Shows
Phase Space Invaders (ψ)Episode 29 - Jérôme Hénin: Free energy methods, building useful software, and human learning from biomolecular systemsSend us a textJerome starts our conversation by reviewing the history of the ABF method and its advantages compared to the main competitors, and connects it to the development of COLVARS, historically very parallel to how the development of the Plumed tool stemmed from the needs of the metadynamics community. We discuss the benefits of graphical interfaces in biomolecular workflows, and touch upon the question of connecting multiple software environments and communities. We then move on to discuss membrane systems and the challenges they pose, both historically and today, and end up on the alchemical side...2025-04-2246 minPhase Space Invaders (ψ)Episode 28 - Yuji Sugita: Replica exchange, software for massive simulations, and importance of long-distance collaborationsSend us a textIn Episode 28, Yuji Sugita shares the story of how he developed temperature replica exchange in the lab of Yuko Okamoto, connecting to his early experience from working with Nobuhiro Go, the father of Go models. We then talk about the process of building up workflows for simulating massive atomistic systems, a multi-year collaboration with Michael Feig, and ponder the question of when one should go about writing their own scientific software rather than reusing existing software packages. Talking about molecular crowding naturally brings us to current and future directions, which for Yuji include...2025-04-1538 minPhase Space Invaders (ψ)Episode 27 - Kresten Lindorff-Larsen: Refining force fields, the science of intrinsically disordered proteins, and writing better grant proposalsSend us a textIn episode 27, Kresten starts by explaining his path from a wet lab biochemist to a computational biophysicist, a story full of open-ended explorations and helpful mentors. He gives us some background on how both the legacy and latest models developed, highlighting how in each case the driving force were experimental results that either weren't quite matching simulations, or were plenty enough to allow for top-down training. We walk through some of the functions and applications of intrinsically disordered regions, or IDRs in short, and their relevance for medical research. Then towards the end...2025-03-2549 minPhase Space Invaders (ψ)Episode 26 - Pratyush Tiwary: Infusing AI with physics, understanding emergent phenomena, the value of education and thinkingSend us a textIn episode 26, we talk about the origins of Pratyush's passion for statistical mechanics, deeply rooted in his background in material science, and think about how we can promote a profound understanding of statmech theory among people working in computational biophysics. From there, we explore ways of re-introducing physical rigor into modern data-driven approaches, which is the main concern that Pratyush says drives his research agenda. He ends up sharing a ton of interesting points on working with the industry, the value of education and knowledge sharing, or the philosophy of complex and cognitive...2025-03-1844 minPhase Space Invaders (ψ)Episode 25 - Ivet Bahar: Elastic network models, targeting hinges for drug discovery, persistence and alertnessSend us a textIn episode 25, Ivet and me start with a general overview of the elastic network theory and its applications to biology, as well as its strengths and limitations. Ivet then tells us about the specific takeaways from the different lines of her research, talking about evolutionary dynamics signatures, mode excitations in allosteric effects, as well as her recent research on the relevance of hinge regions for drug discovery. We talk about the relevance of the proteins-as-graphs picture for machine learning, and end up with a few general reflections about the complementary roles of persistence...2025-03-1139 min
Fakt LIVEStanowski startuje na prezydenta. Co z Mentzenem? I co z Braunem? Ewa Zajączkowska-Hernik, KonfederacjaKrzysztof Stanowski ogłosił start w wyborach prezydenckich. O tym, że będzie kandydował, dziennikarz poinformował we wtorkowy wieczór. Podkreślił jednak, że prezydentem zostać nie chce. — Chcę być kamieniem w bucie innych kandydatów — wyjaśnił. Na antenie Kanału Zero przedstawił też swoje "hasło wyborcze". Konfederacja pożegnała się z Grzegorzem Braunem. To "kara" za ogłoszenie startu w wyborach prezydenckich. Jak te partyjne zawirowania przełożą się na poparcie Sławomira Mentzena? Zapraszamy na program Fakt LIVE. Gościem Miłosza Plocha będzie Ewa Zajączkowska-Hernik - europoseł Konfederacji.2025-01-2243 minPhase Space Invaders (ψ)Episode 24½ - My thoughts on season 3Send us a text2025-01-0726 minPhase Space Invaders (ψ)Episode 24 - Katarzyna Marcinkiewicz [Nature Communications]: The job of a full-time editor, transparency and other novelties in publishing, and coaching the review processSend us a textIn episode 24, Katarzyna talks about the everyday concerns and common threads of an editor's job, from continuously learning about the rapid developments in the field to navigating the review process. She shares some inside stories about the experimental features that journals tinker with these days, and it's good to know that many interesting ideas are being tested out there in the wild. We then discuss a bit about the evolution of the publishing process, including its perception among us research scientists. We largely leave the questions of profits and finance out of the...2024-12-3049 minPhase Space Invaders (ψ)Episode 23 - Zoe Cournia: Precision medicine, designing allosteric drugs, and the role of an academic editorSend us a textIn episode 23, Zoe and me discuss the current status and promises of drug design, a field where many things seem trivial but nothing is really simple. Zoe talks about the challenges that precision medicine is facing, and how it fits into the grand landscape of future therapies. We go through some success stories, and I ask Zoe how the recent additions to drug design workflows help them in everyday scientific practice, both in terms of physics-based and data-driven models. We then spend a moment talking about the opportunities and responsibilities of a journal...2024-12-1750 minPhase Space Invaders (ψ)Episode 22 - Lucie Delemotte: Enhanced sampling methods, alternative publishing models, and becoming a parent in academiaSend us a textIn episode 22, we start by talking about the 2022 review of enhanced sampling methods that Lucie co-authored, one that provides long-needed organizing principles and unifying vocabulary for applications in this field. We also outline some challenges and community needs still waiting for the bold souls out there looking for ambitious projects. Lucie then moves on to share her experience with alternative publishing models, both as a member of Biophysics Colab and a former editor of eLife, and we dwell a bit on the challenges and possible solutions to what some would call a crisis...2024-12-1048 minPhase Space Invaders (ψ)Episode 21 - Tamar Schlick: A mathematician's path to biology, RNA frameshifting, and why scientists (should!) runSend us a textIn episode 21, Tamar first explains how her unique background impacted the way she approached and conceptualized problems in biology, and how her research projects were born in the first place. We talk about the more recent research coming from Tamar's group on frameshifting, a fascinating process by which the readout of the genetic code can be offset by one or two letters to produce multiple proteins from a single viral gene. We then move on to discuss whether it's algorithms or compute that have contributed more to the growth of computational biophysics. Tamar's...2024-12-0344 minPhase Space Invaders (ψ)Episode 20 - Rommie Amaro: Simulating viruses, cross-disciplinary complexity, and the brain drainSend us a textIn 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 upon the exciting experimental developments that enable the realistic modeling of systems as big as entire viruses, and highlight some unexpected findings that came out of the large-scale simulations. Rommie also shares her reflections about the collaboration-driven nature of her lab and the complexities involved in interdisciplinary communication, and we wrap...2024-10-0142 minPhase Space Invaders (ψ)Episode 19 - Alex MacKerell: Simple physics, missing experimental data, and model compatibilitySend us a textIn 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 pragmatic, down-to-earth approach, with the idea of "big molecules, small physics". Alex also highlights the need to augment AI tools with HI, or human intelligence, arguing that so far most attempts at automating model development too much end up with...2024-09-1026 minPhase Space Invaders (ψ)Episode 18 - Erik Lindahl: Finding simple and novel ideas, starting an experimental lab, and ligand-gated ion channelsSend us a textIn 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, highlighting the paradoxical need for both complexity and simplicity in thinking, and talk about what kind of questions in biology will keep us all busy for decades to come. Finally, Erik shares the story behind his series of lectures on concepts in...2024-09-0336 minPhase Space Invaders (ψ)Episode 17 - Caroline Lynn Kamerlin: Deep interdisciplinarity, enzyme promiscuity, and science in societySend us a textIn 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...2024-08-2740 minPhase Space Invaders (ψ)Episode 16½ - End-of-season 2 commentarySend us a text2024-07-1619 minPhase Space Invaders (ψ)Episode 16 - Janusz Bujnicki: Structural modeling, RNA modifications, and advising policy-makers on scienceSend us a textIn 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...2024-07-0928 minPhase Space Invaders (ψ)Episode 15 - Paulo CT Souza: Developing a universal coarse-grained force field, and approaching the science of molecular complexitySend us a textIn 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...2024-07-0226 minPhase Space Invaders (ψ)Episode 14 - Syma Khalid: New ways to fight bacteria, the bacterial envelope, and kindness & openness in academiaSend us a textIn 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.2024-06-2523 minPhase Space Invaders (ψ)Episode 13 - Daniel Zuckerman: Trajectory ensembles, writing books, and learning biology through physicsSend us a textIn 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...2024-06-1729 minPhase Space Invaders (ψ)Episode 12 - Vlad Cojocaru: Simulating transcriptional regulation, returning to our home countries, and the scales of the genomeSend us a textIn 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.2024-06-1127 minPhase Space Invaders (ψ)Episode 11 - Justin Lemkul: Providing technical help online, sharing expertise, and polarization in nucleic acidsSend us a textIn 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...2024-05-2829 minPhase Space Invaders (ψ)Episode 10 - Ariane Nunes-Alves: Kinetics in drug design, molecular crowding, and the social life of a PISend us a textIn 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...2024-05-2119 minPhase Space Invaders (ψ)Episode 9 - Michele Vendruscolo: Preventing protein misfolding, fostering public engagement of scientists, and AI tools in drug designSend us a textIn 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...2024-05-1431 minPhase Space Invaders (ψ)Episode 8½ - My commentary: Wrapping up the first seasonSend us a textIn 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.2024-04-1620 minPhase Space Invaders (ψ)Episode 8 - Rossen Apostolov [BioExcel]: Managing scientific collaboration, the biggest project of European biophysics, and seeding schools of thoughtSend us a textIn 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 funding through maintaining excellence in research, and review ways to share the gained experience with the broader computational world to inspire similar ventures elsewhere. It is a partial attempt to answer questions raised in previous conversations by pointing to existing models for...2024-04-0927 minPhase Space Invaders (ψ)Episode 7 - Aleksei Aksimentiev: Nanobiotechnology, the importance of mentoring, and engineering serendipitySend us a textIn 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 of scientific discovery, openness to new ideas can lead to groundbreaking advancements. Alongside, we discuss the pivotal role of mentorship in fostering scientific curiosity and the pursuit of ambitious goals, illustrating how a supportive mentor can be the key to unlocking potential and driving forward...2024-04-0137 min