Zobrazeno 1 - 10
of 10
pro vyhledávání: '"Enrico Skoruppa"'
Autor:
Enrico Skoruppa, Enrico Carlon
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physical properties have attracted significant interest both from the exper
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::76f0644adb4128665ea8b31e760eaa7f
http://arxiv.org/abs/2205.07735
http://arxiv.org/abs/2205.07735
Autor:
Maxime M. C. Tortora, Hemani Chhabra, Yijing Cao, Garima Mishra, Jonathan P. K. Doye, Enrico Skoruppa, Domen Prešern
Publikováno v:
Journal of Chemical Theory and Computation. 16:7748-7763
To study the elastic properties of rodlike DNA nanostructures, we perform long simulations of these structures using the oxDNA coarse-grained model. By analyzing the fluctuations in these trajectories, we obtain estimates of the bend and twist persis
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4ccb2d2fa58b48d1b9aa385d15295a78
https://doi.org/10.1021/acs.jctc.0c00661
https://doi.org/10.1021/acs.jctc.0c00661
Autor:
Enrico Skoruppa, Jan A. Stevens, Aderik Voorspoels, Enrico Carlon, Merijn Vangilbergen, Midas Segers
Publikováno v:
The Journal of chemical physics. 155(2)
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence length incr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6c8b1b18fb876ced9b82d123cf526cdf
https://pubmed.ncbi.nlm.nih.gov/25833610
https://pubmed.ncbi.nlm.nih.gov/25833610
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are coupled. He
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a2521598d727d2cae6ad4bb693850e8d
http://arxiv.org/abs/2010.01302
http://arxiv.org/abs/2010.01302
Publikováno v:
The Journal of chemical physics. 150(13)
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend coupling, a cross
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0ecbd7b0b5239dfe05d1c971f64e6bf1
https://pubmed.ncbi.nlm.nih.gov/30954045
https://pubmed.ncbi.nlm.nih.gov/30954045
Autor:
Enrico Skoruppa, Michele Caraglio, Michiel Laleman, Enrico Carlon, K. Phillips, Stefanos K. Nomidis
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an imposed bending
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2af2dab940bd0b94477b347ce0745fa9
Publikováno v:
Physical review. E. 99(3-1)
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from the groove a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3f567d4d70f12c4b7a8c00e8ffbdee25
https://pubmed.ncbi.nlm.nih.gov/30999490
https://pubmed.ncbi.nlm.nih.gov/30999490
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling G between twisting and bending, known to arise from the groove asy
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ee429ba2a50c12d4ffa22cc52a18f885
https://doi.org/10.1101/422683
https://doi.org/10.1101/422683
Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend coupling
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::08027a47c7f2b7fb8c70be2a4def5231
https://doi.org/10.1101/256818
https://doi.org/10.1101/256818
It is well-established that many physical properties of DNA at sufficiently long length scales can be understood by means of simple polymer models. One of the most widely used elasticity models for DNA is the twistable worm-like chain (TWLC), which d
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::86e6be387055822961fb31929053065a
http://arxiv.org/abs/1703.02598
http://arxiv.org/abs/1703.02598