Publications

Below is a list of all work published by the group. For convenience, we have compiled a file containing citations formatted for use with BibTex containing all of these publications: A file containing bibtex citations for the work published by the Soft Matter Modelling Lab

• Rouse, I., Power, D., Subbotina, J., Lobaskin, V. NPCoronaPredict: A Computational Pipeline for the Prediction of the Nanoparticle–Biomolecule Corona. J. Chem. Inf. Model. 64, 19, 7525–7543 (2024) (opens in a new window)https://pubs.acs.org/doi/full/10.1021/acs.jcim.4c00434
• Mosaddeghi Amini, P. , Rouse, I., Subbotina, J., Lobaskin, V. Multiscale modelling of biomolecular corona formation on metallic surfaces. Beilstein J. Nanotechnol. 15, 215–229 (2024). (opens in a new window)https://doi.org/10.3762/bjnano.15.21
• Maier, D., Exner, T. E., Papadiamantis, A. G., Ammar, A., Tsoumanis, A., Doganis, P., Rouse, I., Slater, L. T., Gkoutos, G. V., Jeliazkova, N., Ilgenfritz, H., Ziegler, M., Gerhard, B., Kopetsky, S., Joshi, D., Walker, L., Svendsen, C., Sarimveis, H., Lobaskin, V., … Lynch, I. (2023). Harmonising knowledge for safer materials via the “nanocommons” knowledge base. Frontiers in Physics, 11. (opens in a new window)https://doi.org/10.3389/fphy.2023.1271842
• Subbotina, J., Rouse, I., & Lobaskin, V. (2023). In silico prediction of protein binding affinities onto core–shell pegylated noble metal nanoparticles for rational design of drug nanocarriers. Nanoscale, 15(32), 13371–13383. (opens in a new window)https://doi.org/10.1039/d3nr03264g
• Lobaskin, V., Subbotina, J., & Rouse, I. (2023). Computational modelling of bionano interface. Europhysics Letters, 143(5), 57001. (opens in a new window)https://doi.org/10.1209/0295-5075/acf33f
• Exner, T. E., Papadiamantis, A. G., Melagraki, G., Amos, J. D., Bossa, N., Gakis, G. P., Charitidis, C. A., Cornelis, G., Costa, A. L., Doganis, P., Farcal, L., Friedrichs, S., Furxhi, I., Klaessig, F. C., Lobaskin, V., Maier, D., Rumble, J., Sarimveis, H., Suarez-Merino, B., … Lynch, I. (2023). Metadata stewardship in nanosafety research: Learning from the past, preparing for an “on-the-fly” fair future. Frontiers in Physics, 11. (opens in a new window)https://doi.org/10.3389/fphy.2023.1233879
• Rouse, I., & Lobaskin, V. (2023). Machine-learning based prediction of small molecule–surface interaction potentials. Faraday Discussions, 244, 306–335. (opens in a new window)https://doi.org/10.1039/d2fd00155a
• Giudice, G. del, Serra, A., Saarimäki, L. A., Kotsis, K., Rouse, I., Colibaba, S. A., Jagiello, K., Mikolajczyk, A., Fratello, M., Papadiamantis, A. G., Sanabria, N., Annala, M. E., Morikka, J., Kinaret, P. A. S., Voyiatzis, E., Melagraki, G., Afantitis, A., Tämm, K., Puzyn, T., … Greco, D. (2023). An ancestral molecular response to nanomaterial particulates. Nature Nanotechnology, 18(8), 957–966. (opens in a new window)https://doi.org/10.1038/s41565-023-01393-4
• Wyrzykowska, E., Mikolajczyk, A., Lynch, I., Jeliazkova, N., Kochev, N., Sarimveis, H., Doganis, P., Karatzas, P., Afantitis, A., Melagraki, G., Serra, A., Greco, D., Subbotina, J., Lobaskin, V., Banares, M. A., Valsami-Jones, E., Jagiello, K., & Puzyn, T. (2022). Representing and describing nanomaterials in predictive nanoinformatics. Nature Nanotechnology, 17(9), 924–932. (opens in a new window)https://doi.org/10.1038/s41565-022-01173-6
• Hasenkopf, I., Mills-Goodlet, R., Johnson, L., Rouse, I., Geppert, M., Duschl, A., Maier, D., Lobaskin, V., Lynch, I., & Himly, M. (2022). Computational prediction and experimental analysis of the nanoparticle-protein corona: Showcasing an in vitro-in silico workflow providing fair data. Nano Today, 46, 101561. (opens in a new window)https://doi.org/10.1016/j.nantod.2022.101561
• Subbotina, J., & Lobaskin, V. (2022). Multiscale modeling of bio-nano interactions of zero-valent silver nanoparticles. The Journal of Physical Chemistry B, 126(6), 1301–1314. (opens in a new window)https://doi.org/10.1021/acs.jpcb.1c09525
• Rouse, I., Power, D., Brandt, E. G., Schneemilch, M., Kotsis, K., Quirke, N., Lyubartsev, A. P., & Lobaskin, V. (2021). First principles characterisation of bionano interface. Physical Chemistry Chemical Physics. (opens in a new window)https://doi.org/10.1039/d1cp01116b
• Lynch, I., Afantitis, A., Exner, T., Himly, M., Lobaskin, V., Doganis, P., Maier, D., Sanabria, N., Papadiamantis, A. G., Rybinska-Fryca, A., Gromelski, M., Puzyn, T., Willighagen, E., Johnston, B. D., Gulumian, M., Matzke, M., Etxabe, A. G., Bossa, N., Serra, A., … Melagraki, G. (2020). Can an InChI for nano address the need for a simplified representation of complex nanomaterials across experimental and nanoinformatics studies? Nanomaterials, 10(12), 2493. (opens in a new window)https://doi.org/10.3390/nano10122493
• Afantitis, A., Melagraki, G., Isigonis, P., Tsoumanis, A., Varsou, D. D., Valsami-Jones, E., Papadiamantis, A., Ellis, L.-J., Sarimveis, H., Doganis, P., Karatzas, P., Tsiros, P., Liampa, I., Lobaskin, V., Greco, D., Serra, A., Kinaret, P. A. S., Saarimäki, L. A., Grafström, R., … Lynch, I. (2020). NanoSolveIT project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. Computational and Structural Biotechnology Journal, 18, 583–602.
• Alsharif, S. A., Power, D., Rouse, I., & Lobaskin, V. (2020). In silico prediction of protein adsorption energy on titanium dioxide and gold nanoparticles. Nanomaterials, 10(10), 1967. (opens in a new window)https://doi.org/10.3390/nano10101967
• Kokot, H., Kokot, B., Sebastijanović, A., Voss, C., Podlipec, R., Zawilska, P., Berthing, T., Ballester‐López, C., Danielsen, P. H., Contini, C., Ivanov, M., Krišelj, A., Čotar, P., Zhou, Q., Ponti, J., Zhernovkov, V., Schneemilch, M., Doumandji, Z., Pušnik, M., … Štrancar, J. (2020). Prediction of chronic inflammation for inhaled particles: The impact of material cycling and quarantining in the lung epithelium. Advanced Materials, 32(47). (opens in a new window)https://doi.org/10.1002/adma.202003913
• Lobaskin V. (2020) Electrostatic interactions between colloidal particles, in Compendium on Electromagnetic Analysis: From Electrostatics to Photonics: Fundamentals and Applications for Physicists and Engineers, Volume 1 Electrostatic and Magnetic Phenomena, World Scientific, pp. 1-37.
• Power, D., Rouse, I., Poggio, S., Brandt, E., Lopez, H., Lyubartsev, A., & Lobaskin, V. (2019). A multiscale model of protein adsorption on a nanoparticle surface. Modelling and Simulation in Materials Science and Engineering. (opens in a new window)https://doi.org/10.1088/1361-651x/ab3b6e
• Zhernovkov, V., Santra, T., Cassidy, H., Rukhlenko, O., Matallanas, D., Krstic, A., Kolch, W., Lobaskin, V., & Kholodenko, B. N. (2019). An integrative computational approach for a prioritization of key transcription regulators associated with nanomaterial-induced toxicity. Toxicological Sciences, 171(2), 303–314.
• Romenskyy, M., Spaiser, V., Ihle, T., & Lobaskin, V. (2018). Polarized ukraine 2014: Opinion and territorial split demonstrated with the bounded confidence by model, parametrized xy twitter data. Royal Society Open Science, 5(8).
• Puzyn, T., Jeliazkova, N., Sarimveis, H., Robinson, R. L. M., Lobaskin, V., Rallo, R., Richarz, A.-N., Gajewicz, A., Papadopulos, M. G., Hastings, J., Cronin, M. T. D., Benfenati, E., & Fernandez, A. (2018). Perspectives from the nanosafety modelling cluster on the validation criteria for (q)SAR models used in nanotechnology. Food and Chemical Toxicology, 112, 478–494.
• Coburn, L., Lopez, H., Schouwenaar, I.-M., Yap, A. S., Lobaskin, V., & Gomez, G. A. (2018). Role of contact inhibition of locomotion and junctional mechanics in epithelial collective responses to injury. Physical Biology, 15(2), 024001. (opens in a new window)https://doi.org/10.1088/1478-3975/aa976b
• Kabedev, A., & Lobaskin, V. (2018). Structure and elasticity of bush and brush-like models of the endothelial glycocalyx. Scientific Reports, 8(1). (opens in a new window)https://doi.org/10.1038/s41598-017-18577-3
• Rabinovich, A. L., Vysotskaya, R. U., Lyubartsev, A. P., Quirke, N., & Lobaskin, V. A. (2017). ASSESSING the state of an organism and toxicity of substances using biochemical indicators. Trudy Karelskogo Nauchnogo Centra Rossiiskoi Akademii Nauk, 9, 84–97.
• Bañares, M. A., Haase, A., Tran, L., Lobaskin, V., Oberdörster, G., Rallo, R., Leszczynski, J., Hoet, P., Korenstein, R., Hardy, B., & Puzyn, T. (2017). CompNanoTox2015: Novel perspectives from a european conference on computational nanotoxicology on predictive nanotoxicology. Nanotoxicology, 11(7), 839–845. (opens in a new window)https://doi.org/10.1080/17435390.2017.1371351
• Kabedev, A., Ross‐Lonergan, M., & Lobaskin, V. (2017). Hydrodynamic lift forces on solutes in a tilted nanopillar array: A computer simulation study. ELECTROPHORESIS, 38(19), 2479–2487. (opens in a new window)https://doi.org/10.1002/elps.201700130
• Lopez, H., Brandt, E. G., Mirzoev, A., Zhurkin, D., Lyubartsev, A., & Lobaskin, V. (2017). Multiscale modelling of bionano interface. Advances in Experimental Medicine and Biology, 947, 173–206.
• Molotilin, T. Y., Lobaskin, V., & Vinogradova, O. I. (2016). Electrophoresis of janus particles: A molecular dynamics simulation study. The Journal of Chemical Physics, 145(24), 244704. (opens in a new window)https://doi.org/10.1063/1.4972522
• Lobaskin, V., & Netz, R. R. (2016). Diffusive-convective transition in the non-equilibrium charging of an electric double layer. EPL, 116(5).
• Coburn, L., Lopez, H., Caldwell, B. J., Moussa, E., Yap, C., Priya, R., Noppe, A., Roberts, A. P., Lobaskin, V., Yap, A. S., Neufeld, Z., & Gomez, G. A. (2016). Contact inhibition of locomotion and mechanical cross-talk between cell-cell and cell-substrate adhesion determine the pattern of junctional tension in epithelial cell aggregates. Molecular Biology of the Cell, 27(22), 3436–3448.
• Maduar, S. R., Belyaev, A. V., Lobaskin, V., & Vinogradova, O. I. (2015). Electrohydrodynamics near hydrophobic surfaces. Physical Review Letters, 114(11).
• Lopez, H., & Lobaskin, V. (2015). Coarse-grained model of adsorption of blood plasma proteins onto nanoparticles. The Journal of Chemical Physics, 143(24), 243138. (opens in a new window)https://doi.org/10.1063/1.4936908
• Romanczuk, P., Romensky, M., Scholz, D., Lobaskin, V., & Schimansky-Geier, L. (2015). Motion of euglena gracilis: Active fluctuations and velocity distribution. European Physical Journal-Special Topics, 224(7), 1215–1229.
• Romensky, M., & Lobaskin, V. (2015). Orientational hysteresis in swarms of active particles in external field. European Physical Journal-Special Topics, 224(7), 1359–1376.
• Romensky, M., Scholz, D., & Lobaskin, V. (2015). Hysteretic dynamics of active particles in a periodic orienting field. Journal of the Royal Society Interface, 12(108).
• Romensky, M., Lobaskin, V., & Ihle, T. (2014). Tricritical points in a vicsek model of self-propelled particles with bounded confidence. Physical Review E, 90(6).
• Semenov, I., Raafatnia, S., Sega, M., Lobaskin, V., Holm, C., & Kremer, F. (2013). Electrophoretic mobility and charge inversion of a colloidal particle studied by single-colloid electrophoresis and molecular dynamics simulations. Physical Review E, 87(2).
• Lobaskin, V., & Romenskyy, M. (2013). Collective dynamics in systems of active brownian particles with dissipative interactions. Physical Review E, 87(5).
• Romenskyy, M., & Lobaskin, V. (2013). Statistical properties of swarms of self-propelled particles with repulsions across the order-disorder transition. European Physical Journal B, 86(3).
• Maduar, S. R., Lobaskin, V., & Vinogradova, O. I. (2013). Electrostatic interaction of heterogeneously charged surfaces with semipermeable membranes. Faraday Discussions, 166, 317–329.
• Castaneda-Priego, R., Lobaskin, V., Mixteco-Sanchez, J. C., Rojas-Ochoa, L. F., & Linse, P. (2012). On the calculation of the structure of charge-stabilized colloidal dispersions using density-dependent potentials. Journal of Physics-Condensed Matter, 24(6).
• Lobaskin, V., Bogdanov, A. N., & Vinogradova, O. I. (2012). Interactions of neutral semipermeable shells in asymmetric electrolyte solutions. Soft Matter, 8(36), 9428–9435.
• Vinogradova, O. I., Bocquet, L., Bogdanov, A. N., Tsekov, R., & Lobaskin, V. (2012). Electrostatic interaction of neutral semi-permeable membranes. Journal of Chemical Physics, 136(3).