A fast-Fourier-transform method of topography and interferometry is proposed. By computer processing of a noncontour type of fringe pattern, automatic discrimination is achieved between elevation and depression of the object or wave-front form, which has not been possible by the fringe-contour-generation techniques. The method has advantages over moire topography and conventional fringe-contour interferometry in both accuracy and sensitivity. Unlike fringe-scanning techniques, the method is easy to apply because it uses no moving components.

Fourier-transform method of fringe-pattern analysis for computer-based topography and interferometry

On robust estimation of the location parameter

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes. Owing to the tremendous progress in next-generation sequencing technology, ChIP-seq offers higher resolution, less noise and greater coverage than its array-based predecessor ChIP-chip. With the decreasing cost of sequencing, ChIP-seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. In this Review, I describe the benefits and challenges in harnessing this technique with an emphasis on issues related to experimental design and data analysis. ChIP-seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms.

/pdf/chip-seq-advantages-and-challenges-of-a-maturing-technology-57od1mnvrx.pdf

ChIP-Seq: advantages and challenges of a maturing technology

It is shown that the ordinary semiclassical theory of the absorption of light by exciton states is not completely satisfactory (in contrast to the case of absorption due to interband transitions). A more complete theory is developed. It is shown that excitons are approximate bosons, and, in interaction with the electromagnetic field, the exciton field plays the role of the classical polarization field. The eigenstates of the system of crystal and radiation field are mixtures of photons and excitons. The ordinary one-quantum optical lifetime of an excitation is infinite. Absorption occurs only when "three-body" processes are introduced. The theory includes "local field" effects, leading to the Lorentz local field correction when it is applicable. A Smakula equation for the oscillator strength in terms of the integrated absorption constant is derived.

a Quantum-Mechanical Theory of the Contribution of Excitons to the Complex Dielectric Constant of Crystals.

Motivation: Chromatin states are the key to gene regulation and cell identity. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) is increasingly being used to map epigenetic states across genomes of diverse species. Chromatin modification profiles are frequently noisy and diffuse, spanning regions ranging from several nucleosomes to large domains of multiple genes. Much of the early work on the identification of ChIP-enriched regions for ChIP-Seq data has focused on identifying localized regions, such as transcription factor binding sites. Bioinformatic tools to identify diffuse domains of ChIP-enriched regions have been lacking.

Results: Based on the biological observation that histone modifications tend to cluster to form domains, we present a method that identifies spatial clusters of signals unlikely to appear by chance. This method pools together enrichment information from neighboring nucleosomes to increase sensitivity and specificity. By using genomic-scale analysis, as well as the examination of loci with validated epigenetic states, we demonstrate that this method outperforms existing methods in the identification of ChIP-enriched signals for histone modification profiles. We demonstrate the application of this unbiased method in important issues in ChIP-Seq data analysis, such as data normalization for quantitative comparison of levels of epigenetic modifications across cell types and growth conditions.

Availability: http://home.gwu.edu/~wpeng/Software.htm 

Contact: [email protected]

Supplementary information:Supplementary data are available at Bioinformatics online.

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A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

A fast volume rendering process is of primary importance for interactive manipulation of volumetric datasets. This chapter studies acceleration methods of volume rendering.

Fast Multi-Resolution Volume Rendering

Software note: Pattern-constrained multiple polypeptide sequence alignment

A dissipative-driven system can generate steady-state entanglement robust to control parameters, while a quantum plasmonic system has the advantages of being strongly coupled to qubits and manipulation of electromagnetic waves in the subwavelength regime. We propose an effective multiqubit dissipative-driven entanglement model for a plasmonic system which takes into account coupling of the plasmonic cavity and qubits as well as the direct coupling between any two qubits and develop a numerical solution of the effective model on a scalable composite plasmonic structure. In this structure, the multiqubit entanglement under asymmetric detuning, especially for those combinations containing pairs of antisymmetric detuning qubits, achieves stronger steady-state entanglement measured by negativity and pairwise concurrence. The robustness of multiqubit entanglement against variations of the control parameters is also presented. In addition, the phenomenon of entanglement sudden death caused by the driving field in entanglement dynamics is investigated. Our model shows evidence that quantum plasmonics has great potential in multiqubit entanglement.

Plasmonic-modulated dissipative-driven multiqubit entanglement under asymmetric detuning

Cellular Image Classification

Metasurfaces consisted of subwavelength nanostructures can extremely interact with light and manipulate the characteristics of amplitude, phase, and polarization. In particular, on‐chip dielectric metasurfaces have attracted significant attention for optical communication and computing, due to its compact footprint, low loss, and broad bandwidth. Herein, an ultradensely integrated multidimensional optical system with a footprint of only 20 × 30 µm2 based on inverse‐designed dielectric metasurface network, incorporating mode‐division multiplexing, and coherent optical communication technologies that can multiply the system capacity is demonstrated. It is assembled by the ultracompact multifunction on‐chip metasurface devices, including four‐mode demultiplexer, optical hybrid, crossing, and bending, which all have a size of only several micrometers. The inverse‐designed work can significantly broaden the integrated device applications of on‐chip metasurfaces and pave an alternative way for large‐scale high‐capacity optical communication system.

Feng Lin

Papers

Fast Multi-Resolution Volume Rendering

Software note: Pattern-constrained multiple polypeptide sequence alignment

Plasmonic-modulated dissipative-driven multiqubit entanglement under asymmetric detuning

Cellular Image Classification

Dielectric Metasurfaces Enabled Ultradensely Integrated Multidimensional Optical System