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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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Hosted by Ana Oppenheim and Ewa Pospieszyńska, two Poles living in London, this podcast explores Polish politics, culture and history. Expect fascinating guests from Poland and beyond, conversations serious and fun, and a lot of Polish accents. If you'd like to suggest a topic or have a good story to tell, please get in touch at thepolkastpod[at]gmail.com Music: Maciej Czubak. Art: Sahaya James
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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 prag…
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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, highlighti…
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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 v…
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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, an…
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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 adopti…
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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.…
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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 n…
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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…
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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 a…
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Send us a text 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 t…
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Send us a text 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 avenue…
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Send us a text 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 sustaining …
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Send us a text 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 unpredictable path o…
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Send us a text 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, something…
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Send us a text 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, and makes a…
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Send us a text 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 crucial to …
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Send us a text 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 of honesty…
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Send us a text 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, particularly at the …
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Send us a text 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 scientific co…
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Send us a text 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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The Art of Spoken Word with Bob Holman #6 Focus on poets Dennis Cooper, Sparrow, Quincy Troupe, Joseph Brodsky, Miguel Algarin and John Trudell. The podcast is co-produced by Ram Devineni. Find more episodes at https://www.bowerypoetry.com/Oleh Bowery Poetry
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The Art of Spoken Word with Bob Holman #5 Focus on poets Robert Creeley, Czesław Miłosz, James Still, Maggie Estep and Lou Reed. The podcast is co-produced by Ram Devineni. Find more episodes at https://www.bowerypoetry.com/Oleh Bowery Poetry
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The Art of Spoken Word with Bob Holman #3 Focus on poets Tracie Morris, Amiri Baraka, Pearl Cleage, Paul Beatty and Indran Amirthanayagam. The podcast is co-produced by Ram Devineni. Find more episodes at https://www.bowerypoetry.com/Oleh Bowery Poetry
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The Art of Spoken Word with Bob Holman #2 Focus on poets Thylias Moss, Pedro Pietri, Emily XYZ with Myers Bartlett, Matt Cook and Ruth Forman. The podcast is co-produced by Ram Devineni . Find more episodes at https://www.bowerypoetry.com/Oleh Bowery Poetry
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The 15 October general election finally ended Law and Justice's (PiS) parliamentary majority, allowing the “democratic opposition” to form a government. The results were met with celebratory headlines across Europe, but the picture is more complex. As the new coalition government takes shape, we’re taking a closer look at what it might mean for Pol…
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Już 15 października odbędą się w Polsce wybory do Sejmu i Senatu. W głosowaniu wybranych zostanie 460 posłów i 100 senatorów na czteroletnią kadencję. Na ten dzień zaplanowano również referendum ogólnokrajowe. W tym odcinku rozmawiamy z Małgorzatą Hallewell – Polką, która współtworzy inicjatywę „Polonia Głosuje” i angażuje się w działania profrekwe…
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On the 15th of October, Poland is facing a key election. After eight years of ultra-conservative governments and deepening authoritarianism, there’s finally a glimmer of hope for progressive change - but also a real risk of the country shifting even further to the right. Which direction will Poland choose? In this episode, we explain the different …
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The Solidarność movement is one of several events in Polish history that nearly every political tendency tries to claim as their own. Should it be seen primarily as a workers’ struggle? A pro-democracy uprising? A national liberation movement? Or a movement for capitalism? What is the legacy of Solidarność - and who in Poland has got the strongest …
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The slogan “housing is a right, not a commodity” has risen into prominence in Poland, sparking a great deal of debate. But what does the right to housing mean in the Polish context? In this episode, we talk about the housing situation in Poland: its history and how it changed in the era of transformation; current problems and the solutions proposed…
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In today’s episode, we’re discussing a topic that’s impossible to escape when talking about Poland: religion. It’s come up during many of our previous episodes, so it’s time to fill in the gaps. How did religion come to play such a big role in Polish public life? Is Poland following Western Europe and starting to secularise? What does the process o…
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It’s normally the right accusing the left of being easily offended and engaging in cancel culture. But in Poland, artists can be arrested and face trial purely for offending someone’s feelings… In the first episode of season 2, we discuss art and censorship in today’s Poland. We’ll talk about Poland’s blasphemy/'insult laws' and their use by the cu…
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