计算物理学导论

计算机无疑已成为当今物理学不可或缺的最重要工具。它被广泛地应用于计算、显示结果、模拟实验或求解复杂的方程组。在高等学校的物理教学中，计算物理课的地位越来越重要。本书是一本计算物理课程的导论性教材，它给学生们介绍怎样用计算机解物理学的一些数学问题，特别是在解析解不存在，只能用数值解法的复杂情况下，本书教给学生如何选择不同的数值方法，介绍了许多实用程序和可用的软件包。     

Paper tools in experimental cultures

The paper studies various functions of Berzelian formulas in European organic chemistry prior to the mid-nineteenth century from a semiotic, historical and epistemological perspective. I argue that chemists applied Berzelian formulas as productive ‘paper tools’ for creating a chemical order in the ‘jungle’ of organic chemistry. Beginning in the late 1820s, chemists applied chemical formulas to build models of the binary constitution of organic compounds in analogy to inorganic compounds. Based on these formula models, they constructed new classifications of organic substances. They further applied Berzelian formulas in a twofold way to experimentally investigate organic chemical reactions: as tools which supplemented laboratory tools and as tools for constructing interpretive models of organic reactions. The scrutiny of chemists' performances with chemical formulas on paper also reveals a dialectic which contributed considerably to the formation of the new experimental culture of synthetic carbon chemistry that emerged between the late 1820s and the early 1840s. In an unintended and unforeseen way, the tools reacted back on the goals of their users and contributed to conceptual development and a shift of scientific objects and practices (‘substitution’) which transcended the originally intended chemical order.     

Reverse engineering of regulatory networks in human B cells

Cellular phenotypes are determined by the differential activity of networks linking coregulated genes. Available methods for the reverse engineering of such networks from genome-wide expression profiles have been successful only in the analysis of lower eukaryotes with simple genomes. Using a new method called ARACNe (algorithm for the reconstruction of accurate cellular networks), we report the reconstruction of regulatory networks from expression profiles of human B cells. The results are suggestive a hierarchical, scale-free network, where a few highly interconnected genes (hubs) account for most of the interactions. Validation of the network against available data led to the identification of MYC as a major hub, which controls a network comprising known target genes as well as new ones, which were biochemically validated. The newly identified MYC targets include some major hubs. This approach can be generally useful for the analysis of normal and pathologic networks in mammalian cells.     

Physical methods for characterization of microbial surfaces

There are different concepts for explaining the adsorption of microorganisms to solid surfaces: the DLVO theory and the surface free energy. Basic aspects of both theories are discussed. Established methods for determining the surface properties of microbial cells are reviewed: Electrophoretic mobility, colloid titration, electrostatic interaction chromatography, bacterial adherence to hydrocarbons, partitioning in an aqueous two-phase system, hydrophobic interaction chromatography, contact angle measurement and X-ray photoelectron spectroscopy. They are discussed and classified according to their potential for the correlation of cell surface characteristics and adsorption behavior.     

Lubrication by charged polymers

Long-ranged forces between surfaces in a liquid control effects from colloid stability to biolubrication, and can be modified either by steric factors due to flexible polymers, or by surface charge effects. In particular, neutral polymer 'brushes' may lead to a massive reduction in sliding friction between the surfaces to which they are attached, whereas hydrated ions can act as extremely efficient lubricants between sliding charged surfaces. Here we show that brushes of charged polymers (polyelectrolytes) attached to surfaces rubbing across an aqueous medium result in superior lubrication compared to other polymeric surfactants. Effective friction coefficients with polyelectrolyte brushes in water are lower than about 0.0006-0.001 even at low sliding velocities and at pressures of up to several atmospheres (typical of those in living systems). We attribute this to the exceptional resistance to mutual interpenetration displayed by the compressed, counterion-swollen brushes, together with the fluidity of the hydration layers surrounding the charged, rubbing polymer segments. Our findings may have implications for biolubrication effects, which are important in the design of lubricated surfaces in artificial implants, and in understanding frictional processes in biological systems.     

Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm

Stable associations of more than one species of symbiont within a single host cell or tissue are assumed to be rare in metazoans because competition for space and resources between symbionts can be detrimental to the host. In animals with multiple endosymbionts, such as mussels from deep-sea hydrothermal vents and reef-building corals, the costs of competition between the symbionts are outweighed by the ecological and physiological flexibility gained by the hosts. A further option for the coexistence of multiple symbionts within a host is if these benefit directly from one another, but such symbioses have not been previously described. Here we show that in the gutless marine oligochaete Olavius algarvensis, endosymbiotic sulphate-reducing bacteria produce sulphide that can serve as an energy source for sulphide-oxidizing symbionts of the host. Thus, these symbionts do not compete for resources but rather share a mutalistic relationship with each other in an endosymbiotic sulphur cycle, in addition to their symbiotic relationship with the oligochaete host.