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Jerome starts our conversation by reviewing the history of the ABF method and its advantages compared to the main competitors, and connects it to the development of COLVARS, historically very parallel to how the development of the Plumed tool stemmed from the needs of the metadynamics community. We discuss the benefits of graphical interfaces in biomolecular workflows, and touch upon the question of connecting multiple software environments and communities. We then move on to discuss membrane systems and the challenges they pose, both historically and today, and end up on the alchemical side, talking about the latest approaches to alchemical free energy calculations from several exciting angles. Eventually, we agree that regardless of software developments, it's learning and helping others learn to understand molecular systems that's the most rewarding part of the job of a biophysicist.

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In Episode 28, Yuji Sugita shares the story of how he developed temperature replica exchange in the lab of Yuko Okamoto, connecting to his early experience from working with Nobuhiro Go, the father of Go models. We then talk about the process of building up workflows for simulating massive atomistic systems, a multi-year collaboration with Michael Feig, and ponder the question of when one should go about writing their own scientific software rather than reusing existing software packages. Talking about molecular crowding naturally brings us to current and future directions, which for Yuji include simulating increasingly multi-component condensates and exploring multi-resolution schemes in GENESIS. Towards the end, he highlights the need for young researchers to engage with the international community through long-distance collaborations, regardless of where one ends up living and working.

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In episode 27, Kresten starts by explaining his path from a wet lab biochemist to a computational biophysicist, a story full of open-ended explorations and helpful mentors. He gives us some background on how both the legacy and latest models developed, highlighting how in each case the driving force were experimental results that either weren't quite matching simulations, or were plenty enough to allow for top-down training. We walk through some of the functions and applications of intrinsically disordered regions, or IDRs in short, and their relevance for medical research. Then towards the end, Kresten shares some tips and observations from his work in grant evaluation, insisting that internal peer review remains the best source of feedback, but in the end it's one's scientific intuition that has to guide us.

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In episode 26, we talk about the origins of Pratyush's passion for statistical mechanics, deeply rooted in his background in material science, and think about how we can promote a profound understanding of statmech theory among people working in computational biophysics. From there, we explore ways of re-introducing physical rigor into modern data-driven approaches, which is the main concern that Pratyush says drives his research agenda. He ends up sharing a ton of interesting points on working with the industry, the value of education and knowledge sharing, or the philosophy of complex and cognitive systems, and ends up with a call for more time for silent thinking, where - he says - most of his original ideas came from.

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In episode 25, Ivet and me start with a general overview of the elastic network theory and its applications to biology, as well as its strengths and limitations. Ivet then tells us about the specific takeaways from the different lines of her research, talking about evolutionary dynamics signatures, mode excitations in allosteric effects, as well as her recent research on the relevance of hinge regions for drug discovery. We talk about the relevance of the proteins-as-graphs picture for machine learning, and end up with a few general reflections about the complementary roles of persistence and alertness in scientific careers.

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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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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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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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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.