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Items: 18


Mesoscale Liquid Model of Chromatin Recapitulates Nuclear Order of Eukaryotes.

Laghmach R, Di Pierro M, Potoyan DA.

Biophys J. 2019 Sep 17. pii: S0006-3495(19)30787-8. doi: 10.1016/j.bpj.2019.09.013. [Epub ahead of print]


Disorder Mediated Oligomerization of DISC1 Proteins Revealed by Coarse-Grained Molecular Dynamics Simulations.

Roche J, Potoyan DA.

J Phys Chem B. 2019 Nov 14;123(45):9567-9575. doi: 10.1021/acs.jpcb.9b07467. Epub 2019 Oct 30.


Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes.

Di Pierro M, Potoyan DA, Wolynes PG, Onuchic JN.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):7753-7758. doi: 10.1073/pnas.1806297115. Epub 2018 Jul 9.


A stochastic and dynamical view of pluripotency in mouse embryonic stem cells.

Lin YT, Hufton PG, Lee EJ, Potoyan DA.

PLoS Comput Biol. 2018 Feb 16;14(2):e1006000. doi: 10.1371/journal.pcbi.1006000. eCollection 2018 Feb.


Modeling the therapeutic efficacy of NFκB synthetic decoy oligodeoxynucleotides (ODNs).

Wang Z, Potoyan DA, Wolynes PG.

BMC Syst Biol. 2018 Jan 30;12(1):4. doi: 10.1186/s12918-018-0525-6.


Stochastic dynamics of genetic broadcasting networks.

Potoyan DA, Wolynes PG.

Phys Rev E. 2017 Nov;96(5-1):052305. doi: 10.1103/PhysRevE.96.052305. Epub 2017 Nov 3.


Stochastic resonances in a distributed genetic broadcasting system: the NFκB/IκB paradigm.

Wang Z, Potoyan DA, Wolynes PG.

J R Soc Interface. 2018 Jan;15(138). pii: 20170809. doi: 10.1098/rsif.2017.0809.


Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors.

Potoyan DA, Bueno C, Zheng W, Komives EA, Wolynes PG.

J Am Chem Soc. 2017 Dec 27;139(51):18558-18566. doi: 10.1021/jacs.7b08741. Epub 2017 Dec 15.


Molecular stripping, targets and decoys as modulators of oscillations in the NF-κB/IκBα/DNA genetic network.

Wang Z, Potoyan DA, Wolynes PG.

J R Soc Interface. 2016 Sep;13(122). pii: 20160606. Epub 2016 Sep 28.


PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites.

Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, Komives EA.

J Phys Chem B. 2016 Aug 25;120(33):8532-8. doi: 10.1021/acs.jpcb.6b02359. Epub 2016 May 3.


Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network.

Potoyan DA, Zheng W, Komives EA, Wolynes PG.

Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):110-5. doi: 10.1073/pnas.1520483112. Epub 2015 Dec 23.


Dichotomous noise models of gene switches.

Potoyan DA, Wolynes PG.

J Chem Phys. 2015 Nov 21;143(19):195101. doi: 10.1063/1.4935572.


The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects.

Winogradoff D, Echeverria I, Potoyan DA, Papoian GA.

J Am Chem Soc. 2015 May 20;137(19):6245-53. doi: 10.1021/jacs.5b00235. Epub 2015 May 8.


On the dephasing of genetic oscillators.

Potoyan DA, Wolynes PG.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2391-6. doi: 10.1073/pnas.1323433111. Epub 2014 Jan 27.


Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation.

Potoyan DA, Papoian GA.

Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17857-62. doi: 10.1073/pnas.1201805109. Epub 2012 Sep 17.


Computing free energy of a large-scale allosteric transition in adenylate kinase using all atom explicit solvent simulations.

Potoyan DA, Zhuravlev PI, Papoian GA.

J Phys Chem B. 2012 Feb 9;116(5):1709-15. doi: 10.1021/jp209980b. Epub 2012 Jan 26.


Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics.

Potoyan DA, Papoian GA.

J Am Chem Soc. 2011 May 18;133(19):7405-15. doi: 10.1021/ja1111964. Epub 2011 Apr 25.


Computing free energies of protein conformations from explicit solvent simulations.

Zhuravlev PI, Wu S, Potoyan DA, Rubinstein M, Papoian GA.

Methods. 2010 Sep;52(1):115-21. doi: 10.1016/j.ymeth.2010.05.003. Epub 2010 May 20.

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