Diffusion Trapping Research Articles

Fractional differentiation method: Some applications to the theory of subdiffusion-controlled reactions.

The fractional differentiation method's broad possibilities are demonstrated with rather simple but important examples of the anomalous diffusion trapping problems. In particular we evaluate the reaction rate coefficients for the subdiffusion-controlled reactions and for reactions describing by a diffusion equationwith a half-order time derivative as a damping term. The distinctive feature of this aproach is that the reaction rate coefficient may be obtained by means of some factorization procedure immediately, without a preliminary solution to the corresponding initial boundary value diffusion problem. The explanations given in the paper are detailed enough to provide the mathematical background for the fractional differentiation method needed to apply it to a wide range of reaction-diffusion problems with time-fractional derivatives in the Riemann-Liouville sense.

Quantitative evaluation of oncogenic KRAS signaling and therapeutic effects of molecular-targeted drugs in living cells by single-molecule imaging.

76 Background: Oncogenic KRAS mutations pose challenges due to their constitutive activation and resistance to drugs in colorectal cancer. However, several aspects remain unresolved. Single-molecule imaging has revealed distinct behaviors of KRAS. Inactive KRAS wild-type (WT) molecules exhibit continuous lateral diffusion on the plasma membrane, while activated or oncogenic KRAS molecules display slower diffusion and transient trapping due to interactions with signaling molecules. These observations suggest that the overall signal intensity of KRAS within a cell is finely regulated by integrating short-term pulse signals during transient trapping. Methods: We conducted single-molecule observations of KRAS (WT, G13D, and G12D/C/V) in living colon cancer cells, both with and without molecular-targeted drugs, before and after EGF stimulation. We quantitatively analyzed their diffusional behavior to evaluate KRAS signaling and the therapeutic effects of molecular-targeted drugs. Results: The temporal fraction of trapped KRAS WT was highest at 2 minutes (6.4%) and decreased to pre-activation level (3.0%) at 5 minutes after EGF stimulation. Although the temporal fractions of trapped KRAS mutants were higher than those of KRAS WT both before stimulation (5%) and after stimulation (10%), their diffusional behaviors were mutation-specific. The temporal fraction of trapped KRAS G13D increased sharply, and those of KRAS G12D and G12C increased at a moderate rate, while that of KRAS G12V did not elevate after EGF stimulation. Cetuximab treatment significantly reduced the temporal fraction of trapped KRAS WT after stimulation, but only moderately decreased those of KRAS mutants. Notably, transient trappings of KRAS G12D and G12C were abrogated by KRAS inhibitors, and the combined therapy of KRAS inhibitors and cetuximab demonstrated additive effects. Conclusions: Our findings indicate that the mutation-specific diffusional behavior of oncogenic KRAS can be quantitatively assessed by single-molecule imaging. This method serves as a powerful tool to uncover the mechanisms underlying oncogenic KRAS signaling and evaluate the therapeutic efficacy of molecular-targeted drugs in living cells.

Activity-dependent diffusion trapping of AMPA receptors as a key step for expression of early LTP.

This review focuses on the activity-dependent diffusion trapping of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) as a crucial mechanism for the expression of early long-term potentiation (LTP), a process central to learning and memory. Despite decades of research, the precise mechanisms by which LTP induction leads to an increase in AMPAR responses at synapses have been elusive. We review the different hypotheses that have been put forward to explain the increased AMPAR responsiveness during LTP. We discuss the dynamic nature of AMPAR complexes, including their constant turnover and activity-dependent modifications that affect their synaptic accumulation. We highlight a hypothesis suggesting that AMPARs are diffusively trapped at synapses through activity-dependent interactions with protein-based binding slots in the post-synaptic density (PSD), offering a potential explanation for the increased synaptic strength during LTP. Furthermore, we outline the challenges still to be addressed before we fully understand the functional roles and molecular mechanisms of AMPAR dynamic nanoscale organization in LTP. This article is part of a discussion meeting issue 'Long-term potentiation: 50 years on'.

Modeling the effect of grain boundary diffusivity and trapping on hydrogen transport using a phase-field compatible formulation

Hydrogen grain boundary (GB) trapping is widely accepted as the main cause for hydrogen induced intergranular failure. Several studies were conducted to unveil the role of GBs on hydrogen transport; however, a clear understanding is yet to be attained. This is due to the limitations of the state-of-the-art experimental procedures for such highly kinetic processes. In this study, we aim at providing a deeper understanding of hydrogen-GB interactions using full-field representative volume element (RVE). The phase-field method is chosen for generating RVEs, since it is an appropriate numerical tool to represent GBs. A novel fully-kinetic formulation for hydrogen diffusion and GB trapping is presented, which is compatible with the phase-field based RVEs. GB diffusivity (Dgb) and trap-binding energy (Egb) were used as parameters to understand the interactions between diffusion and GB trapping. Uptake and permeation simulations were performed with constant and gradient occupancy boundary conditions respectively. In both cases, increasing Egb, increased the hydrogen GB occupancy. The permeation simulations showed that the hydrogen flux along the GBs increased with increasing both, Dgb and, surprisingly, Egb. Since trapping increases the hydrogen occupancy along GBs, it also increases the occupancy gradients, resulting in a higher flux. This led to the conclusion that, in the case of an external occupancy gradient, GB trapping and diffusion cooperate, rather than compete, to increase the hydrogen flux. On the other hand, the decisive factor for the retention of hydrogen at the GBs in permeation simulations was Dgb rather than Egb.

Imaginary Poynting forces on a magnetodielectric particle under cylindrical vector lights

Particles with magnetodielectric dual responses endure the unique imaginary Poynting force, attributed to the crossed interference between electric and magnetic dipoles. In this work, we theoretically demonstrate that for illumination of cylindrical vector light with azimuthal or radial polarization, the imaginary Poynting force has a radial diffusion or centripetal trapping characteristic exerted on a magnetodielectric particle. Moreover, with a superposition of linearly-polarized light on the cylindrical vector light, an extra transverse force will emerge with a unidirectional characteristic. Our work reveals the unique role of imaginary Poynting force for optical manipulations on magnetodielectric particles by cylindrical vector lights, including radial diffusion, centripetal trapping, and transverse conveying.

Actin filaments form a size‐dependent diffusion barrier around centrosomes

The centrosome, a non‐membranous organelle, constrains various soluble molecules locally to execute its functions. As the centrosome is surrounded by various dense components, we hypothesized that it may be bordered by a putative diffusion barrier. After quantitatively measuring the trapping kinetics of soluble proteins of varying size at centrosomes by a chemically inducible diffusion trapping assay, we find that centrosomes are highly accessible to soluble molecules with a Stokes radius of less than 5.8 nm, whereas larger molecules rarely reach centrosomes, indicating the existence of a size‐dependent diffusion barrier at centrosomes. The permeability of this barrier is tightly regulated by branched actin filaments outside of centrosomes and it decreases during anaphase when branched actin temporally increases. The actin‐based diffusion barrier gates microtubule nucleation by interfering with γ‐tubulin ring complex recruitment. We propose that actin filaments spatiotemporally constrain protein complexes at centrosomes in a size‐dependent manner.

Local structures of phosphorus atoms implanted in crystalline diamond

Effective impurity doping into diamond by an ion implantation technique has been one of the crucial issues for realizing diamond-based high-power electronic devices. Especially for n-type impurity doping, the electrical activation has not been accomplished yet in a practically available level. In this study, local structures and depth profiles of implanted phosphorus atoms were studied by x-ray absorption spectroscopy, secondary ion mass spectroscopy, and first-principles calculations. P ion implantations were performed at two extreme substrate temperatures of room temperature and 900°C at multiple incident energies from 10 to 150 keV for flat doping and a single energy of 200 keV for δ-doping followed by activation annealing at 1300°C. The x-ray absorption spectra and the theoretical calculation showed that most of the implanted phosphorus atoms implanted with a flat doping concentration are existent in the substitutional site; however, they seem to bond with hydroxyl or vacancy complexes, probably resulting in electrical inactivation. Indeed, secondary ion mass analysis showed that a large number of O and H atoms are distributed in the P-doped layer, probably diffused from the surface through a damaged network. On the other hand, impurity diffusion was not observed in the P δ-doped sample followed by high-temperature annealing with a cap layer. It is clearly suggested that a damaged layer by ion irradiation near the surface acts as diffusion channels and trap sites of various impurities. High-temperature annealing with a cap layer is also quite effective in suppressing the formation of the defective layer that becomes a diffusion path of O and H.

Revealing the radiation damage and Al-content impacts on He diffusion in goethite

Over the past few decades, the (U-Th)/He geochronological method on goethite has been more and more applied to date laterite formation and evolution or ore-deposit formation. However, questions remain on possible He loss by diffusion due to the polycrystalline structure of goethite and associated underestimation of the goethite crystallization date given by the (U-Th)/He age. Prior studies estimated helium loss in goethite to range from 2 to 30%, but no relation or models have been produced to explain such values. To clarify the situation, we firstly performed a complete review of experimental He diffusion data in natural goethite, that reveals the link between activation energy and He loss with the damage dose. To understand He diffusion behavior in goethite and model the He loss, natural defect and alpha damage as well as the chemical composition and growth structure effect on He diffusion have been investigated thanks to a multi-scale study. We used numerical simulations combining the Density Functional Theory (DFT) at the atomic scale and Kinetic Monte Carlo (KMC) simulations at the macroscopic scale. We found that He diffusion is purely anisotropic along the preferential elongated axis (i.e., b-axis) and He leaks out easily in defect-free goethite and Al-goethite. The consequence of this anisotropy is that crystallographic defects and alpha damage strongly lower the He diffusivity in goethite and Al-goethite by obstructing the diffusion channel or trapping He along the b-axis. Defect and damage impact on He diffusion is even larger for Al-goethite. The obtained He diffusion parameters for goethite containing defect and damage are similar to the activation energy and He diffusional loss obtained in natural goethite from the literature. We demonstrate the systematic dependence of the diffusion coefficient with damage dose and the impact of Al on He retention. He atoms are retained only at the favor of obstructions blocking the diffusion and vacancies trapping them in the goethite structure. The consequence of the diffusive behavior is that a part of He diffuses out of the crystal until sufficient damage accumulated along the b-axis. The diffusion domain size is the channel length along the b-axis rather than the whole crystallite size. To correct the He loss this study proposes estimation of the He retention and needed corrections for different types of goethite.

An intermediate model for fitting triplet–triplet annihilation in phosphorescent organic light emitting diode materials

Triplet–triplet annihilation (TTA) is one of the primary contributors to efficiency roll-off and permanent material degradation in phosphorescent organic light-emitting diodes. The two limiting case models typically used to quantify this quenching mechanism are multi-step Dexter and single-step Förster, which, respectively, assume ideal Fickian diffusion or perfect trapping of triplet excitons. For device-relevant guest doping levels (typically 5–12 vol. %), both significant diffusion of excitons and trapping due to spatial and energetic disorder exist, so neither conventional model fits experimental data well. We develop and validate an intermediate TTA model, which is a weighted average of the limiting cases of pure radiative decay (no TTA) and multi-step Dexter based TTA that returns an effective TTA rate constant and a parameter quantifying the portion of well-isolated excitons. Kinetic Monte-Carlo simulations and time-resolved photoluminescence measurements of an archetype host–guest system demonstrate that our intermediate model provides significantly improved fits with more realistic physical values, is more robust to variations in experimental conditions, and provides an analysis framework for the effects of trapping on TTA.

Studies of recrystallization in rhenium using positron annihilation spectroscopy

Pure rhenium exposed to cold-rolling was subjected to annealing studies using positron annihilation techniques. The recovery and recrystallization processes were observed using these techniques and they were confirmed by hardness measurement and X-ray diffraction. Using the positron diffusion trapping model the activation energy of the grain boundary migration was determined as 1.08±0.05 eV, and the recrystallization temperature was estimated to be around 950 °C. Additionally, the bulk positron lifetime in this metal determined as 98.38±0.30 ps.

On the phase-field modeling of rapid solidification

The phase-field method has been widely used to study the rapid solidification processes such as additive manufacturing. To lower the computational cost, many simplifications and modifications were made to the original set of phase-field equations for alloy solidification. However, how those simplifications affect the modeling outcome is not well studied. In this work, we developed a phase-field model incorporated with both the coupled thermal-solutal diffusion and solute trapping for the rapid solidification of dilute binary alloys. We focused on the quantification of the influences of the simplifications of interface kinetics, solute trapping, and thermal diffusion on the modeling outcomes. By turning on and off those three effects individually, we explore how the temperature, solute concentration and interfacial velocity are affected. Our investigation shows that the interface kinetics and thermal diffusion cannot be ignored for quantitative modeling of a rapid solidification process for alloys. In the end, we used the rapid solidification of a melt-spun ribbon as an example to show that the phase-field model with all the three aspects considered is capable of capturing the complex interplay among temperature, solute concentration, and interfacial velocity and predicting the resultant solidification structures.

On the use of recombination rate coefficients in hydrogen transport calculations

The commonly accepted picture for the uptake of hydrogen isotopes (HIs) from the gas phase across the surface into a metal with an endothermic heat of solution for HIs is that of dissociation followed by thermalisation in a chemisorbed surface state and finally overcoming a surface barrier to enter the metal bulk where the HIs occupy interstitial solute sites. To leave the metal bulk the HIs first transition to the chemisorbed surface state from which they then enter gas phase by recombining into a diatomic molecule. This model is generally attributed to the work of Pick and Sonnenberg from 1985. They clearly distinguish surface states and subsurface solute sites where the recombination flux is proportional to the square of the concentration of chemisorbed atoms due the diatomic nature of this Langmuir–Hinshelwood process. In an effort to compare their extended model with an earlier surface model by Waelbroeck, which uses an expression for the recombination flux proportional to the square of the sub-surface interstitial solute concentration, they derive an effective recombination coefficient. However, also with the so-derived Pick and Sonnenberg recombination coefficient, the Waelbroeck model is only applicable under certain conditions. But, due to its simplicity, it is often used in boundary conditions of diffusion trapping type calculations, generally ignoring whether or not these conditions are met. This paper will use the full Pick and Sonnenberg model implemented in the TESSIM-X code and in simplified algebraic approximations, to show the limits of applicability of the Waelbroeck–Ansatz in modelling hydrogen transport in metals foreseen for the first wall of magnetic confinement fusion devices.

Revealing Explicit Microsecond Carrier Diffusion from One Emission Center to Another in an All-Inorganic Perovskite Nanocrystal.

Blinking of freely diffusing CsPbBr3 nanocrystals (NCs) is studied using fluorescence lifetime correlation spectroscopy (FLCS). Emitted photons from each NCs are assigned to an emission state (exciton or trap) based on their lifetime. Subsequently, an intrastate autocorrelation function (ACF) and an interstate cross-correlation function (CCF) are constructed. Fitting of the AFCs with an analytical model shows that, at low excitation power, the microsecond blinking timescale of the exciton state matches well with that of the trap state. Most interestingly, both of those timescales further correlate with the microsecond growth timescale of the CCF. The strong anti-correlation of the CCF along with the stretched exponential nature of the blinking kinetics confirms the involvement of carrier diffusion and dispersive trap states in NC blinking. At high excitation power, enhanced sample heterogeneity causes a more dispersive blinking. To the best of our knowledge, this is the first report of a NC blinking study using a single-molecule-based FLCS technique.

Analysis of positron profiling data using e[formula omitted]DSc computer code

The Green’s function method was applied to solve the one-dimensional positron diffusion equation for a system consisting of up to four layers that contain defects with different trapping rates. These allow us to obtain the analytical relationships valid for the evaluation of data obtained from variable energy positron measurements. They have been implemented in user-friendly free computer code available to users. Fitting strategies are presented to extract the relevant physical parameters. The code was used to determine positron diffusion length in samples of polycrystalline pure, well-annealed iron, depleted uranium, and titanium. Program summaryProgram Title: e+DSC-1CPC Library link to program files: https://doi.org/10.17632/jxpj25kjvr.1Licensing provisions: MIT licenseProgramming language: Microsoft Visual Basic 2015External routines/libraries: Accord.NETNature of problem: The program enables the analysis of data obtained from a variable energy positron beam. The shape parameter of the annihilation line as a function of the incident positron energy is evaluated using a positron diffusion trapping model in which the positron trapping rate function is expressed as a four-step function.Solution method: The one-dimensional diffusion equation was solved by the Green’s function method. This allows the use of an exact form for the positron implantation profile, which is used in the program as the Makhov’s function. The parameters of this function are obtained from the MC simulation with GEANT4 and stored in the program.

A semi-physical α-β model on bainite transformation kinetics and carbon partitioning

A semi-physical kinetic model with two adjustable parameters is proposed for prediction of the isothermal bainite transformation and carbon redistribution in steels. The model incorporates the evolution equation of the carbon concentration in bainite, employing the Fermi-Dirac statistic function, and it can phenomenologically capture the evolution of carbon contents of bainite sheaves and the carbon enrichment in the residual austenite. The parameter α reflects the probability for carbon atoms to escape from bainite sheaves into the surrounding bulky austenite, while the parameter β describes the potential for bainite to contribute to the carbon enrichment in bulky austenite. The influence of α on the kinetics of the bainite transformation is explained on the basis of carbon diffusion and carbon trapping, which show a significant temperature dependence. The present model, with its combined adjustment of α and calibrated β, is capable of reproducing the experimental kinetics of bainite transformation for a variety of different steels.

Diffusion, Interactions, and Disparate Kinetic Trapping of Water-Hydrocarbon Mixtures in Nanoporous Solids.

Mixed fluids confined in porous solid hosts present challenges for the accurate characterization of individual-component behavior. NMR diffusometry with chemical resolution is used to identify unexpected loading- and composition-dependent anomalous diffusion in water/cyclohexane mixtures confined to solid nanoporous glass (NPG) hosts. Diffusion NMR results indicate that data obtained on pure-component liquids in confinement cannot be extrapolated to their nonideal liquid mixtures confined in the same solid host. Loading-dependent data must be obtained on each component in the confined mixture in order to determine which of the liquid components exhibits chemical affinity for the host and, conversely, which of the components exhibits anomalous diffusivity. Most notably, NMR diffusometry revealed that cyclohexane diffusivity varied by 2 orders of magnitude in a water-rich mixture depending on the total fluid loading in the NPG host, ranging from anomalously high diffusivities that significantly exceeded that for pure cyclohexane in NPG at low fluid loadings to kinetically trapped sequestration at high fluid loadings. NMR diffusometry indicates that nonideal solution behavior in fluids confined within nanoporous hosts may have practical implications for enhanced oil recovery methods. Specifically, kinetic trapping of hydrocarbons in water-flooding regimes can result from complex liquid-vapor equilibrium that is significantly perturbed from that which exists in bulk or microporous confinement.

Accumulation of Neurofascin at Nodes of Ranvier Is Regulated by a Paranodal Switch.

The paranodal junctions flank mature nodes of Ranvier and provide a barrier between ion channels at the nodes and juxtaparanodes. These junctions also promote node assembly and maintenance by mechanisms that are poorly understood. Here, we examine their role in the accumulation of NF186, a key adhesion molecule of PNS and CNS nodes. We previously showed that NF186 is initially targeted/accumulates via its ectodomain to forming PNS (hemi)nodes by diffusion trapping, whereas it is later targeted to mature nodes by a transport-dependent mechanism mediated by its cytoplasmic segment. To address the role of the paranodes in this switch, we compared accumulation of NF186 ectodomain and cytoplasmic domain constructs in WT versus paranode defective (i.e., Caspr-null) mice. Both pathways are affected in the paranodal mutants. In the PNS of Caspr-null mice, diffusion trapping mediated by the NF186 ectodomain aberrantly persists into adulthood, whereas the cytoplasmic domain/transport-dependent targeting is impaired. In contrast, accumulation of NF186 at CNS nodes does not undergo a switch; it is predominantly targeted to both forming and mature CNS nodes via its cytoplasmic domain and requires intact paranodes. Fluorescence recovery after photobleaching analysis indicates that the paranodes provide a membrane diffusion barrier that normally precludes diffusion of NF186 to nodes. Linkage of paranodal proteins to the underlying cytoskeleton likely contributes to this diffusion barrier based on 4.1B and βII spectrin expression in Caspr-null mice. Together, these results implicate the paranodes as membrane diffusion barriers that regulate targeting to nodes and highlight differences in the assembly of PNS and CNS nodes.SIGNIFICANCE STATEMENT Nodes of Ranvier are essential for effective saltatory conduction along myelinated axons. A major question is how the various axonal proteins that comprise the multimeric nodal complex accumulate at this site. Here we examine how targeting of NF186, a key nodal adhesion molecule, is regulated by the flanking paranodal junctions. We show that the transition from diffusion-trapping to transport-dependent accumulation of NF186 requires the paranodal junctions. We also demonstrate that these junctions are a barrier to diffusion of axonal proteins into the node and highlight differences in PNS and CNS node assembly. These results provide new insights into the mechanism of node assembly and the pathophysiology of neurologic disorders in which impaired paranodal function contributes to clinical disability.

A new perspective on hydrogen diffusion and hydrogen embrittlement in low-alloy high strength steel

Hydrogen diffusion and hydrogen induced embrittlement have been studied in low-alloyhigh strength steel tempered at three different temperature using electrochemical permeation and mechanical tensile tests, respectively. After multiple hydrogen trap sites around dislocation core was first proposed, the quantitative relations between hydrogen diffusivity, hydrogen concentration, as well as activation energy for hydrogen diffusion and hydrogen trap sites density were developed. In addition, the hydrogen-induced embrittlement would result from higher trap density and higher hydrogen concentration. Hence the connection among hydrogen diffusion, microstructure and hydrogen induced embrittlement were established where the hydrogen trap sites density served as a bridge.

Solution‐Processed MAPbBr3 and CsPbBr3 Single‐Crystal Detectors with Improved X‐Ray Sensitivity via Interfacial Engineering

Organic–inorganic hybrid perovskites have been recognized as prospective materials for use in radiation detection application due to their high atomic number, ease of crystal processing, and excellent electronic properties. Herein, solution‐synthesized MAPbBr3 and CsPbBr3 detectors with different structures are constructed. Charge diffusion length and trap density analysis reveal that CsPbBr3 possesses better thermal stability but worse charge‐transport properties than MAPbBr3. To improve the signal current under X‐ray radiation, MoO3 is applied as a hole‐extraction layer to increase hole‐carrier collection. The sensitivity of X‐ray detectors with MoO3 layer can reach up to 2552 μC Gyair−1 cm−2 at an electric field of 45 V cm−1, which is higher than that without the MoO3 layer. It is shown that charge‐transport capability significantly affects the response of the signal current to X‐ray radiation; it also reveals the importance of interface engineering as a means to realize high‐sensitivity X‐ray detectors.

Ultrafast removal of Cu(II) by a novel hierarchically structured faujasite-type zeolite fabricated from lithium silica fume

Novel hierarchically structured Faujasite Type (FAU) zeolite was fabricated from industrial waste lithium silica fume (LSF) via hydrothermal method without the addition of templates. The FAU zeolites exhibited spherical filler morphology with maximum surface area of 372.8 m2/g, enriched microporosity (0.164 cm3/g), and abundant mesoporosity. Owing to its unique structure, the FAU zeolite allowed ultrafast diffusion and rapid trap of copper ion inside the cages of zeolite crystals, and achieved maximum removal (78.76%) of Cu(II) within the very first 2 min, with adsorption rate constant 5.46–6.27 times greater than that of mesoporous commercial zeolite (CZ) between 15 and 45 °C. The physico-chemical structures of the FAU zeolites were carefully studied by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), Fourier Transform Infrared Spectrometry (FT-IR), surface area analyzer (BET) and X-ray photoelectron spectroscopy (XPS). The maximum qe toward Cu(II) achieved by FAU zeolite (i.e., Z9, S/A of 9) featuring a qe of 94.46 mg/g at 25 °C as per calculated from Langmuir model, which is more than twice amount achieved by CZ (39.15 mg/g). Z9 also showed outstanding selectivity for Cu(II) over various coexisting ions. The saturated Z9 can be regenerated with a mild washing procedure, and the spent zeolite can be reused as effective antibacterial agent. This work proposes a cost-effective and green synthesis route for the hierarchically structured zeolite with high copper selective removal capacity from industrial waste.