Výsledky vyhledávání - "Peter C. Kroon"

Akademický článek

Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

Autor: Fabian Grünewald, Riccardo Alessandri, Peter C. Kroon, Luca Monticelli, Paulo C. T. Souza, Siewert J. Marrink

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-12 (2022)

To facilitate the rational design of (nano)-materials and biomacromolecules by MD simulations, the authors present the polyply suite, featuring a graph matching algorithm and a random walk protocol for generating multi-scale polymeric topologies and

Externí odkaz: https://doaj.org/article/2f66b81bff3e43829c65a5e4b1612a5b

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Martini 3

Publikováno v: Nature Methods, 18, 382-388. Nature Publishing Group
Nature Methods
Souza, P C T, Alessandri, R, Barnoud, J, Thallmair, S, Faustino, I, Grünewald, F, Patmanidis, I, Abdizadeh, H, Bruininks, B M H, Wassenaar, T A, Kroon, P C, Melcr, J, Nieto, V, Corradi, V, Khan, H M, Domański, J, Javanainen, M, Martinez-Seara, H, Reuter, N, Best, R B, Vattulainen, I, Monticelli, L, Periole, X, Tieleman, D P, de Vries, A H & Marrink, S J 2021, ' Martini 3 : a general purpose force field for coarse-grained molecular dynamics ', Nature Methods, vol. 18, no. 4, pp. 382-388 . https://doi.org/10.1038/s41592-021-01098-3

The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific inter

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f1fe1d2646ea2c4aa330b9fd3b0ab46d
https://hdl.handle.net/11370/27f1d65b-ff4d-4290-9fc8-b019e36c5c2e

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Stochastic Emergence of Two Distinct Self-Replicators from a Dynamic Combinatorial Library

Autor: Gaël Schaeffer, Marcel J. Eleveld, Jim Ottelé, Peter C. Kroon, Pim W. J. M. Frederix, Shuo Yang, Sijbren Otto

Publikováno v: Journal of the American Chemical Society, 144(14), 6291-6297. AMER CHEMICAL SOC

Unraveling how chemistry can give rise to biology is one of the greatest challenges of contemporary science. Achieving life-like properties in chemical systems is therefore a popular topic of research. Synthetic chemical systems are usually determini

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e0d5a73f59b10a83b1279bf8de7276b1
https://pubmed.ncbi.nlm.nih.gov/35357150

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Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization

Autor: Jim Ottelé, Peter C. Kroon, Wouter H. Roos, Guillermo Monreal Santiago, Omer Markovitch, Sijbren Otto, Marc C. A. Stuart, Pim W. J. M. Frederix, Sourav Maity, Siewert J. Marrink

Publikováno v: J. Am. Chem. Soc.
Journal of the American Chemical Society
Journal of the American Chemical Society, 142(32), 13709-13717. AMER CHEMICAL SOC

Self-assembly features prominently in fields ranging from materials science to biophysical chemistry. Assembly pathways, often passing through transient intermediates, can control the outcome of assembly processes. Yet, the mechanisms of self-assembl

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::febeb8a72691d15c2a46820e7225f964
https://doi.org/10.1021/jacs.0c02635

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Protocol for Simulations of PEGylated Proteins with Martini 3

Autor: Fabian, Grünewald, Peter C, Kroon, Paulo C T, Souza, Siewert J, Marrink

Publikováno v: Methods in molecular biology (Clifton, N.J.). 2199

Enhancement of proteins by PEGylation is an active area of research. However, the interactions between polymer and protein are far from fully understood. To gain a better insight into these interactions or even make predictions, molecular dynamics (M

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::88d21b20082c23bd735b6ac278cc7798
https://pubmed.ncbi.nlm.nih.gov/33125658

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