Rikkert J Nap
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Explore the profile of Rikkert J Nap including associated specialties, affiliations and a list of published articles.
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28
Citations
245
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Recent Articles
1.
Nap R, Carillo Gonzalez P, Coraor A, Virk R, de Pablo J, Backman V, et al.
J Chem Phys
. 2024 Dec;
161(23).
PMID: 39704570
We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP)-the fundamental unit of chromatin consisting of DNA wrapped around a core of histone proteins....
2.
Nap R, Gonzalez P, Coraor A, Virk R, de Pablo J, Backman V, et al.
bioRxiv
. 2024 Nov;
PMID: 39605663
We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP) - the fundamental unit of chromatin consisting of DNA wrapped around a core of...
3.
Frederick J, Virk R, Ye I, Almassalha L, Wodarcyk G, VanDerway D, et al.
bioRxiv
. 2024 Nov;
PMID: 39605341
Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications...
4.
Carignano M, Kroeger M, Almassalha L, Agrawal V, Li W, Pujadas-Liwag E, et al.
Elife
. 2024 Sep;
13.
PMID: 39331520
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV generate conformationally defined domains observed by single-cell...
5.
Carignano M, Kroger M, Almassalha L, Agrawal V, Li W, Pujadas-Liwag E, et al.
ArXiv
. 2024 Mar;
PMID: 38495560
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV generate conformationally-defined domains observed by single cell...
6.
Carignano M, Kroger M, Almassalha L, Agrawal V, Li W, Pujadas E, et al.
Res Sq
. 2023 Oct;
PMID: 37886531
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions that is able to capture the observed behavior across...
7.
Nap R, Qiao B, Palmer L, Stupp S, Olvera de la Cruz M, Szleifer I
Front Chem
. 2022 Apr;
10:852164.
PMID: 35372273
Peptide amphiphiles are a class of molecules that can self-assemble into a variety of supramolecular structures, including high-aspect-ratio nanofibers. It is challenging to model and predict the charges in these...
8.
Gonzalez Solveyra E, Nap R, Huang K, Szleifer I
Polymers (Basel)
. 2020 Oct;
12(10).
PMID: 33027995
Surface functionalization with end-tethered weak polyelectrolytes (PE) is a versatile way to modify and control surface properties, given their ability to alter their degree of charge depending on external cues...
9.
Huang K, Li Y, Shim A, Virk R, Agrawal V, Eshein A, et al.
Sci Adv
. 2020 Jan;
6(2):eaay4055.
PMID: 31950084
With the textbook view of chromatin folding based on the 30-nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10-nm nucleosome polymer structure whose folding...
10.
Shim A, Nap R, Huang K, Almassalha L, Matusda H, Backman V, et al.
Biophys J
. 2019 Dec;
118(9):2117-2129.
PMID: 31818468
The nuclear environment is highly crowded by biological macromolecules, including chromatin and mobile proteins, which alter the kinetics and efficiency of transcriptional machinery. These alterations have been described, both theoretically...