有机肥连续施用对菜田重金属行为的影响——基于地球化学模型研究

2017年起,农业部连续多年出台化肥减量增效行动工作方案,要求适当增加有机肥投入,发展循环农业。但连续施用的有机肥进入土壤后,会对土壤pH、有机质和重金属含量等产生影响,改变土壤重金属行为。科学评估有机肥料施用的影响至关重要。仅通过总含量评估重金属污染风险被认为是片面的,不同化学提取剂提取的重金属含量不能完全代表实际污染状况。地球化学模型具有良好的适用性,比传统的提取方法能够更全面地解释重金属的行为。在集约化农业种植区黄淮海平原,多次施用不同比例的粪源有机肥于旱地菜田,并引入地球化学模型,结合pH依赖性浸出试验,明确连续施肥对菜田土壤重金属行为的主要影响机制。研究发现,有机肥中的铜锌含量远高于土壤中的含量,施用后,它们在土壤中的淋溶浓度随着施用比例增加而显著增加,最多可超过十倍以上,并且活性大大增加,与施肥后溶解性有机物含量的升高呈正相关。不同处理条件下的土壤重金属浸出趋势相似：在中性pH下浸出浓度最低,然后逐渐向强酸和强碱增加,呈现出V型变化。地球化学模型LeachXS展示出较好的模拟结果,其模拟值与实测浓度具有良好的相关性(71.02%)。模拟结果显示,有机肥的施用不会明显改变重金...     

A simulation study of the anomalous osmotic behavior of red cells

The factors responsible for movements of water across cell membranes were described mathematically and incorporated into a model which simulates water balance in the cell. Included in the model are a variable charge and osmotic coefficient of hemoglobin, a Na/K pump whose rate varies with ionic concentrations, and the standard electroneutrality and osmotic equilibrium assumptions. The model was used to investigate the phenomena whereby human red cells placed in media of varying tonicities exhibit steady state volume changes less than those predicted by van't Hoff's Law. The model results showed that this anomalous osmotic behavior was primarily due to changes in the osmotic coefficient of hemoglobin as its concentration in the cell varied. A second factor accounting for a part of this behavior was the alteration in the rate of the Na/K pump due to intracellular ionic concentration changes as cell volume varied. The effect of variable electrical charge on the hemoglobin molecule was found to be in the wrong direction to account for the observed osmotic behavior. Also, this effect was seen to produce relatively large changes in cell membrane potential, a result inconsistent with experimental data. It was concluded from the model results that the anomalous osmotic behavior of human red cells is primarily due to the variation in the osmotic coefficient of hemoglobin as the cell volume changes, and that the variable charge effect on the hemoglobin molecule, if it exists, does not play a role in this response.     

Results from demineralized bone creep tests suggest that collagen is responsible for the creep behavior of bone

Cortical and trabecular bone have similar creep behaviors that have been described by power-law relationships, with increases in temperature resulting in faster creep damage accumulation according to the usual Arrhenius (damage rate approximately exp (-Temp.-1)) relationship. In an attempt to determine the phase (collagen or hydroxyapatite) responsible for these similar creep behaviors, we investigated the creep behavior of demineralized cortical bone, recognizing that the organic (i.e., demineralized) matrix of both cortical and trabecular bone is composed primarily of type I collagen. We prepared waisted specimens of bovine cortical bone and demineralized them according to an established protocol. Creep tests were conducted on 18 specimens at various normalized stresses sigma/E0 and temperatures using a noninvasive optical technique to measure strain. Denaturation tests were also conducted to investigate the effect of temperature on the structure of demineralized bone. The creep behavior was characterized by the three classical stages of decreasing, constant, and increasing creep rates at all applied normalized stresses and temperatures. Strong (r2 > 0.79) and significant (p < 0.01) power-law relationships were found between the damage accumulation parameters (steady-state creep rate d epsilon/dt and time-to-failure tf) and the applied normalized stress sigma/E0. The creep behavior was also a function of temperature, following an Arrhenius creep relationship with an activation energy Q = 113 kJ/mole, within the range of activation energies for cortical (44 kJ/mole) and trabecular (136 kJ/mole) bone. The denaturation behavior was characterized by axial shrinkage at temperatures greater than approximately 56 degrees C. Lastly an analysis of covariance (ANCOVA) of our demineralized cortical bone regressions with those found in the literature for cortical and trabecular bone indicates than all three tissues creep with the same power-law exponents. These similar creep activation energies and exponents suggest that collagen is the phase responsible for creep in bone.     

Hybrid simulation of cellular behavior

MOTIVATION: To be valuable to biological or biomedical research, in silico methods must be scaled to complex pathways and large numbers of interacting molecular species. The correct method for performing such simulations, discrete event simulation by Monte Carlo generation, is computationally costly for large complex systems. Approximation of molecular behavior by continuous models fails to capture stochastic behavior that is essential to many biological phenomena. RESULTS: We present a novel approach to building hybrid simulations in which some processes are simulated discretely, while other processes are handled in a continuous simulation by differential equations. This approach preserves the stochastic behavior of cellular pathways, yet enables scaling to large populations of molecules. We present an algorithm for synchronizing data in a hybrid simulation and discuss the trade-offs in such simulation. We have implemented the hybrid simulation algorithm and have validated it by simulating the statistical behavior of the well-known lambda phage switch. Hybrid simulation provides a new method for exploring the sources and nature of stochastic behavior in cells.     

Solvation free energies of glutamate and its metal complexes: A computer simulation study

Most biological ion channels demonstrate a high degree of selectivity for one type of ion more than others, and in many cases, how they control attaining this is still not clear. So we have studied on some metal ion compounds of glutamate. The Glutamate and its meal ion compounds (Ca²⁺, Na⁺, K⁺ and Li⁺) were first modeled by ab initio calculations and then Monte Carlo simulation was used to calculate solvation free energies and also the complexes free energies for the related structures. The results indicated that Glutamate-Ca²⁺ have more stability in water than other metal ion. Also, it was found out that the more movement in ions; less stability of the structure would result. This trend can be seen both in gas and liquid phase.     

Mechanism of beta-purothionin antimicrobial peptide inhibition by metal ions: molecular dynamics simulation study

Wheat beta-purothionin is a highly potent antimicrobial peptide which, however, is inactivated by metal ions. The key structural properties and mechanisms of inhibition of beta-purothionin were investigated for the first time using unconstrained molecular dynamics simulations in explicit water. A series of simulations were performed to determine effects of temperature and the metal ions. Analyses of the unconstrained simulations allowed the experimentally unavailable structural and dynamic details to be unambiguously examined. The global fold and the alpha1 helix of beta-purothionin are thermally stable and not affected by metal ions. In contrast, the alpha2 helix unfolds with shift of temperature from 300 K and in the presence of metal ions. The network of conserved residues including Arg30 and Lys5 is sensitive to environmental changes and triggers unfolding. Loop regions display high flexibility and elevated dynamics, but are affected by metal ions. Our study provides insights into the mechanism of metal ion-based inhibition.     

A real time finite element based tissue simulation method incorporating nonlinear elastic behavior

This paper presents a new finite element simulation approach for surgical simulators. Based on the solution of the algebraic equations derived from a nonlinear elastic model, we propose a real time simulation rule based on the implicit relation between the displacements of contacted and free nodes. This rule is an analytic expression in the linear case, and an approximation of the implicit relation in the non-linear case. We also remove some of the restrictions on flexibility exhibited by previous linear and nonlinear approaches. In the linear case, real time reconfiguration of the contacted nodes and the boundary constraints is realized using the simulation rule, while in the nonlinear case, a similar result is obtained by employing affine mapping. These methods allow nonlinear material properties to be applied to real time tissue simulation, with an efficiency comparable to that of the tensor matrix method for linear elastic models.     

Reduction reactions of water soluble cyano-cobalt(III)-porphyrins: metal versus ligand centered processes

Reduction reactions of dicyano-cobalt(III)-porphyrins [potential in vivo cyanide scavenger drugs] were studied by radiolytic and electrochemical methods using the water soluble tetrakis(4-sulfonatophenyl)porphyrin (TPPS) and tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP). For [(CN)2CoIIITPPS]-, reduction occurs stepwise to the CoII, CoI, and finally to the phlorin anion. This behavior is similar to that of the cobalt porphyrins in the absence of cyanide, except that the cyanide ligand shifts the reduction potentials to much more negative values. On the other hand, under radiolytic conditions, [(CN)2CoIIITMPyP]- is reduced on the porphyrin macrocycle by one electron to give the CoIII pi-radical anion, which disproportionates into the initial complex and the two-electron ring reduced CoIII phlorin. The radical anion is also formed by intramolecular electron transfer subsequent to the reaction of CoIITMPyP and cyanide. The results are compared with the chemistry of Vitamin B-12.     

Computer simulation of Paramecium chemokinesis behavior

A computer program was designed to simulate the distribution of paramecia in a T-maze assay for chemo-accumulation and dispersal. Simulated values of chemokinesis are compared to experimental values for normal and mutant paramecia. The roles of components of swimming behavior (turning frequency and swimming speed), adaptation, and reaction at the border of solutions are examined.     

Molecular dynamics simulation of the size-dependent morphological stability of cubic shape silver nanoparticles

The morphological stability of sharp-edged silver nanoparticles is examined by the classical molecular dynamics (MD) simulations. The crystalline structure and the perfect fcc atom packing of a series of silver nanocubes (AgNC) of different sizes varying from 63 up to 1099 atoms are compared against quasi-spherical nanoparticles of the same sizes at temperature 303 K. Our MD simulations demonstrate that starting from the preformed perfect crystalline structures the cubic shape is preserved for AgNCs composed of 365–1099 atoms. Surprisingly, the rapid loss of the cubic shape morphology and transformation into the non-fcc-structure are found for smaller AgNCs composed of less than ~256 atoms. No such loss of the preformed crystalline structure is seen for quasi-spherical nanoparticles composed of 38–1007 atoms. The analysis of the temperature dependence and the binding energy of outermost Ag surface atoms suggests that the loss of the perfect cubic shape, rounding and smoothing of sharp edges and corners are driven by the tendency towards the increase in their coordination number. In addition, we revealed that AgNC₁₀₉₉ partially loses its sharp edges and corners in the aqueous environment; however, the polymer coating with poly(vinyl alcohol) (PVA) was able to preserve the well-defined cubic morphology. Finally, these results help improve the understanding of the role of surface capping agents in solution phase synthesis of Ag nanocubes.     

Finite element simulation of early creep and wear in total hip arthroplasty

Polyethylene wear particulate has been implicated in osteolytic lesion development and may lead to implant loosening and revision surgery. Wear in total hip arthroplasty is frequently estimated from patient radiographs by measurement of penetration of the femoral head into the polyethylene liner. Penetration, however, is multi-factorial, and includes components of wear and deformation due to creep. From a clinical perspective, it is of great interest to separate these elements to better evaluate true wear rates in vivo. Thus, the aim of this study was to determine polyethylene creep and wear penetration and volumetric wear during simulated gait loading conditions for variables of head size, liner thickness, and head–liner clearance. A finite element model of hip replacement articulation was developed, and creep and wear simulation was performed to 1 million gait cycles. Creep of the liner occurred quickly and increased the predicted contact areas by up to 56%, subsequently reducing contact pressures by up to 41%. Greater creep penetration was found with smaller heads, thicker liners, and larger clearance. The least volumetric wear but the most linear penetration was found with the smallest head size. Although polyethylene thickness increases from 4 to 16 mm produced only slight increases in volumetric wear and modest effects on total penetration, the fraction of creep in total penetration varied with thickness from 10% to over 50%. With thicker liners and smaller heads, creep will comprise a significant fraction of early penetration. These results will aid an understanding of the complex interaction of creep and wear.     

The behavior of adaptive bone-remodeling simulation models

The process of adaptive bone remodeling can be described mathematically and simulated in a computer model, integrated with the finite element method. In the model discussed here, cortical and trabecular bone are described as continuous materials with variable density. The remodeling rule applied to simulate the remodeling process in each element individually is, in fact, an objective function for an optimization process, relative to the external load. Its purpose is to obtain a constant, preset value for the strain energy per unit bone mass, by adapting the density. If an element in the structure cannot achieve that, it either turns to its maximal density (cortical bone) or resorbs completely.

It is found that the solution obtained in generally a discontinuous patchwork. For a two-dimensional proximal femur model this patchwork shows a good resemblance with the density distribution of a real proximal femur.

It is shown that the discontinuous end configuration is dictated by the nature of the differential equations describing the remodeling process. This process can be considered as a nonlinear dynamical system with many degrees of freedom, which behaves divergent relative to the objective, leading to many possible solutions. The precise solution is dependent on the parameters in the remodeling rule, the load and the initial conditions. The feedback mechanism in the process is self-enhancing; denser bone attracts more strain energy, whereby the bone becomes even more dense. It is suggested that this positive feedback of the attractor state (the strain energy field) creates order in the end configuration. In addition, the process ensures that the discontinuous end configuration is a structure with a relatively low mass, perhaps a minimal-mass structure, although this is no explicit objective in the optimization process.

It is hypothesized that trabecular bone is a chaotically ordered structure which can be considered as a fractal with characteristics of optimal mechanical resistance and minimal mass, of which the actual morphology depends on the local (internal) loading characteristics, the sensor-cell density and the degree of mineralization.     

Modulation of biomolecular phase behavior by metal ions

Liquid–liquid phase separation (LLPS) appears to be a newly appreciated aspect of the cellular organization of biomolecules that leads to the formation of membraneless organelles (MLOs). MLOs generate distinct microenvironments where particular biomolecules are highly concentrated compared to those in the surrounding environment. Their thermodynamically driven formation is reversible, and their liquid nature allows them to fuse with each other. Dysfunctional biomolecular condensation is associated with human diseases. Pathological states of MLOs may originate from the mutation of proteins or may be induced by other factors. In most aberrant MLOs, transient interactions are replaced by stronger and more rigid interactions, preventing their dissolution, and causing their uncontrolled growth and dysfunction. For these reasons, there is great interest in identifying factors that modulate LLPS. In this review, we discuss an enigmatic and mostly unexplored aspect of this process, namely, the regulatory effects of metal ions on the phase behavior of biomolecules.     

A comparative study of the effects of dimethylsulfoxide and glycerol on the bicontinuous cubic structure of hydrated monoolein and its phase behavior

Both dimethylsulfoxide (DMSO) and glycerol act cryoprotectants for biological systems and materials. Knowledge of molecular interactions of DMSO and glycerol with biological lipids is important for understanding of their cryoprotecitive mechanisms. In this study, the phase behavior and structures of hydrated monoolein were investigated in the presence of DMSO or glycerol, using differential scanning calorimetry (DSC) and simultaneous X-ray diffraction/DSC measurements. Based on the results obtained by this study, partial phase diagrams were constructed as a function of DMSO or glycerol concentrations and temperature. DMSO and glycerol hardly affect the enthalpy value for melting temperature of lamellar crystal phase of monoolein and the structure. On the other hand, DMSO and glycerol greatly affect the phase transformations associated with bicontinuous cubic phases of monoolein and the cubic phase structures. DMSO expands Im3m/Pn3m cubic phase co-existence region in the phase diagram and increases the lattice constant of the Pn3m monoolein cubic phase. Glycerol shows opposite effects. The present study suggests that different mechanisms act in the cryopreservation by DMSO and glycerol.     

Phase behavior and dynamic heterogeneities in lipids: A coarse-grained simulation study of DPPC-DPPE mixtures

The coarse-grained Marrink-model for biomembrane simulation is used to study mixtures of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylethanolamine (DPPE) at various concentrations and temperatures. At high temperatures close to ideal mixing is observed. In the low temperature ordered phase dynamic heterogeneities are identified under some conditions. These are correlated with heterogeneities in the local order and define local neighborhoods.     

Phase behavior and dynamic heterogeneities in lipids: a coarse-grained simulation study of DPPC-DPPE mixtures

The coarse-grained Marrink-model for biomembrane simulation is used to study mixtures of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylethanolamine (DPPE) at various concentrations and temperatures. At high temperatures close to ideal mixing is observed. In the low temperature ordered phase dynamic heterogeneities are identified under some conditions. These are correlated with heterogeneities in the local order and define local neighborhoods.     

基于栖息地恢复对群落不同种群演化影响的模拟

通过建立基于栖息地恢复的多种群演化动力学模式,模拟了不同群落结构的不同物种种群的演化特点。模拟结果发现了两类灭绝机制,揭示了(1)小规模栖息地的恢复对群落中的弱小物种的影响是非常有限的,不会给弱小物种种群带来灭绝风险。大幅度的栖息地增加几乎使所有的物种种群都在最初数百年中内都有出现一定的增加,特别是竞争能力最强的物种,其幅度的增加最为显著,但次最强的物种种群可能会在千年左右灭绝。群落内幸存的种群将经历3个阶段迅速壮大(增加)阶段震荡阶段稳定阶段;(2)存在着协同现象,栖息地减少所导致种群的协同演化规律与栖息地恢复所导致的种群的演化规律两者之间既有共同点,又有不同点。毁坏是一种破坏,大规模的栖息地的恢复对已适应于破坏后新环境的某些物种也可能是一种威胁,这类似于生态入侵的初始阶段。