Phase Space Invaders (ψ)
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!
Episodes
23 episodes
Episode 20 - Rommie Amaro: simulating viruses, cross-disciplinary complexity, and the brain drain
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...
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Season 3
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Episode 20
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42:52
Episode 19 - Alex MacKerell: Simple physics, missing experimental data, and model compatibility
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 ...
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Season 3
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Episode 19
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26:14
Episode 18 - Erik Lindahl: Finding simple and novel ideas, starting an experimental lab, and ligand-gated ion channels
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 foll...
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Season 3
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Episode 18
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36:58
Episode 17 - Caroline Lynn Kamerlin: Deep interdisciplinarity, enzyme promiscuity, and science in society
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 na...
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Season 3
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Episode 17
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40:30
Episode 16 - Janusz Bujnicki: Structural modeling, RNA modifications, and advising policy-makers on science
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 res...
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Season 2
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Episode 16
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28:51
Episode 15 - Paulo CT Souza: Developing a universal coarse-grained force field, and approaching the science of molecular complexity
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...
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Season 2
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Episode 15
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26:41
Episode 14 - Syma Khalid: New ways to fight bacteria, the bacterial envelope, and kindness & openness in academia
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 co...
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Season 2
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Episode 14
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23:00
Episode 13 - Daniel Zuckerman: Trajectory ensembles, writing books, and learning biology through physics
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 ea...
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Season 2
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Episode 13
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29:45
Episode 12 - Vlad Cojocaru: Simulating transcriptional regulation, returning to our home countries, and the scales of the genome
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 o...
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Season 2
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Episode 12
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27:12
Episode 11 - Justin Lemkul: Providing technical help online, sharing expertise, and polarization in nucleic acids
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 communit...
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Season 2
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Episode 11
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29:38
Episode 10 - Ariane Nunes-Alves: Kinetics in drug design, molecular crowding, and the social life of a PI
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 explic...
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Season 2
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Episode 10
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19:13
Episode 9 - Michele Vendruscolo: Preventing protein misfolding, fostering public engagement of scientists, and AI tools in drug design
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 perspectiv...
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Season 2
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Episode 9
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31:21
Episode 8½ - My commentary: Wrapping up the first season
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 ...
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Season 1
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Episode 8
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20:15
Episode 8 - Rossen Apostolov: Managing scientific collaboration, the biggest project of European biophysics, and seeding schools of thought
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 wor...
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Season 1
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Episode 8
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27:13
Episode 7 - Aleksei Aksimentiev: Nanobiotechnology, the importance of mentoring, and engineering serendipity
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 ...
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Season 1
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Episode 7
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37:38
Episode 6 - Giulia Palermo: Reimagining scientific creativity, the RNA revolution, and truly multiscale systems
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, t...
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Season 1
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Episode 6
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24:24
Episode 5 - Paul Robustelli: The dissolving barrier between industry and academia, embracing our artistic side, and new models of funding
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 experien...
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Season 1
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Episode 5
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30:04
Episode 4 - Modesto Orozco: Computations driving experiments, opening simulation data, and integrating knowledge across sources and scales
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 sc...
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Season 1
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Episode 4
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24:18
Episode 3 - Wojtek Kopeć: Science as a social endeavor, learning from industry, and the experience of starting a new lab
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 h...
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Season 1
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Episode 3
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35:51
Episode 2 - Max Bonomi: Interoperability, AI-generated ensembles, and recognizing all contributions to science
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 a...
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Season 1
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Episode 2
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24:24
Episode 1 - Pilar Cossio: Modeling experimental setups, overpublishing, and maintaining code
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 publ...
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Season 1
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Episode 1
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27:00
Introduction: Do we really need another podcast?
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 scien...
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Season 1
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Episode 0
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6:39