Uppsala-Stockholm Workshop on Biomolecular Simulation


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The Uppsala-Stockholm Biomolecular Simulation Symposium is a one-day meeting for research groups focusing on computer simulations of biomolecular systems in the Stockholm/Uppsala area. A plenary lecture will be given by Peter Kasson, who recently joined Uppsala university from the University of Virginia, as well as presentations from PhD students and postdocs. A poster session will be organized during coffee breaks and lunch.

Registration to this event has closed!

Free bus shuttle

Bus transportation from/to SciLifeLab in Solna will be arranged. There are still seats available for the bus even though the registration has closed. To sign up for a seat, e-mail to erika.erkstam@scilifelab.uu.se.

  • Departure from Tomtebodavägen 23A, Solna at 08.30.
  • Departure from Husargatan 3, Uppsala at 17:30


If you want to participate or have any inquiries regarding the event or your registration, please contact erika.erkstam@scilifelab.uu.se.



09:30 – 10:00 Coffee

10:00 – 12:05 Session I

10:00 – 10:40 Peter Kasson, University of Virginia and Uppsala University

“Statistical learning on molecular simulations to direct experiments”

10:40 – 10:55 Inna Ermilova. Stockholm University

“Molecular dynamics simulations of cholesterol in polyunsaturated lipid bilayers”

10:55 – 11:10 Pierre Matricon, Uppsala University

”Fragment optimization by molecular dynamics free energy calculations for GPCRs”

11:10 – 11:35 Tyler Harpole, KTH

“Biophysical Properties of voltage gating in K+ channels”

11:35 – 11:50 Nina Fischer, Uppsala University

“Simulating pH-dependent structural changes in L. polyedrum luciferase”

11:50 – 12:05 Annie Westerlund, KTH

“Ca2+-dependent Calmodulin conformational ensemble”


12:05 – 13:30 Lunch & Poster session


13:30 – 15:20 Session II

13:30 – 13:55 Laura Orellana, Stockholm University

“Trapping intermediates in transition pathways: from coarse-grained models to cancer mechanisms”

13:55 – 14:10 Yossa Hartono, Karolinska Institute

”Tautomerisation of pseudoisocytosine investigated by lambda dynamics”

14:10 – 14:25 Matus Rebic, Stockholm University

“Molecular Dynamics Study of Parallel DNA Quadruplex: Evaluation of Water and Ion Models”

14:25 – 14:40 You Xu, Karolinska Institute

“The effects of locked nucleic acid in DNA triplex formation”

14:40 – 15:05 Masoud Kazemi, Uppsala University

”One active site, two reactions”

15:05 – 15:20 Beat Anton Amrein, Uppsala University

“CADEE: Computer-Aided Directed Evolution of Enzymes”


15:20 – 15:40 Coffee & Poster session


15:40 – 17:15 Session III

15:40 – 15:55 Willem Jespers, Uppsala University

“Binding mode prediction using free energy perturbations”

15:55 – 16:20 Lars Sandberg, SciLifeLab Stockholm

”When modelling equilibrium solvation – go implicit not explicit”

16:20 – 16:35 Magnus Lundborg, SciLifeLab Stockholm

”Calculating permeability through the stratum corneum lipid matrix”

16:35 – 17:00 Lorenzo Agosta, Stockholm University

“Structural and reactivity properties of water adsorbed on fully hydrated Titanium oxide surfaces, predicted by ab-initio simulations”

17:00 – 17:15 Petter Johansson, KTH

“Molecular Contact Line Friction in Dynamic Wetting”