Nerukh D - Search Results

1

All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.

Tarasova E, Farafonov V, Khayat R, Okimoto N, Komatsu TS, Taiji M, Nerukh D. Tarasova E, et al. Among authors: nerukh d. J Phys Chem Lett. 2017 Feb 16;8(4):779-784. doi: 10.1021/acs.jpclett.6b02759. Epub 2017 Feb 1. J Phys Chem Lett. 2017. PMID: 28129688 Free PMC article.

2

Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space.

Pavlov E, Taiji M, Scukins A, Markesteijn A, Karabasov S, Nerukh D. Pavlov E, et al. Among authors: nerukh d. Faraday Discuss. 2014;169:285-302. doi: 10.1039/c3fd00159h. Epub 2014 Jun 17. Faraday Discuss. 2014. PMID: 25340552

3

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time.

Korotkin I, Karabasov S, Nerukh D, Markesteijn A, Scukins A, Farafonov V, Pavlov E. Korotkin I, et al. Among authors: nerukh d. J Chem Phys. 2015 Jul 7;143(1):014110. doi: 10.1063/1.4923011. J Chem Phys. 2015. PMID: 26156468 Free article.

4

Ligand Diffusion on Protein Surface Observed in Molecular Dynamics Simulation.

Nerukh D, Okimoto N, Suenaga A, Taiji M. Nerukh D, et al. J Phys Chem Lett. 2012 Dec 6;3(23):3476-9. doi: 10.1021/jz301635h. Epub 2012 Nov 14. J Phys Chem Lett. 2012. PMID: 26290975

5

All-Atom Molecular Dynamics Simulations of Whole Viruses.

Tarasova E, Nerukh D. Tarasova E, et al. Among authors: nerukh d. J Phys Chem Lett. 2018 Oct 4;9(19):5805-5809. doi: 10.1021/acs.jpclett.8b02298. Epub 2018 Sep 24. J Phys Chem Lett. 2018. PMID: 30230849

6

MS2 bacteriophage capsid studied using all-atom molecular dynamics.

Farafonov VS, Nerukh D. Farafonov VS, et al. Among authors: nerukh d. Interface Focus. 2019 Jun 6;9(3):20180081. doi: 10.1098/rsfs.2018.0081. Epub 2019 Apr 19. Interface Focus. 2019. PMID: 31065345 Free PMC article.

7

Disordered protein-graphene oxide co-assembly and supramolecular biofabrication of functional fluidic devices.

Wu Y, Okesola BO, Xu J, Korotkin I, Berardo A, Corridori I, di Brocchetti FLP, Kanczler J, Feng J, Li W, Shi Y, Farafonov V, Wang Y, Thompson RF, Titirici MM, Nerukh D, Karabasov S, Oreffo ROC, Carlos Rodriguez-Cabello J, Vozzi G, Azevedo HS, Pugno NM, Wang W, Mata A. Wu Y, et al. Among authors: nerukh d. Nat Commun. 2020 Mar 4;11(1):1182. doi: 10.1038/s41467-020-14716-z. Nat Commun. 2020. PMID: 32132534 Free PMC article.

8

In Vitro and In Silico Investigation of Water-Soluble Fullerenol C₆₀(OH)₂₄: Bioactivity and Biocompatibility.

Sharoyko VV, Iamalova NR, Ageev SV, Meshcheriakov AA, Iurev GO, Petrov AV, Nerukh DA, Farafonov VS, Vasina LV, Penkova AV, Semenov KN. Sharoyko VV, et al. J Phys Chem B. 2021 Aug 19;125(32):9197-9212. doi: 10.1021/acs.jpcb.1c03332. Epub 2021 Aug 10. J Phys Chem B. 2021. PMID: 34375109

9

Graphene Oxide of Extra High Oxidation: A Wafer for Loading Guest Molecules.

Abdelhalim AOE, Sharoyko VV, Ageev SV, Farafonov VS, Nerukh DA, Postnov VN, Petrov AV, Semenov KN. Abdelhalim AOE, et al. J Phys Chem Lett. 2021 Oct 21;12(41):10015-10024. doi: 10.1021/acs.jpclett.1c02766. Epub 2021 Oct 7. J Phys Chem Lett. 2021. PMID: 34618465

10

Protein-Ligand Dissociation Rate Constant from All-Atom Simulation.

Maximova E, Postnikov EB, Lavrova AI, Farafonov V, Nerukh D. Maximova E, et al. Among authors: nerukh d. J Phys Chem Lett. 2021 Nov 4;12(43):10631-10636. doi: 10.1021/acs.jpclett.1c02952. Epub 2021 Oct 27. J Phys Chem Lett. 2021. PMID: 34704768

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