Biomedical subjects

Xianfeng Chen

Publications and source records attributed to Xianfeng Chen.

15 recordsLinked to original sources

PubMed2007

Dual-peak long-period fiber gratings with enhanced refractive index sensitivity by finely tailored mode dispersion that uses the light cladding etching technique.

We have experimentally investigated the mode dispersion property and refractive index sensitivity of dual-peak long-period fiber gratings (LPGs) that were sensitized by hydrofluoric acid (HF) etching. The nature of the coupled cladding modes close to the dispersion turning point makes the dual-peak LPGs ultrasensitive to cladding property, permitting a fine tailoring of the mode dispersion and index sensitivity by the light cladding etching method using HF acid of only 1% concentration. As an implementation of an optical biosensor, the etched device was used to detect the concentration of hemoglobin protein in a sugar solution, showing a sensitivity as high as 20 nm/1%.

Journal Article↗

PubMed2006

GenomeBlast: a web tool for small genome comparison.

BACKGROUND: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes. RESULTS: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each genome; (2) homologous gene candidates among compared genomes; (3) 2D plots of homologous gene candidates along the all pairwise genome comparisons; and (4) a table of gene presence/absence information and a genome phylogeny. We demonstrated the functions in GenomeBlast with an example of multiple herpesviral genome analysis and illustrated how GenomeBlast is useful for small genome comparison. CONCLUSION: We developed a Web tool for comparative analysis of small genomes, which allows the user not only to identify unique genes and homologous gene candidates among multiple genomes, but also to view their graphical distributions on genomes, and to reconstruct genome phylogeny. GenomeBlast runs on a Linux server with 4 CPUs and 4 GB memory. The online version of GenomeBlast is available to public by using a Web browser with the URL http://bioinfo-srv1.awh.unomaha.edu/genomeblast/.

Algorithms↗

PubMed2006

Molecular basis for differential nucleotide binding of the nucleotide-binding domain of ABC-transporter CvaB.

The cytoplasmic membrane protein CvaB, involved in colicin V secretion in Escherichia coli, belongs to the ABC-transporter family in which ATP hydrolysis is typically the driving force for substrate transport. However, our previous studies indicated that the nucleotide-binding domain of CvaB could also bind and hydrolyze GTP and, indeed, highly preferred GTP over ATP at low temperatures. In this study, we have examined the molecular basis of this preference. Sequence alignment and homology modeling of the CvaB nucleotide-binding domain predicted that the aromatic stacking region of CvaB (Y501DSQ loop) had a role in the differential binding of nucleotides, and Ser503 and Gln504 provided potential hydrogen bonds to GTP but not to ATP. Site-directed mutagenesis of the Y501DSQ loop, mutations S503A, Q504L, and double mutation S503A/Q504L, was made to test the predicted hydrogen bonds with GTP. The double mutation S503A/Q504L increased the affinity for ATP by 6-fold, whereas the affinity for GTP was reduced slightly: the ATP/GTP-binding ratio increased about 10-fold. The temperature effect assays on nucleotide binding and hydrolysis further indicated that the double mutant protein had largely eliminated the difference for substrates ATP and GTP, and behaved more similarly to the NBD of typical ABC-transporter HlyB. Therefore, we conclude that Ser503 and Gln504 in aromatic stacking region of CvaB block the ATP binding and are important for the GTP-binding preference.

ATP-Binding Cassette Transporters↗

PubMed2006

Optic sensors of high refractive-index responsivity and low thermal cross sensitivity that use fiber Bragg gratings of >80 degrees tilted structures.

For the first time to the authors' knowledge, fiber Bragg gratings (FBGs) with >80 degrees tilted structures have been fabricated and characterized. Their performance in sensing temperature, strain, and the surrounding medium's refractive index was investigated. In comparison with normal FBGs and long-period gratings (LPGs), >80 degrees tilted FBGs exhibit significantly higher refractive-index responsivity and lower thermal cross sensitivity. When the grating sensor was used to detect changes in refractive index, a responsivity as high as 340 nm/refractive-index unit near an index of 1.33 was demonstrated, which is three times higher than that of conventional LPGs.

Journal Article↗

PubMed2005

Broadening of the second-harmonic phase-matching bandwidth in type II periodically poled KTP.

We have theoretically demonstrated type II broadband second-harmonic generation (SHG) based on a quasi-phase-matching (QPM) configuration in periodically poled KTP (PPKTP). The wavelength dependence of QPM grating periods at different temperatures of 5 degrees C, 25 degrees C, and 45 degrees C is calculated with the crystal length of 1 cm. We find a very wide bandwidth, as large as 42.6 nm, of fundamental wavelength of 1.58 microm at the telecommunication band with the QPM period of 48.9 microm at 25 degrees C. The corresponding bandwidths of incident angle and temperature are found to be 4.24 degrees and 14.8 degrees C, respectively. The comparison among PPKTP, periodically poled lithium niobate (PPLN), and MgO:PPLN reveals the unique performance of PPKTP in the broadband SHG.

Journal Article↗

PubMed2005

High extinction ratio in-fiber polarizers based on 45 degree tilted fiber Bragg gratings.

We report a near-ideal in-fiber polarizer implemented by use of 45 degrees tilted fiber Bragg grating structures that are UV inscribed in hydrogenated Ge-doped fiber. We demonstrate a polarization-extinction ratio of 33 dB over a 100-nm operation range near 1550 nm. We further show an achievement of 99.5% degree of polarization for unpolarized light with these gratings. We also theoretically investigate tilted grating structures based on the Green's function calculation, therein revealing the unique polarization characteristics, which are in excellent agreement with experimental data.

Journal Article↗

PubMed2005

Direct quasi-phase-matched fourth-harmonic generation.

We have theoretically demonstrated direct fourth-harmonic generation (FHG) based on a quasi-phase-matching (QPM) configuration in periodically poled lithium niobate. The wavelength dependence of period of FHG QPM gratings is calculated. Bandwidths of fundamental wavelength, temperature, and incident angle are also studied. We find a very wide bandwidth, as large as 115 nm, of fundamental wavelength near the wavelength of 3797 nm with the QPM period of 9.73 microm. The numerical calculation shows that the conversion efficiency for QPM FHG and cascading QPM by two-step second-harmonic generation is almost identical.

Journal Article↗

PubMed2005

Simultaneous measurement of temperature and external refractive index by use of a hybrid grating in D fiber with enhanced sensitivity by HF etching.

We propose a dual-parameter optical sensor device achieved by UV inscription of a hybrid long-period grating-fiber Bragg grating structure in D fiber. The hybrid configuration permits the detection of the temperature from the latter's response and measurement of the external refractive index from the former's response. In addition, the host D fiber permits effective modification of the device's sensitivity by cladding etching. The grating sensor has been used to measure the concentrations of aqueous sugar solutions, demonstrating its potential capability to detect concentration changes as small as 0.01%.

Journal Article↗

PubMed2005

Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs.

HIV-1 protease (PR) and two drug-resistant variants--PR with the V82A mutation (PR(V82A)) and PR with the I84V mutation (PR(I84V))--were studied using reduced peptide analogs of five natural cleavage sites (CA-p2, p2-NC, p6pol-PR, p1-p6 and NC-p1) to understand the structural and kinetic changes. The common drug-resistant mutations V82A and I84V alter residues forming the substrate-binding site. Eight crystal structures were refined at resolutions of 1.10-1.60 A. Differences in the PR-analog interactions depended on the peptide sequence and were consistent with the relative inhibition. Analog p6(pol)-PR formed more hydrogen bonds of P2 Asn with PR and fewer van der Waals contacts at P1' Pro compared with those formed by CA-p2 or p2-NC in PR complexes. The P3 Gly in p1-p6 provided fewer van der Waals contacts and hydrogen bonds at P2-P3 and more water-mediated interactions. PR(I84V) showed reduced van der Waals interactions with inhibitor compared with PR, which was consistent with kinetic data. The structures suggest that the binding affinity for mutants is modulated by the conformational flexibility of the substrate analogs. The complexes of PR(V82A) showed smaller shifts of the main chain atoms of Ala82 relative to PR, but more movement of the peptide analog, compared to complexes with clinical inhibitors. PR(V82A) was able to compensate for the loss of interaction with inhibitor caused by mutation, in agreement with kinetic data, but substrate analogs have more flexibility than the drugs to accommodate the structural changes caused by mutation. Hence, these structures help to explain how HIV can develop drug resistance while retaining the ability of PR to hydrolyze natural substrates.

Amino Acid Substitution↗

PubMed2005

Index profiling of anisotropic graded-index planar waveguides from effective indices.

We present a method for recovering the refractive-index profile of an anisotropic graded-index waveguide from the effective indices by using a cubic spline interpolation function. The first and second derivatives of cubic splines are continuous to ensure a smooth index profile, which is consistent with practical graded-index distributions. A straightforward iteration with an exact dispersion equation to verify the interpolated profile makes this method easy and reliable for application. This approach is proved by numerical analysis of several typical index distributions and experimental examples showing that the refractive-index profiles in anisotropy can be reconstructed close to the exact profile. Waveguides with both more modes (more than four guiding modes) and fewer modes (two to four) can be universally profiled with good accuracy.

Journal Article↗

PubMed2004

Bend sensors with direction recognition based on long-period gratings written in D-shaped fiber.

The curvature- or bend-sensing response of long-period gratings (LPGs) UV inscribed in D-shaped fiber has been investigated experimentally. Strong fiber-orientation dependence of the spectral response when such LPGs are subjected to bending at different directions has been observed and is shown to form the basis for a new class of single-device sensor with vector-sensing capability. Potential applications utilizing the linear response and unique bend-orientation characteristics of the devices are discussed.

Journal Article↗

PubMed2004

Molecular dynamics simulations of 14 HIV protease mutants in complexes with indinavir.

The molecular mechanisms of HIV drug resistance were studied using molecular dynamics simulations of HIV-1 protease complexes with the clinical inhibitor indinavir. One nanosecond molecular dynamics simulations were run for solvated complexes of indinavir with wild type protease, a control variant and 12 drug resistant mutants. The quality of the simulations was assessed by comparison with crystallographic and inhibition data. Molecular mechanisms that contribute to drug resistance include structural stability and affinity for inhibitor. The mutants showed a range of structural variation from 70 to 140% of the wild type protease. The protease affinity for indinavir was estimated by calculating the averaged molecular mechanics interaction energy. A correlation coefficient of 0.96 was obtained with observed inhibition constants for wild type and four mutants. Based on this good agreement, the trends in binding were predicted for the other mutants and discussed in relation to the clinical data for indinavir resistance. [figure: see text]. Poincare map representation for WT protease-indinavir complex. The side chain of Tyr 59 showing the positions of hydrogen atoms.

Binding Sites↗

PubMed2004

Explicit analysis of anisotropic planar waveguides by the analytical transfer-matrix method.

The propagation properties of light in anisotropic optical planar waveguides with different index distributions are investigated with the analytical transfer-matrix method. Dispersion equations are analytically deduced by the method in terms of different index profiles. It is shown by examples that this method exhibits good accuracy compared with numerical methods while still holding physical insight.

Journal Article↗

PubMed2003

Electro-optic Solc-type wavelength filter in periodically poled lithium niobate.

We demonstrate an electro-optic Solc-type wavelength filter in periodically poled lithium niobate (PPLN). A Solc-type transmission spectrum is observed experimentally in PPLN with four periods from 20.2 to 20.8 microm. Modulation of the transmission power of the filter is realized by application of electric fields along the Y axis of the PPLN. It is observed that the wavelength can also be tuned by temperature.

Journal Article↗

PubMed2003

Polarization control by use of the electro-optic effect in periodically poled lithium niobate.

We propose a method to control the polarization of light by the electro-optic effect in periodically poled lithium niobate. A single integrated chip of Z-cut lithium niobate having two sections is used. The first section is not periodically poled, whereas the second section is. With an electric field applied along the Z axis of the first section and another electric field applied along the Y axis of the second section, light with an arbitrary elliptical polarization can be converted into a fixed linearly polarized state.

Journal Article↗