Watson-Crick pairing, the Heisenberg group and Milnor invariants

We study the secondary structure of RNA determined by Watson-Crick pairing without pseudo-knots using Milnor invariants of links. We focus on the first non-trivial invariant, which we call the Heisenberg invariant. The Heisenberg invariant, which is an integer, can be interpreted in terms of the Heisenberg group as well as in terms of lattice paths. We show that the Heisenberg invariant gives a lower bound on the number of unpaired bases in an RNA secondary structure. We also show that the Heisenberg invariant can predict \emph{allosteric structures} for RNA. Namely, if the Heisenberg invariant is large, then there are widely separated local maxima (i.e., allosteric structures) for the number of Watson-Crick pairs found.Comment: 18 pages; to appear in Journal of Mathematical Biolog

Old Inflation in String Theory

We propose a stringy version of the old inflation scenario which does not require any slow-roll inflaton potential and is based on a specific example of string compatification with warped metric. Our set-up admits the presence of anti-D3-branes in the deep infrared region of the metric and a false vacuum state with positive vacuum energy density. The latter is responsible for the accelerated period of inflation. The false vacuum exists only if the number of anti-D3-branes is smaller than a critical number and the graceful exit from inflation is attained if a number of anti-D3-branes travels from the ultraviolet towards the infrared region. The cosmological curvature perturbation is generated through the curvaton mechanism.Comment: 31 pages, 3 figures; typos corrected and reference adde

DBI in the Sky

We analyze the spectrum of density perturbations generated in models of the recently discovered "D-cceleration" mechanism of inflation. In this scenario, strong coupling quantum field theoretic effects sum to provide a DBI-like action for the inflaton. We show that the model has a strict lower bound on the non-Gaussianity of the CMBR power spectrum at an observable level, and is thus falsifiable. This in particular observationally distinguishes this mechanism from traditional slow roll inflation generated by weakly interacting scalar fields. The model also favors a large observable tensor component to the CMBR spectrum.Comment: 30 pages latex. v2: references added. v3: correction in three point function. v4: sign of non-Gaussianity corrected; fNL is negativ