Multiscale Coupling in Complex Mechanical Systems

Multiscale coupling attracts broad interests from mechanics, physics and chemistry to biology. The diversity and coupling of physics at different scales are two essential features of multiscale problems in far-from-equilibrium systems. The two features present fundamental difficulties and are great challenges to multiscale modeling and simulation. The theory of dynamical system and statistical mechanics provide fundamental tools for the multiscale coupling problems. The paper presents some closed multiscale formulations, e.g., the mapping closure approximation, multiscale large-eddy simulation and statistical mesoscopic damage mechanics, for two typical multiscale coupling problems in mechanics, that is, turbulence in fluids and failure in solids. It is pointed that developing a tractable, closed nonequilibrium statistical theory may be an effective approach to deal with the multiscale coupling problems. Some common characteristics of the statistical theory are discussed.

Dynamics of quantum dissipation systems interacting with fermion and boson grand canonical bath ensembles: Hierarchical equations of motion approach

A hierarchical equations of motion formalism for a quantum dissipation system in a grand canonical bath ensemble surrounding is constructed on the basis of the calculus-on-path-integral algorithm, together with the parametrization of arbitrary non-Markovian bath that satisfies fluctuation-dissipation theorem. The influence functionals for both the fermion or boson bath interaction are found to be of the same path integral expression as the canonical bath, assuming they all satisfy the Gaussian statistics. However, the equation of motion formalism is different due to the fluctuation-dissipation theories that are distinct and used explicitly. The implications of the present work to quantum transport through molecular wires and electron transfer in complex molecular systems are discussed. (c) 2007 American Institute of Physics.

A delay model for noise-induced bi-directional switching

Many biological systems can switch between two distinct states. Once switched, the system remains stable for a period of time and may switch back to its original state. A gene network with bistability is usually required for the switching and stochastic effect in the gene expression may induce such switching. A typical bistable system allows one-directional switching, in which the switch from the low state to the high state or from the high state to the low state occurs under different conditions. It is usually difficult to enable bi-directional switching such that the two switches can occur under the same condition. Here, we present a model consisting of standard positive feedback loops and an extra negative feedback loop with a time delay to study its capability to produce bi-directional switching induced by noise. We find that the time delay in the negative feedback is critical for robust bi-directional switching and the length of delay affects its switching frequency.

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.

Peeling behavior of a bio-inspired nano-film on a substrate

A peeling model is proposed to analyze the peeling properties of bio-mimetic nano-films using the finite element method (FEM) and theoretical approach. The influences of the nano-film's adhesion length, thickness, elastic modulus, roughness and peeling angle on the peeling force were considered as well as the effect of the viscoelastic behavior. It has been found that the effective adhesion length, at which the peeling force attained maximum, was much smaller than the real length of nano-films; and the shear force dominated in the case of smaller peeling angles, whereas, the normal force dominated at larger peeling angles. The total peeling force decreased with an increasing peeling angle. Two limiting values of the peeling-off force can be found in the viscoelastic model, which corresponds to the smaller and larger loading rate cases. The effects of nano-film thickness and Young's modulus on peeling behaviors were also discussed. The results obtained are helpful for understanding the micro-adhesion mechanisms of biological systems, such as geckos. (C) 2010 Elsevier Ltd. All rights reserved.

Effect of information transmission on cooperative behavior

Considering the fact, in the real world, that information is transmitted with a time delay, we study an evolutionary spatial prisoner's dilemma game where agents update strategies according to certain information that they have learned. In our study, the game dynamics are classified by the modes of information learning as well as game interaction, and four different combinations, i.e. the mean-field case, case I, case II and local case, are studied comparatively. It is found that the time delay in case II smoothes the phase transition from the absorbing states of C (or D) to their mixing state, and promotes cooperation for most parameter values. Our work provides insights into the temporal behavior of information and the memory of the system, and may be helpful in understanding the cooperative behavior induced by the time delay in social and biological systems.

Environmentally friendly synthesis of highly monodisperse biocompatible gold nanoparticles with urchin-like shape

We report a facile and environmentally friendly strategy for high-yield synthesis of highly monodisperse gold nanoparticles with urchin-like shape. A simple protein, gelatin, was first used for the control over shape and orientation of the gold nanoparticles. These nanoparticles, ready to use for biological systems, are promising in the optical imaging-based disease diagnostics and therapy because of their tunable surface plasmon resonance (SPR) and excellent surface-enhanced Raman scattering (SERS) activity.

High resolution mass spectrometric alveolar proteomics: Identification of surfactant protein SP-A and SP-D modifications in proteinosis and cystic fibrosis patients

In the present study, one- and two-dimensional gel electrophoresis combined with high resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) have been applied as powerful approaches for the proteome analysis of surfactant proteins SP-A and SP-D, including identification of structurally modified and truncation forms, in bronchoalveolar lavage fluid from patients with cystic fibrosis, chronic bronchitis and pulmonary alveolar proteinosis. Highly sensitive micro preparation techniques were developed for matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS analysis which provided the identification of surfactant proteins at very low levels. Owing to the high resolution, FT-ICR MS was found to provide substantial advantages for the structural identification of surfactant proteins from complex biological matrices with high mass determination accuracy. Several protein bands corresponding to SP-A and SP-D were identified by MALDI-FT-ICR MS after electrophoretic separation by one- and two-dimensional gel electrophoresis, and provided the identification of structural modifications (hydroxy-proline) and degradation products.

An ESR study on (OH)-O-center dot-radical scavenging activity of water-soluble fullerenols

Water-soluble polyhydroxylated fullerene derivatives (fullerenol) were synthesized, and their scavenging ability for (OH)-O-.-radical was studied by the combination of ESR spectroscopy and spin-trapping technique with phenyl-t-butyl-nitrone. It was found that fullerenols showed an excellent efficiency in eliminating (OH)-O-. free radicals generated by UV photolysis of H2O2. At an applied fullerenol concentration of 0, 3 mg/mL in the final solution, a radical scavenging efficiency of approximate 95% was achieved, revealing the potential use of these compounds as novel potent free radical scavengers in biological systems.

EFFECT OF LANTHANIDE IONS ON THE PHASE-BEHAVIOR OF DIPALMITOYLPHOSPHATIDYLCHOLINE MULTILAMELLAR LIPOSOMES

The effect of lanthanide ions (Ln(3+)) and their coordination compounds of diethylenetriamine pentaacetic acid (DTPA) on the phase behavior of dipalmitoylphosphatidycholine (DPPC) multilamellar liposomes has been studied by differential scanning calorimet

基于代理模型的水下滑翔机机翼设计优化方法

在复杂工程系统的概念设计优化中,高精度数值分析方法得到广泛应用,将高精度数值分析与优化方法有机结合,对设计空间展开全面搜索与寻优,已经成为现代设计优化方法的重要发展方向。以水下滑翔机的概念设计为研究对象,引入代理模型,控制高精度分析试验的数量,有效地化解精度与效率之间的矛盾。将参数化几何建模、网格划分以及流体数值模拟分析集成为自动分析流程,并以此为基础采用试验设计理论,构建代理模型,解决水下滑翔机机翼的多目标设计优化问题。给出基于代理模型的设计优化过程,并系统地比较几种试验设计方法的适应性,重点讨论多项式响应面和径向基函数代理模型,所得代理模型相对误差小于2%。采用梯度寻优方法与遗传算法在给定设计空间内进行全面搜索,获得机翼的最佳平面构形,水下滑翔机的升阻比提高6.76%,俯仰力矩的绝对值由0.2760N•m降低为0.0015N•m,提高水下滑翔机的运动性能。

大型复杂工程系统研究开发中的方法论问题

本文通过大量事例说明了方法论对完成大型工程项目的重要意义,总结了工程技术中方法论的一般原理,并以此为指导,提出了大型自动化系统开发中的新思路。

Screening and analysis of bioactive compounds with biofingerprinting chromatogram analysis of traditional Chinese medicines targeting DNA by microdialysis/HPLC

Biofingerprinting chromatogram, analysis, which is defined as the comparison of fingerprinting chromatograms of the extract of traditional Chinese medicines (TCMs) before and after the interaction with biological systems (DNA, protein. cell. etc.), was proposed for screening and analysis of the multiple bioactive compounds in TCMs. A method of microdialysis sampling combined with high performance liquid chromatography (HPLC) was applied to the study of DNA-binding property for the extracts of TCMs. Seven compounds were found to bind to calf thymus DNA (ct-DNA) from the TCMs of Coptis chinensis Franch (Coptis), but only three ones from Phellodendron amurense Rupr. (Phellodendron) and none from Sophoraflavescens Ait. (Sophora) to bind to ct-DNA. respectively. Three of them were identified as berberine, palmatine and jatrorrhizine and their association constants (K) to ct-DNA were determined by microdialysis/HPLC. Competitive binding behaviors of them to ct-DNA were also investigated. © 2005 Elsevier B.V. All rights reserved.