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Oliver Beckstein [he/him]

@orbeckst.bsky.social

Computational biophysicists at Arizona State University; MDAnalysis (@MDAnalysis.bsky.social) developer. Opinions my own. Research Group: https://becksteinlab.physics.asu.edu/ MDAnalysis: https://www.mdanalysis.org/

30 Posts588 Follower192 Folgt
John Chodera@jchodera.bsky.social · 3mo ago

Tremendously excited to help launch the Open Source for Science Fund, led by a fantastic team with an extraordinary track record of supporting open source software for science.

Open Source for Science Fund@os4science.org · 3mo ago

Today we're launching the Open Source for Science Fund, a new multi-donor philanthropic fund by Renaissance Philanthropy, seeded by @biohub.org and @wellcometrust.bsky.social, with support from @kavlifoundation.org and @researchsoftware.bsky.social 🧵 os4science.org/news/open-so...

MDAnalysis@mdanalysis.bsky.social · 3mo ago

Congratulations to all three of the #GSoC contributors who were accepted to work with MDAnalysis and @westpasoftware.bsky.social mentors this year! 👀 🔜 🤩 Keep an eye out for a blog post coming soon where you can learn more about each of the contributors and their projects.

Google Open Source@opensource.google · 3mo ago

The Journey has begun: Meet the 1,142 Contributors for GSoC 2026, applications stats and what’s next 🧑‍💻✨ ➡️ Read the full announcement here: goo.gle/gsoc-2026-co... #GoogleSummerOfCode #OpenSource #GSoC2026

MDAnalysis@mdanalysis.bsky.social · 5mo ago

MDAnalysis is participating in #GSoC 2026! 👉 Read our blog post for details on how you can apply to work with MDAnalysis through GSoC: www.mdanalysis.org/2026/02/19/g... 🗓️ Pre-proposals must be submitted by March 9. ❗For transparency and fairness, use public forums for all #GSoC communications.

Google Open Source@opensource.google · 6mo ago

📢 Meet the 2026 mentoring organizations for GSoC 2026‼️ Learn about the 185 mentoring orgs and get started with the must application tips to be a Contributor for GSoC 2026🚀 ➡️ Find the full blog here: goo.gle/gsoc2026-org... #GSoC #OpenSource #GoogleSummerofCode #Techcommunities

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Biophysical Society@biophysicalsoc.bsky.social · 5mo ago

Today's President’s Symposium: Communicating the Value of Biophysics in a Changing World features speakers who will discuss perspectives on the current crisis in US investment in science, and approaches for conveying the value of research to human health and prosperity.https://buff.ly/qcRp51M

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Oliver Beckstein [he/him]@orbeckst.bsky.social · 9mo ago

It was a fantastic meeting. It was really great to see so many young and up-and-coming computational scientists all together, showing what they've been working on and learning what they could be doing. I am really happy how @mdanalysis.bsky.social has been bringing people together.

MDAnalysis@mdanalysis.bsky.social · 9mo ago

The 2025 MDAnalysis User Group Meeting wrapped up. If you want to see what great talks and workshops we had, have a look at the UGM2025 repo github.com/MDAnalysis/U... . It was fantastic to have so many of you in Arizona and joining online! See you all again soon.

In-person participants at the MDAnalysis 2025 User Group Meeting (online participants not shown).
Oliver Beckstein [he/him]@orbeckst.bsky.social · 10mo ago

If you're doing #alchemistry (alchemical free energy calculations) then here's release 2.5.0 of alchemlyb for you. github.com/alchemistry/... (There's also the alchemlyb @joss-openjournals.bsky.social paper doi.org/10.21105/jos... if you want to read & cite.)

2.5.0 · alchemistry alchemlyb · Discussion #445

New minor release of alchemlyb with fixes and enhancements. Supports Python 3.11 - 3.14. See CHANGES for details. What's Changed update action/checkout by @orbeckst in #417 Parallel read and prepro...

github.com

Oliver Beckstein [he/him]@orbeckst.bsky.social · last yr.

Ricky Sexton (in collaboration with Mohamadreza Fazel, Maxwell Schweiger and Steve Pressé at ASU) devised a Bayesian nonparametric analysis to robustly and accurately protein-lipid interactions (residence times) from MD simulations – see doi.org/10.1021/acs.... .

Bayesian Nonparametric Analysis of Residence Times for Protein–Lipid Interactions in Molecular Dynamics Simulations

Molecular Dynamics (MD) simulations are a versatile tool to investigate the interactions of proteins within their environments, in particular, of membrane proteins with the surrounding lipids. However, quantitative analysis of lipid–protein binding kinetics has remained challenging due to considerable noise and low frequency of long binding events, even in hundreds of microseconds of simulation data. Here, we apply Bayesian nonparametrics to compute residue-resolved residence time distributions from MD trajectories. Such an analysis characterizes binding processes at different time scales (quantified by their kinetic off-rate) and assigns to each trajectory frame a probability of belonging to a specific process. In this way, we classify trajectory frames in an unsupervised manner and obtain, for example, different binding poses or molecular densities based on the time scale of the process. We demonstrate our approach by characterizing interactions of cholesterol with six different G-protein-coupled receptors (A2AAR, β2AR, CB1R, CB2R, CCK1R, and CCK2R) simulated with coarse-grained MD simulations with the MARTINI model. The nonparametric Bayesian analysis allows us to connect the coarse binding time series data to the underlying molecular picture and thus not only infers accurate binding kinetics with error distributions from MD simulations but also describes molecular events responsible for the broad range of kinetic rates.

doi.org

Don Moynihan@donmoyn.bsky.social · last yr.

You literally cannot tell this incredibly cool part of American history without centering Native American identity. It is an powerful demonstration of how diversity provided tangible military advantages over an enemy committed to White supremacy. donmoynihan.substack.com/p/whitewashi...

As the U.S. entered World Wars I and II, the military needed an efficient means of protecting its radio, telephone, and telegraphic messages from enemy intelligence. During this time, many Native Americans joined the armed forces and had a unique skill that would prove instrumental to the war effort. Each Native American tribe had their own language and dialect that few outside the tribes understood, many of which were not written down. Before their arrival in France during World War I, the Germans had broken every American code used, resulting in the deaths of many U.S. Soldiers. However, the Germans never broke the Native Americans’ “code,” and these Soldiers became affectionately known as Code Talkers.
Don Moynihan@donmoyn.bsky.social · last yr.

Articles about Native Americans, who enroll in the military at much higher rates than other groups, have been removed. This includes Navajo Code Talkers, whose identity was central to their ability to play a crucial role in military intelligence, have disappeared. www.axios.com/local/salt-l...

@darcy-davidson.bsky.social · last yr.

@biophysicalsoc.bsky.social you need to be sharing at the conference this week like our lives depend on it. Because they do. Speak up. Stand up. Get out there and protect out democracy

Stand Up for Science!@standupforscience.net · last yr.

Welcome to the Bluesky account for Stand Up for Science 2025! Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide! #scienceforall #sciencenotsilence