A diffusion model for mesoderm induction in amphibian embryos

In this paper we try to answer the question whether diffusion is a possible mechanism to explain mesoderm induction in Amphibians. First the embryological data are discussed and a hypothesis for mesoderm formation is set forth. The blastula being essentially a hollow sphere, we assume that the induction mechanism in an embryo at the blastula stage can be simulated by diffusion-reaction processes on spherical surfaces. A model is constructed for the simple case when the source is held constant with respect to time, the decay proportional to the concentration and the diffusion coefficient a constant, From simulation we find a (best) value for the decay constant to be 6 × 10^–5/sec and for the diffusion constant to be 0.24 × 10^{– 6} cm²/sec. The relation between the parameters is derived from an analytic solution for the diffusion process on a spherical surface with a continuously producing point source and the concentration proportional to the decay. The form and regulative properties of the steady concentration gradient are discussed.     

Ion Diffusion Selectivity in Lecithin-Water Lamellar Phases

The diffusion coefficients of Na⁺, Rb⁺, and cl^- were determined in lecithin-water lamellar phases at 18°C as a function of phase hydration. Diffusion was measured within the phase with no transfer between phase and bulk aqueous medium. The relative diffusion coefficients of anion and cation depended strongly on phase hydration. At low water content, the diffusion coefficient of Cl^- was greater than that of Na⁺ or Rb⁺ whereas at high water content both cations diffused faster than the anion. The change in relative diffusion coefficient occurred at 0.24 g water/g phase (24% water). The possibility that a change in conformation of the lecithin polar head occurs at a phase water content of 24% is considered. The diffusion coefficients of all three ions decreased at the water content where the relative diffusion rates inverted. Freeze fracture and polarizing microscopy studies were carried out to obtain information on phase structure. The latter study indicated that a change in long-range organization of the phase occured at 24% water. This change accounts for the decrease in the ion diffusion coefficients at this water content. The change in conformation of the choline phosphate group proposed as an explanation for the change in ion selectivity could lead to changes in long-range organization of the phase as a second order-effect.     

Lateral diffusion of gramicidin S,M-13 coat protein and glycophorin in bilayers of saturated phospholipids: Mean field and Monte Carlo studies

We have developed a general model that relates the lateral diffusion coefficient of one isolated large intrinsic molecule (mol. wt. ?1000) in a phosphatidylcholine bilayer to the static lipid hydrocarbon chain order. We have studied how protein lateral diffusion can depend upon protein-lipid interactions but have not investigated possible non-specific contributions from gel-state lattice defects. The model has been used in Monte Carlo simulations or in mean-field approximations to study the lateral diffusion coefficients of Gramicidin S, the M-13 coat protein and glycophorin in dimyristoyl- and dipalmitoylphosphatidylcholine (DMPC and DPPC) bilayers as functions of temperature. Our calculated lateral diffusion coefficients for Gramicidin S and the M-13 coat protein are in good agreement with what has been observed and suggest that Gramicidin S is in a dimeric form in DMPC bilayers. In the case of glycophorin we find that the ‘ice breaker’ effect can be understood as a consequence of perturbation of the lipid polar region around the protein. In order to understand this effect is is necessary that the protein hydrophilic section perturb the polar regions of at least approx. 24 lipid molecules, in good agreement with the numbers of 29–30 measured using ³¹P-NMR. Because of lipid-lipid interactions this effect extends itself out to four or five lipid layers away from the protein so that the hydrocarbon chains of between approx. 74 and approx. 108 lipid molecules are more disordered in the gel phase, so contributing less to the transition enthalpy, in agreement with the numbers of 80–100 deduced from differential scanning calorimetry (DSC). An understanding of the abrupt change in the diffusion coefficient at a temperature below the main bilayer transition temperature requires an additional mechanism. We propose that this change may be a consequence of a ‘coupling-uncoupling’ transition involving the protein hydrophilic section and the lipid polar regions, which may be triggered by the lipid bilayer pretransition. Our calculation of the average number of gauche bonds per lipid chain as a function of temperature and distance away from an isolated polypeptide or integral protein shows the extent of statically disordered lipid around such molecules. The range of this disorder depends upon temperature, particularly near the main transition.     

Diffusion and Electric Mobility of KCI within Isolated Cuticles of Citrus aurantium

Fick's second law has been used to predict the time course of electrical conductance change in isolated cuticles following the rapid change in bathing solution (KCI) from concentration C to 0.1 C. The theoretical time course is dependent on the coefficient of diffusion of KCI in the cuticle and the cuticle thickness. Experimental results, obtained from cuticles isolated from sour orange (Citrus aurantium), fit with a diffusion model of an isolated cuticle in which about 90% of the conductance change following a solution change is due to salts diffusing from polar pores in the wax, and 10% of the change is due to salt diffusion from the wax. Short and long time constants for the washout of KCI were found to be 0.11 and 3.8 hours, respectively. These time constants correspond to KCI diffusion coefficients of 1 × 10⁻¹⁵ and 3 × 10⁻¹⁷ square meters per second, respectively. The larger coefficient is close to the diffusion coefficient for water in polar pores of Citrus reported elsewhere (M Becker, G Kerstiens, J Schönherr [1986] Trees 1: 54-60). This supports our interpretation of the washout kinetics of KCI following a change in concentration of bathing solution.     

Simulation of protein diffusion: a sensitive probe of protein–solvent interactions

Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (R_S), which was derived from the diffusion coefficient and the viscosity. R_S was compared to the geometric radius (R_G) of CALB, which was derived from the protein density. R_S and R_G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.     

Measurement of the apparent diffusion coefficient of N‐butane in soil

Measurements of in‐soil diffusion coefficients and the application of an appropriate diffusional model can allow for a more accurate prediction of soil gas concentrations and movement to locate subterranean contamination of volatile materials. The present study was undertaken to measure and evaluate the “apparent in‐soil diffusion coefficient”; for n‐butane through soil columns under non‐steady‐state conditions. The term “apparent in‐soil diffusion coefficient”; refers to a numerical coefficient that primarily describes the movement of the material by diffusion but also contains effects due to other mechanisms (e.g., adsorption and solubility).

Six test columns were evaluated at three soil porosity levels ranging from 0.30 to 0.43 and at two column temperature conditions, nominally 18°C and 7°C. Soil columns measured 25.4 cm in diameter by 84 cm in height and contained a moist sand/silt/clay mixture. The numerical range for the apparent in‐soil diffusion coefficients for n‐butane was 0.447 × 10^‐3cm²/s to 0.561 × 10^‐3cm²/s. The lower coefficient values were associated with lower soil porosity levels and cooler column conditions.     

Diffusion of phenol through a biofilm grown on activated carbon particles in a draft-tube three-phase fluidized-bed bioreactor

Diffusion of phenol through a biofilm attached to activated carbon particles was investigated. The biofilm was grown on activated carbon particles in a draft-tube three-phase fluidized-bed bioreactor operating in a fed-batch mode. It was found that phenol did not adsorb on the biofilm and that the diffusion coefficient of phenol within the biofilm varied from 13 to 39% of its corresponding value in water. The diffusion coefficient of phenol within the biofilm was reduced by increasing the biofilm density. An extensive literature review of diffusion of substrates through biofilms indicated that this conclusion could be extended to biofilms grown on flat surfaces, rotating cylinders, and even bioflocs.     

Permeability of lysozyme tetragonal crystals to water

Diffusion of water within cross-linked tetragonal crystals of hen egg-white lysozyme has been measured and simulated on a computer using the X-ray structure of water-filled channels within the crystal lattice. Relative to the self-diffusion coefficient of bulk water molecules, the experimental diffusion coefficient of water within the crystal was found to be 13 times reduced in the (001) crystallographic plane and 5 times reduced in the [001] direction. Comparison of the experimental and computer simulated diffusion coefficients shows that steric limitations for water diffusion are mostly responsible for this reduction of the water diffusion in the crystal, with the self-diffusion coefficient of intracrystalline water reduced by no more than 30–40% as compared to that of bulk water.     

Determination of internal diffusion limitation and its macroscopic kinetics of the transesterification of CPB alcohol catalyzed by immobilized lipase in organic media

Optically active cyanohydrin esters such as (S)-α-cyano-3-phenoxybenzyl (CPB) acetate can be obtained with enzymatic transesterification of racemic cyanohydrins in organic media. The influence of internal diffusion limitation on transesterification of CPB alcohol with vinyl acetate catalyzed by immobilized lipase was studied. Internal diffusion limitation could not be ignored since the immobilized lipase granule was not small enough. In order to express the effect of internal diffusion limitation quantitatively, a method was proposed which calculates the effective diffusion coefficient (D_e) first and then calculates apparent Thiele modulus (Φ) and finally obtains internal diffusion effectiveness factor, η value (0.55). D_e was calculated to be 3.1 × 10⁻¹⁰ m² s⁻¹ by supposing that the immobilized lipase was a sphere granule and the diffusion only existed in one dimension. Φ was calculated to be 2.2 by presuming that transport of substrate through the catalyst could be described by Fick's law. Using King–Altman method, a kinetic model of the transesterification of CPB alcohol with vinyl acetate in organic media in the presence of internal diffusion limitation was proposed based on ping-pong bi–bi mechanism. The relative error of the model was 11.18%. A practicable method to evaluate η value and relatively simple model for such kind of reaction system was proposed in this paper.     

Modification of valinomycin-mediated bilayer membrane conductance by 4,5,6,7-tetrachloro-2-methylbenzimidazole

Summary The compound, 4,5,6,7-tetrachloro-2-methylbenzimidazole (TMB), has been found to markedly modify the steady-state valinomycin-mediated conductance of potassium (K⁺) ions through lipid bilayer membranes. TMB alone does not contribute significantly to membrane conductance, being electrically neutral in solution. In one of two classes of experiments (I), valinomycin is first added to the aqueous phases then changes of membrane conductance accompanying stepwise addition of TMB to the water are measured. In a second class of experiments (II), valinomycin is added to the membrane-forming solution, follwed by TMB additions to the surrounding water. In both cases membrane conductance shows an initial increase with increasing TMB concentration which is more pronounced at lower K⁺ ion concentration. At TMB concentrations in excess of 10^–5 m, membrane conductance becomes independent of K⁺ ion concentration, in contrast to the linear dependence observed at TMB concentrations below 10^–7 m. This transition is accompanied by a change of high field current-voltage characteristics from superlinear (or weakly sublinear) to a strongly sublinear form. All of these observations may be correlated by the kinetic model for carriermedicated transport proposed by Läuger and Stark (Biochim. Biophys. Acta 211:458, 1970) from which it may be concluded that valinomycin-mediated ion transport is limited by back diffusion of the uncomplexed carrier at high TMB concentrations. Experiments of class I reveal a sharp drop of conductance at high (>10^–5 m) TMB concentration, not seen in class II experiments, which is attributed to blocked entry of uncomplexed carrier from the aqueous phases. Valinomycin initially in the membrane is removed by lateral diffusion to the surrounding torus. The time dependence of this removal has been studied in a separate series of experiments, leading to a measured coefficient of lateral diffusion for valinomycin of 5×10^–6 cm²/sec at 25°C. This value is about two orders of magnitude larger than the corresponding coefficient for transmembrane carrier diffusion, and provides further evidence for localization of valinomycin in the membrane/solution interfaces.     

Radionuclide transport model for risk evaluation of high-level radioactive waste in Northwestern China

The proper disposal of high-level radioactive waste (HLRW) is highly challenging. Numerical simulations are helpful methods of evaluating the risks of radionuclide transport. This paper examines the hydrogeological conditions of a prospective HLRW repository in China. A regional radionuclide transport model is first constructed using the TOUGH2-MP/EOS7R module at a site in northwestern China to evaluate radionuclide transport behavior. A flow model calibration under a steady state shows that the simulated and observed hydraulic heads match well. Hypothetical radionuclides (⁹⁰Sr, ¹³⁷Cs, ²³⁵U and ²³⁹Pu) are assumed to be instantaneously released at three locations with large groundwater velocities. Transport modeling shows that ²³⁵U is the most sensitive element and has the plume size (2400 m) after 10,000 years. Sensitivity analyses of parameters, including the permeability, distribution coefficient and diffusion coefficient, are carried out. The results show that the distribution coefficient is the most critical parameter for nuclide transport. These findings will provide a preliminary reference for the radionuclide migration process at a prospective HLRW disposal site, which could be informative for safety analyses and further transport in and around the repository system.     

A food web model for fate and direct and indirect effects of Dursban® 4E (active ingredient chlorpyrifos) in freshwater microcosms

An integrated fate and effects model was constructed to simulate direct and indirect effects of chlorpyrifos in experimental indoor ecosystems (microcosms) without macrophytes. These microcosms resembled the ubiquitous drainage ditches in the Netherlands. Observed densities of algae, zooplankton and macrofauna were converted to biomass (g DW m−2) for calibration of a bio-energetics model based on functional groups. The fate of chlorpyrifos could be simulated well by calibrating the sorption coefficient for organic carbon, diffusion rate to the sediment and degradation rates in water and sediment. Direct effects were simulated by integrating a sigmoidal concentration-effect relationship with the population growth model for functional groups. It was hypothesized that indirect effects resulted mostly from resource competition. Functional groups were divided in sensitive and insensitive subgroups to allow such model behaviour. Direct effects of chlorpyrifos affected all arthropods in the microcosms which the model could replicate with reasonable accuracy. Recovery of sensitive zooplankton (consisting of cladocerans and copepods) occurred faster in the microcosms than in the simulation. Indirect effects on algae, rotifers, shredders and tubificids resulted from the direct effects as incorporated in the model. Except for algae, simulations showed good qualitative agreement with observed indirect effects, but no exact quantitative match could be obtained. This revised version was published online in August 2006 with corrections to the Cover Date.     

Permeability characteristics of the basement membrane (basal lamella) of the intestine of Ascaris suum

Permeability characteristics have been determined for isolated ribbons of the basement membrane of the intestine ofAscaris suum. The solute permeability coefficient (P_c) was measured for a series of hydrophobic, nonionic molecules of graded molecular size. The geometric pore area per unit path length (A_o/Δx) was estimated to be 24.0 cm from the diffusion rates for the various solute molecules. A filtration coefficient (L_p) of 18.1×10^?12 cm⁵/dyne-sec was determined by a method that employs osmotic pressure. The preceding values were used to calculate an average pore radius of 24.0 A for the membrane. The unstirred layer was estimated to be 30μm thick from measurements of the change in the rate of diffusion of water across the membrane with change in the rate of perfusion. The preceding values were used to calculate a reflection coefficien (σ), effective permeability coefficient (ω′), and a permeability coefficient (ω). The results support the view that this basement membrane functions as a filter and selective barrier to diffusion of constituents of the worm's body fluid.     

Molecular modelling of the mass density of single proteins

Using molecular dynamics (MD) simulations, the density of single proteins and its temperature dependence was modelled starting from the experimentally determined protein structure and a generic, transferable force field, without the need of prior parameterization. Although all proteins consist of the same 20 amino acids, their density in aqueous solution varies up to 10% and the thermal expansion coefficient up to twofold. To model the protein density, systematic MD simulations were carried out for 10 proteins with a broad range of densities (1.32–1.43?g/cm³) and molecular weights (7–97?kDa). The simulated densities deviated by less than 1.4% from their experimental values that were available for four proteins. Further analyses of protein density showed that it can be essentially described as a consequence of amino acid composition. For five proteins, the density was simulated at different temperatures. The simulated thermal expansion coefficients ranged between 4.3 and 7.1?×?10^?4?K^?1 and were similar to the experimentally determined values of ribonuclease-A and lysozyme (deviations of 2.4 and 14.6%, respectively). Further analyses indicated that the thermal expansion coefficient is linked to the temperature dependence of atomic fluctuations: proteins with a high thermal expansion coefficient show a low increase in flexibility at increasing temperature. A low increase in atomic fluctuations with temperature has been previously described as a possible mechanism of thermostability. Thus, a high thermal expansion coefficient might contribute to protein thermostability.     

Demographic Sensitivity of Population Change in Northern Bobwhite

Abstract: The northern bobwhite (Colinus virginianus) is an economically important gamebird that is currently undergoing widespread population declines. Despite considerable research on the population ecology of bobwhites, there have been few attempts to model population dynamics of bobwhites to determine the contributions of different demographic parameters to variance of the finite rate of population change (Λ). We conducted a literature review and compiled 405 estimates of 9 demographic parameters from 49 field studies of bobwhites. To identify demographic parameters that might be important for management, we used life-stage simulation analyses (LSA) to examine sensitivity of Λ to simulated variation in 9 demographic parameters for female bobwhites. In a baseline LSA based on uniform distributions bounded by the range of estimates for each demographic parameter, bobwhite populations were predicted to decline (Λ = 0.56) and winter survival of adults made the greatest contribution to variance of Λ (r² = 0.453), followed by summer survival of adults (r² = 0.163), and survival of chicks (r² = 0.120). Population change was not sensitive to total clutch laid, nest survival, egg hatchability, or 3 parameters associated with the number of nesting attempts (r²<0.06). Our conclusions were robust to alternative simulation scenarios, and parameter rankings changed only if we adjusted the lower bounds of winter survival upwards. Bobwhite populations were not viable with survival rates reported from most field studies. Survival rates may be depressed below sustainable levels by environmental conditions or possibly by impacts of capture and telemetry methods. Overall, our simulation results indicate that management practices that improve seasonal survival rates will have the greatest potential benefit for recovery of declining populations of bobwhites.     

How do various maize crop models vary in their responses to climate change factors?

Potential consequences of climate change on crop production can be studied using mechanistic crop simulation models. While a broad variety of maize simulation models exist, it is not known whether different models diverge on grain yield responses to changes in climatic factors, or whether they agree in their general trends related to phenology, growth, and yield. With the goal of analyzing the sensitivity of simulated yields to changes in temperature and atmospheric carbon dioxide concentrations [CO₂], we present the largest maize crop model intercomparison to date, including 23 different models. These models were evaluated for four locations representing a wide range of maize production conditions in the world: Lusignan (France), Ames (USA), Rio Verde (Brazil) and Morogoro (Tanzania). While individual models differed considerably in absolute yield simulation at the four sites, an ensemble of a minimum number of models was able to simulate absolute yields accurately at the four sites even with low data for calibration, thus suggesting that using an ensemble of models has merit. Temperature increase had strong negative influence on modeled yield response of roughly ?0.5 Mg ha^?1 per °C. Doubling [CO₂] from 360 to 720 μmol mol^?1 increased grain yield by 7.5% on average across models and the sites. That would therefore make temperature the main factor altering maize yields at the end of this century. Furthermore, there was a large uncertainty in the yield response to [CO₂] among models. Model responses to temperature and [CO₂] did not differ whether models were simulated with low calibration information or, simulated with high level of calibration information.     

Correlation Spectroscopy and Molecular Dynamics Simulations to Study the Structural Features of Proteins

In this work, we used a combination of fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulation methodologies to acquire structural information on pH-induced unfolding of the maltotriose-binding protein from Thermus thermophilus (MalE2). FCS has emerged as a powerful technique for characterizing the dynamics of molecules and it is, in fact, used to study molecular diffusion on timescale of microsecond and longer. Our results showed that keeping temperature constant, the protein diffusion coefficient decreased from 84±4 µm²/s to 44±3 µm²/s when pH was changed from 7.0 to 4.0. An even more marked decrease of the MalE2 diffusion coefficient (31±3 µm²/s) was registered when pH was raised from 7.0 to 10.0. According to the size of MalE2 (a monomeric protein with a molecular weight of 43 kDa) as well as of its globular native shape, the values of 44 µm²/s and 31 µm²/s could be ascribed to deformations of the protein structure, which enhances its propensity to form aggregates at extreme pH values. The obtained fluorescence correlation data, corroborated by circular dichroism, fluorescence emission and light-scattering experiments, are discussed together with the MD simulations results.     

Electrical resistance and ion movement through excised discs of sugar beet root tissue

Electrical and tracer techniques were used to investigate the movement of Na⁺, K⁺ and Cl^? through discs of a range of thicknesses cut from the root tissue of sugar beet, Beta vulgaris L. cv. Amono. At low external concentration the electrical resistance across a discs is less than that of an equivalent volume of solution. This does not appear to be due to a low resistance symplastic pathway but rather, to an enhanced concentration of cation in the apoplast. The resistance is proportional to the thickness of tissue. Although measurement of diffusion potential gives about 25 mV difference across the disc for a ten-fold change in cation concentration, there is little discrimination between K⁺ and Na⁺. The observed tracer kinetics of ⁸⁶Rb through the disc are consistent with those of diffusion, with a coefficient of diffusion, D, of 0.19 × 10^?9 m² s^?1 and a tissue partition coefficient, k, of 0.27 (or of 2.7 if referred to the cell wall phase only). ³⁶Cl gives a similar value for D, but has a k reduced by a factor of 3.3, a result that is consistent with the diffusion potential observation. However, a much larger discrimination would have been expected from the chemically measured cation exchange capacity.     

A pulsed field gradient NMR study of the aggregation and hydration of parvalbumin

Pulsed field gradient NMR is a convenient alternative to traditional methods for measuring diffusion of biological macromolecules. In the present study, pulsed field gradient NMR was used to study the effects of calcium binding and hydration on carp parvalbumin. Carp parvalbumin is known to undergo large changes in tertiary structure with calcium loading. The diffusion coefficient is a sensitive guide to changes in molecular shape and in the present study the large changes in tertiary structure were clearly reflected in the measured diffusion coefficient upon calcium loading. The (monomeric) calcium-loaded form had a diffusion coefficient of 1.4 x 10(-10) m(2) s(-1) at 298 K, which conforms with the structure being a nearly spherical prolate ellipsoid from X-ray studies. The calcium-free form had a significantly lower diffusion coefficient of 1.1 x 10(-10) m(2) s(-1). The simplest explanation consistent with the change in diffusion coefficient is that the parvalbumin molecules form dimers upon the removal of Ca(2+) at the protein concentration studied (1 mM).     

基于SLEUTH模型的阜新市城市扩展模拟

基于SLEUTH模型对1997—2013年阜新市城市扩展进行模拟.结果表明:阜新市转型进程中城市扩展最优系数分别为:扩散系数6、繁衍系数64、蔓延系数44、坡度阻抗系数52、道路引力系数90.阜新市主要表现为新中心增长(自发式增长产生的新城市中心)和边缘增长(新、老城市中心的进一步增长);阜新市转型进程中城市扩展受道路引力影响很大,其值达到90;阜新市作为资源枯竭型城市,矿区枯竭带来了滑坡、塌陷等一系列自然灾害,研究期间城市扩展受到坡度的阻抗是很大的.从城市规模角度看,道路引力对小城市的作用大于大城市;从新中心增长情况来看,小城市更容易出现新中心增长.阜新作为资源型城市,目前确定为资源枯竭型城市,经济转型是头等大事,引进的外资企业、新建的开发区、工业用地等在选址上更偏向道路交通便利区域,受道路影响较大,而且更容易出现飞地式发展.利用SLEUTH模型校正所得的最优参数,对阜新市城市范围进行模拟,其中,城市边缘增长的模拟效果较好,城市新中心即飞地增长的模拟效果较差,主要因为新中心增长受决策影响较大,元胞关系作用不大.2001、2006、2010、2013年的阜新市城市范围模拟精度较高.