Phase Space Invaders (ψ)

Send us a text [https://www.buzzsprout.com/twilio/text_messages/2313153/open_sms] In episode 22, we start by talking about the 2022 review of enhanced sampling methods that Lucie co-authored, one that provides long-needed organizing principles and unifying vocabulary for applications in this field. We also outline some challenges and community needs still waiting for the bold souls out there looking for ambitious projects. Lucie then moves on to share her experience with alternative publishing models, both as a member of Biophysics Colab and a former editor of eLife, and we dwell a bit on the challenges and possible solutions to what some would call a crisis in publishing, where evaluation metrics and publishing companies created unsustainable or even counterproductive incentive structures in sharing scientific results. We end on personal notes: already last year when I was visiting her lab in Stockholm, Lucie agreed to be on the very first list of interviewees, but it took me so long to figure it out that eventually Lucie gave birth to her twins and went on a maternal leave, so now that she's back more than a year later, I also asked her to share a few reflections on becoming a parent in academia.

Send us a text [https://www.buzzsprout.com/twilio/text_messages/2313153/open_sms] In episode 21, Tamar first explains how her unique background impacted the way she approached and conceptualized problems in biology, and how her research projects were born in the first place. We talk about the more recent research coming from Tamar's group on frameshifting, a fascinating process by which the readout of the genetic code can be offset by one or two letters to produce multiple proteins from a single viral gene. We then move on to discuss whether it's algorithms or compute that have contributed more to the growth of computational biophysics. Tamar's textbook and the multiple perspective articles she's written over the years serve us to dwell on the importance of writing for clarity and interdisciplinary collaboration. We end on a people-centric note, talking about the social bonds involved in both running and experimental collaborations.

Send us a text [https://www.buzzsprout.com/twilio/text_messages/2313153/open_sms] In episode 20, I start by asking Rommie how their research on the SARS-CoV-2 virus first unfolded during the early days of the pandemic, and from this story, we move on to discuss her original motivation to study large complex systems. We touch upon the exciting experimental developments that enable the realistic modeling of systems as big as entire viruses, and highlight some unexpected findings that came out of the large-scale simulations. Rommie also shares her reflections about the collaboration-driven nature of her lab and the complexities involved in interdisciplinary communication, and we wrap up with a few thoughts about the AI-driven brain drain from academia to industry.

Send us a text [https://www.buzzsprout.com/twilio/text_messages/2313153/open_sms] In episode 19, Alex and I discuss the history and future of developments in the CHARMM family of force fields, and whether Alex believes there is more physics that we need to include in our classical energy functions to work around our current challenges in biomolecular modeling. Throughout the conversation, he's advocated for a pragmatic, down-to-earth approach, with the idea of "big molecules, small physics". Alex also highlights the need to augment AI tools with HI, or human intelligence, arguing that so far most attempts at automating model development too much end up with parameters that are unphysical and non-transferable. Yet another interesting point is our often surprising reliance on truly ancient experimental data, and we try to make a point that these very non-sexy physical chemistry measurements straight from the 60s and 70s could truly advance the field if anyone was willing to fund them and actually get them done.

Send us a text [https://www.buzzsprout.com/twilio/text_messages/2313153/open_sms] In Episode 18, Erik Lindahl reminds us that despite our dependence on computational power and advanced technology, real breakthroughs are often waiting for those who have the patience to think carefully, come up with eye-opening ideas, and follow their sense of purpose. We discuss the different ways to be smart in science, highlighting the paradoxical need for both complexity and simplicity in thinking, and talk about what kind of questions in biology will keep us all busy for decades to come. Finally, Erik shares the story behind his series of lectures on concepts in molecular biophysics, a great component of the curriculum of every scientist in the field.