Every virus encodes a protein, many copies of which form a shell, called the "capsid", that encloses the viral DNA or RNA until it reaches its host cell. The local pattern is well approximated by a triangular lattice, except at certain "disclinations" the coordination is reduced from 6 to 5. Many viral species (very high) icosahedral symmetry and are relatively large. How (or to what extent) does the capsid manage to reach such a structure in its non-equilibrium growth process? We've focused on retroviruses (of which the best known is HIV, the AIDS virus) which form an ensemble of irregular structures; we are in contact with the retrovirus lab of Prof. Volker Vogt at Cornell. This year, we're trying to extract effective spring constants from molecular dynamics simulations which will let us model the energetics at the coarse-grained scale of the above-mentioned triangular lattice. (Student Steve Hicks.)
Lately, we've been developing methods to extract coarse-grained spring constant parameters from microscopic simulations (by a standard protein routine, NAMD). The goal is to describe each protein unit (or domain) as a single rigid body with six degrees of freedom. Then, the entire capsid can be relaxed as an assembly of such springs and we have an absolute microscopic prediction of the force felt by an atomic-force microscope tip in an indentation experiment. Our approach requires a careful application of stochastically driven dynamics.
By what physical mechanism did life break chiral symmetry? Obviously, an ancient symmetry-breaking led to the handedness of biological molecules, but it's nontrivial how this gets expressed at the level of a multicellular organism. Examples are (1) bilateral asymmetry in vertebrate animals (why isn't your heart on the right side?), and (2) spiral growth in plants. (Student Igor Segota).