A Quick Q&A with NCBI’s Quantitative Molecular Biological Physics Group

What motivates this dedicated group of scientists?

We’re glad we asked.

In this occasional feature we call Quick Q&A, NLM staff share a bit about why they’re motivated and inspired. We also ask them to add something surprising about themselves.

For this Quick Q&A, we reached the seven scientists in the National Center for Biotechnology Information (NCBI) who work in the Quantitative Molecular Biological Physics group.

Driven by curiosity, they investigate biological problems in detail to advance solid connections between medical research and fundamental scientific research.

The group’s leader Yi-Kuo Yu, PhD, says he is excited about his work because he has the pleasure of working with smart people, the excitement of new discoveries, and the joy of understanding and obtaining exact results.

Read on to meet the people who make this happen: Cdr Gelio Alves,PhD; Timothy Doerr, PhD; Solomon Duki, PhD; Mehdi Hamaneh, PhD; Oleg Obolensky, PhD; Aleksey Ogurtsov, PhD; and Yi-Kuo.

Read more Quick Q&As with NCBI scientists.

Quick Q&A with Yu, Doerr, and Duki
Question Yi-Kuo Yu, PhD Timothy Doerr, PhD Solomon Fekade Duki, PhD
casual headshot of Yi-Kuo Yu, PhD casual headshot of Timothy Doerr, PhD casual headshot of Solomon Fekade Duki, PhD
Very briefly, what is your background? Physics Over my career as a physicist I have used a wide range of methods (computer simulations to random matrix theory) to study a broad range of systems (from polymers and liquid crystals to biomolecular interactions). I was born and raised in Addis Ababa, Ethiopia, the sixth child of my parents, along with ten siblings. I am a theoretical physicist by training. I have degrees from AAU Ethiopia (BSc, MSc), ICTP Italy (Diploma) and CWRU in Cleveland (PhD).
In lay terms, what is the focus of your research? Developing firm physics foundations for molecular interactions and computational/statistical methods (often physics-inspired) to mine or uncover information encoded or buried in vast amounts of biological data. I attempt to understand at the most basic physical and chemical levels the interactions of the molecules of biology. The interior of a biological cell is a very crowded environment filled with molecules of many sizes, shapes, and charges that are constantly interacting with each other. The presence of many electrically charged molecules in water—itself a surprisingly difficult to understand biomolecule—makes the situation particularly complex. Analyzing such systems is, therefore, both very challenging and very interesting. Currently I am working on quantum spin-chain models to understand magnetic sensing in animals. The same model is also one of the candidates for quantum computers.
Why is your research significant, in your opinion? If we don’t even understand why life is, it makes little sense to talk about evolution of genomes and so on. If one interprets data by heuristic methods only, it is difficult to discover underlying governing principles. My research addresses both aspects. A full understanding of the interaction of biomolecules will enable reliable computational experimentation and discovery. Tools developed with this knowledge will allow more rapid progress in understanding biology and diseases and will aid drug discovery. The idea that animals can detect magnetic fields has traveled a long way from being fiction to a well-established fact in the last half century. A lot of experimental evidence has shown that many migratory animals, such as birds, whales, sea turtles, etc., use the detection of the earth’s magnetic field to sense the direction of their migrations. Despite the clear experimental evidence, however, the biological mechanisms of magnetic sensing are poorly understood. Our theoretical work is to shed light on this mechanism through quantum magnetism.
What or who inspired you to pursue your career? Mainly curiosity. I have always been curious about why and how things work in certain ways. I was also inspired by great teachers in college and in graduate school: Professors Ching-Liang Lin, Joe Chen, Joaquin Luttinger, and Richard Friedberg all inspired me in different ways. I wanted to be a scientist as long as I can remember, though the branch of science varied from oceanography to astronomy to physics. The fact that both of my parents were physicians encouraged a scientific mindset. Carl Sagan’s “Cosmos” was also a big influence. As a child I was always interested in math and science. The two people who inspired me a great deal in physics are my older brother Endeshaw (also a physicist) and my tenth-grade high school physics teacher. At the time my tenth-grade lessons were only on the basics of electricity and magnetism. However, the teacher taught the class, without detailed math, topics like time dilation and length contraction from the special theory of relativity, wave nature of particles, Compton scattering (scattering of electrons by light), and concepts like discrete energy. By the end of my tenth grade, I knew I would pursue a career in physics.
What really gets you jazzed about science and research? There are several ingredients:

  • the pleasure to work with smart people;
  • the excitement of new discoveries; and
  • the joy of understanding and obtaining exact results.
What amazes me most about science is our ability to discover order in even the most complex systems. And in the process of discovery, it seems that nearly every mathematical structure that we can devise can be made useful in science. The joy of solving physical problems and learning new methods.
If you weren’t doing what you’re doing now, what else might you be doing? This is a tough question for me as I never thought about a career other than physics (and related research). However, I have always been fond of mathematics, classical guitar, and carpentry. That said, other career choices could have been mathematician, classical guitarist, or carpenter. I would be playing the viola. Mathematics is still my other passion, so I might have pursued a career in pure mathematics.
Tell us something surprising about yourself. I enjoy Chinese poetry immensely. I am scared of heights, but I climb mountains anyway. Every year I plan to run a marathon but have never done it. However, I do run about 30 to 35 miles a week, out of which one is a half marathon (which I do it almost every Saturday).
Quick Q&A with Obolensky and Alves
Question Oleg Obolensky, PhD Cdr Gelio Alves, PhD
headshot of Oleg Obolensky, PhD casual headshot of Cdr Alves Gelio, PhD
Very briefly, what is your background? I have a PhD in theoretical physics from the A.F. Ioffe Institute, Russian Academy of Sciences. Over the years I worked first in atomic and then in cluster physics, switching to biophysics not long before coming to NCBI in 2008. My PhD is in statistical physics, and I’m a commander with the United States Public Health Service.
In lay terms, what is the focus of your research? I work on the physical foundations of biomolecular interactions and proteomics. It is no secret that many methods widely employed by biomedical researchers are based on assumptions that are not necessarily valid in all circumstances. I strive to come up with alternatives that would better correspond to processes taking place at the fundamental level. Development of statistical methods and algorithms for the analysis of proteomics data and for the fast identification of pathogens via mass spectrometry.
Why is your research significant, in your opinion? My research helps make sure that conclusions drawn from studies of complex biosystems, be it in proteomics or in the biomedical field, are based on correct assumptions about the fundamentals of the systems under investigation. Having methods that are both rapid and accurate in the identification of pathogens is of extreme importance to public health and safety. Reducing the turnaround time it takes to identify pathogenic microorganisms is especially important in the clinical setting, where patients suffering from infections caused by a single or multiple pathogens can have a faster diagnosis.
What or who inspired you to pursue your career? My grandfather was an electrical engineer who instilled in me a love for inquiry and a desire to know how things work, so, by the age of five I knew exactly what I was going to do with my life. How very complex physical events can be described by simple mathematical equations like Maxwell’s and Einstein’s equations.
What really gets you jazzed about science and research? I am always amazed when I see how purely theoretical concepts manifest themselves in tangible, macroscopic phenomena. When you spent months trying to solve a problem, and one day you wake up in the morning and can see the solution to the problem.
If you weren’t doing what you’re doing now, what else might you be doing? I’d probably be driving an eighteen-wheeler coast to coast. Something else related to science.
Tell us something surprising about yourself. I like traveling by car, and I have been to 47 out of the 48 contiguous states, with trips originating from the DC area. In our last trip to Seattle and the Oregon sand dunes, we traveled  nearly 8,000 miles in three weeks. I grew up in a small island in south Brazil in the country’s third oldest city with a very small population. Growing up, I never thought I would be a scientist working in the United States.
Quick Q&A with Hamaneh and Ogurtsov
Question Mehdi Bagheri Hamaneh, PhD Aleksey Ogurtsov, PhD
casual headshot of Mehdi Hamaneh, PhD casual headshot of Aleksey Ogurtsov, PhD
Very briefly, what is your background? I am a physicist by training, but I am using my knowledge and skills to tackle problems in biology using mathematical and computational approaches. I enrolled in Kolmogorov high school (affiliated with the Lomonosov University in Moscow, Russia) for advanced placement in mathematics and physics. I got my master’s degree at the mechanics and mathematics department of the Lomonosov University in Moscow and completed the graduate program at the same department. In 2003, I got my PhD in biophysics at the Institute of Theoretical and Experimental Biophysics in Moscow.
In lay terms, what is the focus of your research? My research focuses on biological networks. Like a social network in which people are connected to each other, a biological network consists of biological entities (e.g., proteins, genes, or diseases) that are linked to one another based on their biological relations. For example, in a protein-protein interaction network, two proteins are connected if they are known to interact with each other. As another example, consider a disease network in which two diseases are linked if they have the same underlying cause. Once a biological network is constructed, one can use mathematical methods to mine important new information from the network that can help provide insights into many related biological problems. One of the major directions of our group’s efforts is the development of methods to assign statistical significance (also known as P- and E-values) in identification of peptides/proteins/microorganisms using mass spectrometry data. The P- and E-values are unified measures to assess biologically relevant information and extract it from the background noise.

Biological applications of mass spectrometry have grown exponentially during the last decade. Ten years ago, data sets available for downloading and analysis contained only single spectra. Several years ago, a typical mass spectrometer experiment resulted in 10K spectra. Now there are several repositories of thousands of experiments with up to 100K spectra scans each.

Consequently, the range of projects which can be successfully performed using tandem mass spectrometry grew from single peptide identification to identification and quantification of multiple proteins and microorganisms present in a biological sample.

Why is your research significant, in your opinion? My research can potentially answer some important biological questions with real-life consequences. Let me give you an example. We have developed a mathematical method that, given two diseases, determines how likely they are to have the same underlying cause. Since diseases caused by the same mechanism may respond to the same drug, such a method may help treat diseases for which no treatment is still available. For instance, consider disease A, for which a treatment is known, and disease B with no available cure. If, using our method, we find that the two diseases are likely to have the same underpinning mechanism, the treatment used for disease A may also be helpful in curing disease B. The mass spectra data differ between experiments and even between separate scans in a single experiment. Our group develops statistical methods which are based on spectrum specificity and assign statistical significance using the popular P- and E-values. Such an approach is in high demand because it allows the comparison of “apples to apples” in a robust and clear way and results in an accurate statistical assessment. Our group develops these methods into ready-to-go applications that start with a command line or with a user-friendly graphical interface and web server application, capable of processing the whole experiment spectra data.

The areas where mass spectrometry can be applied are quite wide: pharmaceutical, clinical, environmental, geological, biotechnological. Robust and accurate statistics play a critical role in this progress.

What or who inspired you to pursue your career? I pursued this career because it allows me to do two things at the same time: conduct research, which I love, and hopefully improve people’s lives. I would like to thank my middle school math teacher, Tamara Matveyevna Morozova. She influenced my choice of a scientific path by encouraging me to participate in the National Russian Olympiads in math, physics, and chemistry. Later, largely due to success in the Olympiads, I passed the exams to the Kolmogorov high school in Moscow.

Also, I must mention the series of popular science books by Yakov Perelman. These books taught me the beauty of the seemingly boring fundamentals of math and physics.

What really gets you jazzed about science and research? Solving mysteries and finding solutions to important problems. Our group performs the “full circle” of scientific development. That means that we implement the group’s theoretical findings into ready-to-use solutions. The applications include web services, software packages, and user-friendly graphic interfaces. If the theoretical projects are science, then the way they are implemented is art. I like to code, to find non-standard solutions and structures, and to invent special optimal algorithms.
If you weren’t doing what you’re doing now, what else might you be doing? I still would be a physicist but working in a different field like cosmology. When I was a kid I had a dream which I still have. I wanted to become an industrial engineer.

I think I can work in many places in industry and in science. For example, I worked in a branch of a bank for five years. Starting from an entry level position, I was promoted to the head of the analytical and market derivatives group. Our group was the most efficient and produced almost half the profit of the bank’s branch.

Tell us something surprising about yourself. I love movies so much that I watch one every night. Spiritually, I remain young. I adore ice cream and long, animated films such as “Laputa: Castle in the Sky” or “My Neighbor Totoro.”

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One thought on “A Quick Q&A with NCBI’s Quantitative Molecular Biological Physics Group

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