- The meeting is at 15:00 on every Wednesday at POB 2.444 unless otherwise noted.
- The talk would be either speaker's own research (any preliminary and/or technical stuff is good) or introductions of other's paper(s).
- It is preferable that the subject of talk is related to nucleic acids although any other related topics would be also welcomed; e.g. NA-binding proteins, ions, water, experimental/simulation techniques.
- Room reservations can be made here: https://research.utexas.edu/acesit/pob-room-reservations
- Thursday 3:30 PM
Frictional effects on RNA folding.
Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins
Harmon et al. and Pappu (2017) eLife 10.7554/eLife.30294
On a polymer model toward understanding of FRET signals.
Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation
Yoo, Kim, Aksimentiev, Ha, Nat Commun 10.1038/ncomms11045
Duplex and Triplex RNA/DNA
Lesnik & Freier (2002) Biochemistry 10.1021/bi00034a013
Bacolla et al. (2015) PLOS Genetics 10.1371/journal.pgen.1005696
Properties of Gene Expression and Chromatin Structure with Mechanically Regulated Transcription
10.1101/262717
Introduction to OpenMM
Review: Does DNA methylation affect nucleosome dynamics?
Shape, flexibility and packing of proteins and nucleic acids in complexes
Nidhi Rawata and Parbati Biswas (2011) PCCP 10.1039/C1CP00027F
Physics behind the mechanical nucleosome positioning code
Martijn Zuiddam, Ralf Everaers, and Helmut Schiessel (2017) Phys Rev. E 10.1103/PhysRevE.96.052412
Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex
S Chakraborty, PJ Steinbach, D Paul, H Mu, S Broyde, JH Min, A Ansari (2017) NAR 10.1093/nar/gkx1216
Ribosomes are optimized for autocatalytic production
S Reuveni, M Ehrenberg & J Paulsson (2017) Nature 10.1038/nature22998
Sequence-dependent persistence length of DNA
HM Chuang et al. and KD Dorfman (2017) Phys Rev Lett 10.1103/PhysRevLett.119.227802
RNA phase transitions in repeat expansion disorders
Ankur Jain & Ronald D. Vale (2017) Nature 10.1038/nature22386
Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins
Y Lin, et al. and Roy Parker, Mol. Cell (2015) 10.1016/j.molcel.2015.08.018
References :
- http://www.cell.com/cell/abstract/S0092-8674(17)30242-8
- https://www.nature.com/nphys/journal/v11/n11/full/nphys3532.html
- http://www.sciencedirect.com/science/article/pii/S009286741631666X?via%3Dihub
- http://www.cell.com/current-biology/abstract/S0960-9822(15)00014-7
- http://www.cell.com/cell-reports/abstract/S2211-1247(16)31212-8
DNA spools under tension (derivation)
I. M. Kulić and H. Schiessel, PRL (2004) 10.1103/PhysRevLett.92.228101
Crowding-Induced Hybridization of Single DNA Hairpins
L.E. Baltierra-Jasso, ..., S.W. Magennis, JACS (2015) http://dx.doi.org/10.1021/jacs.5b11829
Toehold Switches: De-Novo-Designed Regulators of Gene Expression
A.A. Green, ..., Peng Yin, Cell (2014) http://dx.doi.org/10.1016/j.cell.2014.10.002
Complex cellular logic computation using ribocomputing devices
A.A. Green, ..., Peng Yin, Nature (2017) http://dx.doi.org/10.1038/nature23271
Estimation of Relative Protein–RNA Binding Strengths from Fluctuations in the Bound State
Zhaleh Ghaemi, ..., Martin Gruebele, and Zaida Luthey-Schulten, JCTC (2016) http://dx.doi.org/10.1021/acs.jpcb.7b04318
Packing Defects Propagated During the Growth of Toroidal Condensates by Semiflexible Polymer Chains
Stretching of Homopolymeric RNA Reveals Single-Stranded Helices and Base-Stacking
Seol, Skinner, Visscher, PRL (2007) https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.98.158103
Relevant papers
https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.84.2160
https://journals.aps.org/pre/pdf/10.1103/PhysRevE.70.020902
On the dynamic correlation of water
On the spatial correlation of water
DNA spools under tension
I. M. Kulić and H. Schiessel, PRL (2004) 10.1103/PhysRevLett.92.228101
Why Do Nucleosomes Unwrap Asymmetrically?
Bruin et al. and Helmut Schiessel, JPCB (2016) 10.1021/acs.jpcb.6b00391
Molecular determinants of the interactions between proteins and ssDNA
Mishra and Levy, PNAS (2015) 10.1073/pnas.1416355112
RNA model with explicit Mg and implicit monovalent
Hoogsteen base pairing in DNA
Visualizing the secondary and tertiary architectural domains of lncRNA RepA
Liu, Somarowthu and Pyle (2017) 10.1038/NCHEMBIO.2272
Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
Das and Pappu, PNAS (2013) 10.1073/pnas.1304749110
Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA
Drozdetski et al. and Onufriev, PRL (2016) 10.1103/PhysRevLett.117.028101
Memory-induced anomalous dynamics: Emergence of diffusion, subdiffusion, and superdiffusion from a single random walk model
Kumar et al., Phys. Rev. E (2010) 10.1103/PhysRevE.82.021101
Reconstruction of atomistic model and its application to footprinting data
Riboswitches and cotranscriptional folding.
Cf. Grilley et al., Biochem. (2007) 10.1021/bi062284r
Cf. Leipply et al., Biochem. (2011) 10.1021/bi101948k
Dynamical Disorder in the DNA hydration shell
Duboué-Dijon et al., JACS (2016) 10.1021/jacs.6b02715
Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size
Shin et al., Soft Matter (2015) 10.1039/C4SM02007C
Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response
Riback et al., Cell (2017) 10.1016/j.cell.2017.02.027
On the treatment of electrostatic interaction in coarse-grained models
On the diffusion along DNA
Folding kinetics of Azoarcus ribozyme
On the semi-implicit ion model
Probing helical transition in a DNA duplex
Chakraborty and Wales, PCCP (2017) 10.1039/c6cp06309h