Ateneo Physics faculty Dr. Raphael A. Guerrero is NAST Outstanding Young Scientist and TWAS Prize awardee for 2013

NAST Outstanding Young Scientist Awardees of Ateneo de Manila University: Dr. Raphael A. Guerrero of Physics and Dr. Liane Peña Alampay of Psychology. Dr. Raphael Guerrero also received the Third World Academy of Sciences (TWAS) Prize for Young Scientist in the Philippines.

by Quirino Sugon Jr.

Ateneo Physics faculty Dr. Raphael A. Guerrero received two awards from the National Academy of Sciences (NAST) Philippines during its 35^th Annual Scientific Meeting last 10-11 July 2013 at the Manila Hotel: Outstanding Young Scientist (OYS) and Third World Academy of Sciences (TWAS) Prize. The NAST OYS award is “given to young Filipino scientists…who have made significant contributions to science and technology.” Dr. Guerrero is one of the nine awardees. The NAST TWAS Prize, on the other hand, “is an award given to outstanding young Filipino scientist by the Academy (NAST) and TWAS in the field of Biology, Chemistry, Mathematics, or Physics.” The TWAS award has the same age requirement as that of the OYS award. For the year 2013, the TWAS award was Dr. Raphael Guerrero:

 For 2013, the award is given to outstanding individual in the field of Physics. Dr. Raphael A. Guerrero of the Ateneo de Manila University was declared recipient of the said award, in recognition of his important studies on volume holographic storage and animation which offers a new holographic method for storing multiple pages of data in a nonlinear crystal and his works on the diffraction from relief gratings on a biomimetic elastomer cast from the carapace of a beetle found in Mindanao, Philippines, which have contributed significantly to the visibility of Philippine physics within the global community of scientists.

The other NAST OYS awardee is Dr. Liane Pena-Alampay of the Department of Psychology (see the related news story at the Loyola Schools website).  Below is an an interview with Dr. Raphael Guerrero by the Ateneo Physics News.

Dr. Raphael A. Guerrero in his office at the Photonics Laboratory in Faura Hall

Question 1: Can you tell us more about the award?

I was awarded Outstanding Young Scientist by the NAST, the highest recognition and advisory body regarding S&T in the country. NAST is a body consisting of the premier minds of science in the Philippines. The President of the Philippines listens to the recommendations of NAST. The awarding process started July 11, 2013. Last November 2, the nomination forms and supporting documents were submitted for those who wish to get the award for 2013. The notification letters came by the fourth week of May. It was six months of waiting. There was a screening committee for the Outstanding Young Scientists. They asked me to submit other requirements: descriptions of scientific accomplishments and other stuff needed to get a background on what I do as a scientist.

Question 2. How long have you been in Ateneo?

I started teaching in the second semester of SY 2000-2001. That was 13 years ago. I had just received my master’s degree from UP that April. After a semester of being a research associate at NIP, I decided to give teaching a try. Back then, I walked up to the third floor. The chair was Dr. Holdsworth. I inquired about the possibility of teaching in the department. Luckily, the department was actually looking for an instructor. After submitted my documents, they gave me a load. My load was interesting: I taught all majors for Ps 171 (Classical Electrodynamics I), Ps 113 (Statistical Mechanics and Thermodynamics), and Ps 102 (Classical Mechanics II). Not bad for someone teaching for the first time.

I gave a demonstration lecture. I remember that Gemma Narisma, Ivan Culaba, Obiminda Cambaliza, and Joel Maquiling were part of the audience. We had not really met at that point in time. I gave a demo on diffraction from a slit. It was in F304. I did not notice anybody else or maybe I was scheduled at a different time. I’m not sure if there were other new faculty.

Question 3. What was your career background?

I went to UP Rural High School. It is the official high school of UP Los Baños located next door to my elementary school. After high school, I always wanted to go to UP Diliman. I applied for their Physics program at UP Diliman, a pure physics program. It was a five-year course. (I work mostly on Applied Physics these days.) In 1998, I entered the laser physics lab in my 3rd year doing work on photorefractive crystals. In that same year, I graduated after performing work on Bismuth Silicon Oxide type of photorefractive crystal requiring 5 kV applied voltage. It was the first demo of volume data storage in the Philippines. Back then, it was the best you can possibly do. Holography was still in infancy in the late 1990s. After graduation, I felt I learned nothing from my BS degree, so I took up master’s degree in UP Diliman. It took two years. Different crystals, but still on volume holography and Lithium Niobate. I obtained my masters degree in 2004. Getting a PhD was longer.

I took a break for a semester before proceeding to the PhD program in UP. I started the PhD program while teaching in Ateneo. I mostly teach a series of electives The biggest challenge was coming up with an original work published. After some awkward first few years of trying to find a suitable topic, I was able to publish an article on pattern recognition, still using Lithium Niobate and volume holography. It was accepted June 2004. I graduated with PhD in Physics in 2005. This was while I was teaching full time in Ateneo. In 4.5 years, a Ph.D. can be done full time.

After obtaining the third degree, I was no longer interest in postdoctoral study. It is not something programmed into me. I became busy improving the research capabilities of the Photonics Laboratory in Ateneo. In Physics, we can generate ISI-indexed publications.

I received funding from government over a course of several projects. Previously, the Photonics Laboratory was focused on optical fibers and semiconductor diode lasers. That was the laboratory I saw in 2001 which I inherited under Dr. Holdsworth. Today, the laboratory is mostly on elastomeric optics using PDMS or polydimethylsiloxane, commonly known as silicones. We also have the only working volume in holography set-up in the country. The technology was transplanted from the National Institute of Physics (NIP) to here at the Department of Physics of the Ateneo de Manila University.

In 2005, Ateneo made me assistant professor. No big deal, after getting your PhD. After four years of working and generating papers, I became Associate Professor in 2009, still teaching full time. And here we are in 2013–still teaching, still in the same office.

Dr. Raphael A. Guerrero with his family

Question 4. What led you into physics?

My parents are trying to figure that one out. After the awarding, we were getting coffee and they were just talking, reminiscing whether there were any signs I would go into science. My father, Dr. Rafael D. Guerrero III, is a famous man of science. He developed the method of increasing the productivity of the tilapia industry using the sex reversal technique. He is a legend. His science helped people get food. It is a really important piece of technology. My mother, of course, is a talented zoologist. These fields are loosely related to experimental physics.

I guess, when I was growing up, I remember my father going on trips giving lectures, seminars. Each time he would come home with a souvenir and a toy. All the toys are science-based. The rocket would be launched via water pressure. A He-Man flashlight which you pumped with your hand. There are also Chemistry toys, but I never liked chemistry. I had two telescopes. I had a lot of toys that deals with science in high school.

When we were choosing courses, I joked that that the hardest course in the list is UPCAT. Physics was good. Molecular Biology and Biotechnology were hot, really hot in early ‘90s, but people didn’t know what they were. Physics just sounded really good, so I went to UP Los Baños for Applied Physics. I saw the people working in the farm — that was not really inspiring to me. So I decided to pursue physics. Diliman was the flagship school of UP, the only UP branch that offered physics, and I really wanted to go to Diliman. UPLB was not cool enough for me.

And in the ‘90s, there was MacGyver. He was known for figuring out and solving problems and helping people. There was amazing physics in MacGyver. It was something to do, but in the end it was still a mystery. I don’t know why I went to this field. Interesting. Maybe it’s because people are impressed by physics majors, though scientists find that hard to believe.

Dr. Raphael A. Guerrero and his toy collection

Question 5. Can you tell us about your toys?

Well, they say men never really grow up. I might be the best example of that. Some men have sports cars as toys. Some guys a high-end computers. I just stuck with actual toys. My collection is not random. Some are based on comic characters I resonated with, on stories from Marvel and DC. Like growing up I bought toys and statuettes in some cases, portrayed them in some cases, because the stories are nice. Buying a toy is my way of commemorating how important they were to me growing up. Also with a regular salary, it is easier to buy toys. I was able to buy Voltes V in die-cast metal that I did not get one Christmas. Voltes-V costs a lot of money back then. It costs even more now. It was a lost opportunity; I could have bought it before. Anything that I find interesting that I can afford these days, I look for bargains. I also have a collection of comics in high school, and I never stopped. It has become a major investment in money and space. I have several shelves dedicated to graphic novels. The boxes of comic books increase in number every year. Cliché in Big Bang Theory. That is my life right there. Interesting hobby. Very interesting way to spend your time collecting mementos and reading these fantastic stories.

I give my students a false sense of security in PS1 and PS11. I always start the class with a broad description of physics — really interesting, such as Star Wars, using it after every sentence. that is the fun part of the semester: light sabers, star destroyers, or faster than light travel. They all have physics in them, but no syllabus. I find it really difficult to lecture physics. How I wish I could inject a Star Wars into every lecture. With both content and time constraint, this is not feasible.

6. You travel a lot?

Not as much as I would like to travel for free. I have been lucky having visited many countries because of my physics background–attending conferences, being invited or participating in a certain function. I have a checklist of countries. Egypt, 2008. I am specifically looking forward to a conference in Cairo. I found a military college in Egypt which gave me an excuse to visit Egypt, with support from the University. Subsidized conference expenses. It would be worth it to touch the great pyramids, inhale the dust of Giza Plateau. In Italy, Rome was nice. I was able to see the David sculpture of Michaelangelo. I was able to take a picture of – you are not supposed to do that. I went to Japan several times. US, of course, is my favorite destination for the shopping and for the sheer size of the conferences in optics. Largest Optics Cnference is the SPIE conference in San Diego. It runs for several days. The research areas in optics were vast, so vast that they have become subsections. The plenary talks were from Nobel laureates were humbling and inspiring. Just to mingle with those optical scientists proved inspiring.

Every year I try to go abroad. But I still have to go to Paris. I want to see the Eiffel Tower, Louvre, Taj Mahal. I want to know what is like to travel in another Third World country. I want to go to Angkor Wat in Cambodia, though my wife is terrified of possibly catching diseases. I wish to go to the Great Wall of China. I have not seen in years.

Dr. Raphael A. Guerrero with his graduate and undergraduate thesis students at the Photonics Laboratory

7. Are there other things you wish to add?

I want to thank the department for providing me such a welcoming and supportive home for my professional career. Many faculty members here have become my close friends. I am lucky to be part of the faculty in Ateneo. Ateneo trusted me with a load of teaching these college kids. It feels like it’s a privilege and an honor to be part of this institution. I am very grateful to the Department of Physics, which really supported through these past thirteen years in my accomplishments, awards, publications, action figures, although all that would not have been possible without the support of the university.

8. What are you visions or plans for the Photonics Laboratory?

We talked about this, Pope (Quirino Sugon Jr.). I wish getting published in a journal were easier. Over the next five years, we will have every graduate thesis in Photonics translated in tons of ISI-indexed articles. I plan to translate these into articles this year for all of my graduate students. I would also like to increase the output of papers. Hopefully, we can increase the average number of paper published from one paper a year to two papers a year. I would like to apply for lots of big projects, or maybe buy bigger light sources and lasers and other equipment the lab needs to proceed with research output. I plan to increase publications output. Well, it is still the same goal I had five years ago.

9. Do you have any message to our physics students?

I wish you all the best! I hope physics is as good to you as it is to me. I have been very, very lucky that physics has had to do with my success up to this point, and I hope you will fully enjoy the adventure as physics majors as much as I did. Don’t lose hope! There is a future in physics. You just have to find it.

Dr. Raphael A. Guerrero and Dr. Liane Pena-Alampay with the administrators of NAST and Ateneo de Manila University

Ateneo Physics faculty Dr. Eduardo Cuansing, Jr.: The journey from Creative Writing to Theoretical Physics

Dr. Eduardo Cuansing, Jr. giving a lecture on electron-phonon interaction

by Quirino Sugon Jr.

[Update: As of April 2015, Dr. Ed Cuansing has moved to the University of the Philippines, Los Baños, and is no longer connected with the Ateneo de Manila University. You may contact him at eccuansing(at)up.edu.ph.]

Dr. Eduardo Cuansing Jr. is a new faculty of the Department of Physics of Ateneo de Manila University. He obtained his BS Physics degree from the University of the Philippines, Diliman and his PhD Physics from Purdue University. His undergraduate thesis was on non-Abelian Gauge theories and his doctoral dissertation was on critical phenomena. He did postdoctoral research work at the University of Pittsburgh on the theory of vortices in high-temperature superconductors and at the National University of Singapore on the quantum transport of electrons and phonons. He has recently moved to the Department of Physics, Ateneo de Manila University. This 5 August 2013, he will give a talk entitled, “Electron and phonon transport in nonequilibrium many-body quantum systems with dynamic forces and components.” Below is an interview with Dr. Eduardo Cuansing, Jr. by the Ateneo Physics News:

Question 1. What was your career track?

I studied in Tay Tung High School in Bacolod City. Actually, I passed in Philippine Science High School, but my parents did not allow me to go. I was also accepted in the Ateneo Chemical Engineering and Management Engineering programs, but I studied instead at the University of St. La Salle in Bacolod City.

I like science. I like to write. So I asked my self, “Why not Creative Writing?”After one year, I went to the University of Philippines-Diliman as a Creative Writing major. I was thinking of writing science fiction novels as a career, though I did’nt know yet that I needed to take Chemistry and Physics to do this. Then I met Prof. Yanga in Natural Science 1 in UP Diliman. He convinced me to shift to physics. After one year in Creative Writing, I shifted to physics and then finished my degree. I worked with Dr. Magpantay for my thesis on non-Abelian gauge theories.

I went to the International Center for Theoretical Physics in Trieste, Italy for the diploma program in high energy physics. After that I moved to Purdue University for my PhD. in Physics. In Purdue I did research on Statistical Mechanics and Critical Phenomena. Dissertation with Hisao Nakanishi. After that I moved to University of Pittsburg to work with Yadin Goldschmidt. I was a postdoctoral fellow and we were working on the physics of vortices in high Tc superconductor. I went back to the Philippines and taught at De La Salle University for two years and two trimesters. Then I went to the National University of Singapore. In the first two years I was at the Physics department working with Jian-Sheng Wang on thermal transport in quantum systems. After that I had another postdoctorate, but this time in Electrical Engineering with Albert Liang on electron transport in quantum devices. So finally, after three postdoctorate fellowships, I decided that it was time for me to go back to the Philippines and go to Ateneo de Manila University. Why Ateneo? Ateneo is semestral unlike DLSU which is trimestral. I prefer the semestral system. Ateneo is also close to UP; I can collaborate with people in UP. And the environment in Ateneo is a university setting compared to other universities. Academic setting is more conductive for thinking and doing research.

That is how I went from Tay Tung High School to Ateneo de Manila University. It is a long path. But you know, sometimes you go with the flow. You may also try to find your position, but sometimes you cannot prevent but just go with the flow. There are things that you cannot control.

Carbon nanotube transistor and a graphene transistor

Question 2: What research do you intend to work here in Ateneo?

Right now I am working on quantum transport in really small devices that are small versions of existing ones like transistors or RF receivers and things like that. I am also working on devices that haven’t existed yet, something new. I wish to study how electrons, phonons, or photons and other quantum particles would travel in these really small quantum systems, and how we can manipulate their motions. I wish to take advantage of their properties. Right now I am specifically looking at time dependent behavior of these systems. It is a hot topic. But normally what has been done is on steady state and not on time dependent state. That is, you let the system evolve for a long time and then study the characteristic of the system after this long time. This is the steady state of the system. But what I would like to study is really the real-time behavior of the system. For example, if you have a cellphone, there is a signal impinging on your device. That signal is time-dependent and not steady state. What is the physics of this time-dependent process? There are attempts to study this. It is a very difficult topic. It needs a long of hard work with the help of computers. One advantage for researchers nowadays is the existence of really powerful and cheap computers. We could take advantage of that. Problems that are difficult to solve 20 years ago we can now actually find a numerical solution using these powerful computers.

In quantum transport specifically, I am looking at electrons moving in a system where there are phonons which will carry energy as heat or internal energy. So when an electron interacts with a phonon, what happens? Will the electron slow down? Will they influence the phonons? Will they heat up? Can we make sense of these energies by doing computations? Can we direct energy to another place, to another part of the system? I also wish to find devices involving electron transport that haven’t been discovered yet. I guess the main title for what I am working is time-dependt quantum transport.

There are also questions if you have photons. Photons impinging on your system will interact with the electrons. What will happen to the electron? If the electron absorbs the photon, the electron will increase in energy. In these devices, there are energy barriers like the ones discussed in undergraduate Quantum Mechanics. When particles are moving into a barrier, you either get reflected or transmitted waves. If you have particles with high energy, the transmission is better compared to a particle with that of a slower one. If the particles have energy below that of the energy barrier, the particles can tunnel through; it is going to be difficult for the electron to pass. If you have a photon interacting with an electron, there will be more energy. What happens to things like these? If you shine light on this quantum system, what will happen? What if the light is time-varying? Can we control how the electron moves? Can we have photon-dependent transistors on nanowires?

Now, there is also the question of Non-equilibrium Thermodynamics and Statistical Mechanics. Students may be interested on the open questions on these fields. But solving these questions are more difficult since they are more mathematical. But we can make use of some empirical methods in quantum transport to construct theorems in non-equlibrium systems.

If a student is interested in both quantum transport and non-equilibrium thermodynamics, and he is also interested in computers, then he can apply numerical analysis and programming. Some mathematical problems that were difficult to solve 20 years like triple and multiple integrals can now be solved numerically. We can also apply computers when the system has disorder. There is no good way to analytically treat the system unless disorder is Gaussian, which is not interesting. Computers are actually actually the best used when there is disorder. If you are just interested in theory, then you can also do this.

Question. 3. What are the system requirements for the computers that you need?

Nowadays, we have powerful computers that are cheap, such as quad core I7 costing about Php 30,000. This computer has four processors that are active which you can program in parallel, unlike five years ago when you only have a single core Pentium IV, unlike five years ago when you only have Pentium IV that has only one core. If you have a program, it is 3 gigahertz per CPU. With quad core i7, you can run four programs at the same time or run four calculations at the same time. The program is faster. It is not necessarily four times faster, but definitely faster than one computer alone. It all depends on the programmer.

Programming parallel computers is different from programming serial computers. It is really an art to make good parallel programs that are fast. This means the programs scale linearly with the number of processors. But if you have unlimited resources, you would want to have a supercomputer. But our resources are limited. So we use I7 and a Linux cluster consisting of desktop computers. The one thing nice is the software part: you can make a cluster just by using Linux, not with windows. The Windows OS is expensive and unstable. Linux is best when you want to do clustering of computers.

In my research I use Linux. And I use Fortran and C++ to write my programs. These have languages subroutines or libraries available in the internet that you can download. These libraries were programmed by experts in computer science, so they are really good. For example, if you want to program in linear algebra, it is numerically more efficient if you download the linear algebra package. This is written by computer scientists in University of Tennessee using Fortran 77. But you can use Fortran 90 to make calls to Fortran 77 libraries. You can also use C++ to call Fortran libraries. But just take note that there are differences. For example, in arrays, C++ counts from 0 to n-1, while Fortran counts from 1 to n. Thus, if you want to pass an array or matrix in C++ to Fortran, you must be careful with the language differences before interfacing them.

I prefer to use Fortran. There are libraries in Fortran. Translation is correct donw not have to make sure. But if you know how to program in C++, then you can learn how to program in Fortran. The Fortran compilers are included in Linux, so you don’t have to buy any compiler. I don’t do much graphics, unlike people in Atmospheric Science and Meteorology where they need good graphics. For may cases, we don’t deal with graphics that much. We only calculate integrals and solutions to differential equations for simulations of disordered systems. But for graphics, the requirement is not that high. We only need powerful number-crunching computers.

Question 4. What are you teaching right now?

Ps 52 for sophomore physics majors and Ps21 for sophomore computer science majors. Well, we only met for few weeks. So far the students are attentive and well-behaved. They participate in class. I like the students. But you know it is just a few weeks. The rest of the semester we will see how they would perform. But I think I have high hopes for the physics majors. They are really interested in physics. I am inspired to continue doing things more about physics, even if we are just in the sophomore level. So I try to add as many advanced physics flavors to the class. I am not requiring them to understand everything such as photons, general relativity, and quantum mechanics that we discuss in class but are not part of the syllabus. These are just flavors to get them more curious about advanced topics and learn more on their own, and hopefully inspire them to continue in physics.

The Computer Science students are also ok. I am interested in computing and I can relate to their interests. I am also interested in playing games. The students of this generation studied computers with ipad, iphone, and so on. Most of them are exposed to games. You cannot avoid to not to let them play games. In talking about projectile motion, I use the physics of Angry Birds. The question is this: how do you calculate the angle and height of the projectile? I told my students that they can write their own prototype of the Angry Birds game using the physics we are learning in class. I always try to relate physics to computer science and computing.

I am also teaching Classical Mechanics in Graduate School and in Undergraduate tutorials. So far, it is doing well. Classical mechanics is an important part of a physics student’s education. All the methods such as the Lagrangian, Hamiltonian, and the Principle of Least Action are also used in Quantum Mechanics, Field Theory, Electrodynamics, and Statistical Mechanics. This is just a tutorial course; maybe the department accepts more graduate students so we don’t have to give tutorials. Something must be done to promote the department to get more graduate students.

Question 5. What are your first impressions of Ateneo?

At least there are active research groups here, such as Photonics, Vacuum Coating, and Materials Physics Laboratories. I see students working during their laboratory meetings. They are actively talking about their research. That’s in the first floor of Faura Hall. I don’t know about the third floor. I think the ambiance is nice. If you are thinking about doing research in physics, the academic atmosphere makes makes you feel like doing physics, too. But the teaching can be time-consuming, such as when I prepared for teaching in the first two weeks, the teaching assignments changed; they are not set yet. The system is like that. Something can be done to improve the system. As a new faculty, I don’t have a syllabus. So I just ask a reference syllabus of other people, and construct my syllabus almost a day before the class. It is tough to to think about the syllabus, especially for a new faculty, of how things would progress during the semester. At this point, I don’t know what is going to happen, especially in the laboratory. I am a theorist. The laboratory is difficult for me. Now, I am designing an experiment, hopefully an experiment that is not too easy nor too difficult, because for a theorist all experiments are easy. Designing an experiment for a theorist is not trivial. I cannot really gauge how difficult an experiment is because I am a theorist.

Question 5. Any parting words?

Physics can actually be fun. If you are freshman, you study physics such as Newton’s Laws, Torque, and Statics. At some point, it can be boring if you just learn as much as you can. These are important concepts you learn on which you can build on. All knowledge is based on whatever was done before. Newtons laws–just learn them. When you go to advanced physics, the fun starts with Quantum Mechanics, Statistical Mechanics, Classical Mechanics, and Advanced Electrodynamics. The fun would start you explore cool ideas. And if you keep on, you proceed to graduate school and contribute to discovering new knowledge. The most rewarding thing about being a physicist is when you discover new knowledge and become the first person to realize that a particular system actually acts in a particular way. It is very satisfying feeling.

Also, everybody is curious, but physics satisfies that curiosity. If you have a system, you can be curious about what happens if you change this or change that. So you do an experiment or calculation. If you are an experimentalist, you change the parameters here and see what would happen, e.g. you lower the temperature. It is also possible to satisfy your curiosity if you are a theorist. You can do calculations. Let us say, instead of say , why not ? What happens to physics if you have ma plus a very small term? Would the physics of the universe change? Questions like these can satisfy by doing calculations. What is satisfying about physics is that you can satisfy your curiosity about physical systems.

So as a physicist, you don’t really consider work as work; it is mostly play—playing with ideas using computers and equipments. It is not really work. That is why when you meet a physicist, he will always work, typically always in the laboratory. Form him work ins not work but play. Pleasurable. Something you don’t really feel burdened to do. Enjoyable.

The only thing about being a physicist is that as a career, it is financially not that rewarding. If you become a professor, your salary is not that much. If you like physics, then doing physics is just like getting paid to play. If you really want to earn a lot, you can work in an industry or become a stock market analyst. The things that you learn analytically such as how to solve differential equations and how to construct equations for physical systems may be used here, but nobody has really successfully described the stock market very well. It is very a very difficult differential or integral equation. But people have tried. Success can be fifty percent. You can apply your analytical skills to financial markets and earn than those working in the academe.

Meeting of Filipino physicists at Trieste, Italy (May 2013). From left to right: Ernest Macalalad, Dr. May Lim, Dr. Francis Michael Ian Vega II, Dr. Eduardo Cuansing Jr., and Dr. Quirino Sugon Jr.

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' 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

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.

M.S. Physics offshore program of Ateneo de Manila University and Angeles University Foundation, Pampanga

by Quirino Sugon Jr.

Angeles University Foundation

Every Saturday morning at 6:30 a.m., Jerry Barretto and I arrive at the carpark facing the Science Education Complex A.  There is a van waiting not only for us, but also for two other teachers from Chemistry and Biology Departments.  We are all going to Angeles University Foundation in Pampanga for our offshore graduate program.

The Ateneo-AUF Offshore M.S. scholarship program was proposed by Dean Fabian Dayrit and was funded by CHED.  The students should finish within two years or less.  CHED shall pay all their tuition and fees and allowances.  The lectures are only during Saturdays, so that the teachers can still teach in their classes during weekdays.

We have seven M.S. Physics students in this batch:

1. Alejo, Sherlyn Ambida–Central Luzon College of Science and Technology (Olongapo City)
2. Calugay, Melvin–Lyceum of Subic Bay (SBMA-Olongapo City)
3. De Leon, Analiza–Philippine Science High School, Central Luzon Campus
4. Forteza, Rex–Philippine Science High School, Central Luzon Campus
5. Herrera, Ireneo–Angeles University Foundation
6. Saingan, Ryan–University of Baguio
7. Syhuat, J-Lyn Anicete–Pampanga High School, San Fernando City, Pampanga

These are the only students who passed the post-bridging program exam.  The bridging program started last 2nd Semester of SY 2010-2011, with Jerry teaching Ps 101 Mechanics and me teaching Ps 171 Electromagnetics; we team teach the Ps 121 Vector Analysis.  Last summer the students studied in Ateneo and their teachers were Mr. Joel Maquiling for Ps 113 Statistical Mechanics, Mr. Patricio Dailisan for Ps 122 Matrices and Differential Equations, and Dr. Raphael Guerrero for Quantum Mechanics.  Of the original eight students who entered last November, one shifted to M.S. Biology, two did not pass the qualifying exam.  Last summer, two students from Philippine Science High School-Central Luzon joined the program.  This makes the total number to seven.

Even if the Physics Department has to go to AUF, it is still a long way for some students.  One of them was from University of Baguio.  He leaves his home at 2:30 a.m. in order to reach school by 9:00 a.m.  Others have to take several rides–tricycle, bus, jeep.  It is difficult to reimburse their transportation because, except for buses, there are no formal receipts.  A solution has been proposed: let their own Barangay certify that this such and such amount is their transportation cost.  This shall then be considered by CHED for reimbursement.

The road to Pampanga this past two Saturday’s is unusual.  The great plains of Luzon has become the great flood.  Water, water everywhere, but water mixed with mud.  The white herons or the tagak are gone–perhaps they already migrated.  On a good day, you can see them dotting the rice fields or nesting on the trees.

We passed the long bridge spanning a great river–more like a little stream, but gauging from the distance from bank to bank, this little stream was more than ten times larger at the peak of its tide.

We usually arrive at 8:30 a.m. in Angeles University.  We pass by the graduate school office and get our attendance sheets.  Then we proceed to the cafeteria for our breakfast.  It’s Pampanga, so we get the best of Pampanga specialty: tocino, bacon, longganiza–at least one of them per meal.  Then the waiter shall ask us what we wish to drink.  I get to sample all sugary drinks to the diabetic heart’s content.

Jerry teaches Ps 201 Classical Mechanics from 9:00-12:00 a.m.  I teach Ps 271 Classical Electrodynamics from 1:00-4:00 p.m.  Our friends from Biology and Chemistry asked us why we do not wish to teach for six hours instead.  Our standard reply: we do wish to get tired.  So we’d rather go to AUF every Saturday teaching only 3 hours per meeting, than to go half the number of Saturdays but teach 6 hours.  While waiting, we read our mails, check our papers, and prepare our lessons.  Sometimes, along the way, he would ask me questions regarding the revision of his dissertation on matrix optics and aberration theory, which he successfully defended last March 2011.  Dr. Raphael Guerrero of the Photonics is his adviser and I am a member of his panel.  Time flies fast.

At 4:00 p.m. we leave AUF.  Last two Saturdays, it was drizzling.  And we beheld a rainbow arching over the heavens.  For a moment, all physics of ray tracing, dispersion theory, and wave interference vanished.  And all I hear is a poem by William Wordsworth in our En 14 Poetry class years ago under Dr. Jonathan Chua:

My heart leaps up when I behold
A rainbow in the sky :
So was it when my life began ;
So is it now I am a man ;
So be it when I shall grow old,
Or let me die !
The Child is father of the Man ;
And I could wish my days to be
Bound each to each by natural piety.

The flood plains of Pampanga

A rainbow after a rain in Pampanga

Dr. Fabian Dayrit talks about the Ateneo-AUF Offshore graduate program

Dr. Fabian Dayrit talking to the students of the offshore programs in M.S. Biology, M.S. Chemistry, and M.S. Physics

The M.S. Physics students in the Ateneo-AUF offshore program in one of the classrooms in Angeles University Foundation

Some faculty of Ateneo de Manila University in Angeles University Foundation. From left to right: Dr. Quirino Sugon (Physics), Dr. Christine Lagunzad (Biology), Dr. Rene Macahig (Chemistry), and Jerry Barretto (Physics).