Simulation Application for the LHCb Experiment

We describe the LHCb detector simulation application (Gauss) based on the Geant4 toolkit. The application is built using the Gaudi software framework, which is used for all event-processing applications in the LHCb experiment. The existence of an underlying framework allows several common basic services such as persistency, interactivity, as well as detector geometry description or particle data to be shared between simulation, reconstruction and analysis applications. The main benefits of such common services are coherence between different event-processing stages as well as reduced development effort. The interfacing to Geant4 toolkit is realized through a facade (GiGa) which minimizes the coupling to the simulation engine and provides a set of abstract interfaces for configuration and event-by-event communication. The Gauss application is composed of three main blocks, i.e. event generation, detector response simulation and digitization which reflect the different stages performed during the simulation job. We describe the overall design as well as the details of Gauss application with a special emphasis on the configuration and control of the underlying simulation engine. We also briefly mention the validation strategy and the planing for the LHCb experiment simulation.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 6 pages, LaTeX, 9 eps figures. PSN TUMT00

High-temperature phase transitions in SrBi_2Ta_2O_9 film: a study by THz spectroscopy

Time-domain THz transmission experiment was performed on a $\rm SrBi_2Ta_2O_9$ film deposited on sapphire substrate. Temperatures between 300 and 923 K were investigated and complex permittivity spectra of the film were determined. The lowest frequency optic phonon near 28 cm$^{-1}$ reveals a slow monotonic decrease in frequency on heating with no significant anomaly near the phase transitions. We show that the dielectric anomaly near the ferroelectric phase transition can be explained by slowing down of a relaxational mode, observed in the THz spectra. A second harmonic generation signal observed in a single crystal confirms a loss of center of symmetry in the ferroelectric phase and a presence of polar clusters in the intermediate ferroelastic phase.Comment: subm. to J. Phys.: Condens. Matte

The LHCb trigger and data acquisition system

The LHCb experiment is the most recently approved of the 4 experiments under construction at CERNs LHC accelerator. It is a special purpose experiment designed to precisely measure the CP violation parameters in the B-B system. Triggering poses special problems since the interesting events containing B-mesons are immersed in a large background of inelastic p-p reactions. We therefore decided to implement a 4 level triggering scheme. The LHCb Data Acquisition (DAQ) system will have to cope with an average trigger rate of ~40 kHz, after two levels of hardware triggers, and an average event size of ~100 kB. Thus an event-building network which can sustain an average bandwidth of 4 GB/s is required. A powerful software trigger farm will have to be installed to reduce the rate from the 40 kHz to ~100 Hz of events written to permanent storage. In this paper we outline the general architecture of the Trigger and DAQ system and the readout protocols we plan to implement. First results of simulations of the behavior of the event- building network implementations under the expected traffic patterns are presented. (8 refs)

Epistatic Interactions in the Arabinose Cis-Regulatory Element

Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner

Characterizing and prognosticating chronic lymphocytic leukemia in the elderly: prospective evaluation on 455 patients treated in the United States.

BACKGROUND: Median age at diagnosis of patients with chronic lymphocytic leukemia (CLL) is \u3e 70 years. However, the majority of clinical trials do not reflect the demographics of CLL patients treated in the community. We examined treatment patterns, outcomes, and disease-related mortality in patients ≥ 75 years with CLL (E-CLL) in a real-world setting. METHODS: The Connect® CLL registry is a multicenter, prospective observational cohort study, which enrolled 1494 adult patients between 2010-2014, at 199 US sites. Patients with CLL were enrolled within 2 months of initiating first line of therapy (LOT1) or a subsequent LOT (LOT ≥ 2). Kaplan-Meier methods were used to evaluate overall survival. CLL- and infection-related mortality were assessed using cumulative incidence functions (CIF) and cause-specific hazards. Logistic regression was used to develop a classification model. RESULTS: A total of 455 E-CLL patients were enrolled; 259 were enrolled in LOT1 and 196 in LOT ≥ 2. E-CLL patients were more likely to receive rituximab monotherapy (19.3 vs. 8.6%; p \u3c 0.0001) and chemotherapy-alone regimens (p \u3c 0.0001) than younger patients. Overall and complete responses were lower in E-CLL patients than younger patients when given similar regimens. With a median follow-up of 3 years, CLL-related deaths were higher in E-CLL patients than younger patients in LOT1 (12.6 vs. 5.1% p = 0.0005) and LOT ≥ 2 (31.3 vs. 21.5%; p = 0.0277). Infection-related deaths were also higher in E-CLL patients than younger patients in LOT1 (7.4 vs. 2.7%; p = 0.0033) and in LOT ≥ 2 (16.2 vs. 11.2%; p = 0.0786). A prognostic score for E-CLL patients was developed: time from diagnosis to treatment \u3c 3 months, enrollment therapy other than bendamustine/rituximab, and anemia, identified patients at higher risk of inferior survival. Furthermore, higher-risk patients experienced an increased risk of CLL- or infection-related death (30.6 vs 10.3%; p = 0.0006). CONCLUSION: CLL- and infection-related mortality are higher in CLL patients aged ≥ 75 years than younger patients, underscoring the urgent need for alternative treatment strategies for these understudied patients. TRIAL REGISTRATION: The Connect CLL registry was registered at clinicaltrials.gov: NCT01081015 on March 4, 2010

Finite strain Landau theory of high pressure phase transformations

The properties of materials near structural phase transitions are often successfully described in the framework of Landau theory. While the focus is usually on phase transitions, which are induced by temperature changes approaching a critical temperature T-c, here we will discuss structural phase transformations driven by high hydrostatic pressure, as they are of major importance for understanding processes in the interior of the earth. Since at very high pressures the deformations of a material are generally very large, one needs to apply a fully nonlinear description taking physical as well as geometrical nonlinearities (finite strains) into account. In particular it is necessary to retune conventional Landau theory to describe such phase transitions. In Troster et al (2002 Phys. Rev. Lett. 88 55503) we constructed a Landau-type free energy based on an order parameter part, an order parameter-(finite) strain coupling and a nonlinear elastic term. This model provides an excellent and efficient framework for the systematic study of phase transformations for a wide range of materials up to ultrahigh pressures

First-principles study of the ferroelastic phase transition in CaCl_2

First-principles density-functional calculations within the local-density approximation and the pseudopotential approach are used to study and characterize the ferroelastic phase transition in calcium chloride (CaCl_2). In accord with experiment, the energy map of CaCl_2 has the typical features of a pseudoproper ferroelastic with an optical instability as ultimate origin of the phase transition. This unstable optic mode is close to a pure rigid unit mode of the framework of chlorine atoms and has a negative Gruneisen parameter. The ab-initio ground state agrees fairly well with the experimental low temperature structure extrapolated at 0K. The calculated energy map around the ground state is interpreted as an extrapolated Landau free-energy and is successfully used to explain some of the observed thermal properties. Higher-order anharmonic couplings between the strain and the unstable optic mode, proposed in previous literature as important terms to explain the soft-phonon temperature behavior, are shown to be irrelevant for this purpose. The LAPW method is shown to reproduce the plane-wave results in CaCl_2 within the precision of the calculations, and is used to analyze the relative stability of different phases in CaCl_2 and the chemically similar compound SrCl_2.Comment: 9 pages, 6 figures, uses RevTeX

Phonons from neutron powder diffraction

The spherically averaged structure function \soq obtained from pulsed neutron powder diffraction contains both elastic and inelastic scattering via an integral over energy. The Fourier transformation of \soq to real space, as is done in the pair density function (PDF) analysis, regularizes the data, i.e. it accentuates the diffuse scattering. We present a technique which enables the extraction of off-center phonon information from powder diffraction experiments by comparing the experimental PDF with theoretical calculations based on standard interatomic potentials and the crystal symmetry. This procedure (dynamics from powder diffraction(DPD)) has been successfully implemented for two systems, a simple metal, fcc Ni, and an ionic crystal, CaF$_{2}$. Although computationally intensive, this data analysis allows for a phonon based modeling of the PDF, and additionally provides off-center phonon information from powder neutron diffraction