Department of Medical Biochemistry and Biophysics | LinkedIn Department of Medical Biochemistry and Biophysics | 184 followers on LinkedIn. Driving Discovery in Biochemistry and Biophysics under the Northern Lights | Research at the Department of Medical Bioche...

📢 We’re on Social Media!

Want to keep up with research news, lab highlights, and opportunities from the Department of Medical Biochemistry and Biophysics at Umeå University?

✅ Follow us on LinkedIn:
👉 www.linkedin.com/company/mbb-...

…and here on Bluesky: @mbb-umu.bsky.social

#UmeaUniversity

ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation time scales increase, so does the associated computational cost. To extend simulated time using the same resources, a common strategy is to constrain the fastest degrees of freedom, such as bond lengths, allowing for larger integration time steps without compromising accuracy. The de facto state-of-the-art algorithms for this purpose─SHAKE, LINCS, and P-LINCS─are integrated into most molecular dynamics packages and widely adopted across the field. Despite their impact, these methods exhibit limitations: all converge slowly when high numerical accuracy is required, and the LINCS and P-LINCS algorithms cannot handle general angular constraints, limiting further increases in time step. In this article, we introduce ILVES, a family of parallel algorithms that converge so rapidly that it is now practical to solve bond length and associated angular constraint equations as accurately as the hardware will allow. We have integrated ILVES into Gromacs, and our analysis demonstrates that it is superior to the state-of-the-art when constraining bond lengths. Due to its better convergence properties, we also show that if the time step is increased up to 3.5 fs by enforcing angular constraints, ILVES enables a 1.65× increase in simulated time using the same computational resources and wall-clock time, an outcome unattainable with current methods. This advance can significantly reduce the computational cost of most all-atom molecular dynamics simulations while improving their accuracy and extending access to larger systems and longer time scales.

#iqfpaper ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics. Published in Journal of Chemical Theory and Computation

Collaboration with @diis-uz.bsky.social @i3a.unizar.es @unizar.es #umeauniversity #BSC_CNS #cnr

bit.ly/3IltZ4A

Sunset at open sea.

Could the Bothnian Bay be facing #eutrophication?
There are signs that something is changing in the north.

A new exciting research project is underway to find out why — and what it means. 🌊 🧪🦑

🔗 balticwaters.org/en/...

@balticwaters #BalticSea #MarineScience #ClimateChange #UmeaUniversity

A general rule on the organization of biodiversity in Earth’s biogeographical regions - Nature Ecology & Evolution Ecological assemblages may be spatially organized by both context dependency and general processes. Here the authors find general patterns in the organization of regional biodiversity in biogeographic...

Read the full, open-access paper "A general rule on the organization of biodiversity in Earth’s biogeographical regions" published today in @natecoevo.nature.com. Find the article here: doi.org/10.1038/s415... #biodiversity #biogeography #ecology #evolution #scicomm #UmeaUniversity #IceLab

#Postdoc #ResearchOpportunity #Proteostasis #HighThroughputScreening #Bioinformatics #YeastGenetics #CareerDevelopment #ProfessionalDevelopment #UmeaUniversity #Hiring #WeAreHiring #PostdocOpportunity #OpenPosition #PostdocFellowship

MSc Amy Weisenfeld in the laboratory on Umeå Marine Sciences Centre.

Exciting research ahead! 🧪🌍 Amy Weisenfeld (MSc, @sorbonne-universite.fr) is at #UMF to study phytoplankton responses to long-term brownification & eutrophication in river estuaries at the Gulf of Bothnia. Most welcome, Amy!
#MarineScience #UmeaUniversity #ClimateChange

Adriaen Stigter (Radboud Uni.) and staff scientist Leon Serre-Fredj.

Excited to welcome Adriaen Stigter (Radboud Uni.) to #UMF! With Leon Serre-Fredj, he'll explore how human activities shape fish communities in the Gulf of Bothnia using Generalized Additive Modelling & multivariate analysis.🐟📊🦑
#MarineScience #Ecology #UmeaUniversity @ribesresearch.bsky.social

Alexandra Rouillard, affiliated postdoc at Department of Ecology and Environmental Science and Umeå Marine Sciences Centre, Umeå University.

Proud to share that postdoc Alexandra Rouillard has received a Ymer-80 Foundation scholarship for her research on the role of organic matter on methane microbial dynamics in Greenland!
Congrats, Alex! 👏🚀
#Science #Research #Scholarship #UmeaUniversity #UMF
🌍🧪 🌊

Excited to say I've been offered a Marie Skłodowska-Curie Actions postdoc fellowship! #MSCA

I'll be staying at #umeauniversity, continuing work on the structural biology of Gram-positive type 4 secretion systems.

Two exciting 3-year postdoc positions, on above-/belowground linkages and microbial community structure and genomics, working with one of the best ecologists in the world on the famous islands in northern Sweden! Deadline April 1 #ecology #postdocposition #umeauniversity

Tharindu Herath, researcher at Department of Ecology and Environmental Science (EMG) and Umeå Marine Sciences Centre (UMF), Umeå University, defending his thesis.

Opponent Thorsten Blenckner, Associate Professor at #StockholmUniversity, and Tharindu Herath, researcher at Department of Ecology and Environmental Science (EMG) and Umeå Marine Sciences Centre (UMF), Umeå University.

Congratulations to Tharindu Herath @umeaunimarine.bsky.social for an excellent defense of his thesis: "Marine food webs under changing climate - Impacts on food web efficiency and quality"! 🧪🦑🌍
umu.diva-portal.org/smash/record...

#UmeaUniversity #ClimateResearch #MarineScience

UMF staff sampling in the Baltic Sea.

Winter sampling on the ice with our hovercraft. Photo: Mattias Pettersson/UmU

Ice experiment in the UMF indoor mesocosm facility.

Research vessel KBV181 on winter expedition in the Baltic Sea.

Welcome all new followers on Bsky! 🌊🧪🔬🦑
At @umeaunimarine.bsky.social, we conduct and support #research to drive sustainable development of resilient marine ecosystems in Arctic, sub-Arctic and extreme (inc. coral!) environments. 🌍 Come join us! 🐟

#Sustainability #MarineScience #UmeaUniversity

Visitors in conversation with UMF staff at KBC-days, Umeå University.

Thrilled by the success at KBC Days at #UmeaUniversity! 🎉 Inspiring conversations with scientists on leveraging our advanced infrastructures to push the boundaries of research and innovation! Here’s to supporting breakthrough science!🔬🧪🌊🐋
www.umu.se/en/umea-mari...

#KBCDays #ScienceInfrastructure

Thibaut Cossart, Postdoc fellow at Department of Chemistry.

Coffee break at UMF.

Audience at UMF symposium.

UMF Symposium! Incredible to see the wide range of activities and #research happening at #UMF right now. From #BlueCarbon and #brownification to #CoralBleaching, marine heatwaves and #methylmercury formation in fjord systems... And so much more!
🧪🚢🌊🐋

#umeauniversity #MarineScience

Bad weather on the Baltic Sea.

Water temperature measured with Ferrybox at 5 meters depth.

Salinity in water measured with Ferrybox at 5 meters depth.

Environmental monitoring aboard KBV181 this week. Northern Baltic Sea woke up grumpy, and thanks to hurricane #Kirk's leftovers, things got rougher. But the #Ferrybox worked like a champ, no matter the weather! Glad to be home! 🌊🌪️🚢 🧪

#BalticSea #umeauniversity #UMF

A child explores the aquarium during the European Researchers' Night at Umeå University. Photo: Gabrielle Beans Picón

Children investigating what's in the water during the European Researchers' Night at Umeå University. Photo: Gabrielle Beans Picón

Colorful experiments for kids during the European Researchers' Night at Umeå University. Photo: Gabrielle Beans Picón

A child uses a magnifying glass to find out what is in the water during the European Researchers' Night at Umeå University. Photo: Gabrielle Beans Picón

Lots of activity and young visitors at Curiosum for #EuropeanResearchersNight! #UMF researchers had a great time teaching our scientists of tomorrow about the Baltic Sea and #MarineScience! 🧪🐋🌊

#ForskarFredag #exploREsearch #umeauniversitet #umeauniversity

Home | AQUASERV

Great opportunity! 🐳🧪🌊🦀
#AQUASERV will provide transnational access to advanced research infrastructures such as @umeaunimarine.bsky.social.

Check it out (brand new website is live!) and stay tuned! Calls will open soon! aquaserv-ri.eu

#Sustainability #BlueEconomy #umeauniversity

Diving on closed down fish farm. Photo: Joakim Ahlgren/UMF

This week, we're diving on a closed down #fishfarm area in the High Coast. A multi-year study on recovery of #benthic fauna, vegetation and water chemistry. A unique opportunity, so exciting! 🐋🤿🧪🌊

#biodiversity #MarineScience #research #Baltic #UmeaUniversity #UMF

David Jen, Borealis intern at UMF.

We're excited to welcome Borealis intern David Jen from #UCLA!
He will join our #UMF research team, focusing on how #climatechange and associated stressers may affect the symbiotic community composition within #CoralReefs. 🧪🐋🌊🦐

www.umu.se/en/umea-m...

#umeauniversity

A conceptual summary of the photosynthesis and calcification carbon transport pathways

🌊Out this week in #BiologyLetters! We show that #marine calcifying ecosystem engineers recycle more #carbon than previously thought aiding their role as #BlueCarbon ecosystems! 🦑🧪🌎⚒️🌱https://doi.org/10.1098/rsbl.2023.0598 @hlburdett.bsky.social #JinhuaMao @umeaunimarine.bsky.social #umeauniversity

Dr. Leon Serre-Fredjon, Royal Netherlands Institute for Sea Research. Photo: Kristina Viklund/UMF

Excellent talk! 👍 Dr. Leon Serre-Fredjon on topic ”Quantification of anthropic effects on #phytoplankton using environmental monitoring, times series modelling and bioassays” at seminar @umeaunimarine.bsky.social #UmeaUniversity

Research vessel KBV181 at sea.

Professor Rainer Lohmann, University of Rhode Island, ”Legacy and Emerging Pollutants in the Ocean”.

Speakers at minisymposium: Ashish Verma, Tharindu Bandara Herath, Li Zhao, Rainer Lohmann, Christine Gallampois, Eric Capo.

#UMF celibrate #WorldOceanDay! 🐟🌊🐙🐳
This weeks #EcoChange minisympoium
@umeaunimarine.bsky.social
with keynote Rainer Lohmann from
@universityofri vas a great success! Thanks! 👍
#MarineResearch #OceanClimateAction #WOD2024
#umeauniversity

Postdoctoral Scholarship (2 years) within algal physiology and photophysics - Umeå, Sweden A two-year Postdoctoral Scholarship focused on multiscale (photo)physiology in reef-building marine algae

📣 Last call! 📣 2 year #postdoc position on algal #physiology & #photophysics. Main supervisor @hlburdett.bsky.social. Join us! 👍🦑🧪🌎💧⚒️

📆Deadline 2 June 2024!

www.nature.com/naturecareer...

#UMF #UmeaUniversity #PostDocJobs #MarineScience

Sweden becomes the new hub for European polar research European Polar Board (EPB) and the future European Polar Coordination Office (EPCO) are coming to Umeå.

Happy to share that European Polar Board and the future European Polar Coordination Office are moving to #UmeaUniversity! We are excited to work with them strengthening #Arctic #marine #research and policy development! ❄️❄️❄️
#UMF #EPB #EPCO

www.umu.se/en/news/swed...

Siv Huseby, taxonomist and environmental analyst at Umeå Marine Sciences Centre.

Day after #BiodiversityDay! 🥳
This week we highlight our fantastic taxonomists, doing invaluable work for #environmental #research!
This is Siv Huseby, a specialist in the taxonomy of #phytoplankton and member of the #Helcom Phytoplankton Expert Group! 🐟🐙🐳🦐🌊
#PartOfThePlan #umeauniversity

Petra Rådman, taxonomist at Umeå Marine Sciences Centre.

#BiodiversityDay! 🐟🦀🐙🐬🦪🌊
We want to highlight our fantastic taxonomists, doing invaluable work for #marine #research! This is Petra Rådman, an outstanding specialist in #zooplankton and benthic fauna!
www.umu.se/en/news/vi-f...
#PartOfThePlan #ForNature #umeauniversity #UMF

Mikael Peedu, taxonomist Umea Marine Sciences Centre, collecting samples.

#BiodiversityDay is coming up and we highlight our fantastic taxonomists! Second out is Mikael Peedu, whose expertise is #zooplankton and benthic macrofauna is of great support for environmental #research. Keep up the good work! 🐟🌊👍#PartOfThePlan #ForNature
#umeauniversity

Waves hitting rocks at Ulvön, Bothnian Sea. Photo: Kristina Viklund/UMF

📣Coming up! #EcoChange minisymposium
@umeaunimarine.bsky.social, covering ongoing #marine #research at #umeauniversity. Keynote: Professor Rainer Lohmann, University of Rhode Island, ”Legacy and Emerging Pollutants in the Ocean”. 🌊🧪
📅 Tuesday, June 4
More here: www.umu.se/en/events/mi...

Erik Björn, Professor at Department of Chemistry, Umeå University.

Exciting seminar @umeaunimarine.bsky.social! 👍
Prof. Erik Björn on topic ”Formation and #bioaccumulation of #methylmercury in Baltic Sea waters” and how to gain new knowledge by studies along different types of vertical and spatial gradients in the #BalticSea. 🐟🌊
#umeauniversity #marine #research