Packaging stiff polymers in small containers: A molecular dynamics study

Temperature-dependent ejection evolution arising from active and passive effects in DNA viruses

Recent experiments have demonstrated that the ejection velocity of different species of DNA viruses is temperature dependent, potentially influencing the cellular infection mechanisms of these viruses. However, due to the challenge in quantifying the multiscale characteristics of DNA virus systems, there is currently a lack of systematic theoretical research on the temperature-dependent evolution of ejection dynamics. This work presents a multiscale model to quantitatively explore the temperature-dependent mechanical properties during the virus ejection process, and unveil the underlying mechanisms. Two different assumptions of DNA structures, featuring two or single domains, are used for the early and later stages of ejection, respectively. Temperature is introduced as an influencing variable into the mesoscopic energy model by considering the temperature dependence of Debye length, DNA persistence length, molecular kinetic energy, and other parameters. The results indicate that temperature variations alter the energy landscape associated with DNA structure, leading to the changes in the energy minimum and corresponding DNA structure remaining in the capsid. These changes affect both the active ejection force and passive friction during the DNA ejection, ultimately leading to a significant increase in ejection velocity at higher temperatures. Furthermore, our model supports the previous hypothesis that temperature-induced changes in the size of viral portal pore could dramatically enhance DNA ejection velocity.

Non-equilibrium structural and dynamic behaviors of active polymers in complex and crowded environments

Active matter systems, which convert internal chemical energy or energy from the environment into directed motion, are ubiquitous in nature and exhibit a range of emerging non-equilibrium behaviors. However, most of the current works on active matter have been devoted to particles, and the study of active polymers has only recently come into the spotlight due to their prevalence within living organisms. The intricate interplay between activity and conformational degrees of freedom gives rise to novel structural and dynamical behaviors of active polymers. Research in active polymers remarkably broadens diverse concepts of polymer physics, such as molecular architecture, dynamics, scaling and so on, which is of significant importance for the development of new polymer materials with unique performance. Furthermore, active polymers are often found in strongly interacting and crowded systems and in complex environments, so that the understanding of this behavior is essential for future developments of novel polymer-based biomaterials. This review thereby focuses on the study of active polymers in complex and crowded environments, and aims to provide insights into the fundamental physics underlying the adaptive and collective behaviors far from equilibrium, as well as the open challenges that the field is currently facing.

Orientationally ordered states of a wormlike chain in spherical confinement

One of the basic characteristics of a linear dsDNA molecule is its persistence length, typically of order 50 nm. The DNA chain inflicts a large energy penalty if it is bent sharply at that length scale. Viruses of bacteria, known as bacteriophages, typically have a dimension of a few tens of nanometers. Yet, it is known that a bacteriophage actively packages viral DNA inside the capsid and ejects it afterwards. Here, adopting a commonly used polymer model known as the wormlike chain, we answer an idealized question: Placing a linear DNA molecule inside a spherical cavity, what ordered states can we derive from known tools in statistical physics? Solving the model in a rigorous field-theory framework, we report a universal phase diagram for four orientationally ordered and disordered states, in terms of two relevant physical parameters.

Spontaneous Domain Formation in Spherically Confined Elastic Filaments

Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity driven, suggesting general solutions with DNA organized into spool-like domains. Using analytical calculations and computer simulations of a long elastic filament confined to a spherical container, we show that the ground state is not a single spool as assumed hitherto, but an ordering mosaic of multiple homogeneously ordered domains. At low densities, we observe concentric spools, while at higher densities, other morphologies emerge, which resemble topological links. We discuss our results in the context of metallic wires, viral DNA, and flexible polymers.

Nonmonotonic dependence of polymer-glass mechanical response on chain bending stiffness

We investigate the mechanical properties of amorphous polymers by means of coarse-grained simulations and nonaffine lattice dynamics theory. A small increase of polymer chain bending stiffness leads first to softening of the material, while hardening happens only upon further strengthening of the backbones. This nonmonotonic variation of the storage modulus G^{'} with bending stiffness is caused by a competition between additional resistance to deformation offered by stiffer backbones and decreased density of the material due to a necessary decrease in monomer-monomer coordination. This counterintuitive finding suggests that the strength of polymer glasses may in some circumstances be enhanced by softening the bending of constituent chains.

Rigidity-induced scale invariance in polymer ejection from capsid

While the dynamics of a fully flexible polymer ejecting a capsid through a nanopore has been extensively studied, the ejection dynamics of semiflexible polymers has not been properly characterized. Here we report results from simulations of ejection dynamics of semiflexible polymers ejecting from spherical capsids. Ejections start from strongly confined polymer conformations of constant initial monomer density. We find that, unlike for fully flexible polymers, for semiflexible polymers the force measured at the pore does not show a direct relation to the instantaneous ejection velocity. The cumulative waiting time t(s), that is, the time at which a monomer s exits the capsid the last time, shows a clear change when increasing the polymer rigidity κ. The major part of an ejecting polymer is driven out of the capsid by internal pressure. At the final stage the polymer escapes the capsid by diffusion. For the driven part there is a crossover from essentially exponential growth of t with s of the fully flexible polymers to a scale-invariant form. In addition, a clear dependence of t on polymer length N_{0} was found. These findings combined give the dependence t(s)∝N_{0}^{0.55}s^{1.33} for the strongly rigid polymers. This crossover in dynamics where κ acts as a control parameter is reminiscent of a phase transition. This analogy is further enhanced by our finding a perfect data collapse of t for polymers of different N_{0} and any constant κ.