# Fine Structure of Viral dsDNA Encapsidation

## TL;DR

This paper models the liquid crystal ordering of viral dsDNA within bacteriophage capsids, using advanced numerical methods to analyze phase behavior, core disordering, and potential implications for phage design.

## Contribution

It introduces a combined chromonic and liquid crystal model with a scalar order parameter and develops a finite element algorithm for equilibrium analysis and pressure calculation.

## Key findings

- Identifies well-ordered and disordered DNA regions within capsids.
- Provides phase space analysis of pressure and core radius.
- Enables potential bacteriophage design through parameter exploration.

## Abstract

In vivo configurations of dsDNA of bacteriophage viruses in a capsid are known to form hexagonal chromonic liquid crystal phases. This article studies the liquid crystal ordering of viral dsDNA in an icosahedral capsid, combining the chromonic model with that of liquid crystals with variable degree of orientation. The scalar order parameter of the latter allows us to distinguish regions of the capsid with well-ordered DNA from the disordered central core. We employ a state-of-the-art numerical algorithm based on the finite element method to find equilibrium states of the encapsidated DNA and calculate the corresponding pressure. With a data-oriented parameter selection strategy, the method yields phase spaces of the pressure and the radius of the disordered core, in terms of relevant dimensionless parameters, rendering the proposed algorithm into a preliminary bacteriophage designing tool. The presence of the order parameter also has the unique role of allowing for non-smooth capsid domains as well as accounting for knot locations of the DNA.