Phase Space Invaders (ψ) podcast

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Episode 24 - Katarzyna Marcinkiewicz [Nature Communications]: The job of a full-time editor, transparency and other novelties in publishing, and coaching the review process 49:16

10 weeks fa49:16

49:16

Send us a text In episode 24, Katarzyna talks about the everyday concerns and common threads of an editor's job, from continuously learning about the rapid developments in the field to navigating the review process. She shares some inside stories about the experimental features that journals tinker with these days, and it's good to know that many interesting ideas are being tested out there in the wild. We then discuss a bit about the evolution of the publishing process, including its perception among us research scientists. We largely leave the questions of profits and finance out of the conversation, so this is purely a conversation between two science aficionados who care deeply about the scientific enterprise being transparent, just, open to novelty and focused on quality evidence.…

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Episode 23 - Zoe Cournia: Precision medicine, designing allosteric drugs, and the role of an academic editor 50:00

12 weeks fa50:00

50:00

Send us a text In episode 23, Zoe and me discuss the current status and promises of drug design, a field where many things seem trivial but nothing is really simple. Zoe talks about the challenges that precision medicine is facing, and how it fits into the grand landscape of future therapies. We go through some success stories, and I ask Zoe how the recent additions to drug design workflows help them in everyday scientific practice, both in terms of physics-based and data-driven models. We then spend a moment talking about the opportunities and responsibilities of a journal editor, and what are the lessons Zoe learned from creating her startup.…

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Episode 22 - Lucie Delemotte: Enhanced sampling methods, alternative publishing models, and becoming a parent in academia 48:58

13 weeks fa48:58

48:58

Send us a text 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.…

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Episode 21 - Tamar Schlick: A mathematician's path to biology, RNA frameshifting, and why scientists (should!) run 44:49

14 weeks fa44:49

44:49

Send us a text 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.…

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Episode 20 - Rommie Amaro: Simulating viruses, cross-disciplinary complexity, and the brain drain 42:52

23 weeks fa42:52

42:52

Send us a text 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.…

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Episode 19 - Alex MacKerell: Simple physics, missing experimental data, and model compatibility 26:14

26 weeks fa26:14

26:14

Send us a text 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.…

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Episode 18 - Erik Lindahl: Finding simple and novel ideas, starting an experimental lab, and ligand-gated ion channels 36:58

27 weeks fa36:58

36:58

Send us a text 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.…

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Episode 17 - Caroline Lynn Kamerlin: Deep interdisciplinarity, enzyme promiscuity, and science in society 40:30

28 weeks fa40:30

40:30

Send us a text In episode seventeen, Caroline Lynn Kamerlin talks about the art of asking bold and impactful scientific questions, as well as how to engage in truly interdisciplinary research, something she sees as a consequence of her formal background in natural philosophy. We talk about the emerging concepts around enzyme promiscuity, how this view has steadily become accepted in the field, and how it affects not only research but also human lives. That leads us to consider the ever-emerging problem of bacterial resistance and public health, and since public health is just two steps away from science education, we do venture there too.…

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Episode 16½ - End-of-season 2 commentary 19:23

34 weeks fa19:23

19:23

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Episode 16 - Janusz Bujnicki: Structural modeling, RNA modifications, and advising policy-makers on science 28:51

35 weeks fa28:51

28:51

Send us a text In the sixteenth episode, Janusz Bujnicki tells me about his early switch to bioinformatics, a stroke of serendipity that defined his future career, and how he later managed to reincorporate both biophysics and experimental biology into his research agenda. We talk about the current state of the field of RNA structural prediction, and how we need to bring together physics and data to tackle the ever more complex biological questions that show up on the horizon. Then, we switch gears to discuss the fascinating world of science advisors for policy-making, or to what extent our scientific knowledge can be employed to shape long-term policies, including the blurry borders between science, philosophy and politics. I think it's a laudable aspiration for many of us to understand how we can have a tangible impact on the real world while keeping our humility in check.…

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Episode 15 - Paulo CT Souza: Developing a universal coarse-grained force field, and approaching the science of molecular complexity 26:41

36 weeks fa26:41

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Send us a text In the fifteenth episode, Paulo Souza and I discuss the challenges inherent in managing a project of such a scope, and the philosophy behind the systematic way in which Martini is continuously improved and reparameterized. Paulo describes how a user-centric approach helps refine and troubleshoot the model through its widescale adoption, and how different inherent limitations of coarse-grained modeling can be addressed to progressively make the force field more predictive and less reliant on user-defined biases. Then, we talk about the interplay between force field development and modern trends in biology, biomedicine and computational sciences - from small molecules to lipid nanoparticles, huge systems such as organelles or viruses, and molecular complexity, understood as going beyond simplified model systems and approaching biologically relevant mixtures and compositions.…

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Episode 14 - Syma Khalid: New ways to fight bacteria, the bacterial envelope, and kindness & openness in academia 23:00

37 weeks fa23:00

23:00

Send us a text In the fourteenth episode, Syma Khalid and I talk about the challenges we're faced with when trying to understand the environment of the bacterial cell envelope, and the outer membrane in particular. We discuss how the lessons taken from the computational study of these structures can inform the design of future antibacterial agents. Then, we move on to consider strategies for making the scientific environment of one's research group a place to thrive, develop, and live a happy and fulfilling life.…

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Episode 13 - Daniel Zuckerman: Trajectory ensembles, writing books, and learning biology through physics 29:45

38 weeks fa29:45

29:45

Send us a text In the thirteenth episode, Daniel Zuckerman and I talk about textbooks on statistical biophysics and a physics-based vision of biology, a few of which he himself authored. Daniel reveals that his passion for clarity in writing comes from his early humanities background, and makes a case for how well-thought and physically motivated narratives can unlock profound insights into the inner workings of biology. Then, we move on to discuss the physical theory behind trajectory ensembles, Daniel's preferred lens through which to view statistical mechanics. We dissect the strengths and limitations of this approach, and let ourselves speculate about its future evolution.…

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Episode 12 - Vlad Cojocaru: Simulating transcriptional regulation, returning to our home countries, and the scales of the genome 27:12

39 weeks fa27:12