Ateneo Physics alumnus Jude Salinas is now a PhD student in Earth Systems Science at National Central University, Taiwan

Jude Salinas, PhD Student, Taiwan International Graduate Program - Earth Systems Science Program, Academia Sinica, National Central University, Taiwan

After finishing his BS Applied Physics degree at Ateneo de Manila University in 2012 , Cornelius Csar Jude H. Salinas went on to take his PhD studies at the Taiwan International Graduate Program-Academia Sinica of the National Central University, Taiwan.  Last December 2016, his paper entitled, “Impacts of SABER CO2-based eddy diffusion coefficients in the lower thermosphere on the ionosphere/thermosphere,” was published at the Journal of Geophysical Research-Space Physics. SABER stands for Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument is one of four instruments on NASA’s Thermosphere-Ionosphere-Mesosphere Energetics and Dynamics (TIMED) satellite. To scan the atmosphere, SABER uses a 10-channel broadband limb-scanning infrared radiometer with spectral range of 1.27 µm to 17 µm. Different gases–O3, CO2, H2O, [O], [H], NO, OH, O2, and CO2–have different absorption properties at different electromagnetic wavelengths. This allows the bulk properties of these gases to be measured, such as kinetic temperature, pressure, geopotential height, volume mixing, volume emission rates, and cooling and heating rates–all across different atmospheric heights.

The atmosphere is the layer of the gas molecules surrounding a planet–or even a star like the sun. For the earth, the dominant atmospheric gases are Nitrogen (N2) at 78%, Oxygen (O2) at 21%, and Argon at 0.9%. Different gases have different masses, and the way these gases mix result to different layers of the atmosphere: troposphere (6-20 km), stratosphere (20-50 km), Mesosphere (50-85 km), thermosphere (85-590 km), and exosphere (590-10,000 km). At the thermosphere, the molecules become very hot due to absorption of ultraviolet rays from the sun, with temperatures reaching 2,500 deg Celsius, though it would still feel cold below O deg Celsius since the gases are sparse. Some of these hot molecules gets ionized, i.e. they shed off electrons, transforming the molecules into positive ions. These electrons and ions define the ionosphere. The density of the ionosphere may be determined by the frequency of radio waves that they reflect, which are usually from 2 to 25 MHz. The ionosphere is essentially a plasma, which is affected by the earth’s magnetic field and by the internal electric fields generated by the separation of positive and negative charges. Thus, the motion of the ionosphere is coupled with that of the thermosphere–and even with the lower parts of the atmosphere through wave motion, which makes the problem difficult to observe and model, except through satellite measurements and computational methods, such as those used in Jude Salinas’ work.

Below is an interview with Jude Salinas by Ateneo Physics News.


Jude Salinas with a snowman during an extremely rare event of snow in Taipei in 2016. The last time that it snowed in Taipei was almost 50 years ago.

1. What made you choose to take BS physics in AdMU? 

I chose to take BS Applied Physics with Applied Computer Systems in Ateneo because my particular fascination for airplanes inspired me to understand the physics behind our atmosphere especially turbulence. It definitely helped that I enjoyed my physics class during my highschool, PAREF Westbridge School for Boys in Iloilo City.

2. How were you able to enter the doctoral program at Academia Sinica? Was it through connections or did you pass some tests?

The application procedures didn’t require any tests but it did require recommendation letters and proof of research skills. In my case, I believe showing that I had at least 5 conference presentations (4 international) helped. Indeed, the skills that I learned from my undergraduate research helped me a lot in both course-work and research.

3. What research you currently working on? 

My PhD research specialty is under the fields of atmospheric and space physics. I do research on the coupling of our lower atmosphere (less than 15 km) and our upper atmosphere (greater than 110 km) via the interaction of numerous atmospheric waves (e.g. Rossby/planetary-scale waves, gravity waves, etc.) with the background atmosphere occurring in our middle atmosphere (15 to 110 km). Our middle atmosphere is not in a state of radiative equilibrium everywhere and at all times. For example, in the mesopause (at roughly 90 km), the summer hemisphere is much colder than the winter hemisphere. In fact, the summer mesopause is the coldest point in our atmosphere. The interaction of atmospheric waves with our background atmosphere drives this. This is actually pushed further in that these waves which originated in the neutral atmosphere also affect our ionosphere, a region of our atmosphere that is dominated by charged plasma. Understanding the physics behind the coupling of our atmospheric regions is important in satellite operations, communications and space exploration. My research utilizes physical models to understand and consequently simulate observational data from satellites.

My current research is specifically about understanding the physics and chemistry behind the coupling of our lower atmosphere and our upper atmosphere by looking and explaining the variabilities of CO2 in the middle atmosphere. My JGR Space Physics paper lays the foundation for the rest of my PhD work. It aimed to calculate eddy diffusion coefficient profiles in the Mesosphere and Lower Thermosphere region (80 – 110 km) using satellite observations of CO2 and a one-dimensional photochemical and transport model. Eddy diffusion coefficients are a model parameterization for sub-grid scale motions like mixing due to breaking gravity waves. Calculating this is difficult because it is like calculating the diffusion that occurs when a wave crashes on a sea-shore or the diffusion due to turbulence. Only a few ground-stations have done this but of course, ground-stations don’t give a global coverage which is important. So far, no satellite-derived temperature nor wind dataset can be used to calculate this. Chemical species profiles and a one-dimensional model can also be used to calculate this but the chemistry of the utilized tracer must be well-known or it should be chemically inert. Our work used a CO2 as tracer because it is chemically inert in the Mesosphere and Lower Thermosphere region. We utilized recently retrieved CO2 profiles from the Thermosphere-Ionosphere-Mesosphere Energetics and Dynamics (TIMED) satellite’s Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument. Our work provides the longest dataset on satellite-based eddy diffusion coefficient profiles derived from CO2. We hope to start an effort to calculate these coefficients using other satellite-derived chemical species. After calculating these profiles, we saw that they were very similar to eddy diffusion coefficients calculated by certain models that explicitly parameterizes breaking gravity waves with eddy diffusion coefficients. This led us to think that we may have just indirectly derived eddy diffusion coefficients that could parameterize breaking gravity waves. We are still doing more work to more robustly show this. Noting this though, we set these coefficients as a lower boundary condition in our electrodynamics general circulation model. This checked a recent suggestion that breaking gravity waves was the missing forcing that could completely drive the seasonal variations in thermospheric neutral density and ionospheric electron density. Similar to the aforementioned cold summer mesopause, the ionosphere and thermosphere is also not solely controlled by solar activity (Chapman mechanism) and in this case, geomagnetic activity. There are a lot of phenomena in our upper atmosphere that is found to require additional forcings from lower and middle atmospheric waves. Our work finally showed that our derived eddy diffusion coefficients cannot simulate the seasonal variations in the ionosphere and thermosphere. The first paper to cite our work further supported our suggestions by presenting a different dynamical mechanism centered on first-principles that they showed simulated the seasonal variations in the ionosphere and thermosphere.

4. How is your work in Academia Sinica related to your work at Manila Observatory and the Department of Physics in Ateneo de Manila University?

My current work is related to my undergraduate work at MO and Ateneo in that I utilized satellite data and did a lot of time-series analysis in both works. Interestingly though, I found out that the rainfall data from TRMM (Tropical Rainfall Measuring Mission of NASA) that I used for my undergraduate work was an instrumental observational evidence to the theory that ionospheric plasma bubbles are caused by convective activity in the troposphere via the vertical propagation of convectively-driven atmospheric waves through the middle atmosphere.

5. What is your normal day or week like? Are you a member of a Laboratory? Do you work alone or with a group?

I am a member of a laboratory under the Graduate Institute of Space Science in National Central University and also a laboratory under the Research Center for Environmental Change in Academia Sinica but we all do our research alone. It is our program’s policy that we should belong to two labs. In a normal week, I have one day for our lab meeting. The rest of the week is spent in the lab. On a normal day, I go to the lab and do the most important work from 9 am till 6 pm. It really depends, sometimes this could mean spending an entire day doing observational data analysis or modeling calculations or just reading and writing.

6. Can you describe the physical models and data sets that you use? How much computational power do you need for your models or to analyze your data? What is the computational infrastructure that allows you do such kind of research?

For my work, the data sets that I mostly use are satellite observations. I work with satellite-observations on temperature, CO2, electron density and neutral density. I also work with reanalysis datasets. Reanalysis datasets are datasets formed via complicated interpolation of numerous observations from ground-based stations to satellites. However, for my work, my methodology dictates I prioritize satellite data.

The physical models that I use include one-dimensional models and three-dimensional models. For the one-dimensional model, it is a photochemical and transport model that solves the continuity equation. The model includes the chemistry of the major non-nitrogen chemical species in the altitude range 0 – 130 km.

For the three-dimensional models, they are electrodynamics general circulation models developed by the National Center for Atmospheric Research (NCAR) in the US that solve the fully coupled, nonlinear, hydrodynamic, thermodynamic and continuity equations of neutral gas with the energy, momentum and continuity equations of ions in the thermosphere and ionosphere (from ~97 km to ~500 km). The external forcings accounted for are solar irradiance; geomagnetic energy; ionospheric convection; a specified upward and downward plasma flux at the upper boundary representing the interaction of the system with the plasmasphere; and perturbations at the lower boundary of the model by waves representing the interaction between the ionosphere-thermosphere region and the lower atmosphere.

The datasets that I have are all stored on our lab’s servers because of their massive sizes. The models that I use are also all ran on these servers. While my data-processing work are all done in either MATLAB or IDL, the models are all coded in FORTRAN for efficiency. An entire year’s worth of model run requires two days to finish. I also do decade-long model runs that require roughly a month to finish. In order to do this kind of research, one needs a powerful Linux cluster-system.

7. What are your five-year plans? Are you coming back to the country, pursue postdoctorate, or work in the industry?

My five-year plans include, of course, finishing my PhD and then, I’ll look for opportunities that can allow me to practice my training on atmospheric and space physics.

8. Any parting words for our Physics majors?

Whether you guys immediately opt to work or go to graduate school, understand that you guys will be starting your lives when you graduate. This is particularly difficult to understand for those considering graduate school. Some make the terrible mistake of thinking that graduate school postpones the reality that they are already starting their lives. This hinders them from always keeping in mind the more important things in life like being professional, being disciplined, being humble and thoroughly figuring out what they want in their lives. They’ve become blinded by the pleasure of finding things out (c.f. Richard Feynman). Doing advanced physics is cool but don’t ever lose sight that you have to juggle this with the advanced responsibilities of life. I’ve met numerous top-gun scientists and I’ve seen how their successes were founded not on how amazing they did their calculations and experiments but on how happily they lived their lives with their families. I credit my undergraduate adviser, Dr. Nofel Lagrosas, for constantly reminding me of these things when I was still in Ateneo.


Left: Jude Salinas with his lab-mates and boss (left-most) on their way to an observatory in Taiwan’s Mt. Lulin. They were are setting up a telescope system for observing airglow emissions in the upper atmosphere. Right: Jude Salinas with his poster that won second place under the Mesosphere-Lower Thermosphere division of the Student Poster Competition during the Coupling, Energetics, Dynamics of Atmospheric Regions Workshop in Santa Fe, New Mexico, USA.

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)