Publications

Peer Reviewed Journal Articles:

• NMRlipids VI: Evaluating Polarizable Biomembrane Simulations against Experiments. Hanne S. Antila, Sneha Dixit, Batuhan Kav, Jesper J. Madsen, Markus S. Miettinen, and O. H. Samuli Ollila. J. Chem. Theory. Comput. DOI: 10.1021/acs.jctc.3c01333
• NMRlipids Databank: Overlay databank unlocks data-driven analyses of biomolecules for all. Anne M. Kiirikki, Hanne S. Antila, Lara S. Bort, Pavel Buslaev, Fernando Favela-Rosales, Tiago Mendes Ferreira, Patrick F. J. Fuchs, Rebeca Garcia-Fandino, Ivan Gushchin, Batuhan Kav, Norbert Kučerka, Patrik Kula, Milla Kurki, Alexander Kuzmin, Anusha Lalitha, Fabio Lolicato, Jesper J. Madsen, Markus S. Miettinen, Cedric Mingham, Luca Monticelli, Ricky Nencini, Alexey M. Nesterenko, Thomas J. Piggot, Ángel Piñeiro, Nathalie Reuter, Suman Samantray, Fabián Suárez-Lestón, Reza Talandashti, and O. H. Samuli Ollila. Nat. Commun. DOI: 10.1038/s41467-024-45189-z
• NMRlipids III: Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions. Matti Javanainen, Peter Heftberger, Jesper J. Madsen, Markus S. Miettinen, Georg Pabst, and O. H. Samuli Ollila. J. Chem. Theory. Comput. DOI: 10.1021/acs.jctc.3c00648
• NMRlipids IVb: Inverse Conformational Selection in Lipid–Protein Binding. Amélie Bacle, Pavel Buslaev, Rebeca Garcia-Fandino, Fernando Favela-Rosales, Tiago Mendes Ferreira, Patrick F. J. Fuchs, Ivan Gushchin, Matti Javanainen, Anne M. Kiirikki, Jesper J. Madsen, Josef Melcr, Paula Milán Rodríguez, Markus S. Miettinen, O. H. Samuli Ollila, Chris G. Papadopoulos, Antonio Peón, Thomas J. Piggot, Ángel Piñeiro, and Salla I. Virtanen. J. Am. Chem. Soc. DOI: 10.1021/jacs.1c05549 
• NMRlipids IVa: Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers. Hanne S. Antila, Pavel Buslaev, Fernando Favela-Rosales, Tiago M. Ferreira, Ivan Gushchin, Matti Javanainen, Batuhan Kav, Jesper J. Madsen, Josef Melcr, Markus S. Miettinen, Jukka Määttä, Ricky Nencini, O.H. Samuli Ollila, and Thomas J. Piggot. J. Phys. Chem. B DOI: 10.1021/acs.jpcb.9b06091
• NMRlipids II: Molecular electrometer and binding of cations to phospholipid bilayers. Andrea Catte, Mykhailo Girych, Matti Javanainen, Claire Loison, Josef Melcr, Markus S. Miettinen, Luca Monticelli, Jukka Määttä, Vasily S. Oganesyan, O. H. Samuli Ollila, Joona Tynkkynen, and Sergey Vilov. Phys. Chem. Chem. Phys. DOI: 10.1039/C6CP04883H
• NMRlipids V: Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments. O.H. Samuli Ollila and Georg Pabst. Biochimica et Biophysica Acta (BBA) - Biomembranes DOI:10.1016/j.bbamem.2016.01.019
• NMRlipids I: Towards Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions. Alexandru Botan, Fernando Favela, Patrick Fuchs, Matti Javanainen, Matej Kanduc, Waldemar Kulig, Antti Lamberg, Claire Loison, Alexander Lyubartsev, Markus S. Miettinen, Luca Monticelli, Jukka Määttä, O. H. Samuli Ollila, Marius Retegan, Tomasz Rog, Hubert Santuz, and Joona Tynkkynen. J. Phys. Chem. B DOI:10.1021/acs.jpcb.5b04878

Preprints:

• Alexandru Botan, Andrea Catte, Fernando Favela, Patrick Fuchs, Matti Javanainen, Waldemar Kulig, Antti Lamberg, Markus S. Miettinen, Luca Monticelli, Jukka Määttä, Vasily S. Oganesyan, O. H. Samuli Ollila, Marius Retegan, Hubert Santuz, Joona Tynkkynen. Towards atomistic resolution structure of phosphatidylcholine glycerol backbone and choline headgroup at different ambient conditions. arXiv:1309.2131v2 (2015)
• O. H. Samuli Ollila. Response of the hydrophilic part of lipid membranes to changing conditions — a critical comparison of simulations to experiments. arXiv:1309.2131v1 (2013)

Posters:

Patrick F. J. Fuchs, Matti Javanainen, Antti Lamberg, Markus S. Miettinen, Luca Monticelli, Jukka Määttä, O. H. Samuli Ollila, Marius Retegan, Hubert Santuz. Open Collaboration that uses NMR Data to Judge the Correctness of Phospholipid Glycerol and Head Group Structures in Molecular Dynamics Simulations. Biophysical Journal 108 411a (2015). Presented at the Biophysical Society 59th Annual Meeting in Baltimore, USA in February 2015.

Presented at the International Workshop on Biomembranes — From Fundamentals to Applications in Espoo, Finland in August 2014.

Talks:

Presented at the International Workshop on Biomembranes — From Fundamentals to Applications in Espoo, Finland in August 2014.

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Publications related to the Open Collaboration approach:

September 24th 2015. Markus and Samuli give presentations in the Beyond Open Access session at the Academic Mindtrek 2015. Watch all the talks and discussions below.
May 6th 2015. Article (in Finnish) published by the Open Science and Research Initiative of the Ministry of Education and Culture:  Avointa yhteistyötä lipiditutkimuksessa (Open collaboration in lipid research)

March 27th 2015. Our approach discussed in The Honest Broker blog: Science on Blogspot

March 27th 2015. Samuli in a panel discussion (in Finnish) on open science. Watch the video.

March 10th 2015. Samuli gives a presentation at Open Science Show & Tell event organized by Open Knowledge Finland. Slides available here.