Readings suggested by speakers in week 1 (Click on the title for the material)

1. Christoph Schmidt :

Nonequilibrium Mechanics of Active Cytoskeletal Networks
High-Resolution Probing of Cellular Force Transmission
Brownian Motion of Stiff Filaments in a Crowded Environment
Nonequilibrium Mechanics and Dynamics of Motor-Activated Gels
Diameter-dependent bending dynamics of single-walled carbon nanotubes in liquids

2. Helmut Schiessel:

Rigid-body molecular dynamics of DNA inside a nucleosome
This paper presents a coarse grained nucleosome model that allows to simulate sliding through twist defects.
The dynamics of the nucleosome: thermal effects, external forces and ATP
A small review on the nucleosome discussing most topics from the talk.
The Biology of Chromatin Remodeling Complexes
A review on chromatin remodellers.

3. Moumita Das:

Microrheology of Microtubule Solutions and Actin-Microtubule Composite Networks
Microtubules can bear enhanced compressive loads in living cells because of lateral reinforcement
Buckling and force propagation along intracellular microtubules
Poisson’s Ratio in Composite Elastic Media with Rigid Rods
Redundancy and Cooperativity in the Mechanics of Compositely Crosslinked Filamentous Networks


Readings suggested by speakers in week 2


1. Harald Pleiner

Macroscopic behavior of systems with an axial dynamic preferred direction
Active polar two-fluid macroscopic dynamics
Collective Stop-and-Go Dynamics of Active Bacteria Swarms


2. Mehran Kardar:

Additional material related to Fluctuation Induced Forces is available through links in the web-version of my talk.

3. Silke Henkes

Active Jamming in aligning SPP systems in confinement, and model using the low energy phonons (soft modes) of the packing: HenkesPRE2011
Clustering in systems with no alignment and hydrodynamic model: FilyPRL2012
Full phase diagram of clustering systems, including the high density glassy, liquid and cluster phases: FilySM2014

Readings suggested by speakers in week 3


1. Dhananjay Tambe:

Substrate traction algorithm (Fourier formalism, effect of substrate thickness): ButlerAJP2002, TrepatNP2009, LinPRE2010
Monolayer Stress Microscopy (technique and its validation): TambeNM2011, TambePLoS2013
Plithotaxis (data on cancer cells, rose plots for various stress anisotropy, effect of weakening cell-cell junctions): TambeNM2011
Mechanical waves during tissue spreading (effect of blebbistatin, elastic origin of stresses): Serra-PicamalNP2012
Kenotaxis (tendency of cells to fill free space): KimNM2013
Jamming hypothesis: AngeliniPRL2010, AngeliniPNAS2011, TrepatCOCB2011, SadatiD2013

2. Shiladitya Banerjee:

Continuum model of traction forces by adherent cells on substrates: BanerjeeMCM-EPL2011 Edwards&Schwarz-EPL2011
Dependence of traction forces on substrate thickness and stiffness: BanerjeeMCM-PRL2012
Traction forces by cell colonies: Mertz-etal-PRL2012
Crosstalk of cell-cell and cell-ECM interactions: Mertz-etal-PNAS2013

3. José Alvarado:

Molecular motors robustly drive active gels to a critically connected state [here]

Readings suggested by speakers in week 4


1. Tom Waigh:

Here are a couple of draft chapters for a textbook that I am writing. A book chapter. Another book chapter. They provide some background on active matter for undergraduate physicists.

Otherwise, with respect to my talk, here is some relevant literature from our group:
Particle tracking software in live cells.Tracking.
For the tracking software I attach a bundle that contains the MatLab polyparticletracker software, a parallel (multiple CPU) version of the same code and some other useful algorithms for calculating first passage probabilities, mean square displacements etc.Code.

Pulsatile motion and cytoplasmic streaming in amoeba. Amoeba.
Angular correlations during intracellular vesicle transport. Angular correlations.
First passage probabilities during vesicle transport.SlowFPP, FastFPP, DyneinFPP.
Motion of bacteria through viscoelastic films. Bacterial biofilms.

2. Gautam Menon:

Chromosome Positioning from Activity-based Segregation (Talk): Paper.
Spatio-temporal correlations and nuclear-size fluctuations in stem cells Shefali_StemCellSpatioTemporal_BiophysJ2013.pdf

Readings suggested by speakers in week 3-7 February 2013


1. Peter Olmsted:


Here is a tutorial lecture on banding, which has similar material to my blackboard lecture. Here is a review of shear banding, and here is a Faraday Discussion paper that has a tutorial exposition of banding via a tutorial toy model.

Readings suggested by speakers in week 8, Feb 24-28


1. Cristian Huepe:

The results I presented in my talk on Monday Feb. 24 can be found in these two recent publications:
-"Elasticity-Based Mechanism for the Collective Motion of Self-Propelled Particles with Springlike Interactions:
A Model System for Natural and Artificial Swarms". Phys. Rev. Lett., 111, 268302 (2013)
-"Collective motion dynamics of active solids and active crystals". New J. Phys. 15 095011 (2013)

2. Ulrich Schwarz

1. pushing: models for growing actin networks PNAS Weichsel and Schwarz 2010 Weichsel et al. PRE 2013
2. pulling: models for contracting actomyosin bundles PRL Erdmann and Schwarz 2012 JCP Erdmann et al. 2013

Microtubule Dynamical Instability (Week of April 13)

1. Bulbul Chakraborty:


Following Anatoly's talk, I went back to our work on the 1D random hydrolization model. The results are quite interesting and address some of the questions that came up during the talk. So here are links to two papers:
Phys. Rev. E 76 041907 (2009)
Phys. Rev. E 83 051904 (2011)

2. Anatoly Kolomeisky:
To assist people who are interested in theoretical models to describe microtubule dynamic instability and hydrolysis that I talked in my seminar I am also adding 3 papers that might be useful:
Biophys. J. 102, 1274 (2012)
J. Phys. Chem. B 117, 9217 (2013)
J. Phys. Chem. B 118, 2966 (2014)