Physics with the ALICE Electromagnetic Calorimeter

I will present physics measurements which are achievable in the ALICE experiment at the LHC through the inclusion of a new electromagnetic calorimeter. I will focus on jet measurements in proton proton and heavy ion collisions. Detailed simulations have been performed on jet reconstruction, jet triggering, heavy flavor jet reconstruction through electron identification, gamma-jet reconstruction and the measurements of identified hadrons and resonances in jets. I will show the physics capabilities which are made possible through the combination of calorimeter information with the other detector components in ALICE.Comment: 12 pages, 8 figures, Proceedings for the 25th Winter Workshop on Nuclear Dynamics, Big Sky, Montana (USA), February 1-8, 200

A review of advances in pixel detectors for experiments with high rate and radiation

The Large Hadron Collider (LHC) experiments ATLAS and CMS have established hybrid pixel detectors as the instrument of choice for particle tracking and vertexing in high rate and radiation environments, as they operate close to the LHC interaction points. With the High Luminosity-LHC upgrade now in sight, for which the tracking detectors will be completely replaced, new generations of pixel detectors are being devised. They have to address enormous challenges in terms of data throughput and radiation levels, ionizing and non-ionizing, that harm the sensing and readout parts of pixel detectors alike. Advances in microelectronics and microprocessing technologies now enable large scale detector designs with unprecedented performance in measurement precision (space and time), radiation hard sensors and readout chips, hybridization techniques, lightweight supports, and fully monolithic approaches to meet these challenges. This paper reviews the world-wide effort on these developments.Comment: 84 pages with 46 figures. Review article.For submission to Rep. Prog. Phy

INFN What Next: Ultra-relativistic Heavy-Ion Collisions

This document was prepared by the community that is active in Italy, within INFN (Istituto Nazionale di Fisica Nucleare), in the field of ultra-relativistic heavy-ion collisions. The experimental study of the phase diagram of strongly-interacting matter and of the Quark-Gluon Plasma (QGP) deconfined state will proceed, in the next 10-15 years, along two directions: the high-energy regime at RHIC and at the LHC, and the low-energy regime at FAIR, NICA, SPS and RHIC. The Italian community is strongly involved in the present and future programme of the ALICE experiment, the upgrade of which will open, in the 2020s, a new phase of high-precision characterisation of the QGP properties at the LHC. As a complement of this main activity, there is a growing interest in a possible future experiment at the SPS, which would target the search for the onset of deconfinement using dimuon measurements. On a longer timescale, the community looks with interest at the ongoing studies and discussions on a possible fixed-target programme using the LHC ion beams and on the Future Circular Collider.Comment: 99 pages, 56 figure

The Hot QCD White Paper: Exploring the Phases of QCD at RHIC and the LHC

The past decade has seen huge advances in experimental measurements made in heavy ion collisions at the Relativistic Heavy Ion Collider (RHIC) and more recently at the Large Hadron Collider (LHC). These new data, in combination with theoretical advances from calculations made in a variety of frameworks, have led to a broad and deep knowledge of the properties of thermal QCD matter. Increasingly quantitative descriptions of the quark-gluon plasma (QGP) created in these collisions have established that the QGP is a strongly coupled liquid with the lowest value of specific viscosity ever measured. However, much remains to be learned about the precise nature of the initial state from which this liquid forms, how its properties vary across its phase diagram and how, at a microscopic level, the collective properties of this liquid emerge from the interactions among the individual quarks and gluons that must be visible if the liquid is probed with sufficiently high resolution. This white paper, prepared by the Hot QCD Writing Group as part of the U.S. Long Range Plan for Nuclear Physics, reviews the recent progress in the field of hot QCD and outlines the scientific opportunities in the next decade for resolving the outstanding issues in the field.Comment: 110 pages, 33 figures, 429 references. Prepared as part of the U.S. Long-Range Plan for Nuclear Physic

NOVEL COMPUTATIONAL METHODS FOR CANCER GENOMICS DATA ANALYSIS

Cancer is a genetic disease responsible for one in eight deaths worldwide. The advancement of next-generation sequencing (NGS) technology has revolutionized the cancer research, allowing comprehensively profiling the cancer genome at great resolution. Large-scale cancer genomics research has sparked the needs for efficient and accurate Bioinformatics methods to analyze the data. The research presented in this dissertation focuses on three areas in cancer genomics: cancer somatic mutation detection; cancer driver genes identification and transcriptome profiling on single-cell level. NGS data analysis involves a series of complicated data transformation that convert raw sequencing data to the information that is interpretable by cancer researchers. The first project in the dissertation established a robust, reproducible and scalable cancer genomics data analysis workflow management system that automates the best practice mutation calling pipelines to detect somatic single nucleotide polymorphisms, insertion, deletion and copy number variation from NGS data. It integrates mutation annotation, clinically actionable therapy prediction and data visualization that streamlines the sequence-to-report data transformation. In order to differentiate the driver mutations buried among a vast pool of passenger mutations from a somatic mutation calling project, we developed MEScan in the second project, a novel method that enables genome-scale driver mutations identification based on mutual exclusivity test using cancer somatic mutation data. MEScan implements an efficient statistical framework to de novo screen mutual exclusive patterns and in the meantime taking into account the patient-specific and gene-specific background mutation rate and adjusting the heterogenous mutation frequency. It outperforms several existing methods based on simulation studies and real-world datasets. Genome-wide screening using existing TCGA somatic mutation data discovers novel cancer-specific and pan-cancer mutually exclusive patterns. Bulk RNA sequencing (RNA-Seq) has become one of the most commonly used techniques for transcriptome profiling in a wide spectrum of biomedical and biological research. Analyzing bulk RNA-Seq reads to quantify expression at each gene locus is the first step towards the identification of differentially expressed genes for downstream biological interpretation. Recent advances in single-cell RNA-seq (scRNA-seq) technology allows cancer biologists to profile gene expression on higher resolution cellular level. Preprocessing scRNA-seq data to quantify UMI-based gene count is the key to characterize intra-tumor cellular heterogeneity and identify rare cells that governs tumor progression, metastasis and treatment resistance. Despite its popularity, summarizing gene count from raw sequencing reads remains the one of the most time-consuming steps with existing tools. Current pipelines do not balance the efficiency and accuracy in large-scale gene count summarization in both bulk and scRNA-seq experiments. In the third project, we developed a light-weight k-mer based gene counting algorithm, FastCount, to accurately and efficiently quantify gene-level abundance using bulk RNA-seq or UMI-based scRNA-seq data. It achieves at least an order-of-magnitude speed improvement over the current gold standard pipelines while providing competitive accuracy

The Physics of Ultraperipheral Collisions at the LHC

We discuss the physics of large impact parameter interactions at the LHC: ultraperipheral collisions (UPCs). The dominant processes in UPCs are photon-nucleon (nucleus) interactions. The current LHC detector configurations can explore small $x$ hard phenomena with nuclei and nucleons at photon-nucleon center-of-mass energies above 1 TeV, extending the $x$ range of HERA by a factor of ten. In particular, it will be possible to probe diffractive and inclusive parton densities in nuclei using several processes. The interaction of small dipoles with protons and nuclei can be investigated in elastic and quasi-elastic $J/\psi$ and $\Upsilon$ production as well as in high $t$ $\rho^0$ production accompanied by a rapidity gap. Several of these phenomena provide clean signatures of the onset of the new high gluon density QCD regime. The LHC is in the kinematic range where nonlinear effects are several times larger than at HERA. Two-photon processes in UPCs are also studied. In addition, while UPCs play a role in limiting the maximum beam luminosity, they can also be used a luminosity monitor by measuring mutual electromagnetic dissociation of the beam nuclei. We also review similar studies at HERA and RHIC as well as describe the potential use of the LHC detectors for UPC measurements.Comment: 229 Pages, 121 figure

Particle identification

Particle IDentification (PID) is fundamental to particle physics experiments. This paper reviews PID strategies and methods used by the large LHC experiments, which provide outstanding examples of the state-of-the-art. The first part focuses on the general design of these experiments with respect to PID and the technologies used. Three PID techniques are discussed in more detail: ionization measurements, time-of-flight measurements and Cherenkov imaging. Four examples of the implementation of these techniques at the LHC are given, together with selections of relevant examples from other experiments and short overviews on new developments. Finally, the Alpha Magnetic Spectrometer (AMS 02) experiment is briefly described as an impressive example of a space-based experiment using a number of familiar PID techniques.Comment: 61 pages, 30 figure