Showing posts with label Research. Show all posts
Showing posts with label Research. Show all posts

Tuesday, August 29, 2017

Anomalous Diffusion

I've been taking a deep dive into the world of anomalous diffusion over the past month. It is a fascinating subject that integrates applications from a variety of different fields.

For someone interested, I'd recommend the following resources:

1. A Physics World feature on "Anomalous diffusion spreads its wings" (pdf - currently not paywalled)

2. A YouTube video on anomalous diffusion in crowded environments



3. A gentle introduction/tutorial on normal and anomalous diffusion, which introduces the intuition and mechanics of fractional calculus

4. A more academic review of anomalous diffusion and fractional dynamics (may be paywalled)

Friday, April 8, 2016

Extracting Data from Static Plots

In the past, I have used two programs to extract datapoints from a graph. The typical use case is to save the coordinates extracted from a pdf or png graph, so that you can use them for calculations or to overlay on your graphs.

1. DataThief: A shareware program that is cross platform. It is written in Java and works on Windows, MacOS, and Linux.

2. Engauge Digitizer: This is also cross platform. I have written a little bit about using it here.

In the past month, I discovered WebPlotDigitizer.

It is completely web-based, so on doesn't have to "install" it. This means, it is completely blind to the underlying operating system. The interface overall seems much spiffier, but I haven't taken it out for a serious test drive.

Thursday, December 5, 2013

RIPE: More Polymer Entanglements

In a previous post I discussed entanglements in polymer melts. I thought I’d spend sometime discussing some “practical” matters in which entanglements play a role. Today, lets focus on a very special kind of polymer: DNA.

You have a lot of DNA in your body. In fact, each cell in your body has over 2 meters of DNA packed inside a small bag called the nucleus. The diameter of a typical nucleus is less than 10 microns.

If that hasn’t knocked you off of your seat yet, let me put it in perspective. If all the DNA in your body were set end to end, it would stretch from the Sun to Pluto!

To freaking Pluto; which they say is not even a planet anymore!

I have trouble dealing with headphones in my pocket, and the nucleus manages to pack and use all of that DNA inside it. How the heck does it do that?

The answer turns out to have some parallels in everyday life. How do you deal with a really long water hose or vacuum cleaner cable? You roll it around something! You organize it!

Thus, DNA is not packed randomly. It is organized in a very sophisticated hierarchical manner. This allows the nucleus to sequester a lot of material and information in a very small compartment. Here is a nice video that explains this organization (DNA - nucleosomes - chromatin).

Monday, September 2, 2013

RIPE: Polymers and Entanglements

Let's start with three everyday examples of entanglements.

(i) I am love my iPod and listen to it quite a bit. Usually, after I am done listening, I just stick it, along with headphones, into my pocket. The next time I pull it out, the headphones are all tangled up, and I often wonder what the heck happened to them in my pocket.






(ii) A similar thing happens every time I use my leaf-blower, and don’t stow away the cables carefully. It is a mess!



(iii) As a father of daughters, I am a big fan of short hair. Why? Long hair gets tangled up more easily, and needs more effort combing (de-entangling).

Headphones, cables, and hair – they all have a natural tendency to get all tangled up.

The “longer” these things get, the more trouble they are.

What has this got to do with polymers?

Polymers are long chain-like molecules formed by stringing together units called monomers. As the number of units increases, their “molecular weight” increases, as does their propensity to get tangled up.

Indeed, there is a threshold molecular weight – different for different polymers – called the entanglement molecular weight, beyond which their rheology is strongly influenced by these entanglements. (This opens up a fascinating cascade of research questions that I have spent countless hours pondering!)

Below the entanglement molecular weight, the viscosity (the resistance to flow) of polymer melts increases gently. Double the molecular weight, and you double the viscosity.

Beyond the entanglement molecular weight, this linear increase in viscosity is abruptly disturbed (see a picture here). In this highly entangled regime, a doubling of molecular weight results in nearly a 10-fold increase in viscosity.

Take that!

Footnote: Polyethylene in your milk jars, and polystyrene in Styrofoam cups have entanglement molecular weights of about 1000 and 15,000 daltons respectively.

Footnote2: RIPE = Research In Plain English

Wednesday, January 9, 2013

Molecular Weight Distributions and Size Exclusion Chromatography: Part 1

Size Exclusion Chromatography (SEC) is a commonly used technique to separate molecules dissolved in a solvent on the basis of their size. A sample containing molecules of various sizes is injected at one end of a special SEC column, and monitored at the other end using one or more special detectors.

As an analogy it is useful to think of the column as an obstacle course (a 110 meter hurdle race). Somewhat counter-intuitively, the big fat molecules finish  first, and the small nimble ones finish last. The reason why this happens is the same reason why the tortoise finished first. Despite being slower, he did not pause to examine and explore each nook and cranny.

You can imagine that SEC is a popular technique to get the molecular weight distribution (MWD) of polydisperse polymers. Because of the way in which the calibration process and detectors work, the resulting MWD is usually reported in a somewhat "funky units" of w(log M) versus log M, which looks something like the following.
Note 1: The area under the curve, as reported, is unity.
Note 2: Throughout this discussion, "log" refers to log-base-10, and "ln" refers to log-base-e. In SEC it is more common to use base-10, although as I will show shortly, base-e is more "natural".

Okay, so how is the SEC MWD w(log M) related to quantities we know better such as the number distribution N(M) and the weight distribution W(M)?

To recap, N(M) dM tells us the fraction of molecules with molecular weight between M and M+dM, and W(M) dM tells us the weight fraction of the molecules with molecular weight between M and M+dM. These distributions are normalized which means,

\[ \int_{0}^{\infty} N(M) dM = \int_{0}^{\infty} W(M) dM = 1\]

The first moments of N(M) and W(M) are the number-averaged and weight-averaged molecular weights.

\[ M_n = \int_{0}^{\infty} M N(M) dM\]
\[ M_w = \int_{0}^{\infty} M W(M) dM\]

As you know or expect, N(M) and W(M) contain the same information, and they can be transformed into one other.

\[ W(M) = \frac{M N(M)}{\int_{0}^{\infty} M N(M) dM} = \frac{M N(M)}{M_n}\]


The integral in the denominator ensures the normalization of W(M). The brother of the SEC MWD w(log M) turns out to be closely related to the "next moment"

\[ w(\ln M) \propto M W(M), \]

except that it's normalization is not 

\[\int w(\ln M) dM = 1,\]

but rather,

\[\int_{0}^{\infty} w(\ln M) d \ln M = 1.\]

This is automatically satisfied for w(ln M) = M W(M), since

\[\int_{0}^{\infty} w(\ln M) d \ln M = \int_{0}^{\infty} M W(M) \frac{dM}{M} = \int_{0}^{\infty} W(M) dM.\]

What about w(log M)? Aren't we more interested in that whole shebang?

Sure, no problem. We will find out that w(log M) and w(ln M) are just a constant (2.303) apart.

We start with 

\[ w(\log M) = c M W(M), \]

where c is a constant, and work backwards from the normalization (as in the plot above!)

\[\int_{0}^{\infty} w(\log M) d \log M = 1.\]

This implies

\[\int_{0}^{\infty} c M W(M) \frac{dM}{2.303 M} = 1.\]

This implies c = 2.303, and w(log M) = 2.303 w(ln M) = 2.303 M W(M).

We will apply this to a particular problem in the next post.