Floris van Eerden

Floris Van Eerden Specially-Appointed Assistant Professor florisvaneerden [at] biken.osaka-u.ac.jp


Integrating molecular dynamics simulations and machine learning to study epitope binding by TCR.

During my PhD I studied the behavior of Photosystem II using coarse grained molecular dynamics. This was in the Martini group headed by Siewert-Jan Marrink at the University of Groningen in The Netherlands. I came to Japan to join the lab of Daron Standley to study immunology and to integrate molecular dynamics with machine learning.

Excerpt from a half mili second simulation in which plastoquinone is seen entering Photosystem II, one of the major findings from my PhD.


Year Authors Title Publication Cites
2017 B Liu, C Åberg, FJ van Eerden, SJ Marrink, B Poolman, AJ Boersma Design and properties of genetically encoded probes for sensing macromolecular crowding BIOPHYSICAL JOURNAL, 2017, 112, 1929-1939 29
2013 CA López, Z Sovova, FJ van Eerden, AH de Vries, SJ Marrink Martini force field parameters for glycolipids JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013, 9, 1694-1708 125
2017 FJ Van Eerden, MN Melo, PWJM Frederix, SJ Marrink Prediction of thylakoid lipid binding sites on photosystem II BIOPHYSICAL JOURNAL, 2017, 113, 2669-2681 16
2017 FJ Van Eerden, MN Melo, PWJM Frederix, X Periole, SJ Marrink Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex NATURE COMMUNICATIONS, 2017, 8, 1-8 34
2017 FJ Van Eerden, T Van Den Berg, PWJM Frederix, DH De Jong, X Periole, ... Molecular dynamics of photosystem II embedded in the thylakoid membrane THE JOURNAL OF PHYSICAL CHEMISTRY B, 2017, 121, 3237-3249 24
2016 FJ van Eerden Photosynthesis in Silico: Simulations of Photosystem II and the Thylakoid Membrane RIJKSUNIVERSITEIT GRONINGEN, 2016 0
2009 FJ van Eerden Differential Scanning Calorimetry and Protein Stability FACULTY OF SCIENCE AND ENGINEERING, 2009 0
2015 FJ van Eerden, DH de Jong, AH de Vries, TA Wassenaar, SJ Marrink Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations BIOCHIMICA ET BIOPHYSICA ACTA (BBA)-BIOMEMBRANES, 2015, 1848, 1319-1330 85
2014 FJ van Eerden, DH de Jong, X Periole, SJ Marrink Simulation of Photosystem Ii Dynamics in the Thylakoid Membrane BIOPHYSICAL JOURNAL 106 (2), 181A, 2014 0
2014 HI Ingólfsson, MN Melo, FJ Van Eerden, C Arnarez, CA Lopez, ... Lipid organization of the plasma membrane JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2014, 136, 14554-14559 449
2018 R Friedman, S Khalid, C Aponte-Santamaría, E Arutyunova, M Becker, ... Understanding conformational dynamics of complex lipid mixtures relevant to biology THE JOURNAL OF MEMBRANE BIOLOGY 251 (5-6), 2018, 609-631 13
2019 S Li, J Wilamowski, S Teraguchi, FJ van Eerden, J Rozewicki, A Davila, ... Structural modeling of lymphocyte receptors and their antigens IN VITRO DIFFERENTIATION OF T-CELLS, 2019, 207-229 1