Zobrazeno 1 - 10 of 10 pro vyhledávání: '"Semen A Trygubenko"'
1
A doubly nudged elastic band method for finding transition states
Autor: David J. Wales, Semen A. Trygubenko
Publikováno v: The Journal of Chemical Physics. 120:2082-2094
A modification of the nudged elastic band (NEB) method is presented that enables stable optimisations to be run using both the limited-memory quasi-Newton (L-BFGS) and slow-response quenched velocity Verlet (SQVV) minimisers. The performance of this
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d3b4afc405b60cb3860004b28d844300
https://doi.org/10.1063/1.1636455
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2
Correlated ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment and in Aqueous Solution. Guanine: Surprising Stabilization of Rare Tautomers in Aqueous Solution
Autor: Semen A Trygubenko, Martin Kabeláč, Filip Ryjáček, Tomas Kubar, Michal Hanus, Tetyana V. Bogdan, Pavel Hobza
Publikováno v: Journal of the American Chemical Society. 125:7678-7688
Altogether eight keto and enol tautomers of guanine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in bulk water. The structures of isolated, as well as mono- and dihydrated tautomers were de
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::74ed08f9434e3576800404ae676700b5
https://doi.org/10.1021/ja034245y
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5
Symmetrization of the AMBER and CHARMM force fields
Autor: Birgit Strodel, Semen A. Trygubenko, Szilard N. Fejer, David J. Wales, Edyta Malolepsza, Mey Khalili
Publikováno v: Journal of Computational Chemistry.
The AMBER and CHARMM force fields are analyzed from the viewpoint of the permutational symmetry of the potential for feasible exchanges of identical atoms and chemical groups in amino and nucleic acids. In each case, we propose schemes for symmetrizi
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7390d69a03db55aec30f9b3a2100fb2e
https://doi.org/10.1002/jcc.21425
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6
Kinetic Analysis of Discrete Path Sampling Stationary Point Databases
Autor: David J. Wales, Semen A. Trygubenko
Analysing stationary point databases to extract phenomenological rate constants can become time-consuming for systems with large potential energy barriers. In the present contribution we analyse several different approaches to this problem. First, we
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3d0d61e827c4a3aba1859551f76be2dd
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7
Finding pathways between distant local minima
Autor: Semen A. Trygubenko, David J. Wales, Joanne M. Carr
Publikováno v: The Journal of chemical physics. 122(23)
We report a new algorithm for constructing pathways between local minima that involve a large number of intervening transition states on the potential energy surface. A significant improvement in efficiency has been achieved by changing the strategy
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d6e8e1ffde3f8fe23fa98fb26fb47c4d
https://pubmed.ncbi.nlm.nih.gov/16008483
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8
Analysis of cooperativity and localization for atomic rearrangements
Autor: Semen A. Trygubenko, David J. Wales
We propose new measures of localization and cooperativity for the analysis of atomic rearrangements. We show that for both clusters and bulk material cooperative rearrangements usually have significantly lower barriers than uncooperative ones, irresp
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5be97f42dad46b2c461f6e54b6419605
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