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

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

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

Evidence for Duality of Conifold from Fundamental String

We study the spectrum of BPS D5-D3-F1 states in type IIB theory, which are proposed to be dual to D4-D2-D0 states on the resolved conifold in type IIA theory. We evaluate the BPS partition functions for all values of the moduli parameter in the type IIB side, and find them completely agree with the results in the type IIA side which was obtained by using Kontsevich-Soibelman's wall-crossing formula. Our result is a quite strong evidence for string dualities on the conifold.Comment: 24 pages, 13 figures, v2: typos corrected, v3: explanations about wall-crossing improved and figures adde

Absence of system xc⁻ on immune cells invading the central nervous system alleviates experimental autoimmune encephalitis

Background: Multiple sclerosis (MS) is an autoimmune demyelinating disease that affects the central nervous system (CNS), leading to neurodegeneration and chronic disability. Accumulating evidence points to a key role for neuroinflammation, oxidative stress, and excitotoxicity in this degenerative process. System x(c)- or the cystine/glutamate antiporter could tie these pathological mechanisms together: its activity is enhanced by reactive oxygen species and inflammatory stimuli, and its enhancement might lead to the release of toxic amounts of glutamate, thereby triggering excitotoxicity and neurodegeneration. Methods: Semi-quantitative Western blotting served to study protein expression of xCT, the specific subunit of system x(c)-, as well as of regulators of xCT transcription, in the normal appearing white matter (NAWM) of MS patients and in the CNS and spleen of mice exposed to experimental autoimmune encephalomyelitis (EAE), an accepted mouse model of MS. We next compared the clinical course of the EAE disease, the extent of demyelination, the infiltration of immune cells and microglial activation in xCT-knockout (xCT(-/-)) mice and irradiated mice reconstituted in xCT(-/-) bone marrow (BM), to their proper wild type (xCT(+/+)) controls. Results: xCT protein expression levels were upregulated in the NAWM of MS patients and in the brain, spinal cord, and spleen of EAE mice. The pathways involved in this upregulation in NAWM of MS patients remain unresolved. Compared to xCT(+/+) mice, xCT(-/-) mice were equally susceptible to EAE, whereas mice transplanted with xCT(-/-) BM, and as such only exhibiting loss of xCT in their immune cells, were less susceptible to EAE. In none of the above-described conditions, demyelination, microglial activation, or infiltration of immune cells were affected. Conclusions: Our findings demonstrate enhancement of xCT protein expression in MS pathology and suggest that system x(c)- on immune cells invading the CNS participates to EAE. Since a total loss of system x(c)- had no net beneficial effects, these results have important implications for targeting system x(c)- for treatment of MS

Quivers, YBE and 3-manifolds

We study 4d superconformal indices for a large class of N=1 superconformal quiver gauge theories realized combinatorially as a bipartite graph or a set of "zig-zag paths" on a two-dimensional torus T^2. An exchange of loops, which we call a "double Yang-Baxter move", gives the Seiberg duality of the gauge theory, and the invariance of the index under the duality is translated into the Yang-Baxter-type equation of a spin system defined on a "Z-invariant" lattice on T^2. When we compactify the gauge theory to 3d, Higgs the theory and then compactify further to 2d, the superconformal index reduces to an integral of quantum/classical dilogarithm functions. The saddle point of this integral unexpectedly reproduces the hyperbolic volume of a hyperbolic 3-manifold. The 3-manifold is obtained by gluing hyperbolic ideal polyhedra in H^3, each of which could be thought of as a 3d lift of the faces of the 2d bipartite graph.The same quantity is also related with the thermodynamic limit of the BPS partition function, or equivalently the genus 0 topological string partition function, on a toric Calabi-Yau manifold dual to quiver gauge theories. We also comment on brane realization of our theories. This paper is a companion to another paper summarizing the results.Comment: 61 pages, 16 figures; v2: typos correcte

Wall Crossing, Quivers and Crystals

We study the spectrum of BPS D-branes on a Calabi-Yau manifold using the 0+1 dimensional quiver gauge theory that describes the dynamics of the branes at low energies. The results of Kontsevich and Soibelman predict how the degeneracies change. We argue that Seiberg dualities of the quiver gauge theories, which change the basis of BPS states, correspond to crossing the "walls of the second kind." There is a large class of examples, including local del Pezzo surfaces, where the BPS degeneracies of quivers corresponding to one D6 brane bound to arbitrary numbers of D4, D2 and D0 branes are counted by melting crystal configurations. We show that the melting crystals that arise are a discretization of the Calabi-Yau geometry. The shape of the crystal is determined by the Calabi-Yau geometry and the background B-field, and its microscopic structure by the quiver Q. We prove that the BPS degeneracies computed from Q and Q' are related by the Kontsevich Soibelman formula, using a geometric realization of the Seiberg duality in the crystal. We also show that, in the limit of infinite B-field, the combinatorics of crystals arising from the quivers becomes that of the topological vertex. We thus re-derive the Gromov-Witten/Donaldson-Thomas correspondence

Brezin-Gross-Witten model as "pure gauge" limit of Selberg integrals

The AGT relation identifies the Nekrasov functions for various N=2 SUSY gauge theories with the 2d conformal blocks, which possess explicit Dotsenko-Fateev matrix model (beta-ensemble) representations the latter being polylinear combinations of Selberg integrals. The "pure gauge" limit of these matrix models is, however, a non-trivial multiscaling large-N limit, which requires a separate investigation. We show that in this pure gauge limit the Selberg integrals turn into averages in a Brezin-Gross-Witten (BGW) model. Thus, the Nekrasov function for pure SU(2) theory acquires a form very much reminiscent of the AMM decomposition formula for some model X into a pair of the BGW models. At the same time, X, which still has to be found, is the pure gauge limit of the elliptic Selberg integral. Presumably, it is again a BGW model, only in the Dijkgraaf-Vafa double cut phase.Comment: 21 page

The matrix model version of AGT conjecture and CIV-DV prepotential

Recently exact formulas were provided for partition function of conformal (multi-Penner) beta-ensemble in the Dijkgraaf-Vafa phase, which, if interpreted as Dotsenko-Fateev correlator of screenings and analytically continued in the number of screening insertions, represents generic Virasoro conformal blocks. Actually these formulas describe the lowest terms of the q_a-expansion, where q_a parameterize the shape of the Penner potential, and are exact in the filling numbers N_a. At the same time, the older theory of CIV-DV prepotential, straightforwardly extended to arbitrary beta and to non-polynomial potentials, provides an alternative expansion: in powers of N_a and exact in q_a. We check that the two expansions coincide in the overlapping region, i.e. for the lowest terms of expansions in both q_a and N_a. This coincidence is somewhat non-trivial, since the two methods use different integration contours: integrals in one case are of the B-function (Euler-Selberg) type, while in the other case they are Gaussian integrals.Comment: 27 pages, 1 figur