15 épisodes
Phase Space Invaders (ψ) Miłosz Wieczór
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- Sciences
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're headed for, and which exciting pathways will take us there. Whether you're just thinking of starting your research career or have been computing stuff for decades, come and join the conversation!
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Episode 13 - Daniel Zuckerman: Trajectory ensembles, writing books, and learning biology through physics
Send us a Text Message.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 trajector...
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Episode 12 - Vlad Cojocaru: Simulating transcriptional regulation, returning to our home countries, and the scales of the genome
Send us a Text Message.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...
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Episode 11 - Justin Lemkul: Providing technical help online, sharing expertise, and polarization in nucleic acids
Send us a Text Message.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...
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Episode 10 - Ariane Nunes-Alves: Kinetics in drug design, molecular crowding, and the social life of a PI
Send us a Text Message.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 a...
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Episode 9 - Michele Vendruscolo: Preventing protein misfolding, fostering public engagement of scientists, and AI tools in drug design
Send us a Text Message.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...
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Episode 8½ - My commentary: Wrapping up the first season
Send us a Text Message.In this episode, I'm attempting to string together the most common threads brought up by my guests in the first eight interviews on the podcast. Reflecting on these conversations, I'm suggesting some grand challenges for the field in the years to come.