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STAFF LIST President Marissa Wu Vice Presidents Maggie Chen Vivian Shing Directors of Finance Emily Bi Victoria Li Directors of Editing Executive Editor Anthony Kang Supervising Editors Judy Qin Jessica Shen Directors of Layout Aida Razavilar Heezy Suh Layout Team Emily Bi Emma Boyles Samantha Chai Alyssa Cho Anjali Gopinathan Clara Guo Samruddhi Hande Elizabeth Kwon Harmonie Lau Victoria Li Susan Lin Amanda Tanaka Julie Tran
Cover art by Victoria Li Table of Contents art by Harmonie Lau and Susan Lin
Editing Team Taylor Albizati Emily Bi Emma Boyles Alyssa Cho Sai Gantla Paymon Haddad Amanda Harmon Allen Huang Anusha Jain Hunter Katz Paul Kreymborg Elizabeth Kwon Heloise Leblanc Christina Lee Jessica Li Allison Liu Andrea Liu Nikky Mendoza Rich Murphy Aadil Rehan Julie Tran Ashley Zhang Cecilia Zhang Michelle Zhang Jeanne Zheng Natalia Zorrilla Advisor Michael Gaughen
PRESIDENT CCA— With the arrival of the new year, we are proud to bring you the first issue of Volume 7 of Catalyst Science Magazine. The entire Catalyst team has worked extremely hard on this issue and we hope you enjoy it. In this issue, we introduce the landscape of the future, delving into up-and-coming technology. From redefining parenthood with mitochondrial replacement therapy to integrating lasers into daily life to dissecting a millennial’s posture, you’ll find exciting developments within these pages. Now that you know a little more about the future of science, why not learn about some future career possibilities, too? Take a look at some words of advice from professionals working in STEM fields. After all, as Newton said, “If I have seen further, it is by standing on the shoulders of giants.” We can all learn more about shaping the future by looking to those who have shaped the present. As always, I’d like to thank the Catalyst team for all their hard work in and outside of school on this issue, as well as our advisor, Mr. Gaughen, and our generous sponsors. I also extend my gratitude towards you, reader. Our magazine would not be possible without any of the support that we’ve received from all of you.
Enjoy! Sincerely, Marissa Wu
table of
CONTENTS
LASERS
01
GENERATION HUNCH //HUNTER KATZ
03
THE THREE PARENT TECHNIQUE
05
MALAYSIAN MATH TEACHER: INTERVIEW WITH RON TEH
06
TO BE A CHEMIST: AN INTERVIEW WITH YING QU
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AN INTERVIEW WITH YIFENG CUI: DIRECTOR OF THE HIGH PERFORMANCE GEOCOMPUTING LAB
08
//TARENEH BARJESTAH
//ELIZABETH KWON
//SAMANTHA CHAI
//VICTORIA LI
//PAUL KREYMBORG
LASERS
BY TARANEH BARJESTEH
You’ve seen phasers in Star Trek, lightsabers in Star Wars, and a myriad of other light-related weapons and accoutrements throughout the many science fiction franchises that have captured the world’s attention for the past two centuries. The history of the term “laser” (coined from the acronym “Light Amplification by Stimulated Emission of Radiation”) begins in 1918, when Mark Planck won the Nobel Prize in physics for his discovery of elementary energy. This led into Einstein’s proposal of stimulated emission: electrons could somehow be stimulated to emit light of a certain wavelength, as opposed to spontaneously emitting and absorbing light, the process that makes the modern laser what it is. In 1951, Charles Townes came up with the idea of a “maser,” or “Microwave Amplification by Stimulated Emission of Radiation.” Through collaboration between researchers at Columbia, Harvard, and the P.N. Lebedev Physical Institute in Moscow, “masers” were developed into “optical masers,” and when other types of waves on the electromagnetic spectrum were used in this technology, “masers” became known by their modern term, “lasers.” The light that allows us to see the world around us is only a small portion of the electromagnetic spectrum. We classify visual light as the section of the electromagnetic spectrum where the wavelengths of light range from 380 - 780 nm. Photons are the particles
that make up light, and they exhibit the properties of both a particle and a wave. They are miniscule packages of energy. Photons have no mass, and always move at the speed of light. The amount of energy packaged within photons depends on the wavelength of the electromagnetic spectrum that they are correlated with. Typically photons scatter; a certain quantity of photons bounce off or are absorbed by objects like photoreceptors in our eyes, and the energy from the absorption of photons changes the energy state of the photoreceptor. This change induces the photoreceptor to signal other optic nerve cells. Eventually, this signal reaches the brain, a process occurring within a fraction of a second. Lasers are different from other sources of light, like the sun or a fluorescent lightbulb, in that the light they emit is coherent. Encyclopedia Britannica defines coherence as “a fixed relationship between the phase of waves in a beam of radiation of a single frequency.” Essentially, if the phase difference between two waves of light is constant, then the beams of light are coherent and have a stable interference pattern with each other. A stable interference pattern indicates that when light is shined through two two narrow slits, the resulting light beams form evenly spaced bands. If a wave of light is drawn out, it has peaks and valleys with a “zero
crossing,” like the x axis on a graph representing time, horizontally between them. One “phase” on this graph would be the line beginning at the zero crossing, reaching a peak, crossing the zero crossing into the valley, and then ending at the zero crossing again. Imagine two different waves drawn out on the same graph, one with its phases much shorter than the other, and one where the “peaks” and “valleys” are farther apart. As long as these patterns for each individual wave of light (the phase pattern) and the interactions between the waves (the interference pattern) remain constant over time, the light is coherent. All lasers produce coherent light. Lasers exhibit spatial coherence: their waves have a constant relationship with each other at different points in space, either lateral or longitudinal. Lasers also demonstrate temporal coherence, a constant rate between waves at different moments in time. These properties make lasers incredibly useful, in everything from office supplies to car manufacturing and even medicine. The most common types of lasers in everyday life are semiconductor or diode lasers, which are present in printers, office pointers, and disk players. These lasers are small and use little power, and the majority of them generate a continuous output of light. Diode lasers can comprise a wide range of wavelengths as well. HeNe, or Helium Neon, gas lasers mainly emit red light, and CO2 lasers are generally used for cutting hard materials. Solid state lasers, such as the neodymium YAG (yttrium aluminum garnet) laser contain the material in a solid matrix and may emit infrared light. These lasers have a high output of energy and can vaporize material in machinery, which is useful for cutting portions of steel in industrial manufacturing. Excimer, or “excited dimer,” lasers mix a combination of reactive gases with inert gases. When electrically stimulated, they produce a dimer, and light in the ultraviolet range. Dimer lasers are used in eye surgery, manufacturing of computer chips, and micromachining. In medicine, lasers can be used in surgery to cut precisely, cancer therapies like photodynamic therapy, angioplasty, microscopy for visualization, and melanoma treatment. With this understanding of lasers, we can consider the following qustions: Could lightsabers, phasers and all that other cool tech from your favorite sci-fi movies, books, and T.V. shows be real or even practical in the future? According to Dictionary.com (yes, they have an entry in the dictionary), a light saber is “a sword whose blade is in the form of a laser or powerful beam of light, as used by the Jedi knights in the Star Wars movies.” Wookieepedia adds that this light beam/blade is plasma and is powered by kyber crystals (which unfortunately only exist(ed) a long time ago, in a galaxy far, far away). So, aside from the obvious impracticality of using Force-attuned crystals, how would these lightsabers hold up in real life? The blade would likely be a CO2 laser with a wavelength in the infrared spectrum; it would use a curved mirror or a special lens to focus the light into a beam that would ensure perfectly round shape and consistent energy density. Since the part of the beam that would cut is only ¾ of an inch in diameter, the energy in that area would be extremely powerful. This concept is similar to the common experiment involving starting a fire with a magnifying glass and a leaf, but the effect is much more intense. In addition to CO2, a compressed gas such as nitrogen or oxygen would flow through the nozzle. Colors such as blue or red, could be added for aesthetic effect. But whether combat could actually work with this type of weapon is difficult to determine. The “blade” would be dangerous, for yourself and your opponent, as it would be able to melt, vaporize, or burn upon contact, depending on the intensity of the laser. A mirror wielded by your opponent could easily reflect this energy back onto yourself. Additionally, it would be difficult to shorten the blade without compromising energy, since the speed at which light travels at is extremely fast. In order for this sort of a laser to work properly, it would also need to be plugged into an outlet. And given that there is no sound created by this light, fight scenes would be a whole lot less exciting than the ones depicted on the silver screen. Sorry, Star Wars fans.
Fans of Star Trek may be happy—or terrified—to hear that scientists working for the FBI and CIA are already designing phaser-like weapons for use in the police force and military. Dictionary.com defines a phaser as “a weapon that delivers a particle beam that can stun or annihilate.” In science fiction, the size and intensity of the beam can be shifted at will (“Set phasers to stun!”). The real-life technology uses a laser that has enough energy to ionize atmospheric gas and create a plasma channel, which has an extremely low electrical resistance, allowing continuous high voltage flow so long as there is enough energy to heat the plasma. The microwaves pulsed along this plasma channel potentially have the destructive power of man-made lightning. In theory, this sort of weapon could be used for anything from stunning a violent criminal to stopping a car in its tracks to even destroying cities from afar. Mirrors used to arrange the light, could lower, intensify, or stop the beam. The drawbacks of this sort of weapon are similar to those of lightsabers: an impractical amount of energy is required, and the weapon itself would be bulky and difficult to use. Regardless, nothing resembling the “phasers” of Star Trek has been created so far. While the possibilities of sci-fiesque weapons are exciting, laser technology is now expanding most rapidly in the manufacturing and medical fields, where a whole slew of cures and efficient procedures are waiting to be discovered. Although this article did not delve very deeply into the science of light, if you are more interested in laser technology, here are some great articles and textbooks to help! (Most of the books can be found on Amazon or in the Theodore Geisel library at UCSD). • •
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On the basics regarding the use of lasers in medicine, including laser-tissue interactions: Lasers In Medicine, by Ronald W. Waynant On the basics of photodynamic therapy, from the Department of Molecular Cell Biology, Cell Death Research and Therapy Laboratory, Catholic University of Leuven, Belgium. (This was published on PubMed; links to research on specific types of cancer are included). https://www.ncbi.nlm.nih.gov/pubmed/21617154 On skin cancer treatments using lasers: https://www.ncbi.nlm.nih. gov/pubmedhealth/PMH0032519/ Further exploring the math and programing aspects behind electromagnetic waves for plasma physics and engineering: Electromagnetic Waves, Materials, and Computation with MATLAB® by Dikshitulu K. Kalluri. (Note: this is very calculus-heavy, advanced material). An interesting and clear introduction into lasers: Principles of Lasers (fifth edition) by Orazio Svelto On the use of lasers in manufacturing: Laser Additive Manufacturing: Materials, Design, Technologies, and Applications (Woodhead Publishing Series in Electronic and Optical Materials) 1st Edition by Milan Brandt For an introductory, non-mathematical approach to the science of light and its relation to photography and art: Light Science: Physics and the Visual Arts by Thomas Rossing and Christopher J Chiaverina And of course… Star Wars Light Sabers: A Guide to Weapons of the Force by Pablo Hidalgo, for everything you have ever wanted to know about light-sabers.
Sources (not including books and sites listed above): http://www.physics.org/article-questions.asp?id=59 http://www.ies.org/lighting/science/ http://physics.stackexchange.com/questions/137293/what-happens-to-photons-after-they-hitobjects https://en.wikipedia.org/wiki/Coherence_(physics) https://www.britannica.com/science/coherence http://www.scienceclarified.com/scitech/Lasers/Medical-Uses-of-Lasers.html http://minerva. union.edu/newmanj/Physics100/Applications/lasers_in_industry.htm http://oregonstate.edu/ehs/laser/training/laser-types-and-classification https://www.rp-photonics.com/semiconductor_lasers.html https://www.rp-photonics.com/solid_state_lasers.html http://starwars.wikia.com/wiki/Lightsaber http://www.esabna.com/us/en/education/blog/how-does-laser-cutting-work.cfm https://www.wired.com/2009/04/armys-multimo-1/ https://www.newscientist.com/article/mg20227045.500-microwaves-could-defuse-bombs-fromafar http://www.photonics.com/EDU/Handbook.aspx?AID=42279
Image Credit: Yann Caradec @Flickr
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ith the advancements of technology in the 21st century, many people are developing the ‘hunchback’ posture. Many students at CCA are not aware of the harmful effects of hunching due to their busy schedules. We are constantly slouched over our computers, cell phones, iPads— the list goes on and on. This can be not only a major health concern, but also a social concern as we mature into adults.. Millennials are the first generation where hunching has became the norm, so much so, that one might as well call us ‘Generation Hunch.’ Not only are we hurting our spines, but we are also hindering our everyday life. We as millennials and as Americans need to be able to correct our posture so we can live long healthy lives. Here are a few things to consider the next time we look into our smartphones. Hunching can be detrimental to our health. It causes back pain, neck pain and tension throughout the body. Hunching affects 10 million Americans and can result in Osteoporosis and Parkinson’s disease. Paul Ingram from painscience.com writes that, “After working as a massage therapist for many years, I became confident that poor posture is a “real” thing. I think it is sometimes a factor in chronic pain, mostly later in life, and probably can also be improved in some cases with a little effort.” Due to the advancements in technology, many more people are constantly hunching on a daily basis. Americans use technology over ten hours a day which means that the impacts of computers, smartphones and other electronic devices can be tremendously unhealthy for your neck. When people hunch, they gain 10 pounds to their perceived body weight. Many medical professionals warn of the insidious side effects that come along with hunching. Surgical Technology International states that texting can have serious effects on your spine, including 50 pounds being added on your back. “Many people, upcoming generations especially, essentially grew up in these positions. Much of the entertainment today relies on a screen of some kind, and if it’s not a TV or desktop computer,
it’s a tablet or smartphone that sits comfortably in a person’s hand, but at the same time demands the user crane his or her neck to use it. One estimate suggests people use these devices for roughly two to four hours a day, meaning our necks stay bent for 700 to 1,400 hours in a given year. High school students are even worse, Hansraj says. They may hit 5,000 hours before they graduate,” as noted by Medicaldaily.com. Hunching also leads to more medical health conditions later on in life. People who commonly hunch also are more likely to suffer from scoliosis or kyphosis which are problems specifically for adolescents and the elderly. Poor posture can be grave if not treated early or properly. Hunching can also have a huge impact for adolescents in social situations and can cause emotional pain. Descriptions in literature and films of people with poor posture are viewed in a negative light. In Victor Hugo’s novel The Hunchback of Notre Dame, the main character Quasimodo, although loving and kind, is mocked in society due to his hunchback position. Additionally, Fritz the hunchback in the 1931 film Frankenstein is portrayed as incompetent. Posture and hunching also have a big impact on nonverbal communication and social cues. Those with good posture are often seen in society as ‘confident’ and ‘pleasing’ whereas those with poor posture are often seen as having ‘low self-confidence’ or ‘depressed. People with poor posture are also victims of social stress suffering from insecurity. People with poor posture are also victims of social stress and can suffer from insecurity. “Four studies were conducted in a laboratory setting to examine whether variations in physical posture can have a regulatory or feedback role affecting motivation and emotion. The results of the first study, which were replicated in the second study, revealed that subjects who had been temporarily placed in a slumped, depressed physical posture later appeared to de
H
velop helplessness more readily, as assessed by their lack of persistence in a standard learned helplessness task, than did subjects who had been placed in an expansive, upright posture; surprisingly, there were no differences in verbal reports. The third study established that physical posture was an important cue in observers’ verbal reports of depression in another person. The fourth study further explored the role of posture in self-reports of emotion using another posture. The results indicated that subjects who were placed in a hunched, threatened physical posture verbally reported self-perceptions of greater stress than subjects who were placed in a relaxed position,” as stated in Motivation and Emotion Volume 6, Issue 3.
It is also commonly noted that one’s posture is a gateway to their emotions. The embodied emotion theory suggests that mental events can be interpreted through one’s body whereas disappointment can be attributed to slumped shoulders. Hunching is commonly known as closed posture where a person is giving off an unfriendly or unpleasant vibe to other people. According to a volume 20 of The Arts of Psychotherapy found that people with closed posture give off body sensations through negative emotions. Hunching not only impacts your health but can also your social life. It may seem like a chore, but having good posture will go a long way not just for your health, but also for your everyday life. Millennials need to be willing to lead the way for future generations for a healthy lifestyle. Posture braces and other scientific advancements are currently helping people stand up straight for those who need it. So the next time you use a computer, remember to sit up straight. Not only will it make your back feel better,W but it will also make you look more confident, and feel stronger and better as whole.
h c n u Image Credit: Garry Knight @ Flickr
Image Credit: Caroline Davis @Flickr
Three-Parent Technique by E l i z a b e t h K w o n That’s right: you read that correctly. On April 6, 2016, a Jordanian couple gave birth to the first baby developed through the three-parent technique. This is also known as mitochondrial replacement therapy (MRT). The couple decided on this technique when they found out that the mother of the baby was a carrier of Leigh syndrome, a rare, genetic disease that degenerates the central nervous system and leads to neurological deterioration found in the mitochondria. How exactly is an embryo formed with the DNA of three people? Usually, two eggs (one from the mother, the other from a donor) are fertilized with the father’s sperm. Before the eggs begin dividing, the nuclei are removed from both the donor and the mother’s eggs. Then, the nucleus from the mother’s egg is placed into the donor’s egg. The nucleus contains all the genetic material of the mother and father, except for the mitochondrial DNA that carries Leigh disease. The Jordanian couple, however, chose a different method (called spindle nuclear transfer) due to religious reasons. Instead of having both the donor’s egg and mother’s egg fertilized, only the donor’s egg underwent fertilization. Fortunately, a healthy baby boy was born with less than one percent of his mitochondria carrying the disease.
sons. Zhang’s procedure, carried out in Mexico (a decision often referred to as “medical tourism”), is concerning to many people. The reason why the Jordanian couple had their baby in Mexico was because pronuclear transfer is currently banned in the United States. Zhang told the New Scientist magazine that “there are no rules in Mexico,” which aroused skepticism about whether the experiment was even under proper ethical and regulatory supervision. Rosario Isasi, a legal scholar at the University of Miami, criticized the decision of carrying out the project in Mexico, noting that Mexico had a reputation for attracting patients who receive unproven and possibly unsafe treatments that are illegal in their home countries. Another reason for the project’s controversy was the number of unresolved issues and unanswered questions that came with Zhang’s project. For example, what would be the long-term effects on this child? Although it is highly unlikely the baby boy will develop Leigh syndrome, such major manipulations on the egg cell have unknown effects and could cause problems such as an increased chance of diabetes. Lastly, there are many ethical questions and concerns regarding Zhang’s work, which he self-justified by stating that “to save lives is the ethical thing to do.” The Institute of Medicine, however, disagreed, arguing it “does not address a medical need” and “would not treat an existing person for a disease, illness, or condition.”
MRT has opened a door that doesn’t have to be closed.
This was not the first attempt of spindle nuclear transfer. In the 1990s, three-parent babies were born, but through a different technique of MRT where the mitochondrial and cellular material was transferred into the mother’s fertilized egg instead of the donor’s egg. Additionally, at Sun Yat-Sen University in China in 2003, five embryos were implanted in a woman through a project led by John Zhang, the doctor who also monitored the Jordanian couple’s delivery. One of the five embryos was aborted to increase the chance of survival of the other four. The mother became pregnant with twins but miscarried them a couple months into the pregnancy. After the failed attempt, the approach was banned in China and sparked much controversy, receiving criticism from anti-abortion groups. The Jordanian baby project was similarly controversial for a variety of rea-
While opinions about the ethicality and necessity of this project differ, the impact MRT will have for people who do have mitochondrial DNA mutations will overall be positive. Especially for cases like that of the Jordanian couple, where there are few other options due to religious reasons, the spindle nuclear transfer method will give people opportunities to have children. Despite the currently unanswered questions regarding spindle nuclear transfer, MRT has opened a door that doesn’t have to be closed. After more regulation and testing of the procedures, mitochondrial replacement therapy may become legal in the U.S. and other countries. Hopefully, as mitochondrial replacement therapy becomes more commercial, families with terminal or lifelong genetic diseases will be able to safely have children.
Image Credit: Kevin Poh @ Flick
Malaysian Math Teacher
Interview with Ron Teh
by Samantha Chai
Image Credit: Abul Az Abu Jamil @ Flickr
Ronald Teh grew up in the small rural village of Perak, Malaysia. During his school years, he was a below-average student, but later became a well-respected mathematics teacher in his hometown. In the early 1990s, he moved to the United States where he utilized his skills to work as a senior tech for Micron. He retired in the early 2000s, and now resides in Boise, Idaho. He enjoys spending his free time biking along the Boise Greenbelt trails, cooking his favorite hometown Malaysian dishes, and travelling the world. Teh also enjoys helping his godchildren in California with their integrated math homework. Canyon Crest Academy 10th grader, Samantha Chai, had the chance to ask Ron Teh a few questions regarding his career of teaching in a foreign country and being an engineering senior technician.
Ron Teh pictured above
How long have you/had you worked in the STEM field? Twenty years as a math teacher and 12 years as a senior tech in the semi-conductor field. How and why did you pursue a career in teaching and working in the semiconductor industry? Teaching: I loved mathematics as a child and found it as a universal language that anyone from any part of the world could decipher. My passion for sports also helped with being relevant to students, since math could easily be applied to sports. As for my career as a senior tech in Micron, my interest in new technology and innovation inspired me. What is your favorite part of the job? As a teacher, my favorite part was definitely the human feedback when my students do well and score high grades in the exams. Receiving recognition from students and parents is a very motivating push. Later, as a semiconductor tech, being able to write a program to find the cause of defects on wafers was memorable. What part of your job do you find most difficult? Helping students who are having very little knowledge of basic math, coupled with a lack of effort and absent mindset to learn, proved to be difficult as a teacher. As a semiconductor tech, frustrations would arise when the cause of the defects on the wafers in order to eliminate them immediately from the original source could not be identified. But it was worth it at the end since I was able to devise a program to identify them.
Which skills and abilities do you find to be the most important in this career? Making math an interesting and easy-to-learn subject is vital since many people view it as a difficult subject. If students have genuine interest, they can solve problems on their own. Then, the ability to apply math skills to write a useful program was important in my later career. What is/was your typical day like? Just like the typical day of a student, a typical day of a teacher can be happy, present frustrations at times, anxious, stressful! Every day as a semiconductor tech presented a new challenge because I had to create a new program for each job. Are there any memorable stories from your time as a teacher in Malaysia or a tech in Idaho? As a teacher, the best job satisfaction feeling is keeping in touch with my students after four decades or more and seeing them doing well in life. Also, the feeling of achievement after my students would walk out of the exam room with full confidence that they did not make any mistakes made me proud. Getting praise for a job well done really boosts self-confidence and motivation, which I also experienced after receiving praise from other engineers and my supervisors. Do you have any advice to students aspiring to be a teacher or tech? Go for it and fully enjoy what you love to do even when things get tough. And don’t underestimate your abilities.
TO BE A CHEMIST: An Interview with Ying Qu by Victoria Li Ying Qu, Ph.D. is currently a senior scientist at Exagen Diagnostics, where she led a project to develop a new biomarker for monitoring therapeutic drug use for diseases like rheumatoid arthritis and lupus. She has a bachelor’s and master’s degree in chemistry from Lanzhou University and a Ph.D. in neuroscience from the Catholic University of Leuven. Q: How and why did you pursue a career in chemistry? A: In high school, I competed in the city-wide— and eventually provincial—chemistry competition back in my hometown in China. To my surprise, I actually placed in the top thirty! I was very proud and never considered anything besides becoming a chemist after that. After I moved to the U.S., I was interviewed for a job where I could work for the sake of patients, and that’s where I am at now. Q: What is your favorite part about your job? A: It’s very rewarding to know that you contributed to something new that changes people’s lives for the better; instead of having patients having to give 10 milliliters of venous blood, they now only have to have 10 microliters of capillary blood extracted from the fingertips. Also, it was originally very difficult to transport the glass containers of blood in a controlled temperature to be tested at a lab, but now it can just be stuffed into an envelope and mailed! Q: What part of your job do you find the most difficult? A: Well, it seemed impossible at first to accomplish my goal, because the instruments provided to me were not sensitive enough to detect the tiny amounts of medicine in the tiny amounts of blood. I had to stay optimistic that this new method would eventually succeed—even with insufficient materials—and it was hard doing so. Q: What skills and abilities do you find to be the
most important in this career? A: I have had more than thirty years of work experience in analytical chemistry and mass spectrometry prior to working on this project. But more importantly, I was motivated to do my work everyday, because I could use my experience to solve problems and the impossible… Yep, that’s it! Q: How would you describe your typical workday? A: I get to work early, make myself some coffee, and check the latest data. Usually I discuss the results from the mass spectrometer with the younger scientists, to help them in their training. Then, we start designing the next experiment. After lunch, I start writing up the results from previous experiments, and I sometimes read the scientific journal if I have time. What I do varies day to day, but read, write, and design: that’s basically what I do. Q: Are there any memorable stories from your time as a neuropharmacologist or analytical chemist? A: When I was at the NIH, I researched the effectiveness of antidepressants on chronic mental illnesses. This went on for three years. At the end, I felt very helpless when my results showed the bad side effects of the commercial antidepressants on the market outweighed the benefits; it kind of made me think that it was impossible to cure anything with medicine, and it was discouraging. Q: Do you have any advice for students aspiring to pursue your career? A: Hm... I really haven’t thought about this before... Do it! You will like it!
Image: Exagen Diagnostics, Inc.
An Interview with Yifeng Cui
Director of the High Performance Geocomputing Lab BY PAUL KREYMBORG
Dr. Yifeng Cui is the director of the High Performance Geocomputing Lab, a laboratory “conducting research on high performance computing, data intensive computing, and grid computing to support geoscience applications, with particular emphasis on computational seismology” ( http://hpgeoc.sdsc.edu/). The research that he currently leads could be especially useful for predicting the outcomes of earthquakes. Seismologists today predict earthquakes by analyzing measurements taken by seismographs that were active during past earthquakes. This method, however, is limited in that it only provides information on what would happen in earthquakes similar to those that have been recorded before and, even then, only with information on what the earthquake would be like at the specific locations of the seismographs during the recorded earthquake. Future computer-predicted earthquakes could place virtual seismographs at any point in the region simulated for an earthquake, then simulate the earthquake and find what kind of shaking would be experienced on those points. The applications of this technology would be numerous: an architect could simulate a location-specific earthquake on a 3D model of their proposed building, or an insurance company could use earthquake models to determine how much their earthquake insurance should cost. While the software and hardware to perform these simulations don’t provide enough accuracy for detailed data yet, it’s only a matter of time before exponentially increasing computer power and researchers like Dr. Cui make it possible. Here is an email interview conducted with Yifeng Cui. - What operating system is used by the HPGeoC Lab when it runs earthquake simulations? What sets it apart from the operating systems commonly used on PCs? Large-Scale 3D ground motion simulations are run on supercomputers. Earthquake threat is highly time-dependent and involves terribly violent, but known, physics. Accurate simulations must span an enormous range of scale, from meters near the earthquake source to hundreds of kilometers across entire region, and time scales from hundredths of a second to capture the higher frequencies. Modeling of earthquake dynamics is one of the most challenging computational problems in science. PCs are not fast enough to solve these complex problems, not even the fastest supercomputer in the world today. - What are the limiting factors that prevent earthquake simulations from being more complex than they are right now? Do the accuracy and detail of the simulation depend more on the software of the simulations or the computing abilities of the supercomputer? Earthquake simulations used to be 2D, but advanced computing technology made it possible to run full scale 3D dynamic rupture and wave propagation simulations today. Carrying out large-scale, high-resolution simulations, however, requires orders of magnitude more computing power than studies done to date. More advanced physics is needed to improve the accuracy of the models; for example, the nonlinearity must be addressed in order to produce more realistic seismograms at high frequencies. Faster supercomputers are needed when moving to high frequency simulations . We are capable of running 2-Hz wall-to-wall scenarios on the Southern California region with today’s computing capabilities, but our goal is to include frequencies up to 10-Hz, which is relevant to building engineering design. - Where does funding for the HPGeoC Lab come from? Most of our funding comes from the National Science Foundation through the Southern California Earthquake Center at USC. We also receive funds from Intel, NVIDIA, and the Keck Foundation. We also receive support from the NSF-funded Extreme Science and Engineering Discovery Environment, also known as XSEDE. - What are the applications of your work for California and the world? Why is this research worthwhile? The software developed at our lab can be used to predict realistic ground motions anywhere in the world, though our emphasis has been on Southern California. We will have our open source software released soon on GitHub. We have used the software for multiple San Andreas fault scenario
Image Credit: JoL @ YouTube
simulations called TeraShake, ShakeOut-D, and M8, which revealed order-of-magnitude San Andreas to Los Angeles wave-guide amplification. We also used the software for a Pacific Northwest megathrust scenario, causing 5 of minutes shaking in Seattle. The software is community code that has been used by Southern California Earthquake Center seismologists for production runs, in particular for seismic hazard analysis. Our code, for example, is making a statewide hazard model a goal reachable with existing supercomputers. - How long has the HPGeoC Lab existed? Around 12 years since TeraShake simulation. - What programming languages are used to run the simulations? We have a CPU-based Fortran+MPI code. MPI is a standardized and portable message-passing interface, used for programming parallel computers. We also have a GPU version C+CUDA+MPI code that runs on NVIDIA-based accelerators. The GPU code is particularly powerful and efficient. We are in the process of developing a hybrid C/MPI/OpenMP code preparing for Intel’s next generation many-core architecture. Architectures are changing rapidly, and so are programming models. - What advancements in earthquake simulations do you predict will occur in the next 10 years? Earthquake prediction problems remain mostly unsolved. Probabilistic seismic hazard analysis will play a central role in earthquake forecasting in coming years. This is a great opportunity for a new generation of computational seismologists to take on the challenge of earthquake system science. - What are the largest obstacles in researching at the HPGeoC Lab? Earthquake simulations are interdisciplinary, multi-institutional efforts. Our research is done in the best spirit of collaboration. Computational science as a “third pillar,” however, still has significant obstacles today in rigid disciplinary silos in academia that mirror our organizational structure.
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