Molecular Dynamics Simulation of the Diffusion Dynamics of Linear DNA Fragments in Dilute Solution with the Parmbsc1 Force Field and Comparison with Experimental Data and Theoretical Models

Terpsichori S. Alexiou; Dimitris G. Mintis; Vlasis G. Mavrantzas

doi:10.1021/acs.macromol.0c00222

Molecular Dynamics Simulation of the Diffusion Dynamics of Linear DNA Fragments in Dilute Solution with the Parmbsc1 Force Field and Comparison with Experimental Data and Theoretical Models

Macromolecules ◽

10.1021/acs.macromol.0c00222 ◽

2020 ◽

Vol 53 (15) ◽

pp. 6135-6150

Author(s):

Terpsichori S. Alexiou ◽

Dimitris G. Mintis ◽

Vlasis G. Mavrantzas

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Force Field ◽

Theoretical Models ◽

Dynamics Simulation ◽

Dilute Solution ◽

Linear Dna ◽

Diffusion Dynamics ◽

Comparison With Experimental Data

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Molecular dynamics simulation of cis-1,4-polybutadiene. 1. Comparison with experimental data for static and dynamic properties

Polymer ◽

10.1016/s0032-3861(01)00628-0 ◽

2002 ◽

Vol 43 (3) ◽

pp. 971-976 ◽

Cited By ~ 20

Author(s):

O Okada

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamic Properties ◽

Dynamics Simulation ◽

Comparison With Experimental Data

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Microscopic Dynamics and Topology of Polymer Rings Immersed in a Host Matrix of Longer Linear Polymers: Results from a Detailed Molecular Dynamics Simulation Study and Comparison with Experimental Data

Polymers ◽

10.3390/polym8080283 ◽

2016 ◽

Vol 8 (8) ◽

pp. 283 ◽

Cited By ~ 19

Author(s):

George Papadopoulos ◽

Dimitrios Tsalikis ◽

Vlasis Mavrantzas

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Linear Polymers ◽

Host Matrix ◽

And Topology ◽

Comparison With Experimental Data ◽

Microscopic Dynamics

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Adsorption of organic molecules on carbon surfaces: Experimental data and molecular dynamics simulation considering multiple protonation states

Journal of Colloid and Interface Science ◽

10.1016/j.jcis.2020.12.107 ◽

2021 ◽

Author(s):

Robin Wagner ◽

Saientan Bag ◽

Tatjana Trunzer ◽

Paula Fraga-García ◽

Wolfgang Wenzel ◽

...

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Organic Molecules ◽

Dynamics Simulation ◽

Adsorption Of Organic Molecules ◽

Carbon Surfaces

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Molecular Dynamics Simulation of Silicon Dioxide Etching by Hydrogen Fluoride Using the Reactive Force Field

ACS Omega ◽

10.1021/acsomega.1c01824 ◽

2021 ◽

Author(s):

Dong Hyun Kim ◽

Seung Jae Kwak ◽

Jae Hun Jeong ◽

Suyoung Yoo ◽

Sang Ki Nam ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Silicon Dioxide ◽

Force Field ◽

Hydrogen Fluoride ◽

Dynamics Simulation ◽

Reactive Force ◽

Reactive Force Field

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Molecular Dynamics Simulation of Tri-n-butyl-Phosphate Liquid: A Force Field Comparative Study

The Journal of Physical Chemistry B ◽

10.1021/jp207089e ◽

2011 ◽

Vol 116 (1) ◽

pp. 305-313 ◽

Cited By ~ 33

Author(s):

Shengting Cui ◽

Valmor F. de Almeida ◽

Benjamin P. Hay ◽

Xianggui Ye ◽

Bamin Khomami

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Comparative Study ◽

Force Field ◽

Dynamics Simulation

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Molecular Dynamics Simulation of Membrane Free Energy Profiles Using Accurate Force Field for Ionic Liquids

Scientific Computing and Algorithms in Industrial Simulations ◽

10.1007/978-3-319-62458-7_14 ◽

2017 ◽

pp. 265-284

Author(s):

Thorsten Köddermann ◽

Martin R. Schenk ◽

Marco Hülsmann ◽

Andreas Krämer ◽

Karl N. Kirschner ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ionic Liquids ◽

Molecular Dynamics Simulation ◽

Force Field ◽

Dynamics Simulation ◽

Energy Profiles ◽

Free Energy Profiles

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GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Soft Matter ◽

10.1039/c2sm26007g ◽

2012 ◽

Vol 8 (37) ◽

pp. 9617 ◽

Cited By ~ 134

Author(s):

Callum J. Dickson ◽

Lula Rosso ◽

Robin M. Betz ◽

Ross C. Walker ◽

Ian R. Gould

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Force Field ◽

Dynamics Simulation ◽

Amber Force Field

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Reactive force-field molecular dynamics simulation for the surface reaction of SiH (x = 2–4) species on Si(1 0 0)-(2 × 1):H surfaces in chemical vapor deposition processes

Computational Materials Science ◽

10.1016/j.commatsci.2022.111193 ◽

2022 ◽

Vol 204 ◽

pp. 111193

Author(s):

Naoya Uene ◽

Takuya Mabuchi ◽

Masaru Zaitsu ◽

Shigeo Yasuhara ◽

Takashi Tokumasu

Keyword(s):

Molecular Dynamics ◽

Chemical Vapor Deposition ◽

Molecular Dynamics Simulation ◽

Force Field ◽

Vapor Deposition ◽

Surface Reaction ◽

Chemical Vapor ◽

Dynamics Simulation ◽

Reactive Force ◽

Deposition Processes

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Dataset of molecular dynamics simulation trajectories of amino-acid solutions with various force fields, water models and modified force field parameters

Data in Brief ◽

10.1016/j.dib.2020.105483 ◽

2020 ◽

Vol 30 ◽

pp. 105483

Author(s):

Jiří Průša ◽

Michal Cifra

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Molecular Dynamics Simulation ◽

Force Field ◽

Force Fields ◽

Dynamics Simulation ◽

Acid Solutions ◽

Amino Acid Solutions ◽

Water Models ◽

Force Field Parameters

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New all-atom force field for molecular dynamics simulation of an AlPO4-34 molecular sieve

Journal of Computational Chemistry ◽

10.1002/jcc.20774 ◽

2007 ◽

Vol 29 (1) ◽

pp. 122-129 ◽

Cited By ~ 9

Author(s):

Matej Praprotnik ◽

Stanko Hočevar ◽

Milan Hodošček ◽

Matej Penca ◽

Dušanka Janežič

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Force Field ◽

Molecular Sieve ◽

Dynamics Simulation

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