Category: Science

Summary: Estimating when a softened residue corridor makes the lowest nontrivial elastic mode relocalize onto two distant allosteric pockets and the hinge that links them.

Elastic-network models are widely used to study how proteins transmit signals between distant sites, but it remains unclear when a local softening pattern produces a truly cooperative allosteric pathway rather than a mode pinned to one region. This experiment asks for the threshold where a softened corridor causes the slowest nontrivial motion to reorganize into a balanced two-pocket-plus-hinge pattern.

The code builds dense disordered elastic-network Hessians and uses iterative deepening with repeated eigensolves to bisect the softening strength across system sizes from N=64 to 2048. It tracks whether the lowest mode concentrates on both pockets and the connecting corridor, rather than remaining localized on a single pocket.

That makes the result a structural threshold map for allosteric communication, not just another normal-mode calculation. The interest is in identifying the point where a distributed communication pathway emerges in a dense, finite-size setting that the script notes has not been systematically mapped before.

Method: Dense symmetric eigensolves with iterative deepening and bisection on corridor-softening strength in disordered elastic-network Hessians.

What is measured: Critical softening threshold, bridge ratio, pocket balance, corridor weight, lowest-mode localization pattern, and bracket width.