Discussion+Groups


 * Topics to be discussed either by all members or a smaller subset of the members is listed here. Date and time for each session and a short abstract about each topic will be provided by the moderator of each topic. Click to see NEW TOPICS starting from 5/31/2011.**

**Transcriptional proofreading beyond Hopfield** (Discussion leader: Martin Depken) (Thursday May 19, 2.30 PM, room SSR)

 * **Abstract:** Martin will kick off by describing RNAP backtracking and its implications for (nested) kinetic proofreading in transcription. Through this I hope to initiate a discussion regarding the generalizations of Hopfield's original scheme (PNAS, 1974) as well as of the mechanistic details of how backtracking contributes to suppress errors in transcription.
 * **Participants:** Martin Depken, Ludvig Lizana, Anatoly Kolomeisky, Alexander Grosberg
 * **Discussion summary:**

**Electrophoresis** (Discussion leader: Ludvig Lizana) (Thursday May 12, 2.30 PM, room "the tower" (2514))

 * **Abstract:** Ludvig will start the discussion by presenting new analytical results on the electrophoretic motion of a charged colloidal particle in an ionic liquid.
 * **Participants:** Payam Rowghanian, Ludvig Lizana, Alexander Grosberg, Michael Rubinstein, Liheng Cai, Stefan Kesselheim, Alexander Chervanyov
 * **Discussion summary:**

**DNA Translocation and Capture** (Discussion initiator: Payam Rowghanian) (Tuesday May 17, 2:30 PM, Room 2514)

 * **Abstract:**
 * **Participants:** Payam Rowghanian, Anatoly Kolomeisky, Alexander Grosberg, Ludvig Lizana, Stefan Kesselheim, Alexander Chervanyov, Tannie Liverpool, Martin Depken, Paul van der Schoot
 * **Discussion summary:**

**Melt of Rings**

 * **Abstract:** The problem is quite generic and has projections on both chromosome (nuclear) physics and polymer physics. It can be formulated in the following way: consider a system of unconcatenated rings filling the space with volume fraction close to 100%. What will be the scaling of a typical ring size and its internal fractal structure? There were two theoretical predictions, Cates and Deutsch predicted $R \sim N^{2/5}$ and "crumpled globule" model $R \sim N^{1/3}$. The recent advances in simulation suggest that 2/5 is an intermediate asymptotics and 1/3 is the final one with respect to large $N$. Open questions include understanding the roughness of surfaces separating rings.
 * **Participants:** Ralf Everaers, Franco Ferrari, Michael Rubinstein, Alexander Grosberg, Ludvig Lizana, Liheng Cai, Rony Granek, Paul van der Schoot, Mike Hagan, Martin Depken, Payam Rowghanian
 * **Discussion summary:** The discussion evolved to focus on the question of how many subchains of some length $s$ share the same volume, and how this number $P(s)$ depends on the scale $s$. Naive crumpled globule model suggests that $P(s) \sim 1$ for any $s$. Clearly, this cannot be true on the length scale small compared at the entanglement length, at $s<N_{e}$; in this range $P(s)$ must grow with $s$. Indeed, simulations by both Everaers group (looking at not-necessarily-equilibrated systems) and Kremer group (more equilibrated) indicate $P(s)$ growing and reaching as much as about $60$ or so. For comparison, the parameter $P(s)$ for a Hilbert curve in 3D is close to 22, so this is what should be understood as being ``of order unity'' in this context. Thus, simulation shows that $P(s)$ is about 3 times larger for rings in the melt or for Everaers chains than it is for an ideal crumpled globule, which is the Hilbert curve.

**Fractal Structure of Biopolymers** (Discussion leader: Rony Granek) (Friday May 6, 11AM, SSR, room 2514)

 * **Abstract:** We will discuss the fractal nature of RNA, chromatin, and proteins, and possible connection between the three.
 * **Participants:**Payam Rowghanian, Alexander Grosberg, Ralf Everaers, Franco Ferrari, Michael Rubinstein, Liheng Cai, Tannie Liverpool, Paul van der Schoot
 * **Discussion summary:** This was an open (and unorganized...) discussion that followed Kay Wiese talk, in which I (RG) presented the question of how should RNA fold in 3D given a known self-similarity in the secondary structure, as Wiese finds (that does not contain, however, pseudoknots). Kay Wiese presented a back-of-the-envelope Flory-type calculation (done just an hour before the discussion...) to obtain the fractal dimension in 3D. However, Rubinstein (correctly, as always...) suggested that this calculation contradicts the Flory theory that one does for branched polymers with Gaussian (entropic) springs, where the spectral dimension is 4/3 (Gaussian branched polymer fractal dim. dfg=2*ds/(2-ds)=4), and the excluded volume driven fractal dimension is found to be (in 3D) df=5*ds/(2+ds)=2, e.g. Cates calculation. The discussion continued in the courtyard... It looks that Kay's calculation, which is similar to the calculation done in the past for random surfaces, coincides with the polymer-type Flory theory only if one takes the manifold dimension D to be equal to the spectral dimension ds, rather than using D=1/zeta where zeta is the self-similarity dimension (h~L^(zeta)) that Kay mentioned in his talk (go to his video recording), zeta\simeq 2/3. Some other things I realized later... One important thing should be mentioned. Henri Orland taught us that pseudoknot pairs are 10% of all pairs, which suggests (to me at least) that the 3D fold structure is determined mainly by pseudoknots (some disordered regions are still left, I believe). Hence, the calculation remains mainly of "academic interest"...

**Polymer Adsorption Near Surfaces**

 * **Abstract:**
 * **Participants:** Michael Rubinstein, Franco Ferrari, Liheng Cai, Paul van der Schoot, Mike Hagan, Payam Rowghanian, Alexander Chervanyov, Arlette Baljon, Martin Depken
 * **Discussion summary:**

**Sequence Dependence vs. Universality** (Discussion leader: Alexei Kornyshev)

 * **Abstract:**
 * **Participants:** Alexander Grosberg, Ralf Everaers, Franco Ferrari, Michael Rubinstein, Ludvig Lizana, Liheng Cai, Rony Granek, Paul van der Schoot, Mike Hagan, Martin Depken, Payam Rowghanian, Tannie Liverpool, Arlette Baljon
 * **Discussion summary:**

**Virus/RNA Self-organization/self-assembly** (Discussion leader: )

 * **Abstract:**
 * **Participants:** Michael Rubinstein, Payam Rowghanian, Liheng Cai
 * **Discussion summary:**

**Cytoskeleton** (Discussion leader: Garyk Papoian)

 * 1) Action networks
 * 2) Motors vs. effective temperature
 * 3) Microtubules
 * **Abstract:**
 * **Participants:**Arlette Baljon, Michael Rubinstein, Chase Broedersz, Jay Schieber, Dima Makarov, Rony Granek, Payam Rowghanian, Liheng Cai, Andreas Bausch, Franco Ferrari, Christoph Weber.
 * **Discussion summary:** Thefluctuation-dissipation relations in active gels were discussed. One may define effective temperature as a frequency dependent quantity, however the usefulness and the predictive nature of such a concept was questioned.

**Structure of bio-polyelectrolytes, e.g. mucins, and their interaction with substrates** (Discussion leader: Katharina Ribbeck)

 * **Abstract:** Oliver Lieleg will show single particle tracking data that demonstrate how particle surface charges retards particle diffusion in biological hydrogels.
 * **Participants:**Arlette Baljon, Michael Rubinstein, Oliver Lieleg, Payam Rowghanian, Franco Ferrari, Christoph Weber, Liheng Cai
 * **Discussion summary:**

**Extra cellular matrix** (Discussion leader: Frederick MacKintosh)

 * **Abstract:**
 * **Participants:**Arlette Baljon, Michael Rubinstein, Chase Broedersz, Jay Schieber, Garyk Papoian, Oliver Lieleg, Franco Ferrari, Dima Makarov, Katharina Ribbeck, Rony Granek, Payam Rowghanian, Liheng Cai, Andreas Bausch, Christoph Weber.
 * **Discussion summary:**

**Response of biomolecules to mechanical forces (single-molecule pulling, the origin of catch-bonds etc.)** (Discussion leader: Dima Makarov)

 * **Abstract:**
 * **Participants:** Chase Broedersz, Franco Ferrari, Yann von Hansen, Nicolas Clauvelin, Rony Granek, Payam Rowghanian, Liheng Cai, Andreas Bausch
 * **Discussion summary:** While macroscopic analogs of catch-bonds are ubiquitous, our microscopic understanding of the physics of catch bonds is rather incomplete. It is however clear that one-dimensional free-energy models, which are commonly employed to describe the effect of mechanical force on molecules, cannot describe catch-bonds. Higher-dimensional models naturally allow for the catch-bond effect. Knotted proteins are examples of microscopic systems that may show catch-bond behavior, which may have biological significance.

=**Self-assembled lipid bilayers**= (Discussion leader: Carlos Marques) (Friday June 17, 10.00 AM, room SSR)
 * **Abstract:**We will look into interactions of lipid bilayers with single DNA molecules (Marques, [|1],[|2]), tube extraction (Baljon) and area storage (Papoian) by curvature induced proteins ... and more.
 * **Participants:**
 * **Discussion summary:**

=**Gels:** Strings, droplets and tubes- how does phase separation take place in a connected network?= (Discussion leader: Yitzhak Rabin, June 20)
 * Abstract: We introduce the elastic Lennard-Jones model of a polymer network of particles connected by harmonic springs and interaction through LJ potential. The network undergoes microphase separation at low temperature. In 2d and intermediate range of spring constants, this results in a super-network of high density filaments in a matrix of low density background.

=Models of Active Systems=
 * (Discussion leaders: Rony Granek & Michael Cates) (Friday June 23, 2:00 pm, SSR)**
 * **Abstract:** RG will present two complementary models for active transport in living cells and model systems: i) small cargos carried by motor proteins that move on disordered microtubule networks, and ii) large cargos moving in viscoelastic media. MEC will elaborate on his model of bacteria motion and pattern formation in colonies as described in his short talk. Fred and Nir are not here anymore but others are welcome to present their models/viewpoints.
 * **Participants:**
 * **Discussion summary:** Different model systems were presented, see recording.