Journal club

Journal club meetings are on Mondays at 2-3 pm through video conference.

October 26, 2020
Unraveling Molecular Interactions in Liquid–Liquid Phase Separation of Disordered Proteins by Atomistic Simulations

M. Paloni, R. Bailly, L. Ciandrini, and A. Barducci J. Phys. Chem. B (2020), 124, 41, 9009–9016

Abstract PDF | SI

presented by Gilberto

October 19, 2020
Simulation of FUS protein condensates with an adapted coarse-grained model

Z. Benayad, S. von Bulow, L. S. Stelzl, and G. Hummer
bioRxiv, 2020

Abstract / PDF

presented by Bercem

October 12, 2020
End-to-End Differentiable Molecular Mechanics Force Field Construction

Yuanqing Wang, Josh Fass, and John D. Chodera, arXiv (2020).

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presented by Lim

October 5, 2020
Tunable multiphase dynamics of arginine and lysine liquid condensates

Fisher, R.S., Elbaum-Garfinkle, S.  Nat Commun 11, 4628 (2020)

Abstract PDF | SI

presented by Gilberto

September 28, 2020
Nucleated transcriptional condensates amplify gene expression

M.-T. Wei, Y.-C. Chang, S. F. Shimobayashi, Y. Shin, A. R. Strom and C. P. Brangwynne
Nature Cell Biology, 2020

Abstract / PDF

presented by Bercem

September 21, 2020
Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics

Yihang Wang, João Marcelo Lamim Ribeiro & Pratyush Tiwary, Nature Communications (2019).

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presented by Lim

September 14, 2020
Sequence dependent co-phase separation of RNA-protein mixtures elucidated using molecular simulations.

Roshan M. Regy, Gregory L. Dignon, Wenwei Zheng, Young C. Kim & Jeetain Mittal (2020) bioRxiv

Abstract PDF

presented by Gilberto

August 31, 2020
The Interplay between Phase Separation and Gene- Enhancer Communication: A Theoretical Study

A. M. Chiariello, F. Corberi, and Mario Salerno
Biophysical Journal 119, 873–883, 2020

Abstract / PDF

presented by Bercem

August 24, 2020
IG-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation

Raphael R. Eguchi, Namrata Anand, Christian A. Choe, Po-Ssu Huang, bioRxiv (2020).

PDF 

presented by Lim

August 17, 2020
DNA sequence-directed cooperation between nucleoid-associated proteins

Japaridze A, Yang W, Dekker C, Nasser W & Muskhelishvili G (2020) bioRxiv

Abstract PDF

presented by Gilberto

August 10, 2020
Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid–liquid phase separation

A.-M. Ladouceur et al
PNAS, , 2020

Abstract / PDF

presented by Bercem

August 3, 2020
Improved protein structure refinement guided by deep learning based accuracy estimation

Naozumi Hiranuma, Hahnbeom Park, Ivan Anishchanka, Minkyung Baek, David Baker, bioRxiv (2020).

PDF 

presented by Lim

July 27, 2020
Bacterial chromosome organization by collective dynamics of SMC condensins

Miermans C.A. and Broedersz C.P. (2018) J. R. Soc. Interface. 15(147):20180495

Abstract PDF | SI

presented by Gilberto

July 20, 2020
Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

G. Krainer et. al
bioRxiv, 2020

Abstract / PDF

presented by Bercem

July 13, 2020
Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach

Zosel, F. et al., JCP (2020).

PDF 

presented by Lim

July 6, 2020
Impact of crowders on the morphology of bacterial chromosomes

Kumar A, Swain P, Mulder BM and Chaudhuri D (2019) Europhysics Letters,128:68003

Abstract PDF

presented by Gilberto

June 29, 2020
Closing and opening of the RNA polymerase trigger loop

A. Mazumdera, M. Lina, A. N. Kapanidis, and R. H. Ebright
PNAS, 2020

Abstract / PDF

presented by Bercem

June 22, 2020
Depletion interactions modulate the binding between disordered proteins in crowded environments

Zosel, F. et al., Proc. Natl. Acad. Sci. USA (2020).

Abstract PDF 

presented by Lim

June 15, 2020
The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid

D Yang, J Männik, ST Retterer, J Männik (2020) Mol. Microbiol. 113, 1022–1037

Abstract PDF | SI

presented by Gilberto

June 8, 2020
Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components

J. R. Espinosa, J. A. Joseph, I. Sanchez-Burgos, A. Garaizar, D. Frenkel, and R. Collepardo-Guevara
PNAS, 2020

Abstract / PDF

presented by Bercem