scholarly journals Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute–solvent interactions

2014 ◽  
Vol 16 (38) ◽  
pp. 20639-20649 ◽  
Author(s):  
Petr Štěpánek ◽  
Petr Bouř
Keyword(s):  
Amino Acids ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Electronic Spectra ◽  
Aromatic Amino Acids ◽  
Molecular Structures ◽  
Solvent Interactions ◽  
Multi Scale ◽  
Scale Modeling ◽  
Multi Scale Modeling

Electronic spectra provide a wealth of information on molecular structures. We demonstrate a very satisfactory agreement between experimental and modeled spectra, as obtained by combined molecular mechanics/quantum mechanics computations for three aromatic amino acids.

scholarly journals Multiscale Modeling of Amyloid Fibrils Formed by Aggregating Peptides Derived from the Amyloidogenic Fragment of the A-Chain of Insulin

2021 ◽  
Vol 22 (22) ◽  
pp. 12325
Author(s):  
Michał Koliński ◽  
Robert Dec ◽  
Wojciech Dzwolak
Keyword(s):  
Structure Prediction ◽  
Amyloid Fibrils ◽  
Md Simulations ◽  
Molecular Structures ◽  
Coarse Grained ◽  
Multi Scale ◽  
Modeling Procedure ◽  
Scale Modeling ◽  
Multi Scale Modeling ◽  
A Chain

Computational prediction of molecular structures of amyloid fibrils remains an exceedingly challenging task. In this work, we propose a multi-scale modeling procedure for the structure prediction of amyloid fibrils formed by the association of ACC1-13 aggregation-prone peptides derived from the N-terminal region of insulin’s A-chain. First, a large number of protofilament models composed of five copies of interacting ACC1-13 peptides were predicted by application of CABS-dock coarse-grained (CG) docking simulations. Next, the models were reconstructed to all-atom (AA) representations and refined during molecular dynamics (MD) simulations in explicit solvent. The top-scored protofilament models, selected using symmetry criteria, were used for the assembly of long fibril structures. Finally, the amyloid fibril models resulting from the AA MD simulations were compared with atomic force microscopy (AFM) imaging experimental data. The obtained results indicate that the proposed multi-scale modeling procedure is capable of predicting protofilaments with high accuracy and may be applied for structure prediction and analysis of other amyloid fibrils.

scholarly journals Application of transfer Hamiltonian quantum mechanics to multi-scale modeling

2004 ◽  
Vol 100 (6) ◽  
pp. 1019-1025 ◽  
Author(s):  
Aditi Mallik ◽  
DeCarlos E. Taylor ◽  
Keith Runge ◽  
James W. Dufty
Keyword(s):  
Quantum Mechanics ◽  
Multi Scale ◽  
Scale Modeling ◽  
Multi Scale Modeling

Multi-Scale Modeling of Cementitious Materials (Briefing Chart)

2014 ◽  
Author(s):  
M. M. Shahzamanian ◽  
T. Tadepalli ◽  
A. M. Rajendran ◽  
W. D. Hodo ◽  
R. Mohan ◽  
...  
Keyword(s):  
Cementitious Materials ◽  
Multi Scale ◽  
Scale Modeling ◽  
Multi Scale Modeling

Multi-Scale Modeling of Neural Structure in X-Ray Imagery

2021 ◽  
Author(s):  
Aishwarya Balwani ◽  
Joseph Miano ◽  
Ran Liu ◽  
Lindsey Kitchell ◽  
Judy A. Prasad ◽  
...  
Keyword(s):  
Neural Structure ◽  
X Ray ◽  
Multi Scale ◽  
Scale Modeling ◽  
Multi Scale Modeling

Multi-scale modeling and experimental study of fatigue of plain-woven SiC/SiC composites

2021 ◽  
pp. 106725
Author(s):  
Hongnian Dong ◽  
Xiguang Gao ◽  
Sheng Zhang ◽  
Guoqiang Yu ◽  
Yingdong Song ◽  
...  
Keyword(s):  
Experimental Study ◽  
Multi Scale ◽  
Scale Modeling ◽  
Multi Scale Modeling ◽  
Sic Composites
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