Send us a text 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 d...
Send us a text 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 softwar...
Send us a text 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 application...
Send us a text 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 ...
Send us a text 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 pic...
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 percept...
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 th...
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 ...
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 ...
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 a...
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...
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 ...
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-emergi...
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 ...
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 le...
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...
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 ensemb...
Send us a text In the twelfth episode, Vlad Cojocaru and I discuss how the simulation field can integrate further layers of complexity in modeling transcription control and genome organization in humans. Vlad shares his insights on the computational biology of transcription factors, including DNA-mediated allostery and pioneer transcription factors, which are crucial for cellular reprogramming. Our discussion then shifts to the underexplored topic of researchers' returning to our home countri...
Send us a text In the eleventh episode, Justin Lemkul and I talk about the motivations and challenges behind providing technical help on online forums and mailing lists. Justin shares his story of becoming a prolific technical advisor for the Gromacs community, which evolves into a discussion about automatability, the role of expertise in running and documenting simulation-based projects, and the incentives for people who contribute their time to helping the community. We then move on to disc...