Non-Abelian Wilson Surfaces

A definition of non-abelian genus zero open Wilson surfaces is proposed. The ambiguity in surface-ordering is compensated by the gauge transformations.Comment: JHEP Latex, 10 pages, 6 figures; v2, refs and comments added in sec.

Path Integral for Space-time Noncommutative Field Theory

The path integral for space-time noncommutative theory is formulated by means of Schwinger's action principle which is based on the equations of motion and a suitable ansatz of asymptotic conditions. The resulting path integral has essentially the same physical basis as the Yang-Feldman formulation. It is first shown that higher derivative theories are neatly dealt with by the path integral formulation, and the underlying canonical structure is recovered by the Bjorken-Johnson-Low (BJL) prescription from correlation functions defined by the path integral. A simple theory which is non-local in time is then analyzed for an illustration of the complications related to quantization, unitarity and positive energy conditions. From the view point of BJL prescription, the naive quantization in the interaction picture is justified for space-time noncommutative theory but not for the simple theory non-local in time. We finally show that the perturbative unitarity and the positive energy condition, in the sense that only the positive energy flows in the positive time direction for any fixed time-slice in space-time, are not simultaneously satisfied for space-time noncommutative theory by the known methods of quantization.Comment: 21 page

Hard Non-commutative Loops Resummation

The non-commutative version of the euclidean $g^2\phi^4$ theory is considered. By using Wilsonian flow equations the ultraviolet renormalizability can be proved to all orders in perturbation theory. On the other hand, the infrared sector cannot be treated perturbatively and requires a resummation of the leading divergencies in the two-point function. This is analogous to what is done in the Hard Thermal Loops resummation of finite temperature field theory. Next-to-leading order corrections to the self-energy are computed, resulting in $O(g^3)$ contributions in the massless case, and $O(g^6\log g^2)$ in the massive one.Comment: 4 pages, 3 figures. The resummation procedure is now discussed also at finite ultraviolet cut-off. Minor changes in abstract and references. Final version to be published in Physical Review Letter

Non-renormalizability of noncommutative SU(2) gauge theory

We analyze the divergent part of the one-loop effective action for the noncommutative SU(2) gauge theory coupled to the fermions in the fundamental representation. We show that the divergencies in the 2-point and the 3-point functions in the $\theta$-linear order can be renormalized, while the divergence in the 4-point fermionic function cannot.Comment: 15 pages, results presented at ESI 2d dilaton gravity worksho

Self-organizing ontology of biochemically relevant small molecules

<p>Abstract</p> <p>Background</p> <p>The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest.</p> <p>Results</p> <p>To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development.</p> <p>Conclusions</p> <p>We conclude that the proposed methodology can ease the burden of chemical data annotators and dramatically increase their productivity. We anticipate that the use of formal logic in our proposed framework will make chemical classification criteria more transparent to humans and machines alike and will thus facilitate predictive and integrative bioactivity model development.</p

Magnetic Backgrounds and Noncommutative Field Theory

This paper is a rudimentary introduction, geared at non-specialists, to how noncommutative field theories arise in physics and their applications to string theory, particle physics and condensed matter systems.Comment: 26 pages, 3 figures, uses ws-ijmpa.cls; Invited review to be published in International Journal of Modern Physics A; v2: References adde

Some comments about Schwarzschield black holes in Matrix theory

In the present paper we calculate the statistical partition function for any number of extended objects in Matrix theory in the one loop approximation. As an application, we calculate the statistical properties of K clusters of D0 branes and then the statistical properties of K membranes which are wound on a torus.Comment: 15 page

Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

<p>Abstract</p> <p>Background</p> <p>The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in the hands of human curators using manual or semi-automated protocols, leaving many novel entities unclassified. Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality.</p> <p>Results</p> <p>As part of an exploratory study, we have investigated the utility of semantic web technologies in automated chemical classification and annotation of lipids. Our prototype framework consists of two components: an ontology and a set of federated web services that operate upon it. The formal lipid ontology we use here extends a part of the LiPrO ontology and draws on the lipid hierarchy in the LIPID MAPS database, as well as literature-derived knowledge. The federated semantic web services that operate upon this ontology are deployed within the Semantic Annotation, Discovery, and Integration (SADI) framework. Structure-based lipid classification is enacted by two core services. Firstly, a structural annotation service detects and enumerates relevant functional groups for a specified chemical structure. A second service reasons over lipid ontology class descriptions using the attributes obtained from the annotation service and identifies the appropriate lipid classification. We extend the utility of these core services by combining them with additional SADI services that retrieve associations between lipids and proteins and identify publications related to specified lipid types. We analyze the performance of SADI-enabled eicosanoid classification relative to the LIPID MAPS classification and reflect on the contribution of our integrative methodology in the context of high-throughput lipidomics.</p> <p>Conclusions</p> <p>Our prototype framework is capable of accurate automated classification of lipids and facile integration of lipid class information with additional data obtained with SADI web services. The potential of programming-free integration of external web services through the SADI framework offers an opportunity for development of powerful novel applications in lipidomics. We conclude that semantic web technologies can provide an accurate and versatile means of classification and annotation of lipids.</p

Exact Solution of Quantum Field Theory on Noncommutative Phase Spaces

We present the exact solution of a scalar field theory defined with noncommuting position and momentum variables. The model describes charged particles in a uniform magnetic field and with an interaction defined by the Groenewold-Moyal star-product. Explicit results are presented for all Green's functions in arbitrary even spacetime dimensionality. Various scaling limits of the field theory are analysed non-perturbatively and the renormalizability of each limit examined. A supersymmetric extension of the field theory is also constructed in which the supersymmetry transformations are parametrized by differential operators in an infinite-dimensional noncommutative algebra.Comment: 70 pages AMSTe

On the UV renormalizability of noncommutative field theories

UV/IR mixing is one of the most important features of noncommutative field theories. As a consequence of this coupling of the UV and IR sectors, the configuration of fields at the zero momentum limit in these theories is a very singular configuration. We show that the renormalization conditions set at a particular momentum configuration with a fixed number of zero momenta, renormalizes the Green's functions for any general momenta only when this configuration has same set of zero momenta. Therefore only when renormalization conditions are set at a point where all the external momenta are nonzero, the quantum theory is renormalizable for all values of nonzero momentum. This arises as a result of different scaling behaviors of Green's functions with respect to the UV cutoff ($\Lambda$) for configurations containing different set of zero momenta. We study this in the noncommutative $\phi^4$ theory and analyse similar results for the Gross-Neveu model at one loop level. We next show this general feature using Wilsonian RG of Polchinski in the globally O(N) symmetric scalar theory and prove the renormalizability of the theory to all orders with an infrared cutoff. In the context of spontaneous symmetry breaking (SSB) in noncommutative scalar theory, it is essential to note the different scaling behaviors of Green's functions with respect to $\Lambda$ for different set of zero momenta configurations. We show that in the broken phase of the theory the Ward identities are satisfied to all orders only when one keeps an infrared regulator by shifting to a nonconstant vacuum.Comment: 29 pages, 8 figures, uses JHEP.cls, references adde