Kenneth Curtis

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Clemson Research Experiences for Undergraduates

Collaborative Data Visualization Applications Summer 2014

Home Institution

The University of Alabama at Birmingham

Clemson Research Mentor

Dr. Andrew Tennyson
Inorganic Chemistry

Clemson Visualization Mentor

Dr. Jill Gemmill
Department of Electrical and Computer Engineering

About Me

  • Interests
    • Computers(Programming)
    • Music
    • Art
    • Traveling
    • Food
    • Fitness
  • Hobbies
    • Programming
    • Learning New Programming Languages
    • Cooking
    • Weight Lifting
    • Gaming
  • Something intersting about meself
    • My siblings and I all have "Marqu" in our names.(Marques, Marquita,Marquez)
  • Computer Science Classes I've Taken
    • Intro to Programming-Java
    • Object Oriented Design-Java
    • Algorithms and Data Structures
    • Automata and Formal Language Theory
    • x86 Assembly
  • Awards/Recognitions
    • Ford Family Foundation Scholarship

My name is Kenneth Marquez Curtis, I am 23 yrs old, and I am from Louisville,MS. I am currently a Senior majoring in Computer Science at The University of Alabama at Birmingham set to gradate in May of 2015. I am very spontaneous and talkative but you might not able to tell at first glance. I am the youngest of 3 children, I have an older brother and an older sister. In my spare time I like spending time with my girlfriend, cooking, working out, as well as an assortment of other activities as mentioned in the list above. I love watching cartoons, my favorite to watch is Tom and Jerry. Aside form cartoons, I also enjoy watching educational programs on channels such as Discovery, History, NatGeo, and the Science channel to name a few. I'll try almost any thing once and I am spicy food fanatic. Upon graduating from college, I plan to pursue a career in software/web development.

Project Description

The objective of this project is to create compounds effective against multidrug resistant diseases. Complexes of silver (Ag) and gold (Au) supported by N-heterocyclic carbene (NHC) ligands have recently demonstrated effectiveness against methicillin-resistant stapholycoccus aureus but cannot be modified for bioconjugation or cell-trapping. To address this shortcoming, we have created a synthetic approach that allows incorporation of multiple functionalities into NHCs. We have emphasized chelating NHCs, which bind metals with more than one atom, because their complexes are more kinetically resistant to metal dissociation. Building from this foundation, we will create new classes of chelating NHC ligands for Ag and Au, metals with the geometric requirement of being able only to bind a ligand at two sites 180 degrees apart (i.e. trans-chelating). A visualization REU student will obtain experimental proof that the complexes are monometallic with trans-chelating ligands or are instead multimetallic with non-chelating ligands via single-crystal X-ray diffraction (XRD). This technique reveals the locations, numbers and identities of atoms in a molecule via the scattering of focused X-rays off the core electrons of each atom. This raw image data is indexed and converted to points in 3D reciprocal space. These points can then be projected in real 3D space, assigned to specific elements (i.e., carbon, Ag, etc), and generate a representation of the atoms and bond connectivity in the molecule. Knowledge of the molecular structure enables determination of bond lengths and geometries, information essential to rational design of the target trans-chelating NHC ligands.

Week 1

During the first week of the REU program, I spent a lot of time getting settled into the program. I got to meet my Project Mentor Dr. Tennyson and have him explain in more details what he was trying to accomplish which was the best way to visualize simple and complex crystallography structures. With these ideas in mind and a few visualization programs he'd given me to play around with, I set out to learn how to better use them and to see if I could find any other programs to use that would help accomplish our goal. I become competent in using the software my research mentor had given me, downloaded and tested at least 10 other visualization programs. I met again with my research mentor demonstrating to him what I had accomplished with the software he had given me. Afterwards we then discussed my idea of using a combination of visualization techniques such as such as videos, interactive models, and picture and set a goal to meet next week with some rough working examples and models that he could look at. Dr. Tennyson got me to schedule to meet with Dr. McMillen, who is an X-ray guru in the chemistry department and with his help I would learn how they take raw data from the X-ray crystallography, process it, and convert it to a format that visualization programs can use to make images so I would be able to take part in the whole scientific process.

Week 2

The majority of the second week was spent testing the capabilities of the different visualization programs to narrow down which ones would best be suited to use for the research project. After narrowing it six programs, I began to take some of the sample data given to me by Dr. Tennyson and used it in the programs to make rough models and videos to show Dr. Tennyson at our next meeting to get feedback. During our meeting I presented the rough models and afterwards Dr. Tennyson gave me some tips on how to best represent complex crystal structures and he also went into further detail about the type of things he would like to see in the video representations.

Week 3

During the third week I spent most of my time looking up different methods to show video representations of the 3D molecules. I spent time learning to use BioBlender so that I would be able to make presentation quality videos that Dr.Tennyson could use on the research project. Blender is an open source 3D computer software product that allows you to create models and make animations. BioBlender the Blender program with a built in plug-in that allows you to upload PDB files and renders a 3D model of the molecule. I also got to start my training with Dr.McMillen an together we used the Shelxlt program to figure what the new crystal structure that Dr.Tennyson and his team created looks like. Shelxlt is a program that takes the data file from the X-ray diffraction machine and based on the different intensity values, it plots many points where it thinks atoms are. Users then select individual points which might be atoms checking the distance between it and the possible atoms bonded to it along with their bond angles so that each point can then be correctly labeled as an atom or deleted because it was useless. After doing this serveral times and refining the data as needed, the structure of the molecule is obtained and is now ready to be render in visualization programs such Ortep3 or Mercury.

Week 4

During the forth week I did some research on UCSF Chimera, another visualization program I downloaded to test its video making capabilities to see if it would be useful for the project. After reading the documentation provided on the software's website and looking on Youtube to see example videos of what it was capable of, I decided to use this program instead of BioBlender to make the presentation videos because it would be easier and more time efficient. I then completed another one of my milestones by figuring out how a make a video of a molecule transforming into another molecular structure after it has combined with another molecule.

Week 5

During week 5, I spent time reading the user guides for UCSF Chimera and Jmol to learn how to use different features like fade-in/out and showing the thermal ellipsoid view of molecules which shows how much motion is going in each atom. As I read, I tested the features by using some sample data to make some rough video examples. I also made notes on how to use each feature and those notes will be incorporated into the tutorial I make for each program in the coming weeks. In addition to working on my research project, I also prepared for and presented at our midterm presentations. Test link Click

Week 6

During the sixth week, I met with Dr. Tennyson to find out which data sets he wanted presentation quality visualizations for and what all he wanted to be seen in them. Using this picture drawn by Dr. Tennyson as guidance, I then started to work on making the final visualizations. That Friday, I met with Dr. Tennyson to show him what I done so far and the get more clarification about what he wanted done in the visualizations. After getting some feedback, went back to work on correcting the models. Besides working on the final visualizations, I also prepared to attend the XSEDE14 Conference in Atlanta, GA from July 13 - July 17.

Week 7

During week 7 I attended the XSEDE14 Conference in Atlanta, GA. At the conference I volunteered at 2 sessions by taking count of how many people attended, handing out surveys, and by getting copies of the lecture materials so they could be uploaded to the XSEDE website. I got a chance to meet new people and network with Professors from other school, as well as attend other lectures where I learned about things such as High Performance Computing. Also while at the conference I continued my research by working on my final visualizations for Dr. Tennyson when I wasn't attending conference events.

Week 8

During the last week of the REU i spent the majority of my time getting ready for the final presentation and finishing up any last minute work that needed to be completed. Also while working on my final video presentation, I figured out why some models didn't show the morph animation that they were supposed to. I turns out that in order for the program to show morph transformation, which is where a new model is created and transposed on to a pre-existing structure showing that it is derived from another pre-exinting model, would only work if the models had the same atom labels. This means that even if 2 structures had the same exact atoms and build that the morph animation would only happen between atom with the same label. So C19 in model 1 would only transpose with C19 in model 2 if it had one. I also got am extension to finish the tutorial I decided to create for Dr. Tennyson and his team so they would be able to continue creating visualizations for his research project and any future works.

Last updated: 07/26/2014