Fully quantum mechanical dynamic analysis of single-photon transport in a single-mode waveguide coupled to a traveling-wave resonator

We analyze the dynamics of single photon transport in a single-mode waveguide coupled to a micro-optical resonator using a fully quantum mechanical model. We examine the propagation of a single-photon Gaussian packet through the system under various coupling conditions. We review the theory of single photon transport phenomena as applied to the system and we develop a discussion on the numerical technique we used to solve for dynamical behavior of the quantized field. To demonstrate our method and to establish robust single photon results, we study the process of adiabatically lowering or raising the energy of a single photon trapped in an optical resonator under active tuning of the resonator. We show that our fully quantum mechanical approach reproduces the semi-classical result in the appropriate limit and that the adiabatic invariant has the same form in each case. Finally, we explore the trapping of a single photon in a system of dynamically tuned, coupled optical cavities.Comment: 24 pages, 10 figure

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications

Cataloged from PDF version of article.High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or more) in the multi-mapping mode. Furthermore, mrsFAST-Ultra has an index size of 2GB for the entire human reference genome, which is roughly half of that of Bowtie2. mrsFAST-Ultra is open source and it can be accessed at http://mrsfast.sourceforge.net

Fast and accurate mapping of Complete Genomics reads

Many recent advances in genomics and the expectations of personalized medicine are made possible thanks to power of high throughput sequencing (HTS) in sequencing large collections of human genomes. There are tens of different sequencing technologies currently available, and each HTS platform have different strengths and biases. This diversity both makes it possible to use different technologies to correct for shortcomings; but also requires to develop different algorithms for each platform due to the differences in data types and error models. The first problem to tackle in analyzing HTS data for resequencing applications is the read mapping stage, where many tools have been developed for the most popular HTS methods, but publicly available and open source aligners are still lacking for the Complete Genomics (CG) platform. Unfortunately, Burrows-Wheeler based methods are not practical for CG data due to the gapped nature of the reads generated by this method. Here we provide a sensitive read mapper (sirFAST) for the CG technology based on the seed-and-extend paradigm that can quickly map CG reads to a reference genome. We evaluate the performance and accuracy of sirFAST using both simulated and publicly available real data sets, showing high precision and recall rates. © 2014 Elsevier Inc

Dissect: detection and characterization of novel structural alterations in transcribed sequences

Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of identifying structural alterations in the transcriptome is now attracting significant attention

Developing surrogate markers for predicting antibiotic resistance "hot spots" in rivers where limited data are available

Pinpointing environmental antibiotic resistance (AR) hot spots in low-and middle-income countries (LMICs) is hindered by a lack of available and comparable AR monitoring data relevant to such settings. Addressing this problem, we performed a comprehensive spatial and seasonal assessment of water quality and AR conditions in a Malaysian river catchment to identify potential "simple"surrogates that mirror elevated AR. We screened for resistant coliforms, 22 antibiotics, 287 AR genes and integrons, and routine water quality parameters, covering absolute concentrations and mass loadings. To understand relationships, we introduced standardized "effect sizes"(Cohen's D) for AR monitoring to improve comparability of field studies. Overall, water quality generally declined and environmental AR levels increased as one moved down the catchment without major seasonal variations, except total antibiotic concentrations that were higher in the dry season (Cohen's D > 0.8, P < 0.05). Among simple surrogates, dissolved oxygen (DO) most strongly correlated (inversely) with total AR gene concentrations (Spearman's ρ 0.81, P < 0.05). We suspect this results from minimally treated sewage inputs, which also contain AR bacteria and genes, depleting DO in the most impacted reaches. Thus, although DO is not a measure of AR, lower DO levels reflect wastewater inputs, flagging possible AR hot spots. DO measurement is inexpensive, already monitored in many catchments, and exists in many numerical water quality models (e.g., oxygen sag curves). Therefore, we propose combining DO data and prospective modeling to guide local interventions, especially in LMIC rivers with limited data

On the evolution of superposition of squeezed displaced number states with the multiphoton Jaynes-Cummings model

In this paper we discuss the quantum properties for superposition of squeezed displaced number states against multiphoton Jaynes-Cummings model (JCM). In particular, we investigate atomic inversion, photon-number distribution, purity, quadrature squeezing, Mandel $Q$ parameter and Wigner function. We show that the quadrature squeezing for three-photon absorption case can exhibit revivals and collapses typical to those occurring in the atomic inversion for one-photon absorption case. Also we prove that for odd number absorption parameter there is a connection between the evolution of the atomic inversion and the evolution of the Wigner function at the origin in phase space. Furthermore, we show that the nonclassical states whose the Wigner functions values at the origins are negative will be always nonclassical when they are evolving through the JCM with even absorption parameter. Also we demonstrate that various types of cat states can be generated via this system.Comment: 27 pages, 10 figure