Peanut butter in water - doubling the amount

A quick experiment today around boiling peanut butter in water.  I doubled the amount of peanut butter to 56 g in 1 cup of water.  During the boil it formed a complete emulsion, as far as I could tell there was no water, it was all very foam-like.  After the boil, I transferred to a mason jar with total volume slightly more than 4 cups.  It was initially uniformly cloudy white, but then settled into the 3 layers previously observed.  The bottom layer was bigger than previously observed.

I used a baster to extract the middle layer (water) and tasted it - tasted like peanut butter, but not more so than previously.

There doesn't appear to be any major benefit of using double the amount of peanut butter, and the downside is that the greater amount of bottom sediment might mean less usable / uncloudy beer.

Previous post about peanut butter in water: Testing boiling peanut butter in water: results

Next post: Brewing a peanut butter porter - the wort

Hydrogen bonding in drugs

A member of my group, Patrick McCarren, worked on modeling the hydrogen bonds in some molecules at the Broad Institute that we screen as potential drugs.  It was part of a very nice paper which included a lot of solid experimental work:
http://pubs.acs.org/doi/abs/10.1021/jm500059t

It got a write up here:
http://wavefunction.fieldofscience.com/2014/02/hiding-hydrogen-bonding-groups-in-large.html

and here:
http://pipeline.corante.com/archives/2014/02/28/computational_nirvana.php

STEM Career talk at Cambridge Rindge and Latin School

I gave an ~11 min talk at Cambridge Rindge and Latin about my job / career and how I ended up in it:
https://drive.google.com/file/d/0Bwt7GLsjfgEdS2FHSW9rV2tVNFE/edit?usp=sharing

Testing boiling peanut butter in water: results

Following up on preparing to test boiling peanut butter in water, after letting the mixtures sit for a day, I tested them.  They looked very similar - they hadn't noticeably separated further.  The oil layer (top) was about the same thickness, same color, possibly less homogeneous.  The other two layers also appeared the same (thickness, color / cloudiness).

Bottling the carob porter

I bottled the carob porter (previous posts: initial brew, racking into secondary) today.

Cleaning / sterilization

I washed everything with soap and water yesterday, I used a brush to scrub inside of bottles and auto-siphon.  I sterilized my equipment and the bottles using iodine solution, prepared by filling the bottling bucket with the hottest possible water. I added about ~3 splashes of iodine solution from the bottle until the the color of the solution was light orange.  Everything sat in solution at least 2 minutes, and then was allowed to drain / dry for several minutes.

Testing boiling peanut butter in water: preparation

In preparation for making a peanut butter beer, I ran some small scale experiments boiling peanut butter in water, to mimic what will happen during the brew.  I had read the biggest concern was avoiding having the beer be oily, so last time I tried peanut butter flavored beer, I centrifuged the peanut butter for ~90 minutes, which separated the it pretty well into oil and dry solids.  I discarded the oil and boiled the solids in the wort.  After bottling (after a secondary fermentation), I tried the liquid at the bottom of the carboy and it had a very strong peanut butter flavor.  However, the bottled beer had no peanut butter flavor.  My guess is that since the beer I sampled had a lot of solids, but the bottled beer had none, the solids were the source of the flavor.  That presents two possible next steps:

1. prepare the beer with the peanut butter with its oil to try to extract some amount of flavor and or oil into the beer mixture, then remove excess oil
2. leave the peanut butter solids in the bottled beer, and like a hefewezein or wheat beer, serve with the sediment

Matlab spconvert function - undocumented "feature"

Matlab has a useful function for loading data that is in a sparse format - spconvert.  Basically, you create a file where each row contains the row, column, and data of the matrix you wish to load.  The first column is indicates the destination row, the second column indicates the destination column and the third column indicates the value at that row and column.  You load that into matlab (using, e.g., csvread):
sparse = csvread('mydata.csv');

example:
sparse = [1 1 2
2 1 3
2 2 5
3 3 7];

"sparse" is now have a N by 3 matrix, where N is the number of non-zero entries in your data.  With the command:
mat = spconvert(sparse)

yields:
2 0 0
3 5 0
0 0 7

Warning!!!! This doesn't appear to be documented!!! If you repeat a location in sparse, the value that appears in the result (mat) will be the sum of the entries in sparse.  For example, if sparse is modified to be:
sparse = [1 1 2
2 1 3
2 2 5
3 3 7
1 1 11];

then mat = spconvert(sparse) yields:
13 0 0
3 5 0
0 0 7

Note that the (1,1) entry of mat is 13, the sum of 2 + 11, the first and last rows of sparse.