I have envisioned this site as an electronic version of my CV. For those that would prefer to download a pdf copy of my CV, please click here.
I am an experimentalist who has tinkered with a great number of disciplines. I have experience in the following areas.
I have been given the honor of receiving several grants to help in my research. I would like to acknowledge and thank the following agencies.
Addgene, Cambridge, MA.I have been very fortunate to be able to participate in several fellowship programs at UNM. Most of my funding has come from the IGERT program which is an amazing NSF funded interdisciplinary program. Through my participation, I have been able to broaden my scientific knowledge in optics, biology, and even nanotechnology. I was also the recipient of a small grant from Emcore which is a fiber optics and photovoltaics company based in Albuquerque NM.
The University of New Mexico, Albuquerque, NMTeaching can be one of the most difficult challenges that anyone can attempt. It requires a certain skill, art form, attention to detail, and willingness to listen to a novice that can be near impossible to master with every student. "Teaching" can, however, be easily achieved if all the teacher wants to do is impress upon the student and have them regurgitate factual knowledge without any learning on the student's part.
These polar opposite concepts to teaching; attention to the individual and factual, regurgitant knowledge, are not mutually exclusive. To be a good teacher, you need to be able to teach someone the facts about things. On the other hand, you need to be tuned to the student in order to observe if they are either "getting it" or not. So, the teacher must be able to present boring concepts at the same time, they are listening to how the students respond to the new concepts. This can be difficult as every student is different and everyone requires different levels of attention for them to understand things. Presenting material and adjusting the presentation dependent on how the students respond can be especially difficult with typical college classroom sizes of over a hundred students.
I have had the pleasure of teaching small classrooms of students in a lecture format and individuals in a research environment format. I have also taught a limited number of lectures were there were a large number of students. When teaching the larger classes, it became essential for me to use active electronic feedback in order to assess if the class was understanding the concepts being taught. I am a big proponent for using social media, MediaWikis, and in class feedback technologies to help aid the instructor in understanding if what is being taught, is being comprehended.
When teaching small classrooms and individuals, I always actively adjust how I am presenting the material to the students by watching their reactions. If something is not understood, I immediately try to explain a concept in a different manner and gauge how the new explanation is working or not. This type of instruction is great for small classrooms and individuals and is my preferred way of teaching. However, I do understand that this way of teaching is not always viable and it is always the job of the teacher to change how they teach in order to accommodate the number of students being taught.
I feel that the most important thing about teaching is to never forget what it is like to be a student.
Below are the publications I have contributed to.
As an open notebook scientist, I have decided to make my entire dissertation open and freely available to the public. I feel that none of the information or data I have taken belongs to me. It doesn't belong just to the scientific community either. It belongs to the entire global community. Anyone can use the data and any portion of my dissertation, freely. I strongly feel that progress is dictated by communication and, if we want progress to succeed, we all must be willing to freely communicate.
Being an open scientist is my choice since it is available to me. I do understand that in many cases, complete disclosure of projects may not be in the best interest of a company or a lab. Trade secrets and security should be a top consideration before anyone decides to take the leap into open science. And, as always, communication about doing open science should always be done with your superiors or PI before launching into it.
Since this is my dissertation, it is a work in progress. I will post links to new chapters as I complete them. The main theme to my dissertation is to investigate the interactions of kinesin and microtubules via the gliding motility assay by varying surface passivation, water isotopes, and osmotic stresses.
Today I read more about roughness and started a LaTeX document with my re-derivation of Hamaker’s constant. I also got a nice paper discussing theoretical models of adhesion using different roughness models.
I am still working on the complete derivation and once I am finished, I will post it in my notebook.
I spoke with Oli today about some high speed imaging techniques and experiments to do. I am engineering a chamber for the inhalers now.
I still have not gotten the sputter coater working. I am going to try vacuum greasing the chamber a lot and see if that does anything.
I was able to contact an engineer at nanoTherics today. Hopefully we can figure out what is wrong with our device. So far, my interactions with them indicate that they are an awesome company and anyone reading this should buy stuff from them.
Damian and I tried even more things. Including removing and cleaning all connections to the chamber. Nothing worked. We even globed on a bunch of vacuum grease every where to see if there were inadvertent leaks. Again, nothing worked.
Sarah and I completed the power supply modifications today. This is good news as we can now start looking at the accelerometer for the pendulum
Tommy needed a stirrer for magnetic nanoparticles. So, I ripped apart a hand drill that functioned off of a 6V battery pack. Unfortunately, the battery pack was dead and the charger didn’t work. So, I swapped out the battery pack for a 6V wall wart with not a lot of current. This is fine as the stirring doesn’t need to be fast. By removing the battery pack, the ability to change the speed went away. I’m guessing that there is some way to reinstate this. In the mean time, sorry Hugh for ripping apart your old hand drill. I will fix it when it is no longer needed. The stir bar is a glass pipet that was cleaved and the paddle is a microscope slide that is epoxied to the pipet. No metal!
The sputter coater has 2 valves that control the exhaust (for when you want the chamber to return to atmospheric pressure) and the other for filling the chamber with the gas of your choice. In order to determine if the release valve is the culprit for our leak, I did the following things.
Neither of these things worked. Rather than try to fuss with the valves, I am going to remove all connections to the chamber and try to find a way to test pressure inline with the vacuum pump. Perhaps the actual chamber is the problem.
If the chamber isn’t the problem, then it may be the pressure gauge. That, I can’t fix and will be an absolute bear if we need to replace it since the machine is out of production.
Continuing with my other interests in roughness, I obtained the original Hamaker publication which talks about the aptly “Hamaker coefficient” that I have been reading about. I plan to rederive the coefficient for two spherical bodies as it should be interesting.
I have been able to read Hamaker’s original article
Hamaker HC (1937) The London-van der Waals attraction between spherical particles. Physica 4:1058–1072. http://dx.doi.org/10.1016/S0031-8914(37)80203-7.
and I have worked through his calculations. I am getting a sign error for some reason and will have to investigate that later. In the very least, it feels good to do some math and flex my integrating muscles. I’ll post my calculations in a later post.
The sputter coater is down due to the device’s inability to pump the sample chamber to the required pressures to sputter. Damian and I have tried the following things to try and fix it.
Unfortunately, neither of those fixed the problem. I just now switched out the pump with a different one and the same problem is occurring. My next steps are:
Changing the hose material did nothing for the pumping. Actually, it made it worse so it is most definitely not the hose, nor is it the pump. This leaves the following connections that need to be checked:
Drat…a lack of Teflon tape is preventing me from looking at the rest of the valves.
Another project that is related to fixing the sputter coater is to investigate roughness. I feel like I am spinning my wheels on this one a good amount as the paper I am reviewing:
is not easy to follow as there seem to be missing steps with the RMS roughness calculations. Especially since I feel like equation 4 is coming out of left field with its coefficients. Of course, this is probably because I don’t know the field well enough…I am currently investigating other references but I am finding it difficult to find articles.
Citation style language (CSL) is an XML format that allows for easy mark-up of citations. This is great as tons of popular reference managers use it. My manager of choice is Mendeley as I particularly like the ability to share references within groups and, I can get my papers on all my devices. Plus Mr. Gunn (of Mendeley) is a super badass genius and why wouldn’t you want to use something that Mr. Gunn recommends?
I particularly like the PLoS citation format as it is clean looking and, presents all the relevant information that a person would need in order to find the article being referenced.
1. Maloney A, Herskowitz LJ, Koch SJ (2011) Effects of surface passivation on gliding motility assays. PloS one 6: e19522. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3108588&tool=pmcentrez&rendertype=abstract. Accessed 23 July 2011.
It shows:
I’m not too keen having the Available:… tag as it doesn’t give relevant information for locating an article. This stems from my belief that URLs are not forever and neither are websites. Remember Geocities? What I do want to have is the DOI in place of the Available:… since DOIs have been deemed forever static as issued forth from the electronic scribes in the cloud. At least I hope so.
In order to ensure that I don’t have the Available: section in my citation and I do have the DOI, I had to change the CSL file to do what I wanted. First, I had to find where Mendeley stored the CSL files on my computer. Since I’m using a Mac, I found they needed to be stored in:
~/Library/Application Support/Mendeley Desktop/citationStyles-1.0/
Which are my user specified csl files. I downloaded a copy of the plos.csl file from here and copied it into the above folder. I then made a copy of the plos.csl file and opened it up with my text editor and started modifying it. The beginning of the file has the info tag which houses the title of the file and the author etc.
<info> <title>Public Library of Science (PLoS)</title> <id>http://www.zotero.org/styles/plos</id> <link href="http://www.zotero.org/styles/plos" rel="self"/> <author> <name>Julian Onions</name> <email>julian.onions@gmail.com</email> </author> <category citation-format="numeric"/> <category field="science"/> <updated>2011-12-23T01:16:03+00:00</updated> <summary>Public Library of Science Journal style.</summary> <link href="http://journals.plos.org/plosbiology/guidelines.php" rel="documentation"/> <rights>This work is licensed under a Creative Commons Attribution-Share Alike 3.0 License: http://creativecommons.org/licenses/by-sa/3.0/</rights> </info>
I didn’t need all this so I shortened it to the following. This is purely aesthetic but, doing so helped me figure out how to read the code and what the tags meant. I changed the info tag to be:
<info> <title>custom</title> <id>http://www.zotero.org/styles/custom</id> <category citation-format="numeric"/> <category field="science"/> <summary>doi, bolded journal, italics title</summary> </info>
Note that I left the id tag alone. Turns out that if you get rid of it, then your word processor freaks out and says that the citation style is not available at this time. So, leave it in there and just change the URL to indicate that it is a custom style. Doesn’t seem to matter what goes there, as long as it points to the zotero styles.
The next chunks of code are the “macro” chunks. These are “functions” if you will that are reusable bits of code that you can call in the “bibliography” block. The macro blocks in the PLoS CSL are the following:
In the access macro, the XML looks like this:
<macro name="access"> <group> <choose> <if variable="URL"> <text variable="URL" prefix="Available:" suffix="."/> <group prefix=" " suffix="."> <text term="accessed" text-case="capitalize-first" suffix=" "/> <date variable="accessed"> <date-part name="day" suffix=" "/> <date-part name="month" suffix=" "/> <date-part name="year"/> </date> </group> </if> <else> <text variable="DOI" prefix="doi:"/> </else> </choose> </group> </macro>
In this block of code, there are two variables used, the URL and the DOI. Initially I just nixed the entire block for the URL in order to get the citations to have just the DOIs in them. However, this is not entirely advantageous as sometimes I will want the URL because I do not have a DOI. It turns out that just reordering the variables so that the DOI comes in the if statement instead of the else statement will fix this problem.
<macro name="access"> <group> <choose> <if variable="DOI"> <text variable="DOI" prefix="http://dx.doi.org/"/> </if> <else variable="URL"> <text variable="URL" prefix="Available:" suffix="."/> <group prefix=" " suffix="."> <text term="accessed" text-case="capitalize-first" suffix=" "/> <date variable="accessed"> <date-part name="day" suffix=" "/> <date-part name="month" suffix=" "/> <date-part name="year"/> </date> </group> </else> </choose> </group> </macro>
Now my citations look like:
1. Maloney A, Herskowitz LJ, Koch SJ (2011) Effects of surface passivation on gliding motility assays. PloS one 6: e19522. http://dx.doi.org/10.1371/journal.pone.0019522.
Notice that I replaced the “doi: ” with “http://dx.doi.org/” in order to get a URL. Unfortunately, I have not figured out how to make it into a link yet.
The next thing I wanted was to get rid of the space between the “volume: pages”. This is changed way down in line 140 of the plos.csl file. Before I show what I changed, it is important to understand a bit about the code. In this section, I’m in the actual bibliography section that will format the citation in the way that I want. Within the bibliography section is a layout tag. This is just a tag that indicates the layout of the citation. In other words, this is the way the citation will look. The flow of the code is as follows:
In this else statement, there is a text tag for the variable “page”. Getting rid of the space in the prefix attribute fixes the space problem.
<choose> ... <else> <group delimiter=" " prefix=". "> <text variable="container-title" form="short" strip-periods="true" font-weight="bold"/> <text variable="volume"/> </group> <text variable="page" prefix=":"/> </else> </choose>
So I also decided to make the journal name bold. Hence the font-weight attribute above. I also decided to make the article title italics so back up in the first group section of the bibliography, I attached a font-type attribute. Now my citations look like the following.
1. Maloney A, Herskowitz LJ, Koch SJ (2011) Effects of surface passivation on gliding motility assays. PloS one 6:e19522. http://dx.doi.org/10.1371/journal.pone.0019522.
The only thing I can’t seem to do is actually make the doi a real link so I have to go through the bibliography to make them ones. Oh well…
The following review is my own interpretation of the linked-to article. Please do not use my review as a complete reference for the article as I will most likely skip important information that you feel is relevant. If I do miss something, please feel free to comment about it in the comments section below. Please read the article before reading my review and remember, this is my notebook, which means these are my notes on the article and they will more-than-likely hold no relevance to you or your research.
In this paper, the authors did both experiments and calculations on biofilms. They used an interesting device called a Biofilm Airlift Suspension device which, is used to study wastewater treatment.
I think the take-home from this paper is that they were able to model biofilms. This was definitely a review paper even though it didn’t state that it was. The important things I learned were:
Also, I completely agree with the author’s desire to get more experimental data in their closing remarks. Actually, everything they suggested are questions that I have about biofilms and I need to search for every term above.
The following review is my own interpretation of the linked-to article. Please do not use my review as a complete reference for the article as I will most likely skip important information that you feel is relevant. If I do miss something, please feel free to comment about it in the comments section below. Please read the article before reading my review and remember, this is my notebook, which means these are my notes on the article and they will more-than-likely hold no relevance to you or your research.
I decided to ask the question; what is a biofilm? Usually, I would start with a review on the subject to try and answer this question and this is exactly what I decided to do. Again, as usual, I “picked” the first review article I found from a Google Scholar Search. Too bad the article isn’t OA.
So, the second half of the paper talked about biofilms on implants and cystic fibrosis. There was a ton of stuff in this section that I didn’t quite grasp so I’ll have to revisit it in the future. Overall, this was a good review of what makes biofilms, where they form, and some characteristics of them once they are created.
So, the next step for the pendulum was to try and hold it in one spot and let it go in a reproducible way. To do this, Sarah and I decided to use some 1/4″ Loc-Line coolant tubing. This stuff is great and will become a staple in my tool arsenal from now on. The concept is not new and was repurposed from an Instructables post that I came across a while ago. We purchased ours from McMaster-Carr part number 10095K11. The point of using the Loc-Line tubing is to release the pendulum in a reproducible manner. We want to know what forces the pendulum will hit the target when it is let go at a specified angle and using the tubing is an attempt to reduce error when letting go of the pendulum.
The first thing to do was to modify one of the adapters that came with the package from McMaster-Carr to allow it to be mounted to the Thorlabs breadboard. To do this, I sawed the adapter shown in Figure 1 in half.
| Figure 1: Loc-Line Adapter. In order to attach the Loc-Line coolant system to the breadboard, I had to saw one of the adapters in half. I used the one that a 1/4-20 screw could fit through. |
Figure 1 shows one of the two adapters that came in the package. I sawed it in half and stuck a 1/4-20 through it and mounted it on the breadboard, Figure 2.
Once the Loc-Line Breadboard Adapter is positioned where one wants it, it’s just a matter of sticking the tubing on the adapter. This is no small feat of strength but, it can be done. Figure 3 shows the Loc-Line Pendulum Holder in action. It basically just holds the pendulum up from the bottom. When you want to let it go, you just move the tubing out of the way. This configuration was found to be the most stable.
| Figure 3: Loc-Line Adapter. The Loc-Line pendulum holder in all it’s glory. It works quite well. To release the pendulum, one just moves the Loc-Line system out of the way. |
The magnet holder was another complicated issue that needed addressing. When the pendulum came to the bottom of its swing, it would impact the magnet. The impact of the pendulum on the magnet is not whimpy and would cause the magnet to shatter. This was a problem as I’d like to prevent the device from destroying itself. To prevent this from occurring, a suitable spacer was needed. This came in the form of a hard drive compression gasket seen in Figure 4. Ahh computer junk, the source of so many DIY devices.
| Figure 4: HD gasket.. The wonky looking thing is a hard drive compression gasket used to keep the HD from spinning out of its box. There is a magnet epoxied to the other side. |
Figure 5 shows the pendulum spacer, magnet, and the pendulum together. The spacer prevents the pendulum from coming in contact with the magnet thus preserving it. I’m not sure what the material is of the HD gasket. I think it’s titanium as it is nonferrous and tougher than aluminum.
| Figure 5: Magnet spacer. The pendulum ball fits nicely in the center hole of the HD gasket. The pendulum does not impact the magnet directly thus preventing it from shattering. |
As much fun as it is to get to build something, this bugger is becoming irritating due to the fact that we have been having to epoxy things together. While epoxy is good for somethings, I dislike the stuff and would much rather use mechanical fasteners when ever I have the chance. Glue is good for wood but, not so much so for metal. Que sera…
The point of this device is to be able to measure quantities of chemicals coming off of different chemical substrates. To do this, we have to collect the chemicals being flung off of the substrate. We decided on using scintillation vials as the way to collect materials being de-adhered from a substrate due to the impact of the pendulum. Hmm, I like that sentence. In order to mount the vial in the pendulum, the optics holder was used, see Figure 6.
| Figure 6: 4th iteration. Fourth version of the pendulum. The scintillation vial is being held by the optics holder. It is prevented from moving backwards with the optical posts due to an impact. |
The amount of force being imparted to the scintillation vial is enough to cause the holder’s grip on the vial to slip. This is why a set of optical posts were used to prevent the vial from moving backwards, seen as the metal posts opposite to the pendulum weight. The cap of the vial is attached to the magnet holder which creates a mechanical connection to the vial. Thus, when the pendulum hits the magnet, its impact force will be imparted to the objects of interest attached to the cap.
I’ll show a movie of the pendulum in action once the epoxy on the cap dries. Sarah and I already tried it before the epoxy had time to cure and it just destroyed the epoxy on the cap. So, rather than have to re-epoxy it again, I’m not going to try it now. I’ve done a couple of dry run whacks with the pendulum and a blank cap and so far, it looks great.
I’ll admit that I’m irritated with myself about how long it took to debug this thing. Although, I’m super excited that the problems that did arise were solved easily through communication. Be it with open notebook science, talking with the students in the lab, or Hugh, the pendulum progressed into a solid device in a relatively short period of time. The only two possible kinks left are force calibration and the epoxied cap that holds the substrates.
Still working on debugging the pendulum. Thanks to Hugh for figuring this little quirk out. The bearing that I was using previously was not up to cutting the mustard so, I culled one from a hard drive. The hard drive bearing worked great but, it didn’t fit properly in the Thorlabs holder. Hugh came in this morning and started playing around with the items and figured out that the new bearing I was using could be put in the right angle optical post holder with no problem. Unfortunately, doing so would cause a redesign that wasn’t the quickest thing to do. It did, however, fix a lot of issues and so, it won in the end because I’d rather have something working that can take data than redesigning it to make it keep original aspects. In life, business, and the lab, never get emotionally attached to a design because it’s either what your customer wants, or what makes you get the data that will win.
So, Sarah and I removed epoxy and re-epoxied things back together to incorporate this design shift. See Figure 1 for the new look.
| Figure 1: Pendulum V3.0. This is the third design of the pendulum. It fixes some issues about stability with the bearing. |
It is much more compact and the most important thing, works nicely. The other issue with the pendulum was that the protractor was wonky. Meaning that it did not display angles correctly because of poor mounting. In order to mount the protractor read head properly, Sarah came up with the idea of using a grommet. I had a couple extra grommets lying around at home and brought one in. Thankfully it was a 1/4″ ID grommet that accepted the 6mm shaft properly. We decided to epoxy the grommet into place to prevent any movement of the read head from causing problems with measurements. See Figure 2.
So far, this is robust. The next step is to figure out the whole magnet thing and a better method for placing the pendulum at some height and letting it go. I think better magnets and the coolant hose idea will work.
The bearing I purchased from McMaster-Carr had way too much slack in it. This caused the weight to acquire a tilt to it when it was at rest, see Figure 1.
| Figure 2: Ball bearing slack. The above image shows the slack in the ball bearing that was purchased from McMaster-Carr. The red lines are there to help guide the viewer. |
To alleviate this, I opened up an old hard drive lying around the lab and salvaged the voice-coil hard drive head-reader, see Figure 2.
Of course, the new bearing doesn’t fit into the holder I got for the original bearing. This isn’t a problem as I found a nut that Sarah epoxied onto the bearing. The epoxy takes 3 days to cure so we will know if it will work on Monday. I did use some 5 min epoxy on it to show that it will work. 5 min epoxy is not good enough for the parts unfortunately. The retaining ring is a bit more difficult to get into place but, that will just have to be the way it is.
The next issue is to try and get the pendulum to be held in one place and release without issues. One thing I noticed when both Sarah and I were attempting to release the weight, we both gave it a little upward kick without realizing it. This is an issue that needs to be resolved. In Figure 3, I have setup a simple mockup behind what we would like to do. It doesn’t work that great but it does remove me or another user from giving the weight an upward motion before release.
| Figure 3: Pendulum holder. A simple (and bad) way for holding the pendulum in place. There has to be a better way. |
I have Sarah right now investigating different materials that we could use in order to make a better holder. She is right now looking at different materials we can use that would fit better on the base. Things such as flexible coolant hoses, third hands, etc.