Examination of the LBM in simulation of microchannel flow in transitional regime

The gas flows in micro-electro-mechanical systems possess relatively large Knudsen number and usually belong to the slip flow and transitional flow regimes. Recently the lattice Boltzmann method (LBM) was proposed by Nie et al. in Journal of Statistical Physics, vol. 107, pp. 279-289, in 2002 to simulate the microchannel and microcavity flows in the transitional flow regime. The present article intends to test the feasibility of doing so. The results of using the lattice Boltzmann method and the direct simulation Monte Carlo method show good agreement between them for small Kn (Kn = 0.0194), poor agreement for Kn = 0.194, and large deviation for Kn = 0.388 in simulating microchannel flows. This suggests that the present version of the lattice Boltzmann method is not feasible to simulate the transitional channel flow.

A scaling law of photoionization in few-cycle regime

In this paper, a scaling law of photoionization of atoms irradiated by intense, few- cycle laser pulses is established. The scaling law sets a relation to the phase- dependent ionization with the kinetic energy of photoelectrons, the duration and peak intensity of short pulses, and the ionization potential of the target atoms. We find that it will be advantageous to manifest the phase- dependent photoionization by choosing the target atoms with larger ionization potential, using laser with smaller carrier- frequency, and increasing the pulse intensity. (c) 2007 Optical Society of America.

Electron injection by a nanowire in the bubble regime

The triggering of wave-breaking in a three-dimensional laser plasma wake (bubble) is investigated. The Coulomb potential from a nanowire is used to disturb the wake field to initialize the wave-breaking. The electron acceleration becomes more stable and the laser power needed for self-trapping is lowered. Three-dimensional particle-in-cell simulations were performed. Electrons with a charge of about 100 pC can be accelerated stably to energy about 170 MeV with a laser energy of 460 mJ. The first step towards tailoring the electron beam properties such as the energy, energy spread, and charge is discussed. (C) 2007 American Institute of Physics.

Quantum path control in few-optical-cycle regime

We theoretically show that selection of a single quantum path in high-order harmonics generation can be realized in a few-optical-cycle regime with two-color schemes. We also demonstrate, in theory as well, the generation of spectrally smooth and ultrabroad extreme ultraviolet supercontinuum in argon gas which can produce single similar to 79 as pulses with currently available ultrafast laser sources. Our finding can be beneficial for generating isolated sub-100 as extreme ultraviolet pulses.

Bubble regime for ion acceleration in a laser-driven plasma

Proton trapping and acceleration by an electron bubble-channel structure in laser interaction with high-density plasma is investigated by using three-dimensional particle-in-cell simulations. It is shown that protons can be trapped, bunched, and efficiently accelerated for appropriate laser and plasma parameters, and the proton acceleration is enhanced if the plasma consists mainly of heavier ions such as tritium. The observed results are analyzed and discussed in terms of a one-dimensional analytical three-component-plasma wake model.

De novo origination of a new protein-coding gene in Saccharomyces cerevisiae

Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes of creating new genes using preexisting genes as the raw materials are well characterized, such as exon shuffling, gene duplicat

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

Recent transcription profiling studies have revealed an unexpectedly large proportion of antisense transcripts in eukaryotic genomes. These antisense genes seem to regulate gene expression by interacting with sense genes. Previous studies have focused on the non-coding antisense genes, but the possible regulatory role of the antisense protein is poorly understood. In this study, we found that a protein encoded by the antisense gene ADF1 acts as a transcription suppressor, regulating the expression of sense gene MDF1 in Saccharomyces cerevisiae. Based on the evolutionary, genetic, cytological and biochemical evidence, we show that the protein-coding sense gene MDF1 most likely originated de novo from a previously non-coding sequence and can significantly suppress the mating efficiency of baker's yeast in rich medium by binding MAT alpha 2 and thus promote vegetative growth. These results shed new light on several important issues, including a new sense-antisense interaction mechanism, the de novo origination of a functional gene, and the regulation of yeast mating pathway.

The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

EXPERIMENTS ON AQUATIC ECOSYSTEM REGIME SHIFT IN ENCLOSURES NEAR LAKE DIANCHI, CHINA

To discover how a lake converts from a turbid state to clean state, and what drives this process, we constructed controlled enclosure ecosystems and used the ecological remediation method to force ecosystems to convert from the turbid state to the clean state. Our results show that the driving forces include temperature., macrophyte, silver carp and mussel, which form a combined force to drive the controlled ecosystem to switch. There is a threshold existing in treated enclosure ecosystem during the conversion from turbid to clean state. When TP <0.09 mg.L-1, Chl-a <0.036 mg.L-1, transparency >62 cm, TN <2.15 mg.L-1, CODMn <13.7 mg.L-1, tubidity <10, and the number of algal cells <10(6) cells.L-1, the treated ecosystem changes sharply from turbid to clean state. The conversion process can be divided into three phases: turbid state, clean-turbid transitional state as well as clean state, and described with the power function Y = a*X-b (where Y is water parameter, X is time, a and b are constants), which indicates that the shift in the enclosure ecosystem from turbid to clean state is discontinuous.

De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase

Classical swine fever virus (CSFV) non-structural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp), a key enzyme which initiates RNA replication by a de novo mechanism without a primer and is a potential target for anti-virus therapy. We expressed the NS5B protein in Escherichia coli. The rGTP can stimulate de novo initiation of RNA synthesis and mutation of the GDD motif to Gly-Asp-Asp (GAA) abolishes the RNA synthesis. To better understand the mechanism of viral RNA synthesis in CSFV, a three-dimensional model was built by homology modeling based on the alignment with several virus RdRps. The model contains 605 residues folded in the characteristic fingers, palm and thumb domains. The fingers domain contains an N-terminal region that plays an important role in conformational change. We propose that the experimentally observed promotion of polymerase efficiency by rGTP is probably due to the conformational changes of the polymerase caused by binding the rGTP. Mutation of the GDD to GAA interferes with the interaction between the residues at the polymerase active site and metal ions, and thus renders the polymerase inactive. (c) 2005 Elsevier B.V. All rights reserved.

Single-photon source in strong photon-atom interaction regime in quasiperiodic photonic crystals

The antibunching properties of the fluorescence from a two-level ideal system in a 12-fold quasiperiodic photonic crystal are investigated based on the calculated local density of states. We found that the antibunching phenomenon of the fluorescence from two-level ideal systems could be significantly changed by varying their positions, i.e., perfect antibunching and antibunching with damped Rabi oscillation phenomenon occurred in different positions and at different frequencies in photonic crystals as a result of the large differences in the local density of states. This study revealed that the multi-level coherence of fluorescence from a two-level ideal system could be manipulated by controlling the position of the two-level ideal system in photonic crystals and the emission frequency in the photonic band structure. Copyright (C) EPLA, 2008