scholarly journals Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials

2019 ◽  
Vol 2 (11) ◽  
pp. 1900135 ◽  
Author(s):  
David Dubbeldam ◽  
Krista S. Walton ◽  
Thijs J. H. Vlugt ◽  
Sofia Calero
Keyword(s):  
Force Fields ◽  
Nanoporous Materials ◽  
Atomic Force ◽  
Design Parameterization

Mechanical characterization of nanoporous materials by use of atomic force acoustic microscopy methods

2013 ◽  
Vol 24 (35) ◽  
pp. 355703 ◽  
Author(s):  
M Kopycinska-Müller ◽  
K-B Yeap ◽  
S Mahajan ◽  
B Köhler ◽  
N Kuzeyeva ◽  
...  
Keyword(s):  
Mechanical Characterization ◽  
Nanoporous Materials ◽  
Acoustic Microscopy ◽  
Atomic Force

scholarly journals Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions

2011 ◽  
Vol 32 (8) ◽  
pp. 1680-1686 ◽  
Author(s):  
Shide Liang ◽  
Yaoqi Zhou ◽  
Nick Grishin ◽  
Daron M. Standley
Keyword(s):  
Force Fields ◽  
Side Chain ◽  
Series Expansions ◽  
Atomic Force

A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

2017 ◽  
Vol 19 (21) ◽  
pp. 13629-13639 ◽  
Author(s):  
Jie Hu ◽  
Tao Chen ◽  
Moye Wang ◽  
Hue Sun Chan ◽  
Zhuqing Zhang
Keyword(s):  
Protein Folding ◽  
Force Fields ◽  
Coarse Grained ◽  
Unfolded Proteins ◽  
Critical Comparison ◽  
Atomic Models ◽  
Atomic Force

The predicted dimension of unfolded proteins is quite different using native-centric Gō-like models and transferrable (non-structure-based) models based on current atomic force fields.

Recent developments in first-principles force fields for molecules in nanoporous materials

2014 ◽  
Vol 2 (2) ◽  
pp. 274-291 ◽  
Author(s):  
Hanjun Fang ◽  
Hakan Demir ◽  
Preeti Kamakoti ◽  
David S. Sholl
Keyword(s):  
First Principles ◽  
Force Fields ◽  
Nanoporous Materials ◽  
Recent Developments

Atomic Force Fields*

1924 ◽  
Vol 9 (3) ◽  
pp. 237
Author(s):  
F. S. Brackett
Keyword(s):  
Force Fields ◽  
Atomic Force

scholarly journals Exploiting a Mechanical Perturbation of Titin Domain to Identify How Force Field Parameterization Affects Protein Refolding Pathways

2019 ◽  
Author(s):  
David Wang ◽  
Piotr E. Marszalek
Keyword(s):  
Force Field ◽  
Force Fields ◽  
Direct Transition ◽  
Mechanical Perturbation ◽  
Atomic Force ◽  
Force Field Parameterization ◽  
Helical Peptide ◽  
Perturbed Model ◽  
Simulation Time ◽  
Insight Into

AbstractMolecular mechanics force fields have been shown to differ in their predictions of processes such as protein folding. To test how force field differences affect predicted protein behavior, we created a mechanically perturbed model of the beta-stranded I91 titin domain based on atomic force spectroscopy data and examined its refolding behavior using six different force fields. To examine the transferability of the force field discrepancies identified by this model, we compared the results to equilibrium simulations of the weakly helical peptide Ac-(AAQAA)3-NH2. The total simulation time was 80 µs. From these simulations we found significant differences in I91 perturbation refolding ability between force fields. Concurrently, Ac-(AAQAA)3-NH2 equilibration experiments indicated that although force fields have similar overall helical frequencies, they can differ in helical lifetimes. The combination of these results suggests that differences in force field parameterization may allow a more direct transition between the beta and alpha regions of the Ramachandran plot thereby affecting both beta-strand refolding ability and helical lifetimes. Furthermore, the combination of results suggests that using mechanically perturbed models can provide a controlled method to gain more insight into how force fields affect protein behavior.

Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

2009 ◽  
Vol 130 (19) ◽  
pp. 195103 ◽  
Author(s):  
Marcos R. Betancourt ◽  
Sheyore J. Omovie
Keyword(s):  
Force Fields ◽  
Coarse Grained ◽  
Atomic Force
Sign in / Sign up

Export Citation Format

Share Document