Week of 10/10/08

In attempt to make these posts more regular I will be trying a different approach of simply posting links to various papers of interest, without much graphics or commentary.

• V. A. Martinez, G. Bryant and W. van Megen, “Slow Dynamics and Aging of a Colloidal Hard Sphere Glass,” Physical Review Letters 101, 135702-4 (2008)
• J. M. Brader, M. E. Cates and M. Fuchs, “First-Principles Constitutive Equation for Suspension Rheology,” Physical Review Letters 101, 138301-4 (2008)  also reviewed by
  N. Wagner, “How colloidal dispersions relax under stress,” Physics 1, 22 (2008)
• D. K. Satapathy, O. Bunk, K. Jefimovs et al., “Colloidal Monolayer Trapped near a Charged Wall: A Synchrotron X-Ray Diffraction Study,” Physical Review Letters 101, 136103-4 (2008)

Nanoparticle Self-assembly with DNA

Image on the left is the cover of Jan. 31 issue of Nature.

Anyone who took high school chemistry has played with “sticks and balls” models of molecules or crystalline atoms. There are magnetic toy sets which allow kids to assemble their own version of crystals.

A similar feat, but on nanoscale, was accomplished by two groups – one at Brookhaven (Nykypanchuk et. al  Nature 451, 549-552 (2008)) and another at Northwestern (Park et. al, Nature 451, 553-556 (2008)).

The basic idea behind these two experiments is to graft different strands of DNA molecules onto particles, creating two “species” of particles with complimentary pairs of DNA strands. These two different types of strands can merge together into a double helix at high temperatures, making a strong connection between particles of the opposite species. The result is a cubic structure, similar to ion salts.

The nanoparticle crystals held together by DNA molecules are rather fragile, and most of volume is occupied by water. The typical size of the unit cell is on the order of 35-50 nm, with particle size just 10 nm in size. The nanoparticles therefore occupy only a tiny fraction of the total crystal volume, with density of such “fluffy” crystals less than milk foam in your latte.

DNA capture and recapture with nanopores

The featured article is “Recapturing and trapping single molecules with a solid-state nanopore” by Gershow, M. & Golovchenko, J. A. Nature Nanotech. 2, 775–779 (2007).

The idea behind nanopore-based DNA sequencing is relatively simple – pass a DNA molecule through a nanopore channel, sort of the same way you pass a thread through an eye of the needle. As the DNA is passing through the pore, it can be “read out” by looking for specific signatures of the four bases in, for example, electrical capacitance. Experimental implementation of this idea is of course very challenging.

Gershow and Golovchenko demonstrate that they have ability to “suck” the DNA molecule back into the pore, sufficiently long time after it left the pore. The figure above demonstrates this process schematically.

See also a News and Views by Derek Stein, as well as “Colloquium” review of DNA sequencing approaches in Review of Modern Physics paper by DiVentra and Zwolak.

How ropes coil and knot

Two papers featured this week, both relating to behavior of macroscopic “soft” matter – namely ropes, threads, spaghetti and other linear elastic and flexible objects.

The first one is a PRL by Habibi et al., “Coiling of elastic ropes” Phys. Rev. Lett. 99, 154302 (2007).
If you drop a rope on the floor (also works for spaghetti), it tends to coil up. The authors investigate how this coiling comes about, what conditions lead to simple circular coiling, as opposed to figure 8 coling, etc.

The second paper is a PNAS publication by Reymer and Smith “Spontaneous knotting of an agitated string” PNAS 104, 16432 (2007).

If you throw a long rope in a box and tuble it around (think about a rope in a dryer), it tends to tangle up in a knot. The authors did series of experiments for various lengths and types of ropes, analyzing resulting knots, in addition to complex mathematical simulations. It is a test of self-avoiding random walk theory, except applied to real objects with finite flexibility.

Quasi-Forbidden Bragg peaks from soft matter

This week’s item is a rather technical Nature Materials paper by Forster et al., “Order causes secondary Bragg peaks in soft materials”[Nature Materials 6, 888 - 893 (2007)].

Atomic crystals can often be well-ordered, meaning that the correlation length on which “perfect” atomic order exist can extend over many thousands (or even millions) unit cells. Grain boundaries, dislocations and other defects are a common cause of breaking the perfectly ordered chain of atoms.

Soft materials – liquid crystals, colloids, mesoporous materials etc. – typically consist of fairly large unit cells and it is more difficult to get these materials as well-ordered as atomic crystals. All atoms are identical, but colloidal solutions, for example, are often fairly polydisperse, and therefore crystallize with some difficulty – if at all. It is no surprise that the correlation lengths – especially when expressed in unit cells – is far shorter in soft matter, compared to atomic crystals, such as Si or Pb.

Correlation lengthscales can be determined via Debye-Scherrer formalism that relates width of the x-ray or neutron scattering peak to the typical coherent domain size within the sample.

Forster et al. address the issue of finite correlation lengths by analysis of secondary “forbidden” (or quasi-forbidden) Bragg reflections. For example, for a perfect body-centered cubic lattice 001 reflection does not exist – only (002), (011) and other indices that add up to an even number. But once you introduce some disorder, these forbidden peaks become “alive”, since destructive interference responsible for precisely canceling out contributions to these forbidden reflections becomes somewhat faulty.

Surprisingly enough, people haven’t dealt much with ordered, but only over short-range distances materials, at least not to the extent of coming up with sophisticated treatment of intensities of these secondary Bragg peaks that can answer questions like: is the material truly homogeneous but has a lot of disorder, or is it “patchy”? Forster’s paper represents a key step in dealing with these important issues.

Glass on cooling OR heating

This week’s item is a paper that just appeared on arxiv.org by Simon Mochrie’s Yale group and Argonne collaborators on a unique situation that occurs in a liquid that becomes a glass upon cooling OR heating: X. Lu et al., “How a liquid becomes a glass both on cooling and on heating” arxiv.org/0708.3663v1

Typically we think of glasses that vitrify when the temperature is (suddenly) lowered. The unique situation explored in this paper is a situation where at high temperature system forms a glass dominated by repulsive interactions, and at low temperatures due to attractive interactions.

By tracking the glass transition using coherent x-ray scattering techniques (XPCS in this case) the authors look in great detail at the logarithmically decaying slow fluctuations in the same system under very different circumstances – and therefore able to study not a single but two glass transitions with either repulsive or attractive interactions.

Soap Bubble Clusters

Rev. Mod. Phys. features a short (and quite mathematically inclined) Colloquium on Soap Bubble Clusters by Frank Morgan.

It discusses things like “Double Bubble Conjecture” and other fun geometrical work on soap bubbles.