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TheoBiophysics

TheoBiophysics

By TheoBiophysics

Podcast discussing recent advances in the field of biophysics.

Check us out on Twitter @theobiophysics
21 - First Hydration Shell Around Biomolecules
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 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
45:32
December 09, 2022
20 - Local temporal acceleration in kinetic monte carlo models
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 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
35:37
September 15, 2022
19 - Modeling transitions between lag, exponential, stationary, and death phases of bacteria
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
28:45
July 27, 2022
18 - lifespan of starving bacteria
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 ORCID: https://orcid.org/0000-0002-5952-8817
26:22
July 19, 2022
17 - Optimal Work Protocols
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 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   
41:13
June 27, 2022
14 - Metastable Characterization
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 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
59:24
May 26, 2022
16- Stochastic logistic models reveal microbial communities
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 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
36:44
May 25, 2022
15- Short-range interactions of microbial communities
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. Enjoy! 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). Website: https://www.dalcolab.com/ And follow our initiative on @theobiophysics
29:42
May 24, 2022
13 - Modeling Bursty Transcription
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! 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
44:34
March 29, 2022
12 - Interplay between Brownian motion and cross-linking
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 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
41:38
March 17, 2022
11 - Introducing new hosts and interesting papers in the field
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 https://www.jstor.org/stable/2460550 https://arxiv.org/abs/cond-mat/9610209 https://www.sciencedirect.com/science/article/pii/S2589004221016485?via%3Dihub
54:51
March 08, 2022
5-Extending the timescale of molecular simulations using time-temperature superposition
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.    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
44:55
February 17, 2022
6 - Free Energy and Kinetics of cAMP permeation through connexin26
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    https://www.biorxiv.org/content/10.1101/2021.01.18.427208v1.abstract
30:31
February 17, 2022
7 - Survival in Branching Cellular Population Networks
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
30:11
February 16, 2022
8 - VAE for Collective Variables
8 - VAE for Collective Variables
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
38:20
February 16, 2022
9 - Transitions Path Times
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 https://pubs.rsc.org/en/content/articlehtml/2021/cp/d1cp03296h  Be sure to follow us on Twitter for more theoretical biophysics! @theobiophysics
36:30
February 16, 2022
10 - Thermodynamic Constraints on Microbial Ecosystems
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!  https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1009643  Be sure to follow us on Twitter @theobiophysics
56:55
February 16, 2022