Wall-crossing, open BPS counting and matrix models

We consider wall-crossing phenomena associated to the counting of D2-branes attached to D4-branes wrapping lagrangian cycles in Calabi-Yau manifolds, both from M-theory and matrix model perspective. Firstly, from M-theory viewpoint, we review that open BPS generating functions in various chambers are given by a restriction of the modulus square of the open topological string partition functions. Secondly, we show that these BPS generating functions can be identified with integrands of matrix models, which naturally arise in the free fermion formulation of corresponding crystal models. A parameter specifying a choice of an open BPS chamber has a natural, geometric interpretation in the crystal model. These results extend previously known relations between open topological string amplitudes and matrix models to include chamber dependence.Comment: 25 pages, 8 figures, published versio

Instantons on ALE spaces and orbifold partitions

We consider N=4 theories on ALE spaces of $A_{k-1}$ type. As is well known, their partition functions coincide with $A_{k-1}$ affine characters. We show that these partition functions are equal to the generating functions of some peculiar classes of partitions which we introduce under the name 'orbifold partitions'. These orbifold partitions turn out to be related to the generalized Frobenius partitions introduced by G. E. Andrews some years ago. We relate the orbifold partitions to the blended partitions and interpret explicitly in terms of a free fermion system.Comment: 28 pages, 10 figures; reference adde

KnotProt: a database of proteins with knots and slipknots.

The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints

ABJM theory as a Fermi gas

The partition function on the three-sphere of many supersymmetric Chern-Simons-matter theories reduces, by localization, to a matrix model. We develop a new method to study these models in the M-theory limit, but at all orders in the 1/N expansion. The method is based on reformulating the matrix model as the partition function of an ideal Fermi gas with a non-trivial, one-particle quantum Hamiltonian. This new approach leads to a completely elementary derivation of the N^{3/2} behavior for ABJM theory and N=3 quiver Chern-Simons-matter theories. In addition, the full series of 1/N corrections to the original matrix integral can be simply determined by a next-to-leading calculation in the WKB or semiclassical expansion of the quantum gas, and we show that, for several quiver Chern-Simons-matter theories, it is given by an Airy function. This generalizes a recent result of Fuji, Hirano and Moriyama for ABJM theory. It turns out that the semiclassical expansion of the Fermi gas corresponds to a strong coupling expansion in type IIA theory, and it is dual to the genus expansion. This allows us to calculate explicitly non-perturbative effects due to D2-brane instantons in the AdS background.Comment: 52 pages, 11 figures. v3: references, corrections and clarifications added, plus a footnote on the relation to the recent work by Hanada et a

Multiple D4-D2-D0 on the Conifold and Wall-crossing with the Flop

We study the wall-crossing phenomena of D4-D2-D0 bound states with two units of D4-brane charge on the resolved conifold. We identify the walls of marginal stability and evaluate the discrete changes of the BPS indices by using the Kontsevich-Soibelman wall-crossing formula. In particular, we find that the field theories on D4-branes in two large radius limits are properly connected by the wall-crossings involving the flop transition of the conifold. We also find that in one of the large radius limits there are stable bound states of two D4-D2-D0 fragments.Comment: 24 pages, 4 figures; v2: typos corrected, minor changes, a reference adde