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The virus bacteriophage T4, from the family Myoviridae, employs an intriguing contractile injection machine to inject its genome into the bacterium Escherichia coli. Although the atomic structure of phage T4 is largely understood, the dynamics of its injection machinery remains unknown. This study contributes a system-level model describing the nonlinear dynamics of the phage T4 injection machinery interacting with a host cell. The model employs a continuum representation of the contractile sheath using elastic constants inferred from atomistic molecular-dynamics (MD) simulations. Importantly, the sheath model is coupled to component models representing the remaining structures of the virus and the host cell. The resulting system-level model captures virus–cell interactions as well as competing energetic mechanisms that release and dissipate energy during the injection process. Simulations reveal the dynamical pathway of the injection process as a “contraction wave” that propagates along the sheath, the energy that powers the injection machinery, the forces responsible for piercing the host cell membrane, and the energy dissipation that controls the timescale of the injection process. These results from the model compare favorably with the available (but limited) experimental measurements.

We have performed constrained molecular dynamics simulations of magnesium chloride in water-ethanol mixtures. From the potentials of mean force (PMFs) of the Mg(2+)-Cl(-) ion pair, we notice that, as the mole fraction of ethanol increases, the depths of the minima of the contact ion pair (CIP) and solvent assisted ion pair (SAIP) increase, but the depth of the CIP minimum increases more in comparison to the SAIP minimum. This shows that ion pairing becomes more favorable with an increase in the mole fraction of ethanol. Significant differences in the PMFs between the Mg(2+) and the Cl(-) ion (depending upon whether the second Cl(-) ion is present in the first coordination shell of the Mg(2+) ion or not) seem to have been reported for the first time in this work. The local mole fraction of water molecules in the first solvation shell of ions is generally greater than in the bulk. The diffusional behavior of solvent molecules in solvation shells of the ion-pair indicates that the ions as well as the first solvation shells of the ions diffuse at much slower rates. Also, the diffusion constant of bulk water in the mixtures is greatly reduced compared to the pure solvent value.