scholarly journals Progress in deep Markov State Modeling: Coarse graining and experimental data restraints

Author(s):  
Andreas Mardt ◽  
Frank Noé
2015 ◽  
Vol 143 (4) ◽  
pp. 044119 ◽  
Author(s):  
B. Fačkovec ◽  
E. Vanden-Eijnden ◽  
D. J. Wales

2021 ◽  
Author(s):  
Lazaros Melidis ◽  
Iain B. Styles ◽  
Michael J. Hannon

MD simulations and Markov state modeling explore induced fit binding of metallo-helicates to bulges in dynamic TAR RNA, reproduce experimental data, show how RNA conformational flexibility is reduced, and give mechanistic insight into insertion.


2016 ◽  
Vol 94 (5) ◽  
Author(s):  
F. Pellegrini ◽  
François P. Landes ◽  
A. Laio ◽  
S. Prestipino ◽  
E. Tosatti

2020 ◽  
Author(s):  
Michael Johnston ◽  
Andrew Duff ◽  
Richard L. Anderson ◽  
William Swope

<div><div><div><p>Using a comprehensive set of recently published experimental results for training and validation, we have developed computational models appropriate for simulations of aqueous solutions of poly(ethylene oxide) alkyl ethers, an important class of micelle- forming nonionic surfactants, usually denoted CnEm. These models are suitable for use in simulations that employ a moderate amount of coarse graining and especially for dissipative particle dynamics (DPD), which we adopt in this work.</p><p><br></p><p>The experimental data used for training and validation were reported earlier and produced in our laboratory using dynamic light scattering (DLS) measurements per- formed on twelve members of the CnEm compound family yielding micelle size dis- tribution functions and mass weighted mean aggregation numbers at each of several surfactant concentrations. The range of compounds and quality of the experimental results were designed to support the development of computational models. An es- sential feature of this work is that all simulation results were analysed in a way that is consistent with the experimental data. Proper account is taken of the fact that a broad distribution of micelle sizes exists, so mass weighted averages (rather than num- ber weighted averages) over this distribution are required for the proper comparison of simulation and experimental results.</p><p><br></p><p>The resulting DPD force field reproduces several important trends seen in the exper- imental critical micelle concentrations and mass averaged mean aggregation numbers with respect to surfactant characteristics and concentration. We feel it can be used to investigate a number of open questions regarding micelle sizes and shapes and their dependence on surfactant concentration for this important class of nonionic surfactants.</p></div></div></div>


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