An Efficient Bayesian Inference Framework for Coalescent-Based Nonparametric Phylodynamics

Phylodynamics focuses on the problem of reconstructing past population size dynamics from current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology, but is particularly useful for studying the spread of quickly evolving infectious diseases agents, e.g.,\ influenza virus. Phylodynamics inference uses a coalescent model that defines a probability density for the genealogy of randomly sampled individuals from the population. When we assume that such a genealogy is known, the coalescent model, equipped with a Gaussian process prior on population size trajectory, allows for nonparametric Bayesian estimation of population size dynamics. While this approach is quite powerful, large data sets collected during infectious disease surveillance challenge the state-of-the-art of Bayesian phylodynamics and demand computationally more efficient inference framework. To satisfy this demand, we provide a computationally efficient Bayesian inference framework based on Hamiltonian Monte Carlo for coalescent process models. Moreover, we show that by splitting the Hamiltonian function we can further improve the efficiency of this approach. Using several simulated and real datasets, we show that our method provides accurate estimates of population size dynamics and is substantially faster than alternative methods based on elliptical slice sampler and Metropolis-adjusted Langevin algorithm

A high-order fully coupled electro-fluid-dynamics solver for multiphase flow simulations

A high-order discontinuous Galerkin Finite Element solver is developed for solving electro-fluid-dynamics problems. The solver is employed to perform numerical simulations of deformation of a droplet suspended in another immiscible liquid by applying steady and oscillatory electric fields. The level set method is adopted to represent the common interface of the droplet and surrounding medium. Electrostatics equation with a jump in the dielectric property at the interface is solved to find the electric field distribution. The incompressible Navier-Stokes equations including the surface tension force are solved to find the flow field. The Electrostatics and Navier-Stokes equations are coupled through changes in the geometry because of the deformation of the droplet and the dielectrophoretic body force, which is present at the interface

Reassessing accounting faculty scholarly expectations: Journal classification by author affiliation

An extensive literature exists that determines accounting journal rankings and top research producers both individually and by program. While this research stream provides valuable insights to the Association to Advance Collegiate Schools of Business International (AACSB) accredited programs and to programs working to achieve such accreditation, it frequently is based on quality perceptions or considers top-rated programs only. This study extends previous research by reviewing authorship by faculty at a wider range of institutions. The results of this study suggest that lists based on the “top” journals may be unrealistic for many institutions. The information provided in this manuscript should assist programs, program leaders, and faculty members address AACSB accreditation issues, promotion and tenure decisions, and annual faculty evaluations

Progress of the ECHo SDR Readout Hardware for Multiplexed MMCs

The electron capture in $^{163}$Holmium (ECHo) experiment seeks to achieve sub-eV sensitivity of the electron neutrino mass through calorimetric decay spectroscopy of $^{163}$Ho in large arrays of cryogenic magnetic microcalorimeters (MMCs). Microwave SQUID multiplexing serves to efficiently increase the number of readout channels, thus calorimeters per array and ultimately per cryostat. A corresponding frequency multiplexing room temperature software-defined radio (SDR) system is in development to enable the readout of this increased number of MMCs per cable. The SDR consists of a custom FPGA platform that provides signal generation and analysis capabilities, as well as tailored signal conversion and analog conditioning front end electronics that enable the room-temperature-to-cryogenic interface. Ultimately, the system will read out 400 multiplexer channels with double pixel detectors through a bandwidth of 4 GHz (IEEE C band). As high-resolution data converters are limited in sample rate, the C-band is split into five sub-bands using a two-stage mixing method. In this contribution, a prototype of the heterodyne RF design is presented. It comprises one of the five 800 MHz sub-bands for a target frequency range between 4 and 8 GHz. Furthermore, the second version of the A/D converter stage is presented, capable of generating and digitizing up to five complex basebands using 1 GSs$^{-1}$ converters, the reference clocks and a flux-ramp signal. We will show first results of their single and combined characterization in the lab. The current state of the prototype hardware enables preliminary measurements, only limited in bandwidth and with slightly higher noise. Potential improvements could be derived and will be implemented in the full bandwidth, 5-sub-band RF PCB design

Complete Embedded Self-Translating Surfaces under Mean Curvature Flow

We describe a construction of complete embedded self-translating surfaces under mean curvature flow by desingularizing the intersection of a finite family of grim reapers in general position.Comment: 42 pages, 8 figures. v2: typos correcte

Online Demodulation and Trigger for Flux-ramp Modulated SQUID Signals

Due to the periodic characteristics of SQUIDs, a suitable linearization technique is required for SQUID-based readout. Flux-ramp modulation is a common linearization technique and is typically applied for the readout of a microwave SQUID multiplexer as well as since recently also for dc-SQUIDs. Flux-ramp modulation requires another stage in the signal processing chain to demodulate the SQUID output signal before further processing. For cryogenic microcalorimeters, the signal contains events that are given by a fast exponentially rising and slowly exponentially decaying pulses shape. The events shall be detected by a trigger engine and recorded by a storage logic. Since the data rate can be decreased significantly by demodulation and event detection, it is desirable to do both steps on the deployed fast FPGA logic during measurement before passing the data to a general-purpose processor. In this contribution, we show the implementation of efficient multi-channel flux-ramp demodulation computed at run-time on a SoC-FPGA. Furthermore, a concept and implementation for an online trigger and buffer mechanism with its theoretical trigger loss rates depending on buffer size is presented. Both FPGA modules can be operated with up to 500 MHz clock frequency and can efficiently process 32 channels. Correct functionality and data reduction capability of the modules are demonstrated in measurements utilizing magnetic microcalorimeter irradiated with an Iron-55 source for event generation and read out by a microwave SQUID multiplexer

SDR-Based Readout Electronics for the ECHo Experiment

Due to their excellent energy resolution, the intrinsically fast signal rise time, the huge energy dynamic range, and the almost ideally linear detector response, metallic magnetic calorimeters (MMC)s are very well suited for a variety of applications in physics. In particular, the ECHo experiment aims to utilize large-scale MMC-based detector arrays to investigate the mass of the electron neutrino. Reading out such arrays is a challenging task which can be tackled using microwave SQUID multiplexing. Here, the detector signals are transduced into frequency shifts of superconducting microwave resonators, which can be deduced using a high-end software-defined radio (SDR) system. The ECHo SDR system is a custom-made modular electronics, which provides 400 channels equally distributed in a 4 to 8 GHz frequency band. The system consists of a superheterodyne RF frequency converter with two successive mixers, a modular conversion, and an FPGA board. For channelization, a novel heterogeneous approach, utilizing the integrated digital down conversion (DDC) of the ADC, a polyphase channelizer, and another DDC for demodulation, is proposed. This approach has excellent channelization properties while being resource-efficient at the same time. After signal demodulation, on-FPGA flux-ramp demodulation processes the signals before streaming it to the data processing and storage backend

Versatile Configuration and Control Framework for Real Time Data Acquisition Systems

Modern physics experiments often utilize field-programmable gate array (FPGA)-based systems for real-time data acquisition (DAQ). Integrated analog electronics demand for complex calibration routines. Furthermore, versatile configuration and control of the whole system are key requirements. Besides a low-level register interface to the FPGA, also, access to I 2 C and SPI buses is often needed to configure the complete system. Calibration through an FPGA is inflexible and yields a complex hardware implementation. On the contrary, calibration through a remote system is possible but considerably slower due to repetitive network accesses. By using system-on-chip (SoC)-FPGA solutions with a microprocessor, more sophisticated configuration and calibration solutions, as well as standard remote access protocols, can be efficiently integrated into the software. Based on Xilinx Zynq US+ SoC-FPGAs, we implemented a versatile control framework. This software framework offers convenient access to the hardware and a flexible abstraction via remote-procedure calls (RPCs). Based on the open-source RPC library gRPC, functionality with low-latency control flow, complex algorithms, data conversions and processing, and configuration via external buses can be provided to a client via Ethernet. Furthermore, client interfaces for various programming languages can be generated automatically, which eases collaboration among different working groups and integration into existing software. This contribution presents the framework and benchmarks regarding latency and data throughput

DTS-100G — a versatile heterogeneous MPSoC board for cryogenic sensor readout

Heterogeneous devices such as the Multi-Processor System-on-Chip (MPSoC) from Xilinx are extremely valuable in custom instrumentation systems. This contribution presents the joint development of a heterogeneous MPSoC board called DTS-100G by DESY and KIT. The board is built around a Xilinx Zynq Ultrascale+ chip offering all available high-speed transceivers using QSFP28, 28 Gbps FireFly, FMC, and FMC+ interfaces. The board is not designed for a particular application, but can be used as a generic DAQ platform for a variety of physics experiments. The DTS-100G board was successfully developed, built and commissioned. ECHo-100k is the first experiment which will employ the board. This contribution shows the system architecture and explains how the DTS-100G board is a crucial component in the DAQ chain