Zahmeeth Sayed Sakkaff

Institution/Organization: University of Nebraska – Lincoln

Department: Computer Science and Engineering.

Academic Status: Graduate Student.

What conference theme areas are you interested in:

Computational science and machine learning;
Statistical modeling, methods, and computation;
High performance software: packages and design;
Algorithms at extreme scales;
High-order methods, novel discretizations, and scalable solvers;
Data science, analytics, and visualization;
Biological and biomedical computations;
Numerical optimization: methods and applications;
Emerging trends in CS&E education and training.


In my eyes, education means hope for a more favorable future. Pursuing a Ph.D. in the U.S. despite growing up in war-torn Sri Lanka fills me with incomprehensible gratitude. For my future career, I wish to serve society by both inspiring students through academic mentorship to pursue high levels of education and conduct excellent interdisciplinary research. I am currently a Research Assistant and lab manager in the Molecular and Biochemical Telecommunications (MBiTe) lab under the supervision of Dr. Massimiliano Pierobon. My research interests are focused primarily on the intersection of computational systems biology, bioinformatics, molecular communication, and information and coding theory. In particular, my main interest is the realization of telecommunication systems in signaling pathways, gene regulation and metabolic pathways underlying cell-to-cell communication, how cells send and receive information to/from their environment and within themselves. Understanding the complete mechanism lying behind cell-to-cell communication is one of the most challenging research problems addressed by the biology, biochemistry, engineering, and biophysics research communities. Although we have made huge progress in our understanding of biology, our overall understanding of cell-to-cell communication, its internal hierarchies, and its highly integrated and extremely dynamic nature remain largely mysterious. Hence, my research interests involve applying telecommunication systems, engineering concepts, and information theory to cell-to-cell communication to explore the quantitative modeling of information exchange among cells with a transformative layer-by-layer abstraction approach. I will also propose design techniques to leverage these interactions for the realization of novel artificial communication systems. 

As a part of my master’s thesis, I studied the regulation of metabolism in the standard non-pathogenic lab-safe strain of E. coli organism as a molecular communication channel, which resulted in novel information theoretic models to characterize communications between cells and their environment. This work was presented and published at the 17th IEEE International Workshop on Signal Processing Advances in Wireless Communications in July 2016. Based on this work, I completed my MS degree in Computer Science in Dec 2016. This work won the 2017 UNL CSE Outstanding Master’s Thesis Award and was nominated for the 2016-17 Folsom Distinguished Master’s Thesis Award. Subsequently, I developed a complete end-to-end model of the communication channels underlying the cell metabolism and applied it to two human gut organisms, i.e., B. theta and M. smithii which are directly linked to nutrition-related disorders such as obesity, to demonstrate the versatility of this approach and its potential practical applications. The latter has been published as “End-to-end Molecular Communication Channels in Cell Metabolism: an Information Theoretic Study,” at ACM International Conference on Nanoscale Computing and Communication 2017 and won the Best Paper Award. My work previous works have led me to the synthesis of the journal paper titled “Molecular Communication Based on Cell Metabolism: A Case Study with Human Gut Microbes” which will be submitted to IEEE Transactions on NanoBioscience by May 2018. This is the very first time the regulation of the cell metabolism is fully abstracted and modeled as an end-to-end communication system. This paper contains innovative and insightful contributions in the field of communication theory applied to biological systems. 

At the beginning of Spring 2018, I started exploring the potential of biochemical communication channels on signaling pathways in eukaryotic cells. This is particularly interesting to me since their communication performance is directly linked to organisms’ health, which can be clearly seen in the case of cancer. This work was submitted to 19th IEEE International Workshop on Signal Processing Advances in Wireless Communications in March 2018. I also have an ongoing research collaboration with Dr. Chris Henry’s Lab at Argonne National Laboratory (ANL). In 2017 and 2018, I worked as a graduate summer research intern where I developed Software Development Kit tools for a public application in the U.S. Department of Energy Systems Biology Knowledge Base. 

In the past several years, with the help of others, I have been diligently preparing myself to become a skilled researcher and a professional through my graduate education. My experiences have bolstered me with skills in research techniques, collaboration, creative problem solving, perseverance, and dissemination of knowledge. I believe that being a graduate student at UNL built a solid foundation from which I can become a successful scientist. By working in a multidisciplinary field conducting cutting-edge research, I aspire to build a career as a female scientist at a National Research Laboratory where I can continue bridging disciplines while working on novel and meaningful research. I believe obtaining a Ph.D. at UNL will formally prepare me as a scientist so that, one day, I can lead my own research team and contribute to the scientific community. 

I believe that I am well aware of the challenges that students face, especially women, in the STEM fields of education. The challenges I have faced growing up as a woman in a harsh civil war region has driven my passion to maximize the value of opportunities before me. Most importantly, my experiences have inspired my ultimate goals: to help female students join the STEM educational fields and to share my experience and passion for sciences. Achieving the aforementioned goals most effectively will not be possible without the continued academic, professional, and personal training accessed through graduate education. In fact, my journey at UNL has been very enriching and rewarding in many ways which are vital for my future academic career. I am very thankful to the graduate program at UNL because I have already had the opportunity to take large strides toward my academic, career, and life goals through my education and also through opportunities to attend prestigious research conferences along with other professional development conferences like the Grace Hopper Conference (GHC) and the Computing Research Association-Women (CRA-W). Going forward, I would like to continue to develop cutting-edge technologies for the molecular communication field. I will use my extensive background in research as a springboard for my future career in research and education. Through my future interdisciplinary research, I intend to bridge the gap between engineering and biology and achieve my most cherished career intention which is to share my knowledge, skills, and resources to students in STEM education, especially women in computing.

Non-Work Related Activities/Interests:

I involve in the several activities apart from my academic life. I love sports very much, especially I like to run every day during weekdays to enjoy the morning spirits and beauty of nature. I formed a running group at UNL with 5 members and we maintain our run routing daily during the school semester. Apart from this, I am a good swimmer, a bicycle rider, a yoga practitioner, a female cricket and basketball player, and a rock climber. I also currently involved in pottery class offered at UNL. Here, I am learning to put my creative ideas into different projects. Moreover, I am a strong mentor for most of my college friends not only for their academic career but also for their personal life. One of my great interest is meeting different people from different countries and becoming good friends where we share our common interests such as participating for to cooking competitions, improving reading and wrings skills, stitching, and sewing, sometimes exchanging coding tricks as well.