O. Kimchi

Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays

This paper introduces a method to measure intramolecular connectivity in long RNA molecules using DNA patch-probe arrays and validates it on STMV RNA, revealing coexisting global and local structures.

Lytic and temperate phage naturally coexist in a dynamic population model

The paper shows that lytic and temperate phage can coexist in a bacterial community through chaotic dynamics, with lytic phage populations fluctuating to extinction despite dominance.

The assembly yield of complex, heterogeneous structures: A computational toolbox

The paper introduces a computational framework to predict assembly yields of complex structures by combining statistical mechanics with automatic differentiation, validated through simulations and applied to protein and colloidal systems.

Uncovering the mechanism for aggregation in repeat expanded RNA reveals a reentrant transition

This study develops a framework to predict RNA repeat aggregation by analyzing bonding and entropy, revealing reentrant transitions and sequence-dependent behavior.

RNA structure prediction including pseudoknots through direct enumeration of states

This paper introduces a new RNA secondary structure prediction method that accurately predicts pseudoknots by combining a polymer physics model with exhaustive enumeration of possible structures.