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Tariq, Syeda Sumayya, Zia, Komal, Nur-e-Alam, Mohammad, Nerukh, Dmitry, Farafonov, Vladimir S. and Ul-Haq, Zaheer (2024). Impact of mutations in SARS-CoV-2 recombinant sub-variant XBB.1.16 on the binding affinity with human ACE2 receptor. Journal of Molecular Graphics and Modelling, 131 ,

Abdjan, Muhammad Ikhlas, Shafiq, Muhammad, Nerukh, Dmitry, Nur-e-Alam, Mohammad and Ul-Haq, Zaheer (2024). Exploring the mechanism of action of spirooxindoles as a class of CDK2 inhibitors: a structure-based computational approach. Physical Chemistry Chemical Physics, 26 (22), pp. 16139-16152.

Sharoyko, Vladimir V., Kukaliia, Olegi N., Darvish, Diana M., Meshcheriakov, Anatolii A., Iurev, Gleb O., Andoskin, Pavel A., Penkova, Anastasia V., Ageev, Sergei V., Petukhova, Natalia V., Timoshchuk, Kirill V., Petrov, Andrey V., Akentev, Aleksandr V., Nerukh, Dmitry A., Mazur, Anton S., Maistrenko, Dmitrii N., Molchanov, Oleg E., Murin, Igor V. and Semenov, Konstantin N. (2024). Protective action of water-soluble fullerene adducts on the example of an adduct with L-arginine. Journal of Molecular Liquids, 401 ,

Munsif, Sajida, Ayub, Khurshid, Nur-e-Alam, Mohammad, Nerukh, Dmitry and Ul-Haq, Zaheer (2024). Alkali metal decorated BC3 monolayer as sensing material for warfare agents. Computational and Theoretical Chemistry, 1234 ,

Laguta, Anna, Vodolazkaya, Natalya and Nerukh, Dmitry (2024). The Spectrophotometric Determination of the Patchy Surface Potential of Viruses Using pH-Sensitive Molecular Probes. Journal of Chemical Education, 101 (3), pp. 1190-1197.

Ahmad, Nadeem, Ali Khan, Salman, Sardar, Madiha, Mushtaq, Mamona, Siddiqui, Ali Raza, Munsif, Sajida, Nur-e-Alam, Mohammad, Nerukh, Dmitry and Ul-Haq, Zaheer (2024). Mutant anaplastic lymphoma kinase inhibitor identification by integrated in silico approaches. Molecular Simulation, 50 (5), pp. 404-419.

Farafonov, Vladimir S., Stich, Michael and Nerukh, Dmitry A. (2023). Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome. Journal of Chemical Theory and Computation, 19 (21), pp. 7924-7933.

Vodolazkaya, Natalya, Laguta, Anna, Farafonov, Vladimir, Nikolskaya, Marina, Balklava, Zita, Khayat, Reza, Stich, Michael, Mchedlov-Petrossyan, Nikolay and Nerukh, Dmitry (2023). Influence of various colloidal surfactants on the stability of MS2 bacteriophage suspension. The charge distribution on the PCV2 virus surface. Journal of Molecular Liquids, 387 ,

Sharoyko, Vladimir V, Berdichevsky, Grigory M, Vasina, Lubov V, Shemchuk, Olga S, Maystrenko, Dmitriy N, Molchanov, Oleg E, Abdelhalim, Abdelsattar O E, Nashchekin, Alexey V, Nerukh, Dmitry A, Tochilnikov, Grigorii V, Murin, Igor V and Semenov, Konstantin N (2023). Covalent conjugates based on nanodiamonds with doxorubicin and a cytostatic drug from the group of 1,3,5-triazines::Synthesis, biocompatibility and biological activity. BBA - General Subjects, 1867 (9), p. 130384.

Karabasov, Sergey A., Zaitsev, Mihail A. and Nerukh, Dmitry A. (2023). The nut-and-bolt motion of a bacteriophage sliding along a bacterial flagellum: a complete hydrodynamics model. Scientific Reports, 13 (1),

Farafonov, Vladimir S., Lebed, Alexander V., Nerukh, Dmitry A. and Mchedlov-Petrossyan, Nikolay O. (2023). Estimation of Nanoparticle’s Surface Electrostatic Potential in Solution Using Acid–Base Molecular Probes I: In Silico Implementation for Surfactant Micelles. Journal of Physical Chemistry: Part B, 127 (4), 1022–1030.

Farafonov, Vladimir S., Lebed, Alexander V., Nerukh, Dmitry A. and Mchedlov-Petrossyan, Nikolay O. (2023). Estimation of Nanoparticle’s Surface Electrostatic Potential in Solution Using Acid–Base Molecular Probes II: Insight from Atomistic Simulations of Micelles. Journal of Physical Chemistry: Part B, 127 (4), 1031–1038.

Lebedev, Vasiliy T., Charykov, Nikolay A., Shemchuk, Olga S., Murin, Igor V., Nerukh, Dmitry A., Petrov, Andrey V., Maystrenko, Dmitriy N., Molchanov, Oleg E., Sharoyko, Vladimir V. and Semenov, Konstantin N. (2023). Endometallofullerenes and their derivatives:Synthesis, physicochemical properties, and perspective application in biomedicine. Colloids and Surfaces B: Biointerfaces, 222 ,

Farafonov, Vladimir, Stich, Michael and Nerukh, Dmitry (2022). Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density. Faraday Discussions, 240 , pp. 152-167.

Vodolazkaya, Natalya, Nikolskaya, Marina, Laguta, Anna, Farafonov, Vladimir, Balklava, Zita, Stich, Michael, Mchedlov-Petrossyan, Nikolay and Nerukh, Dmitry (2022). Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes. III. Experimental Hydrophobicity/Hydrophilicity and Charge Distribution of MS2 Virus Surface. Journal of Physical Chemistry: Part B, 126 (41), pp. 8166-8176.

Mikolaichuk, Olga V., Popova, Elena A., Protas, Alexandra V., Rakipov, Ilnaz T., Nerukh, Dmitry A., Petrov, Andrey V., Charykov, Nikolay A., Ageev, Sergei V., Tochilnikov, Grigorii V., Zmitrichenko, Iulia G., Stukov, Aleksandr N., Semenov, Konstantin N. and Sharoyko, Vladimir V. (2022). A cytostatic drug from the class of triazine derivatives:Its properties in aqueous solutions, cytotoxicity, and therapeutic activity. Journal of Molecular Liquids, 356 ,

Abdelhalim, Abdelsattar O.E., Semenov, Konstantin N., Nerukh, Dmitry A., Murin, Igor V., Maistrenko, Dmitrii N., Molchanov, Oleg E. and Sharoyko, Vladimir V. (2022). Functionalisation of graphene as a tool for developing nanomaterials with predefined properties. Journal of Molecular Liquids, 348 ,

Tarasova, Elvira, Okimoto, Noriaki, Feng, Shanshan, Nerukh, Dmitry, Khayat, Reza and Taiji, Makoto (2021). Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly. Physical Chemistry Chemical Physics, 23 (43), pp. 24617-24626.

Maximova, Ekaterina, Postnikov, Eugene B., Lavrova, Anastasia I., Farafonov, Vladimir and Nerukh, Dmitry (2021). Protein–Ligand Dissociation Rate Constant from All-Atom Simulation. Journal of Physical Chemistry Letters, 12 (43), 10631–10636.

Abdelhalim, Abdelsattar O.E., Sharoyko, Vladimir V., Ageev, Sergei V., Farafonov, Vladimir S., Nerukh, Dmitry A., Postnov, Viktor N., Petrov, Andrey V. and Semenov, Konstantin N. (2021). Graphene Oxide of Extra High Oxidation: A Wafer for Loading Guest Molecules. Journal of Physical Chemistry Letters, 12 (41), 10015–10024.

Sharoyko, Vladimir V., Iamalova, Nailia R., Ageev, Sergei V., Meshcheriakov, Anatolii A., Iurev, Gleb O., Petrov, Andrey V., Nerukh, Dmitry A., Farafonov, Vladimir S., Vasina, Lubov V., Penkova, Anastasia V. and Semenov, Konstantin N. (2021). In Vitro and In Silico Investigation of Water-Soluble Fullerenol C60(OH)24:Bioactivity and Biocompatibility. Journal of Physical Chemistry: Part B, 125 (32), 9197–9212.

Qaiser, Hina, Saeed, Maria, Nerukh, Dmitry and Ul-Haq, Zaheer (2021). Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation. Journal of Biomolecular Structure and Dynamics, 39 (16), pp. 5920-5939.

Vus, Kateryna, Tarabara, Uliana, Balklava, Zita, Nerukh, Dmitry, Stich, Michael, Laguta, Anna, Vodolazkaya, Natalya, Mchedlov-Petrossyan, Nikolay O., Farafonov, Vladimir, Kriklya, Nika, Gorbenko, Galyna, Trusova, Valeriya, Zhytniakivska, Olga, Kurutos, Atanas, Gadjev, Nikolai and Deligeorgiev, Todor (2020). Association of novel monomethine cyanine dyes with bacteriophage MS2:A fluorescence study. Journal of Molecular Liquids, 302 ,

Wu, Yuanhao, Okesola, Babatunde O, Xu, Jing, Korotkin, Ivan, Berardo, Alice, Corridori, Ilaria, di Brocchetti, Francesco Luigi Pellerej, Kanczler, Janos, Feng, Jingyu, Li, Weiqi, Shi, Yejiao, Farafonov, Vladimir, Wang, Yiqiang, Thompson, Rebecca F, Titirici, Maria-Magdalena, Nerukh, Dmitry, Karabasov, Sergey, Oreffo, Richard O C, Carlos Rodriguez-Cabello, Jose, Vozzi, Giovanni, Azevedo, Helena S, Pugno, Nicola M, Wang, Wen and Mata, Alvaro (2020). Disordered protein-graphene oxide co-assembly and supramolecular biofabrication of functional fluidic devices. Nature Communications, 11 (1),

Atamas, Natalia, Bardik, Vitalii Y., Komisarenko, Serhiy, Makogonenko, Yevgen M., Lugovskoi, Edward V., Malomuz, Nikolai P., Nerukh, Dmitry and Solonin, Pavlo K. (2019). Water dynamics and stability of major blood proteins at pre-denaturation stage. Atti della Accademia Peloritana dei Pericolanti, 97 (Suppl ),

Farafonov, Vladimir S. and Nerukh, Dmitry (2019). MS2 bacteriophage capsid studied using all-atom molecular dynamics. Interface Focus, 9 (3),

Mchedlov-Petrossyan, Nikolay O., Farafonov, Vladimir S., Cheipesh, Tatyana A., Shekhovtsov, Sergey V., Nerukh, Dmitry A. and Lebed, Alexander V. (2019). In search of an optimal acid-base indicator for examining surfactant micelles:Spectrophotometric studies and molecular dynamics simulations. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 565 , pp. 97-107.

Tarasova, Elvira and Nerukh, Dmitry (2018). All-Atom Molecular Dynamics Simulations of Whole Viruses. Journal of Physical Chemistry Letters, 9 , pp. 5805-5809.

Tarasova, Elvira, Farafonov, Vladimir, Taiji, Makoto and Nerukh, Dmitry (2018). Details of charge distribution in stable viral capsid. Journal of Molecular Liquids, 265 , pp. 585-591.

Tarasova, Elvira, Korotkin, Ivan, Farafonov, Volodymyr, Karabasov, Sergey and Nerukh, Dmitry (2017). Complete virus capsid at all-atom resolution:simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function. Journal of Molecular Liquids, 245 , pp. 109-114.

Atamas, N., Bardik, V., Bannikova, A., Grishina, O., Lugovskoi, E., Lavoryk, S., Makogonenko, Y., Korolovych, V., Nerukh, D. and Paschenko, V. (2017). The effect of water dynamics on conformation changes of albumin in pre-denaturation state:photon correlation spectroscopy and simulation. Journal of Molecular Liquids, 235 , pp. 17-23.

Tarasova, Elvira, Farafonov, Vladimir, Khayat, Reza, Okimoto, Noriaki, Komatsu, Teruhisa, Taiji, Makoto and Nerukh, Dmitry (2017). All-atom molecular dynamics simulations of entire virus capsid reveal the role of ion distribution in capsid’s stability. Journal of Physical Chemistry Letters, 8 (4), pp. 779-784.

Korotkin, Ivan, Nerukh, Dmitry, Tarasova, Elvira, Farafonov, Vladimir and Karabasov, Sergey (2016). Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution. Journal of Computational Science, 17 (part 2), pp. 446-456.

Scukins, A., Nerukh, D., Pavlov, E., Karabasov, S. and Markesteijn, A. (2015). Multiscale molecular dynamics/hydrodynamics implementation of two dimensional “Mercedes Benz” water model. The European Physical Journal: Special Topics, 224 (12), pp. 2217-2238.

Korotkin, Ivan, Karabasov, Sergey, Nerukh, Dmitry, Markesteijn, Anton, Scukins, Arturs, Farafonov, Vladimir and Pavlov, Evgen (2015). A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time. Journal of Chemical Physics, 143 (1),

Scukins, Arturs, Bardik, Vitaliy, Pavlov, Evgen and Nerukh, Dmitry (2015). Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model. Computer Physics Communications, 190 , pp. 129-138.

Karabasov, Sergey, Nerukh, Dmitry, Hoekstra, Alfons, Chopard, Bastien and Coveney, Peter V. (2014). Multiscale modelling:approaches and challenges. Philosophical Transactions A, 372 (2021),

Pavlov, Evgen, Taiji, Makoto, Scukins, Arturs, Markesteijn, Anton, Karabasov, Sergey and Nerukh, Dmitry (2014). Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space. Faraday Discussions, 169 , pp. 285-302.

Nerukh, Dmitry and Karabasov, Sergey (2013). Water-peptide dynamics during conformational transitions. Journal of Physical Chemistry Letters, 4 (5), pp. 815-819.

Bardik, V.Yu., Nerukh, D., Pavlov, E. and Zhyganiuk, I. (2012). Equation of state for water in the small compressibility region. Ukrainian Journal of Physics, 57 (1), pp. 47-51.

Ryabov, Vladimir and Nerukh, Dmitry (2011). Computational mechanics of molecular systems:quantifying high-dimensional dynamics by distribution of Poincaré recurrence times. Chaos, 21 (3),

Nerukh, Dmitry and Ryabov, Vladimir (2011). Quantifying long time memory in phase space trajectories of molecular liquids. Journal of Molecular Liquids, 159 (1), pp. 99-104.

Fedorov, Maxim V., Goodman, Jonathan M., Nerukh, Dmitry and Schumm, Stephan (2011). Self-assembly of trehalose molecules on a lysozyme surface: the broken glass hypothesis. Physical Chemistry Chemical Physics, 13 (6), pp. 2294-2299.

Ruzhytska, Svitlana, Jacobi, Martin N., Jensen, Christian H. and Nerukh, Dmitry (2010). Identification of metastable states in peptide's dynamics. Journal of Chemical Physics, 133 (16), p. 164102.

Nerukh, Dmitry, Jensen, Christian H. and Glen, Robert C. (2010). Identifying and correcting non-Markov states in peptide conformational dynamics. Journal of Chemical Physics, 132 (8), 084104.

Nerukh, Dmitry, Ryabov, Vladimir and Taiji, Makoto (2009). Molecular phase space transport in water:non-stationary random walk model. Physica A, 388 (22), pp. 4719-4726.

Nerukh, Dmitry and Taiji, Makoto (2009). 21-residue peptide's dynamics at and between elementary structural transitions. Journal of Molecular Liquids, 147 (1-2), pp. 124-127.

Nerukh, D. (2009). Dynamical frustration of protein's environment at the nanoseconds time scale. Journal of Molecular Liquids, 145 (3), pp. 139-144.

Jensen, Christian H., Nerukh, Dmitry and Glen, Robert C. (2008). Controlling protein molecular dynamics:how to accelerate folding while preserving the native state. Journal of Chemical Physics, 129 (22),

Buts, V.A., Nerukh, A.G., Ruzhytska, N.N. and Nerukh, Dmitry (2008). Wave chaotic behaviour generated by linear systems. Optical and Quantum Electronics, 40 (8), pp. 587-601.

Nerukh, D. (2008). Computational mechanics reveals nanosecond time correlations in molecular dynamics of liquid systems. Chemical Physics Letters, 457 (4-6), pp. 439-443.

Nerukh, Dmitry, Ryabov, Vladimir and Glen, Robert C. (2008). Complex temporal patterns in molecular dynamics:a direct measure of the phase-space exploration by the trajectory at macroscopic time scales. Physical Review E, 77 (3),

Jensen, Christian H., Nerukh, Dmitry and Glen, Robert C. (2008). Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory. Journal of Chemical Physics, 128 (11),

Jensen, Christian H., Nerukh, Dmitry and Glen, Robert C. (2007). Calculating mean first passage times from Markov models of proteins. AIP Conference Proceedings, 940 , pp. 150-157.

Karvounis, George, Nerukh, Dmitry and Glen, Robert C. (2004). Water network dynamics at the critical moment of a peptide's ß-turn formation:a molecular dynamics study. Journal of Chemical Physics, 121 (10), pp. 4925-4935.

Nerukh, Dmitry, Karvounis, George and Glen, Robert C. (2002). Complexity of classical dynamics of molecular systems. I. Methodology. Journal of Chemical Physics, 117 (21), pp. 9611-9617.

Nerukh, Dmitry, Karvounis, George and Glen, Robert C. (2002). Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a water-Na+ system. Journal of Chemical Physics, 117 (21), pp. 9618-9622.

Nerukh, Dimitry and Frederick, John H. (2000). Multidimensional quantum dynamics with trajectories: a novel numerical implementation of Bohmian mechanics. Chemical Physics Letters, 332 (1-2), pp. 145-153.

Book Section

Nerukh, Dmitry (2010). Why are MD simulated protein folding times wrong? IN: Advances in Computational Biology. Arabnia, Hamid R. (ed.) Advances in Experimental Medicine and Biology, Part 3 . Springer.

Nerukh, A., Ruzhytska, N. and Nerukh, D. (2006). Quasi-intermittency of waves and their complexity in modulated dielectric medium. IN: Conference Proceedings - 11th International Conference on Mathematical Methods in Electromagnetic Theory, MMET'06. UKR: UNSPECIFIED.

Monograph

Maximova, Ekaterina, Postnikov, Eugene, Lavrova, Anastasia, Farafonov, Vladimir and Nerukh, Dmitry (2021). Protein-ligand dissociation rate constant from all-atom simulation. Other. Research Square.

Other

Nerukh, Alexander G., Zolotariov, Denis A. and Nerukh, Dmitry (2011). Bifurcating trajectory of non-diffractive electromagnetic airy pulse. UNSPECIFIED. (Unpublished)