scholarly journals Thermal Response in Cellulose Iβ Based on Molecular Dynamics

2019 ◽  
Vol 7 (1) ◽  
pp. 85-97
Author(s):  
Xuewei Jiang ◽  
Yu Chen ◽  
Yue Yuan ◽  
Lu Zheng
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
High Temperatures ◽  
Structural Information ◽  
Structural Parameters ◽  
Thermal Response ◽  
Intermediate Temperature ◽  
Cellulose I ◽  
Cellulose Iβ ◽  
Dynamics Simulations

AbstractThe structural details of cellulose I β were discussed according to molecular dynamics simulations with the GLYCAM-06 force field. The simulation outcomes were in agreement with previous experimental data, including structural parameters and hydrogen bond pattern at 298 K. We found a new conformation of cellulose Iβ existed at the intermediate temperature that is between the low and high temperatures. Partial chain rotations along the backbone direction were found and conformations of hydroxymethyl groups that alternated from tg to either gt or gg were observed when the temperature increased from 298 K to 400 K. In addition, the gg conformation is preferred than gt. For the structure adopted at high temperature of 500 K, major chains were twisted and two chains detached from each plain. In contrast to the observation under intermediate temperature, the population of hydroxymethyl groups in gt exceeded that in gg conformation at high temperature. In addition, three patterns of hydrogen bonding were identified at low, intermediate and high temperatures in the simulations. The provided structural information indicated the transitions occurred around 350 K and 450 K, considered as the transitional temperatures of cellulose Iβ in this work.

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

2019 ◽  
Vol 25 (31) ◽  
pp. 3339-3349 ◽  
Author(s):  
Indrani Bera ◽  
Pavan V. Payghan
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Molecular Dynamics Simulations ◽  
Drug Target ◽  
Structural Information ◽  
Drug Binding ◽  
Structure Based Drug Design ◽  
Drug Designing ◽  
Target Binding ◽  
Dynamics Simulations

Background: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. Objective: The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. Method: This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. Results: This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. Conclusion: The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

scholarly journals Study of High-Temperature Behaviour of ZnO by Ab Initio Molecular Dynamics Simulations and X-ray Absorption Spectroscopy

Materials ◽  
2021 ◽  
Vol 14 (18) ◽  
pp. 5206
Author(s):  
Dmitry Bocharov ◽  
Inga Pudza ◽  
Konstantin Klementiev ◽  
Matthias Krack ◽  
Alexei Kuzmin
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Mean Square ◽  
Structural Anisotropy ◽  
X Ray ◽  
Temperature Dependences ◽  
Dynamics Simulations ◽  
X Ray Absorption

Wurtzite-type zinc oxide (w-ZnO) is a widely used material with a pronounced structural anisotropy along the c axis, which affects its lattice dynamics and represents a difficulty for its accurate description using classical models of interatomic interactions. In this study, ab initio molecular dynamics (AIMD) was employed to simulate a bulk w-ZnO phase in the NpT ensemble in the high-temperature range from 300 K to 1200 K. The results of the simulations were validated by comparison with the experimental Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra and known diffraction data. AIMD NpT simulations reproduced well the thermal expansion of the lattice, and the pronounced anharmonicity of Zn–O bonding was observed above 600 K. The values of mean-square relative displacements and mean-square displacements for Zn–O and Zn–Zn atom pairs were obtained as a function of interatomic distance and temperature. They were used to calculate the characteristic Einstein temperatures. The temperature dependences of the O–Zn–O and Zn–O–Zn bond angle distributions were also determined.

scholarly journals Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

2009 ◽  
Vol 62 (9) ◽  
pp. 1054 ◽  
Author(s):  
Defang Ouyang ◽  
Hong Zhang ◽  
Dirk-Peter Herten ◽  
Harendra S. Parekh ◽  
Sean C. Smith
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Structural Information ◽  
Structural Parameters ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Viral Gene ◽  
Conformational Structure ◽  
Crystal Forms ◽  
Gene Delivery Vectors

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A′-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA – namely major groove width, inclination and the number of base pairs in a helical twist – over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A′-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).

Schwarzites to schwarzynes: A new class of superdeformable materials

MRS Advances ◽  
2020 ◽  
Vol 5 (37-38) ◽  
pp. 1947-1954
Author(s):  
Eliezer Fernando Oliveira ◽  
Douglas Soares Galvao
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Elastic Properties ◽  
High Temperatures ◽  
Preliminary Results ◽  
New Class ◽  
Elastic Regime ◽  
Dynamics Simulations

AbstractIn this work, we have investigated the structural and mechanical properties of a new class of soft and superelastic materials, called schwarzynes. These materials are obtained by inserting sp carbon atoms (acetylenic groups) into the schwarzite framework. Using fully atomistic molecular dynamics simulations with the AIREBO force field, our results show that schwarzynes are stable materials up to high temperatures (1000K). Schwarzynes exhibit a very wide elastic regime, some of them up to 70% strain without structural fractures. Our preliminary results show that the elastic properties can be easily engineered by tuning the number of acetylenic groups and the crystallographic directions where they are inserted.

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