Biological systems are inherently very complex in nature, typically consisting of multiple highly non-linear molecular interactions. As a result, even relatively small networks, such as the lactose regulation network in bacteria, tend to display very complex behaviors.
One such network is the DNA damage response network which plays a major role in tumor suppression. The central hub of this network is the p53 protein; it plays a critical role in guarding against cancer development. In humans, p53 is part of a sophisticated network of proteins that mediate cell fate decisions such as the initiation of cell-cycle arrest, DNA repair and apoptosis. Aside from p53, this network includes a set of core regulation proteins among a host of other upstream, downstream and intermediate species involved in sensing, transduction and regulation.
In collaboration with the Proulx lab in the Evolution, Ecology and Molecular Biology (EEMB) department, we explored the evolutionary history of the DNA damage response network. While the p53 protein’s function seems to have been preserved for over one billion years, this is not the case for the other core regulation proteins in the network.
We use the evolutionary analysis as the starting point to partition our dynamical model of the p53 network into smaller sub-units or "modules", such that properties of the network can be inferred from properties of these modules. Using this modular analysis, we attempt to infer the function of each module within the network. Our results show an evolutionary path towards networks with an increasingly complex structure of multi-stability, which we conjecture is associated with cell fate decisions.
I will never forget that when I first came to UCSB as a PhD student in Controls, I thought I would choose any project other than one that involved Systems Biology! I met Prof. Mustafa Khammash (then at UCSB) casually and he gave me a set of papers to read. One paper that he co-authored changed my entire perspective on the field. It was a paper about calcium homeostasis in cows. The paper went on to mention that two hormones are known to control this homeostasis, although one is thought by Biologists to be redundant. By modeling the network as an integral feedback loop the authors showed that both hormones are actually necessary, otherwise after lactation, the calcium levels would not return to their nominal level. The thought that simple ideas from undergraduate control theory could be so powerful in explaining complex biological phenomena was what lead me to pursue Systems Biology related research.
Due to the highly interdisciplinary nature of my work, I find it most rewarding when I am able to present my work to both engineers and biologists in a way that they can understand.
UCSB has one of the strongest Control theory groups in the country. To get an opportunity to work and interact with the faculty here is an honor.
My advisor Prof. Joao Hespanha has been incredibly supportive throughout my PhD. He has been instrumental in me pursuing Systems Biology research, even though I had very limited prior knowledge in Biology. Whenever I have problems with my research, he is always able to offer a very simple (although incredibly insightful) solution. I'm also thankful to have a great set of lab-mates that I see every day. We have a very diverse lab with students, post-docs and visitors of multiple nationalities. When we're not discussing work, a lot of our conversations center around football (soccer) and world politics!
I hope to use my quantitative background and interdisciplinary experience in both Engineering and Biology to study and infer the plethora of data that is available about complex biological networks. I believe that this is certainly the future when it comes to studying complex biological networks. I hope to become a Data Scientist in the industry in the short-term future. I also hope to get an opportunity to teach in an academic environment, as teaching is a strong passion of mine.
The greatest strength of the program is how approachable the faculty are. I have taken so many classes and learned so much from them, in no small part thanks to the faculty. I have never felt inadequate, even when asking the most fundamental questions to my Professors in class. Of course, it is worth mentioning that the department is engaged in cutting-edge research.
My favorite courses as a graduate student are ME 215A and B (Dynamical Systems Theory) taught by Profs Igor Mezic and Jeff Moehlis. As a Control Theory student with an ECE background, I somewhat understood the underlying dynamics in systems. However, most of the focus in Control is on the design and analysis of the controllers. Taking Dynamical Systems Theory opened up my mind to how and why systems behave in the way they do, and I highly recommend all Control students with an ECE background to take these two classes.
Screening exam: The screening exam was quite an experience; essentially, 5 Professors ask you any question under the sun about all your relevant undergraduate work. Although I was extremely nervous before the exam, one of my lab mates told me something on the morning of my exam that certainly helped me, and I hope will help others as well. Don't worry, the Professors are there to help you and not to fail you. Just relax and work through the questions with them.
Qualifying exam: The qualifying exam was a less intense experience, since one is talking about one's own work. Preparing for the qualifying exam certainly helped me to organize my thoughts and my findings, which I feel is an extremely important part of the PhD. It also helped to build my presentation skills; speaking out loud in a clear fashion is certainly very different from mulling over thoughts in my head!
I am currently working on my thesis.
TA – In my first year, I taught ECE 130A, 130B and 139. Every week, I would plan a 1.5 hour lecture to deliver during the discussion section (for all 3 classes), and of course hold office hours as well. Teaching is my greatest passion, and I really enjoy being able to simplify concepts to teach students. I think it is key to bring oneself down to the level of the students. As someone who struggled with these 3 (very mathematical) classes as an undergrad myself, I was able to identify the concepts that confused me and therefore what would probably confuse other students. Graphical convolution is certainly one of the most confounding things when one first learns about it, only to realize that one will never have to use it again!
GSR – Research on its own is very interesting, which is why I pursued a graduate degree. I think the key thing I didn't realize as an undergraduate student was how challenging it can be to define a research problem, and communicate the idea behind this problem effectively. It is almost like designing your own product. What is it? Why is it useful? Why is it novel? Moreover,as time passed during my PhD and I became more familiar with the research area, the problem definition itself (along with the solution) morphed a little bit. It was unexpected at first, but I slowly got the hang of it.
I have a time table which I try to follow. I make sure I reserve time on the weekends to take care of myself (cooking, grocery shopping, cleaning), be involved in music and speak to my wife (who is a PhD student in the East Coast). I think it is also very important to stay mentally relaxed, so I do actively have to disconnect my mind from research on most nights. I also ensure that I run in the evenings a few times a week.
Till the Fall of 2014, on nights and weekends, I was actively involved in 2 student groups on campus. With some close friends, I founded UCSB Agni, an Indian Classical music and dance group that fosters student artists and organizes performances on campus for students and the community. I was also part of UCSB Ravaani, the university's South Asian Acapella team. Going for Acapella practices, making music with my friends and preparing for performances used to take up most of my evenings and weekends. I also made some great friends in the process, many of whom have graduated but are still in touch. Since then I have gotten busier with my research, but still perform sporadically around campus. I hope to be more active in music once I graduate!
Fingers crossed, I am looking to graduate by the end of this summer. So I'll definitely be here!
My advice is as follows:
1) Be patient. If positive results came quickly, we would all be done with our PhDs in a year! We are all swimming in unknown territory, but if we keep at it, results will certainly come.
2) Stay calm. Unlike in undergrad when stress levels elevate before exams and then drop, the stress slowly and gradually builds up in the PhD. I did not even realize the stress levels building up until others pointed it out to me! It helps to actively engage in research when you are at work, and actively disengage when you are relaxing. Set aside time to relax, and try to focus better when you are doing work. It also helps to exercise regularly, even if it is for a short while.
3) Avoid competition. It is very easy to get caught up in comparing the number of publications, citations and time to graduation against others. However, I think that time is better spent focusing on one's own research problem. Remember, everyone's PhD is different. The PhD is a journey in academic maturity, and avoiding unnecessary competition and barometers for success helps make it much more pleasurable.
Typical light-matter interactions have size scales in which the wavelength of light and the size of the object it is interacting with are very different. When light interacts with objects that have sizes similar to the wavelength of light, then interesting things start happening and we can actually start to control the way light behaves. In this size regime, objects exhibit a series of resonances at certain wavelengths, known as multipolar resonances. By manipulating these resonances, researchers have created new materials with very interesting optical properties beyond those of naturally occurring materials, known as metamaterials. Typically, researchers manipulate these multipolar resonances by changing the physical properties of the objects (e.g., size, shape, material, etc.). Instead, my research focuses on manipulating the properties of the light. This enables a completely different way of manipulating multipolar phenomena.
When I started college I wanted to be an engineer, but didn't know what kind. I initially wanted to be any kind of engineer except an Electrical Engineer, because that's what my father is and I wanted to do something different. But after I started taking college classes, I realized EE is actually what I really like. I enjoyed physics in high school but never wanted to be a physicist, and EE is a happy medium between physics and engineering.
I selected the ECE department at UCSB because it has a fantastic reputation and because I had lived in Michigan my whole life before then, and I wanted to experience living somewhere different. I had applied to the Master's program at first as I wasn't sure I wanted to do a PhD, but that quickly changed after I arrived at UCSB.
When things go right in research, it's one of the most satisfying feelings in the world!
Although our research group is the only one at UCSB that works on metamaterials, we collaborate with other groups for a variety of purposes. One of my labmates is working on building a specialized measurement setup, and he gets his samples from a group in the Materials department. Another labmate of mine is working on a reconfigurable metamaterial that requires a lot of semiconductor device design, and he collaborates with the Mishra and Palmstrom groups to figure out his design and to get material to actually fabricate his design. We also have collaborations with Brown University and UCSD.
I really enjoy working with my research group. We fit really well together. They are all really interesting people and I enjoy learning from them and being exposed to things I normally wouldn't be exposed to. Many of my labmates possess important research skills that I lack, and it's extremely beneficial to be surrounded by them so I can learn from them. Additionally, when I started out with Jon, my advisor, I didn't have a background in this field. Jumping into something completely new was intimidating, at first, but partly because our research group is so new (Jon joined UCSB in 2012), we were all new to the field and all learning together.
I plan to transition into a career in which I can more directly see the impacts of the work I do by bridging the gap between science and society. I don't think there are enough scientists in positions where they are regularly interacting with and impacting the public in meaningful ways, which has contributed to a disconnect between the scientific realm and the public. Specifically, I plan to go into a career related to science education or policy.
There are many knowledgeable students and professors who excel at a wide variety of research. If there is any question you have about some type of software, or some type of circuit or device you are trying to design, a useful conversation about it is just an email away. Also, many students in ECE research groups are actually from other departments which naturally encourages multidisciplinary projects.
My favorite course at UCSB was Digital Circuit Design taught by Luke Theogarajan. I doubt I would have said that at the time I was taking the course, and even though I learned only half of what was taught, even that half was an incredible amount of information. A lot of my appreciation for that class was because Luke was teaching it. He is one of those rare professors who actually takes a personal interest in the success of the students he encounters.
Preparing for the screening exam was pretty stressful at the time. I was preparing for the screening exam over the summer, when I was also doing a full time internship. I was grateful when it was over. The qualifying exam was far less stressful, since it is a presentation about my research, which I already knew. There is less room for the unexpected in a qualifying exam.
It's a see-saw. Sometimes research is extremely busy and I have a ton of deadlines and there is no balance, and other times I can breathe a little and there is time to have fun. I try to take advantage of that time when it comes.
I lived in San Clemente my first year, which was fun as I got to meet many grad students in a variety of departments. However, I have since moved into an off-campus apartment which I also very much enjoy. I am in an apartment complex where plenty of UCSB grad students live. Santa Barbara public transportation is great and it's easy to get around by bus. I also really appreciate the location of Santa Barbara in terms of where it is in the state of California. SB is about equidistant from both Yosemite National Park and Las Vegas. There are so many places to explore in this region of the U.S. and they are all a road trip away, which also makes SB a great place to live.
This summer I stayed in SB and did research.
The typical advice is to make sure you and your advisor get along and have a good relationship, but I would say it is equally if not more important to make sure this is true for your labmates as well. They are the people you will see and interact with the most often. Being friends with them and genuinely liking them will make grad school life much more bearable. Also, after you stop taking classes, realize that there is no longer an externally imposed structure on your life. Recognize this and impose your own structure so you make sure you get things done.
My fascination with computers began at an early age. The more I learned, the more complex and intriguing further learning became. As a high school student, I chose UCSB for the location and its prominent social scene. What got me to stay for grad school were UCSB's excellent academic standings and the beautiful campus which provides a relaxing atmosphere.
Very large amounts of data are produced during manufacture and test of semiconductors, but analysis techniques applied in practice do not utilize all the information available in that data. Our research focuses on applying state-of-the-art approaches from the machine learning field to advance semiconductor testing, as well as developing novel techniques suited for the specific problems at hand. The goal of test data analysis is to find the right balance while attempting to improve quality, reduce test cost, and increase yield.
I took Professor Li-C. Wang's courses as an undergraduate and was quickly captivated by his way of thinking and approaching problems. I reached out to him to learn about his group's research and was so fascinated by it that I eagerly decided to try to join the group and help move the research forward. I think what persuaded me the most was how clear the application of the research was to real problems.
Doing my undergrad at UCSB exposed me to our phenomenal faculty. The professors in our ECE department are great mentors and are some of the top experts in their fields. I also looked at PhD program rankings in ECE across the country, and at the time UCSB was ranked 5th so that was a huge plus.
Since we work closely with industry, we actually get to see our methodologies applied in practice. It's very exciting to see our ideas come to life, and getting praise from engineers for helping them solve critical problems is very rewarding. This close industry partnership is rather unique for academic research groups, which pushes us to do our best to maintain it.
From what I've seen so far, collaboration is the single most important element of successful research. The atmosphere in the ECE department is always very encouraging towards collaborating with peers and faculty. I feel very comfortable discussing my research with students from other groups, and I also find it interesting to hear about the research they are working on. Such discussions often lead to exchanges of ideas which help to uncover new perspectives of the problem at hand.
The collaborative aspect of research is what truly enables rapid and meaningful progress. I consider every single one of my group mates a good friend. We often spend time together in all kinds of social situations, and new research ideas sometimes spring up at the most unexpected times. Our advisor, Li-C. Wang, is very hands on with all our research. He is always very closely involved with all the little details of our projects and is available for consultation at virtually all times.
Throughout my research, I've had the privilege of working with companies which are considered technology leaders in semiconductor manufacturing. This experience has opened many doors for jobs in the industry. As of now, I believe after graduation I will go directly into industry, and I will choose the company where I feel I can make the biggest contribution.
The main strength has to be attributed to the outstanding faculty. The research conducted by all of their groups is cutting edge and they strive to always be the leading researchers in their fields with their continuous involvement in global research communities.
Having taken most of the offered undergrad and grad courses related to Computer Engineering, it is very difficult to single one out as the favorite. I think an honorable mention definitely has to go to the CE Senior Capstone project (ECE 189B) that I took with Professor Steve Butner. That course really helped tie together a lot of the concepts learned throughout my first four years, but also made me realize how much I still didn't know which contributed to my decision to continue on to grad school.
The screening exam sounded very scary at first. The idea of being orally examined by five professors sounded more stressful than any exam I had taken in the past. However, I found that with thorough preparation it was not as bad as I anticipated.
I have been a GSR for almost every quarter, and I was a TA for two courses (Digital Design with VHDL & Synthesis — ECE 156A and Computer-Aided Design of VLSI Circuits — ECE 156B). The GSR experience can sometimes truly push you to your limits. It taught me a lot about self-motivation and organization, both of which are absolutely necessary to make it as a GSR. The TA experience, on the other hand, was less hectic but just as rewarding. Although I did get overwhelmed with questions at times, especially near project deadlines, the experience was always positive. It is a great feeling to have students look up to you and to be able to help them truly grasp the concepts taught in class.
Work-life balance does get out of hand at times, but usually only around important deadlines. During those times, it may feel like every waking hour is spent on research. However, when there are no imminent deadlines, even as a grad student I get plenty of time to socialize and take part in fun activities. Getting the most out of life may require slightly better time management skills than back during undergrad, but it's definitely achievable.
I lived in IV for a while and enjoyed my stay there, but after becoming a grad student and focusing more on my work I moved to Family Housing, which is probably the best housing deal available in the area.
This summer I will go to Phoenix, AZ for an internship. My advisor's close relationship with industry has made finding internships every summer very easy. This will be my third summer interning for research related work and I did not have to interview for any of them.
Don't get consumed by research and academics. Try surfing, check out the many hiking trails, see a movie at the drive-in theater, go wine tasting, join an adult sports league, or just try something new. Venturing beyond what you're normally comfortable with can really help with personal development which ultimately reflects back on your research.
My research is related to computational photography and computer vision. My aim is to develop algorithms and if possible, hardware, to make smarter cameras with better functionality. Specifically, I have worked on projects related to High Dynamic Range Imaging, Light Field Processing and Image Animation until now. All the projects are in the pipeline for completion and publication. In my latest project on image animation, I worked in collaboration with my advisor and two experienced researchers from the Imaging team at Nokia (in Sunnyvale) to develop an efficient and accurate algorithm that requires minimal effort on the part of the user. I recently submitted a paper on this project to Eurographics Symposiumon Rendering. This project started during my internship at Nokia in Summer of 2014.
The course on Signal Processing taught during my undergrad came very naturally to me, it was very easy to be the best in class without putting in much effort. I knew the subject was tough because everyone around me was struggling with it. And so it occurred to me that I might be good at this. Image processing, computer vision, computational photography depends heavily on signal processing. In addition these fields seem very cool and impactful to me. So, after the realization of my natural expertise in signal processing, I leaned towards understanding these related fields and decided to choose these for my research.
I interviewed with Professor Pradeep Sen before I received a decision letter from UCSB. During the interview, Pradeep was enthusiastic, encouraging and full of energy. UCSB's ECE department was popular among my fellow undergraduate students and Pradeep seemed like a good person to work with — so I decided to go for UCSB. Plus the location needs a mention as well.
The ability of cameras to capture the world in a manner that we do as humans and the possibility of computers being able to perceive, understand and learn from pictures just like humans fascinates me. The idea of being able to contribute to this very fascinating and quickly advancing field motivates me. The nature of this field of study also makes it possible to convert research into product-ready technology without years of delay. It is very gratifying for me to be able to foresee that it won't take way too many years for the technology I or anyone in my field creates to reach the hands of consumers. I like the fact that it is possible to have an impact sooner, rather than later, in my field of study.
In keeping with UCSB's tradition of a collaborative environment, my lab as a whole also enjoys a highly collaborative work process. My advisor, Professor Sen, encourages collaboration among students and with experts from outside the lab as we truly believe that great ideas are not born in isolation. Outside of UCSB, as a part of Nokia-UCSB collaboration, I have worked with experts at Nokia, Sunnyvale, on High Dynamic Range imaging and Image Animation projects. This collaboration has proved very instrumental in helping me mature as a researcher in the past year at UCSB.
This is my first ever research environment and the transition from being an undergrad to becoming a Ph.D. student in fall 2013 was difficult. This was in addition to adjusting to a completely new culture in United States. It took time to find my footing, but now I am much more comfortable and productive. Working in a group research environment has been very fulfilling so far, especially because of the weekly lab meetings and discussions. My advisor has been kind and supportive.
Research is unpredictable. So it is hard to answer where my research will take me next. I would like to work with Computational Imaging and novel camera designs. My personal goal is to be the best and one of the most impactful people in my field of study. This is somewhat vague, because I have not quantitatively defined what I mean by best, but I will know I have become the best when I am convinced.
Collaboration with industry, very useful graduate coursework, freedom and flexibility for graduate students to find and work on problems that excite them the most.
Pattern Recognition (ECE 277) taught by Professor Kenneth Rose in Winter 2014 was my favorite. I couldn't complete the course due to personal reasons, but I attended almost all the classes. It was so exciting to see a professor always smiling and teaching the subject with so much energy. It never troubled him if someone asked a tough question, on the contrary, he would actually smile, as if grateful to the student for having asked the question. He is the only professor I have met this far who has a knack at teaching some really complicated mathematical concept so very beautifully and simply. If I ever become a professor, I want to be as great a teacher as him.
I recently took the Ph.D. screening exam and succeeded in it. It can be a stressful experience, so it is important to be well prepared. I was somewhat nervous throughout the exam, but the professors understand this and they help you out. The aim is not to intimidate the students, but to see if they have the necessary skills and minimum required knowledge to be Ph.D. students. Overall, it helped me realize how much I know and how much I still need to do.
My experience as a GSR has been great so far. I have worked on a variety of projects and also had the chance to collaborate with industry and witness first-hand what it takes to convert a research prototype into a product.
It is a little challenging to manage personal life and work, I started to realize that when I came to the US. Sometimes I get too engrossed with work and my personal life suffers and sometimes it is the other way around. Research is not easy, and as young students just beginning to understand this, it is often overwhelming. But I truly feel I have gotten better at it in the past year. So things are going smoother now.
I live in Goleta, previously I lived in Isla Vista (in student housing on El Colegio) but I soon realized it is not a very grad-student-friendly environment, especially for grad students who wish to simply enjoy some quiet time after a day's work. So my friends and I moved away from Isla Vista.
I plan to intern in the Bay Area for the summer, it is a beautiful place to be in summer. Looking forward to it!
Always start from basics and build each concept from ground up. Very few people practise this very effective strategy, since it seems to be slow initially. Personal: It is important to stay in touch with family, especially if the students are coming from very far away countries (like India) and it is not quick and cheap to travel back home. I strongly advise all grad students to be mindful of their health. It is not good to loose your health to your work while you are in your 20s.