Lightnews — Scholar-powered news

MDAnalysis @mdanalysis.bsky.social · Jul 18

Matthias Heyden focuses on anharmonic low-frequency vibrations, which play a critical role in #molecular behavior but are often overlooked in harmonic models. His talk will show how sub-picosecond data can reveal key insights — and how data #streaming via #MDAnalysis makes it possible.

Dr. Matthias Heyden, Associate Professor, Arizona State University. Prof. Heyden's research group studies the dynamics and function of biomolecules with molecular simulations and Monte Carlo simulations. A special interest of his is anharmonic low-frequency vibrations, which are easily excitable by molecular collisions and can exhibit large deviations from harmonic approximations.

1 2

MDAnalysis @mdanalysis.bsky.social · Jul 18

@ltchong.bsky.social develops methods to simulate rare but important biological events — leading the team behind @westpasoftware.bsky.social, an #OSS for weighted ensemble (WE) path sampling. Her talk will explore how #WE methods and #ML can uncover hidden protein states and rare transitions.

Dr. Lillian Chong, Professor, University of Pittsburgh. Prof. Chong's research focuses on developing and applying advanced simulation methods to investigate rare but biologically important events, with an emphasis on capturing rigorous kinetics. Her group leads the development of the open-source WESTPA software, which implements weighted ensemble path sampling strategies for efficient simulation of rare events. She also works on the development of implicitly polarized force fields and rational design of protein conformational switches.

1 4

MDAnalysis @mdanalysis.bsky.social · Jul 18

🧵 In this thread, we introduce Lillian Chong (Univ. of Pittsburgh) and Matthias Heyden (ASU) as keynote speakers for the #mdaUGM2025! Register now to hear these talks on novel molecular simulation and analysis strategies.

📅 Nov 9–11
📍 Arizona State University
🔗 www.mdanalysis.org/2025/07/15/u...

UGM 2025 Announcements – Keynote Speakers, Workshop Hosts, and Registration Deadline Extension · MDAnalysis

www.mdanalysis.org

1 2

Reposted by MDAnalysis

Oliver Beckstein [he/him] @orbeckst.bsky.social · Jul 16

Come to the @mdanalysis.bsky.social User Group Meeting at Arizona State University in November. See www.mdanalysis.org/2025/07/15/u... for our keynote speakers and more updates.

Great opportunity for junior researchers to present their work and to network with the MDAnalysis community.

3 8

MDAnalysis @mdanalysis.bsky.social · Jul 18

🗞️ Good news! Abstract and travel bursary applications for #mdaUGM2025 (Nov 9–11 @ ASU) are still being accepted — registration is now on a rolling basis.

Details and a link to the registration form are found on the #MDAnalysis blog: www.mdanalysis.org/2025/07/15/u...

#MolecularDynamics #OpenSource

MDAnalysis @mdanalysis.bsky.social · Jul 11

🚨 Deadline coming up!
🎯 Don’t miss your chance to present at the #mdaUGM2025 — abstract + travel bursary applications due July 15!

Meet the community, share your work, learn from others, and get support to attend.

🔗 Info: www.mdanalysis.org/pages/ugm2025/

#MDAnalysis #OSS #MolecularDynamics #UGM

1 4

MDAnalysis @mdanalysis.bsky.social · Jul 11

🚨 Deadline coming up!
🎯 Don’t miss your chance to present at the #mdaUGM2025 — abstract + travel bursary applications due July 15!

Meet the community, share your work, learn from others, and get support to attend.

🔗 Info: www.mdanalysis.org/pages/ugm2025/

#MDAnalysis #OSS #MolecularDynamics #UGM

2 3

MDAnalysis @mdanalysis.bsky.social · May 20

#mdaUGM2025 is officially happening! Abstracts and travel bursary applications are being accepted from now until the July 15, 2025 deadline: www.mdanalysis.org/2025/04/13/u....

🗓️ November 9-11, 2025
📍Tempe, Arizona, USA (and online)

#open-source-software #molecular #simulations #streaming

1 3 10

MDAnalysis @mdanalysis.bsky.social · Mar 19

Do you like coding in #Python? Have you been using #MonteCarlo methods or running #MD simulations?

Working with MDAnalysis and @westpasoftware.bsky.social on a GSoC 2025 project may be just for you! For details, read our blog post: www.mdanalysis.org/2025/02/28/g....

Pre-proposal deadline: Mar 21

1 2

MDAnalysis @mdanalysis.bsky.social · Mar 17

Friendly reminder that this is the last week to submit your pre-proposals if you are interested in working with MDAnalysis in the GSoC 2025 program (⏱️ **Deadline: March 21st**). Read our GSoC blog post for full details: www.mdanalysis.org/2025/02/28/g....

2 4

MDAnalysis @mdanalysis.bsky.social · Mar 17

MDAnalysis 2.9.0 (and its blog post) is out: www.mdanalysis.org/2025/03/11/r...!

Includes:
* Additional Gromacs/distopia/parallel analysis support
* New "water"/"precision" keywords

🙏 to the release's 10 contributors (3 new), and to @numfocus.bsky.social/@chanzuckerberg.bsky.social for support.

Release 2.9.0 of MDAnalysis · MDAnalysis

www.mdanalysis.org

12 31

MDAnalysis @mdanalysis.bsky.social · Mar 3

MDAnalysis is participating in Google Summer of Code 2025! Do you like #coding to solve problems in #biophysics #chemistry or #materials?

Read our blog on how to apply: www.mdanalysis.org/2025/02/28/g.... Pre-proposals are due March 21st.

We value transparency; please communicate in public forums.

4 9

MDAnalysis @mdanalysis.bsky.social · Dec 12

Making the image not transparent (sorry!) actually shows you the simple Python code that one uses to generate it: Make a MDAnalysis AtomGroup and call the visualize() method.

4

MDAnalysis @mdanalysis.bsky.social · Dec 12

🎉 Small Development Grant by @numfocus.bsky.social for Advanced Molecular Visualizations with #MolecularNodes and @blender3d.bsky.social! @yuxuanzhuang.bsky.social and @bradyajohnston.bsky.social will build an API & integrate with @projectjupyter.bsky.social. See www.mdanalysis.org/2024/12/12/s...

Visualization of part of a protein with MDAnalysis and Blender/MolecularNodes together with Python code to generate the image.

1 6 41

MDAnalysis @mdanalysis.bsky.social · Nov 27

We released MDAnalysis 2.8.0 🚀 See the blog post www.mdanalysis.org/2024/11/22/r... . Highlights: (1) all code under the GNU Lesser General Public License, (2) new Guesser API, (3) general parallelization for analysis tools, (3) DSSP analysis class, (4) more MDAKits.

Release 2.8.0 of MDAnalysis · MDAnalysis

www.mdanalysis.org

17 58

MDAnalysis @mdanalysis.bsky.social · Aug 16

Your opinion matters! 🌟 If you haven't already, please take a moment to share your thoughts about MDAnalysis communications and resources: www.mdanalysis.org/2024/07/31/s....

The survey deadline is August 31st.

2 3

MDAnalysis @mdanalysis.bsky.social · Aug 1

Do you use or contribute to MDAnalysis? Have you attended MDAnalysis events? We invite all community members to participate in a survey before Aug 31 to help us foster an inclusive and supportive community and develop a communications strategy: www.mdanalysis.org/2024/07/31/s.... Thanks in advance!

MDAnalysis Community Survey 2024 · MDAnalysis

www.mdanalysis.org

1

MDAnalysis @mdanalysis.bsky.social · Jul 12

⏰ It's almost that time for the #mdaUGM2024 registration deadline (July 14, midnight anywhere on Earth). Sign up now to secure your spot: www.mdanalysis.org/pages/ugm202...

We look forward to seeing you there!

MDAnalysis @mdanalysis.bsky.social · Jul 8

🚨 There is only ~1 week left to register for the #mdaUGM2024 before the deadline, July 14th!

Register now to join us in London Aug 21-23 for exciting talks, interesting discussions and an interactive hackathon related to all things #MD and #OSS: mdanalysis.org/pages/ugm202...

1

MDAnalysis @mdanalysis.bsky.social · Jul 8

🚨 There is only ~1 week left to register for the #mdaUGM2024 before the deadline, July 14th!

Register now to join us in London Aug 21-23 for exciting talks, interesting discussions and an interactive hackathon related to all things #MD and #OSS: mdanalysis.org/pages/ugm202...

1

MDAnalysis @mdanalysis.bsky.social · Jun 25

Greetings from the joint MDAnalysis / MolSSI hybrid workshop at ASU: from users to developers in the analysis of molecular simulations with software engineering best practices and MDAKits mdanalysis.org/2024/05/14/A... : ~45 in-person attendees+instructors and ~80 online.

group photo from the MDAnalysis/MolSSI Workshop at ASU, June 24-25, 2024

3

MDAnalysis @mdanalysis.bsky.social · Jun 18

📢 One of MDAnalysis's very own core developers, Richard Gowers, will be giving a CCPBioSim industry talk June 19th, from 14:00-15:30 BST. Read more and access the link to register in our latest blog post: www.mdanalysis.org/2024/05/30/c....

CCPBioSim Industry Talk by Richard Gowers (MDAnalysis Core Developer) · MDAnalysis

www.mdanalysis.org

1

MDAnalysis @mdanalysis.bsky.social · May 29

MDAnalysis is thrilled to be working with 4 amazing new contributors through the @ggl.bsky.social Summer of Code and Outreachy programs. Meet them all and learn more about the projects they will be working on over the next few months in our new blog post: www.mdanalysis.org/2024/05/27/g...

1 4

MDAnalysis @mdanalysis.bsky.social · May 17

📢📢 Registration for #mdaUGM2024 is now open! Join us in London from 21-23 Aug to talk about all things MDAnalysis. You also won't want to miss the talks from our keynote speakers, Drs. Antonia Mey and Francesca Stanzione.

Register now to secure your place:
www.mdanalysis.org/pages/ugm202...

UGM 2024 · MDAnalysis

www.mdanalysis.org

1 2

MDAnalysis @mdanalysis.bsky.social · May 14

Register for our joint MDAnalysis/MolSSI workshop at Arizona State University on June 24th-25th 2024. Attendance is free, travel bursaries are available, register for in-person or online attendance at www.mdanalysis.org/2024/05/14/A... Registration deadline is soon, May 27, 2024.

1 2

MDAnalysis @mdanalysis.bsky.social · Apr 24

Save the date: June 24th & 25th: Joint MDAnalysis/MolSSI workshop at Arizona State University. Details to follow.

www.mdanalysis.org/2024/04/24/A...

1 2

MDAnalysis @mdanalysis.bsky.social · Apr 15

🚨 Last call (TODAY) for abstract submissions for the #mdaUGM2024 !

Submit here: docs.google.com/forms/d/e/1F...

Read more about the user group meeting here: www.mdanalysis.org/pages/ugm2024/