Purdue NSF Quantitative Physiology Scholars
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# [http://openwetware.org/wiki/User:Cal_Rabang Cal Rabang]
# [http://openwetware.org/wiki/User:Cal_Rabang Cal Rabang]
# Sean Connell
# Sean Connell
# : [http://openwetware.org/wiki/User:Danielle_R._Kalajian Danielle Kalajian], Danielle Nelson
# Sarah Noble: Lindsay Wendel, Teresa Lin
# Sarah Noble: Lindsay Wendel, Teresa Lin
Revision as of 11:55, 29 September 2010
Welcome Quantitative Physiology Scholars
This wiki is for you to communicate as a community. The QP scholar community consists of undergraduate scholars, graduate mentors, and faculty mentors that are all working and training in interdisciplinary project and mentoring teams.
Thank you NSF
This work is funded by the National Science Foundation S-STEM program. If you are an NSF QP scholar, please do acknowledge this source of funding in your presentations and scholarly works.
Not yet a QP scholar but want to be?? See our website at QP Scholars for application details. We are accepting applications annually.
A list of all of the members of the Purdue University NSF Quantitative Physiology Scholars
Graduate Students (PI in parentheses): David Jaroch (Rickus), Sal Sommakia (Otto, Rickus), Sean Connell (Shi), Cal Rabang(Bartlett), Brittany Book (Irudayaraj), Stephen Chabot (Bartlett), Vu Dinh (Buzzard), Anne Dye (Nauman), Sarah Noble (Rundell)
Undergraduate Students: Kristy Bielak, Katie Boehm, Brittany Book, Kaitlyn Edwards, Danielle Kalajian, Dong Lim, Teresa Lin, Tiffany Miller, Amanda Pannell, Si Min Su, Lindsay Wendel, Amanda Smith, Lauren Schuler, Marshal Huang, Chad Tuchek, Danielle Nelson, Alex Fickes, Taylor Willett, Sanjay Gunashekar, Annamarie Bustion, Michael Comasco, Mark Hamilton
Fall 2010 Schedule (updated regularly)
08/27: Introductions, surveys, topics for QP
09/03: Prof. Eric Nauman, "Are you ready for some head injuries! (I mean, Football!)"
09/10: Lab tour
09/17: Prof. Jenna Rickus, Lab tour of Bindley Bioscience Center and Birck Nanotechnology Center.
09/24: Ranulfo Romo lecture, hosted by Prof. Kevin Otto
More to follow...
- Vu Dinh
- Sal Sommakia
- David Jaroch
- Stephen Chabot
- Brittany Book
- Cal Rabang
- Sean Connell
- : Danielle Kalajian, Danielle Nelson
- Sarah Noble: Lindsay Wendel, Teresa Lin
What We Do
As Quantitative Physiology Scholars at Purdue University, we strive to bring together the theoretical and empirical sides of physiology.
What do we mean by that?
Following the footsteps of premier quantitative physiologists, such as A. L. Hodgkin and A. F. Huxley, we are learning to prove points in a way that is complete: looking at a problem (and our solution) not only with laboratory data, but marrying it with principles that can be mathematically found while sitting at a desk. Bridging these two together, we can complete our research, ensuring its reliability. Doing so will make our findings more understandable in that the scientist reading our work or the student whom we are trying to teach can grasp it where they are able – at their strengths, whether mathematics, visual graphs, or written findings from the lab – and therefore, gain so much more.
In this program we are trying to gain knowledge in quantitative physiology through classroom discussions, lab visitations, research, and outreach projects of our own. Through these different pathways, we will put into practice our method of “theoretical and empirical” and try to enrich the world doing so.
Edited by *Danielle R. Kalajian 17:38, 15 October 2008 (EDT)
Things we have done so far to acheive these goals include:
- Read and discuss "A quantitative description of membrane current and its application to conductance and excitation in nerve," by A.L. Hodgkin and A.F. Huxley (The Journal of Physiology, 1952) - Visit Dr. Nauman's Biomechanics Lab to see the different projects that the graduate students in his lab work on. - Read and discuss "Metabolic gene regulation in a dynamically changing environment," by Mattew R. Bennett (Nature, 2008) - Create outreach projects to be used to interest students (predominantly middle school age) in and teach then about quantitative physiology (see below for project descriptions)
Edited by *Lindsay Wendel
Tips for Creating Teams
As Purdue Quantitative Physiology Scholars, teamwork is important to us, and is an integral part of our studies, both in the classroom and in the laboratory. Here we would like to present some guidelines to create good teams.
- Pick teammates that have similar interests and you do. This will ensure that when doing projects or research, everyone keeps their attention on the project. The more they like what they are doing, the more time spent on the project, and the better the results will be!
- Look for teammates what different strengths than you have. This will ensure that lively discussions take place. The different strengths will keep the projects rolling at a good pace, because if one person is having trouble on something, instead of becoming a road block (and therefore delaying the project), one of the other teammates may be able to help! This will keep teammates from becoming discouraged and help the group move at a good pace. Different strengths to oppose other’s weaknesses becomes critical when we are talking about quantitative physiology: some teammates need the theoretical finesse, while others need to have the experimental good standing in order to make a well-rounded team.
- However, don’t have teammates that are so diverse that you cannot agree on anything. This will not only have potential to cause hard feelings within the group, but will slow down the project because every fork-in-the-road will be a cause of argument and much time will be wasted disputing the point.
- Remember: your teammates may make good friends, but your friends may not always make good teammates. Keep the goal in mind when creating teams!
Edited by *Danielle R. Kalajian 20:12, 22 October 2008 (EDT)
Mentor Research Projects
Dynamical systems can be used to describe cardiac action potentials and are thus an invaluable tool used in the pursuit to understand the electrical activity of the heart. An arrhythmia is any disturbance from the normal periodicity of the heart beat and may lead to serious and even fatal conditions of the heart. Alternans is one such abnormal heart rhythm in which the length of time that the cardiac cells are excited alternates between long and short.
We are studying the traveling waves in cardiac models and working to use analytical methods to describe patterns of alternation. The following are a few of the main references that we are currently using in our work.
- J.P. Keener and J. Sneyd, Mathematical Physiology, Springer, New York, 1998, 766 pages (ISBN 0-387-98381-3; hardcover).
- B. Echebarria and A. Karma, Amplitude equation approach to spatiotemporal dynamics of cardiac alternans, Phys. Rev. E 76, 051911 (2007).
- E. Cytrynbaum and J. P. Keener, Stability conditions for the traveling pulse: Modifying the restitution hypothesis, Chaos 12, 788 (2002).
For Students: An undergraduate interested in working with us in the area of cardiac modeling will be mentored on a project tailored to his or her interests. Whether it be analytical, computational, or more on the biological side, we will aim to relate a level-appropriate project to our current mathematical investigations. Because MATLAB is an effective tool that may be used to explore abnormal wave patterns and system bifurcations, a student would ideally be familiar with differential equations and either comfortable with computing or willing to learn the marvels of MATLAB.
Current Outreach Projects
In this section, we encourage each team to discuss the projects they are currently working on.
Hormones: Fight or Flight
Graduate Students: Craig Barcus & David Jaroch, Undergraduate Students: Kristy Bielak & Danielle Kalajian, Taylor Willett
- Physiological Concept we wish to convey.
For this project, we would like to present how hormones can affect what people/animals do and how they act. By this, we would show how humans/animals are born with genetic tendencies and instincts that naturally lead us to act certain ways.
- The best way to present this concept/make it happen.
We are going to let the students put ants and a specific ant hormone together and see how it affects the ant. We would talk about hormones and natural responses, such as ‘fight or flight’, and let the students conduct a hands-on demonstration as to how animals respond to these hormones and their natural instinct concerning them.
- What we would need to make the presentation.
In order to do this presentation, we will assume that the class is made out of 20-30 students. There will need to be one set of supplies for each group of students. The number of students per group will depend on how old (read: mature) the class is, and the younger they are, the more students per group, so that there can always be someone supervising, and less people per group if the students are older.
Each set of supplies will include: • Petri dish • A few ants • Ant pheromones • Cotton swabs (such as q-tips)
The presentation would go something like this: First, we would explain how hormones work, and also cover some natural instincts that are found in humans. Then we would briefly give them an idea of what they might discover as they perform the experiment. The students would then be broken into groups and given the supplies. They would be given an opportunity to draw paths of hormones with the cotton swab and the pheromones. We would give them a few pointers as to what to try, and then let them do things on their own, such as make their own hormone paths. After the experiment was conducted, we would hold a wrap-up session, where we would ask the students what they discovered with their experiment, ask them why they thought it happened, and lastly, how it applies to all living things, especially humans.
Edited by *Danielle R. Kalajian 17:38, 15 October 2008 (EDT)
Biomedical Prosthetics: Classroom Experiment
By: Brittany Book, Bryan Schlink, Max Haddan, Dong Lim, Mandy Su
The concept we are going to implement in the classroom setting is an explanation of implantable prostheses. We will contact companies and professors here at Purdue University to attain samples of current prosthetic implants. We will take these samples into schools and show them to students. The students will guess the use of each implant. This will facilitate discussion on the application, design logic, and history of implants. We will then show a short powerpoint on the history, design, production, and use of implants. We will allow the students to ask questions at this time. We will pass the implants around the room to increase student interaction. This presentation and question session will last around 20 to 30 minutes. It will be applicable for elementary to high school students. The powerpoint itself and presentation length can be adapted to meet the attention spans and needs of the different age ranges.
To prepare for this outreach endeavor we will implement the following process: 1. Create a list of current prosthetic companies who may be willing to help facilitate this program. 2. Divide the companies among group members. 3. Create a contact with company representatives. Ask the representatives for any samples or assistance they may provide. 4. Have samples shipped to the Martin Jischke Building for inspection and presentation set-up. 5. Create labels for prostheses. 6. Research history of implants. 7. Create an adaptable powerpoint to present in the classroom. 8. Contact schools to determine interest and availability.
By: Kara, Lindsay, Teresa
A lot of teenagers are active in afterschool sports programs or at least have required physical education classes. As their body changes and they start training for the competitive nature of high school sports, we can introduce the concepts of muscular control and skeletal muscle anatomy.
The best way to present it interactively is to develop a robust model using representative rigid and contractile elements. We propose creating a representation of a thigh and shank with a knee joint using PVC pipe or saw bones. With this model we can attach rope or tethers at muscle origins. The rope will be unraveled and divided to represent as many heads and alternate ending attachment points. The students can experience hands on the number of muscles that need to be contracted in various sequences in order to do a simple task like kick a ball.
To begin the presentation, there would be a brief discussion of a lever arm and quick demonstration of a simple fulcrum and slab to balance the moments on each side. Then we show example pictures of the anatomy and explain that muscles act as actuators. To show this we could have the student lift the shank and compare that force to pulling on the rope that would represent the quad. Asking him/her to explain why it was so much harder to get the shank to rotate by pulling on the quad rope would hopefully induce thinking of the body in terms of simple mechanisms like lever arms. Due to the close attachment point of the patellar tendon, their “lever arms” may be very small in comparison to the length of the muscle.
Now looking at the amount of forces required just to simply move in one plane, we can un-brace the leg model and ask them if they could make it “stand.” We would use this opportunity to explain co-contraction of agonist and antagonist muscles to stabilize joints. Note the number of actively contracted muscles in a passive activity like standing.
Now hook the leg back up to the hip joint and have several students volunteer to pull on the rope to make it kick a soccer ball into a goal. Watch as they talk about who needs to pull first and which muscles need to pull at the same times. (Use this to explain all of the task that the nervous system has to figure out with each simple movement.) Now have them estimate with all of them pulling how much force they are putting on the knee joint. Show a video of a world cup soccer player kick. Then show an free body diagram of the forces that the world cup player’s knee experiences during the kicking motion. Do the same analysis related to body weight and add other tasks like jumping and walking forces on the knee. Sum up by reviewing lever arms and thinking of the body as a big machine and explain that the cool part about engineering is you can not only explain how things like this work, but you can also solve for injury tolerances and predict the forces needed to hurt a basketball player, etc.
Edited by *Teresa Lin 15:11, 20 October 2008 (EDT)
Graduate App Resources By Kara
Resources & Hints:
Here is a copy of the powerpoint slides on grad school presented in class by the graduate students: The_Graduate_School_Presentation
Funding Opportunities: Explains fellowships, scholarships, grants. Lists national fellowships as well as the ones available at Purdue. Search for this type of page at prospective institutions. 
1. NIGMS Quantitative Biology : Progress in several areas of biological science supported by the National Institute for General Medical Sciences (NIGMS), is critically dependent on the involvement of scientists with training in both traditional quantitative disciplines (such as mathematics, physics, engineering, and computer science) and biology. Therefore, the NIGMS is encouraging applications for individual postdoctoral and senior fellowships from highly qualified individuals with doctoral training in the above quantitative areas who are seeking additional training in biological areas congruent to the mission of NIGMS. 
2. NIH-Funded Training in Cell Signaling and Lung Pathobiology: The NHLBI-funded Institutional Training Program in Cell Signaling and Lung Pathobiology supports predoctoral fellows who have completed the one-year interdisciplinary core curriculum in the Basic Medical Sciences PhD program at the University of South Alabama . Trainees receive the current year NIH predoctoral stipend, full tuition remission and health insurance. The Training Program combines state-of-the-art research training with Program faculty with advanced course work in lung biology, lung pathobiology and signal transduction. Training resources include facilities in the Center for Lung Biology and the Cancer Research Institute. Program faculty provide a breadth of expertise with respect to lung biology and pathobiology, with extramurally funded research focusing on regulation of lung endothelial barrier function, acute lung injury, lung remodeling in pulmonary hypertension, sickle cell disease, airway solute transport, cystic fibrosis, and alveolar epithelial cell function. We have the expertise to train students in research approaches to understanding mechanisms at the molecular to integrative level of function. For more information, contact Dr. Mary Townsley, Program Director (460-6815, firstname.lastname@example.org). 
- Bryan R. Schlink 10:48, 27 October 2008 (EDT):
Purdue CCO: How to write a resumé and CV. 
Workshops: Purdue’s graduate school sponsors a bunch of workshops on everything from proposal writing (integral to applying for funding) to different fellowship specific info sessions. 
Hints to remember: • Look at professors in each department and what research they do, not just the department. • Email the professors and their grad students ahead of time to get the down low on if there is funding, how that prof is as an advisor, what it’s like to live there…etc. • Keep emailing around, but do not send form letters. Write something to the effect of I have read one of your recent papers and am interested in this work because... otherwise they won’t respond. • Start early with the things that aren’t controlled by you (ex: GRE reporting, submitting transcripts, getting recommendation letters)
Links to Purdue Opportunities
- SURF Summer undergraduate research fellowships for research under the guidance of engineering faculty (including some of the QP faculty mentors).
- Purdue Research Park Internship Postings
- Louis Stokes Alliance for Minority Participation. LSAMP Indiana.
Reimbursement Form: Image:Form25.xls
Links to External Opportunities
- Computational and Systems Biology Summer Institute. Computational and Systems Biology Summer Institute (CSBSI) at Iowa State University is jointly supported by the National Institutes of Health (NIH) and the National Science Foundation (NSF). The purpose of this program is to provide undergraduate and graduate students majoring in sciences and engineering with an introduction to integrated biology and Systems Biology.
- "The Program in Neural Computation (PNC) offers undergraduate training in computational neuroscience for students seeking training in the application of quantitative and computational approaches to the study of the brain. The Program is coordinated by the Center for the Neural Basis of Cognition (CNBC) a joint project of Carnegie Mellon University and University of Pittsburgh. This NIH-funded training program supports "summer students" from around the country to come to Pittsburgh and do research."
- Hertz Graduate Fellowships. "The Hertz Foundation identifies the rare young scientists and engineers with the potential to change the world for the better and supports their research endeavors from an early stage"
Links to Career/Jobs Resources & Tools
- Institute of Biological Engineering Career Center. Upload your resume information. See job postings. Get emails when jobs are posted that fit your criteria. Get a one year free membership in IBE for participating.
- Win a Nobel Prize!
- National Geographic
- How Stuff Works
- Scientific American
- Discover Magazine
- List of Science Museums
- Wired Magazine
- Dana Alliance for Brain Initiatives
- NERVE: Neuroscience Education Resources Virtual Encycloportal
- BrainFacts Document
"Somatosensory discrimination based on cortical microstimulation" by Ranulfo Romo, Nature, 1998: A Discussion
On Friday, September 24th from 9:30-10:10am in MJIS 1001, there will be a scientific lecture presented by Dr. Ranulfo Romo. A biography of Dr. Romo can be found here: http://www.hhmi.org/research/international/romo_bio.html.
Please add your thoughts on the following two questions:
1. What are the Quantitative Physiological (QP) implications of electrical vs. natural somatosensory discrimination?
i) With the aid of computer models, we can directly determine mathematically the underlying relationships between artificially-induced flutter and naturally-induced flutter. One goal could be to utilize this technology in virtual reality. - Marshal
Danielle R. Kalajian: The study shows that the monkey’s did not have statistically different results based on whether the sensory was triggered electrically or mechanically, with there only being a difference of 2% on how many times they answered correctly (83% and 85%, respectively). From a quantitative physiology perspective, this study shows us that there are different methods available to quantify a physiological response.
2. What are the QP implications of the periodic vs. aperiodic results?
Danielle R. Kalajian: The results were almost identical with the periodic and aperiodic tests. This teaches us that from a quantitative standpoint, you could have different inputs and still come out with the same output. That is to say, in this case, changing something about the stimuli input didn’t make a difference once it was interpreted by the monkey’s brain.
Edited by *Danielle R. Kalajian 23 September 2010