Electron and proton transfer in chloroplasts in silico. 2: The effect of diffusion limitations on the process of photosynthesis in spatially inhomogeneous thylakoids

The lateral mobility of protons and mobile electron carriers (plastoquinone and plastocyanin) is subjected to diffusion limitations; the effect of these limitations on the kinetics of photoinduced pH _i changes has been investigated in the present work for metabolic states 3 (conditions of intensive ATP synthesis) and 4 (the state of photosynthetic control). Computer simulations were based on a mathematical model of electron and proton transport in chloroplasts developed earlier by the authors. Non-uniform distribution of electron carriers and ATP synthase complexes in the membranes of grana and intergranal thylakoids was taken into account in the model. The kinetics of intrathylakoid pH _i changes and the lateral profiles of distribution of the mobile electron transporters in granal and intergranal thylakoids were studied. The formation of non-uniform pH _i profiles (with lumen acidification in the central parts of the grana being substantially slower than in the stromal thylakoids) was shown to occur under the conditions of ATP synthesis. Variation of the diffusion coefficients of intrathylakoid hydrogen ions and mobile electron carriers (plastoquinone and plastocyanin) can have substantial effects on the lateral pH _i profiles and the redox state of the mobile electron carriers.     

Systematic features of diffusion and aggregation of intrinsic defects in dielectric crystals

It has been shown that the kinetics of reactions involving mobile intrinsic defects in the crystal is described by the exponential dependence in many cases. Based on this dependence and the fact that random-walk diffusion occurs in the cases under consideration, the distribution of diffusion paths traveled by mobile defects before entering into the reaction has been found. An expression for the arithmetic mean of these paths has been obtained. For lithium fluoride crystals irradiated with gamma-rays, the pre-exponential factors in the temperature dependences of the diffusion coefficients of F ₂ ⁺ color centers and anion vacancies have been determined and the diffusion coefficients of these types of defects have been estimated.     

Derivation of a closed form analytical expression for fluorescence recovery after photo bleaching in the case of continuous bleaching during read out

Measurements of very slow diffusive processes in membranes, like the diffusion of integral membrane proteins, by fluorescence recovery after photo bleaching (FRAP) are hampered by bleaching of the probe during the read out of the fluorescence recovery. In the limit of long observation time (very slow diffusion as in the case of large membrane proteins), this bleaching may cause errors to the recovery function and thus provides error-prone diffusion coefficients. In this work we present a new approach to a two-dimensional closed form analytical solution of the reaction-diffusion equation, based on the addition of a dissipative term to the conventional diffusion equation. The calculation was done assuming (i) a Gaussian laser beam profile for bleaching the spot and (ii) that the fluorescence intensity profile emerging from the spot can be approximated by a two-dimensional Gaussian. The detection scheme derived from the analytical solution allows for diffusion measurements without the constraint of observation bleaching. Recovery curves of experimental FRAP data obtained under non-negligible read-out bleaching for native membranes (rabbit endoplasmic reticulum) on a planar solid support showed excellent agreement with the analytical solution and allowed the calculation of the lipid diffusion coefficient.     

Effect of a Hydrogen-Bonding Layer on a Hollow Capsule's Permeability

Hollow capsules formed by layer-by-layer self-assembly polymers have been intensively studied for their potential applications in medicine and biotechnology. We have controlled such capsules’ permeability with a hydrogen-bonding layer. Scanning electron microscopy and Fourier transform infrared results showed the fabrication of multilayer polyelectrolyte films. Z-potential results were employed to record the deposition of the polyelectrolyte. The diffusion coefficients for 6-carboxyfluorescein (6-CF) and fluorescently labeled goat anti-human IgG-FITC molecules passing through the wall were calculated based on the fluorescence recovery after photobleaching experiment. The results show that 6-CF molecules can pass through the capsule wall more easily than IgG-FITC molecules. By decreasing the solution's pH, the capsule's permeability to macromolecular dyes or small molecular dyes can be controlled, i.e., the capsule's permeability can be tuned by the hydrogen-bonding interaction.     

Diffusion Coefficients of Several Rhodamine Derivatives as Determined by Pulsed Field Gradient–Nuclear Magnetic Resonance and Fluorescence Correlation Spectroscopy

Rhodamine derivatives are popular, photostable fluorophores that are used in a number of fluorescent based techniques, including fluorescence correlation spectroscopy (FCS). Indeed, in FCS, both rhodamine 6G (R6G) and rhodamine 110 (R110) are used as calibration standards to determine the dimensions of the instrument confocal volume. In spite of a requirement for precise values of the diffusion coefficients, literature values are scarce and vary over an order of magnitude. In this paper, the diffusion coefficients of four rhodamine fluorophores (rhodamine 6G (R6G), rhodamine B (RB), rhodamine 123 (R123), rhodamine 110 (R110)) were determined by pulsed field gradient nuclear magnetic resonance (PFG-NMR) spectrometry and then validated by comparison with fluorescence correlation spectroscopy. With the objective of validating the FCS calibration, diffusion coefficients of several dextrans and a polystyrene nanoparticle were also determined and compared with literature values or theoretical values that were based upon the Stoke–Einstein equation. The work presented here lead us to conclude that the diffusion coefficients for R6G and R110 have generally been underestimated in the literature. We propose revised values of 4.4 × 10⁻¹⁰ m² s⁻¹ for R110 and 4.0 × 10⁻¹⁰ m² s⁻¹ for R6G. Using the revised D value for R110 to calibrate the FCS instrument, diffusion coefficients have then been systematically determined for different conditions of pH, ionic strength and concentration. To correct for differences due to solvent effects (D₂O vs. H₂O), an isotopic correction factor, of 1.23, was determined from both FCS and from the solvent auto-diffusion coefficients obtained by NMR.     

Probing passive diffusion of flagellated and deflagellated Escherichia coli

Using particle-tracking techniques, the translational and rotational diffusion of paralyzed E. coli with and without flagella are studied experimentally. The position and orientation of the bacteria are tracked in the lab frame and their corresponding mean-square displacements are analyzed in the lab frame and in the body frame to extract the intrinsic anisotropic translational diffusion coefficients as well as the rotational diffusion coefficient for both strains. The deflagellated strain is found to show an anisotropic translational diffusion, with diffusion coefficients that are compatible with theoretical estimates based on its measured geometrical features. The corresponding translational diffusion coefficients of the flagellated strain have been found to be reduced as compared to those of the deflagellated counterpart. Similar results have also been found for the rotational diffusion coefficients of the two strains. Our results suggest that the presence of flagella --even as a passive component-- has a significant role in the dynamics of E. coli, and should be taken into account in theoretical studies of its motion.     

Diffusion of D2O in archaeological wood measured by 1-D NMR profiles

1-D¹H nuclear magnetic resonance profiles have been used to image the penetration of D₂O into waterlogged archaeological wood. A series of well characterised plugs were sampled from different depths, reflecting different degrees of degradation and orientation with respect to the wood structure, of an oak timber from the Mary Rose. The ingress of D₂O was Fickian in character and the diffusion coefficients,D, are reported as a function of depth into the timber for each orientation. The behaviour ofD could be approximated by a surface layer, with a higher diffusion coefficient, and a lower diffusion core region. The differences in the values ofD in the different orientations are rationalised in terms of the known structure of decayed wood. Theoretical uptake curves were calculated from a numerical evaluation of the analytical solution for diffusion into a multiple-layer model. Saturation of the surface layer was predicted to occur prior to diffusion into the core, with a characteristic change of gradient displayed in the uptake curve. Good agreement was achieved with experiments that sampled the different decay environments. Concentration distributions, and uptake curves, were calculated using these models for a typical archaeological timber.     

Diffusion of particles over strongly anisotropic surface with traps

We investigate surface diffusion in a system of particles adsorbed on a two-dimensional strongly anisotropic lattice. There are two kinds of the lattice sites - ordinary sites and deep traps. Particles adsorbed in the ordinary sites can migrate over the surface, but particles adsorbed in traps are immobile. These particles do not move over the surface and they obstacle also the mobile particles migration (surface defects). Using kinetic Monte Carlo simulations we obtained coverage dependencies of the tracer, jump, and chemical diffusion coefficients. The coefficients are rather sensitive to the defect concentration. Even small admixture of the defects decreases drastically the fast diffusion. The effect is rather specific: strong dependence of the pre-exponential factor on the defect concentration and almost independent activation energy. The defect influence on the slow diffusion is weak. It results in strong decreasing of the surface diffusion anisotropy with the defect concentration. Such unusual behavior of the diffusion coefficients was observed in many experimental investigations of the surface diffusion of lithium, cesium, potassium, and strontium over strongly anisotropic W(1 1 2) and Mo(1 1 2) planes. It was shown that this specific behavior arises exclusively due to the surface anisotropy, and does not depend on the lateral interaction between the particles.     

Control of frictional coupling of transmembrane cell receptors in model cell membranes with linear polymer spacers

The planar plasma membrane model with linear polymer spacers with defined lengths enables the control of the frictional coupling between incorporated transmembrane proteins (human platelet integrin) and the solid substrate. This mimics the viscous environment provided by the extracellular matrix of cells. The friction coefficient can be calculated quantitatively from the diffusion coefficient of integrin, measured by fluorescence recovery after photobleaching. The obtained results demonstrate a clear influence of the length and lateral density of polymer chains on the mobility of transmembrane proteins.     

Self-diffusion and sedimentation of tracer spheres in (semi)dilute dispersions of rigid colloidal rods

Long-time self-diffusion and sedimentation of fluorescent tracer spheres in electrostatically stabilized dispersions of rigid colloidal host rods have been measured in situ with fluorescence recovery after photobleaching, and gravitational and ultracentrifugal sedimentation. The dynamics of silica tracer spheres of 39 and 370 nm radius was monitored in dispersions of host rods with aspect ratios 9.6 and 25.7 at various rod volume fractions. The translational and rotational diffusion coefficient of the host rods was obtained independently with dynamic light scattering and birefringence decay measurements. Our results indicate that sedimentation and long-time self-diffusion are determined by the same friction factor. Furthermore we find that, as long as the host rods are relatively mobile, tracer sphere sedimentation and long-time self-diffusion are governed by the macroscopic solution viscosity, regardless of the tracer and host rod size. However, when the host rods are immobilized, due to rod entanglements at higher volume fractions, tracer sphere dynamics depends strongly on the tracer size relative to the pore size of the host rod network. The large tracers are completely trapped in the network whereas the small tracer spheres remain mobile. Current models for tracer sphere motion in rod assemblies do not satisfactorily explain the complete dynamic regime covered by our experimental model system because the effect of host rod mobility is not properly taken into account.     

Viscosity critical behaviour at the gel point in a 3d lattice model

Within a recently introduced model based on the bond-fluctuation dynamics, we study the viscoelastic behaviour of a polymer solution at the gelation threshold. We here present the results of the numerical simulation of the model on a cubic lattice: the percolation transition, the diffusion properties and the time autocorrelation functions have been studied. From both the diffusion coefficients and the relaxation times critical behaviour a critical exponent k for the viscosity coefficient has been extracted: the two results are comparable within the errors giving , in close agreement with the Rouse model prediction and with some experimental results. In the critical region below the transition threshold the time autocorrelation functions show a long-time tail which is well fitted by a stretched exponential decay. Received 20 December 1999 and Received in final form 18 February 2000     

Estimation of diffusion coefficients by a capillary method in the presence of oppositely directed convection of the melt

The paper presents a theoretical analysis of linear diffusion in the presence of convection with a constant flow rate for an instantaneous plane source and for diffusion in infinite capillary. A conclusion can be drawn that diffusion in the melt moving at the ratev together with the source is described, with respect to the system of coordinates connected with the capillary, by a superposition of molecular diffusion and translational motion of the melt. Self-diffusion of⁵¹Cr in Fe-Cr-O systems of different compositions and self-diffusion of⁵⁹Fe in molten iron at 1860 K have been investigated experimentally. The results of theoretical analysis have been applied in the evaluation of diffusion coefficients in the presence of convection.     

Investigation of Molecular Diffusion at Block Copolymer Thin Films Using Maximum Entropy Method-Based Fluorescence Correlation Spectroscopy and Single Molecule Tracking

Fluorescence correlation spectroscopy (FCS) has been widely used to investigate molecular diffusion behavior in various samples. The use of the maximum entropy method (MEM) for FCS data analysis provides a unique means to determine multiple distinct diffusion coefficients without a priori assumption of their number. Comparison of the MEM-based FCS method (MEM-FCS) with another method will reveal its utility and advantage as an analytical tool to investigate diffusion dynamics. Herein, we measured diffusion of fluorescent probes doped into nanostructured thin films using MEM-FCS, and validated the results with single molecule tracking (SMT) data. The efficacy of the MEM code employed was first demonstrated by analyzing simulated FCS data for systems incorporating one and two diffusion modes with broadly distributed diffusion coefficients. The MEM analysis accurately afforded the number of distinct diffusion modes and their mean diffusion coefficients. These results contrasted with those obtained by fitting the simulated data to conventional two-component and anomalous diffusion models, which yielded inaccurate estimates of the diffusion coefficients. Subsequently, the MEM analysis was applied to FCS data acquired from hydrophilic dye molecules incorporated into microphase-separated polystyrene-block-poly(ethylene oxide) (PS-b-PEO) thin films characterized under a water-saturated N₂ atmosphere. The MEM analysis revealed distinct fast and slow diffusion components attributable to molecules diffusing on the film surface and inside the film, respectively. SMT studies of the same materials yielded trajectories for mobile molecules that appear to follow the curved PEO microdomains. Diffusion coefficients obtained from the SMT data were consistent with those obtained for the slow diffusion component detected by MEM-FCS. These results highlight the utility of MEM-FCS and SMT for gaining complementary information on molecular diffusion processes in heterogeneous material systems.

Graphical Abstract

     

Fluorescence Lifetime Tuning—A Novel Approach to Study Flip-Flop Kinetics in Supported Phospholipid Bilayers

In the present work we introduce a straightforward fluorescent assay that can be applied in studies of the transbilayer movement (flip-flop) of fluorescent lipid analogues across supported phospholipid bilayers (SPBs). The assay is based on the distance dependent fluorescence quenching by light absorbing surfaces. Applied to SPBs this effect leads to strong differences in fluorescence lifetimes when the dye moves from the outer lipid leaflet to the leaflet in contact with the support. Herein, we present the basic principles of this novel approach, and comment on its advantages over the commonly used methods for investigating flip-flop dynamics across lipid bilayers. We test the assay on the fluorescent lipid analog Atto633-DOPE and the 3-hydroxyflavone F2N12S probe in SPBs composed of DOPC/ DOPS lipids. Moreover, we compare and discuss the flip-flop rates of the probes with respect to their lateral diffusion coefficients.     

Surface diffusion of particles adsorbed on an inhomogeneous lattice with two non-equivalent sites

We investigate surface diffusion in a system of particles with the nearest neighbor pairwise lateral interaction adsorbed on a two-dimensional inhomogeneous lattice of square symmetry with deep and shallow sites. General analytical expressions for the chemical and jump diffusion coefficients have been derived in case of strong inhomogeneity. The expressions are valid for the inhomogeneous lattices with different geometries and dimensionalities. We have calculated the coverage dependencies of the tracer, jump and chemical diffusion coefficients for different temperatures using the real-space renormalization group (RSRG) method and compared the data with the numerical results obtained by the MC simulations. The coincidence between the data obtained by these quite different methods is rather good.     

Investigations on Afterglows of Neon Gas Discharges

We report on the experimental and numerical investigations on afterglows of neon gas discharges, which are performed at the Eindhoven University of Technology. The studied gas pressure range extends from 1 to 100 torr, the discharge current from 1 to 100 mA. The densities of the 1s-levels are measured with the help of the selective excitation spectroscopy (fluorescence technique). In this way a great number of decay curves of the 1s-densities have been measured in the afterglow of neon gas discharges. From these curves the diffusion coefficient of the metastable 1s-atoms, the coefficients of atomic collisional transfer between the 1s₅- and 1s₄-level, as well as the three body collision coefficient between metastable 1s₅-atoms and neon ground state atoms have been determined. Besides these experiments a numerical model of the neon afterglows has been developed. With this model the afterglow phenomena can be simulated and the influence of the particular processes on the whole afterglow can be studied conveniently. Comparison is made between the experimentally and numerically obtained decay curves. For the application of the numerical model a number of starting conditions, such as radial density profiles, gas temperature, (relative) densities of the 1s-levels, have been measured. Results of these measurements are presented. Also with the help of the selective excitation spectroscopy the coefficients of atomic collisional transfer between the 2p-levels have been measured in the afterglow. From these results, together with the measured (relative) intensities of the neon spectral lines in the afterglow the partial recombination coefficients for the 2p-levels were calculated.     

Determination of the diffusion and viscosity coefficients from the properties of dual fluorescence of molecules in solutions

We have proposed and substantiated an approach that makes it possible to determine the diffusion and microviscosity coefficients in solutions from characteristics of the dual fluorescence of molecular probes. This approach uses the Stern-Volmer constants obtained upon fluorescence dynamic quenching in solutions. The relations that follow from the balance equations in terms of the formalism of two-level reactions in the excited state for the case of photoreactions of the kinetic character yield the dependences of the intensity ratio of the fluorescence bands of the normal form and tautomer on the degree of quenching. In accordance with these dependences, the dynamic quenching of the diffusion character (including the temperature quenching) changes the intensity distribution, and, based on these dependences, the Stern-Volmer constants and the bimolecular quenching constants can be determined, from which, using appropriate models, the diffusion and viscosity coefficients can be found. The merit of the method is its simplicity and availability, since it is based on the use of the data of steady-state measurements of fluorescence spectra with widespread standard instruments.     

Fluorescence lifetimes in the biphenyl-tetracyanobenzene crystal doped with TCNQ

Summary Transient optical emission spectra of biphenyl-1,2,4,5-tetracyanobenzene crystal doped with TCNQ have been investigated in the (77÷300) K temperature range. Host prompt fluorescence lifetimes have been measured by cross-correlation phase fluorometry. The decay signal is fitted by a biexponential function whose coefficients are strongly dependent on temperature. A thermal activation energy of 300 cm⁻¹ for the diffusion of singlet exciton has been determined. This work was supported in part by the Italian National Research Council (CNR) through its Centro di Studio sugli Stati Molecolari Radicalici ed Eccitati.     

First principles calculations of alloying element diffusion coefficients in Ni using the five-frequency model

The diffusion coefficients of several alloying elements(Al,Mo,Co,Ta,Ru,W,Cr,Re) in Ni are directly calculated using the five-frequency model and the first principles density functional theory.The correlation factors provided by the five-frequency model are explicitly calculated.The calculated diffusion coefficients show their excellent agreement with the available experimental data.Both the diffusion pre-factor(D 0) and the activation energy(Q) of impurity diffusion are obtained.The diffusion coefficients above 700 K are sorted in the following order:DAl>DCr>DCo>DTa>DMo>DRu>DW>D Re.It is found that there is a positive correlation between the atomic radius of the solute and the jump energy of Ni that results in the rotation of the solute-vacancy pair(E 1).The value of E 2-E 1(E 2 is the solute diffusion energy) and the correlation factor each also show a positive correlation.The larger atoms in the same series have lower diffusion activation energies and faster diffusion coefficients.     

Investigation of radiological properties of some shielding materials on charged and uncharged radiation interaction for neutron generator

Radiation interaction parameters such as total stopping power, projected range (longitudinal and lateral) straggling, mass attenuation coefficient, effective atomic number (Z_eff) and electron density (N_eff) of some shielding materials were investigated for photon and heavy charged particle interactions. The ranges, stragglings and mass attenuation coefficients were calculated for the high-density polyethylene(HDPE), borated polyethylene (BPE), brick (common silica), concrete (regular), wood, water, stainless steel (304), aluminum (alloy 6061-O), lead and bismuth using SRIM Monte Carlo software and WinXCom program. In addition, effective atomic numbers (Z_eff) and electron densities (N_eff) of HDPE, BPE, brick (common silica), concrete (regular), wood, water, stainless steel (304) and aluminum (alloy 6061-O) were calculated in the energy region 10?keV–100?MeV using mass stopping powers and mass attenuation coefficients. Two different methods namely direct and interpolation procedures were used to calculate Z_eff for comparison and significant differences were determined between the methods. Variations of the ranges, longitudinal and lateral stragglings of water, concrete and stainless steel (304) were compared with each other in the continuous kinetic energy region and discussed with respect to their Z_effs. Moreover, energy absorption buildup factors (EABF) and exposure buildup factors (EBF) of the materials were determined for gamma rays as well and were compared with each other for different photon energies and different mfps in the photon energy region 0.015–15?MeV.