Preferential Flux Research Articles

Habitat heterogeneity drives arbuscular mycorrhizal fungi and shrub communities in karst ecosystems

Arbuscular mycorrhizal fungi (AMF) constitute one of the factors that regulate the success of vegetation restoration. Karst ecosystems are heterogenous in nutrient content and plant communities because of preferential water fluxes within cracks and gullies in the soil parent material. The effects of habitat on soil nutrients, shrub, and AMF diversity in karst ecosystems are yet to be established. Thus, we investigated the diversity of shrubs and AMF within three habitats: i) rocky soil surface (Rock), ii) soil surface (Soil), and iii) rocky gully (Gully) in a typical karst shrub ecosystem. We observed that AMF diversity was independent of the sampling location, whereas AMF abundance and the shrub Shannon index increased with sampling distance, reaching a plateau in a sampling area of 1000 m2. The AMF community composition was driven by dominating shrubs (Vitex negundo, Tirpitzia ovoidea). Higher shrub diversity and AMF abundance occurred in Rock than in Soil and Gully areas, suggesting higher habitat heterogeneity in Rock areas. Based on co-occurrence network analysis, interactions with a high link number among the AMF taxa were stronger in Rock than in Gully because the network complexity in the Rock areas strongly depended on symbiosis with AMF taxa to cope with high habitat heterogeneity. The Random forest model revealed that AMF abundance was mainly affected by available phosphorous, total potassium, and shrub diversity. Available phosphorous, soil pH, and exchangeable Ca2+, rather than plant diversity, were the main factor controlling AMF community composition. Overall, the results suggest that the increase in shrub diversity raised AMF abundance and richness, and strengthened the interactions among AMF taxa because of nutrient exchange. Thus, increasing habitat heterogeneity with abundant shrub diversity, but soil nutrient limitation, enriches AMF abundance and diversity.

Seasonal and deep groundwater‐surface water interactions in the tropical Middle Magdalena River basin of Colombia

AbstractThis study is an attempt to understand flow patterns in the Middle Magdalena Valley River basin (MMV), a tropical lowland humid forest. For this purpose, we used δ2H and δ18O water stable isotopes measured in different surface and groundwater sources collected in the area both during the dry and the wet seasons. Two hundred and forty‐five water samples were collected in rainfall, springs, rivers, swamps, and wells (from 10 to 350 m depth). Thus, we were able to establish three tendencies that suggest the existence of surface‐groundwater interactions or preferential groundwater fluxes in the MMV: (i) samples with an isotopic enrichment from the wet to the dry season (groundwater samples following the rainfall isotopic variability), (ii) groundwater samples with an isotopic depletion from the wet to the dry season (opposite to the rainfall isotopic signal), and (iii) groundwater samples whose isotopic composition did not change significantly among seasons. However, none of these tendencies could be related to geology or the type of sampled site, which suggests that some not fully understood processes must be taking place in the hydrological system of the MMV. Both, surface, and groundwater samples are grouped close to the Colombian meteoric line, with exception of some swamp samples collected during the dry period, which displayed the expected evaporation trend line tendency. This may be an indicator of the connection/disconnection of swamps with the river during the hydrological year. Finally, this study aims to fulfil the gap in water‐stable isotope data in Colombia and provide insights about the hydrological setup of a lowland tropical basin.

Scalar gradient and flame propagation statistics of a flame-resolved laboratory-scale turbulent stratified burner simulation

A bluff-body stabilised turbulent jet flame burning in a stratified mode of combustion for fuel-lean methane/air mixtures is investigated by a flame-resolved simulation. A tabulated chemistry approach based on premixed flamelet generated manifolds (PFGM) accounts for thermochemistry. The computations are performed for a grid-resolution of 100 µm, sufficient to resolve the thermal flame thickness. The look-up table is generated with a mixture-averaged diffusivity assumption and the preferential diffusion fluxes are included in the simulation, using an efficient method without increasing the dimensionality of the manifold. The predicted mean and RMS quantities are found to be in good agreement with the experiment. The investigation focuses on the comparison of the combustion behaviour of the upstream locations close to the inlet with weak mixture fraction gradients to the downstream locations away from the inlet with strong mixture fraction gradients. Statistical analysis of the diffusion terms within the flame revealed that the preferential diffusion remains significant near the inlet, in the recirculation zone over the bluff-body. The structure of the stratified flame in downstream locations is statistically analysed in terms of displacement speed and scalar gradients by comparing against the corresponding quantities in upstream locations with weak mixture fraction gradients. It is shown that the displacement speed is statistically different between the flames under weak or strong mixture fraction gradients due to the influence of molecular diffusion and reaction rate components. However, increased curvature effects and cross-dissipation component also play a role. Finally, scalar dissipation and cross-dissipation rates of the mixture fraction fluctuation and the reaction progress variable fluctuation within the flame-brush are investigated, and their closure approaches are discussed.

Impact of geometry on the magnetic flux trapping of superconducting accelerating cavities

Controlling trapped magnetic flux in superconducting radiofrequency (RF) cavities is of crucial importance in modern accelerator projects. In order to study flux trapping efficiency and sensitiv- ity of surface resistance, dedicated experiments have been carried out on different types of low-\b{eta} superconducting accelerating cavities. Even under almost full trapping conditions, we found that the measured magnetic sensitivities of these cavity geometries were significantly lower than the theoretical values predicted by commonly-used models based on local material properties. This must be resolved by taking account of geometrical effects of flux trapping and flux oscillation under RF surface current in such cavity shape. In this paper, we propose a new approach to convolute the influence of geometries. We point out a puzzling contradiction between sample measurements and recent cavity experiments, which leads to two different hypotheses to simulate oscillating flux trapped in the cavity surface. A critical reconsideration of flux oscillation by the RF Lorentz force, compared with temperature mapping studies in elliptical cavities, favoured the results of previous sample measurements, which suggested preferential flux trapping of normal component to the cavity inner surface. Based on this observation, we builded a new model to our experimental results and the discrepancy between old theory and data were resolved.

Direct evidence of microstructure dependence of magnetic flux trapping in niobium

Elemental type-II superconducting niobium is the material of choice for superconducting radiofrequency cavities used in modern particle accelerators, light sources, detectors, sensors, and quantum computing architecture. An essential challenge to increasing energy efficiency in rf applications is the power dissipation due to residual magnetic field that is trapped during the cool down process due to incomplete magnetic field expulsion. New SRF cavity processing recipes that use surface doping techniques have significantly increased their cryogenic efficiency. However, the performance of SRF Nb accelerators still shows vulnerability to a trapped magnetic field. In this manuscript, we report the observation of a direct link between flux trapping and incomplete flux expulsion with spatial variations in microstructure within the niobium. Fine-grain recrystallized microstructure with an average grain size of 10–50 µm leads to flux trapping even with a lack of dislocation structures in grain interiors. Larger grain sizes beyond 100–400 µm do not lead to preferential flux trapping, as observed directly by magneto-optical imaging. While local magnetic flux variations imaged by magneto-optics provide clarity on a microstructure level, bulk variations are also indicated by variations in pinning force curves with sequential heat treatment studies. The key results indicate that complete control of the niobium microstructure will help produce higher performance superconducting resonators with reduced rf losses1 related to the magnetic flux trapping.

Ore shoots in folded and fractured rocks – Insights from 3D modelling of the Fosterville gold deposit (Victoria, Australia)

At the Fosterville gold deposit, high concentrations of visible and refractory gold are hosted in arrays of quartz and quartz-carbonate veins. They are distributed in elongate zones to form south plunging ore shoots within a folded and fractured turbidite sequence. Here we distinguish the influence of faults versus folds at Fosterville, by assessing the deposit-scale structural framework and hydrothermal fluid flow using a combination of 3D implicit modelling, structural analysis and 3D fault slip/dilation tendency analyses. Gold assay and bedding trend data, from a large drillhole dataset, were spatially interpolated and used to analyse and measure the orientation of ore bodies and folded host rocks. Field measurements of fold axis orientations were compared to bedding measurements in oriented drillcore, Bingham axial analysis of bedding trends, and orientation data from a 3D implicit model. Both field and drill core structural data show that ore shoots at Fosterville do not parallel the first order, gently (≤10°) south-plunging folds. Instead the orientation of the ore shoots is coincident with an intersection lineation between steeply west-dipping bedding-parallel faults and moderately dipping linkage faults that obliquely cut across the main structural grain, resulting in ore shoot plunges larger than 20°. Slip and dilation tendencies suggest that linkage faults had a higher likelihood of activity in the inferred far-field stress regimes at the time of mineralisation, relative to other structures at Fosterville. These linkage faults are therefore interpreted to have been preferential fluid flux conduits in the system despite appearing to be subordinate structures at the scale of the deposit. This new structural model for Fosterville highlights that fluid flow and ore shoot formation are strongly controlled by obliquely oriented structures that are unlike the main structural grain of first order folds and faults.

Mechanisms of radiation-induced segregation around He bubbles in a Fe-Cr-Ni crystal

Fe-15Cr-15Ni (wt.%) austenitic stainless steel was irradiated with 200 keV 4He+ ions to a fluence of 5 × 1016/cm2 at 500 °C. Radiation-induced segregation (RIS) at He bubbles in the irradiated steel was measured using Energy Dispersive X-ray Spectroscopy (EDS) coupled with Scanning Transmission Electron Microscopy (STEM). The RIS measurements exhibited an enrichment of Ni and a depletion of Cr and Fe at the bubbles. To determine the underlying mechanisms of the RIS, the prediction of the Marwick model was compared with the RIS measurements. The model with parametric input in accordance with the Inverse Kirkendall effect (IKE), i.e. a preferential flux of elements associated with vacancy flux, was inadequate in explaining the observed amount of segregation of Fe, Cr and Ni. Specifically, a considerably lower ratio of the concentration gradient between Cr and Fe, ∇Cr∇Fe, of 0.53 was obtained from the RIS measurements versus the model-predicted value of 2.3, indicating an overestimation of Cr depletion at the bubbles by the Marwick model. To explain this difference between the model prediction and the RIS measurements, in addition to the Cr depletion at the bubbles by IKE due to the fastest diffusion via vacancy flux, a preferential interstitial flux of Cr from the matrix to the bubbles is discussed as a possible concurrently operating mechanism.

Evidence for preferential flux flow at the grain boundaries of superconducting RF-quality niobium

The question of whether grain boundaries (GBs) in niobium can be responsible for lowered operating field (BRF) or quality factor (Q0) in superconducting radio frequency (SRF) cavities is still controversial. Here, we show by direct DC transport across planar GBs isolated from a slice of very large-grain SRF-quality Nb that vortices can preferentially flow along the grain boundary when the external magnetic field lies in the GB plane. However, increasing the misalignment between the GB plane and the external magnetic field vector markedly reduces preferential flux flow along the GB. Importantly, we find that preferential GB flux flow is more prominent for a buffered chemical polished than for an electropolished bi-crystal. The voltage–current characteristics of GBs are similar to those seen in low angle grain boundaries of high temperature superconductors where there is clear evidence of suppression of the superconducting order parameter at the GB. While local weakening of superconductivity at GBs in cuprates and pnictides is intrinsic, deterioration of current transparency of GBs in Nb appears to be extrinsic, since the polishing method clearly affect the local GB degradation. The dependence of preferential GB flux flow on important cavity preparation and experimental variables, particularly the final chemical treatment and the angle between the magnetic field and the GB plane, suggests two more reasons why real cavity performance can be so variable.

Adsorption-Mediated Mass Streaming in a Standing Acoustic Wave.

Oscillating flows can generate nonzero, time-averaged fluxes despite the velocity averaging zero over an oscillation cycle. Here, we report such a flux, a nonlinear resultant of the interaction between oscillating velocity and concentration fields. Specifically, we study a gas mixture sustaining a standing acoustic wave, where an adsorbent coats the solid boundary in contact with the gas mixture. It is found that the sound wave produces a significant, time-averaged preferential flux of a "reactive" component that undergoes a reversible sorption process. This effect is measured experimentally for an air-water vapor mixture. An approximate model is shown to be in good agreement with the experimental observations, and further reveals the interplay between the sound-wave characteristics and the properties of the gas-solid sorbate-sorbent pair. The preferential flux generated by this mechanism may have potential in separation processes.

Functional behavior of the anomalous magnetic relaxation observed in melt-textured YBa2Cu3O7-δ samples showing the paramagnetic Meissner effect

We have studied the functional behavior of the field-cooled (FC) magnetic relaxation observed in melt-textured YBa2Cu3O7-δ (Y123) samples with 30 wt% of Y2Ba1Cu1O5 (Y211) phase, in order to investigate anomalous paramagnetic moments observed during the experiments. FC magnetic relaxation experiments were performed under controlled conditions, such as cooling rate and temperature. Magnetic fields up to 5T were applied parallel to the ab plane and along the c-axis. Our results are associated with the paramagnetic Meissner effect (PME), characterized by positive moments during FC experiments, and related to the magnetic flux compression into the samples. After different attempts our experimental data could be adequately fitted by an exponential decay function with different relaxation times. We discuss our results suggesting the existence of different and preferential flux dynamics governing the anomalous FC paramagnetic relaxation in different time intervals. This work is one of the first attempts to interpret this controversial effect in a simple analysis of the pinning mechanisms and flux dynamics acting during the time evolution of the magnetic moment. However, the results may be useful to develop models to explain this interesting and still misunderstood feature of the paramagnetic Meissner effect.

Computational simulations of asymmetric fluxes of large molecules through gap junction channel pores

Gap junction channels are formed out of connexin isoforms, which enable molecule and ion selective diffusion amongst neighboring cells. HeLa cells expressing distinct connexins (Cx) allow the formation of heterotypic channels, where we observed a molecular charge-independent preferential flux of large fluorescent molecules in the Cx45 to Cx43 direction. We hypothesize that the pore's shape is a significant factor along-side charge and transjunctional voltages for this asymmetric flux. To test this hypothesis, we developed a 3D computational model simulating Brownian diffusion of large molecules in a gap junction channel pore. The basic pore contour was derived from x-ray crystallographic structures of Cx43 and Cx26 and approximated using basic geometric shapes. Lucifer yellow dye molecules and cesium counter-ions were modeled as spheres using their respective Stokes radii. Our simulation results from simple diffusion and constant concentration gradient experiments showed that only charged particles yield asymmetric fluxes in heterotypic pores. While increasing the inner mouth size resulted in a near-quadratic rise in flux, the rise was asymptotic for outer mouth radii increase. Probability maps and average force per particle per pore section explain the asymmetric flux with variation in pore shape. Furthermore, the simulation results are in agreement with our in vitro experimental results with HeLa cells in Cx43-Cx45 heterotypic configurations. The presence of asymmetric fluxes can help us to understand effects of the molecular structure of the pore and predict potential differences in vivo.

Regulation of genetic flux between bacteria by restriction–modification systems

Restriction-modification (R-M) systems are often regarded as bacteria's innate immune systems, protecting cells from infection by mobile genetic elements (MGEs). Their diversification has been recently associated with the emergence of particularly virulent lineages. However, we have previously found more R-M systems in genomes carrying more MGEs. Furthermore, it has been suggested that R-M systems might favor genetic transfer by producing recombinogenic double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic exchanges, we analyzed their frequency with respect to the inferred events of homologous recombination and horizontal gene transfer within 79 bacterial species. Genetic exchanges were more frequent in bacteria with larger genomes and in those encoding more R-M systems. We created a recognition target motif predictor for Type II R-M systems that identifies genomes encoding systems with similar restriction sites. We found more genetic exchanges between these genomes, independently of their evolutionary distance. Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange within and between lineages with cognate R-M systems. Because the repertoire and/or specificity of R-M systems in bacterial lineages vary quickly, the preferential fluxes of genetic transfer within species are expected to constantly change, producing time-dependent networks of gene transfer.

Quantitative Framework for Preferential Flow Initiation and Partitioning

Core Ideas Preferential flow can be predicted from the distribution of mesoscale matrix infiltrability. Soil matrix material, rather than the characteristics of macropores, largely controls preferential flow. Two different scales of representative areas are needed to predict matrix–macropore partitioning. A model for preferential flow in macropores is based on the short‐range spatial distribution of soil matrix infiltrability. It uses elementary areas at two different scales. One is the traditional representative elementary area (REA), which includes a sufficient heterogeneity to typify larger areas, as for measuring field‐scale infiltrability. The other, called an elementary matrix area (EMA), is smaller, but large enough to represent the local infiltrability of soil matrix material, between macropores. When water is applied to the land surface, each EMA absorbs water up to the rate of its matrix infiltrability. Excess water flows into a macropore, becoming preferential flow. The land surface then can be represented by a mesoscale (EMA‐scale) distribution of matrix infiltrabilities. Total preferential flow at a given depth is the sum of contributions from all EMAs. Applying the model, one case study with multi‐year field measurements of both preferential and diffuse fluxes at a specific depth was used to obtain parameter values by inverse calculation. The results quantify the preferential–diffuse partition of flow from individual storms that differed in rainfall amount, intensity, antecedent soil water, and other factors. Another case study provided measured values of matrix infiltrability to estimate parameter values for comparison and illustrative predictions. These examples give a self‐consistent picture from the combination of parameter values, directions of sensitivities, and magnitudes of differences caused by different variables. One major practical use of this model is to calculate the dependence of preferential flow on climate‐related factors, such as varying soil wetness and rainfall intensity.

Preferential Magnetic Flux Invasion and Heat Generation Owing to Macrostructure in HTS Bulk Magnets in Pulse Field Magnetization Processes

In order to clarify the behavior of the magnetic flux that invade into the melt-processed Dy123-based high-temperature superconducting bulk magnet, the motions of magnetic fluxes and the phenomena of heat generation were precisely measured during the pulsed field magnetization processes. In the experiments, we estimated the time evolutional profiles that were measured at two portions in the growth sector region and the growth sector boundary. They are characterized as the areas of lower and higher critical current densities than each other, respectively. The serial pulsed magnetic fields of 5 T were applied to the sample at 30 K, and the data were obtained in turn by the Hall sensor and thermometer that were put at several positions along the radial rows on the growth sector boundary and the growth sector region. The profiles of magnetic flux during the pulsed field application actually proved that the magnetic flux invades the sample through the growth sector regions in shorter time and with stronger magnitude than through the growth sector boundaries. Since the low magnetic field application leads to low heat generation, it is expected to achieve the higher trapped field performances than ever.

Approximate models for the ion-kinetic regime in inertial-confinement-fusion capsule implosions

“Reduced” (i.e., simplified or approximate) ion-kinetic (RIK) models in radiation-hydrodynamic simulations permit a useful description of inertial-confinement-fusion (ICF) implosions where kinetic deviations from hydrodynamic behavior are important. For implosions in or near the kinetic regime (i.e., when ion mean free paths are comparable to the capsule size), simulations using a RIK model give a detailed picture of the time- and space-dependent structure of imploding capsules, allow an assessment of the relative importance of various kinetic processes during the implosion, enable explanations of past and current observations, and permit predictions of the results of future experiments. The RIK simulation method described here uses moment-based reduced kinetic models for transport of mass, momentum, and energy by long-mean-free-path ions, a model for the decrease of fusion reactivity owing to the associated modification of the ion distribution function, and a model of hydrodynamic turbulent mixing. The transport models are based on local gradient-diffusion approximations for the transport of moments of the ion distribution functions, with coefficients to impose flux limiting or account for transport modification. After calibration against a reference set of ICF implosions spanning the hydrodynamic-to-kinetic transition, the method has useful, quantifiable predictive ability over a broad range of capsule parameter space. Calibrated RIK simulations show that an important contributor to ion species separation in ICF capsule implosions is the preferential flux of longer-mean-free-path species out of the fuel and into the shell, leaving the fuel relatively enriched in species with shorter mean free paths. Also, the transport of ion thermal energy is enhanced in the kinetic regime, causing the fuel region to have a more uniform, lower ion temperature, extending over a larger volume, than implied by clean simulations. We expect that the success of our simple approach will motivate continued theoretical research into the development of first-principles-based, comprehensive, self-consistent, yet useable models of kinetic multispecies ion behavior in ICF plasmas.

Asymmetry of radiation damage properties in Al–Ti nanolayers

Molecular dynamics (MD) simulations were employed with empirical potentials to study the effects of multilayer interfaces and interface spacing in Al–Ti nanolayers. Several model interfaces derived from stacking of close-packed layers or face-centered cubic {100} layers were investigated. The simulations reveal significant and important asymmetries in defect production with ∼60% of vacancies created in Al layers compared to Ti layers within the Al–Ti multilayer system. The asymmetry in the creation of interstitials is even more pronounced. The asymmetries cause an imbalance in the ratio of vacancies and interstitials in films of dissimilar materials leading to >90% of the surviving interstitials located in the Al layers. While in the close-packed nanolayers the interstitials migrate to the atomic layers adjacent to the interface of the Al layers, in the {100} nanolayers the interstitials migrate to the center of the Al layers and away from the interfaces. The degree of asymmetry and defect ratio imbalance increases as the layer spacing decreases in the multilayer films. Underlying physical processes are discussed including the interfacial strain fields and the individual elemental layer stopping power in nanolayered systems. In addition, experimental work was performed on low-dose (1016atoms/cm2) helium (He) irradiation on Al/Ti nanolayers (5nm per film), resulting in He bubble formation ∼1nm in diameter in the Ti film near the interface. The correlation between the preferential flux of displaced atoms from Ti films to Al films during the defect production that is revealed in the simulations and the morphology and location of He bubbles from the experiments is discussed.

Improved horizontal installation of large soil moisture content sensors and interpretation of their readings in terms of preferential flow / Zlepšená vodorovná instalace velkých čidel půdní vlhkosti a interpretace jejich čtení ve smyslu preferenčního proudění

Soil moisture content was measured by TDR sensors Aqua-Tel-TDR (Automata, Inc., today McCrometer CONNECT) in a loamy Chernozem on carbonate-rich loess substrate. The sensors, wrapped in slurry made of local soil and water, were installed horizontally into pre-made holes. The bias caused by imperfectly filled gaps between the wall of the hole and the sensor surface was reduced by field calibration. The same gaps made it possible to detect the preferential flow in soil macropores, due to which the reflectometric readings were perceivably higher than analogous readings before percolation events and sometimes higher than the native soil porosity. One typical event is presented. It is envisaged that sensors of this type can be used for semi-quantitative estimation of the preferential flux density, e.g. with the help of dual or multiple porous medium models or the momentum dissipation theory.

Percolation in macropores and performance of large time-domain reflectometry sensors

  The large-diameter time-domain reflectometry soil water sensors placed horizontally in a structured loamy soil are very sensitive to rapid preferential percolation events. Their readings on these occasions rise considerably, often becoming higher than the native soil’s porosity. The effect is caused by gaps between the native soil and the sensors. The geometry of the gaps, even if filled with soil slurry at installation, is not exactly reproducible, which leads to sensor-to-sensor variability of readings. Field calibration in percolation-free periods lead to non-unique trajectories rather than monotonous calibration curves, which can be commented in terms of soil heterogeneity and the dual porosity theory. Data of two typical percolation events are presented. Sensors of this type can be used for detection of preferential flux.  

Evaluating Coupled Water, Vapor, and Heat Flows and Their Influence on Moisture Dynamics in Arid Regions

The flow and thermal driven processes are crucial for the soil water dynamics in the vadose zone in arid regions. The understanding of the soil moisture and heat distribution is important for assessing the fate and transport of contaminants for the waste-burial site in a desert setting. A coupled water, vapor, and heat flow model was used in this study for evaluating the interactions of these processes and their influence on the moisture dynamics in the Amargosa Desert Research Site (ADRS) in southern Nevada. The treatment of preferential flow was also included in the model. Data from a previously conducted tracer experiment were used for estimating initial parameters of preferential flux and the parameters in pedotransfer functions (PTFs), while the Levenberg-Marquardt algorithm was used to optimize various parameters in the model calibration on the basis of the observation data. After the model calibration, three-year simulations (1998–2000) were conducted for evaluating the spatiotemporal variability of soil moisture and temperature in the site. The simulation results show that the performance of thermal model with vapor and preferential flow is close to those of isothermal model without vapor and preferential flow as compared with the observed records in ADRS, while critical physical mechanisms could be well described with the thermal model. The vapor flow for the water budget on the upper boundary is insignificant while it influences the water content distribution in the soil profile; the wetting front depth of preferential flow and water budget has increased in rain days; however, the high evaporation counteracts it in the annual water budget. The thermal diffusion of water vapor and thermal liquid fluxes were affected by temperature fluctuation and soil water saturation status. Comparison between the flux components shows that the thermal driven flux has more weight on the water movement in the soil profile. Results indicate that the coupled flow and thermal model could well describe the natural condition in arid regions and is more efficient in simulating mutual effects among various processes.

Brownian Permeability Computation Model Predicts That Differences in the Internal Radii of the Pore are Determinant for Unidirectional and Reversal Fluxes through Gap Junction Channels

Gap junctions are vital in multiple organs’ physiology and are linked to severe genetic diseases. Connexins are the proteins forming these gap junction channels which allow molecular and ionic selective-diffusion amongst neighboring cells. Selectivity is connexin-type dependent. In between HeLa cells expressing distinct connexins (e.g. Cx43 and Cx45), heterotypic channels formed induce a preferential flux of large fluorescent molecules towards the Cx43 side. The independence to molecule's charge, points towards a high relevance of the channel's pore shape. To study the effects of pore shape on particles movement, a 3D-computational channel model was developed, emulating X-ray crystallographic structures from Cx43 and Cx26. The sections of the pore were approximated to standard geometric shapes including a central ellipsoidal vestibule. Ellipsoids were placed on either ends of the pore, representing controlled volumes from coupled cells. Particles were modeled as spheres and Brownian dynamics was used to model particles’ interactions. Simulations for different pore geometries show that against conventional thought, some shapes can explain the direction of the preferential flux data that comply with the electrical resistances measured through electrophysiological recordings. This pore-geometry causes a different intra-pore mechanism that requires an asymmetric vestibule with radii comparable to the particle size. In our simulations when particles were introduced from the side of the pore where the inner mouth is larger, particles reside longer in the vestibule using it as an intermediate stop and forcing the particles to cross faster to the other side of the pore.