## Bookbinding Class Notes – Part 1

Isn’t it a hassle when you go try to keep your class notes organized and bound, but your professor loves handouts?  Just take to bookbinding class notes into a copy worth keeping, like I have.  This and the post next week will show the steps I took to bind the notes from one of my classes into a hardbound copy.

## Printing and Sizing the Paper

When preparing my notes for bookbinding, I had to deal with a combination of page sizes.  I took my notes on lined paper which was slightly smaller than the handouts, which were printed on standard US Letter sized paper.  This was fixed by cutting down the letter paper with a straightedge and razor.  I chose to cut from the bottom edge of the letter paper rather than the top to resize.  Either works, and it is a matter of preference.  Be sure not to cut off something important!

## Binding with String and Glue

Once you have all of your notes ready to go, place the copies in a stack and secure with clamps.  For this book, I used a piece of wood on either side of the stacked papers to prevent the C-clamps I was using from damaging the notes.  The wood was positioned to leave a margin on the binding side of the documents.

Next, line was traced on the top page 1 cm from the edge.  This line was marked at regular intervals (I think I used 1 cm for my intervals on this copy).  At each of these intervals, I drilled a small hole all the way through the papers.  I used a 3/32″ diameter drill bit.  It is important to note that while drilling these holes, the papers will tend to splay out.  I mitigated this issue by securing the area adjacent to the drill hole with channel lock pliers.

When all of the holes are drilled, use a needle and thread to bind the book.  There are several different binding techniques you can use, but I have found that a simple looping forward and backward along the spine of the book was sufficient.  With the string tied off, I used a liberal amount of PVA glue along the spine to further hold the pages together.

Next week I will describe how I make my covers.

## LaTeX: Drawing MOSFET in TikZ – Labels and Animation

Continuing from last week’s post, this week we will be adding labels to our MOSFET in TikZ and adding slide animations with Beamer.

As a reminder, last week we drew our image of a MOSFET in Tikz before adding colors. The colors we added were based on the materials used in each part of the n-type MOSFET. Now let’s add some labels to make sure that anyone we present this image to can understand what is going in.

## Centered Labels

Now we take the code from last week and add “nodes” to certain of our shapes. We tell these nodes to have certain text and compile.

\documentclass{beamer}

\usepackage{tikz}
\usetikzlibrary{patterns}

\title{\LaTeX~Surface Science and Electronics}
\author{Wesley T. Honeycutt}
\date{\today}

\newcommand{\metalone}{[pattern= horizontal lines, pattern color=blue]}
\newcommand{\metaltwo}{[pattern= vertical lines, pattern color=purple]}
\newcommand{\poly}{[pattern= grid, pattern color=red]}
\newcommand{\pdiff}{[pattern= north east lines, pattern color=orange]}
\newcommand{\ndiff}{[pattern= north west lines, pattern color=green]}
\newcommand{\pwell}{[pattern= crosshatch dots, pattern color=orange]}
\newcommand{\nwell}{[pattern= crosshatch dots, pattern color=green]}
\newcommand{\oxide}{[pattern = bricks, pattern color = olive]}
\newcommand{\silicon}{[fill = white]}
\newcommand{\metalthree}{[fill = teal]}

\begin{document}

\frame{\titlepage}

\frame{\frametitle{MOSFET}
% General n-type mosfet
\begin{tikzpicture}
\draw \pdiff (0,.25) -- (0,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3) -- (11,3) -- (11,.25) -- (0,.25) node {p-type};
\draw \metalthree (0,0) rectangle (11,.25) node {Si Substrate};
\draw \oxide (4,3) rectangle (7,4) node {oxide};
\draw \metalone (4,4) rectangle (7,4.5);
\draw \ndiff (4.25,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3) node {n-type};
\draw \ndiff (10,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3) node {n-type};
\draw \metalone (1.25,3) rectangle (3,3.5);
\draw \metalone (8,3) rectangle (9.75,3.5);
\end{tikzpicture}
}

\end{document}


This gives us the following image with ill-placed text:

The text looks odd because the node location in TikZ defaults to the last point in the drawing. We can tell it to place the node in a certain location with respect to this anchor point. Additionally, I might want to change some other properties such as text color for my labels. This can all be done in brackets after declaring the node. Now my code becomes:

\documentclass{beamer}

\usepackage{tikz}
\usetikzlibrary{patterns}

\title{\LaTeX~Surface Science and Electronics}
\author{Wesley T. Honeycutt}
\date{\today}

\newcommand{\metalone}{[pattern= horizontal lines, pattern color=blue]}
\newcommand{\metaltwo}{[pattern= vertical lines, pattern color=purple]}
\newcommand{\poly}{[pattern= grid, pattern color=red]}
\newcommand{\pdiff}{[pattern= north east lines, pattern color=orange]}
\newcommand{\ndiff}{[pattern= north west lines, pattern color=green]}
\newcommand{\pwell}{[pattern= crosshatch dots, pattern color=orange]}
\newcommand{\nwell}{[pattern= crosshatch dots, pattern color=green]}
\newcommand{\oxide}{[pattern = bricks, pattern color = olive]}
\newcommand{\silicon}{[fill = white]}
\newcommand{\metalthree}{[fill = teal]}

\begin{document}

\frame{\titlepage}

\frame{\frametitle{MOSFET}
% General n-type mosfet
\begin{tikzpicture}
\draw \pdiff (0,.25) -- (0,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3) -- (11,3) -- (11,.25) -- (0,.25) node [midway,above] {p doped Si};
\draw \metalthree (0,0) rectangle (11,.25) node [midway, color=white]
{Si Substrate};
\draw \oxide (4,3) rectangle (7,4) node [pos=.5,font=\bf\Large] {oxide};
\draw \metalone (4,4) rectangle (7,4.5);
\draw \ndiff (4.25,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3) node at (2.625,2.5) [align=center] {n-type};
\draw \ndiff (10,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3) node at (8.375,2.5) [align=center] {n-type};
\draw \metalone (1.25,3) rectangle (3,3.5);
\draw \metalone (8,3) rectangle (9.75,3.5);
\end{tikzpicture}
}

\end{document}


In this case, I have added some alignment options for different locations.

• For the silicon substrate, I have told the node [midway, color=white] so the text appears in the middle of the rectangle and white to show up against the color of metalthree
• For the p doped region, I have told the node [midway,above] so that the text is in the middle of the picture and at the bottom. Notice how midway does not place the text at the true center of custom shapes. It only knows to place it relative to the previous line.
• For the n doped regions, I did not want the text to sit relative to the line, I wanted it to be in the center of the shape. Thus, I told the node to be at a certain set of coordinates which I calculated to be the center of that shape, and set [align=center].
• For the oxide layer, I wanted the text to show up against the oddly colored bricks. Therefore, I used [pos=.5,font=\bf\Large]. The “pos=.5” argument is functionally the same as “midway”, but offers greater freedom to customize. The font arguments tell the node to use text in boldface with a Large size.

The image ends up looking like this:

## Labels on Arrows

I’ve decided that I want to label the metal connections on our MOSFET, but I don’t want to place the text directly over the shape. Instead, I want to tell TikZ to draw little arrows pointing to what is labeled. This is easy. We just draw a line, which we tell to have an arrowhead, from a point to another point. At the first point, we tell it to have a label. I have used:

\draw [->] (1,5) node [above] {Source} -- (2.125,3.5);
\draw [->] (10,5) node [above] {Drain} -- (8.975,3.5);
\draw [->] (5.5,5) node [above] {Gate} -- (5.5,4.5);


Which when implemented, looks like this:

## Animation with Beamer

Did you know that the same person that wrote TikZ wrote Beamer, the LaTeX slideshow creator? It’s true. This makes things quite convenient, as the author has designed it such that it is easy to integrate slide animations into your TikZ code.

For the final part of our MOSFET in TikZ, I’m going to add some animation. I want to make it obvious to the viewer how my MOSFET works going from the off state to saturation mode. I will do this by adding nodes to present the voltage relationship of each state on the screen, then pop up an image of the electron rich areas of the MOSFET. This is very easy to do with \only. Check out the final code below:

\documentclass{beamer}

\usepackage{tikz}
\usetikzlibrary{patterns}

\title{\LaTeX~Surface Science and Electronics}
\author{Wesley T. Honeycutt}
\date{\today}

\newcommand{\metalone}{[pattern= horizontal lines, pattern color=blue]}
\newcommand{\metaltwo}{[pattern= vertical lines, pattern color=purple]}
\newcommand{\poly}{[pattern= grid, pattern color=red]}
\newcommand{\pdiff}{[pattern= north east lines, pattern color=orange]}
\newcommand{\ndiff}{[pattern= north west lines, pattern color=green]}
\newcommand{\pwell}{[pattern= crosshatch dots, pattern color=orange]}
\newcommand{\nwell}{[pattern= crosshatch dots, pattern color=green]}
\newcommand{\oxide}{[pattern = bricks, pattern color = olive]}
\newcommand{\silicon}{[fill = white]}
\newcommand{\metalthree}{[fill = teal]}

\begin{document}

\frame{\titlepage}

\frame{\frametitle{MOSFET}
% General n-type mosfet
\begin{tikzpicture}
\draw \pdiff (0,.25) -- (0,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3) -- (11,3) -- (11,.25) -- (0,.25) node [midway,above] {p doped Si};
\draw \metalthree (0,0) rectangle (11,.25) node [midway, color=white]
{Si Substrate};
\draw \oxide (4,3) rectangle (7,4) node [pos=.5,font=\bf\Large] {oxide};
\draw \metalone (4,4) rectangle (7,4.5);
\draw \ndiff (4.25,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3) node at (2.625,2.5) [align=center] {n-type};
\draw \ndiff (10,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3) node at (8.375,2.5) [align=center] {n-type};
\draw \metalone (1.25,3) rectangle (3,3.5);
\draw \metalone (8,3) rectangle (9.75,3.5);
\draw [->] (1,5) node [above] {Source} -- (2.125,3.5);
\draw [->] (10,5) node [above] {Drain} -- (8.975,3.5);
\draw [->] (5.5,5) node [above] {Gate} -- (5.5,4.5);
\only<1> {\node at (5.5,-.5) [align=center] {$V_{GS} < V_{threshold}$};}
\only<2-3> {\node at (5.5,-.5) [align=center] {$V_{GS} \geq V_{threshold}$};
\node at (5.5,-1) [align=center] {$V_{DS} < V_{GS} - V_{threshold}$};
}
\only<3> {\draw [fill=white] (4.25,3) rectangle (6.75,2.5);
\draw \ndiff (4.25,3) rectangle (6.75,2.5);
}
\only<4-5> {\node at (5.5,-.5) [align=center] {$V_{GS} \geq V_{threshold}$};
\node at (5.5,-1) [align=center] {$V_{DS} = V_{GS} - V_{threshold}$};
}
\only<5> {\draw [fill=orange,orange] (4.25,3) rectangle (6.75,2.5);
\draw [fill=white] (4.25,3) -- (4.25,2.65) -- (6.75,3) -- (4.75,3);
\draw \ndiff (4.25,3) -- (4.25,2.65) -- (6.75,3) -- (4.75,3);
}
\only<6-7> {\node at (5.5,-.5) [align=center] {$V_{GS} \geq V_{threshold}$};
\node at (5.5,-1) [align=center] {$V_{DS} > V_{GS} - V_{threshold}$};
}
\only<7> {\draw [fill=orange,orange] (4.25,3) rectangle (6.75,2.5);
\draw [fill=white] (4.25,3) -- (4.25,2.85) -- (6.75,3) -- (4.75,3);
\draw \ndiff (4.25,3) -- (4.25,2.85) -- (6.75,3) -- (4.75,3);
}
\end{tikzpicture}
}

\end{document}


Each time I add an \only, I put slide numbers in pointed braces. The code between the curly braces will “only” show up on the slides listed in the pointed braces. The result of this code is shown in the following gif:

## Wrap Up

I know that creating a MOSFET in TikZ is a bit specific. Still, I hope that this little tutorial gives everyone a feel for how to take make nice scale-able images in LaTeX using TikZ.

## LaTeX: Drawing MOSFET in TikZ

I’m a big fan of using LaTeX for my scientific writing.  (What is LaTeX? It is a typesetting programming language that gives you much more flexibility than other writing environments.  wikipedia)  Since I have some time on my hands, I wanted to prepare for future presentations by writing up some notes and slides using in LaTeX for future use.  This includes drawing diagrams using TikZ.  This post describes how to draw a simple, generalized MOSFET in TikZ while standardizing some of the layer notation.

## Setting up the Beamer environment

Before we get started with our drawing, let’s first set up a simple LaTeX environment.  Let’s say we want to make some slides for a lecture.  We can use the Beamer class in LaTeX to make these slides.  We tell LaTeX what we what to do.

\documentclass{beamer}

\begin{document}

\end{document}


Now, we add some title information into the preamble of the code, and we tell the document to produce a title slide.

\documentclass{beamer}

\title{Dr. Honeycutt's \LaTeX Surface Science and Electronics}
\author{Wesley T. Honeycutt}
\date{\today}

\begin{document}

\frame{\titlepage}

\end{document}


The “\frame” command tells the LaTeX compiler to produce a single slide with the content in the curly braces. For our title slide, we want the content to be the information title information we included in the preamble. After compiling, it should look like this:

If you want to make your slides look fancy, there are plenty of things you can do. For this demonstration, we are only need a simple framework for the TikZ drawing, so we will just leave it at the default.

## Drawing the MOSFET in TikZ

Now we are going to make a new slide with our drawing. We tell LaTeX that we will be using TikZ in the preamble. Then, we start a new slide (“\frame”) and begin our drawing. If you don’t know what a MOSFET is, or you just need a bit of a refresher, check out this for reference. Here is what my code looks like:

\documentclass{beamer}

\usepackage{tikz}

\title{\LaTeX~Surface Science and Electronics}
\author{Wesley T. Honeycutt}
\date{\today}

\begin{document}

\frame{\titlepage}

\frame{\frametitle{MOSFET}
% General n-type mosfet
\begin{tikzpicture}
\draw (0,.25) -- (0,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3) -- (11,3) -- (11,.25) -- (0,.25);
\draw (0,0) rectangle (11,.25);
\draw (4,3) rectangle (7,4);
\draw (4,4) rectangle (7,4.5);
\draw (4.25,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3);
\draw (10,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3);
\draw (1.25,3) rectangle (3,3.5);
\draw (8,3) rectangle (9.75,3.5);
\end{tikzpicture}
}

\end{document}


In the preamble, I have told LaTeX I will be using the TikZ package. After the title slide, I added a new “\frame” and gave it a “\frametitle”. Note how the curly brace of the “\frame” does not close until line 25. In this “\frame” I have started a tikzpicture environment. This tells LaTeX that it should start using the TikZ code in this section. I have two types of drawings here. The first are simple rectangles. These rectangles are bounded by the opposing corners in (x,y) coordinates. The default units here are cm. The second type of drawing is a complex line shape. The code tells TikZ that I want a line “–” drawn from one (x,y) coordinate to a second coordinate. Multiples of these lines can be drawn in a single line. I have drawn curved lines with a different notation. I tell TikZ to draw from the first (x,y) coordinate “to [out=a,in=b]” where “a” and “b” are angles. This creates a curved line which connects to the previous and next segment at the defined angles. There are many ways to draw curves in TikZ, but for simple figures such as depicted here, this approach is sufficient. Finally, note how each line of the “tikzpicture” code is ended by a semicolon. This line ending is not something that you normally see in LaTeX, so be sure you don’t forget it.

When I compile my code, the slide with the drawing of the MOSFET in TikZ looks like this:

Now let’s add some color to our image. Using TikZ, adding a color is as easy as mentioning a fill color. But this is a special case. When drawing electronic components at the surface level, there are standard colors used for certain things. The standardized colors make it easy for Engineers to understand how a circuit works at a glance. These colors, from the classic VLSI design program “Magic”, are show in the picture (from Prof. Stine’s guide to Magic) below:

I want to use these colors for all of the drawings in my slides and notes. Therefore, I am going to make a new command for the colors in LaTeX. Additionally, since I expect my drawings to overlap at times, I want to give the colors patterns as well. I add the following code to my preamble:

\newcommand{\metalone}{[pattern= horizontal lines, pattern color=blue]}
\newcommand{\metaltwo}{[pattern= vertical lines, pattern color=purple]}
\newcommand{\poly}{[pattern= grid, pattern color=red]}
\newcommand{\pdiff}{[pattern= north east lines, pattern color=orange]}
\newcommand{\ndiff}{[pattern= north west lines, pattern color=green]}
\newcommand{\pwell}{[pattern= crosshatch dots, pattern color=orange]}
\newcommand{\nwell}{[pattern= crosshatch dots, pattern color=green]}
\newcommand{\oxide}{[pattern = bricks, pattern color = olive]}
\newcommand{\silicon}{[fill = white]}
\newcommand{\metalthree}{[fill = teal]}


In this section, I am defining a new custom command for LaTeX with the command name in the first set of curly braces, and the action to be performed in the second set of curly braces. The actions include a pattern and a pattern color in a format acceptable to TikZ notation. All I have to do is include the command in my drawing for the color and pattern to apply. If I decide to change a color later on (maybe metalthree needs to be pink instead of teal), all I have to do is change the command in one location and every instance of the command in the code is changed.

Additionally, since we decided to use patterns with the color fill commands, we need to add a line in the preamble declaring that we are going to use patterns. This is the case for all optional TikZ libraries we use in the future.

When we take a look at the complete code for the MOSFET in TikZ slide, it should look like this:

\documentclass{beamer}

\usepackage{tikz}
\usetikzlibrary{patterns}

\title{\LaTeX~Surface Science and Electronics}
\author{Wesley T. Honeycutt}
\date{\today}

\newcommand{\metalone}{[pattern= horizontal lines, pattern color=blue]}
\newcommand{\metaltwo}{[pattern= vertical lines, pattern color=purple]}
\newcommand{\poly}{[pattern= grid, pattern color=red]}
\newcommand{\pdiff}{[pattern= north east lines, pattern color=orange]}
\newcommand{\ndiff}{[pattern= north west lines, pattern color=green]}
\newcommand{\pwell}{[pattern= crosshatch dots, pattern color=orange]}
\newcommand{\nwell}{[pattern= crosshatch dots, pattern color=green]}
\newcommand{\oxide}{[pattern = bricks, pattern color = olive]}
\newcommand{\silicon}{[fill = white]}
\newcommand{\metalthree}{[fill = teal]}

\begin{document}

\frame{\titlepage}

\frame{\frametitle{MOSFET}
% General n-type mosfet
\begin{tikzpicture}
\draw \pdiff (0,.25) -- (0,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3) -- (11,3) -- (11,.25) -- (0,.25);
\draw \metalthree (0,0) rectangle (11,.25);
\draw \oxide (4,3) rectangle (7,4);
\draw \metalone (4,4) rectangle (7,4.5);
\draw \ndiff (4.25,3) -- (1,3) -- (1,2.5) to [out=270,in=180] (1.5,2) -- (3.75,2) to [out=0,in=270] (4.25,2.5) -- (4.25,3);
\draw \ndiff (10,3) -- (6.75,3) -- (6.75,2.5) to [out=270,in=180] (7.25,2) -- (9.5,2) to [out=0,in=270] (10,2.5) -- (10,3);
\draw \metalone (1.25,3) rectangle (3,3.5);
\draw \metalone (8,3) rectangle (9.75,3.5);
\end{tikzpicture}
}

\end{document}


Compiling this code will give us this as our second slide:

## Acetone Melted Goggles

I remember back in undergrad when I had a small safety incident in one of my labs.  We were doing an extraction of . . . something or other.  Part of the experiment involved an extraction using a cooled Rotovap extraction.  This particular extraction needed a very cold trap.  We were using dry ice in an acetone bath (-78℃/-108℉).  As I was putting in a block of dry ice into the acetone, the warm (relatively speak) acetone flash sublimated the dry ice.  This  sudden expulsion of nitrogen gas splashed the acetone out of the container and all over me.  Thankfully, I was wearing my safety goggles.  The acetone splash dissolved the plastic of the clear shield on the goggles and permanently ruined it.  Thus, I now have a set of acetone melted goggles.

My acetone melted goggles are actually a handy little accessory to have on hand.  I always take it to the first day of any lab section I teach.  When I give the requisite lecture about appropriate lab behavior, I like to pass these around.  Even if the students are fresh and don’t know about acetone on plastic or sublimation, they will recognize that goggles saved my eyes.  Hopefully the point sticks a bit better with them, and they understand the importance of safety in the chemistry lab.

## Blue Canola Oil or Dye Another Day

Did you know that if things go just wrong enough, you can create blue canola oil?  I didn’t either until the other day when I decided to make some fries to go with some burgers I made.

### Hungry Yet?

It was going to be a delicious meal.  Some big Idaho potatoes were into thick fries (the best kind when you make them at home).  I was making sliders with ground beef and just a little bit of sausage.  I had fresh buns, salad greens, Vidalia onions, and spicy mustard all ready to go.  The fries were timed just right with the patties so that everything would be ready to go at the exact same time.  It was going to be perfect.  I grabbed a metal colander to scoop out the fries (I couldn’t find a slotted spatula), dipped it in to grab my deep fried potato prize, but suddenly my cooking oil turned a bright turquoise.

I scooped out the fries and laid them to cool on a paper plate.  The color change had gotten to the fries.  They were contaminated.  I wasn’t sure what caused this horrific turn of events, but something told me that these were inedible.

Unless it comes with the suffix -berry, I’m hesitant to trust blue food.

I was stymied.  What could create blue canola oil?  I knew it had to be linked to the metal strainer, but how?  I always thought the strainer was steel, had it magically turned into copper?  Even if it did have copper in it, how did that suddenly dissolve into canola oil?

And then the solution hit me:

### Keyboards!

Remember a few posts ago when I was going over my Model M mods?  You know, this one.  Remember how I dyed my keycaps blue?  Yeah…. about that…

It seems that I somehow mixed in my crafting colander with my food-safe cookware.  The iDye Poly I used for that project was formulated to dye polymers.  Most polymers a craft oriented person would want to color are hydrophobic in nature.  It follows that a very hydrophobic liquid (canola oil) would dissolve the dye quite readily.

Since this little event, I have separated my metal strainers in a more obvious manner.  Accidentally using lab ware for human consumption is no joke.  Now the real question: what do I do with all this blue canola oil?

## Fountain Pen Ink pH – A Comparison of Five Commercial Inks

A while back, there was some discussion about fountain pen ink pH.  During that discussion, I offered to test inks and my friend from the Geekhack forum, CPTBadass, offered to donate some samples for my tests.  I received samples from my good CPT in the mail, and I went about running tests.  This post is the outcome of that work.

## The Samples

Four samples were procured from CPTBadass and one was supplied by the author.

Noodler’s Baystate Blue – a vibrant royal blue ink
Rohrer & Klingner Scabiosa – an iron gall ink
Noodler’s North African Violet – an intense violet ink
Diamine Soft Mint – an ink that appeared turquoise or aqua in the bulk solution
Noodler’s Polar Brown – a somewhat rust tinged brown ink

Upon receipt, the samples were transferred to 20mL plastic scintillation vials.  The original containers’ opening was too small to accomodate the probe used in the pH experiments.

## 1. Shake Tests

### Method

Samples in scintillation vials were given a quick shake and observed for fluid and surface characteristics.

Results

 Ink Observations Noodler’s Baystate Blue Ink left a thin layer coating the wall that persisted for a long time.  This thin layer did not show any detail of the plastic surface.  It produced bubbles, Rohrer & Klingner Scabiosa Ink left a very thin layer coating the wall that persisted for some time.  The layer highlighted plastic imperfections of the bottle by contrast.  It produced bubbles. Noodler’s North African Violet Ink left a very thin layer coating the wall that persisted for some time.  The layer highlighted some plastic imperfections of the bottle by contrast.  It produced bubbles. Diamine Soft Mint Ink did not coat walls.  Preferred cohesion and formed small islands of liquid on the plastic surface.  It produced NO bubbles. Noodler’s Polar Brown Ink left a very thin layer coating the wall that persisted for a long time.  The layer highlighted plastic imperfections of the bottle by contrast.  It produced many/large bubbles.  Bubbles appeared to grow over time.

Discussion

The surface coating indicates that there was interaction with the walls of the container.  Since the plastic was either polyethylene or polypropylene, we expect the walls to be hydrophobic.  The inks which wetted the surface well interacted with the plastic surface.  Since bubbles were formed, we can assume that the interaction with the wall was due to surfactant in the ink reducing the surface energy allowing this prolonged contact.  The lack of coating in the Diamine sample suggests that it is highly hydrophilic.  The lack of bubbles suggests that no surfactant was added to the ink during manufacturing.

## 2. pH Test

### Method

Samples were tested for hydrogen ion concentration using a Vernier pH probe connected to a computer running the logging software.  The probe was calibrated immediately before the experiment with a pH 4.00 buffer standard (Fisher – methyl alcohol, formaldehyde, and potassium hydrogen phthalate) and a pH 10.00 buffer standard (Fisher – disodium EDTA dihydrate, potassium carbonate, potassium borate, potassium hydroxide).  The lab temperature was 25C, and the standard pH did not need adjusted from the label value based on this temperature.

Results

 Ink pH Noodler’s Baystate Blue 3.97 Rohrer & Klingner Scabiosa 2.33* Noodler’s North African Violet 4.60 Diamine Soft Mint 4.00 Noodler’s Polar Brown 8.78

### Discussion

The majority of the inks were slightly acidic in nature, and the Polar Brown ink was slightly basic.  The iron gall based ink was quite acidic.  This ink pH is marked with an asterisk(*) since the pH was not stable.  The value continually drifted downward, trending toward acidity.  The value used here was the observed pH value after 15 minutes of attempted stabilization.  After the experiments were complete, the pH probe was observed to be slightly discolored.  To determine how this effected the results, the standards were measured with the discolored probe.  The 4.00 buffer measured 3.74, and the 10.00 buffer measured 9.88.  This indicates that the results are probably skewed downward by ~0.25 pH units.  The results were not corrected for this error, since it would be difficult to quantify the error without much experimentation.  The probe was cleaned by soaking in 2% nitric acid for 30 minutes.  After this time, the probe was deemed ‘clean’ and returned to storage.

The results of this experiment should clear up a few misconceptions.  Notably, none of the inks in this less than comprehensive test were pH neutral.  Some sources discussed previously make claims based on the acid or base nature of inks based on brand.  Clearly, this is not a wise assessment.  The brand with three different inks in the test (Noodler’s) showed a wide range of pH values.  Some outside sources suggest that acidic inks may damage pens.  Most of the inks tested were acidic.  No metal based tests were performed in this experiment, but this author believes that the correlation between metal pitting and acid content of an ink may be spurious.

## 3. Solvent Tests

### Method

In this test, a small quantity of ink was deposited onto a strip of printer paper (Staples Brand) and partially submerged in solvent.  The ink was applied to the paper by smearing one or two drops from a disposable plastic pipette on the paper.  All labels on the samples were written in pencil.  The ink was allowed to dry then tested.  Most strips were folded so they would stand and set in a petri dish with the testing solution for five minutes. These tests were broken up into aqueous, organic, and chlorinated solvent groups to prevent unwanted reactions.

The wet papers were then taped to a rail in the hood to dry.

One strip was tested under a 18.4 W long wave UV lamp for one hour.  One strip was left as a control.

Results

#### Control

The numbers represent the inks Noodler’s Baystate Blue, Rohrer & Klingner Scabiosa, Noodler’s North African Violet, Diamine Soft Mint, and Noodler’s Polar Brown respectively.  The inks were not applied evenly, and some spreading, especially in samples 3-5 was due to large drops.  The Polar Brown ink naturally feathers a great deal on this paper, and the Scabiosa and North African Violet inks showed some feathering.  The Soft Mint ink naturally spread, but did not show feathering.

#### Water

 1 2 3 4 5 minimal feathering feathering feathering spread and loss No Change (NC)

#### Ethanol

 1 2 3 4 5 upward drift some upward spread upward drift upward drift edge reddening

#### Acetone

 1 2 3 4 5 some spread NC feathering upward drift NC

#### Isopropanol

 1 2 3 4 5 upward drift some feathering some feathering/drift some drift NC

#### Toluene

 1 2 3 4 5 upward drift NC minor drift NC edge reddening

#### Nitric Acid (~4%)

 1 2 3 4 5 gone, yellow edge almost gone, blue edge almost gone, green edge gone NC

#### Hydrochloric Acid (~4%)

 1 2 3 4 5 gone, yellow edge almost gone, blue edge almost gone, green edge gone/upward drift edge reddening

#### Dichloromethane

 1 2 3 4 5 upward drift feathering upward drift/feathering minor upward drift yellow color separation

#### UV Exposure

 1 2 3 4 5 NC NC NC NC NC

Discussion

There is a great deal of information to be learned from these tests.  What we are looking at is actually a very rudimentary form of thin layer chromotography.  The paper acts as a stationary phase and the solvent as a mobile phase.  The mobile phase moves our eluent along the capillaries within the paper fiber matrix.  If we let this go for a long time, we would see the individual components separate from each other.  There are better methods to perform that experiment though, and it was not in the scope of this one.  The goal of the test was to determine the stability of the ink when in contact with the solvents.  In doing this, we can learn something about the character of the ink.

Different solvents have different polarities.  The polarity of a molecule being the concentration of electrons on one side of an atom and exposed protons on the other side.  We can relate these by a polarity index.  Since “like dissolves like” if something is moved or dissolved by more polar solvents, then the material must be polar.  So we can see that the Diamine ink is more polar than the quite nonpolar Baystate Blue based on what different solvents do to it.

The Polar Brown ink interestingly slightly drifts in both polar and nonpolar solvents.  If you look closely (probably not visible in pictures), you can see a yellow component separate out in nonpolar solvents and a red component separate out in polar solvents.  These colors moving out of the bulk drop only slightly affect a color change in the brown.

I chose the two acids to test here on purpose.  We would expect the HCl to react mostly as an acid, whereas the HNO3 would react as both an acid and a strong oxidizer.  Since both of the acids had similar effects on the inks, we can see that none of the inks oxidize easily – which speaks well for the permanence of these inks.

Future tests would include solvents with polarity index of 0.

The lack of change due to UV light is good, though this author would like to point out that this was not a very strong source.  Future tests should attempt to use more powerful sources such as a laser.

## A. Errata

All solvents were obtained from Pharmaco Aaper with purity >99.5% except the nitric acid, which was obtained from Fisher.

All water used in the experiments was reagent grade, purified by reverse osmosis to resistance of >18Mohms.

I would like to thank CPTBadass again for his donations and my advisor for being out of town this week so I could do silly experiments like this without getting yelled at.

## SEM of Uranium Adsorption Sites

Before my dissertation project got underway, I was working on a project describing the kinetics of adsorption of uranyl ions onto a metal oxide thin film.  The thin film was impregnated onto pellets of silica and alumina, then I would submerge the pellets in a solution of uranium nitrate in water.  After being submerged for a while, the white pellets would come out with intense yellow-green coloration, as seen in the picture below:

There is a lot of interesting stuff happening with the kinetics there as you adjust things like ion concentration, pH, mixing speed, etc.  We think that there is an ion exchange happening at the surface sites, but the kinetics get complicated.  There are clearly some Langmuir adsorption effects going on. But that isn’t what I want to show you today.  During my time doing my PhD, I was fortunate enough to get into a course on microscopy which was offered by the veterinary biology school.  When we weren’t busy looking at mouse blood and sickly tree leaves (those pics will come later), we had an opportunity to bring in our own samples to explore.  I decided I wanted to take a look at one of these pellets.  We mounted a sample onto a platen, coated it with some carbon, and took a gander at it through the scanning electron microscope.

Now here is the fun part.  This wasn’t your grandma’s SEM.  This one was equipped with an optional x-ray spectrometer for elemental analysis.  To generate an SEM image, we fire electrons at a surface and analyze the backscattered electrons and secondary electrons.  Not all of the electrons that hit the target generate the backscattering we need to ‘see’ a sample. Some of them wiggle and release the energy from the absorbed electron as a photon.  This means that while we are blasting the surface in the picture above we can analyze the photons that come off.  X-ray photons from atoms have particular binding energies which allow us to identify what is present in the sample.  In the sample I’m looking at, I can run a check and make a pretty graph of what is detected:

## Elemental Analysis of the Thin Film under the SEM

The instrument we use to check the elements in the sample come up on the plot as a color.  Since the instrument also saves each pass, I can look at them as overlays on the original SEM image.  I can see what goes where:

That’s neat and all, but so what?  Well that is best part.  Did you notice how some of the colors in the animation above sort of glomp together?  I did. There is some significance to that grouping.  If we combine the overlays for the calcium and [metal X] onto one image, we see that these pair together nicely. This is because of the thin film we use: CaXOy.  The calcium starts out bonded to the XOy complex.  In the ion exchange mechanism, which is proposed as the primary mechanism for action in this system, the uranium/uranyl comes along and knocks off the calcium and takes over that spot.  When we see [metal X] and calcium together, we know that these are unreacted sites.  If we combine the overlays for both uranium peaks and the oxygen peak, these materials match up.  This suggests something important:

Uranium is adsorbing as the uranyl (UO_4) species, not the bare atom.

Now if we compare these two images side by side, we see that there are areas which are distinctly different.

In the bright blue spots in the left image, there is little to no oxygen showing up on the right image.  This means that all of the oxygen in our metal oxide thin film as well as the oxygen in the structure of the alumina is sufficiently buried so that we can’t see it on the surface.  This also means that there is something about those locations that makes the uranyl not ‘want’ to bind there.  What is it about those sites?  I’ve included the original image here too so you can compare.  You can actually see that the blank areas have distinct features, even if it isn’t high enough resolution to make out the exact shape of those features.   There is clearly a preference for binding sites in this material.  This has ramifications for the kinetics experiments I was running a on the material.  If we classify sites that uranyl ‘wants’ to bind to as SITE1 and sites that uranyl doesn’t ‘want’ to bind to as SITE2, we can think about it like this:  The kinetics of adsorption would have a single mathematical model to describe how fast it adsorbs at SITE1, and it would likely have a distinct mathematical model to describe SITE2 locations.  But when all of the SITE1 locations run out, and the remaining uranyl is forced to bind at SITE2 locations, is there a smooth transition?  Is there some energy barrier separating these that we would see as a hiccup on the uptake curve?  There are some anomalies on the curves that still need explained.  Could this be the answer?

Unfortunately, I didn’t have the time or funding to answer those questions when I got these data.  I presented my findings on the uranium uptake at two ACS meetings already(cited below), and I needed to move on to bigger projects.  So all I can do for now is to communicate to you, humble reader, how interesting this finding is.  These data may be published in the future when we finalize the uranium adsorption project into a paper, but until then I will leave this up for you to enjoy.

## References

1. Honeycutt, W. T., Hamby, H., Apblett, A. & Materer, N. F. Uptake kinetics of heavy metals from water using a high surface area supported inorganic metal oxide. in Abstracts of Papers, 247th ACS National Meeting & Exposition, Dallas, TX, United States, March 16-20, 2014 ENVR-272 (American Chemical Society, 2014).
2. Honeycutt, W. T., Kadossov, E. B., Apblett, A. W. & Materer, N. F. Selectivity and kinetic behavior of heavy metal and radionuclides on supported ion-exchange adsorbant. in Abstracts of Papers, 249th ACS National Meeting & Exposition, Denver, CO, United States, March 22-26, 2015 I+EC-44 (American Chemical Society, 2015).

## UHV Electron Beam Fluorescence of UOx

Let’s get this thing started. This is a new blog which will be used to act as a frontpage for my projects. Since I have a few years of interesting stuff worth posting, I’m going to post old things every week. Each of these posts will be categorized as “backlog” and will be dated if possible.

I will start this with a gif I found from one of my old experiments.

This video was taken using my cellphone of a sample inside our UHV-XPS.  What you are looking for is in the center of the image.  There is a dark square which has some glowing spots.  The dark square is uranium oxide powder which is held to the sample holder by an advanced fixative (double-sided scotch tape).  In this image, we are not running the x-ray source.  Instead, we are blasting the surface with electrons to clean it off for the analysis.  In this process, a beam of electrons are shot at the sample, and the energy imparted will remove any adsorbed contaminants one layer at a time.  When we shoot these electrons at uranium oxide, there is a luminescent phenomenon.  The incident electron knocks around the electrons of the molecule and  the molecule wiggles away the energy by ejecting a photon.  This one happens to have a pretty green glow, which unfortunately doesn’t come across in the gif.

Another interesting part of this is the way the glowing portion seems to go from one blob, to two blobs, then back again to one blob, and so on.  This appearance is due to the shutter speed of the camera.  The electron gun is programmed to raster the beam across an area.  Imagine rastering an area similar to mowing a lawn.  You push the mower back and forth in lines to cover the area of the lawn.  Our electron beam is sweeping across the uranium oxide like a high voltage power-washer.  It just so happens that the zig-zag of this sweeping pattern syncs up with the shutter speed of the camera in such a way as to make it appear like there are little dancing blobs.  Pretty neat!