User:Andy Maloney

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About me

I am a member of the Koch lab at the University of New Mexico in the Physics & Astronomy department. Below, in the projects section, you will find links to my public lab notebook and various projects I have done in the lab. The dissertation section is where I am actively writing my dissertation in an open format and I welcome anyone to comment on it. Directly below, you can find links to various other endeavors I have worked on.


Below are the chapters to my open dissertation. This is going to be an experiment where I post all my revisions and my completed dissertation openly so that the public can access it. This experiment is to see if an open dissertation is viable and can be achieved through open discussion on the subjects that I post below.

The whole point of this experiment is to be as transparent as possible, as well as to note that science and scientific discovery is not written in stone. Since the dissertation is in a media wiki format, the documents below can be viewed as a "living" description of the experiments that I have run. With the ever evolving dissertation, it is very important to understand that changes will be made to it. These changes are all documented in the history for each page and can be viewed by anyone. All pages can also be commented on in the associated talk pages for the dissertation. I welcome any and all comments to the talk pages. All relevant suggestions will be taken into consideration and will help to make this dissertation navigable and easy to read.

General discussions about open notebook science or my open dissertation can be done on the associated talk page for this page. Any comments specific to the other chapters to my dissertation can be done on that chapter's talk page. In order to comment, you must become a member of the wiki. If for some reason you do not want to join the wiki in order to post comments, feel free to email me using the link below and specify if you want to remain anonymous or not.

I would like to have the associated talk pages used as resources for anyone that is attempting to write a dissertation as well as a spot where open discussions can occur on my dissertation. Writing a dissertation is not easy and anyone that wishes to give advice or suggestions on the process is encouraged to comment on the talk page. I strongly believe that science progresses in a much more efficient manner when it can be discussed openly. I hope that this first attempt at making the process of writing a dissertation open to everyone can help researchers in the future as well as help new scientists that wish to conduct kinesin and microtubule experiments.

As of right now, the dissertation is not complete. It is in the process of being written. This means that I will be updating it periodically. I will post a link to the pdf version of the dissertation once it has been completely written.

Preface   Here I discuss the tone of my dissertation and how I feel the mentality of preparing experiments should be done.
Chapter 1 - Introduction   This is the introduction to my dissertation. It was suggested by the committee that I include an introduction chapter to the thesis and this is it.
Chapter 2   This page describes how to conduct a gliding motility assay using kinesin and microtubules. It also talks about the equipment, supplies, and chemicals necessary to complete the assay. I also go into some important reasons about why I have designed this experiment in this manner and some of the failures I have faced along the way. This is also my first chapter in my attempt at a completely Open Notebook Science dissertation.
Chapter 3   This page looks at how gliding speeds are affected by different surface passivations. It is the first experiment that I conducted investigating the kinesin and microtubule system. It is also the second chapter to my dissertation.
Chapter 4   Here, I discuss the results of how the kinesin and microtubule system is affected by changing the isotope of water.
Chapter 5   This is the fourth chapter to my thesis. It basically describes what I feel open science is, some success stories, and recent advancements at UNM for doing open science.


Below is a list of projects that I have, or I am actively working on. Each link will ultimately take you to a page where I point out the important characteristics, motivation, and the science being done with each project.

As this is an entirely new endeavor on my part, organization will be somewhat chaotic at first. Most notably my notebook. I will try to link my notebook entries to the below pages and I am currently in the process of doing so. As my knowledge of how to work wikis increase, this page will undoubtedly get better. Until then, please forgive my dust.

Notebook   This is my scientific notebook. This is where I write down any data that I collect, reviews to some papers I have read, and most of all my musings. I will attempt to link all my notebook entries to pages in the below projects. My notebook is somewhat chaotic so if you are looking for something specific, your best bet is to just do a search.
Java   I am going to learn how to use Java and this page will house all of my notebook entries on Java. As well as some insights when I become competent with the language.
Tobacco seeds   This page is about reproducing and extending the classic experiment by Gilbert Lewis with deuterium oxide and tobacco seeds.
Laser diode build   This is a link to an Instructable I made outlining how to build an OEM laser diode system.
Fluorescence Schlieren Microscope   This is a dead project that combines Schlieren imaging with fluorescent imaging. The goal was to look at membrane dynamics in an ultrasonic field.
Optical tweezers   This is an ongoing project where I built my first optical tweezers. It has now past through my hands and into the hands of other students. But, I can't help but feel pleasantly attached to the project.
CV   Here you will find my ever growing CV.
Osmotic stress effects on kinesin and microtubules   This is work showing how kinesin and microtubules are affected by osmotic stressors.
Temperature effects on kinesin velocity   There are a great number of things that can affect how kinesin and microtubules interact with one another. Temperature is one of them.
Engineering   This showcases any pages in my notebook where I talk about engineering hurdles that slow down science. It also houses my notebook entries where I talk about any open science things I find interesting and any new technologies that can be used for open science.
Heavy water storage   This page describes my observations when storing proteins in heavy water.
DNA   There's not much here. Just some musings about DNA unzipping and optical tweezers.
Uploaded files   This page attempts to catalog all the files I've uploaded since OWW does not have the Special:FileLists page.

Notebook entries for papers

Surface passivation study   The entries in this page are listings of my notebook that are related to the surface passivation study using various bovine caseins. The goal of this page is to be able to create a URL that is used as a reference for the paper about this study.