TheoBiophysics

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

https://doi.org/10.1021/acs.jctc.2c00823

and Oliver at

@olliemelling_

Be sure to follow us on Twitter for more

@theobiophysics

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

https://doi.org/10.1021/acs.jctc.2c00889

And be sure to follow us on Twitter @theobiophysics

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

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

https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.2c07672

Check out their lab website to stay up to date on their work

http://ncasd.org/

And be sure to follow us on twitter @theobiophysics

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

https://www.ibps.sorbonne-universite.fr/fr/IBPS/annuaire/10714-Maxime-Deforet

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.

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

https://pubs.acs.org/doi/full/10.1021/acscentsci.2c00702

You can follow Ethan on twitter at 

@perets_ea

or check out his podcast title "Picturing Knowledge"

https://open.spotify.com/show/1tKiW9tSQnScVQJGY5q3Rx?si=-2OPCTklRcKFdiS4YgP9xQ

And be sure to follow us on Twitter!

@theobiophysics

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

https://pubs.acs.org/doi/abs/10.1021/acs.jctc.1c01010

You can check out more about this topic and their funding source at

@eu_lionhearted

Be sure to follow us on twitter and stay tuned for more episodes!

@theobiophysics

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

ORCID: https://orcid.org/0000-0002-5952-8817

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

https://aip.scitation.org/doi/10.1063/5.0086079

And if you are interested in more of this type of work follow similar work of her group 

@DavidASivak

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

https://arxiv.org/abs/2204.07391

Link to github repo

https://github.com/luigibonati/md-stateinterpreter

Be sure to check us out on Twitter @theobiophysics

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
https://journals.aps.org/pre/abstract/10.1103/PhysRevE.104.034404

Stochastic logistic models reproduce experimental time series of microbial communities
Lana Descheemaeker, Sophie de Buyl
https://elifesciences.org/articles/55650

Make sure to follow our next broadcast @theobiophysics

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!

https://pubmed.ncbi.nlm.nih.gov/35143775/

Keep an eye on his work 

@GorinGennady

And be sure to follow us on twitter for more updates

@theobiophysics

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

https://doi.org/10.1016/j.bpj.2022.02.030

And Ondrej's website for any future updates

https://cims.nyu.edu/~om759/

Be sure to follow us on twitter @theobiophysics

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

https://www.jstor.org/stable/2460550

https://arxiv.org/abs/cond-mat/9610209

https://www.sciencedirect.com/science/article/pii/S2589004221016485?via%3Dihub

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.   

https://pubs.rsc.org/en/content/articlelanding/2021/sm/d1sm00701g 

Extending the timescale of molecular simulations by using time–temperature superposition: rheology of ionic liquid 

Adegbola Balogun, Daria Lazarenko, Fardin Khabaz and  Rajesh Khare

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   

https://www.biorxiv.org/content/10.1101/2021.01.18.427208v1.abstract

A discussion with Satyabrata Bandyopadhyay on using deep learning to deduce suitable coarse variables in biophysics.

https://aip.scitation.org/doi/10.1063/5.0059965

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

https://pubs.rsc.org/en/content/articlehtml/2021/cp/d1cp03296h 

Be sure to follow us on Twitter for more theoretical biophysics! @theobiophysics

Tune in to a conversation with Jacob Cook (@jacobcook1995) in which we discuss their recent publication on incorporating thermodynamic constraints into microbial ecosystems! 

https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1009643 

Be sure to follow us on Twitter @theobiophysics