Journal club

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

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

June 1, 2020
Ultrafast Spectroscopy of Lipid–Water Interfaces: Transmembrane Crowding Drives H-Bond Dynamics

Jennifer C. Flanagan, Alfredo E. Cardenas, Carlos R. Baiz

J. Phys. Chem. Lett. 2020, 11, 4093-4098

Abstract  PDF SI

presented by Michael

May 18, 2020
GANcon: protein contact map prediction with deep generative adversarial network

Yang, H., et al., IEEE Access (2020).

PDF 

presented by Lim

May 11, 2020
Composition-dependent thermodynamics of intracellular phase separation

Joshua Riback, Lian Zhu, Mylene Ferrolino, Michele Tolbert, Diana Mitrea, David Sanders, Ming-Tzo Wei, Richard Kriwacki, Clifford Brangwynne (2020) Nature

Abstract PDF | SI

presented by Michael

May 4, 2020
Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox

Guang Shi and D. Thirumalai (2019) Nat. Commun. 10, 3894

Abstract PDF | SI

presented by Gilberto

April 27, 2020
Generating functional protein variants with variational autoencoders

Hawkins-Hooker et al.,
bioRxiv preprint

Abstract / PDF

presented by Bercem

April 20, 2020
Machine Learning Driven Analysis of Large Scale Simulations Reveals Conformational Characteristics of Ubiquitin Chains

Berg, A., Franke, L, Scheffner, M., and Peter, C., JCTC (2020).

PDF 

presented by Lim

April 13, 2020
Organization of the Escherichia coli Chromosome by a MukBEF Axial Core

Mäkelä, J and Sherratt, D (2020) Molecular Cell 78, 1–11

Abstract PDF

presented by Gilberto

April 6, 2020
Elastic ripening and inhibition of liquid–liquid phase separation

Rosowski et al.,
Nature Physics, 16, 422-425, 2020

Abstract / PDF

presented by Bercem

March 30, 2020
Development of a Force Field for the Simulation of Single-Chain Proteins and Protein−Protein Complexes

Piana, S., Robustelli, P., Tan, D., Chen, S., and Shaw, E. D., JCTC (2020).

Abstract PDF 

presented by Lim

March 23, 2020
Resolving the degree of order in the bacterial chromosome using a statistical physics approach

J J.B. Messelink, J Janssen, M C.F. van Teeseling, M Thanbichler, C P. Broedersz arXiv 2002.03880 (2020)

Abstract PDF w/ SI

presented by Gilberto