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

Expression of the apoptotic markers in normal breast epithelium, benign mammary dysplasia and in breast cancer

Apoptosis and proliferation are processes associated with the development and progression of breast cancer. The sensitivity of tumour cells to the induction of apoptosis depends on the balance between pro- and anti-apoptotic proteins. The expression of Bak and Bcl-2 was examined using an immunohistochemical method in 71 primary breast cancers. Furthermore, Bcl-2 and Bak were assessed in the normal mammary gland as well as in benign mammary dysplasia adjacent to breast cancer. Positive immunostaining for Bcl-2 was observed in 77.8% of cases of normal breast epithelium (NBE), 93% of benign dysplasia without intraductal proliferation (BBD) as well as in 94% of intraductal proliferative lesions of the breast (BIPL). Expression of Bak was detected in 39% of cases of NBE, 45% of BBD and in 67% of BIPL. In breast cancer Bcl-2 and Bak expression was found in 83% and 70% of the cases studied, respectively. Increased Bcl-2 expression in primary tumours significantly correlated with favourable prognostic factors, namely pT1, G2 and lack of metastases to the regional lymph nodes (p < 0.01, p < 0.03, p < 0.02, respectively). There were no relationships between Bak and the clinicopathological features studied, but our results indicate changes in the expression of Bak during breast cancer development and progression. It would appear to be important to assess and compare pro- and anti-apoptotic proteins between normal mammary gland, benign mammary dysplasia and the primary tumours of breast cancer. This knowledge should be helpful in understanding breast cancer development and progression

Oral Direct-Acting Agent Therapy for Hepatitis C Virus Infection: A Systematic Review

Rapid improvements in hepatitis C virus (HCV) therapy have led to the approval of multiple oral direct-acting antiviral (DAA) regimens by the U.S. Food and Drug Administration (FDA) for treatment of chronic HCV infection

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

Statistical model and BPS D4-D2-D0 counting

We construct a statistical model that correctly reproduces the BPS partition function of D4-D2-D0 bound states on the resolved conifold. We prove that the known partition function of the BPS indices is reproduced by the counting "triangular partitions" problem. The wall-crossing phenomena in our model are also studied.Comment: 9 pages, 6 figures; v2: typos corrected, minor change

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

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