Radiation of an electric charge in the field of a magnetic monopole

We consider the radiation of photons from quarks scattering on color-magnetic monopoles in the Quark-Gluon Plasma. We consider a temperature regime T\gsim2T_c, where monopoles can be considered as static, rare objects embedded into matter consisting mostly of the usual "electric" quasiparticles, quarks and gluons. The calculation is performed in the classical, non-relativistic approximation and results are compared to photon emission from Coulomb scattering of quarks, known to provide a significant contribution to the photon emission rates from QGP. The present study is a first step towards understanding whether this scattering process can give a sizeable contribution to dilepton production in heavy-ion collisions. Our results are encouraging: by comparing the magnitudes of the photon emission rate for the two processes, we find a dominance in the case of quark-monopole scattering. Our results display strong sensitivity to finite densities of quarks and monopoles.Comment: 28 pages, 8 figure

The role of monopoles in a Gluon Plasma

We study the role of magnetic monopoles at high enough temperature $T>2T_c$, when they can be considered heavy, rare objects embedded into matter consisting mostly of the usual "electric" quasiparticles, quarks and gluons. We review available lattice results on monopoles at finite temperatures. Then we proceed to classical and quantum charge-monopole scattering, solving the problem of gluon-monopole scattering for the first time. We find that, while this process hardly influences thermodynamic quantities, it does produce a large transport cross section, significantly exceeding that for pQCD gluon-gluon scattering up to quite high $T$. Thus, in spite of their relatively small density at high $T$, monopoles are extremely important for QGP transport properties, keeping viscosity small enough for hydrodynamics to work at LHC.Comment: 60 pages, 15 Figure

Dimension 2 condensates and Polyakov Chiral Quark Models

We address a possible relation between the expectation value of the Polyakov loop in pure gluodynamics and full QCD based on Polyakov Chiral Quark Models where constituent quarks and the Polyakov loop are coupled in a minimal way. To this end we use a center symmetry breaking Gaussian model for the Polyakov loop distribution which accurately reproduces gluodynamics data above the phase transition in terms of dimension 2 gluon condensate. The role played by the quantum and local nature of the Polyakov loop is emphasized.Comment: 3 pages, 1 figure. Talk given at the IVth International Conference on Quarks an Nuclear Physics, Madrid, June 5th-10th 200

Mol-CycleGAN - a generative model for molecular optimization

Designing a molecule with desired properties is one of the biggest challenges in drug development, as it requires optimization of chemical compound structures with respect to many complex properties. To augment the compound design process we introduce Mol-CycleGAN - a CycleGAN-based model that generates optimized compounds with high structural similarity to the original ones. Namely, given a molecule our model generates a structurally similar one with an optimized value of the considered property. We evaluate the performance of the model on selected optimization objectives related to structural properties (presence of halogen groups, number of aromatic rings) and to a physicochemical property (penalized logP). In the task of optimization of penalized logP of drug-like molecules our model significantly outperforms previous results

THE CONTEXT OF DISCOVERY OF DATA-DRIVEN BIOLOGY

My PhD dissertation aims (1) at reconstructing the structure of the context of discovery of \u2018data-driven\u2019 (big data, data intensive) biology and (2) at comparing it to traditional molecular approaches. Within the current debate in philosophy of science, \u2018traditional approaches\u2019 in molecular biology should be understood as the discovery and heuristics strategies identified by mechanistic philosophers such as Carl Craver and Lindley Darden. Therefore, key questions of my thesis are: what is the structure of discovery of data-driven biology? Is data-driven biology methodology different from traditional molecular approaches? The reason for doing such an analysis comes from a recent controversy among biologists. In particular, sides disagree on whether high throughput sequencing technologies are stimulating the development of a new scientific method somehow irreducible to traditional approaches. I will try to disentangle the debate by reconstructing and comparing data-driven and traditional methodologies. The dissertation is composed of five chapters. The first chapter deals with methodological issues. How do I compare data-driven and traditional molecular biology structures of discovery? Mechanistic philosophers have extensively characterized the discovery structure of traditional molecular biology. However, there is not such an analysis for data-driven biology. In order to do this, I will critically revise the discovery/justification distinction. The debate on discovery/justification has provided valuable tools on how discovery strategies might be conceived, and it is clearly one of the main forefathers of recent philosophical discussions on scientific methodologies in biology and physics. In Chapter 2 I shall to try to infer a full-fledged account of discovery for data-driven biology by means of the philosophical tools developed in Chapter 1. This analysis will be done in parallel to the investigation of key examples of data-driven biology, namely genome-wide association studies and cancer genomics. In Chapter 3 I analyze the epistemic strategies enabled by biological databases in data-driven biology. In Chapter 4, I will show how the discovery structure of \u2018traditional molecular biology\u2019 can be more efficiently rephrased through the same theoretical framework that I use to characterize data-driven biology. Since data-driven and traditional molecular biology seem to adopt the same discovery structure, one might consider the controversy motivating my research ill posed. However, in Chapter 5 I shall argue that there is still a valuable reason of disagreement between the sides. Actually, data-driven and traditional molecular biology endorse different cognitive values, which provide the criteria for evaluating models and findings as adequate or not. Here one might say that, although the structures of discovery (i.e. how reasoning and experimental strategies are structured and depend on each other) of the two sides are the same, the contexts of discovery (i.e. the set of both reasoning/experimental strategies and epistemic values/background assumptions that motivate discovery) are different. Therefore, in this last chapter I shall pinpoint the cognitive values behind traditional and data-driven biology, and how these commitments stimulate the heated disagreement motivating my research

A General Optimization Technique for High Quality Community Detection in Complex Networks

Recent years have witnessed the development of a large body of algorithms for community detection in complex networks. Most of them are based upon the optimization of objective functions, among which modularity is the most common, though a number of alternatives have been suggested in the scientific literature. We present here an effective general search strategy for the optimization of various objective functions for community detection purposes. When applied to modularity, on both real-world and synthetic networks, our search strategy substantially outperforms the best existing algorithms in terms of final scores of the objective function; for description length, its performance is on par with the original Infomap algorithm. The execution time of our algorithm is on par with non-greedy alternatives present in literature, and networks of up to 10,000 nodes can be analyzed in time spans ranging from minutes to a few hours on average workstations, making our approach readily applicable to tasks which require the quality of partitioning to be as high as possible, and are not limited by strict time constraints. Finally, based on the most effective of the available optimization techniques, we compare the performance of modularity and code length as objective functions, in terms of the quality of the partitions one can achieve by optimizing them. To this end, we evaluated the ability of each objective function to reconstruct the underlying structure of a large set of synthetic and real-world networks.Comment: MAIN text: 14 pages, 4 figures, 1 table Supplementary information: 19 pages, 8 figures, 5 table

On the Reconstruction of Cavities in a Nonlinear Model Arising from Cardiac Electrophysiology

In this paper, we deal with the problem of determining perfectly insulating regions (cavities) from one boundary measurement in a nonlinear elliptic equation arising from cardiac electrophysiology. Based on the results obtained in [9] we propose a new reconstruction algorithm based on Gamma-convergence. The relevance and applicability of this approach are then shown through several numerical experiments

A new PCR based molecular method for early and precise quantification of parasitization in the emerging olive pest Dasineura oleae

BACKGROUND: Dasineura oleae (Angelini 1831) (Diptera: Cecidomyiidae) was considered a minor pest in olive orchards, but in recent years severe outbreaks have been registered in several Mediterranean countries. Damage is caused by the feeding activity of larvae that induce gall formations and alters the physiological activity of the leaves. In Italy, this pest may be controlled by four Hymenoptera parasitoid species belonging to Platygaster and Mesopolobus genera such as Platygaster demades Walker 1835, Platygaster oleae Szelenyi 1940 (Hymenoptera: Platygastridae), Mesopolobus aspilus (Walker 1835) and Mesopolobus mediterraneus (Mayr 1903) (Hymenoptera: Pteromalidae), but parasitization becomes evident only after gall dissection. RESULTS: In this study, we aim to: (i) design a primer for the detection of specimens belonging to Platygaster and Mesopolobus genera; (ii) develop a multiplex quantitative polymerase chain reaction (qPCR) protocol combined to a fast samples DNA extraction method; (iii) apply the developed protocol to field-collected specimens and compare this method with traditional techniques based on visual estimation of parasitism rate on larvae. Primers were designed to anneal with cytochrome oxidase subunit I (COI) sequences of Platygaster and Mesopolobus genera while protocols were developed to be fast and capable to process several samples at the same time. Molecular analyses demonstrated to provide almost double of the parasitism rate assessed by visual inspection. Furthermore, on second instar larvae the PCR-based method was able to detect ten-fold times the parasitization rate estimated by visual inspection. CONCLUSION: The application on a greater scale of this newly developed method could be fundamental in the determination of the biological control potential in olive orchards

Debye mass and heavy quark potential in a PNJL quark plasma

We calculate the Debye mass for the screening of the heavy quark potential in a plasma of massless quarks coupled to the temporal gluon background governed by the Polyakov loop potential within the PNJL model in RPA approximation. We give a physical motivation for a recent phenomenological fit of lattice data by applying the calculated Debye mass with its suppression in the confined phase due to the Polyakov-loop to a description of the temperature dependence of the singlet free energy for QCD with a heavy quark pair at infinite separation. We compare the result to lattice data.Comment: 6 pages, 1 figure, contribution to Proceedings of the 6th International Conference on "Critical Point and Onset of Deconfinement", to appear in Phys. At. Nucl., vol. 7

Thermodynamics of the PNJL model

QCD thermodynamics is investigated by means of the Polyakov-loop-extended Nambu Jona-Lasinio (PNJL) model, in which quarks couple simultaneously to the chiral condensate and to a background temporal gauge field representing Polyakov loop dynamics. The behaviour of the Polyakov loop as a function of temperature is obtained by minimizing the thermodynamic potential of the system. A Taylor series expansion of the pressure is performed. Pressure difference and quark number density are then evaluated up to sixth order in quark chemical potential, and compared to the corresponding lattice data. The validity of the Taylor expansion is discussed within our model, through a comparison between the full results and the truncated ones.Comment: 6 pages, 5 figures, Talk given at the Workshop for Young Scientists on the Physics of Ultrarelativistic Nucleus-Nucleus Collisions (Hot Quarks 2006), Villasimius, Italy, 15-20 May 200