Theoretical physics of polymers, biopolymers, and soft matter

Below is more or less random sample of topics and images. For the more complete picture, look at the publication list.

List of Publications in pdf format
Topologically Constrained Polymers

Image on the right shows how un-concatenated rings are "territorially segregated" for purely topological reasons. The image was generated by Jonathan Halverson and Kurt Kremer, it is MD simulation of a set of 200 rings, 1600 monomers each. Entanglement length of this polymer model is 28.

We hypothesize that this effect is behind the phenomenon of chromosome territories.

Link to the review of this subject...
... and also to the video abstract of that review.
Statistical Physics Away from Detailed Balance

With Jean-Francois Joanny, we were able to develop a surprisingly complete theory for the out-of-equilibrium system which consists of two types of particles, A and B, interacting with two different heat reservoirs. Although our theory is an analog of only second virial approximation, but it is nevertheless complete in the sense that all approximations are strictly parameter-based.

The image on the right shows detailed balance violating loopy currents on the phase plane of coordinates of two particles.

Link to the paper on this subject, With Jean-Francois Joanny
Variations on the theme of crumpled globule

Although we invented crumpled globule (with S.Nechaev and E.Shakhnovich) a long time ago (1988), and then applied it to DNA in the cell (with Y.Rabin, S.Havlin, and A.Neer) also a long time ago (1993), understanding of it is still far from complete, and we keep working on it.

This image, generated by Jan Smrek, shows minimal surfaces spanned on various types of polymer rings and allowing (we hope) to understand them better.

Link to the paper (ACS MACRO Letters) on minimal surfaces, with Jan Smrek
Minimal Surfaces
Space filling curves

Also on the subject of crumpled globules, Jan Smrek was able to invent space filling curves with fractal dimension of the boundary arbitrary close to the dimension of embedding space (here shown in d=2).


By the way, the inspiration for this work came from the drawings of Escher...

Link to the paper about it.
Chromatin hydrodynamics

Chromatin is of great to interest to us not only in connection with topology and crumpled globule issues, but also in the context of its driven non-equilibrium dynamics.

This particular image is a cartoon showing scalar and vector sources in chromatin hydrodynamics.

Link to the paper about this, with Robijn Bruinsma, Yitzhak Rabin, and Alexandra Zidovska.
Scalar and Vector Sources
Electrophoresis, translocation, trumpet...

Usually electric field is screened at a rather short Debye length in molecular systems in water. But this is only true in equilibrium. In a driven system, such as in the vicinity of nanopore when aan ionic current is driven through, there is an electric field proportional to the current which is not screened. Moreover, this field nicely behaves just like an electrostatic field of a point charge, like 1/r, except it looks like a positive charge on one side of the pore and negative on the other.

This has far reaching consequences, such as, e.g., iso-flux trumpet.

Link to the paper about this, with Payam Rowghanian.
Lattice proteins

Lattice proteins are not very fashionable these days, and some people are sceptical about them, but I think they are gorgeous.

This particular image was generated a long time ago by Vijay Pande when we worked together.

Link to the old review, with Toyoichi Tanaka and Vijay Pande
Lattice Protein
Other interesting things

With Edo Kussel and Stan Leibler, we managed to make a map between polymers and populations. This paper does not seem to be very popular, but I still like it!

There is not even a single figure in that paper, so I show a table instead of a figure...

Link to the paper with Edo Kussel and Stan Leibler