News

Group Retreat 2019

Thirty members of Molecular Biophysics Stockholm, representing thirteen countries and a range of research areas, gathered for our annual spring retreat on 8 April 2019 at the Science for Life Laboratory in Solna, Sweden. Gabriella Fägerlind of Uppsala’s Implement Diversity AB led a workshop on inclusivity and psychological safety in the academic workplace, followed by small- and large-group exercises around goal-setting and group resource development, and an evening pizza party.

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Workshopping Sharing

Eight members of Molecular Biophysics Stockholm helped host an international workshop on Sharing Data from Molecular Simulations, 25–27 November on Lidingö in the Stockholm archipelago. Researchers from 13 institutions in 8 countries sought to explore and improve the dissemination of data and code related to molecular simulations and related methods in computational biology/chemistry. Major topics included:

  • Standardization of file formats
  • Tools for trajectory sharing
  • Streamlining molecular simulations data
  • Reproducibility of molecular simulations

Lucie Delemotte and Reba Howard co-organized the workshop with Matthieu Chavent (IPBS), Daniel Smith (MolSSI), and Mikael Trellet (Utrecht), with sponsorship from Rossen Apostolov at BioExcel. Among the participants were session chair Mark Abraham and invited speaker Erik Lindahl.

Although this exploratory workshop was limited in scale, organizers sought to maximize transparency by live-tweeting the proceedings (#SDMS18) and making videos of all talks and roundtable discussions, as well as original presentation slides, available for download via BioExcel.

A follow-up event, organized by MolSSI, is planned for 2019 in the USA.

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Biophysics Abroad

Molecular Biophysics Stockholm was the first external research site to host US undergraduates through the recently launched DIS-Study Abroad in Scandinavia Stockholm program in Fall 2018. Under the supervision of Reba Howard, Isabel Anaya (Northwestern University) and Jaewon Kang (Vassar College) worked ≥20 hours per week on independent research projects in the Ligand-Gated Ion Channels team throughout the term. Both presented posters on their work at the DIS End-of-Semester Symposium, 11 December 2018 at Stockholm’s Kungliga Musikhögskolan.

Two new DIS students will initiate new research projects with the team in Spring 2019. For more information, contact Reba or DIS-Stockholm.

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Multiscale Modeling in Tokyo

Five members of Molecular Biophysics Stockholm presented their research and discussed prospective collaborations at the 2nd Stockholm-Tokyo University Partnership Workshop, held this year in Japan, 28–30 October 2018. Among others, Erik Lindahl co-chaired a plenary session on Biological Mechanisms Regulating Healthy and Maladaptive Aging, and co-coordinated a satellite workshop on New Technologies: Multiscale Computation. Following the workshop, group members were generously hosted by their University of Tokyo colleagues in multiscale simulations and electron microscopy for a traditional meal in the Hongō district.

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Grattis till Docent Delemotte

Members of Molecular Biophysics Stockholm celebrated Lucie Delemotte’s Swedish-language Docent Lecture in Applied Physics at KTH Royal Institute of Technology, Structural dynamics of voltage-gated ion channels and implications for health and disease, 24 October 2018 at AlbaNova Universitetscentrum in Stockholm, Sweden. With new funding recently awarded by Vetenskapsrådet, the Delemotte team stands poised grow in size and contribution. Check back soon for new openings!

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GROMACS Workshop October 2018

The 2018 workshop, 17–19 October in Göttingen, set out to provide opportunities for GROMACS developers and power-users to use or implement their own enhanced simulation protocols, involving for example fast multipole methods, constant pH, or experimental constraints from microscopy/spectroscopy. Key questions included:

  • How can a highly optimized, parallel simulation code provide a general infrastructure that allows incorporation of new methods in a straightforward way?
  • Can it do so without sacrificing (parallel) performance?
  • Can the software be made less monolithic and blackbox-like, but more modular and extensible?
  • Can providing an own method become less of a challenge for the average scientist who is not at the same time a GROMACS coding expert?

Thanks to sponsors BioExcel and SPPEXA, and to the Theoretical and Computational Biophysics group at the Max Planck Institute for Biophysical Chemistry for venue and other support.

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Grattis till Licentiate Westerlund

Members of Molecular Biophysics Stockholm celebrated Annie Westerlund’s successful defense of her Licentiate thesis in Biophysics from KTH Royal Institute of Technology, Computational Study of Calmodulin’s Ca2+-dependent Conformational Ensembles, 3 October 2018 at the Science for Life Laboratory in Solna, Sweden. Professor Björn Wallner (Linköping University) served as opponent, and Professors Lucie Delemotte (KTH) and Erik Lindahl (KTH & Stockholm University) led a toast to their advisee of two years.

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Grattis till Dr Heusser

Members of Molecular Biophysics Stockholm joined family and friends in celebrating Stephanie Heusser’s successful defense of her PhD thesis in Biochemistry & Biophysics from Stockholm University, Allosteric Modulation of Pentameric Ligand-Gated Ion Channels by General Anesthetics, 4 May 2018 in Magnélisalen, Stockholm University. Professor Pierre-Jean Corringer (Pasteur Institute, Paris, France) served as opponent, and Professor Erik Lindahl (Stockholm University, KTH Royal Institute of Technology) led a toast to his advisee of four years.

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Biophysics in San Francisco

Eleven members of Molecular Biophysics Stockholm traveled to San Francisco, CA to present their research at the 62nd Annual Meeting of the Biophysical Society. Among others, Lucie Delemotte was an invited speaker in the Membrane Biophysics Subgroup, describing her work On the selective promiscuity of calmodulin. Prior to the meeting, group members also found time for a quick hike through glorious Muir Woods National Monument.