Microchannel avalanche photodiode with wide linearity range

Design and physical operation principles of new microchannel avalanche photodiode (MC APD) with gain up to 10^5 and linearity range improved an order of magnitude compared to known similar devices. A distinctive feature of the new device is a directly biased p-n junction under each pixel which plays role of an individual quenching resistor. This allows increasing pixel density up to 40000 per mm^2 and making entire device area sensitive.Comment: Submitted to Journal of Technical Physic

A parallel method for enumerating amino acid compositions and masses of all theoretical peptides

<p>Abstract</p> <p>Background</p> <p>Enumeration of all theoretically possible amino acid compositions is an important problem in several proteomics workflows, including peptide mass fingerprinting, mass defect labeling, mass defect filtering, and de novo peptide sequencing. Because of the high computational complexity of this task, reported methods for peptide enumeration were restricted to cover limited mass ranges (below 2 kDa). In addition, implementation details of these methods as well as their computational performance have not been provided. The increasing availability of parallel (multi-core) computers in all fields of research makes the development of parallel methods for peptide enumeration a timely topic.</p> <p>Results</p> <p>We describe a parallel method for enumerating all amino acid compositions up to a given length. We present recursive procedures which are at the core of the method, and show that a single task of enumeration of all peptide compositions can be divided into smaller subtasks that can be executed in parallel. The computational complexity of the subtasks is compared with the computational complexity of the whole task. Pseudocodes of processes (a master and workers) that are used to execute the enumerating procedure in parallel are given. We present computational times for our method executed on a computer cluster with 12 Intel Xeon X5650 CPUs (72 cores) running Windows HPC Server. Our method has been implemented as a 32- and 64-bit Windows application using Microsoft Visual C++ and the Message Passing Interface. It is available for download at <url>https://ispace.utmb.edu/users/rgsadygo/Proteomics/ParallelMethod</url>.</p> <p>Conclusion</p> <p>We describe implementation of a parallel method for generating mass distributions of all theoretically possible amino acid compositions.</p

On features of potential distribution in avalanche photodiodes with deeply buried pixels

The shape of potential distribution in micro-pixel avalanche photodiodes (MAPD) with deeply buried pixels is investigated. It was found that the electrons created in the photosensitive part of the device are collected to the corresponding n-pixel and multiplied in the avalanche region. At the same time the holes generated in the semiconductor substrate passes through the gaps between the n-pixels and therefore they are not amplified. This results in improvement the both signal/noise ratio and radiation resistance of the devic

Study of timing performance of Silicon Photomultiplier and application for a Cherenkov detector

Silicon photomultipliers are very versatile photo detectors due to their high photon detection efficiency, fast response, single photon counting capability, high amplification, and their insensitivity to magnetic fields. At our institute we are studying the performance of these photo detectors at various operating conditions. On the basis of the experience in the laboratory we built a prototype of a timing Cherenkov detector consisting of a quartz radiator with two $3\times 3$ mm$^2$ MPPCs S10362-33-100C from Hamamatsu Photonics as photodetectors. The MPPC sensors were operated with Peltier cooling to minimize thermal noise and to avoid gain drifts. The test measurements at the DA$\Phi$NE Beam-Test Facility (BTF) at the Laboratori Nazionali di Frascati (LNF) with pulsed 490 MeV electrons and the results on timing performance with Cherenkov photons are presented.Comment: Conference proceedings of 12th Vienna Conference on Instrumentation 201

PROPERTIES OF THE BISUBDIFFERENTIAL OF BICONVEX FUNCTIONS

In this work, a number of properties of bisubdifferential and biconjugate functions for biconvex functions are studied. Necessary and sufficient conditions for the equality of the bisubdifferential of the sum and the sum of the bisubdifferentials of two biconvex functions are obtained. A biconvex mathematical programming problem is considered

Proteome Dynamics with Heavy Water — Instrumentations, Data Analysis, and Biological Applications

The quantitative assessment of the synthesis of individual proteins has been greatly hindered by the lack of a high-throughput nonradioactive method. We recently developed a method that we call “proteome dynamics” and software that enables high-throughput kinetic analyses of peptides on a proteome-wide scale. Previous studies established that oral administration of heavy water (2H2O or deuterium oxide, D2O) is safe and well tolerated in humans. Briefly, a loading dose of 2H2O, a nonradioactive isotope, is administered in drinking water. 2H2O rapidly labels body water and transfers 2H from 2H2O to 2H-labeled amino acids, which incorporates into proteins dependent upon the rate of synthesis of the specific protein. Proteins are analyzed by high-resolution mass spectrometry and protein synthesis is calculated using specialized software. We have established the effectiveness of this method for plasma and mitochondrial proteins. We demonstrated that fasting has a differential effect on the synthesis rates of proteins. We also applied this method to assess the effect of heart failure on the stability of mitochondrial proteins. In this review, we describe the study design, instrumentation, data analysis, and biological application of heavy water-based proteome turnover studies. We summarize this chapter with the challenges in the field and future directions