scholarly journals How Short Is Too Short for the Interactions of a Water Potential? Exploring the Parameter Space of a Coarse-Grained Water Model Using Uncertainty Quantification

2014 ◽  
Vol 118 (28) ◽  
pp. 8190-8202 ◽  
Author(s):  
Liam C. Jacobson ◽  
Robert M. Kirby ◽  
Valeria Molinero
Keyword(s):  
Water Potential ◽  
Uncertainty Quantification ◽  
Parameter Space ◽  
Coarse Grained ◽  
Water Model

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

2017 ◽  
Vol 146 (5) ◽  
pp. 054501 ◽  
Author(s):  
Julian Michalowsky ◽  
Lars V. Schäfer ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field

Four-to-one coarse-grained polarisable water model for dissipative particle dynamics

2017 ◽  
Vol 44 (7) ◽  
pp. 540-550 ◽  
Author(s):  
Rakesh Vaiwala ◽  
Sameer Jadhav ◽  
Rochish Thaokar
Keyword(s):  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Water Model

Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis

Nanoscale ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 1647-1660 ◽  
Author(s):  
Chao-Min Huang ◽  
Anjelica Kucinic ◽  
Jenny V. Le ◽  
Carlos E. Castro ◽  
Hai-Jun Su
Keyword(s):  
Uncertainty Quantification ◽  
Dna Origami ◽  
Variance Analysis ◽  
Coarse Grained ◽  
Computational Framework ◽  
Coarse Grained Model

We report a hybrid computational framework combining coarse-grained modeling with kinematic variance analysis for predicting uncertainties in the motion pathway of a multi-component DNA origami mechanism.

scholarly journals Data-driven uncertainty quantification for systematic coarse-grained models

2020 ◽  
Vol 18 (2-3) ◽  
pp. 348-368
Author(s):  
Tangxin Jin ◽  
Anthony Chazirakis ◽  
Evangelia Kalligiannaki ◽  
Vagelis Harmandaris ◽  
Markos A. Katsoulakis
Keyword(s):  
Uncertainty Quantification ◽  
Data Driven ◽  
Coarse Grained

scholarly journals Constructing a coarse-grained water model based on non-Markovian dissipative particle dynamics

2018 ◽  
Vol 84 (865) ◽  
pp. 18-00193-18-00193
Author(s):  
Gengo KIHARA ◽  
Yuta YOSHIMOTO ◽  
Takuma HORI ◽  
Shu TAKAGI ◽  
Ikuya KINEFUCHI
Keyword(s):  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Water Model ◽  
Model Based
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