Phase Space Invaders (ψ)

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Phase Space Invaders (ψ)

Miłosz Wieczór

33 episodes

6 months ago

Send us a text Jerome 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 d...

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Send us a text Jerome 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 d...

Show more...

Episodes (20/33)

Phase Space Invaders (ψ)

Episode 29 - Jérôme Hénin: Free energy methods, building useful software, and human learning from biomolecular systems

Send us a text Jerome 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 d...

6 months ago

46 minutes

Phase Space Invaders (ψ)

Episode 28 - Yuji Sugita: Replica exchange, software for massive simulations, and importance of long-distance collaborations

Send us a text In 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 softwar...

6 months ago

38 minutes

Phase Space Invaders (ψ)

Episode 27 - Kresten Lindorff-Larsen: Refining force fields, the science of intrinsically disordered proteins, and writing better grant proposals

Send us a text In 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 application...

7 months ago

49 minutes

Phase Space Invaders (ψ)

Episode 26 - Pratyush Tiwary: Infusing AI with physics, understanding emergent phenomena, the value of education and thinking

Send us a text In 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 ...

7 months ago

44 minutes

Phase Space Invaders (ψ)

Episode 25 - Ivet Bahar: Elastic network models, targeting hinges for drug discovery, persistence and alertness

Send us a text In 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 pic...

7 months ago

39 minutes

Phase Space Invaders (ψ)

Episode 24½ - My thoughts on season 3

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10 months ago

26 minutes

Phase 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 process

Send 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 percepti...

10 months ago

49 minutes

Phase Space Invaders (ψ)

Episode 23 - Zoe Cournia: Precision medicine, designing allosteric drugs, and the role of an academic editor

Send 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 the...

10 months ago

50 minutes

Phase Space Invaders (ψ)

Episode 22 - Lucie Delemotte: Enhanced sampling methods, alternative publishing models, and becoming a parent in academia

Send 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 o...

11 months ago

48 minutes

Phase Space Invaders (ψ)

Episode 21 - Tamar Schlick: A mathematician's path to biology, RNA frameshifting, and why scientists (should!) run

Send 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 o...

11 months ago

44 minutes

Phase Space Invaders (ψ)

Episode 20 - Rommie Amaro: Simulating viruses, cross-disciplinary complexity, and the brain drain

Send 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 ab...

1 year ago

42 minutes

Phase Space Invaders (ψ)

Episode 19 - Alex MacKerell: Simple physics, missing experimental data, and model compatibility

Send 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 ...

1 year ago

26 minutes

Phase Space Invaders (ψ)

Episode 18 - Erik Lindahl: Finding simple and novel ideas, starting an experimental lab, and ligand-gated ion channels

Send 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 d...

1 year ago

36 minutes

Phase Space Invaders (ψ)

Episode 17 - Caroline Lynn Kamerlin: Deep interdisciplinarity, enzyme promiscuity, and science in society

Send 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-emergin...

1 year ago

40 minutes

Phase Space Invaders (ψ)

Episode 16½ - End-of-season 2 commentary

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1 year ago

19 minutes

Phase Space Invaders (ψ)

Episode 16 - Janusz Bujnicki: Structural modeling, RNA modifications, and advising policy-makers on science

Send 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 g...

1 year ago

28 minutes

Phase Space Invaders (ψ)

Episode 15 - Paulo CT Souza: Developing a universal coarse-grained force field, and approaching the science of molecular complexity

Send 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 les...

1 year ago

26 minutes

Phase Space Invaders (ψ)

Episode 14 - Syma Khalid: New ways to fight bacteria, the bacterial envelope, and kindness & openness in academia

Send 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 ...

1 year ago

23 minutes

Phase Space Invaders (ψ)

Episode 13 - Daniel Zuckerman: Trajectory ensembles, writing books, and learning biology through physics

Send 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 ensembl...

1 year ago

29 minutes

Phase Space Invaders (ψ)

Episode 12 - Vlad Cojocaru: Simulating transcriptional regulation, returning to our home countries, and the scales of the genome

Send 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 countrie...

1 year ago

27 minutes