More than twenty current and former members of Molecular Biophysics Stockholm had the rare opportunity to be visited by over 1000 scientists at the biannual Congress of the European Biophysical Societies’ Association (EBSA), held 31 July–4 August for its first time in Stockholm. The event culminated months of preparation by Congress Co-Chair Erik Lindahl, and included selected oral presentations by Nandan Haloi and Marie Lycksell, as well as poster awards to Anton Jansen and Antoni Marciniak (pictured at bottom).
Members of Molecular Biophysics Stockholm joined family and friends in celebrating Cathrine Bergh’s successful spikning and defense of her PhD from KTH in Applied Physics, From static structures to free energy landscapes: characterizing conformational transitions in biological macromolecules. Cathrine nailed her thesis on 29 May, and defended it 13 June at SciLifeLab, with Professor Gerhard Hummer (Max Planck Institute of Biophysics) as opponent. Professor Erik Lindahl and Ligand-Gated Ion Channels team-lead Reba Howard led a toast to their advisee of over five years, as she prepares to join the GROMACS software development team.
Members of Molecular Biophysics Stockholm joined family and friends in celebrating Koushik Choudhury’s successful spikning and defense of his PhD from KTH in Applied Physics, Gating and modulation mechanism of voltage gated sodium channels. Koushik nailed his thesis on 30 May, and defended it 2 June at SciLifeLab, with Professor Phil Biggin (University of Oxford) as opponent. Professor Lucie Delemotte led a toast to her advisee of over four years, as he prepares to embark on a postdoctoral fellowship at AstraZeneca.
Eight members of Molecular Biophysics Stockholm traveled to San Diego, CA this year to present research at the 67th Annual Meeting of the Biophysical Society. Among others, Will Pipatpolkai spoke in the Platform on General Protein-Lipid Interactions, and Reba Howard spoke in the Best of Biophysical Journal Symposium.
Members of Molecular Biophysics Stockholm joined family and friends in celebrating Linnea Yvonnesdotter’s licentiate in Biophysics, Intersection of model and experiments: Combining cryo-electron microscopy data and molecular dynamics simulations. Linnea defended on 24 January at Stockholm University, with Dr Erik Marklund (Uppsala University) as opponent. Professor Erik Lindahl and Ligand-Gated Ion Channels team-lead Reba Howard led a toast to their advisee of over four years.
Members of Molecular Biophysics Stockholm helped install seasonal spirit and decor in our SciLifeLab offices on 6 December. Wishing all our members and colleagues a god jul and fine New Year!
Members of Molecular Biophysics Stockholm joined family and friends in celebrating Marie Lycksell‘s successful spikning and defense of her PhD in Biophysics, Combining low resolution, high resolution, functional, and simulation techniques: In the study of pentameric ligand-gated ion channels. Marie nailed her thesis on 9 November 2022, and defended it 1 December 2022 at Stockholm University, with Professor Kresten Lindorff-Larsen (University of Copenhagen) as opponent. Professor Erik Lindahl and Ligand-Gated Ion Channels team lead Reba Howard led a toast to their advisee of over five years, as she prepares to embark on a postdoctoral fellowship at the Institut Laue-Langevin in Grenoble, France.
Thirty members of Molecular Biophysics Stockholm finally gathered 25–26 August at Skepparholmen Nacka, our first such off-site group program since 2019. The program included workshops on interdisciplinary communication, popular science, course development, and networking skills, as well as bonding over wonderful meals, pools, and saunas. Big thanks to Alessandra, Anton, Michele, and Reba for co-organizing this long-awaited retreat.
Members of Molecular Biophysics Stockholm joined SciLifeLab colleagues in hosting local high school students for an introduction to life sciences research on 11 March—the first such event possible since the onset of the COVID-19 global pandemic. Among others, Nandan Haloi, Marie Lycksell, and Will Pipatpolkai introduced visiting students to principles of molecular dynamics simulations, including a virtual-reality tour of membrane proteins in motion.
Twelve members of Molecular Biophysics Stockholm traveled to San Francisco, CA to present their research at the 66th Annual Meeting of the Biophysical Society, back on-site after a remote meeting in 2021. Among others, Lucie Delemotte spoke in and chaired the Symposium on Peripheral Membrane Proteins, Anton Jansen spoke in the Platform on Molecular Dynamics (II), and Erik Lindahl spoke in and co-chaired the Platform on Computational Methods and Bioinformatics (I). Cathrine Bergh was an invited speaker in the Platform on Protein-Lipid Interactions, with her talk delivered by Urška Rovšnik due to COVID-19 infection; Koushik Choudhury and Yuxuan Zhuang were invited speakers in the Platforms on Voltage-Gated Channels (I) and Ligand-Gated Ion Channels (II), though both talks were delivered by Reba Howard due to travel limitations.
Members of Molecular Biophysics Stockholm braved the winter weather on 8 February for an afternoon hike around Brunnsviken, a couple kilometers east of our SciLifeLab campus. Though we look forward to being able to socialize indoors, we are privileged to work so close to such beautiful and accessible spots.
Twenty-nine members of Molecular Biophysics Stockholm, along with colleagues in the Cryo-EM Swedish Infrastructure Unit, finally gathered for an outdoor mini-retreat on 23 August 2021 on the Karolinska Institute campus. Although plans for a longer off-site event were again postponed by the ongoing COVID-19 pandemic, it was a tremendous opportunity to reconnect in person with our collegial community, including several members joined within recent months. Many thanks to co-organizers Alessandra, Michele, Anton, Reba, and especially Linnea for the afternoon activities.
Members of Molecular Biophysics Stockholm joined colleagues in our local structural-biology community, as well as invited speakers from France, Germany, Canada, Australia, and the USA, for the 24th annual Swedish Conference on Macromolecular Structure and Function (SWEPROT) 20–23 June 2021. In contrast to previous gatherings — with the exception of 2020, which was cancelled due to COVID-19 precautions — this year’s program was relocated from its foundational Tällberg venue in central Sweden, to be hosted instead by Linköping University and Around the Corner as a Video and Virtual Reality Conference.
Congratulations especially to MBS doctoral student Marie Lycksell, who was selected among submitted abstracts to present a virtual talk on Solution structure of the pentameric ligand-gated ion channel GLIC probed by small-angle neutron scattering, and further awarded runner-up for Best Oral Presentation.
Members of Molecular Biophysics Stockholm joined family and friends in celebrating Oliver Fleetwood‘s successful defense of his PhD thesis in Biophysics, New approaches to data-driven analysis and enhanced sampling simulations of G protein-coupled receptors, 2 June 2021 at the KTH Royal Institute of Technology, Stockholm, Sweden. Professor Ulrich Zachariae (University of Dundee, UK) served as opponent via videoconference. Despite ongoing pandemic precautions, Associate Professor Lucie Delemotte (KTH) led a toast to her advisee of four years, accompanied by co-advisor Professor Erik Lindahl and a small group of family and team members.
Members of Molecular Biophysics Stockholm joined family and friends in celebrating Annie Westerlund‘s successful defense of her PhD thesis in Biophysics, Deciphering conformational ensembles and communication pathways in biomolecules, 18 December 2020 at the KTH Royal Institute of Technology, Stockholm, Sweden. Professor Kresten Lindorff-Larsen (University of Copenhagen, Denmark) served as opponent via videoconference. Associate Professor Lucie Delemotte (KTH) led a toast to her advisee of four years, while Delemotte group members awarded an equally merited honorary diploma from the Hogwarts School of Witchcraft and Wizardry to their Network Witch.
Since its initiation by the Royal Swedish Academy of Sciences in 2011, the Young Academy has provided an independent, interdisciplinary platform for the most prominent younger researchers in Sweden. Its ~35 members meet regularly across institutional and disciplinary borders during their 5-year terms to discuss research, science policy, and related topics.
Read more here (press release, Swedish).
As we return to the (semi-) normal academic year, Molecular Biophysics Stockholm also celebrated PhD student Yuxuan Zhuang‘s successful completion of a competitive summer internship contributing to MDAnalysis, a freely available, open-source object-oriented Python library to analyze trajectories from molecular dynamics simulations.
Zhuang’s internship was awarded through the Google Summer of Code, focused on bringing more student developers into open source software development. Just past its 15th year, the global program has produced over 38 million lines of code for 715 open source organizations.
Read Zhuang’s final remarks on his summer project, Serialization of the MDAnalysis-Universe for Parallelism, here.
While many seminars in our science communities have been suspended this spring, EU-funded Centre of Excellence BioExcel has stepped up its promotion of educational webinars for computational biomolecular research.
In support of this effort, Molecular Biophysics Stockholm (MBS) members delivered two presentations in the spring series.
- Christian Blau introduced new tools for guiding simulations with cryo-electron microscopy data: Density guided simulations – combining cryo-EM data and molecular dynamics simulation, 28 April 2020
- Lucie Delemotte and Annie Westerlund presented tools for clustering of computational free-energy landscapes: Clustering free energy landscapes from molecular dynamics simulations, 12 May 2020
Conceived in 2016, BioExcel webinars cover broad topics related to the latest development of major software packages; their application to modeling and simulation; best practices for performance tuning and efficient usage on HPC and novel architectures; introductory tutorials for novel users; and much more. Prior to this spring, MBS members also contributed regularly to the series on optimizing molecular dynamics simulations in GROMACS.
Webinar slides and video recordings are freely available from BioExcel; for updates and registration on upcoming events, subscribe to the community newsletter.
Three remarkable members of Molecular Biophysics Stockholm celebrated completion of their doctoral degrees this spring.
Though their presentations had to be revised to meet public-health recommendations, including video-casting to off-site opponents and committee members, all three delivered polished, informative defenses of their respective theses to enthusiastic remote audiences.
- Petter Johansson, Department of Applied Physics, KTH Royal Institute of Technology. Molecular processes in dynamic wetting, 16 April 2020. Opponent: Professor Guillaume Galliero, University of Pau and Pays de l’Adour, France.
- Björn O Forsberg, Department of Biochemistry & Biophysics, Stockholm University. Fast and reliable alignment and classification of biological macromolecules in electron microscopy images, 24 April 2020. Opponent: Professor Sriram Subramanian, University of British Columbia, Canada.
- Ali Narangifard, Department of Medicine, Karolinska Institute. Molecular structure of the human skin’s barrier: elucidation, formation and utilization, 5 May 2020. Opponent: Professor Johan Engblom, Malmö University, Sweden.
We regret missing out on traditional festivities in honor of these fine colleagues, and hope to properly celebrate with them soon.
Like so many of our colleagues worldwide, Molecular Biophysics Stockholm (MBS) has been engaged in various efforts to navigate and combat the novel coronavirus. Although the group’s past research rarely intersected with virology or clinical work, and none of us are are experts in the field, we hope to help where we can.
Among others, members of the Membrane-Protein Modeling and GROMACS Development teams have joined the Folding@home consortium to apply the power of distributed computing to understanding SARS-CoV-2 membrane proteins. Listen to Professor Erik Lindahl speak about this work on Sveriges Radio (Swedish), read about it on Videnskab.dk (Danish)—or contribute your own compute time to active projects managed by Associate Professor Lucie Delemotte!
Members of the GROMACS team and BioExcel Centre also contribute to Exscalate4CoV, a consortium awarded €3 million by the European Commission for research on COVID-19 vaccines, treatment, and diagnostics. Key tasks at MBS include deployment of molecular-dynamics code and free-energy calculations for coronavirus protein simulations and drug-candidate scoring. For an overview of relevant targets, data repositories, and community collaborations, watch Lindahl’s presentation to the Centre Européen de Calcul Atomique et Moléculaire (English, 4:13–36:04).
On the clinical side, members of the Ligand-Gated Ion Channels (LGICs) team have worked with fellow chemists at Stockholm University to alleviate urgent needs for medical supplies, helping coordinate donations of masks, gloves, and other personal protective equipment from SciLifeLab to local hospitals. With reagents contributed by academic groups, the Museum of Natural History, and companies including GE Health, Petrolia, Runa and Absolut Vodka, we also assisted in the department’s production and distribution of over 20,000 liters of hand sanitizer to medical and care facilities. Read more in recent coverage by the university (English) and national (Swedish) media.
MBS is also involved in an accelerated grant by the KAW Foundation to iLACO-Sweden, a multi-institution project led by Professor Vicent Pelechano (Karolinska Institute) to develop a rapid, low-cost color-based test for COVID-19 infection. The method was recently covered on Sveriges Television, including an interview with LGICs team-lead Reba Howard (Swedish, some English audio).
We are deeply grateful for the dedication and compassion of all MBS members, who continue to find creative paths to productivity even at a distance. Many have managed unprecedented disruptions to academic, research, and development work, including DIS students Jojo Scott and Phaedra Robinson, whose time abroad was truncated months early by US travel restrictions. We so look forward to collaborating again at higher density on the other side of this pandemic.
Members of Molecular Biophysics Stockholm celebrated Berk Hess‘ promotion to full Professor in Applied Physics at KTH Royal Institute of Technology, 15 November 2019, conferred by President Sigbritt Karlsson at Konserthuset in Stockholm, Sweden. With funding recently awarded by Vetenskapsrådet to the INTERFACE project, Hess’ team stands poised grow in size and contribution; check back soon for new openings!
Twenty-three members of Molecular Biophysics Stockholm gathered for our fall off-site retreat, 24–25 October 2019 at historic Vår Gård in Saltsjöbaden, Sweden, workshopping topics related to individual core competencies, academic and industry CVs, group networking, and team communication. Thanks to co-organizers Annie, Joe, Lucie, Reba, and Urška, and to Vår Gård for a beautiful autumn getaway!
Four current and former members of Molecular Biophysics Stockholm, along with multiple collaborators, presented their research at the 2019 Jacques Monod Conference Canaux ioniques activés par les ligands: de la structure atomique à la transmission synaptique (Ligand-gated ion channels from atomic structure to synaptic transmission) 24–29 May 2019 in Roscoff, France. Among others, Reba Howard gave an invited talk on Biochemical and simulation studies of allosteric mechanisms in a model Cys-loop receptor.
Molecular Biophysics Stockholm again hosted two US undergraduates through the DIS-Study Abroad in Scandinavia Stockholm program in Spring 2019. Under the supervision of Reba Howard and Urška Rovšnik, Sarah Komon (Wheaton College) and Nicole Sanford (St Olaf College) worked ≥20 hours per week on independent projects in the Ligand-Gated Ion Channels team throughout the term, including data collection at both the Science for Life Laboratory and Umeå University. Each presented a research poster at the DIS End-of-Semester Symposium, 7 May 2019 at Stockholm’s Kungliga Musikhögskolan. For an interview with Komon and Sanford regarding their experiences, visit the DIS blog Discover Study Abroad.