This free resource is developed and maintained by the Laboratory for Computational Biology & Biophysics at MIT, which is directed by Professor Mark Bathe.
The 3D solution shape and flexibility of programmed DNA assemblies are predicted using a mechanical model of DNA that assumes the DNA double-helix to be a homogeneous elastic rod with axial, twisting, and bending moduli that have been measured experimentally . These mechanical elements that are constrained to neighbors using double-stranded crossovers provide internal constraints that deform DNA from its straight, rod-like conformation to complex shapes as shown in detail in [4, 9-10].
Computational prediction of deformed DNA shapes is performed using the Finite Element Method implemented in the commercial software program ADINA (ADINA R&D, Inc.), which is a well established numerical technique for the analysis of complex structural mechanics and dynamics . The thermally-induced fluctuations of DNA nanostructures are computed using the equipartition theorem of statistical mechanics and normal mode analysis , as shown for proteins in [15-16]. Atomic models of DNA nanostructures are generated from 3D solution shapes and thermal fluctuations, as shown for the design of light-harvesting nanodevices  and DNA casting molds for inorganic structures .
Setting up the preceding finite element model using CanDo requires input files that specify the sequence topology of the underlying DNA nanostructure, as well as its initial configuration (basepair coordinates and orientations). Our lab has developed the ability to read in these model features from either caDNAno or Tiamat files, which are two popular drawing programs, as well as from our own file format with extension cndo.
The source code needed to generate the finite element models are available upon request by e-mailing Daniel Dardani (firstname.lastname@example.org).
The Laboratory for Computational Biology & Biophysics is grateful to its sponsors for financial support including the Office of Naval Research, the Army Research Office, and the National Science Foundation.
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