scholarly journals Microbial diversity affects self-organization of the soil–microbe system with consequences for function

2011 ◽  
Vol 9 (71) ◽  
pp. 1302-1310 ◽  
Author(s):  
John W. Crawford ◽  
Lewis Deacon ◽  
Dmitri Grinev ◽  
James A. Harris ◽  
Karl Ritz ◽  
...  
Keyword(s):  
Structural Changes ◽  
Bacterial Biomass ◽  
Soil Nutrient ◽  
Physical Structure ◽  
Self Organization ◽  
Pore Scale ◽  
Lattice Boltzmann Simulation ◽  
Unique Material ◽  
Terrestrial Life ◽  
Measured Change

Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits.

scholarly journals Protein Sensing Device with Multi-Recognition Ability Composed of Self-Organized Glycopeptide Bundle

2020 ◽  
Vol 22 (1) ◽  
pp. 366
Author(s):  
Mao Arai ◽  
Tomohiro Miura ◽  
Yuriko Ito ◽  
Takatoshi Kinoshita ◽  
Masahiro Higuchi
Keyword(s):  
Binding Site ◽  
Lipid Bilayer ◽  
Structural Changes ◽  
Bilayer Membrane ◽  
Lipid Bilayer Membrane ◽  
Target Protein ◽  
Self Organization ◽  
Specific Response ◽  
Target Proteins ◽  
Recognition Ability

We designed and synthesized amphiphilic glycopeptides with glucose or galactose at the C-terminals. We observed the protein-induced structural changes of the amphiphilic glycopeptide assembly in the lipid bilayer membrane using transmission electron microscopy (TEM) and Fourier transform infrared reflection-absorption spectra (FTIR-RAS) measurements. The glycopeptides re-arranged to form a bundle that acted as an ion channel due to the interaction among the target protein and the terminal sugar groups of the glycopeptides. The bundle in the lipid bilayer membrane was fixed on a gold-deposited quartz crystal microbalance (QCM) electrode by the membrane fusion method. The protein-induced re-arrangement of the terminal sugar groups formed a binding site that acted as a receptor, and the re-binding of the target protein to the binding site induced the closing of the channel. We monitored the detection of target proteins by the changes of the electrochemical properties of the membrane. The response current of the membrane induced by the target protein recognition was expressed by an equivalent circuit consisting of resistors and capacitors when a triangular voltage was applied. We used peanut lectin (PNA) and concanavalin A (ConA) as target proteins. The sensing membrane induced by PNA shows the specific response to PNA, and the ConA-induced membrane responded selectively to ConA. Furthermore, PNA-induced sensing membranes showed relatively low recognition ability for lectin from Ricinus Agglutinin (RCA120) and mushroom lectin (ABA), which have galactose binding sites. The protein-induced self-organization formed the spatial arrangement of the sugar chains specific to the binding site of the target protein. These findings demonstrate the possibility of fabricating a sensing device with multi-recognition ability that can recognize proteins even if the structure is unknown, by the protein-induced self-organization process.

Evaluating the interaction of biofilms, organic matter and soil structures at the pore scale

2021 ◽  
Author(s):  
Alexander Prechtel ◽  
Simon Zech ◽  
Alice Lieu ◽  
Raphael Schulz ◽  
Nadja Ray
Keyword(s):  
Organic Matter ◽  
Structural Changes ◽  
Effective Diffusivity ◽  
Computational Domain ◽  
Pore Scale ◽  
Gas Phases ◽  
Soil Structures ◽  
Ldg Method ◽  
Conventional Models ◽  
Diffusive Processes

<div class="description js-mathjax"> <p>Key functions of soils, such as permeability or habitat for microorganisms, are determined by structures at the microaggregate scale. The evolution of elemental distributions and dynamic processes can often not be assessed experimentally. So mechanistic models operating at the pore scale are needed.<br />We consider the complex coupling of biological, chemical, and physical processes in a hybrid discrete-continuum modeling approach. It integrates dynamic wetting (liquid) and non-wetting (gas) phases including biofilms, diffusive processes for solutes, mobile bacteria transforming into immobile biomass, and ions which are prescribed by means of partial differential equations. Furthermore the growth of biofilms as, e.g., mucilage exuded by roots, or the distribution of particulate organic matter in the system, is incorporated in a cellular automaton framework (CAM) presented in [1, 2]. It also allows for structural changes of the porous medium itself (see, e.g. [3]). As the evolving computational domain leads to discrete discontinuities, we apply the local discontinuous Galerkin (LDG) method for the transport part. Mathematical upscaling techniques incorporate the information from the pore to the macroscale [1,4].<br />The model is applied for two research questions: We model the incorporation and turnover of particulate OM influencing soil aggregation, including ‘gluing’ hotspots, and show scenarios varying of OM input, turnover, or particle size distribution. <br />Second, we quantify the effective diffusivity on 3D geometries from CT scans of a loamy and a sandy soil. Conventional models cannot account for natural pore geometries and varying phase properties. Upscaling allows also to quantify how root exudates (mucilage) can significantly alter the macroscopic soil hydraulic properties.</p> </div> <div id="field-23"> <p>[1]  Ray, Rupp, Prechtel (2017). AWR (107), 393-404.<br />[2] Rupp, Totsche, Prechtel, Ray (2018). Front. Env. Sci. (6) 96.<br />[3] Zech, Dultz, Guggenberger, Prechtel, Ray (2020). Appl. Clay Sci. 198, 105845.<br />[4] Ray, Rupp, Schulz, Knabner (2018). TPM 124(3), 803-824.</p> </div>

Near-Infrared Spectroscopic Measurements of Structural Changes in Starch-Containing Extruded Products

1996 ◽  
Vol 50 (9) ◽  
pp. 1134-1139 ◽  
Author(s):  
S. Millar ◽  
P. Robert ◽  
M. F. Devaux ◽  
R. C. E. Guy ◽  
P. Maris
Keyword(s):  
Structural Changes ◽  
Near Infrared ◽  
Mechanical Energy ◽  
Principal Component ◽  
Physical Structure ◽  
Extrusion Cooking ◽  
Absorption Bands ◽  
Energy Inputs ◽  
Specific Mechanical Energy ◽  
Extruded Products

Near-infrared spectroscopy was evaluated as a means of following physical and chemical changes in starch during the extrusion cooking of wheat flour under the Measurements and Testing Program of the European Commission. With the use of principal component (PC) and canonical correlation (CC) analyses, samples could be classified according to the severity of the extrusion cooking conditions. An interpretation of the spectra showed that the different processing conditions modified the physical structure of the starch molecules. At low values of specific mechanical energy inputs, starch was partially crystalline and the near-infrared spectra exhibited characteristic absorption bands at about 1428, 1520, and 1587 nm. As the energy inputs increased, causing a change to molten starch, the intensity of the bands at 1520 and 1587 nm decreased, with a shift of the 1428-nm absorption band towards longer wavelengths also being observed. The changes that occurred were thought to be due to a disruption of the intra- and intermolecular hydrogen bonding of the starch. At the higher levels of specific mechanical energy inputs, the starch molecules underwent further structural modification, resulting in their partial degradation.

Lattice Boltzmann Simulation of Lithium Peroxide Formation in Lithium–Oxygen Battery

2016 ◽  
Vol 13 (3) ◽  
Author(s):  
M. Jithin ◽  
Malay K. Das ◽  
Ashoke De
Keyword(s):  
Porous Media ◽  
Lattice Boltzmann ◽  
Pore Scale ◽  
Peroxide Formation ◽  
Initial Current ◽  
Lattice Boltzmann Simulation ◽  
Lithium Peroxide ◽  
Lower Porosity ◽  
Lithium Oxygen Battery ◽  
Boltzmann Method

Present research deals with multiphysics, pore-scale simulation of Li–O2 battery using multirelaxation time lattice Boltzmann method. A novel technique is utilized to generate an idealized electrode–electrolyte porous media from the known macroscopic variables. Present investigation focuses on the performance degradation of Li–O2 cell due to the blockage of the reaction sites via Li2O2 formation. Present simulations indicate that Li–air and Li–O2 batteries primarily suffer from mass transfer limitations. The study also emphasizes the importance of pore-scale simulations and shows that the morphology of the porous media has a significant impact on the cell performance. While lower porosity provides higher initial current, higher porosity maintains sustainable output.

scholarly journals Self-Organization Characteristics of Lunar Regolith Inferred by Yutu-2 Lunar Penetrating Radar

2021 ◽  
Vol 13 (15) ◽  
pp. 3017
Author(s):  
Xiang Zhang ◽  
Wenmin Lv ◽  
Lei Zhang ◽  
Jinhai Zhang ◽  
Yangting Lin ◽  
...  
Keyword(s):  
Root Mean Square ◽  
Structural Changes ◽  
Structural Characteristics ◽  
Lunar Regolith ◽  
Homogeneous Medium ◽  
Self Organization ◽  
Mean Square ◽  
Organization Model ◽  
Correlation Distance ◽  
Regolith Layer

Most previous studies tend to simplify the lunar regolith as a homogeneous medium. However, the lunar regolith is not completely homogeneous, because there are weak reflections from the lunar regolith layer. In this study, we examined the weak heterogeneity of the lunar regolith layer using a self-organization model by matching the reflection pattern of both the lunar regolith layer and the top of the ejecta layer. After a series of numerical experiments, synthetic results show great consistency with the observed Chang’E-4 lunar penetrating radar data and provide some constraints on the range of controlling parameters of the exponential self-organization model. The root mean square permittivity perturbation is estimated to be about 3% and the correlation distance is about 5–10 cm. Additionally, the upper layer of ejecta has about 1–2 rocks per square meter, and the rock diameter is about 20–30 cm. These parameters are helpful for further study of structural characteristics and the evolution process of the lunar regolith. The relatively small correlation distance and root mean square perturbation in the regolith indicate that the regolith is mature. The weak reflections within the regolith are more likely to be due to structural changes rather than material composition changes.

scholarly journals The Effect of Atmospheric Plasma on Cold Thermal Stability of Powdered Whey Protein Isolate

2018 ◽  
Author(s):  
Michael D Birnbaum
Keyword(s):  
Thermal Stability ◽  
Whey Protein ◽  
Structural Changes ◽  
Thermal Conditions ◽  
Whey Protein Isolate ◽  
Physical Structure ◽  
Protein Isolate ◽  
Atmospheric Plasma ◽  
Relative Temperature ◽  
Food Applications

Thermostability is the capacity of a material to withstand irreversible change in its structure by resisting extreme external factors such as high relative temperature. Extensive efforts toward making protein-based biological substances such as vaccines thermally stable have been made by implementing treatments such as lyophilisation, biomineralization, and encapsulation in sugar glass and organic polymers. These substances have a typically short shelf life, as they denature and degrade at room temperature over time. Furthermore, efficient storage and distribution relies on continuous refrigeration in order to preserve protein stability. However, this is costly and not always effective, as any disturbance in storage and distribution conditions may lead to rapid loss of effectiveness and potency. Whey protein isolate is used in a wide variety of food applications and is at risk of exposure to freezing temperatures during its transportation, which in turn could affect its stability as well as chemical and physical structure. This study examines the effects of plasma surface modification (PSM) on whey protein thermostability. Here we report on structural changes in commercially available whey protein exposed to cold thermal conditions, as reported by the Protein Thermal Shift Assay (PTSA). An improvement of 48% in protein thermal stability was observed upon treatment with PSM, suggesting that PSM may reduce damage caused by temperature fluctuations.

scholarly journals E-Commerce Credit Risk Assessment Based on Fuzzy Neural Network

2022 ◽  
Vol 2022 ◽  
pp. 1-10
Author(s):  
Lina Wang ◽  
Hui Song
Keyword(s):  
Supply Chain ◽  
Credit Risk ◽  
Parameter Optimization ◽  
Structural Changes ◽  
Electronic Device ◽  
Self Organization ◽  
Principal Component Factor Analysis ◽  
The Core ◽  
Optimization Mechanism ◽  
Organization Mechanism

In this paper, we propose a cooperative strategy-based self-organization mechanism to reconstruct the network. The mechanism includes a comprehensive evaluation algorithm and structure adjustment mechanism. The self-organization mechanism can be carried out simultaneously with the parameter optimization process. By calculating the similarity and independent contribution of normative neurons, the effectiveness of fuzzy rules can be jointly evaluated, and effective structural changes can be realized. Moreover, this mechanism should not set the threshold in advance in practical application. In order to optimize the parameters of SC-IR2FNN, we developed a parameter optimization mechanism based on an interaction strategy. The parameter optimization mechanism based on a joint strategy, namely multilayer optimization engine, can split SC-IR2FNN parameters into nonlinear and linear parameters for joint optimization. The nonlinear parameters are optimized by an advanced two-level algorithm, and the linear parameters are updated with the minimum biological multiplication. Two parameter optimization algorithms optimize nonlinear and linear parameters, reduce the computational complexity of SC-IR2FNN, and improve the learning rate. Using the principal component factor analysis method, seven representative common factors are selected to replace the original variables, which include the profitability factor of the financing enterprise, the solvency factor of the financing enterprise, the profitability factor of the core enterprise, the operation guarantee factor, and the growth ability of the financing enterprise. Factors, supply chain online degree factors, financing enterprise quality, and cooperation factors, can well measure the credit risk of online supply chains. The logistic model shows that the profitability factor of the financing company, the debt repayment factor of the financing company, and the profitability of the core company are three factors that have a significant impact on the credit risk of online supply chain finance. Based on the improved credit calculation model, we developed an online clue risk calculation. This method is based on site conditions and can evaluate credit risk. From the test results, the improved credit scoring system is the result of facing speculative and circular credit fraud and implies that the traders of risk commentators are in a leading position in each electronic device. The results show that risk analysis is effective in any case.

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