Exploring the role of topology in biological phase transitions

Phase transitions where matter changes from one form to another due to altering parameters such as temperature, are common in nature.  At a fundamental level, many phase transitions can be understood as a competition between energy and entropy  (disorder). Because of these underlying universal properties, physical theories once developed for phase transitions in non-living matter, turn out to be very effective at describing biological processes as well. One such biological process is the melting of DNA, where the two strands making up the double helix unwind and separate from each other. 

Circular DNA (cDNA), found in viruses and bacteria, behaves differently from linear DNA in humans due to its complex topology. cDNA is more stable and has a higher melting temperature. Topology, a branch of mathematics, examines the connections between geometric shapes that can be smoothly transformed into each other without cutting or tearing – as an old joke goes, a donut and a coffee mug look the same in topology, because they both have one hole. Souradeep aims to understand DNA melting in circular DNA, and specifically how the topology of circular DNA affects the melting phase transition. 

Using statistical physics models and dynamical simulations run on Ashoka’s High-Performance-Computing cluster, Souradeep’s research investigates how DNA melting is affected by basic topological constraint – gluing the two ends of a DNA chain together and making it circular. He found that in the absence of any further twisting (known as supercoiling), circular DNA behaved similarly to linear DNA, when the DNA molecule was very long. Just as the Earth appears flat to us instead of curved due to its immense size, simple circular DNA also could not recognize its own curvature if it became very long. 

Biological systems are enormously complex and hard to grasp in their totality – this is where interdisciplinary approaches from physics can help delineate the importance of different aspects of biological systems.  It helps provide a generalized framework, e.g. how much of any biomolecule’s behavior can be understood from its geometry and topology alone? Souradeep aims to contribute to the interdisciplinary effort to unravel the mysteries of our biology.

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Edited by Yukti Arora and Kangna Verma (Academic Communications, RDO)