Statistical physics and stromatolite growth: new perspectives on an ancient dilemma

This paper outlines our recent attempts to model the growth and form of microbialites from the perspective of the statistical physics of evolving surfaces. Microbialites arise from the environmental interactions of microbial communities (microbial mats). The mats evolve over time to form internally laminated organosedimentary structures (stromatolites). Modern day stromatolites exist in only a few locations, whereas ancient stromatolitic microbialites were the only form of life for much of the Earth's history. They existed in a wide variety of growth forms, ranging from almost perfect cones to branched columnar structures. The coniform structures are central to the heated debate on the oldest evidence of life. We proposed a biotic model which considers the relationship between upward growth of a phototropic or phototactic biofilm and mineral accretion normal to the surface. These processes are sufficient to account for the growth and form of many ancient stromatolities. These include domical stromatolites and coniform structures with thickened apical zones typical of Conophyton. More angular coniform structures, similar to the stromatolites claimed as the oldest macroscopic evidence of life, form when the photic effects dominate over mineral accretion.     

Investigation of microbial—mineral interactions by Mössbauer spectroscopy

Mössbauer spectroscopy was used to investigate the reactions of microbes with iron minerals in aqueous solutions and as components of rocks in banded iron formations and granite. A microbial biofilm that formed on a wall of an excavated granite vault in a deep underground laboratory initiated this research. At the aerobic face of the biofilm, iron was found in a form of ferrihydrite; in the anaerobic face against the rock, iron was found as very small siderite particles. Laboratory incubations of the biofilm microbial consortium showed different mineral species could be formed. When the microbial consortium from the biofilm was incubated with magnetite grains, up to about 10% of the iron was altered in three weeks to hematite. The ability of the consortium to precipitate iron both as Fe²⁺ and Fe³⁺ in close proximity may have a bearing on the deposition of banded iron formations. These reactions could also be important in microbially induced corrosion.     

槽道湍流展向振荡电磁力控制的实验研究

对槽道湍流的展向振荡电磁力控制进行了实验研究,讨论了展向振荡电磁力对宏观流场、近壁湍流结构以及壁面阻力的影响.采用谱方法进行了数值模拟的对比.数值模拟和实验结果均表明展向振荡电磁力能够使近壁区域的宏观流场产生周期性振荡,并影响壁湍流的条带结构,使其在展向上发生倾斜,从而使壁面阻力减小.     

Variation in the biological characteristics of BAC during ultrasonic regeneration

Ultrasonic treatment has been shown to have a favorable effect on the regeneration of spent biological activated carbon (BAC) from drinking water treatment plants. In this study, the use of ultrasound as a regeneration method had a significant effect on the recovery of spent BAC after 7.5 years of use; it effectively increased the iodine value from 300 mg/g to 600 mg/g and restored the specific surface area and pore volume of BAC. Ultrasound effectively changed the structure of the biofilm inside and on the surfaces of BAC particles, on the basis of confocal laser scanning microscopy (CLSM) images. The thickness of the surface biofilm attached to BAC reached an “active” level (about 100 μm) at the regeneration frequency of 40 kHz. The dehydrogenase activity significantly improved from 4.50 mg TF/g BAC to 9.13 mg TF/g BAC, and the content of adenosine-triphosphate (ATP) in regenerated BAC was maintained at a high level (2.501 × 10⁻⁶g ATP/g BAC), thus allowing the development of microbial growth. The production of soluble microbial products (SMPs) from regenerated BAC decreased during the reuse process. The removal efficiency of DOC, COD_Mn, NH₄⁺ and NO₃^– control increased by approximately 78%, 71%, 50% and 20%, respectively.     

A multi-scale numerical simulation of the crystallisation and temperature field of glass

There is a big difference in the spatial scale between temperature field simulation and crystallisation simulation of the glass cooling process. The temperature field belongs to the macroscopic scale, while crystallisation is on the mesoscopic scale. In this paper, a coupled algorithm for the temperature field and crystallisation calculation is established in which the macroscopic temperature simulation is based on the finite element method while the mesoscopic crystallisation simulation is based on the Monte Carlo method using the Uhlmann model. In calculations, the temperature value is regarded as the input condition of the crystallisation calculation while the results of crystallisation in the form of latent heat are used as the input conditions for the temperature calculation. The pixel method is employed to deal with the collision process of crystal grain interfaces. A corresponding numerical simulation scheme has been developed and a multi-scale simulation of glass crystallisation and the cooling temperature field has been carried out. Finally, the presented model and developed simulation scheme have been shown to be very reasonable in comparison to both numerical predictions and with previous results from the literature.     

Atomic force microscopy: A nanoscopic view of microbial cell surfaces

The atomic force microscope (AFM) is a powerful instrument for microbiological investigation. It has evolved from an imaging tool used to investigate microbial surfaces at high resolution in their physiological environment into a lab-on-a-tip device, which allows more quantitative analysis of biological samples (from molecules to cells) in aqueous liquids. Atomic force microscopy provides information about the nanoscale architecture of microbes and about the localization and interactions of their individual constituents. Microbial interactions play essential roles in biology, medicine, ecology, biotechnology, food science and contribute to phenomena as varied as bacterial infections, biofilm formation, and bacterial adhesion to surfaces. In this review, we focus on recent developments offered by the rapid advances in AFM imaging and force spectroscopy with emphasizes on microbial research.     

Lehmann effect in a compensated cholesteric liquid crystal: Experimental evidence with fixed and gliding boundary conditions

In a recent letter (Europhys. Lett. 80, 26001 (2007)), we have shown that a compensated cholesteric liquid crystal (in which the macroscopic helix completely unwinds) may be subjected to a thermomechanical torque (the so-called Lehmann effect), in agreement with previous findings of éber and Jánossy (Mol. Cryst. Liq. Cryst. Lett. 72, 233 (1982)). These results prove that one must take into account the chirality of the molecules and the absence of inversion symmetry at the macroscopic scale when deriving the constitutive equations of the phase at the compensation temperature. In this paper, we present the details of our experimental work and a new experiment performed in a sample treated for planar gliding anchoring. The latter experiment, coupled with a numerical simulation, supports the existence of a thermomechanical coupling in a compensated cholesteric.     

A simulation model of biofilms with autonomous cells: I. Analysis of a two-dimensional version

We introduce a single-cell based simulation model of biofilm growth. Each microbial cell is modelled as an autonomous agent whose behavior is controlled by thermodynamic parameters, mechanical properties, physiological rules and environmental conditions. In the two-dimensional version presented here, a cell is represented by a closed chain of self-avoiding beads linked together using the bond fluctuation algorithm. The cell is thus controlled both by the rigidity of its membrane and a pressure difference. The model is complemented by key features such as the explicit presence of nutrient diffusion and flow, the processes of cell-division and cell-death, and the attractive interactions between the cell and the surface on which the colony grows. Tuning the parameters of the model can lead to the growth and maturation of various types of biofilms. In this first article, we describe the main properties of a two-dimensional version of the model, and we discuss the extension to three dimensions.     

Role of spectral cues in median plane localization

The role of spectral cues in the sound source to ear transfer function in median plane sound localization is investigated in this paper. At first, transfer functions were measured and analyzed. Then, these transfer functions were used in experiments where sounds from a source on the median plane were simulated and presented to subjects through headphones. In these simulation experiments, the transfer functions were smoothed by ARMA models with different degrees of simplification to investigate the role of microscopic and macroscopic patterns in the transfer functions for median plane localization. The results of the study are summarized as follows: (1) For front-rear judgment, information derived from microscopic peaks and dips in the low-frequency region (below 2 kHz) and the macroscopic patterns in the high-frequency region seems to be utilized; (2) for judgment of elevation angle, major cues exist in the high-frequency region above 5 kHz. The information in macroscopic patterns is utilized instead of that in small peaks and dips.     

Phase-resolved photoacoustic spectroscopy to monitor dental plaque on tooth enamel

Dental plaque is a biofilm on the enamel surface of the teeth, formed by colonizing bacteria. It is essential to monitor the biofilm presence on the surface of the enamel of the teeth, since plaque is a reason for periodontal disease and dental caries. This paper proposes applying photoacoustic spectroscopy to monitor and the phase-resolved photoacoustic method to analyze the biofilm plaque on samples of human dental enamel facets. The biofilm growth occurred in the oral cavity environment at deposition time of 48 and 72?h. Photoacoustic ex vivo monitoring found that: (1) Photoacoustic spectroscopy is a helpful tool to identify the bactericidal effect on dental plaque; (2) the biofilm deposition provides an optical absorption of the Soret band at 410?nm and increase of hydroxyl absorption band; (3) the biofilm thickness by phase-resolved photoacoustic method is in agreement with the literature in situ measurements. These new knowledges may help in development of a greater practicality and safety equipment able to identify and quantify dental biofilm, which may be achieved with low-cost Soret-band light emitting diode as light excitation.     

A novel macroscopic traffic model based on generalized optimal velocity model

In this paper, we adopt the coarse graining method proposed by Lee H K et al. to develop a macroscopic model from the microscopic traffic model-GOVM. The proposed model inherits the parameter p which considers the influence of next-nearest car introduced in the GOVM model. The simulation results show that the new model is strictly consistent with the former microscopic model. Using this macroscopic model, we can avoid considering the details of each traffic on the road, and build more complex models such as road network model easily in the future.     

光波长对平板反应器成膜及产氢特性影响

实验研究了不同光波长对生物膜平板反应器中光合细菌(Rhodopseudomonas palustris CQK 01)吸附、生长及产氢性能的影响。结果表明:在相同条件下,波长为590 nm时形成的生物膜具有最大的细菌覆盖率和生物膜密度,以及较高的产氢性能。不同光波长条件下形成的生物膜均在运行入射光波长为590 nm时产氢速率达到最大。在最佳光波长条件下,底物浓度为60 mmol/L时得到最大产氢速率11.2 mmol/(m~2·h)。     

A higher-order macroscopic model for pedestrian flows

This paper develops a higher-order macroscopic model of pedestrian crowd dynamics derived from fluid dynamics that consists of two-dimensional Euler equations with relaxation. The desired directional motion of pedestrians is determined by an Eikonal-type equation, which describes a problem that minimizes the instantaneous total walking cost from origin to destination. A linear stability analysis of the model demonstrates its ability to describe traffic instability in crowd flows. The algorithm to solve the macroscopic model is composed of a splitting technique introduced to treat the relaxation terms, a second-order positivity-preserving central-upwind scheme for hyperbolic conservation laws, and a fast-sweeping method for the Eikonal-type equation on unstructured meshes. To test the applicability of the model, we study a challenging pedestrian crowd flow problem of the presence of an obstruction in a two-dimensional continuous walking facility. The numerical results indicate the rationality of the model and the effectiveness of the computational algorithm in predicting the flux or density distribution and the macroscopic behavior of the pedestrian crowd flow. The simulation results are compared with those obtained by the two-dimensional Lighthill-Whitham-Richards pedestrian flow model with various model parameters, which further shows that the macroscopic model is able to correctly describe complex phenomena such as “stop-and-go waves” observed in empirical pedestrian flows.     

Modeling the elimination of mature biofilms formed by Staphylococcus aureus and Salmonella spp. Using combined ultrasound and disinfectants

Biofilm formation by foodborne pathogens on food processing surfaces has contributed to numerous disease outbreaks and food recalls. We evaluated the following strategies for elimination of mature biofilm formed by Staphylococcus aureus and Salmonella spp. on stainless steel surfaces: acidic electrolyzed water (AEW), ozone water (OW), or ultrasound (40 kHz) alone, and combinations of ultrasound and disinfectants. The dynamics of elimination by combinations were determined using the Weibull and biphasic models. Treatment with AEW alone reduced the number of biofilm cells by approximately 3.0 log cfu/cm², whereas less than 0.8 log cfu/cm² of cells reduction was observed in biofilm exposed to OW or ultrasound alone, even with treatment for 20 min. The combination of AEW and ultrasound produced an obvious synergistic effect on biofilm reduction, achieving approximately 4.8 log cfu/cm² reduction in Salmonella spp. biofilm. Interestingly, the biphasic model was a better fit than the Weibull model for the elimination process of mature biofilm formed by both pathogens and subjected to a combination of ultrasound and AEW, as determined by smaller values of the statistical parameters RMSE and AIC, although both models could evaluate the dynamic processes. Our findings indicated that a combination of ultrasound and AEW could effectively reduce the biofilm formed by pathogens on food contact surfaces, and that the biphasic model could predict the number of residual cells after biofilm exposure to this intervention approach.     

Discharge characteristics in plasma display cell at high frequency

We present the experimental and simulation studies of the glow discharge plasma in a macroscopic AC plasma display panel cell operating at a high frequency. We find that at high frequencies the plasma from the previous pulse has a significant influence on the discharge properties. The xenon excitation efficiency is larger than that at low frequencies.The discharge mode and efficiency at high frequencies have been discussed in this paper.     

GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows

We have developed a GPU-based molecular dynamics simulation for the study of flows of fluids with anisotropic molecules such as liquid crystals. An application of the simulation to the study of macroscopic flow (backflow) generation by molecular reorientation in a nematic liquid crystal under the application of an electric field is presented. The computations of intermolecular force and torque are parallelized on the GPU using the cell-list method, and an efficient algorithm to update the cell lists was proposed. Some important issues in the implementation of computations that involve a large number of arithmetic operations and data on the GPU that has limited high-speed memory resources are addressed extensively. Despite the relatively low GPU occupancy in the calculation of intermolecular force and torque, the computation on a recent GPU is about 50 times faster than that on a single core of a recent CPU, thus simulations involving a large number of molecules using a personal computer are possible. The GPU-based simulation should allow an extensive investigation of the molecular-level mechanisms underlying various macroscopic flow phenomena in fluids with anisotropic molecules.     

Effect of an aggressive medium on discontinuous deformation of aluminum–magnesium alloy AlMg6

It is experimentally shown that the molecular (chemical) process of surface etching of deformed aluminum–magnesium alloy AlMg6 causes the development of a macroscopic plastic strain step with an amplitude of a few percent. Using numerical simulation of the polycrystalline solid etching process, it is shown that the corrosion front morphology varies during etching from Euclid (flat) to fractal (rough). The results obtained show the key role of the surface state on the development of macroscopic mechanical instability of a material exhibiting the Portevin–Le Chatelier effect.     

棒状分子聚合物溶液的微宏观数值模拟

利用微宏观耦合方法模拟了棒状分子聚合物溶液在平板Couette流动中的复杂流变行为,其中微宏观模型通过非均匀Doi理论来描述.数值模拟中,应用有限体积方法耦合求解了介观尺度上的Smoluchowski方程和宏观尺度上的流场守恒方程.数值结果不仅得到了若干种典型的流动类型,而且还预测了另外两种新的复合瑕疵结构.数值试验表明：棒状分子聚合物的流变结构主要依赖于De数、分子相对尺度以及溶液浓度常数的取值;并且De数对分子指向矢的翻滚周期、随流取向角等微观特性也均有明显影响. 关键词： 棒状分子 聚合物溶液 微宏观模拟