A DNA length reducing computing model for maximum independent set problem

In this paper, a new molecular computing model is developed to solve the maximum independent set problem, based on the method of DNA length reducing. To solve the maximum independent set problem with n-vertices and m-edges, the time complexity is O(n+m). With the enlargement of the problem scale, the numbers of the required tubes will increase linearly. Two important methods in this experiment are single strand DNA (ssDNA) circularization and DNA length reducing. In addition, using reverse polymerase chain reaction (PCR) and circligase, the structure of DNA molecules is changed in each computing step, transforming from linear double strand DNA (dsDNA) to linear ssDNA and circular ssDNA. Using the circular DNA structure, the recombina-tion among DNA molecules is avoided. To verify this computing model, a small maximum independent set problem was solved.     

Predicted methylation landscape of all CpG islands on the human genome

CpG island methylation plays important role in various biological processes. To investigate methylation landscape of all CpG islands on the human genome, we develop a model for predicting the CpG island methylation status. This model outperforms other existing methods. We apply the model on the whole human genome and predict the landscape of DNA methylation of all CpG islands. Based on the methylation profile, we find that about 31% of CpG islands are methylation-prone and CpG islands located in promoter regions are seldom methylated. There is no significant difference in the CpG island methylation level between R and G bands among the chromosomes. The occupancy of RNA polymerase II is significantly higher in methylation-resistant promoter CpG islands, indicating that genes with such promoter CpG islands tend to be more active.     

Identification of petroleum aromatic fraction by comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry

Comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS) is com-mercially available in the 1990s, with the characteristics of large peak capacity, high resolution, high sensitivity, etc. However, its application to the petroleum and geological analyses is just emerging in China and overseas. In this research, the analytical method for petroleum aromatic fraction using GC×GC-TOFMS is set up, via the choice of the column system and optimization of setting parameters, such as temperature programming, modulation time, hot pulse time, flow rate of carrier gas, data acquisition rate and data processing. The results indicate that different polar compounds of aromatic fraction distribute as bands on structured GC×GC chromatogram. Within each band, homologous compounds appear as a roof-tile structure based on the number of substituent residues. The aromatic compounds are identified and characterized according to the GC×GC chromatogram and mass spectra. According to the polarity and the number of rings, aromatic compounds are spatially present on one chromatogram, which directly reflects the distribution characteristics of complex compounds of aromatic hydrocarbons. In addition, quantitative analysis is favored as some overlapped peaks on traditional GC-MS chromatogram have been separated completely on GC×GC. Some heterocyclic atom aromatic compounds at trace level can be clearly identified using this method, for polarity differences from other interfered aromatic compounds. The development of this method and chromatogram recognition offer petroleum geologists a practical example for the application performance of GC×GC-TOFMS.     

Response of Zhadang Glacier runoff in Nam Co Basin,Tibet, to changes in air temperature and precipitation form

This paper describes 2007/2008 inter-annual changes in runoff from the Zhadang Glacier located on the northern slope of Nyainqêntanglha Range, Tibet, and analyzes their causes. Precipitation increased by 17.9% in summer months of 2008 compared with the same period in 2007, drainage basin runoff decreased by 33.3%, and glacial meltwater decreased by 53.8%. Change in positive accumulated air temperature explained approximately half of the inter-annual difference in glacial meltwater using a de-gree-day model. This suggests that the glacier is extremely sensitive to changes in air temperature. Energy balance analysis showed that change in glacier surface albedo, considered to be caused by difference in precipitation form, resulted in the large inter-annual difference in glacial meltwater. It was shown statistically that precipitation form in the summer months of 2007 was mainly rainfall which comprised 71.5% of total precipitation, while during the same period in 2008 rainfall accounted for 30.7%, with the majority of precipitation falling as snow. Precipitation form should be considered an independent factor when analyzing glacier sensitivity to climate change or forecasting the runoff from certain glaciers.     

Ultafast organic nonlinear optical molecules and the realization of mesoscopic photonic devices

In the twentieth century, revolutionary changes took place in the human society and people’s life-style due to the improvement of the optoelectronic information technology based on the second-order nonlinear optical effects, such as the electro-optic effect, the second harmonic generation (SHG), and so on. Along with the rapid development of light information technology, new principles and methods of nonlinear optics are needed, and the third-order nonlinear optical effects attract great attention. The research progress of nonlinear optics is reviewed in this article. Our research work on the third-order nonlinear optical materials, ultrafast and low-power organic all-optical photonic crystal switching are introduced.     

Responses of soil respiration in non-growing seasons to environmental factors in a maize agroecosystem,Northeast China

Based on continuous three-year measurements (from 2004 to 2007) of eddy covariance and related environmental factors, envi-ronmental controls on variation in soil respiration (R_s) during non-growing season were explored in a maize agroecosystem in Northeast China. Our results indicated that during non-growing seasons, daily Rs was 1.08–4.08 g CO2 m^–2 d^–1, and the lowest occurred in late November. The average R_s of non-growing season was 456.06 ± 20.01 g CO2 m^–2, accounting for 11% of the gross primary production (GPP) of the growing season. Additionally, at monthly scale, the lowest value of R_s appeared in January or February. From the beginning to the end of non-growing season, daily R_s tended to decrease first, and then increase to the highest. There was a significant quadratic curve relationship between Rs and soil temperature at 10 cm depth when soil temperature was more than 0°C (P<0.001), with the explaining ratio of 38%–70%. When soil water content was more than 0.1 m³ m^–3, soil moisture at 10 cm depth was significantly parabolically correlated with R_s (P<0.001), explaining the rate of 18%–60%. Based on all the data of soil temperature of more than 0°C, a better model for R_s was established by coupling soil temperature and moisture, which could explain the rate of up to 53%–79%. Meanwhile, the standard error of regression estimation between the values of prediction and observation for R_s could reach 2.7%–11.8%. R_s in non-growing season can account for 22.4% of R_s in growing season, indicating that it plays a critical role in assessing the carbon budget in maize agroecosystem, Northeast China.     

A novel self-promoted Morita-Baylis-Hillman-like dimerization

While stable in CH₂Cl₂, hexane or THF, in the presence of MeOH, self-promoted dimerization of the triarylphosphine-alkene 1, a ligand for Pd-catalyzed reactions, produced an unusual racemic bis(phosphine) 2 in high yield. The reaction of 2 with Pd(dba)₂, followed by oxidative addition of p-IC₆H₄NO₂, yielded a trans-chelated Pd(II) aryl iodide complex.     

Solving surface plasmon resonances and near field in metallic nanostructures: Green’s matrix method and its applications

With the development of nanotechnology, many new optical phenomena in nanoscale have been demonstrated. Through the coupling of optical waves and collective oscillations of free electrons in metallic nanostructures, surface plasmon polaritons can be excited accompanying a strong near field enhancement that decays in a subwavelength scale, which have potential applications in the surface-enhanced Raman scattering, biosensor, optical communication, solar cells, and nonlinear optical frequency mixing. In the present article, we review the Green’s matrix method for solving the surface plasmon resonances and near field in arbitrarily shaped nanostructures and in binary metallic nanostructures. Using this method, we design the plasmonic nanostructures whose resonances are tunable from the visible to near-infrared, study the interplay of plasmon resonances, and propose a new way to control plasmonic resonances in binary metallic nanostructures.     

Advances in the hyperlens

As a superlens to overcome the well-known diffraction limit, the hyperlens has received much attention due to its super resolving power and magnifying capabilities. In this article, we review the recent developments, including theoretical and experimental studies on the hyperlens. We also discuss its limitations and potential.     

Infrared phononic nanoantennas: Localized surface phonon polaritons in SiC disks

The electromagnetic interaction of light with polar materials shows a sharp and well defined electromagnetic response in the infrared (IR) region that consists mainly of excitation of optical phonons. Similar to surface plasmons in the visible region, surface phonons can couple efficiently to infrared light in micron-sized antennas made of polar materials. We applied the boundary element method to calculating the infrared electromagnetic response of single SiC disks acting as effective infrared antennas as a function of different parameters such as disk size and thickness. We also analyzed the effect of locating a probing metallic tip near the SiC disk to scatter light in the proximity of the SiC disk, thereby obtaining new spectral peaks connected with localized modes between the tip and the SiC disk. We then further investigated their application in IR scanning probe microscopy. A near-field map of the phononic resonances enhances the understanding of the nature of the IR extinction peaks.