Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study

2015 ◽  
Vol 17 (45) ◽  
pp. 30307-30317 ◽  
Author(s):  
Sathish Kumar Mudedla ◽  
Ettayapuram Ramaprasad Azhagiya Singam ◽  
Kanagasabai Balamurugan ◽  
Venkatesan Subramanian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Simulation Study ◽  
Gold Nanoclusters ◽  
Dynamics Simulation ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
Positively Charged

The complexation of siRNA with positively charged gold nanoclusters has been studied using classical molecular dynamics simulations.

scholarly journals Formation mechanism of bound rubber in elastomer nanocomposites: a molecular dynamics simulation study

RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Bound Rubber ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

The formation mechanism of the bound rubber in elastomer nanocomposites using the coarse-grained molecular-dynamics simulations.

Solvation of cholesterol in different solvents: a molecular dynamics simulation study

2020 ◽  
Vol 22 (3) ◽  
pp. 1154-1167 ◽  
Author(s):  
Khair Bux ◽  
Syed Tarique Moin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dimethyl Sulfoxide ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Dynamical Properties ◽  
Dynamics Simulations

Molecular dynamics simulations were applied to an isolated cholesterol immersed in four different solvents of varying polarity, such as water, methanol, dimethyl sulfoxide and benzene, to gain insights into the structural and dynamical properties.

Molecular dynamics simulation study of various zeolitic imidazolate framework structures

2016 ◽  
Vol 45 (10) ◽  
pp. 4289-4302 ◽  
Author(s):  
Min Gao ◽  
Alston J. Misquitta ◽  
Leila H. N. Rimmer ◽  
Martin T. Dove
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Simulation Study ◽  
Lattice Dynamics ◽  
Dynamics Simulation ◽  
Zeolitic Imidazolate Framework ◽  
Dynamics Simulations

We report the results of a series of molecular dynamics simulations on a number of zinc zeolitic imidazolate framework (ZIF) structures together with some lattice dynamics calculations on ZIF-4, providing information about the flexibilities of these structures.

Molecular dynamics simulation study of distribution and dynamics of aqueous solutions of uranyl ions: the effect of varying temperature and concentration

2015 ◽  
Vol 17 (41) ◽  
pp. 27840-27850 ◽  
Author(s):  
Manish Chopra ◽  
Niharendu Choudhury
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Uranyl Ions ◽  
Orientational Distribution ◽  
Dynamics Simulations

Orientational distribution and dynamics of aqueous solutions of uranyl ions are studied at different concentrations and temperatures using molecular dynamics simulations.

scholarly journals Complexation of single stranded RNA with an ionizable lipid: an all-atom molecular dynamics simulation study

Soft Matter ◽  
2020 ◽  
Vol 16 (30) ◽  
pp. 6993-7005
Author(s):  
Anastassia N. Rissanou ◽  
Andreas Ouranidis ◽  
Kostas Karatasos
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Aqueous Medium ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Dynamics Simulations

Complexation of a lipid-based ionizable cationic molecule with RNA in an aqueous medium was examined in detail by means of fully atomistic molecular dynamics simulations.

Influence of the interfacial interaction strength on the viscoelasticity of hard–soft block copolymer based nanocomposites: a molecular dynamics simulation study

2020 ◽  
Vol 22 (7) ◽  
pp. 3897-3905
Author(s):  
Ruiqi Zhao ◽  
Yu Wang ◽  
Xinglong Gong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Block Copolymer ◽  
Molecular Dynamics Simulations ◽  
Simulation Study ◽  
Interaction Strength ◽  
Interfacial Interaction ◽  
Dynamics Simulation ◽  
Dynamics Simulations

The evolution of the polymer–nanofiller interface and hard domains during deformation was characterized by molecular dynamics simulations.

scholarly journals Exploring interfacial dynamics in homodimeric S-ribosylhomocysteine lyase (LuxS) from Vibrio cholerae through molecular dynamics simulations

RSC Advances ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 1700-1714
Author(s):  
Khair Bux ◽  
Thomas S. Hofer ◽  
Syed Tarique Moin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Vibrio Cholerae ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Interfacial Dynamics ◽  
Dimeric Form ◽  
Dynamical Properties ◽  
Dynamics Simulations

To the best of our knowledge, this is the first molecular dynamics simulation study on the dimeric form of the LuxS enzyme from Vibrio cholerae to evaluate its structural and dynamical properties including the dynamics of the interface formed by the two monomeric chains of the enzyme.

The interfacial structure and dynamics in a polymer nanocomposite containing small attractive nanoparticles: a full atomistic molecular dynamics simulation study

2020 ◽  
Vol 22 (20) ◽  
pp. 11400-11408 ◽  
Author(s):  
Xiang-Meng Jia ◽  
Hu-Jun Qian ◽  
Zhong-Yuan Lu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Simulation Study ◽  
Polymer Nanocomposite ◽  
Interfacial Structure ◽  
Dynamics Simulation ◽  
Structure And Dynamics ◽  
Dynamics Simulations ◽  
Oligomeric Silsesquioxane

We study the interfacial structure and dynamics of a polymer nanocomposite (PNC) composed of octaaminophenyl polyhedral oligomeric silsesquioxane (OAPS) and poly(2-vinylpyridine) (P2VP) by performing full atomistic molecular dynamics simulations.

scholarly journals An introduction to classical molecular dynamics simulation for experimental scattering users

2019 ◽  
Vol 52 (3) ◽  
pp. 665-668
Author(s):  
Andrew R. McCluskey ◽  
James Grant ◽  
Adam R. Symington ◽  
Tim Snow ◽  
James Doutch ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Theory And Practice ◽  
Dynamics Simulation ◽  
Scattering Data ◽  
Open Educational Resource ◽  
Common Component ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

Classical molecular dynamics simulations are a common component of multi-modal analyses of scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a `black box' analysis technique. This article describes an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open-source software repository, which can be freely copied, modified and redistributed by educators. The topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.

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.

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