Zobrazeno 1 - 10
of 14
pro vyhledávání: '"Fabian, Grünewald"'
Autor:
Benjamin R. Gilbert, Zane R. Thornburg, Troy A. Brier, Jan A. Stevens, Fabian Grünewald, John E. Stone, Siewert J. Marrink, Zaida Luthey-Schulten
Publikováno v:
Frontiers in Cell and Developmental Biology, Vol 11 (2023)
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial
Externí odkaz:
https://doaj.org/article/42b2539a78d14ebabeca3d47e234ce28
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
Autor:
Jan A. Stevens, Fabian Grünewald, P. A. Marco van Tilburg, Melanie König, Benjamin R. Gilbert, Troy A. Brier, Zane R. Thornburg, Zaida Luthey-Schulten, Siewert J. Marrink
Publikováno v:
Frontiers in Chemistry, Vol 11 (2023)
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell’s components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge
Externí odkaz:
https://doaj.org/article/ec6346a36976419a93f6e9f4abc90255
Autor:
Selim Sami, Riccardo Alessandri, Jeff B. W. Wijaya, Fabian Grünewald, Alex H. de Vries, Siewert J. Marrink, Ria Broer, Remco W. A. Havenith
Publikováno v:
JOURNAL OF PHYSICAL CHEMISTRY C
Journal of Physical Chemistry C, 126(45):2c05682, 19462-19469. AMER CHEMICAL SOC
Journal of Physical Chemistry C, 126(45):2c05682, 19462-19469. AMER CHEMICAL SOC
High dielectric constant organic semiconductors, often obtained by the use of ethylene glycol (EG) side chains, have gained attention in recent years in the efforts of improving the device performance for various applications. Dielectric constant enh
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::196545c945c1be367f3df7c2f828c8ad
https://doi.org/10.1021/acs.jpcc.2c05682
https://doi.org/10.1021/acs.jpcc.2c05682
Publikováno v:
A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules ISBN: 9780735425248
The Martini force-field for molecular dynamics (MD) simulations is suitable for running MD simulations of complex bio(molecular) systems and nano-materials. Recently, titratable Martini was developed, which is an extension of the popular force-field
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::cbca994478c88d1e0022784dd5f008ce
https://doi.org/10.1063/9780735425279_004
https://doi.org/10.1063/9780735425279_004
Autor:
Fabian Grünewald, Mats H. Punt, Elizabeth E. Jefferys, Petteri A. Vainikka, Melanie König, Valtteri Virtanen, Travis A. Meyer, Weria Pezeshkian, Adam J. Gormley, Maarit Karonen, Mark S. P. Sansom, Paulo C. T. Souza, Siewert J. Marrink
Publikováno v:
Journal of Chemical Theory and Computation, 18(12). AMER CHEMICAL SOC
Grünewald, F, Punt, M H, Jefferys, E E, Vainikka, P, König, M, Virtanen, V, Meyer, T A, Pezeshkian, W, Gormley, A, Karonen, M, Sansom, M S P, Souza, P C T & Marrink, S 2022, ' Martini 3 Coarse-Grained Force Field for Carbohydrates ', Journal of Chemical Theory and Computation, vol. 18, no. 12, pp. 7555-7569 . https://doi.org/10.1021/acs.jctc.2c00757
Grünewald, F, Punt, M H, Jefferys, E E, Vainikka, P, König, M, Virtanen, V, Meyer, T A, Pezeshkian, W, Gormley, A, Karonen, M, Sansom, M S P, Souza, P C T & Marrink, S 2022, ' Martini 3 Coarse-Grained Force Field for Carbohydrates ', Journal of Chemical Theory and Computation, vol. 18, no. 12, pp. 7555-7569 . https://doi.org/10.1021/acs.jctc.2c00757
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ed2775c6911d458d8f4bc2eddd1acc5f
https://doi.org/10.1021/acs.jctc.2c00757
https://doi.org/10.1021/acs.jctc.2c00757
Publikováno v:
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 14, 905-911. AMER CHEMICAL SOC
The photosystem II PsbS protein triggers the photo-protective mechanism of plants – nonphotochemical quenching (NPQ) – by sensing the acidification of the thylakoid lumen. A popular model of the NPQ activation involves the monomerization of the P
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0fea8e0c1c7408975d663630d1d33ac5
https://doi.org/10.26434/chemrxiv-2022-7zgw4
https://doi.org/10.26434/chemrxiv-2022-7zgw4
Autor:
Vincent Nieto, Valentina Corradi, Siewert J. Marrink, Matti Javanainen, Peter C. Kroon, Ilpo Vattulainen, Hector Martinez-Seara, D. Peter Tieleman, Alex H. de Vries, Jan Domański, Hanif M. Khan, Robert B. Best, Ilias Patmanidis, Sebastian Thallmair, Ignacio Faustino, Xavier Periole, Jonathan Barnoud, Tsjerk A. Wassenaar, Josef Melcr, Nathalie Reuter, Haleh Abdizadeh, Bart M H Bruininks, Paulo C. T. Souza, Fabian Grünewald, Riccardo Alessandri, Luca Monticelli
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
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
https://hdl.handle.net/11370/27f1d65b-ff4d-4290-9fc8-b019e36c5c2e
Autor:
Weria Pezeshkian, Fabian Grünewald, Oleksandr Narykov, Senbao Lu, Valeria Arkhipova, Alexey Solodovnikov, Tsjerk A Wassenaar, Siewert J. Marrink, Dmitry Korkin
Publikováno v:
Structure, 31(4):202302006, 492-503. CELL PRESS
Despite tremendous efforts by the research community during the COVID-19 pandemic, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. Being a key structural component of the SARS-CoV-2 virion, the envelope encapsulates v
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::837a0d3f52cd005a54ea449750a7d0f4
https://doi.org/10.1101/2021.09.15.459697
https://doi.org/10.1101/2021.09.15.459697
Publikováno v:
Advanced materials, 33(24):e2008635. WILEY-V C H VERLAG GMBH
The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::599686a4b711767efee058d1ae09467f
https://research.rug.nl/en/publications/02a7f046-3ce7-477c-9204-32aae654a5a8
https://research.rug.nl/en/publications/02a7f046-3ce7-477c-9204-32aae654a5a8