Nonsupersymmetric Brane/Antibrane Configurations in Type IIA and M Theory

We study metastable nonsupersymmetric configurations in type IIA string theory, obtained by suspending D4-branes and anti-D4-branes between holomorphically curved NS5's, which are related to those of hep-th/0610249 by T-duality. When the numbers of branes and antibranes are the same, we are able to obtain an exact M theory lift which can be used to reliably describe the vacuum configuration as a curved NS5 with dissolved RR flux for g_s<<1 and as a curved M5 for g_s>>1. When our weakly coupled description is reliable, it is related by T-duality to the deformed IIB geometry with flux of hep-th/0610249 with moduli exactly minimizing the potential derived therein using special geometry. Moreover, we can use a direct analysis of the action to argue that this agreement must also hold for the more general brane/antibrane configurations of hep-th/0610249. On the other hand, when our strongly coupled description is reliable, the M5 wraps a nonholomorphic minimal area curve that can exhibit quite different properties, suggesting that the residual structure remaining after spontaneous breaking of supersymmetry at tree level can be further broken by the effects of string interactions. Finally, we discuss the boundary condition issues raised in hep-th/0608157 for nonsupersymmetric IIA configurations, their implications for our setup, and their realization on the type IIB side.Comment: 84 pages (57 pages + 4 appendices), 18 figure

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Does urinary peptide content differ between COPD patients with and without inherited alpha-1 antitrypsin deficiency?

Differentiating between chronic obstructive pulmonary disease (COPD) patients with normal (PiMM) or deficient (PiZZ) genetic variants of alpha-1 antitrypsin (A1AT) is important not only for understanding the pathobiology of disease progression but also for improving personalized therapies. This pilot study aimed to investigate whether urinary peptides reflect the A1AT-related phenotypes of COPD. Urine samples from 19 clinically stable COPD cases (7 PiMM and 12 PiZZ A1AT) were analyzed by capillary electrophoresis coupled to mass spectrometry. We identified 66 peptides (corresponding to 36 unique proteins) that differed between PiZZ and PiMM COPD. Among these, peptides from the collagen family were the most abundant and divergent. A logistic regression model based on COL1A1 or COL5A3 peptides enabled differentiation between PiMM and PiZZ groups, with a sensitivity of 100% and specificity of 85.71% for COL1A1 and a sensitivity of 91.67% and specificity of 85.71% for COL5A3. Furthermore, patients with PiZZ presented low levels of urinary peptides involved in lipoproteins/lipids and retinoic acid metabolism, such as apolipoprotein A-I and C4, retinol-binding protein 4 and prostaglandin-H2 d-isomerase. However, peptides of MDS1 and EVII complex locus, gelsolin and hemoglobin alpha were found in the urine of COPD cases with PiZZ, but not with PiMM. These capillary electrophoresis coupled to mass spectrometry-based results provide the first evidence that urinary peptide content differs between PiMM and PiZZ patients with COPD

Emergence and Correspondence for String Theory Black Holes

This is one of a pair of papers that give a historical-\emph{cum}-philosophical analysis of the endeavour to understand black hole entropy as a statistical mechanical entropy obtained by counting string-theoretic microstates. Both papers focus on Andrew Strominger and Cumrun Vafa's ground-breaking 1996 calculation, which analysed the black hole in terms of D-branes. The first paper gives a conceptual analysis of the Strominger-Vafa argument, and of several research efforts that it engendered. In this paper, we assess whether the black hole should be considered as emergent from the D-brane system, particularly in light of the role that duality plays in the argument. We further identify uses of the quantum-to-classical correspondence principle in string theory discussions of black holes, and compare these to the heuristics of earlier efforts in theory construction, in particular those of the old quantum theory.Comment: 40 page

Soft matrix models and Chern-Simons partition functions

We study the properties of matrix models with soft confining potentials. Their precise mathematical characterization is that their weight function is not determined by its moments. We mainly rely on simple considerations based on orthogonal polynomials and the moment problem. In addition, some of these models are equivalent, by a simple mapping, to matrix models that appear in Chern-Simons theory. The models can be solved with q deformed orthogonal polynomials (Stieltjes-Wigert polynomials), and the deformation parameter turns out to be the usual $q$ parameter in Chern-Simons theory. In this way, we give a matrix model computation of the Chern-Simons partition function on $S^{3}$ and show that there are infinitely many matrix models with this partition function.Comment: 13 pages, 3 figure

Conceptual Analysis of Black Hole Entropy in String Theory

The microscopic state counting of the extremal Reissner-Nordstr\"om black hole performed by Andrew Strominger and Cumrun Vafa in 1996 has proven to be a central result in string theory. Here, with a philosophical readership in mind, the argument is presented in its contemporary context and its rather complex conceptual structure is analysed. In particular, we will identify the various inter-theoretic relations, such as duality and linkage relations, on which it depends. We further aim to make clear why the argument was immediately recognised as a successful accounting for the entropy of this black hole and how it engendered subsequent work that intended to strengthen the string theoretic analysis of black holes. Its relation to the formulation of the AdS/CFT conjecture will be briefly discussed, and the familiar reinterpretation of the entropy calculation in the context of the AdS/CFT correspondence is given. Finally, we discuss the heuristic role that Strominger and Vafa's microscopic account of black hole entropy played for the black hole information paradox. A companion paper analyses the ontology of the Strominger-Vafa black hole states, the question of emergence of the black hole from a collection of D-branes, and the role of the correspondence principle in the context of string theory black holes.Comment: 70 page