Marina Katava
computational biophysics
Information encoding to polymers
Data acquisition and mining is currently the principal driving force of technological advances. New solutions in data storage and retrieval are necessary to sustain current data production rates. Polymers represent natural candidates for the task, as nucleic acids already efficiently encode for vast biological complexity.
However, the synthesis of long sequence-ordered polymers in vitro has proven to be challenging and remains an open question. I wish to address whether conditions of spontaneous sequence ordering can be achieved under
non-equilibrium conditions, as well as the timescales pertinent to sequence ordering under non-equilibrium conditions. I also aim to understand the conditions which allow for creation of autocatalytic self-replicative sequence sets, with emphasis on timescales relevant to this process.
Project name 02
Role Title
I'm a paragraph. Click here to add your own text and edit me. It’s easy. Just click “Edit Text” or double click me to add your own content and make changes to the font. I’m a great place for you to tell a story and let your users know a little more about you.
Information encoding to polymers
Data acquisition and mining is currently the principal driving force of technological advances. New solutions in data storage and retrieval are necessary to sustain current data production rates. Polymers represent natural candidates for the task, as nucleic acids already efficiently encode for vast biological complexity.
However, the synthesis of long sequence-ordered polymers in vitro has proven to be challenging and remains an open question. I wish to address whether conditions of spontaneous sequence ordering can be achieved under
non-equilibrium conditions, as well as the timescales pertinent to sequence ordering under non-equilibrium conditions. I also aim to understand the conditions which allow for creation of autocatalytic self-replicative sequence sets, with emphasis on timescales relevant to this process.
Spreading of epigenetic modifications
It has been long thought that nucleic acids such as DNA are the sole carriers of information in living organisms. DNA, being a very long linear chain, is condensed into a more compact form with the help of histone proteins. The histone proteins and the DNA can be chemically modified by the application of epigenetic markers, which are chemical 'tags' that carry information on the gene expression patterns. These modifications are at the basis of obivous cellular diversity in higher organisms, they control development and aging, and are linked to numerous diseases.
The mechanism of spreading and inheritance of these modifications is currently unknown. I am interested in providing possible scenarios that could explain the spreading and inheritance of these modifications. In addition, I aim to address the interplay between genome folding and the spreading of epigenetic modifications.
Protein (in)stability at high temperatures
A typical human cell contains billions of proteins. These molecules are linear sequences built of 20 sub-units arranged in patterns that determine their structure and function. Prediction of protein structure and its relationship to function is one of the classical problems in computational biophysics present since the very beginning of the field.
During my PhD thesis, I addressed several subjects related to protein stability at high temperatures. Proteins in organisms that survive temperatures above the boiling point of water are built of same sub-units as human proteins that lose activity above 40°C. The key idea was the exploration of protein flexibility/rigidity at different time- and length scales. I quantified the thermal effects on mechanical properties, stability, and activity of the proteins. Among others, we have established that atomistic fluctuations can serve as a signature of protein melting, we have studied the effect of solvent and crowding to the melting point, and have determined relevant functional modes by comparing protein pairs that perform similar function in organisms which survive moderate and high temperatures.
