implied a monolayer coating for low surfactant coverage and a disordered bilayer arrangement at high surfactant uptakes. Molecular dynamics simulations showed that for very high cation uptake a quasi-paraffin-like configuration is also possible. The combination of experimental and modelling methods yielded congruent information on the molecular-scale arrangement of organic cations at the organoclay surfaces and the controlling mechanisms.

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