Evaluating Simple Ab Initio Models of the Hydrated Electron: The Role of Dynamical Fluctuations

2020 ◽  
Vol 124 (43) ◽  
pp. 9592-9603 ◽  
Author(s):  
Sanghyun J. Park ◽  
Benjamin J. Schwartz
Keyword(s):  
Ab Initio ◽  
Hydrated Electron ◽  
Dynamical Fluctuations ◽  
Ab Initio Models

The role of density reduction in lithiated amorphous silicon: Molecular dynamics and ab-initio studies

2021 ◽  
Author(s):  
Jay Krishan Dora ◽  
Charchit Saraswat ◽  
Ashish Gour ◽  
Sudipto Ghosh ◽  
Natraj Yedla ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Amorphous Silicon ◽  
Density Reduction

scholarly journals A Peptides Prediction Methodology for Tertiary Structure Based on Simulated Annealing

2021 ◽  
Vol 26 (2) ◽  
pp. 39
Author(s):  
Juan P. Sánchez-Hernández ◽  
Juan Frausto-Solís ◽  
Juan J. González-Barbosa ◽  
Diego A. Soto-Monterrubio ◽  
Fanny G. Maldonado-Nava ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Ab Initio ◽  
Primary Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Golden Ratio ◽  
Small Peptides ◽  
Hybrid Simulated Annealing ◽  
Ab Initio Models

The Protein Folding Problem (PFP) is a big challenge that has remained unsolved for more than fifty years. This problem consists of obtaining the tertiary structure or Native Structure (NS) of a protein knowing its amino acid sequence. The computational methodologies applied to this problem are classified into two groups, known as Template-Based Modeling (TBM) and ab initio models. In the latter methodology, only information from the primary structure of the target protein is used. In the literature, Hybrid Simulated Annealing (HSA) algorithms are among the best ab initio algorithms for PFP; Golden Ratio Simulated Annealing (GRSA) is a PFP family of these algorithms designed for peptides. Moreover, for the algorithms designed with TBM, they use information from a target protein’s primary structure and information from similar or analog proteins. This paper presents GRSA-SSP methodology that implements a secondary structure prediction to build an initial model and refine it with HSA algorithms. Additionally, we compare the performance of the GRSAX-SSP algorithms versus its corresponding GRSAX. Finally, our best algorithm GRSAX-SSP is compared with PEP-FOLD3, I-TASSER, QUARK, and Rosetta, showing that it competes in small peptides except when predicting the largest peptides.

On the role of hydrogen filled vacancies on the embrittlement of zirconium: An ab initio investigation

2015 ◽  
Vol 467 ◽  
pp. 311-319 ◽  
Author(s):  
Pär A.T. Olsson ◽  
Kwadwo Kese ◽  
Anna-Maria Alvarez Holston
Keyword(s):  
Ab Initio

Role of the Catalytic Triad and Oxyanion Hole in Acetylcholinesterase Catalysis:  An ab initio QM/MM Study

2002 ◽  
Vol 124 (35) ◽  
pp. 10572-10577 ◽  
Author(s):  
Yingkai Zhang ◽  
Jeremy Kua ◽  
J. Andrew McCammon
Keyword(s):  
Ab Initio ◽  
Catalytic Triad ◽  
Oxyanion Hole

Erratum: The role of the frontier orbitals in acid-base chemistry of organic amines probed by ab initio and chemometric techniques

2010 ◽  
Vol 111 (15) ◽  
pp. 4505-4505 ◽  
Author(s):  
Felipe A. La Porta ◽  
Regis T. Santiago ◽  
Teodorico C. Ramalho ◽  
Matheus P. Freitas ◽  
Elaine F. F. Da Cunha
Keyword(s):  
Ab Initio ◽  
Frontier Orbitals ◽  
Acid Base ◽  
Chemometric Techniques ◽  
Organic Amines
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