Date of download: 7/10/2016 Copyright © ASME. All rights reserved. From: A Model for Highly Strained DNA Compressed Inside a Protein Cavity J. Comput. Nonlinear Dynam. 2012;8(3): doi: / A schematic of mature bacteriophage φ29 based on the cryo-electron micoscopy reconstruction [6,28]. The toroidal DNA is contained within a cavity just below the capsid and suspected to contain 30–40 bp of DNA. The cavity is formed from the void between the connector and the lower collar. Shown inside the capsid is a cross sectional view of concentric hoops of DNA which ultimately fill the entire capsid. Figure Legend:

Date of download: 7/10/2016 Copyright © ASME. All rights reserved. From: A Model for Highly Strained DNA Compressed Inside a Protein Cavity J. Comput. Nonlinear Dynam. 2012;8(3): doi: / The atomic structure of DNA superimposed with a an elastic rod with equivalent elastic properties. R→(s,t) tracks the position of the helical axis as a function of contour length s and time t with respect to the inertial frame e. We also define a body-fixed reference frame a(s,t) which is also a function of s and t. Figure adaped from [29]. Figure Legend:

Date of download: 7/10/2016 Copyright © ASME. All rights reserved. From: A Model for Highly Strained DNA Compressed Inside a Protein Cavity J. Comput. Nonlinear Dynam. 2012;8(3): doi: / Side view of the 3-D cavity structure estimated from the connector and lower collar geometry in the cryo-EM images [6] with relevant dimensions labeled. We assume the cavity is symmetric about the vertical axis. Cavity grid points are spaced in stacked rings of points separated by dc above and below one another and dc along the circumference of each ring (see red arrows). Here, we have set dc to 4 Å to reduce the number of grid points by an order of magnitude (over 1 Å separation) and thereby gain computational efficiency. The shaded blue box indicates the approximate area A=dc2 surrounding each grid point. Figure Legend:

Date of download: 7/10/2016 Copyright © ASME. All rights reserved. From: A Model for Highly Strained DNA Compressed Inside a Protein Cavity J. Comput. Nonlinear Dynam. 2012;8(3): doi: / The interaction forces are dependent on all pairwise vectors between rod grid points p and points q representing the cavity surface which are fixed in space Figure Legend:

Date of download: 7/10/2016 Copyright © ASME. All rights reserved. From: A Model for Highly Strained DNA Compressed Inside a Protein Cavity J. Comput. Nonlinear Dynam. 2012;8(3): doi: / (a) Computational snapshots (aligned to the dots on the plot directly below) from simulating 90 bp of DNA compressed within the cavity. (b) Internal (compressive) force (pN) and elastic energy (kT) following Eq. (6) as functions of the shortening of the rod δ = L – d where L is the length of DNA (306 Å) and d is the distance between the upper and lower rod boundaries. The green box illustrates where we report internal force along the contour length. (c) Top and side view of the final toroidal structure. Figure Legend:

Date of download: 7/10/2016 Copyright © ASME. All rights reserved. From: A Model for Highly Strained DNA Compressed Inside a Protein Cavity J. Comput. Nonlinear Dynam. 2012;8(3): doi: / Equilibrium conformation from Fig. 5(c) upon altering the cavity grid spacing parameter dc to (a) 8 Å, (b) 4 Å, (c) 2 Å, (d) 1 Å Figure Legend:

Date of download: 7/10/2016 Copyright © ASME. All rights reserved. From: A Model for Highly Strained DNA Compressed Inside a Protein Cavity J. Comput. Nonlinear Dynam. 2012;8(3): doi: / (a) Dynamic ejection and toroid collapse. Snapshots illustrate DNA conformation at each of the 5 ns increments denoted in the figure below. (b) DNA reaction force (solid green line and circles) and torque (solid red line and circles) on the remaining capsid/DNA (upper end) as a function of time. The solid blue line represents the component of the viscous drag force (integrated over the length of the rod) acting along the z-axis (vertical axis). Figure Legend: