Chunxiong Luo | Searcharxiv

arXiv2022

Identifying the phase diagram structure for optimal information integration in morphogen systems

Gene regulatory networks (GRNs) perform a wide range of biological functions. It is, however, often challenging to reveal their functioning mechanism with the conventional approach focusing on the network topological structure from a bottom-up perspective. Here, we apply the top-down approach based on the optimality theory to study the information integration in morphogen systems, and show that the optimal integration strategy raises requirement on the phase diagram, rather than the topological structure, of a GRN. For the morphogen system in early fly embryos, our parameter-free model can quantitatively predict the patterning position shifts upon the dosage change of the morphogen Bicoid.

physics.bio-ph↗

arXiv2005

Monte Carlo simulation of melting transition on DNA nanocompartment

DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force microscopy. Interesting and novel phenomena emerged during the switching of the device. We have found that DNAs in this system exhibit a much steep melting transition compared to ones in bulk solution or conventional DNA array. To achieve an understanding to this discrepancy, we introduced DNA-DNA interaction potential to the conventional Ising-like Zimm-Bragg theory and Peyrard-Bishop model of DNA melting. To avoid unrealistic numerical calculation caused by modification of the Peyrard-Bishop nonlinear Hamiltonian with the DNA-DNA interaction, we established coarse-gained Monte Carlo recursion relations by elucidation of five components of energy change during melting transition. The result suggests that DNA-DNA interaction potential accounts for the observed steep transition.

physics.bio-ph↗