Dr. Rhonald Lua of Lichtarge Computational Biology Lab gave a workshop on Protein Bioinformatics

by Quirino Sugon Jr.

Last 18-21 October 2011, Dr. Rhonald Lua  of Lichtarge Computational Biology Lab of Baylor College of Medicine gave a workshop on Protein Bioinformatics entitled, “Evolution-directed visualization using PyMOL and docking using AutoDock Vina.”  The workshop was held at the PLDT-CTC Building Room 215 in Ateneo de Manila University.  The workshop was organized by Dr. Nina Rosario Rojas of the Chemistry Department and was attended by about twenty participants.

Dr. Rhonald Lua  finished his B.S. Physics in Ateneo de Manila University last 1996 and graduated Cum Laude.  A year after, he earned his second degree in B.S. Computer Engineering.  He then continued graduate studies abroad at the University of Minnesota and earned his M.S. in Physics in 2002 and his Ph.D. in Physics in 2005.  Dr. Lua worked for a year as postdoctoral researcher at the National Institute of Standards and Technology before transferring to his present job at the Lichtarge Computational Biology Lab.

After his workshop, Dr. Lua went to Manila Observatory and met with his college classmate, Dr. Quirino Sugon Jr. who works at the Ionosphere Research Building.  Dr. Lua also met his former student, Genie Lorenzo, who now works at the Urban Air Quality program and Michael Andrews, Dr. Sugon’s graduate student. Dr. Lua talked about the mathematical theory of knots and their invariants and how these are related to protein structures.  Since we all have physics backgrounds, Dr. Lua presented his talk in physics terms.  He talked about Hamiltonian walks or the travelling salesman problem: how to go from one place to another in the shortest path, passing only each station once.  He also talked about entropy functions for protein sequence alignments and evolutionary traces. The aim of Dr. Lua’s protein research is drug design.

Below is an interview with Dr. Rhonald Lua:

Dr. Rhonald Lua, Genie Lorenzo, and Dr. Quirino Sugon Jr. at Manila Observatory

Dr. Rhonald Lua, Genie Lorenzo, and Dr. Quirino Sugon Jr. at Manila Observatory' Lobby

1.  How were you able to apply for Ph.D.?

I just looked for the schools online and got into the University of Minnesotta.  Last July 2000,  I went to the US. At first, I just thought that I would get an M.S. degree, but everyone was automatically enrolled to Ph.D. My adviser was Alexander Grosberg, whose adviser was I. M Lifshitz. I am not sure if he was related to the author of the Landau and Lifshitz series of physics books that we know. But this one is famous in polymer physics. In my thesis I was looking at knots in lattices and proteins. I developed software that determines what kind of knot you can find in a lattice. Specifically,  I developed algorithms for computing knot invariants. I actually spoke about this topic a total of six times including this morning. This protein, for example, is a hemoglobin. It is a globular protein, very dense, about 1.3 times the density of water. Proteins are like nanoscale machines. If you look at its backbone traced by C alpha atoms, you would expect that it is entangled. We want to know if this is really the case.

2.  Did you have to take biology classes.

I did read books but not text books. The book by Watson and popular accounts of Biology.  I learned about the Nature and Science journals. I highly recommend them. I did not appreciate the research journals earlier in my career. When I was in Ateneo, I like browsing American Journal of Physics, College Mathematics, and American Mathematical Monthly. We attended seminars, too. It was inspiring if the speaker is good.  I just read a lot and listened and talk to researchers–something like that.  Giving talks is a good idea, because it forces yourself to stand and present your work in front of people.

3.  What made you decide to work on this field?

I knew Python and Java and I am comfortable with computing, but Biology was new to me at that time. I used what I learned in Physics. I get to learn more physics, too. I read physics while I was a postdoc here. I have time to indulge in topics I liked.

4.  Do you use Monte Carlo simulation?

You want to create a distribution of velocities and energies. The name, Monte Carlo, came from a gambling joint in Las Vegas. For example, in docking, you can generate solutions by randomly selecting shapes and trying them on the receptor. If it increases energy, throw it away. Explore the search space. Monte Carlo is just a technique. You need random number generators. Some generators are poor. Default libraries on number generators are poor. I often see this. For my project, I use the code in Numerical Recipes. The problem of other random number generators is that they have a short cycle. Your simulation should not be longer than the period of your random number generator. Some people are afraid to try out new things or to fail. I don’t understand this. This is discouraging. I learned that it is ok to figure things out as you go along. Then you build  confidence. Eventually you shall figure it out. It is ok if you don’t know now. It does not make you inferior.

5.  What is your normal day like in the research?

I come in at around 10 a.m. in the morning. Then I check my email.  I don’t really have a set thing to do. It depends on what is required. Most of the time I develop software and write programs to do computations. My greatest contribution is the plug-in to PyMol for visualization of molecules. I work previously with another viewer in Java. I also make software available in the web so that ET is available for everyone. I am also dabbling with docking and molecular dynamics.

Dr. Quirino Sugon Jr., Dr. Rhonald Lua, and Michael Andrews at the Ionosphere Research Building, Manila Observatory

Dr. Quirino Sugon Jr., Dr. Rhonald Lua, and Michael Andrews at the Ionosphere Research Building, Manila Observatory

6.  How did you acclimatize?

Houston is very like Manila.  Hot and humid . It is an hour from Galveston and the Gulf of Mexico. Houston is very diverse. There are many Filipinos there. There are many Latinos whose culture I can relate to. Of course, I am still doing science. I do science on a day to day basis.

7.  What are your plans five years from now?

I live in an apartment right now.  But I want to live in a real house with a garden.  My coworkers live in a house and tend a garden. My recreation is to run and walk around the neighborhood, which is difficult to do here.

8.  Does ateneo education have any difference?

I am not a great speaker in English. But the non-science courses helped me express myself better. I really love history. My favorite was Fr. Leonard. I have a few other excellent teachers. One was in English. He rides a motorbike and does Aikido. He is a big guy but I forgot his name. I have fond memories of some other classes: (Physics/CE) Mr. Tecson, Mr. Montuno, Fr. McNamara, Sir Carlos Oppus, Dr. Nathaniel Libatique, Sir Bong Monje, and others in the department; (Math/CS) Dr. Quimpo, Dr. Marasigan, Dr. Manalastas, Dr. Vistro-Yu; (Theo) Dr. Astorga, Sir Bobby Guevarra. I heard that Fr. Ferriols is sick.

I look back fondly at the wide variety of classes that we had to take at the Ateneo, and I am proud to tell my colleagues here in the US when I get the chance.

9.  Any message for the physics majors in Ateneo?

I would say if you really like physics, just read on your own . I can’t think of anything funny or creative to say. I was not really into volunterering then, but I would encourage the physics majors to do volunteer work and engage in extra-curricular activities.  In the US, I was not really outgoing then. I volunteer at the local humane society, an adoption center for dogs and cats. We have many stray dogs and cats. Also, the physics majors should not be ashamed going to the library. Start reading journals early if they are serious about research and about science in general. American Journal of Physics is not really a research journal, but I did enjoy photocopying and reading their articles. I would suggest reading Science and Nature as early as possible.

10.  Do you have any regrets?

One regret I have is that I did not dabble and become proficient with electronics and
machining. I like to make and tinker with stuff, but at that time, I felt I have to understand the physics of something (like an electronic component) well before using it. That is related to what I said earlier about not letting uncertainty or lack of knowledge prevent you from experimenting and treating it in the meantime like a black box just to get something done. I tried to rectify that by taking a machining course (a long time ago) and building with LEGO Mindstorms, Basic Stamp, and Nitinol.


About ateneophysicsnews
Physics News and Features from Ateneo de Manila University

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