Photo credit: Safar Safarov
I used to be afraid of computers.
Like Heath-Ledger-as-the-Joker afraid. (To give you a frame of reference: after seeing that movie, I slept with my bedroom light on for a month … and I was eighteen.
To me, computers were as foreign as hieroglyphics, and I had convinced myself I wasn’t smart enough to literally “crack the code.” However, I knew I wanted to work in a lab and decided to apply for a research internship at the University of Massachusetts-Amherst, convinced that my willingness to apply myself to any type of research project would work in my favor. In an ironic convergence of circumstances, my “free-spiritedness” landed me in a computational lab tasked with modeling DNA.
Photo credit: Joshua Sortino
Basically, I was sentenced to using a computer to answer questions that I barely understood, let alone had any intuition as to how to answer them. The project entailed simulating how DNA is packaged into and released from a virus. My brain was immediately flooded with questions: How do I tell a computer what DNA is? How do I make the DNA move? How do I even get it inside the virus? While these questions arose from panic, I realized much later that these were legitimate questions with non-intuitive answers.
I don’t know if I should say in spite of or because of this weird twist of fate, but regardless, this exposure did propel me into more than a decade’s worth of computational research - a career move I simultaneously praise and curse, especially when my data behave like my two-year-old niece alternating between loving me (“HIIIII, DODAAAAA!”) and barely tolerating me (“Buh-bye, Doh Doh”). But with each setback and success, I am reminded of how this area of research provides a window into a world otherwise unseen.
Atomic simulations, a major field of computational research, are used to study and predict how different systems like DNA, solar cell materials, and lipid bilayers behave under different conditions such as temperature changes and solvent interactions. Understanding how the individual atoms perform paints a more accurate picture of how structure affects outcome. For instance, modeling the interactions between a specific group of molecules in DNA and molecules in the virus allowed us to see how the DNA coiled itself inside the viral capsid. In fact, we were able to visualize intricate details of DNA entry, like how the DNA chain would actually pause and wait for the coiled section to relax before the next part of the chain made its way into the virus.
Photo credit: Piotr Makowski
But how do we even get the computer to understand what the different atoms are, let alone how they interact with one another? In a way, it’s somewhat similar to playing chess: each piece has its own identity and set position on the board. They each have specific movements they’re allowed to make, and there is a hierarchy of interaction (i.e., which piece “takes” another piece). The player, like the mathematical model upon which a simulation relies, is the brain of the operation; nothing moves until its scrupulous survey of the board prompts a decision.
In atomic simulations, each atom has its own identity and its own set of coordinates to set its location. When the simulation begins, the mathematical equations used to govern the system act as the brain, telling which atoms where they can move and how they can affect their surroundings. At each step, those new coordinates and interactions are recorded to provide a map of each atom’s progress throughout the calculation.
For my master’s thesis, I modeled an organic solar cell material in the figure to the right to see how its stability was affected by its atomic and molecular arrangements. Through a series of calculations, I was able to witness how atoms were contorting different sections of molecules when closely interacting, almost as if they were repelling each other before they got too close. For one of the early projects of my Ph.D., I studied enzyme transfer and could see how different enzymes “choose” different paths to take as they “walk” along the backbone of a ligand.
Nearly every day, I am made privy to the subtlest and nearly-undetectable inner workings of the universe. What can’t be seen with the naked eye, I can “see” replicated on my laptop; and it is a marvelous sight to behold. It never ceases to amaze me how the effects of the smallest participants in our world can be felt like tidal waves. And it is equally unnerving to know that I could have missed out on this wonder because of fear of the unknown. Yet it is the unknown that drives research forward into new arenas and opens our eyes to what has always existed that we were never able to see. What can be more humbling and thrilling than that?
-Kristina
Photo credit: Philipp Katzenberger
