Information Preservation (IP) Method in Simulation

This paper reviews firstly methods for treating low speed rarefied gas flows: the linearised Boltzmann equation, the Lattice Boltzmann method (LBM), the Navier-Stokes equation plus slip boundary conditions and the DSMC method, and discusses the difficulties in simulating low speed transitional MEMS flows, especially the internal flows. In particular, the present version of the LBM is shown unfeasible for simulation of MEMS flow in transitional regime. The information preservation (IP) method overcomes the difficulty of the statistical simulation caused by the small information to noise ratio for low speed flows by preserving the average information of the enormous number of molecules a simulated molecule represents. A kind of validation of the method is given in this paper. The specificities of the internal flows in MEMS, i.e. the low speed and the large length to width ratio, result in the problem of elliptic nature of the necessity to regulate the inlet and outlet boundary conditions that influence each other. Through the example of the IP calculation of the microchannel (thousands long) flow it is shown that the adoption of the conservative scheme of the mass conservation equation and the super relaxation method resolves this problem successfully. With employment of the same measures the IP method solves the thin film air bearing problem in transitional regime for authentic hard disc write/read head length ( ) and provides pressure distribution in full agreement with the generalized Reynolds equation, while before this the DSMC check of the validity of the Reynolds equation was done only for short ( ) drive head. The author suggests degenerate the Reynolds equation to solve the microchannel flow problem in transitional regime, thus provides a means with merit of strict kinetic theory for testing various methods intending to treat the internal MEMS flows.

Information preservation (IP) method in simulation of internal rarefied gas flows in MEMS

This paper reviews firstly methods for treating low speed rarefied gas flows: the linearised Boltzmann equation, the Lattice Boltzmann method (LBM), the Navier-Stokes equation plus slip boundary conditions and the DSMC method, and discusses the difficulties in simulating low speed transitional MEMS flows, especially the internal flows. In particular, the present version of the LBM is shown unfeasible for simulation of MEMS flow in transitional regime. The information preservation (IP) method overcomes the difficulty of the statistical simulation caused by the small information to noise ratio for low speed flows by preserving the average information of the enormous number of molecules a simulated molecule represents. A kind of validation of the method is given in this paper. The specificities of the internal flows in MEMS, i.e. the low speed and the large length to width ratio, result in the problem of elliptic nature of the necessity to regulate the inlet and outlet boundary conditions that influence each other. Through the example of the IP calculation of the microchannel (thousands m ? long) flow it is shown that the adoption of the conservative scheme of the mass conservation equation and the super relaxation method resolves this problem successfully. With employment of the same measures the IP method solves the thin film air bearing problem in transitional regime for authentic hard disc write/read head length ( 1000 L m ? = ) and provides pressure distribution in full agreement with the generalized Reynolds equation, while before this the DSMC check of the validity of the Reynolds equation was done only for short ( 5 L m ? = ) drive head. The author suggests degenerate the Reynolds equation to solve the microchannel flow problem in transitional regime, thus provides a means with merit of strict kinetic theory for testing various methods intending to treat the internal MEMS flows.

Information Preservation Modeling of Rayleigh-Benard Transition from Thermal Conduction to Convection

Onset and evolution of the Rayleigh-Benard (R-B) convection are investigated using the Information Preservation (IP) method. The information velocity and temperature are updated using the Octant Flux Splitting (OFS) model developed by Masters & Ye based on the Maxwell transport equation suggested by Sun & Boyd. Statistical noise inherent in particle approaches such as the direct simulation Monte Carlo (DSMC) method is effectively reduced by the IP method, and therefore the evolutions from an initial quiescent fluid to a final steady state are shown clearly. An interesting phenomenon is observed: when the Rayleigh number (Ra) exceeds its critical value, there exists an obvious incubation stage. During the incubation stage, the vortex structure clearly appears and evolves, whereas the Nusselt number (Nu) of the lower plate is close to unity. After the incubation stage, the vortex velocity and Nu rapidly increase, and the flow field quickly reaches a steady, convective state. A relation of Nu to Ra given by IP agrees with those given by DSMC, the classical theory and experimental data.

Reduced deep-tissue image degradation in three-dimensional multiphoton microscopy with concentric two-color two-photon fluorescence excitation

We theoretically demonstrate that enhanced penetration depth in three-dimensional multiphoton microscopy can be achieved using concentric two-color two-photon (C2C2P) fluorescence excitation in which the two excitation beams are separated in space before reaching their common focal spot. Monte Carlo simulation shows that, in comparison with the one-color two-photon excitation scheme, the C2C2P fluorescence microscopy provides a significantly greater penetration depth for imaging into a highly scattering medium. (C) 2008 Optical Society of America.

苦苣苔科植物的组织培养和离体保存

苦苣苔科(Gesneriaceae)植物种类繁多, 全世界约150属3700余种,我国有58属470余种，大部分具有极高的观赏价值，许多是传统的民间草药。虽然我国苦苣苔科植物资源丰富，然而很多种类分布区域狭窄，种群数量稀少，加之生境受到破坏，许多已经面临灭绝的危险。本研究拟通过组织培养、玻璃化超低温保存以及快速繁殖，达到保护和扩繁珍稀濒危苦苣苔科植物的目的。 以药用唇柱苣苔（Chirita medica D. Fang ex W. T. Wang）和粉绿异裂苣苔（Pseudochirita guangxiensis W.T.Wang var. glauca Y. G. Wei et Y. Liu）为材料，取幼嫩叶片为外植体，通过组织培养实验得到最佳诱导不定芽培养基：MS培养基附加30 g l-1蔗糖，7.5 g l-1琼脂，药用唇柱苣苔附加0.10 mg l-1 BA ，0.10 mg l-1 NAA，粉绿异裂苣苔附加0.05 mg l-1IAA，1.00 mg l-1BA。最高不定芽诱导率分别为：90.3%和85.0%。最佳生根培养基：1/2MS培养基附加30 g l-1蔗糖，5 g l-1活性炭，7 g l-1琼脂，生根率为100%，诱导产生6.11条根，根长为18.8mm（药用唇柱苣苔）；1/2MS培养基附加10-20g l-1蔗糖，1 g l-1活性炭，7 g l-1琼脂，诱导生成6.8-7.4条根，均长17.7-22.0mm（粉绿异裂苣苔）。 在组织培养的基础上进行了苦苣苔科植物的玻璃化超低温冷冻保存研究。以烟叶唇柱苣苔（C. heterotricha Merr.）和濒危植物药用唇柱苣苔叶片外植体为材料，经过自然干燥、装载液处理、玻璃化溶液处理、液氮冷冻保存，成功实现了玻璃化超低温冷冻保存，经过液氮冷冻保存后的材料可以继续分化、生长。适当时间的玻璃化试剂处理对于材料无致死作用，不经液氮冷冻，可以达到100%存活。-20 oC 、-40 oC、液氮保存后，存活率随温度下降而下降，表明冷冻致死的原因在于冰晶形成；提高冷冻后成活率的关键是控制干燥脱水，经过适当的自然干燥，材料存活率分别达到50.0%和27.8%。 以叶片为外植体材料，通过组织培养和快速繁殖可以大规模扩繁苦苣苔科植物。主要步骤为：外植体叶片消毒→不定芽诱导培养→生根诱导培养→继代保存或炼苗移栽，经过3-4个月时间可获得大量栽培植株。已成功保存并培养了40余种苦苣苔科植物，包括濒危苦苣苔及高观赏价值苦苣苔。

Characterization and Comparison of the Tissue-Related Modules in Human and Mouse

Background: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches. Results: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity,'' a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse. Conclusions: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions.