## Jaren Ryan Rex (BS APS/ACS): Magna Cum Laude and Physics Program Awardee for 2017

From left to right: VP for Loyola Schools Dr. Maria Luz P. Vilches, Physics Department Chair Dr. Raphel Guerrero, SOSE Awardee Jaren Ryan Rex, and SOSE Dean Dr. Evangeline Bautista at the SOSE Recognition Program for Distinguished Students held at Leong Hall Auditorium last 24 May 2017, 10:00 a.m.

by Ellice Dane Ancheta and Quirino Sugon Jr

BS Applied Physics with Applied Computer Systems student Jaren Ryan Rex is one of the students recognized by School of Science and Engineering (SOSE) of Ateneo de Manila University in a Recognition Program for Distinguished Students held in Leong Hall Auditorium last 24 May 2017, 10:00 a.m. Jaren finished Magna Cum Laude and was chosen as the Program Awardee of the Department of Physics. He finished his elementary at Multiple Intelligence International School and his high school at Philippine Science High School Main Campus where he graduated with Highest Honors. Upon entering Ateneo de Manila University for his undergraduate studies, Jaren was given the Fr. Thomas B. Steinbugler, SJ Academic Scholarship, a 100% tuition and fees scholarship for valedictorians from Jesuit and science high schools.

Below is an interview with Jaren Ryan Rex by Ateneo Physics News.

1. Why did you choose Ateneo in college?

It is an interesting piece of information. I was diagnosed with mild Asperger’s syndrome, which means my social and physical skills were underdeveloped. So when deciding where to study for college, my parents and I were discussing whether I would go to UP or Ateneo. We weighed the pros and cons, and we decided that Ateneo would be a more friendly and nurturing environment to help me overcome my challenges better. And I think it did. And also, my choice of a double major course, BS Applied Physics/ BS Applied Computer Systems is only offered here.

2. What was your BS Applied Physics thesis?

In my undergraduate thesis, I simulated typhoon Haiyan (Yolanda) several times using the weather model called WRF, short for Weather Research and Forecasting model. The WRF model has many different physical parameters that represent physical assumptions made by the model, such as the amount of air that flows between atmospheric columns, the mixing ratios of different states of water in clouds, and the interaction between the air and the ocean. These are just a few parameters that can be varied in the WRF mode. In my thesis I tried varying all of these to see which parameters caused Haiyan to be most intense. I hoped we would be able to understand more the physics of how Haiyan became so destructive.

For each of these parameters there are different schemes that we set for the parameters, and each parameter affected a different part of the simulation. Some parameters affected the typhoon’s track. Some affected the minimum sea level pressure. Some affected the wind speed. For each parameter, there were settings that produced the most intense typhoon in the simulation: that’s what I assumed to be closest to the actual state of the atmosphere and the ocean during the typhoon. Some settings would make the track very accurate, but the sea level pressure would be too high. It would not be as intense as observed—in fact, very far away from observed intensity. On the other hand, there were settings of the same parameters that made Haiayan more intense but also caused it to deviate far away from its observed track. The model itself could use some improvements.

3. What was your BS Applied Computer Systems thesis?

I got concrete blocks and dropped weights on them so they would crack. I dropped the weight repeatedly and took a picture of the block after I dropped the weight. A new crack would form, and would appear in the picture. I would then have a series of pictures that show how the crack propagates after each impact. Then I would run different image processing operations on the pictures to analyze the properties such as the length and the branching patterns of the cracks. For image processing, I used OpenCV (CV stands for Computer Vision) for Python, which I learned on my own. I did not simulate. All the experiments were actual physical experiments.

I had experiments where I varied the height from which I dropped the weight, to measure the rate at which the crack propagates in relation to the energy of impact. I have another set of experiments where I had different compositions of the concrete. They are mixtures of cement and sand. I varied the ratio of cement to sand by volume. For the experiments where I varied the mixture, I found that pure cement is much weaker compared to mixtures of cement and sand, meaning it cracks with much fewer impacts. The cement-sand mixtures crack after about three times as many impacts as pure cement. But on the other hand, for the cement-sand mixtures, it does not seem to matter how much sand is there. The strength of the block is relatively constant with respect to the amount of sand. For the experiments where I varied the height, I got the obvious results. The blocks crack faster when the weight is dropped from a higher distance, since more energy is input into the block for each impact. And also actually what is interesting is, for the higher impact distance, the crack forms more branches than with lower heights.

Actually I was supposed to predict quantitatively how cracks propagate but my thesis was submitted in a somewhat unfinished state based on the results I was able to produce. My plan was to use the image processing techniques to get a measure of the crack length, crack area and even the speed of propagation. But what I ended up doing was trying so many image processing techniques to isolate the crack in the image. It was hard to find a good algorithm because usually there was a lot of black noise in the image background, making it hard to see the cracks.

I eventually found an image processing technique that makes the crack stands out from the background much more compared to the other image processing technique. It is called bottom-hat filter. I just put in the recommendations that the results of applying the bottom-hat filter can then be analyzed further to extract those quantitative parameters, such as crack length and area. There were a lot of previous studies about image processing of cracks where I found out about the suitability of this kind of image processing. I did not exactly base it on quality control. The intent of this thesis was more of studying how cracks propagate for computational fracture mechanics. I deduce the theory from what is observed.

4. Do you have extra-curricular activities?

I was part of the Ateneo programming varsity team. We competed in programming contests like the ACM-ICPC (Association for Computing Machinery – International Collegiate Programming Contest) among other various local contests. There is also a programming contest hosted by UP Diliman called Algolympics. There are many contests with a similar nature. In programming contest we are usually given problems that have a certain specification and given input. We need to do some computations and process data in some way to produce a certain output. Our goal is to write programs to solve those problems such that whenever you input anything into the program, it will produce the correct output. Most of the time the programming languages we use are limited to C++ and Java.

This semester, I have won two champion titles. One of them is the UP ACM Algolympics. This is by team. (We usually compete in teams.) The other contest was the HP Code Wars. It was hosted by HP (Hewlett-Packard), the company. The way we’re teamed up depends on the circumstances. Most of the time we have the same team for most of our contests, but in some circumstances some members are not available, so teams are shuffled a bit. Sometimes, some members are ineligible, e.g. the HP Code Wars was only for graduating students. So instead of my usual team I was teamed up with other graduating students in the Programming Varisity. The members of the programming varsity are mostly Computer Science majors. I was the only Physics major there. At some point there were two physics majors there, but one of them shifted to Computer Science as well. He was also from my course, BS Applied Physics with BS Applied Computer Systems.

5. Do you have a blog?

I write for leisure but I don’t write regularly for any organizations or school publications. I have a blog on Blogspot, entitled Overcoming. I’ve been posting on this blog since 4th year high school. I’ve written over one hundred posts–mostly just personal reflections.

6. What can you say being in the last batch taking BS APS/ACS program? (Note: the program is still listed in the Registrar and may be offered again.)

I would say it is a little sad. I met freshmen who said this is their dream course. It would have been the course they would take if it was still offered. I believe it was mistake on the part of the Registrar or so I heard. Since last semester, when Dr. Guerrero talked to our batch, he mentioned something about making curriculum for something that could be a replacement for this course. I hope it would be similar or even better.

One thing I really enjoyed doing apart from studying physics itself is tutoring physics. I have given a lot of tutorials for my block mates in Physics and Math that I have lost count. I even tutored other students in Ateneo who have asked for help in Physics and Math. The tutoring has helped me understand the topics even more and deepened my appreciation for them. Because of this experience in tutorials, I planned to someday return to Ateneo and teach Physics.

After Ateneo, I may take a vacation for a year before working here in RCS (Regional Climate Systems Program of Manila Observatory) where I did my thesis. I have talked to Dr. Gemma Narisma about this already. I shall work there for maybe one or two years to have good working experience. After this, I shall go to graduate school either in Europe or Japan because I want to specialize in Particle Physics. My dream is work with CERN (European Organization for Nuclear Research). I don’t know how many years I would spend there, but I plan to return to Ateneo to teach physics.

8. Any parting words?

Maybe I would say if anyone asked us for advice about how to being in a Physics major, I think the best I can say is to keep reading not just the lessons you are taking up, but anything that interests you within physics, because that’s how you keep yourself motivated. Practice makes perfect. You develop an intuition on how to solve or approach problems even if you have never seen the problem before.

## Electrowetting actuation of gold nanofluid droplets: a physics dissertation defense by Crismar Patacsil

The Department of Physics of Ateneo de Manila University cordially invites you to a Physics Dissertation Defense:

• Dissertation title: ELECTROWETTING ACTUATION OF GOLD NANOFLUID DROPLETS
• PhD candidate: Crismar P. Patacsil
• Date and Venue: April 8, 2017, 1:00 PM at Faura Hall F-106

Panel members:

• Raphael A. Guerrero, Ph.D., Dissertation Supervisor
• Benjamin O. Chan, Ph.D., Dissertation Examiner
• Gil Nonato C. Santos, Ph.D., Dissertation Examiner
• Erwin P. Enriquez, Ph.D., Dissertation Reader
• Joel T. Maquiling, Ph.D., Dissertation Reader

Abstract:
Nanoparticles exhibit completely different properties (physical, chemical, electronic, magnetic and optical) from their bulk material counterparts. This study explores the interaction of gold nanoparticle (AuNP) suspensions in a liquid droplet with an applied electric field. A basic planar electrowetting set-up is employed, consisting of a bottom copper electrode coated with a thin insulating layer of uncured polydimethysiloxane (PDMS) silicone oil mounted on an adjustable stage and a platinum wire upper electrode in contact with the sessile gold nanofluid droplet sitting on the dielectric layer. A voltage source is connected across the top and bottom electrodes. Changes in the contact angle of the droplet, as voltage is varied, is captured using a USB microscope camera. The contact angles of the images are determined using ImageJ software. The electrowetting on dielectric (EWOD) experiment is done with varying concentrations (in µM) of gold nanofluid (deionized water containing gold nanoparticles with an average size of 10 nm): 0.5, 0.33, 0.25, 0.05 and deionized water (no gold nanoparticles) as a control fluid. Results show a different electrowetting response for each concentration. The contact angle is found to decrease with increasing nanoparticle concentration, indicating a decrease in the liquid-gas surface tension as concentration increases. Increasing the nanoparticle content also lowers the required voltage for effective actuation. Contact angle saturation is observed with nanofluid droplets, with the threshold voltage decreasing as nanoparticle concentration rises. Maximum droplet actuation before contact angle saturation is achieved at only 10 V for a concentration of 0.5 μM. To explain the mechanism for the observed enhanced electrowetting actuation, the specific capacitance C is calculated from the voltage versus contact angle data for each concentration. For the control fluid, the calculated specific capacitance is 0.0012 F/m^2. Specific capacitances are C = 0.0097 F/m^2, C = 0.0049 F/m^2, and C = 0.0015 F/m^2 for 0.5µM, 0.33µM, and 0.05µM gold nanofluid concentrations, respectively. The presence of gold nanoparticles affects electrowetting response by increasing the capacitance with increasing concentration of the nanoparticles. Higher specific capacitance results in increased induced charges at the solid-liquid interface which would result in increased electro-mechanical force on the droplet as voltage is applied.

## Ateneo Physics Talk: “Theoretical study of hydrogen interaction with metal surfaces” by Allan Padama of Osaka University

Title: Theoretical study of hydrogen interaction with metal surfaces
Speaker: Allan Abraham Padama, Department of Applied Physics, Osaka University
Date and Time: January 15, 2014 at 4:30 pm
Place: Faura 304 (Coffee and cookies will be provided)

Abstract:
The interaction of hydrogen atoms with metal surfaces is a fundamental concept in the field of surface science and is an important factor in the realization of a sustainable hydrogen-based economy. The absorption of hydrogen, in particular, is a very crucial process for hydrogen storage, hydrogen purification and hydrogenation/dehydrogenation applications. Pd and Pd-based materials are popular for such applications due to their capability to absorb large quantities of hydrogen. This present work investigates the absorption of hydrogen atom in Pd(110) and Pd3Ag(110) surfaces and elucidates the effect of Ag in the absorption phenomenon. Furthermore, hydrogen-induced reverse segregation of Pd atoms in the PdAg alloy is examined.

Allan Abraham Padama is currently finishing his doctoral studies at Osaka University. He works in the Kasai Laboratory, doing research on the theory of the dynamics and characteristics of materials. He employs density functional theory techniques to calculate the physical properties of materials with potential practical applications.

## Ateneo Physics faculty Artoni Ang went to a two-week internship at NAIST

by Quirino Sugon Jr.

Artoni Ang setting up of the UHV SEM for Auger Electron Spectroscopy

Artoni Ang, an Assistant Instructor and a graduate student of the Department of Physics of Ateneo de Manila University, went to Narra Institute of Technology (NAIST) last October 2012 for a two-week internship.  NAIST is a graduate school for Material Science, Information Science and Biological Sciences in Nara, Japan. Since 2006, it has been holding the NAIST Project for Interns (NAPI) where qualified students from the Ateneo de Manila University are invited to the laboratory of their choice for a 2 week internship.  For his internship, Artoni went to the Surface and Materials Laboratory under Professor Hiroshi Daimon.  This laboratory focuses on the study of nanomaterials, surfaces, and interfaces using the 10 m long Ultra High Vacuum (UHV) total analysis system developed by the laboratory.

Below is an interview of Artoni by the Ateneo Physics News:

1. How long have you been teaching in Ateneo?

Less than a year.  This is my second semester. I am teaching Ps 1 and 2 (Natural Science course) and various lab classes for Health Science and Biology majors. I am teaching 13 units this semester.

2.  Where do you do your research in Ateneo?

I work in Mr. Ivan Culaba’s Vacuum Coating Laboratory at the first floor of Faura Hall. Right now I am working on thin films on elastomeric substrates. I am trying to make stretchable diffraction grating. Specifically, I wish to reduce the cracking on the metal film as the grating is stretched. Metal films on stretchable substrates have many applications.  Diffraction gratings are just one of them.  Diffraction gratings are surfaces with very fine line grooves like furrows in a field, except that the distance between furrows is in the order of the wavelength of light, which is a few hundred nanometers or a fraction of the width of a hair strand.  Reducing cracking of the grating would increase the lifetime of such material.  I am working on the optical properties of materials by using the grating as a beam scanner. If we have a beam incident to the grating, we can change the angle of the of the reflected beam by stretching the grating. Stretching would change of the grating pitch or the distance between the line grooves.

3.  How is your work in the lab related to your work in the NAIST laboratory?

It is not exactly related but similar . Here we work with thin films with thickness levels in the nanometer and micrometer range in the wavelength of light. In NAIST we work with even thinner films in the Angstrom level or about 10 layers of atoms thick. Here we have high vacuum systems with pressures of $10^{-5}$ torr. In NAIST they have ultra high vacuum high systems of $10^{-10}$ torr. Most of the procedures in running the equipment are the same, except when the pressures reach $10^{-10}$: they have to bake the chambers. They wrap the chambers with heating blankets and bake the chambers for a month to get it to $10^{-10}$ torr. In our case to reach $10^{-5}$ torr, we only need 2 hours to pump it down. We use rotary pump and oil diffusion pump. In NAIST they use turbo molecular pumps and titanium sublimation pumps. After they bake their chambers they leave it at that pressure range. Then they leave all their pumps turned on 24 hours a day. In our case, we shut the system down once we are done with a specific experiment. We don’t need to keep it turned it overnight, because we can regain the same pressure the next day after 2 hours.

The panel that controls the substrate holders in their UHV system

3.  How many interns were from Ateneo?

There were 10 of us: 1 from Biology, 4 from Materials Science, and 5 from Information Science. I am part of the Material Science group. We were all assigned to different labs. We only see each other during scheduled trips or if we run into each other during the day. I am on my own from 9:00 a.m. to 5:00 p.m.

4.  What was your day like in the NAIST laboratory?

During my first day there, they held a welcoming tea party for me. So all of the grad students and most of the pofessors were there. I get to meet everyone. Since they were around 20 of them, I can’ t remember all their names. They opened the dried mangoes I brought. They all liked it. It wasn’t a formal Japanese tea ceremony.

I was there for 2 weeks. But lab work was only about 8 days. The usual day starts with me going to the laboratory at around 9:00 a.m, though I usually try to arrive a bit later. I don’t like to be the first one in the laboratory alone. And I stay outside to wait for a graduate student to arrive. They actually they told me where they hide the key, but I am not comfortable going inside without them. My day actually starts around 10:00 a.m. I waste an hour waiting outside.

Their lab is divided into two main parts: experimental section and the offices. In my  first day they assigned  me to an empty desk. And that is where I stay. In my first day, too, I met with one of the professors: Sakura Takeda-sensei. She created a schedule for me so that I will be working with different students with their own research projects. When working with them, they perform their experiments and explain the details to me. And in some cases. I get hands-on. In one particular case, we were working for two days on a scanning tunneling microscope. But it was repair and maintenance duties. We have to remove some of the main components. It was a long job. I think they finished all the maintenance work a few days before I left. And they started baking it. I guess they had to wait a month before they can even start using it.

I was assigned to do analysis on the data we collected in the experiments. I did image processing on diffraction patterns from RHEED (Reflection High Energy Electron Diffraction) experiments. I analyzed the data collected using ARPES (Angle Resolved Photoelectron Spectroscopy). From that data we were able to obtain the electron band structure of the Lead monolayer on Germanium. I was  suppose to get the mass of heavy hole from that data, but I did not get to finish the calculations. They had their own software which came with equipment. And there was another software that I think one of the graduate students wrote using java. It just converts the data collected from ARPES to electron band diagram we are all familiar with.

I worked with another student doing RHEED experiments on Indium monolayer on Silicon substrates. I also used the Scanning Electron Microscopes on Iron polycrystalline sample. I was suppose to help on the experiment involving Bismuth on Silicon, but one of the major gauges broke down, so we have to stop.

I attended study sessions, a laboratory meeting, and a laboratory colloquium. In the study session, we spent around an hour discussing theoretical principles behind ARPES. In the colloquium, we spent the entire morning listening to two graduate students presenting papers relevant to their work. It would have been were more interesting if they were reporting in English, but they were speaking in Japanese. I sat there the entire morning looking at their slides. In the afternoon is the colloquium where every graduate student presented a slide or two about their progress since the last lab meeting. Some of the students were presenting slides whose only progress is that  they attended courses or studied their exam. Nevertheless, they still have to present those because it is apart of their process. There are also students who made a lot of progress. They presented a lot of the data they were collecting. They also made me present a brief overview of the research that I do in the Philippines. I had to leave after 4 hours. I think their meeting lasted 6 hours–the whole afternoon. Between the colloquium and laboratory meeting is lunch break. And there is 30 minutes of general laboratory cleanup.  Everybody cleans by sweeping or mopping the floors.

During the first week my sensei gave me a lot of books. After 5:00 p.m. , I usually go straight to the dorm and read the books–not the entire book but only the selected chapters. I think she was surprised that I can read them overnight, because she is just used that her students have difficulty reading books in English. So from their point of view, I read really fast.

A group photo with the professors and students of the Surface and Material Science Laboratory

5.  What do you like best during your stay in Japan?

Their transportation system is very organized. If the train is scheduled to arrive at 8:02 a.m., it will actually arrive at 8:02 a.m..  So if we go out for dinner or cultural trip, our entire travel itinerary was already arranged, because they know the schedules of the trains and buses. It was easy getting around even without a car.  And this was in Narra which is not one of the big urbanized area. But despite that the transportation system is very good. In fact when you go out to the gate of NAIST, the first thing that you see is a rice field and it smells like a rice field. But then there is a bus station in front of the gate.  So even if it is in the rural part of Narra, we can still get around. We can also actually walk to the closest train station, but it takes 40 minutes.

It seems very safe there. There were times we walked to the train station in the middle of the night beside the big mall at around 10 or 11 p.m. We were not worried about being held up. The sense of security is also visible in the campus itself. They don’t have a close gate. It is just an open road that goes toward the campus. I don’t see any security guard walking around.

Of course the food was great. The organizers brought us to Japanese restaurants. We got to try sushi, yakiniku, okonomiyaki, ramen, and some other Japanese foods. Before I went there, I promised myself that I will never say no. I will eat whatever served to me. Half of what I ate there, I don’t know what it was. And then we had weekend trips to Kyoto, Osaka, and Narra. We got to visit some of the old temples and an aquarium in Osaka. During our last day there, they took us to the shopping district in Osaka,where they sold everything from electronics to anime things to clothes.

6.  Any parting thoughts?

Overall it was a good experience. You get to see how research is done in universities in other countries. The research culture is very different. Most of the students are full-time researchers. They don’t attend courses. They only worry about their research projects. They spend an entire day in the lab, because they have a desk there. They are really focused on what they are doing in the lab. Unlike in my experience as a student, my attention is divided in the courses I am taking and the research I am doing. Of course, it would be easier if you are only focused on research work.

It was also eye-opening to me to see how disciplined the Japanese people are.  After eating in the cafeteria, they clean up. We don’t see people littering. They all follow traffic rules, unlike here in the Philippines where traffic is very chaotic.

After I finish my Masters degree, I plan to apply for Ph.D. degree outside the Philippines. I am now looking at Erasmus Mundus program for Materials Science. I have already informed my Professors in NAIST that I will be applying there, too. Hopefully, I get accepted to one of them. If not , I shall also apply to universities in the United States.

## Dr. Jer-Lai Kuo of Academia Sinica to give a talk on synthesis of semiconductor alloys and on graduate programs in Taiwan

Dr. Jer-Lai Kuo of Academia Sinica shall give a talk on November 29, 2011 entitled, “Synthesizing semiconductor alloys on the CLOUD–A 1st principles based multi-scale approach to map out the phase diagrams of semiconductor alloys.  The talk will be from 10:30 a.m. to 12:00 noon at the Department of Chemistry, Room C-109.   After the talk, Dr. Kuo shall give an introduction to the Taiwan International Graduate Program.

Synthesizing Semiconductor Alloys on the CLOUD – A 1st-Principles Based Multi-scale approach to Map out the Phase Diagrams of Semiconductor Alloys

Jer-Lai Kuo
Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan

Binary semiconductor alloys have been commonly proposed/synthesized to provide a much wider range of material properties than their parent compounds. However, theoretical studies are hindered by the intrinsic complexity. We have developed a CLOUD-ready multi-scale algorithm to effectively explore the configurational space (~2N) and applied it to study the newly synthesized BexZn1-xO. Examining the formation enthalpy we found the possible existence of three meta-stable order states. The calculated band-gap of the BexZn1-xO is also compared with the experimental measurements and surprisingly we found that some alloy configurations with the same concentration can have band-gaps differed by ~ 1.5 eV1,2. We have also considered the composition-temperature phase diagram of BexZn1-xO alloys3. The predicted phase diagram is consistent with the experimental observation that alloying Mg with BexZn1-xO suppresses phase separation. Furthermore, we have also looked into anionic replacements – ZnOxS1-x4 and other BN and C alloys5-7.

We are working toward to port our methods to CLOUD facility not only to speed up this process but also to make it more accessible to experimentalists. Thus, we believe that our work reported here is not only related to material simulations but also should be of interests to experimentalists who are working on synthesizing the binary semiconductor alloys.
[1] Fan X.F., Zhu Z, Ong YS, Shen Z.X, and Kuo J-L, Lu Y.M., Appl. Phys. Lett. 91, 121121 (2007).
[2] Fan X.F., Sun H.D., Lu Y.M. , Shen Z.X, and Kuo J-L, J. Phys. Cond. Matt. 20, 235221 (2008)
[3] Gan C.K, Fan X.F., and Kuo J-L, Comp. Mater. Sci. 49, S29 (2010)
[4] Xiao-feng Fan, Y.M. Lu, Zexiang Shen, and Jer-Lai Kuo, New J. Phys. 11, 093008 (2009)
[5] Fan X.F., Zhu ZX. , Shen Z.X, and Kuo J-L, J. Phys. Chem. C 112, 15691 (2008)
[6] Fan X.F., Wu H, Shen Z.X. and Kuo J-L, Diamond and Related Materials, 18, 1278 (2009)
[7] Wu H, Fan X.F. and Kuo J-L, Diamond and Related Materials, 19, 100 (2010)