Influence of an inhomogeneous and expanding medium on signals of the QCD phase transition

According to a fluid dynamic expansion of the fireball we investigate how the inhomogeneity of the system influences the chiral phase transition of QCD. We compare the averaged values of the order parameter in equilibrium with that of a homogeneous system. If the temperature is averaged over a certain region of the fireball the corresponding correlation length does not diverge in an expansion with a critical point.Comment: proceedings for Quark Matter 201

A composite parameterization of unitary groups, density matrices and subspaces

Unitary transformations and density matrices are central objects in quantum physics and various tasks require to introduce them in a parameterized form. In the present article we present a parameterization of the unitary group $\mathcal{U}(d)$ of arbitrary dimension $d$ which is constructed in a composite way. We show explicitly how any element of $\mathcal{U}(d)$ can be composed of matrix exponential functions of generalized anti-symmetric $\sigma$-matrices and one-dimensional projectors. The specific form makes it considerably easy to identify and discard redundant parameters in several cases. In this way, redundancy-free density matrices of arbitrary rank $k$ can be formulated. Our construction can also be used to derive an orthonormal basis of any $k$-dimensional subspaces of $\mathbb{C}^d$ with the minimal number of parameters. As an example it will be shown that this feature leads to a significant reduction of parameters in the case of investigating distillability of quantum states via lower bounds of an entanglement measure (the $m$-concurrence).Comment: 13 pages, 1 figur

Hybrid approaches to heavy ion collisions and future perspectives

We present the current status of hybrid approaches to describe heavy ion collisions and their future challenges and perspectives. First we present a hybrid model combining a Boltzmann transport model of hadronic degrees of freedom in the initial and final state with an optional hydrodynamic evolution during the dense and hot phase. Second, we present a recent extension of the hydrodynamical model to include fluctuations near the phase transition by coupling a chiral field to the hydrodynamic evolution

Chiral fluid dynamics with explicit propagation of the Polyakov loop

We present a fully dynamical model to study nonequilibrium effects in both the chiral and the deconfinement phase transition. The sigma field and the Polyakov loop as the corresponding order parameters are propagated by Langevin equations of motion. The locally thermalized background is provided by a fluid of quarks and antiquarks. Allowing for an exchange of energy and momentum through dissipative and stochastic processes we ensure that the total energy of the coupled system remains conserved. We study its relaxational dynamics in different quench scenarios and are able to observe critical slowing down as well as the enhancement of long wavelength modes at the critical point. During the fluid dynamical expansion of a hot plasma fireball typical nonequilibrium effects like supercooling and domain formation occur when the system evolves through the first order phase transition.Comment: 20 pages, 22 figure

Towards automatic classification within the ChEBI ontology

*Background*
Appearing in a wide variety of contexts, biochemical 'small molecules' are a core element of biomedical data. Chemical ontologies, which provide stable identifiers and a shared vocabulary for use in referring to such biochemical small molecules, are crucial to enable the interoperation of such data. One such chemical ontology is ChEBI (Chemical Entities of Biological Interest), a candidate member ontology of the OBO Foundry. ChEBI is a publicly available, manually annotated database of chemical entities and contains around 18000 annotated entities as of the last release (May 2009). ChEBI provides stable unique identifiers for chemical entities; a controlled vocabulary in the form of recommended names (which are unique and unambiguous), common synonyms, and systematic chemical names; cross-references to other databases; and a structural and role-based classification within the ontology. ChEBI is widely used for annotation of chemicals within biological databases, text-mining, and data integration. ChEBI can be accessed online at "http://www.ebi.ac.uk/chebi/":http://www.ebi.ac.uk/chebi/ and the full dataset is available for download in various formats including SDF and OBO.

*Automated Classification*
The selection of chemical entities for inclusion in the ChEBI database is user-driven. As the use of ChEBI has grown, so too has the backlog of user-requested entries. Inevitably, the annotation backlog creates a bottleneck, and to speed up the annotation process, ChEBI has recently released a submission tool which allows community submissions of chemical entities, groups, and classes. However, classification of chemical entities within the ontology is a difficult and niche activity, and it is unlikely that the community as a whole will be able or willing to correctly and consistently classify each submitted entity, creating required classes where they are missing. As a result, it is likely that while the size of the database grows, the ontological classification will become less sophisticated, unless the classification of new entities is assisted computationally. In addition, the ChEBI database is expecting substantial size growth in the next year, so automatic classification, which has up till now not been possible, is urgently required. Automatic classification would also enable the ChEBI ontology classes to be applied to other compound databases such as PubChem. 

*Description Logic Reasoning*
Description logic based reasoning technology is a prime candidate for development of such an automatic classification system as it allows the rules of the classification system to be encoded within the knowledgebase. Already at 18000 entities, ChEBI is a fair size for a real-world application of description logic reasoning technology, and as the ontology is enhanced with a richer density of asserted relationships, the classification will become more complex and challenging. We have successfully tested a description logic-based classification of chemical entities based on specified structural properties using the hypertableaux-based HermiT reasoner, and found it to be sufficiently efficient to be feasible for use in a production environment on a database of the size that ChEBI is now. However, much work still remains to enrich the ChEBI knowledgebase itself with the properties needed to provide the formal class definitions for use in the automated classification, and to assess the efficiency of the available description logic reasoning technology on a database the size of ChEBI's forecast future growth.

*Acknowledgements*
ChEBI is funded by the European Commission under SLING, grant agreement number 226073 (Integrating Activity) within Research Infrastructures of the FP7 Capacities Specific Programme, and by the BBSRC, grant agreement number BB/G022747/1 within the “Bioinformatics and biological resources” fund

Minocycline is cytoprotective in human corneal endothelial cells and induces anti-apoptotic B-cell CLL/lymphoma 2 (Bcl-2) and X-linked inhibitor of apoptosis (XIAP)

Introduction Loss of corneal endothelial cells (CECs) is one major factor limiting transplant clarity and survival after keratoplasty. Amongst other factors, apoptosis due to cellular stress is responsible for these problems. This study investigates the possible anti-apoptotic and cytoprotective effects of minocycline on a human corneal endothelial cell line (HCEC-SV40) cultured under oxidative stress and with transforming growth factor beta (TGF-beta). Methods CECs were treated with 1-150 mM minocycline. Cell viability and the median inhibitory concentration (IC(50)) were evaluated after 48 h and after H(2)O(2) treatment (tetrazolium dye reduction assay and liveedead assay). Expression of B-cell CLL/lymphoma 2 (Bcl-2) and X-linked inhibitor of apoptosis (XIAP) and their mRNA were assessed by reverse transcriptase (RT)-PCR and western blot analysis after treatment with minocycline alone and consecutive incubation with 200 mM H(2)O(2) and TGF-beta 2. A quantitative detection of histone-associated DNA fragmentation by ELISA was performed. Results Minocycline concentrations from 1-50 mM showed no toxic effects on CECs. Pre-treatment with 10-40 mM minocycline led to an increase in viability after H(2)O(2) treatment. In addition, minocycline pretreatment attenuated the increase of histone-associated DNA fragmentation after treatment with H(2)O(2) and TGF-beta 2 significantly. When CECs were treated with minocycline and then consecutively with H(2)O(2) or TGF-beta 2, RT-PCR and western blot analysis yielded an overexpression of Bcl-2 and XIAP. Conclusion In this study minocycline prevented apoptotic cell death in cultured CECs in vitro. Our results suggest that minocycline might offer cytoprotective properties that might help to prevent loss of corneal endothelial cells in vivo