Inexact Newton Dogleg Methods

The dogleg method is a classical trust-region technique for globalizing Newton\u27s method. While it is widely used in optimization, including large-scale optimization via truncated-Newton approaches, its implementation in general inexact Newton methods for systems of nonlinear equations can be problematic. In this paper, we first outline a very general dogleg method suitable for the general inexact Newton context and provide a global convergence analysis for it. We then discuss certain issues that may arise with the standard dogleg implementational strategy and propose modified strategies that address them. Newton-Krylov methods have provided important motivation for this work, and we conclude with a report on numerical experiments involving a Newton-GMRES dogleg method applied to benchmark CFD problems

Construction and Performance of a Micro-Pattern Stereo Detector with Two Gas Electron Multipliers

The construction of a micro-pattern gas detector of dimensions 40x10 cm**2 is described. Two gas electron multiplier foils (GEM) provide the internal amplification stages. A two-layer readout structure was used, manufactured in the same technology as the GEM foils. The strips of each layer cross at an effective crossing angle of 6.7 degrees and have a 406 um pitch. The performance of the detector has been evaluated in a muon beam at CERN using a silicon telescope as reference system. The position resolutions of two orthogonal coordinates are measured to be 50 um and 1 mm, respectively. The muon detection efficiency for two-dimensional space points reaches 96%.Comment: 21 pages, 17 figure

Ground-State Electromagnetic Moments of Calcium Isotopes

High-resolution bunched-beam collinear laser spectroscopy was used to measure the optical hyperfine spectra of the $^{43-51}$Ca isotopes. The ground state magnetic moments of $^{49,51}$Ca and quadrupole moments of $^{47,49,51}$Ca were measured for the first time, and the $^{51}$Ca ground state spin $I=3/2$ was determined in a model-independent way. Our results provide a critical test of modern nuclear theories based on shell-model calculations using phenomenological as well as microscopic interactions. The results for the neutron-rich isotopes are in excellent agreement with predictions using interactions derived from chiral effective field theory including three-nucleon forces, while lighter isotopes illustrate the presence of particle-hole excitations of the $^{40}$Ca core in their ground state.Comment: Accepted as a Rapid Communication in Physical Review

Certainty Closure: Reliable Constraint Reasoning with Incomplete or Erroneous Data

Constraint Programming (CP) has proved an effective paradigm to model and solve difficult combinatorial satisfaction and optimisation problems from disparate domains. Many such problems arising from the commercial world are permeated by data uncertainty. Existing CP approaches that accommodate uncertainty are less suited to uncertainty arising due to incomplete and erroneous data, because they do not build reliable models and solutions guaranteed to address the user's genuine problem as she perceives it. Other fields such as reliable computation offer combinations of models and associated methods to handle these types of uncertain data, but lack an expressive framework characterising the resolution methodology independently of the model. We present a unifying framework that extends the CP formalism in both model and solutions, to tackle ill-defined combinatorial problems with incomplete or erroneous data. The certainty closure framework brings together modelling and solving methodologies from different fields into the CP paradigm to provide reliable and efficient approches for uncertain constraint problems. We demonstrate the applicability of the framework on a case study in network diagnosis. We define resolution forms that give generic templates, and their associated operational semantics, to derive practical solution methods for reliable solutions.Comment: Revised versio

Cones, pringles, and grain boundary landscapes in graphene topology

A polycrystalline graphene consists of perfect domains tilted at angle {\alpha} to each other and separated by the grain boundaries (GB). These nearly one-dimensional regions consist in turn of elementary topological defects, 5-pentagons and 7-heptagons, often paired up into 5-7 dislocations. Energy G({\alpha}) of GB computed for all range 0<={\alpha}<=Pi/3, shows a slightly asymmetric behavior, reaching ~5 eV/nm in the middle, where the 5's and 7's qualitatively reorganize in transition from nearly armchair to zigzag interfaces. Analysis shows that 2-dimensional nature permits the off-plane relaxation, unavailable in 3-dimensional materials, qualitatively reducing the energy of defects on one hand while forming stable 3D-landsapes on the other. Interestingly, while the GB display small off-plane elevation, the random distributions of 5's and 7's create roughness which scales inversely with defect concentration, h ~ n^(-1/2)Comment: 9 pages, 4 figure

Beam test results of silicon sensor module prototypes for the Phase-2 Upgrade of the CMS Outer Tracker

The start of the High-Luminosity LHC (HL-LHC) in 2027 requires upgrades to the Compact Muon Solenoid (CMS) Experiment. In the scope of the upgrade program the complete silicon tracking detector will be replaced. The new CMS Tracker will be equipped with silicon pixel detectors in the inner layers closest to the interaction point and silicon strip detectors in the outer layers. The new CMS Outer Tracker will consist of two different kinds of detector modules called PS and 2S modules. Each module will be made of two parallel silicon sensors (a macro-pixel sensor and a strip sensor for the PS modules and two strip sensors for the 2S modules). Combining the hit information of both sensor layers it is possible to estimate the transverse momentum of particles in the magnetic field of 3.8 T at the full bunch-crossing rate of 40 MHz directly on the module. This information will be used as an input for the first trigger stage of CMS. It is necessary to validate the Outer Tracker module functionality before installing the modules in the CMS experiment. Besides laboratory-based tests several 2S module prototypes have been studied at test beam facilities at CERN, DESY and FNAL. This article concentrates on the beam tests at DESY during which the functionality of the module concept was investigated using the full final readout chain for the first time. Additionally the performance of a 2S module assembled with irradiated sensors was studied. By choosing an irradiation fluence expected for 2S modules at the end of HL-LHC operation, it was possible to investigate the particle detection efficiency and study the trigger capabilities of the module at the beginning and end of runtime of the CMS experiment.The start of the High-Luminosity LHC (HL-LHC) in 2027 requires upgrades to the Compact Muon Solenoid (CMS) experiment. In the scope of the upgrade program the complete silicon tracking detector will be replaced. The new CMS Tracker will be equipped with silicon pixel detectors in the inner layers closest to the interaction point and silicon strip detectors in the outer layers. The new CMS Outer Tracker will consist of two different kinds of detector modules called PS and 2S modules. Each module will be made of two parallel silicon sensors (a macro-pixel sensor and a strip sensor for the PS modules and two strip sensors for the 2S modules). Combining the hit information of both sensor layers, it is possible to estimate the transverse momentum of particles in the magnetic field of 3.8 T at the full bunch-crossing rate of 40 MHz directly on the module. This information will be used as an input for the first trigger stage of CMS. It is necessary to validate the Outer Tracker module functionality before installing the modules in the CMS experiment. Besides laboratory-based tests several 2S module prototypes have been studied at test beam facilities at CERN, DESY and FNAL. This article concentrates on the beam tests at DESY during which the functionality of the module concept was investigated using the full final readout chain for the first time. Additionally the performance of a 2S module assembled with irradiated sensors was studied. By choosing an irradiation fluence expected for 2S modules at the end of HL-LHC operation, it was possible to investigate the particle detection efficiency and study the trigger capabilities of the module at the beginning and end of the runtime of the CMS experiment

Spatial and topological organization of DNA chains induced by gene co-localization

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close-by. This is motivated by recurrent evidence that there exists physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.Comment: Figures and Supplementary Material freely available on http://dx.doi.org/10.1371/journal.pcbi.100067

Virtual Resection: A New Tool for Preparing for Nephron-Sparing Surgery in Wilms Tumor Patients

Nephron-sparing surgery (NSS) in Wilms tumor (WT) patients is a surgically challenging procedure used in highly selective cases only. Virtual resections can be used for preoperative planning of NSS to estimate the remnant renal volume (RRV) and to virtually mimic radical tumor resection. In this single-center evaluation study, virtual resection for NSS planning and the user experience were evaluated. Virtual resection was performed in nine WT patient cases by two pediatric surgeons and one pediatric urologist. Pre- and postoperative MRI scans were used for 3D visualization. The virtual RRV was acquired after performing virtual resection and a questionnaire was used to assess the ease of use. The actual RRV was derived from the postoperative 3D visualization and compared with the derived virtual RRV. Virtual resection resulted in virtual RRVs that matched nearly perfectly with the actual RRVs. According to the questionnaire, virtual resection appeared to be straightforward and was not considered to be difficult. This study demonstrated the potential of virtual resection as a new planning tool to estimate the RRV after NSS in WT patients. Future research should further evaluate the clinical relevance of virtual resection by relating it to surgical outcome

In vitro efficacy and safety of a system for sorbent-assisted peritoneal dialysis

In vitro efficacy and safety of a system for sorbent-assisted peritoneal dialysis. Am J Physiol Renal Physiol 319: F162-F170, 2020. First published June 1, 2020; doi:10.1152/ajprenal. 00079.2020.-A system for sorbent-assisted peritoneal dialysis (SAPD) was designed to continuously recirculate dialysate via a tidal mode using a single lumen peritoneal catheter with regeneration of spent dialysate by means of sorbent technology. We hypothesize that SAPD treatment will maintain a high plasma-to-dialysate concentration gradient and increase the mass transfer area coefficient of solutes. Thereby, the SAPD system may enhance clearance while reducing the number of exchanges. Application is envisaged at night as a bedside device (12 kg, nighttime system). A wearable system (2.0 kg, daytime system) may further enhance clearance during the day. Urea, creatinine, and phosphate removal were studied with the daytime and nighttime system (n = 3 per system) by recirculating 2 liters of spent peritoneal dialysate via a tidal mode (mean flow rate: 50 and 100 mL/min, respectively) for 8 h in vitro. Time-averaged plasma clearance over 24 h was modeled assuming one 2 liter exchange/day, an increase in mass transfer area coefficient, and 0.9 liters ultrafiltration/day. Urea, creatinine, and phosphate removal was 33.2 ± 4.1, 5.3 ± 0.5, and 6.2 ± 1.8 mmol, respectively, with the daytime system and 204 ± 28, 10.3 ± 2.4, and 11.4 ± 2.1 mmol, respectively, with the nighttime system. Time-averaged plasma clearances of urea, creatinine and phosphate were 9.6 ± 1.1, 9.6 ± 1.7, and 7.0 ± 0.9 mL/min, respectively, with the nighttime system and 10.8 ± 1.1, 13.4 ± 1.8, and 9.7 ± 1.6 mL/min, respectively, with the daytime and nighttime system. SAPD treatment may improve removal of uremic toxins compared with conventional peritoneal dialysis, provided that peritoneal mass transport will increase