Zobrazeno 1 - 10
of 15
pro vyhledávání: '"Alfred C.K. Farris"'
Publikováno v:
American Journal of Physics. 87:310-316
We describe a minimalistic model of a protein undergoing folding into its native (ground) state. This HP protein model is composed of a lattice polymer with two types of monomers: hydrophobic (H) and polar (P). The specific sequence of the two types
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::4a5b0ce1cfd791d54b2178e2e2cb663c
https://doi.org/10.1119/1.5093292
https://doi.org/10.1119/1.5093292
Publikováno v:
The Journal of chemical physics. 154(8)
We compare and contrast folding behavior in several coarse-grained protein models, both on- and off-lattice, in an attempt to uncover the effect of lattice constraints in these kinds of models. Using modern, extended ensemble Monte Carlo methods—Wa
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8abe4bab656cef96197d2a6bcc001e84
https://pubmed.ncbi.nlm.nih.gov/33639740
https://pubmed.ncbi.nlm.nih.gov/33639740
Autor:
Alfred C.K. Farris, David P. Landau
Publikováno v:
Journal of Physics: Conference Series. 2207:012002
The longest sequence in the literature of the HP model of protein folding is studied on a simple cubic lattice using replica-exchange Wang-Landau sampling. We find a lower ground state energy than found in previous studies, and, for the first time, s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::a403b60fa1e4d3ac529ee1838a1abdf7
https://doi.org/10.1088/1742-6596/2207/1/012002
https://doi.org/10.1088/1742-6596/2207/1/012002
Publikováno v:
Journal of Physics: Conference Series, 1290 (1)
To compare folding behavior among lattice proteins which have similar corresponding structures in nature, Crambin homologues are tested in the semi-flexible H0P lattice model using replica-exchange Wang-Landau sampling. Our simulation shows that, at
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d88e9302dc543f846619551b2b5b0e8b
Autor:
Alfred C.K. Farris, David P. Landau
Publikováno v:
Physica A: Statistical Mechanics and its Applications. 569:125778
Long sequences of the HP model of protein folding are studied using replica exchange Wang–Landau sampling. We find lower ground state energies than found from earlier simulations using PERM and replica exchange Monte Carlo and, for the first time,
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7ee07832ef51207e7f837543131fc243
https://doi.org/10.1016/j.physa.2021.125778
https://doi.org/10.1016/j.physa.2021.125778
We report a new multicanonical Monte Carlo algorithm to obtain the density of states for physical systems with continuous state variables in statistical mechanics. Our algorithm is able to obtain a closed-form expression for the density of states exp
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7408b29c3fd46a80a13f9cdc510dccb0
http://arxiv.org/abs/1811.07715
http://arxiv.org/abs/1811.07715
Publikováno v:
Journal of Physics: Conference Series, 1012 (1)
Many studies inspired by the HP lattice protein model have helped to confirm the importance of the hydrophobic "driving force" during folding. Unfortunately, the high level of coarse-graining inherent to this model leads to significant limitations; r
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf926d7b941ca9eee5a27ac8186d40a1
Publikováno v:
Journal of Physics: Conference Series. 1290:012019
In order to study the effects of lattice constraints on coarse-grained protein models, we apply Wang-Landau sampling to the continuum analogue of the hydrophobic-polar (HP) lattice protein model. The continuum version is inspired by the AB polymer mo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7c475f85eadf7e5654178c70ca85aac8
https://doi.org/10.1088/1742-6596/1290/1/012019
https://doi.org/10.1088/1742-6596/1290/1/012019
Publikováno v:
The Journal of Chemical Physics. 149:125101
Using Monte Carlo simulations, we investigate simple, physically motivated extensions to the hydrophobic-polar lattice protein model for the small (46 amino acid) protein Crambin. We use two-dimensional replica-exchange Wang-Landau sampling to study
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2786e6fdaec2b7ce56fe3d00147b8d37
https://doi.org/10.1063/1.5045482
https://doi.org/10.1063/1.5045482
We analyze a semi-infinite one-dimensional random walk process with a biased motion that is incremental in one direction and long-range in the other. On a network with a fixed hierarchy of long-range jumps, we find with exact renormalization group ca
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::70a585b7bb06c1e6b0890467efc8f8f2
http://arxiv.org/abs/1410.2092
http://arxiv.org/abs/1410.2092