Phase Space Invaders (ψ)

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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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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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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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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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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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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 countries as group leaders. We examine the hopes, fears, and conditions for success in making this transition, aiming to rewrite common narratives from our unique perspectives.

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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 discuss polarizable force fields for nucleic acids, including the problems they might help solve and the practical ways in which we might arrive at these solutions. We conclude by pointing out the need for more nuanced undergraduate curricula that reflect the current open questions in nucleic acids research to attract students who will make the future discoveries.

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In the tenth episode, Ariane Nunes-Alves and I talk about a kinetics-centric view of drug design, making the case that modeling kinetics in atomistic simulation is an important frontier that, despite clear biomedical relevance, is rarely explicitly addressed either in model parameterization or with the latest AI methods. We discuss the need to turn to a more explicit image of the drug's pathway towards its target, including not only affinities and residence times, but also the cellular environment. Then, we switch to the social sphere to discuss how much of a PI's professional time circles around interpersonal interactions, and where can we computational scientists go to find our community in the era of fragmentation and specialization of social media.

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In the ninth episode, Michele Vendruscolo and I discuss the current state of research on misfolding diseases, typically associated with excessive protein aggregation and formation of insoluble amyloids. Michele presents an optimistic perspective in which the convergence of recent clinical and software developments opens up new avenues for efficient treatment of such debilitating conditions as Alzheimer's and Parkinson's disease. This interconnection between the everyday work of scientists and the experience and outlook of affected individuals inspires us to reflect on the societal responsibilities of a scientist, from disseminating our results to inspiring newcomers to engage with urgent global crises to mentoring the next generation of problem-solvers and revolutionary thinkers.