Journal club

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

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

March 16, 2020
Proteome-wdie observation of the phenomenon of life on the edge of solubility

G. Vecchi, P. Sormanni, B. Mannini, A. Vandelli, G. Tartaglia, C. Dobson, F. U. Hartl, M. Vendruscolo
PNAS, 117, 1015-1020, 2020

Abstract / PDF

presented by Michael

March 9, 2020
Multiphase Complex Coacervate Droplets

T. Lu and E. Spruijt
J. Am. Chem. Soc., 142, 6, 2905-2914, 2020

Abstract / PDF

presented by Bercem

March 2, 2020
Deciphering protein evolution and fitness landscapes with latent space models

Ding, X., Zou, Z. & Brooks III, C.L. Deciphering protein evolution and fitness landscapes with latent space models. Nat Commun 10, 5644 (2019). 

Abstract PDF 

presented by Lim

February 24, 2020
Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

Fabai Wu, et al. Current Biology (2019), 29(13):2131-2144.e4 doi:10.1016/j.cub.2019.05.015

Abstract / PDF / SI

presented by Gilberto

February 10, 2020
Enhancer Features that Drive Formation of Transcriptional Condensates

K. Shrinivas et al.
Molecular Cell, 75, 549–561, 2019

Abstract / PDF

presented by Bercem

February 3, 2020
Improved protein structure prediction using potentials from deep learning

Andrew W. Senior et al., Nature 577, 706-710.

Abstract PDF 

presented by Lim

January 27, 2020
EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm

Hua, K. and Ma, B. BMC Genomics 20, 738 (2019) doi: 10.1186/s12864-019-6096-0 

Abstract / PDF / SI

presented by Gilberto

January 20, 2020
Protein Network Structure Enables Switching between Liquid and Gel States

J.D. Schmit, J.J. Bouchard, E. W. Martin and T. Mittag
J. Am. Chem. Soc., 142, 874-883, 2020

Abstract / PDF

presented by Bercem

January 13, 2020
Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation

Leandro Oliveira Bortot, Zahedeh Bashardanesh, and David van der Spoel, J. Chem. Inf. Model. (2019).

Abstract PDF 

presented by Lim

April 11, 2016
pKa Values of Titrable Amino Acids at the Water/Membrane Interface

Vitor H. Teixeira, Diogo Vila-Vicosa, Pedro B. P. S. Reis, and Miguel Machuqueiro

Journal of Chemical Theory and Computation (2016, 12 (3), 930-934)

Abstract / PDF

presented by Nawrocki