Publications

Antila, H.; Dixit, S.; Kav, B.; Madsen, J. J.; Miettinen, M. S.; Ollila, O. H. S.: Evaluating polarizable biomembrane simulations against experiments. Journal of Chemical Theory and Computation 20 (10), pp. 4325 - 4337 (2024)

Hernández-Sánchez, I.; Rindfleisch, T.; Alpers, J.; Dulle, M.; Garvey, C. J.; Knox-Brown, P.; Miettinen, M. S.; Nagy, G.; Pusterla, J. M.; Rekas, A. et al.; Shou, K.; Stadler, A. M.; Walther, D.; Wolff, M.; Zuther, E.; Thalhammer, A.: Functional in vitro diversity of an intrinsically disordered plant protein during freeze–thawing is encoded by its structural plasticity. Protein Science 33 (5), e4989 (2024)

Kiirikki, A. M.; Antila, H.; Bort, L. S.; Buslaev, P.; Favela-Rosales, F.; Ferreira, T. M.; Fuchs, P. F. J.; Garcia-Fandino, R.; Gushchin, I.; Kav, B. et al.; Kučerka, N.; Kula, P.; Kurki, M.; Kuzmin, A.; Lalitha, A.; Lolicato, F.; Madsen, J. J.; Miettinen, M. S.; Mingham, C.; Monticelli, L.; Nencini, R.; Nesterenko, A. M.; Piggot, T. J.; Piñeiro, Á.; Reuter, N.; Samantray, S.; Suárez-Lestón, F.; Talandashti, R.; Ollila, O. H. S.: Overlay databank unlocks data-driven analyses of biomolecules for all. Nature Communications 15, 1136 (2024)

Parlato, R.; Volarić, J.; Lasorsa, A.; Bagherpoor Helabad, M.; Kobauri, P.; Jain, G.; Miettinen, M. S.; Feringa, B. L.; Szymanski, W.; van der Wel, P. C. A.: Photocontrol of the β-Hairpin polypeptide structure through an optimized azobenzene-based amino acid analogue. Journal of the American Chemical Society 146 (3), pp. 2062 - 2071 (2024)

Lipowsky, R.; Ghosh, R.; Satarifard, V.; Sreekumari, A.; Zamaletdinov, M.; Różycki, B.; Miettinen, M. S.; Grafmüller, A.: Leaflet tensions control the spatio-temporal remodeling of lipid bilayers and nanovesicles. Biomolecules 13 (6), 926 (2023)

Zamaletdinov, M. F.; Miettinen, M. S.; Lipowsky, R.: Probing the elastic response of lipid bilayers and nanovesicles to leaflet tensions via volume per lipid. Soft Matter 19 (36), pp. 6929 - 6944 (2023)

Antila, H.; Wurl, A.; Ollila, O. H. S.; Miettinen, M. S.; Ferreira, T. M.: Rotational decoupling between the hydrophilic and hydrophobic regions in lipid membranes. Biophysical Journal 121, pp. 68 - 78 (2022)

Castillo, S. R.; Rickeard, B. W.; DiPasquale, M.; Nguyen, M. H. L.; Lewis-Laurent, A.; Doktorova, M.; Kav, B.; Miettinen, M. S.; Nagao, M.; Kelley, E. G. et al.; Marquardt, D.: Probing the link between pancratistatin and mitochondrial apoptosis through changes in the membrane dynamics on the nanoscale. Molecular Pharmaceutics 19 (6), pp. 1839 - 1852 (2022)

Schullian, O.; Antila, H.; Heazlewood, B. R.: A variable time step self-consistent mean field DSMC model for three-dimensional environments. The Journal of Chemical Physics 156 (12), 124309 (2022)

Antila, H.; M. Ferreira, T.; Ollila, O. H. S.; Miettinen, M. S.: Using open data to rapidly benchmark biomolecular simulations: phospholipid conformational dynamics. Journal of Chemical Information and Modeling 61 (2), pp. 938 - 949 (2021)

Bacle, A.; Buslaev, P.; Garcia-Fandino, R.; Favela-Rosales, F.; Mendes Ferreira, T.; Fuchs, P. F. J.; Gushchin, I.; Javanainen, M.; Kiirikki, A. M.; Madsen, J. J. et al.; Melcr, J.; Milán Rodríguez, P.; Miettinen, M. S.; Ollila, O. H. S.; Papadopoulos, C. G.; Peón, A.; Piggot, T. J.; Piñeiro, Á.; Virtanen, S. I.: Inverse conformational selection in lipid–protein binding. Journal of the American Chemical Society 143 (34), pp. 13701 - 13706 (2021)

Yuan, J.; Antila, H.; Luijten, E.: Particle–particle particle–mesh algorithm for electrolytes between charged dielectric interfaces. The Journal of Chemical Physics 154 (9), 094115 (2021)

Knox-Brown, P.; Rindfleisch, T.; Günther, A.; Balow, K.; Bremer, A.; Walther, D.; Miettinen, M. S.; Hincha, D. K.; Thalhammer, A.: Similar yet different–structural and functional diversity among Arabidopsis thaliana LEA_4 proteins. International Journal of Molecular Sciences 21 (8), 2794 (2020)

Schullian, O.; Woodard, J.; Tirandaz, A.; Mashaghi, A.: A circuit topology approach to categorizing changes in biomolecular structure. Frontiers in Physics 8, 5 (2020)

Yuan, J.; Antila, H.; Luijten, E.: Structure of polyelectrolyte brushes on polarizable substrates. Macromolecules 53 (8), pp. 2983 - 2990 (2020)

Antila, H.; Buslaev, P.; Favela-Rosales, F.; Mendes Ferreira, T.; Gushchin, I.; Javanainen, M.; Kav, B.; Madsen, J. J.; Melcr, J.; Miettinen, M. S. et al.; Määttä, J.; Nencini, R.; Ollila, O.H. S.; Piggot, T. J.: Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers. The Journal of Physical Chemistry B 123 (43), pp. 9066 - 9079 (2019)

Schullian, O.; Heazlewood, B.: Beyond direct simulation Monte Carlo (DSMC) modelling of collision environments. Molecular Physics 117 (21), pp. 3076 - 3087 (2019)

Miettinen, M. S.: Refined molecular dynamics simulations of phospholipid bilayers. In: Advances in Biomembranes and Lipid Self-Assembly, Vol. 30, pp. 1 - 38 (2019)

Antila, H.; Miettinen, M. S.: Data-driven development of lipid force fields for molecular dynamics simulations. In Biophysical Journal, 118 (3, Supplement 1), pp. 141a - 142a. Cell Press, Cambridge, Mass. (2020)

Miettinen, M. S.; Lipowsky, R.: Spontaneous curvature generation in asymmetric lipid bilayers with tensionless leaflets. In Biophysical Journal, 118 (3, Supplement 1). Cell Press, Cambridge, Mass. (2020)