TheoBiophysicsJul 18, 2023
28 - Enhanced Grand Canonical Sampling
Join us for another episode where we talk with lead author Oliver Melling about their recent work on improving the efficiency of Grand Canonical Sampling. We discuss why this is a challenging problem, why moving to non-equilibrium offers a new perspective, and the findings in protein systems that come from it.
Check out their paper at
and Oliver at
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27 - Rigid Base Biasing
Discussion with researcher Aderik about his recent work on DNA conformation biasing. We discuss the key aspects of software development, what this allows researchers to do, and probing new regimes to match with predictions from prior theories.
Follow Aderik @AderikVoorspoel and his institute @PoL_KULeuven
Link to paper
And be sure to follow us on Twitter @theobiophysics
26 - 'Aha' Moments and Reinforcement Learning with Gautam Reddy
Today we will be talking with Dr. Gautam Reddy about his research on reinforcement learning, discontinuous learning, animal behavior, mice, mazes, and more!
Please find the paper that we discuss here: https://www.pnas.org/doi/abs/10.1073/pnas.2215352119
25 - Network Hamiltonians
Join in for a conversation with Liz Diessner as we discuss Network Hamiltonian models in describing protein-protein interactions. We talk about challenges in parameterizing this type of model, interesting finding when examining mutations, and what type of time/length scales using this approach unlocks.
Here is a link to the paper
Check out their lab website to stay up to date on their work
And be sure to follow us on twitter @theobiophysics
24- Evolution at the edge of expanding populations
Talking science with Maxime Deforet, CNRS researcher at Sorbonne University's Jean Perrin lab. Maxime, who studies bacterial colonies, shares a recent story he wrote telling the evolution taking place at the fringe of growing populations. https://doi.org/10.1086/704594
23 - Firefly Synchronisation with Dr. Raphael Sarfati
A discussion with Dr. Raphael Sarfati (from Prof. Orit Peleg's lab at the University of Colorado, Boulder) about fireflies, collective behavior, and synchronization. We discuss his paper, Self-organization in natural swarms of Photinus carolinus synchronous fireflies (https://www.science.org/doi/10.1126/sciadv.abg9259).
We also recommend his gorgeous and enthralling website (lucidluminescence.org) on fireflies, which includes many visuals to help understand how mesmerizing fireflies are!
22 - Overview on the preprint initiatives
A discussion with Iratxe Puebla, the director of ASPABio https://asapbio.org/, who sheds insight on the preprint process. If you want to know where and how to use preprint servers such as biorxiv, peercomunity in, and prereview, this podcast is for you.
NB: Colin Favrebulle, the sound engineer, has graciously smoothed out this episode.
21 - First Hydration Shell Around Biomolecules
Join us for a conversation with Dan & Ethan, two researchers out of Yale, as we discuss their recent work on studying the hydration layer around biomolecules. In this episode we discuss the nuances of chiral sum frequency generation, how we can use experiment and theory to probe deeper into molecular structures, and what new things we can hope to study by getting a better understanding of the first hydration layer.
Check out their work at
You can follow Ethan on twitter at
or check out his podcast title "Picturing Knowledge"
And be sure to follow us on Twitter!
20 - Local temporal acceleration in kinetic monte carlo models
A conversation with Manuel Gößwein, a researcher from TU-Munich, on their recent work on making reducing the cost of kinetic monte carlo models by speeding up certain steps. We discuss how to define quasi-equilibrium, parameter sensitivity, and how get better sampling with systems with time-disparity.
Link to publication
You can check out more about this topic and their funding source at
Be sure to follow us on twitter and stay tuned for more episodes!
19 - Modeling transitions between lag, exponential, stationary, and death phases of bacteria
A chat with Yusuke Himeoka from University of Tokyo on his recent work to model typical transitions among the lag, exponential, stationary, and death phases. His work provides universal growth laws beyond the exponential phase, offering insight into how cells halt growth without entering the death phase. Below the link to the paper we are talking about.
Link to the paper: https://journals.aps.org/prx/pdf/10.1103/PhysRevX.7.021049
Link to Yusuke website: https://www.yhimeoka.com/en
18 - Lifespan of starving bacteria
A chat with Severin Schink from Harvard Medical School on his recent work to reveal mechanisms underpinning the dynamics of a dying bacterial population. We discuss how he uses bacterial physiology and microscopy to uncover the cannibalism behaviour of cells that consequently damps out the death of the population. This leads the population to follow a stupendous law of exponential decay.
link to the preprint: https://doi.org/10.1101/2021.11.22.469587
17 - Optimal Work Protocols
A discussion with Miranda Louwerse, a researcher from Canada, on her recent work exploring the benefits of multidimensional control for work. We talk about how moving into higher dimensions gives the system a way to extract more work, what role energy and entropy have, and how this could be extended to more complex networks.
Checkout the original article:
Multidimensional minimum-work control of a 2D Ising model
And if you are interested in more of this type of work follow similar work of her group
14 - Metastable Characterization
A conversation with two researchers out of Italy Pietro Novelli and Luigi Bonati on their recent work in analyzing molecular dynamic simulations. We discuss how to distinguish metastable states, what data science can tell us in term of molecular simulations, and how we can interpret highly complex systems.
Link to paper
Link to github repo
Be sure to check us out on Twitter @theobiophysics
16- Stochastic logistic models reveal microbial communities
A chat with Sophie de Buyl from the Vrije Universiteit of Brussel on her recent work to reveal the underpinning mechanisms of noisy time series monitoring microbial communities. We discuss how she uses Lokta-Volterra models to investigate the source of noise in experimental time series and her explanation of the heavy-tailed abundance distributions in microbial communities.
Heavy-tailed abundance distributions from stochastic Lotka-Volterra models
Lana Descheemaeker, Jacopo Grilli, and Sophie de Buyl
Stochastic logistic models reproduce experimental time series of microbial communities
Lana Descheemaeker, Sophie de Buyl
Make sure to follow our next broadcast @theobiophysics
15- Short-range interactions of microbial communities
A chat with Alma Dal Co from the University of Lausanne on her recent work to uncover how individual bacterial cells interact inside microbial communities. We discuss how she uses microfluidic techniques to measure these interactions, and mathematical modeling to uncover what biophysical parameters determine these interactions.
Ref: Co, A. D., van Vliet, S., Kiviet, D. J., Schlegel, S. & Ackermann, M. Short-range interactions govern the dynamics and functions of microbial communities. Nat. Ecol. Evol. 4, 366–375 (2020).
And follow our initiative on @theobiophysics
13 - Modeling Bursty Transcription
A chat with Gennady Gorin, a researcher from Cal Tech on their recent working using the chemical master equation to model transcription. We discuss matching to experiments, the beauty of simplicity, and mathematical description of complex processes. Enjoy!
Keep an eye on his work
And be sure to follow us on twitter for more updates
12 - Interplay between Brownian motion and cross-linking
A discussion with Ondrej Maxian, a researcher out of New York, on their recent work looking at bundling dynamics in actin networks. We discuss building a actin molecules using Chebyshev interpolants, the relevant forces for the current length scale, and the molecular underpinnings behind why bundles form in certain conditions.
Check out the paper here
And Ondrej's website for any future updates
Be sure to follow us on twitter @theobiophysics
11 - Introducing new hosts and interesting papers in the field
Introducing new cohosts Maxime and Avaneesh to the show. After a brief introduction each of us discuss a paper we found interesting/influential in the field of biophysics.
The three papers discussed
5-Extending the timescale of molecular simulations using time-temperature superposition
A discussion with Adegbola Balogun, a research out of Texas Tech, on his work trying to use molecular simulations to determine rheological and dynamic properties of ionic liquids. We discuss the viscoelastic properties, mean squared displacements, and why it can be hard to compare the timescales of simulation and theory.
Extending the timescale of molecular simulations by using time–temperature superposition: rheology of ionic liquid
Adegbola Balogun, Daria Lazarenko, Fardin Khabaz and Rajesh Khare
6 - Free Energy and Kinetics of cAMP permeation through connexin26
A chat with Lyna Luo, a researcher from Western University, about her recent work on the study of connexin channels. We talk about how hard it is to study kinetics and how multiple simulation techniques can help shed insight onto the complex interplay between messenger molecules and membrane proteins.
Be sure to check out her group on Twitter @lyna_yunluo for the latest updates.
Free energy and kinetics of cAMP permeation through connexin26 hemichannel with and without voltage.
Wenjuan Jiang, Yi-Chun Lin, Wesley Botello-Smith, Jorge Contreras, Andrew L. Harris, Luca Maragliano, Yun Lyna Luo
7 - Survival in Branching Cellular Population Networks
A discussion with Adam Bryant and Maxim Lavrentovich, two researchers from the University of Tennessee - Knoxville. We discuss why to not put all your eggs in one basket and the effects of stochastic behavior in propagating your offspring forward.
Check out the paper here: https://arxiv.org/abs/2108.04992
8 - VAE for Collective Variables
A discussion with Satyabrata Bandyopadhyay on using deep learning to deduce suitable coarse variables in biophysics.
9 - Transitions Path Times
A conversation with Prof Eli Pollak at the Weizmann Institute of Science on his recent work examining transition path times and what can theory tell us in helping decipher experimental data. We discuss the importance of boundary conditions, physical relevance, and outlooks for the future. What can we learn from transition path time distributions for protein folding and unfolding?
Rajesh Dutta, Eli Pollak. PCCP 2021
Be sure to follow us on Twitter for more theoretical biophysics! @theobiophysics
10 - Thermodynamic Constraints on Microbial Ecosystems
Tune in to a conversation with Jacob Cook (@jacobcook1995) in which we discuss their recent publication on incorporating thermodynamic constraints into microbial ecosystems!
Be sure to follow us on Twitter @theobiophysics