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Biomedical subjects

Jian Zi

Publications and source records attributed to Jian Zi.

18 recordsLinked to original sources
PubMed2006

Diamagnetic response of metallic photonic crystals at infrared and visible frequencies.

We show analytically and numerically that diamagnetic response (effective magnetic permeability mue<1) at infrared and visible frequencies can be achieved in photonic crystals composed of metallic nanowires or nanospheres when the wavelength is much larger than the lattice constant a (lambda approximately 2000a). When lambda approximately100a, the metallic photonic crystals will exhibit strong diamagnetic response (mue<0.8), leading to many interesting phenomena such as the unusual Brewster angle for s waves and incident-angle-and-polarization-independent reflection and transmission.

Journal Article↗
PubMed2006

Omnidirectional total reflection for liquid surface waves propagating over a bottom with one-dimensional periodic undulations.

We study theoretically the propagation of liquid surface waves over a bottom with one-dimensional (1D) periodic undulations. We find a general criterion for omnidirectional total reflection in such a system. Numerical simulations based on a transfer matrix method demonstrate unambiguously the existence of omnidirectional total reflection for liquid surface waves propagating over a bottom with 1D periodic undulations.

Journal Article↗
PubMed2006

Anomalous Doppler effects in phononic band gaps.

Doppler effects in periodic acoustic media were studied theoretically and experimentally. Analytical formulas are derived using the Green's function formalism. We found that a far field observer cannot hear the sound inside a band gap from a stationary source, but a moving source can be heard even if the frequency is inside the gap, and the Doppler shifts can be inverted or anomalously large.

Journal Article↗
PubMed2006

Acoustic backward-wave negative refractions in the second band of a sonic crystal.

Acoustic negative refractions with backward-wave (BW) effects were both theoretically and experimentally established in the second band of a two-dimensional (2D) triangular sonic crystal (SC). Intense Bragg scatterings result in the extreme deformation of the second band equifrequency surface (EFS) into two classes: one around the K point and the other around the point of the reduced Brillouin zone. The two classes can lead to BW negative refractions (BWNRs) but with reverse negative refraction dependences on frequencies and incident angles. Not only BWNR but BW positive refraction can be present at EFSs around the K point, so it is possible to enhance the resolution of acoustic waves with a subdiffraction limit regardless of refractions, which is no analogy in both left-handed material and SCs' first band. These abundant characters make refractions in the second band distinguished.

Journal Article↗
PubMed2005

Structural origin of the brown color of barbules in male peacock tail feathers.

We report detailed optical measurements and numerical simulations of brown barbules in male peacock tail feathers. Our results indicate that brown coloration is predominantly produced structurally by the two-dimensional (2D) photonic-crystal structure in the cortex layer of a barbule. The constructing strategies of brown coloration revealed by numerical simulations are indeed subtle, which are of great significance in the artificial constructions of mixed structural coloration. It is found that the structural configurations of the 2D photonic-crystal structure such as the lattice constant, the number of periods, and even the interdistance and missing holes between the two melanin layers nearest to the cortex surface, are important in the production of structural brown colors.

Animals↗
PubMed2005

Two-dimensional sonic crystals with Helmholtz resonators.

We present a type of sonic crystal composed with an array of two-dimensional Helmholtz resonators, which in the long-wave regime have both a high relative acoustic refractive index n and at the same time, a small acoustic impedance Z mismatch with air for airborne sound. We analyze the n and Z of such sonic crystals by finite-difference time-domain simulations, and by mapping our results to a corresponding electromagnetic (EM) model, and we find that our Helmholtz resonant sonic crystal has a bigger effective magnetic permeability mu than the conventional rigid-cylinder sonic crystal in its EM counterpart. As a result, a thin convergent lens with very good focusing effect is demonstrated based on our crystal.

Journal Article↗
PubMed2005

Self-collimation in liquid surface waves propagating over a bottom with periodically drilled holes.

Liquid surface waves propagating over a bottom with periodically drilled holes are studied experimentally and theoretically. Point source waves are generated in the center of the array of the periodically drilled holes in order to observe the evolvements of these waves. We successfully observe the self-collimation phenomenon in liquid surface waves. Band structures and constant-frequency surfaces are calculated, which can give a satisfactory interpretation of the experimental observations.

Journal Article↗
PubMed2005

Protein flexibility prediction by an all-atom mean-field statistical theory.

We extended a mean-field model to proteins with all atomic detail. The all-atom mean-field model was used to calculate the dynamic and thermodynamic properties of a three-helix bundle fragment of Staphylococcal protein A (Protein Data Bank [PDB] ID 1BDD) and alpha-spectrin SH3 domain protein (PDB ID 1SHG). We show that a model with all-atomic detail provides a significantly more accurate prediction of flexibility of residues in proteins than does a coarse-grained residue-level model. The accuracy of flexibility prediction is further confirmed by application of the method to 18 additional proteins with the largest size of 224 residues.

Mathematics↗
PubMed2004

Properties of one-dimensional photonic crystals containing single-negative materials.

The transmission properties of a one-dimensional photonic crystal containing two kinds of single-negative (permittivity- or permeability-negative) media are studied theoretically. We show that this structure can possess a type of photonic gap with zero effective phase (phi(eff) ). The zero-phi(eff) gap distinguishes itself from a Bragg gap in that it is invariant with a change of scale length and is insensitive to thickness fluctuation. In contrast to a photonic gap corresponding to zero averaged refractive index, the zero-phi(eff) gap can be made very wide by varying the ratio of the thicknesses of two media. An equivalent transmission-line model is utilized to explain the properties. A photonic quantum-well structure based on zero-phi(eff) gaps is proposed as a multiple channeled filter that is compact and robust against disorder.

Journal Article↗
PubMed2004

Superlensing effect in liquid surface waves.

We present experimental observations and numerical simulations of superlensing effect in liquid surface waves. We use rigid cylinders to create a two-dimensional periodic lattice, in which liquid surface waves propagate. Through the observation of a superlensing effect, we demonstrate the existence of negative refraction in surface waves. In addition, a complete band gap is found.

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PubMed2003

Complete band gaps for liquid surface waves propagating over a periodically drilled bottom.

A plane-wave expansion approach is developed to solve the mild-slope equation for liquid surface waves propagating over a bottom with periodic structures. Band structures are calculated for the bottom periodically drilled with the square or triangular lattice of holes. Complete band gaps are found for both lattices. Parameters that influence the formation of band gaps are discussed.

Journal Article↗
PubMed2003

Determining a detectable threshold of signal intensity in cDNA microarray based on accumulated distribution.

In microarray data mining, one of the key problems is how to handle weak signals. Based on a bent piecewise linear accumulated distribution generally found in the microarray data, a new detectable threshold finding method is proposed to filter genes with unreliable information in this paper. More reliable and reproducible data is produced for the subsequent data mining.

DNA, Complementary↗
PubMed2003

Coloration strategies in peacock feathers.

We report the mechanism of color production in peacock feathers. We find that the cortex in differently colored barbules, which contains a 2D photonic-crystal structure, is responsible for coloration. Simulations reveal that the photonic-crystal structure possesses a partial photonic bandgap along the direction normal to the cortex surface, for frequencies within which light is strongly reflected. Coloration strategies in peacock feathers are very ingenious and simple: controlling the lattice constant and the number of periods in the photonic-crystal structure. Varying the lattice constant produces diversified colors. The reduction of the number of periods brings additional colors, causing mixed coloration.

Animals↗
PubMed2003

Universal behavior of localization of residue fluctuations in globular proteins.

Localization properties of residue fluctuations in globular proteins are studied theoretically by using a Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship between participation ratio and frequency is similar for all globular proteins, indicating a universal behavior in spite of their different size, shape, and architecture.

Animals↗
PubMed2003

Lattice Boltzmann model for photonic band gap materials.

An efficient technique for computing photonic band structure and defect modes is proposed based on the lattice Boltzmann model. Physically, it is a scheme based on the kinetics of the virtual microscopic process, rather than a solution of the macroscopic Maxwell equations. The method has significant advantages of being naturally suited for massively parallel machine, as well as speed and convenience, providing another methodology for photonic band gap materials and, also, for general electromagnetic scattering problems in open region when incorporated with the perfectly matched layer technique.

Journal Article↗