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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 14 - Syma Khalid: New ways to fight bacteria, the bacterial envelope, and kindness & openness in academia
23:00
23:00
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23:00
Send us a Text Message. 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 antibacteria…
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Episode 13 - Daniel Zuckerman: Trajectory ensembles, writing books, and learning biology through physics
29:45
29:45
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29:45
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 mo…
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Episode 12 - Vlad Cojocaru: Simulating transcriptional regulation, returning to our home countries, and the scales of the genome
27:12
27:12
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27:12
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 transcriptio…
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Episode 11 - Justin Lemkul: Providing technical help online, sharing expertise, and polarization in nucleic acids
29:38
29:38
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29:38
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 …
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Episode 10 - Ariane Nunes-Alves: Kinetics in drug design, molecular crowding, and the social life of a PI
19:13
19:13
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19:13
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 …
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Episode 9 - Michele Vendruscolo: Preventing protein misfolding, fostering public engagement of scientists, and AI tools in drug design
31:21
31:21
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31:21
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 n…
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Episode 8½ - My commentary: Wrapping up the first season
20:15
20:15
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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.By Miłosz Wieczór
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Episode 8 - Rossen Apostolov: Managing scientific collaboration, the biggest project of European biophysics, and seeding schools of thought
27:13
27:13
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27:13
Send us a Text Message. In the eight episode, Rossen Apostolov and I depart from the standard format to talk about the core concepts behind BioExcel, the European Center of Excellence for computational biology. We discuss their main objectives and challenges, from working with code to organizing schools and webinars, talk about the challenges of su…
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Episode 7 - Aleksei Aksimentiev: Nanobiotechnology, the importance of mentoring, and engineering serendipity
37:38
37:38
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37:38
Send us a Text Message. In the seventh episode, Aleksei Aksimentiev and I delve into the intersection of physics, biology, and nanotechnology, exploring the innovative world of nanopores and biomolecular sequencing. Aleksei shares his journey from particle physics in Ukraine to leading-edge research in the US, and underscores how on the unpredictab…
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Episode 6 - Giulia Palermo: Reimagining scientific creativity, the RNA revolution, and truly multiscale systems
24:24
24:24
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24:24
Send us a Text Message. In the sixth episode, Giulia Palermo and I discuss the challenges of studying truly multiscale biomolecular systems, such as the CRISPR/Cas9 complex she famously got involved with. While such problems can take us way out of our comfort zones, they also provide us with clear pathways to innovative and transformative science, …
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Episode 5 - Paul Robustelli: The dissolving barrier between industry and academia, embracing our artistic side, and new models of funding
30:04
30:04
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30:04
Send us a Text Message. In the fifth episode, Paul Robustelli and I discuss how the once very sharp boundary between academia and industry has been becoming increasingly porous, and what implications it will have for future careers in science. Paul shares his experiences and observations about the competing models of funding scientific research, an…
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Episode 4 - Modesto Orozco: Computations driving experiments, opening simulation data, and integrating knowledge across sources and scales
24:18
24:18
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24:18
Send us a Text Message. In the fourth episode, Modesto Orozco and I talk about the rough path to the predictive power modern computational science has achieved in biology, and the immense possibilities it opens to today's computational biologists working across the scales of space and time. Modesto also reflects on why sharing simulation data is cr…
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Episode 3 - Wojtek Kopeć: Science as a social endeavor, learning from industry, and the experience of starting a new lab
35:51
35:51
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35:51
Send us a Text Message. In the third episode, Wojtek Kopeć and I discuss the overlooked yet exciting social aspect of scientific collaboration, and what the world of academia could learn from the industry and statisticians to avoid falling behind. Wojtek also shares his personal experience of starting a lab as a new PI, and we reflect on the role o…
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Episode 2 - Max Bonomi: Interoperability, AI-generated ensembles, and recognizing all contributions to science
24:24
24:24
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24:24
Send us a Text Message. In the second episode, Max Bonomi and I discuss efforts to achieve interoperability and portability in the computational community, and how the AI structural revolution will unfold to bring us realistic molecular ensembles. We then move on to ask how the entire range of contributions to science can be recognized, particularl…
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Episode 1 - Pilar Cossio: Modeling experimental setups, overpublishing, and maintaining code
27:00
27:00
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27:00
Send us a Text Message. In the first episode, Pilar Cossio and I discuss the radical progress in integrating simulations with experiments, and the excitement about recent progress in modeling cryo-EM tomography data. We share thoughts on the sustainability of our publishing practices, and comment on the challenges of funding the maintenance of scie…
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Introduction: Do we really need another podcast?
6:39
6:39
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Send us a Text Message. What is this all about? Does the computational community need a podcast? Along with the first interview, I'm sharing the idea behind PSI, and explaining why the time is ripe for a new marketplace of ideas to drive the changes in how we do science. Everyone is invited, from ambitious undergraduates to seasoned veterans!…
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