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Serdal Kirmizialtin

Publications and source records attributed to Serdal Kirmizialtin.

2 recordsLinked to original sources

RNA Dynamics from Experimental and Computational Approaches

Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining the ensemble of conformations that they populate is crucial not only to elucidate their biological functions, but also for their potential use as therapeutic targets. Computational and experimental techniques provide complementary views on RNA dynamics, and their integration is fundamental to improve the accuracy of computations and the resolution of experiments. Recent exciting developments in this field, were discussed at the CECAM workshop ``RNA dynamics from experimental and computational approaches'', in Paris, June 26-28, 2023. This report outlines key `take-home' messages that emerged during this workshop from the presentations and discussions.

q-bio.BM↗

Untying molecular friction knots

Motivated by recent advances in single molecule manipulation techniques that enabled several groups to tie knots in individual polymer strands and to monitor their dynamics, we have used computer simulations to study "friction knots" joining a pair of polymer strands. The key property of a friction knot splicing two ropes is that it becomes jammed when the ropes are pulled apart. In contrast, molecular friction knots eventually become undone by thermal motion. We show that depending on the knot type and on the polymer structure, a friction knot between polymer strands can be strong (the time t the knot stays tied increases with the force F applied to separate the strands) or weak (t decreases with increasing F). We further present a simple model explaining these behaviors.

physics.bio-ph↗