User:BPappas

From Soft-Matter
Revision as of 03:05, 12 January 2009 by Morrison (Talk | contribs) (Protected "User:BPappas" [edit=autoconfirmed:move=autoconfirmed])

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Home

About Me

I am a first year biophysics graduate student, currently studying the molecular motor dynein with Samara Reck-Peterson. My undergraduate institution was the Rochester Institute of Technology, where I studied biochemistry and dabbled in physics (and Portuguese!).

My research has involved concentrated eye-lens crystallin protein analysis (read: soft condensed matter, ooo) with George Thurston, optical tweezers setup and bacteriophage packaging application with Douglas Smith, unconventional myosin purification and crystallization with Jon Kull, and lifetime analysis on green fluorescent protein with Martin Gruebele.

E-mail is the best way to get in touch with me: bpappas at fas.harvard.edu


Miscellany

  • Fun fact: Prof Morrison wrote a, and I quote, "highly popular" book on Colloidal Systems that "should be available in all polymer sciences libraries"; not too shabby. Unfortunately not a Google book, though available in the McKay library.
  • For the talk of Lightning storms, I found a book on the Microphysics of Clouds and Precipitation. Checked out of our library currently (12 November), but a lot of it is available online. It has a whole chapter on the Electricity of Clouds.
  • The Complex Fluids Workshop is coming up at Harvard shortly: December 5th, all day in Maxwell Dworkin. Here is the link to the work group: http://www.complexfluids.org/necf/index.php. The keynote is from Cal Berkley.
  • If anyone is having trouble with typing equations into the wiki, this is a great reference: http://en.wikibooks.org/wiki/LaTeX/Mathematics. I will not even claim to be a novice at LaTeX, but that wikibook definitely helped me to become at least mildly literate.
  • This paper from PNAS by Brent Christner, LSU, is regarding evidence that bacteria play an important role in cloud formation and precipitation. They are called "Biological Ice Nucleators" in the paper.

Final Project for the Wiki

Soft Matter and Clouds

Plan

Clouds! Dr. Morrison and I talked about doing another, perhaps longer, talk about Clouds as Soft Matter for the March Complex Fluids Workshop, so for my final project I am going to try to cull together what we as a class thought was interesting, add some more fun facts, and try to organize it in a way that is persuasive.

Notes

What is soft matter? Foams, emulsions, gels, all have certain characteristics that cause us to classify them as soft condensed matter.

Length scale is very important. Typically in soft condensed matter the self assembled structures are between atomic sizes and macroscopic scales. Many of the behaviors of this type of matter come from the topological implications of the assembled units, and are not necessarily dictated by the chemistry of the units. In the case of clouds, we see that the droplet sizes range from on the order of 10um to 3mm.

Fluctuations in soft matter is also an important feature, with the typical energies associated with the bonds between structures and with the distortions of those structures comparable in size to thermal energies, kT. Soft matter systems are visualized as being in a constant state of motion--the tumbling of cloud over itself, the formation of "cloud highways", all indicating that clouds are experiencing some form of long range interactions.

Self assembly, too, is a key feature in soft matter, and even more interesting when molecular level assembly (free water droplets coming together around nucleating sites, for instance) leads to supramolecular structure and a higher level of order, perhaps a massive cloud.

So this got us all thinking about clouds as soft matter, and then really the coup de grat came when some of us found that the nucleating sites of clouds actually might be so much more interesting than we thought. Bacteria! Who knew? Well actually a lot of people knew that there were microbes in clouds and throughout the atmosphere, but some recent work by Brent Christner's lab at LSU actually showed that biological nuclei may be the only things that can cause warmer weather clouds to form the droplet sizes they need to begin precipitation.

Ice formation in tropospheric clouds is required for snow and most rainfall. At temperatures > –40°C, ice formation is not spontaneous, and diverse substrates can act as catalysts of ice nucleation. Biological ice nucleators (IN) are the most active IN in nature, and some bacterial plant pathogens can catalyze ice formation at temperatures near –2°C. The activity of most known biological IN is mediated by proteins or proteinaceous compounds. Results from Brent Christner's lab at LSU indicate that these particles are widely dispersed in the atmosphere, and, if present in clouds, they are likely to have an important role in the initiation of ice formation, especially when minimum cloud temperatures are relatively warm.

Proof of bacteria shown in lysozyme sensitivity (damages the peptidoglycan cell wall of bacteria), heat sensitivity, and DNA presence. Some were also cultured from samples.

Bacteria: “The most widespread and well-studied biological aerosols with ice-nucleating activity are comprised of certain species of plant-associated bacteria (Pseudomonas syringae, Pseudomonas viridiflava, Pseudomonas fluorescens, Pantoea agglomerans, and Xanthomonas campestris), but also fungi (e.g., Fusarium avenaceum), algae such as Chlorella minutissima, and birch pollen. P. syringae and F. avenaceum in particular have been detected in atmospheric aerosols and clouds. Ice-nucleating strains of P. syringae possess a 120- to 180-kDa ice nucleation active protein in their outer membrane comprised of contiguous repeats of a consensus octapeptide; the protein binds water molecules in an ordered arrangement, providing a nucleating template that enhances ice crystal formation” from PNAS December 2, 2008 vol. 105 no. 48

Questions remaining: Is this a dispersion strategy developed by bacteria and plant pathogens? In the absence of biological IN, can clouds form at these higher temperatures? Did bacteria develop extracellular proteins specifically for ice nucleation?

Notes from last day of class

We are dealing with fluctuations when dealing with soft matter. The lengths are constantly fluctuating, like in polymers. Forces are on the order of kT. Forces are unbalanced in soft matter often, which causes much fluctuation.

There are many assertions in simple polymers, like no matter how big the area gets, the distribution of end-to-end distance will be the same. How does the density of the

Random walk: Density goes as the square of the polymer MW? Not tightly packed, as things get bigger the density decreases. But in self-avoiding, the repulsive forces get less and less as the density gets greater, and you see an average density on the 5/3 power. Cube of the MW? Tightly packed.

Elasticity is energy per unit volume. Viscosity is a time scale for systems to relax--viscosity increases as the relaxation time increases. Entangling effects this greatly.

Time scale and force scale for soft matter is relevant to us.

Are there phase diagrams for clouds? Water phase diagram.

Dispersion attractions