Diffusion Mode Research Articles

Thymine DNA glycosylase combines sliding, hopping, and nucleosome interactions to efficiently search for 5-formylcytosine

Base excision repair is the main pathway involved in active DNA demethylation. 5-formylcytosine and 5-carboxylcytosine, two oxidized moieties of methylated cytosine, are recognized and removed by thymine DNA glycosylase (TDG) to generate an abasic site. Using single molecule fluorescence experiments, we study TDG in the presence and absence of 5-formylcytosine. TDG exhibits multiple modes of linear diffusion, including hopping and sliding, in search of base modifications. TDG active site variants and truncated N-terminus, reveals these variants alter base modification search and recognition mechanism of TDG. On DNA containing an undamaged nucleosome, TDG is found to either bypass, colocalize with, or encounter but not bypass the nucleosome. Truncating the N-terminus reduces the number of interactions with the nucleosome. Our findings provide mechanistic insights into how TDG searches for modified DNA bases in chromatin.

Optical scattering methods for the label-free analysis of single biomolecules.

Single-molecule techniques to analyze proteins and other biomolecules involving labels and tethers have allowed for new understanding of the underlying biophysics; however, the impact of perturbation from the labels and tethers has recently been shown to be significant in several cases. New approaches are emerging to measure single proteins through light scattering without the need for labels and ideally without tethers. Here, the approaches of interference scattering, plasmonic scattering, microcavity sensing, nanoaperture optical tweezing, and variants are described and compared. The application of these approaches to sizing, oligomerization, interactions, conformational dynamics, diffusion, and vibrational mode analysis is described. With early commercial successes, these approaches are poised to have an impact in the field of single-molecule biophysics.

POSSIBILITIES OF SYNTHESIS OF UNCHARGED STABLE LATEX PARTICLES FOR IMMUNOANALYSIS

Objective: The objective of this study is to find a method for synthesizing uncharged polystyrene latex particles whose surface can be easily modified. Theoretical basis: The main method of latex synthesis is emulsion polymerization. Latexes for a specific purpose can be obtained by polymerization in heterogeneous monomer-water systems, without the use of emulsifiers, both with intensive mixing of the system and under static conditions. In this work, polymerization was carried out without the use of emulsifiers in a static monomer-water system. Method: To achieve the set goal, the possibility of obtaining latex particles using a hydrophobic initiator - ditrile of azoisobutyric acid - was investigated by carrying out polymerization in a diffusion mode in a three-phase system monomer - water - initiator. Results and discussion: The results of the study showed that the latex obtained in the three-phase system is stable. It is assumed that the stability is due to the presence of hydroxyl end groups groups of polymer molecules on the surface of the latex particles, which are formed as a result of the reaction of the initiator with water and initiate polymerization. The synthesized latexes retained stability for a year. Practical value: Latexes can be used in all those areas of science and technology where the absence of a charge on the surface of latex particles is required. Originality/value: The originality of the work lies in the fundamental simplicity of the synthesis and the unambiguity of the results obtained.

The research of knowledge diffusion network model for Tourism Destination-Public ecological civilization.

Visitor education plays a crucial role in the knowledge diffusion process in outdoor recreation and nature-based tourism. It entails sharing information, experiences, and insights with visitors to enhance their understanding and appreciation of the natural environment. Our methodology for investigating the diffusion of ecological civilization knowledge in tourism destinations involves constructing a knowledge diffusion network model. In this model, scenic spots, tourists, and the public are defined as network nodes, with the communication channels between them representing the edges of the network. By constructing a scale-free complex network, the knowledge diffusion mode of scenic spots can be depicted. The layer of resource supply node consists of different scenic spots, forming the core nodes set for knowledge diffusion in the tourism industry. This research aims to further explore the social and economic value of the tourism areas' ecological civilization knowledge diffusion, as well as analyze the path, quantity, and cost of knowledge diffusion. by analyzing this knowledge diffusion network model, insights into the effectiveness and impact of visitor education in promoting ecological civilization and sustainable practices in tourism destinations can be gained. Overall, this approach provides a theoretical framework for investigating and comprehending the knowledge diffusion process in Tourism Destination-Public ecological civilization, thereby shedding light on the social and economic benefits that can be derived from sustainable tourism practices.

Elemental diffusion coefficient prediction in conventional alloys using machine learning

This paper presents the Machine Learned Diffusion Coefficient Estimator, a comprehensive machine learning framework designed to predict diffusion coefficients in impure metallic (IM) and multi-component alloy (MCA) media. The framework incorporates five machine learning models, each tailored to specific diffusion modes: (1) impurity and (2) self-diffusion in IM media, and (3) self, (4) impurity, and (5) chemical diffusion in MCA media. These models use statistical aggregations of atomic descriptors for both the diffusing elements and the diffusion media, along with the temperature of the diffusion process, as features. Models are trained using the random forest and deep neural network algorithms, with performance evaluated through the coefficient of determination (R2), mean squared error (MSE), and uncertainty estimates. The models within this framework achieve an impressive R2 score above 0.90 with MSE less than 10−16 m2/s, demonstrating high predictive accuracy and reliability for diffusion coefficient.

Ultrafast Charge Separation Driven by Solvation-Coupled Intramolecular Torsion.

Photoinduced intramolecular charge separation in a pyrene- and triarylamine-based donor-acceptor dyad was studied by polarization-dependent femtosecond time-resolved transient absorption (TA) spectroscopy in polar solvents. Photoexcitation forms an excited state with charge transfer (CT) character due to the intrinsic electronic coupling between the triarylamine and pyrene groups, resulting in ultrafast charge separation (CS) in polar solvents. TA measurements reveal a correlation between the rate of CS and solvation dynamics, which implies that solvation is involved in the CS reaction. In addition, polarization-dependent TA spectroscopy was devoted to tracking the ultrafast anisotropy evolution of the cationic absorption band, which is attributed to intramolecular torsional motion and is proposed to be coupled to diffusive orientational solvent modes. The results therefore reveal that the evolution of the CT state in the condensed phase is driven by solvation-coupled excited-state structural relaxation. In other words, intramolecular torsional motion is directly confirmed to be involved in the reaction coordinate of the CS reaction in a strongly coupled donor-acceptor dyad.

Exploiting Materials Binding Peptides for the Organization of Resilient Biomolecular Constructs.

Elastomers based on the resilin protein confer exceptional mechanical resilience in nature, but it remains elusive to recover the remarkable properties of these materials when they are made in the laboratory. This is possibly due to preorganized conformations of resilin in its natural setting, facilitating Tyr-based cross-linking. Here, resilin-like peptides (RLPs) are conjugated with a graphene-binding peptide, P1, to produce P1/RLP conjugates, in which the P1 domain may provide favorable preorganization on a graphene surface. Experiments using quartz crystal microbalance analysis and atomic force microscopy identified that the parent RLPs demonstrate negligible graphene binding; however, integration of the P1 with the RLPs resulted in the formation of dense, patterned bioligand overlayers on graphene. To complement this, molecular simulations revealed a notable difference in binding mode of the conjugates compared with typical materials binding peptides. Specifically, the adsorption of the P1/RLP conjugates did not focus on a few strongly bound "anchor" residues, but instead supported a more diffuse mode of binding, with many more participating residues featuring moderate contact. Analysis of the number of available Tyr residues (i.e., those not adsorbed at the surface) indicate that the RLP2-based conjugates will provide greater opportunity for cross-linking when adsorbed on graphene, providing a framework to generate patterned elastomeric materials.

High-fidelity predictions of diffusion in the brain microenvironment

Multiple-particle tracking (MPT) is a microscopy technique capable of simultaneously tracking hundreds to thousands of nanoparticles in a biological sample and has been used extensively to characterize biological microenvironments, including the brain extracellular space (ECS). Machine learning techniques have been applied to MPT data sets to predict the diffusion mode of nanoparticle trajectories as well as more complex biological variables, such as biological age. In this study, we develop a machine learning pipeline to predict and investigate changes to the brain ECS due to injury using supervised classification and feature importance calculations. We first validate the pipeline on three related but distinct MPT data sets from the living brain ECS—age differences, region differences, and enzymatic degradation of ECS structure. We predict three ages with 86% accuracy, three regions with 90% accuracy, and healthy versus enzyme-treated tissue with 69% accuracy. Since injury across groups is normally compared with traditional statistical approaches, we first used linear mixed effects models to compare features between healthy control conditions and injury induced by two different oxygen glucose deprivation (1) exposure times. We then used machine learning to predict injury state using MPT features. We show that the pipeline predicts between the healthy control, 0.5 h OGD treatment, and 1.5 h OGD treatment with 59% accuracy in the cortex and 66% in the striatum, and identifies nonlinear relationships between trajectory features that were not evident from traditional linear models. Our work demonstrates that machine learning applied to MPT data is effective across multiple experimental conditions and can find unique biologically relevant features of nanoparticle diffusion.

Change-point detection in anomalous-diffusion trajectories utilising machine-learning-based uncertainty estimates

Abstract When recording the movement of individual animals, cells or molecules one will often observe changes in their diffusive behaviour at certain points in time along their trajectory. In order to capture the different diffusive modes assembled in such heterogeneous trajectories it becomes necessary to segment them by determining these change-points. Such a change-point detection can be challenging for conventional statistical methods, especially when the changes are subtle. We here apply Bayesian Deep Learning to obtain point-wise estimates of not only the anomalous diffusion exponent but also the uncertainties in these predictions from a single anomalous diffusion trajectory generated according to four theoretical models of anomalous diffusion. We show that we are able to achieve an accuracy similar to single-mode (without change-points) predictions as well as a well calibrated uncertainty predictions of this accuracy. Additionally, we find that the predicted uncertainties feature interesting behaviour at the change-points leading us to examine the capabilities of these predictions for change-point detection. While the series of predicted uncertainties on their own are not sufficient to improve change-point detection, they do lead to a performance boost when applied in combination with the predicted anomalous diffusion exponents.

Analytic structure of diffusive correlation functions

Diffusion is a dissipative transport phenomenon ubiquitously present in nature. Its details can now be analyzed with modern effective field theory (EFT) techniques that use the closed-time-path (or Schwinger-Keldysh) formalism. We discuss the structure of the diffusive effective action appropriate for the analysis of stochastic or thermal loop effects, responsible for the so-called long-time tails, to all orders. We also elucidate and prove a number of properties of the EFT and use the theory to establish the analytic structure of the n-loop contributions to diffusive retarded two-point functions. Our analysis confirms a previously proposed result by Delacrétaz that used microscopic conformal field theory arguments. Then, we analyze a number of implications of these loop corrections to the dispersion relations of the diffusive mode and new, gapped modes that appear when the EFT is treated as exact. Finally, we discuss certain features of an all-loop model of diffusion that only retains a special subset of n-loop “banana” diagrams. Published by the American Physical Society 2024

An interfacial dual-regulation strategy for ultra-stable 3D Zn metal anodes

The development of Zn metal-batteries, which are viewed as one of the most potential alternatives to lithium ion batteries, is severely hindered by sluggish ion diffusion kinetics and uncontrollable dendritic growth for anodes. Herein, we propose an interfacial dual-regulation strategy for the fabrication of 3D Zn anode through the direct in-situ treatment of benchmark Zn foil. Both rapid ion migration dynamics and homogeneous bottom-up Zn2+ deposition are achieved due to the unique open nanoarray structure with superhydrophilic and zincophilic interface to the electrolyte. Theoretical calculations and finite element simulations reveal this design can effectively redistribute Zn2+ and increase ion flux with a long-lasting 3D diffusion mode, enabling exceptional reversibility during Zn plating/stripping. The as-prepared anode therefore achieves an ultralong lifespan over 3000 h along with high rate capability even at 40 mA cm−2 (depth of discharge ≈ 68.4%). Furthermore, its practical feasibility is validated by a superior capacity retention of 92.5% after 1000 cycles for full cell and high capacity of 112.2 mAh g−1 for pouch cell. This study opens up new opportunities for the development of dendrite-free anodes for aqueous metal batteries.

Minimal wave speed and spreading speed in predator-prey systems with stage structure

This article studies the minimal wave speed of traveling wave solutions as well as spreading speed in predator-prey systems. The model divides the prey into the immaturity and maturity, and the predator feeds on the immature individuals. For the traveling wave solutions connecting the predator-free equilibrium with the coexistence state, we consider two different diffusion modes. For both modes, the minimal wave speed is shown by presenting the existence or nonexistence of nontrivial traveling wave solutions for all wave parameters. When the diffusion is local, the minimal wave speed is the spreading speed of the corresponding initial value problem, in which the initial condition implies that the predator is the invader while the prey is the aborigine in the whole habitat. Under the persistence assumption in the corresponding kinetic systems, our conclusion coincides with the fact that the diffusion of the prey may have less effect on the invasion ability of the predator.

The evolutionary process of W-V mixed dumbbell in tungsten crystals: A study about W-V alloy as a plasma-facing material in fusion devices

Alloying is widely used to improve the radiation resistance of plasma-facing materials. The first-principles method based on density function theory was used in this work to study the stability and mobility properties of the W-V mixed dumbbell pair. The diffusion of monovacancy and recovery of mixed dumbbell pairs were also studied. The rotations and diffusion results indicated that the W-V mixed dumbbell pair diffusions are favored in two/three-dimensional motion because of low energy barriers. And the results are also suggested the mixed dumbbell lowers the diffusion energy barriers of the monovacancy. New vacancy diffusion modes were also observed along the 〈110〉 direction during the simulation. Besides, the addition of V may also moderate the diffusion of W SIA in 〈111〉 direction.

Dynamic behaviors of interfacial oxides and elements during the ultrasonic-assisted diffusion bonding of 6063Al alloys

Efficiently breaking the oxide layer and rapidly diffusing of elements at low-temperature has been a longstanding goal in the diffusion bonding (DB) of Al alloys. To break the interfacial oxide layers and accelerate atomic diffusion, ultrasound energy was introduced during the DB of 6063Al. A full Zn–Al eutectoid joint was manufactured via a pure Zn interlayer at 360 °C in atmospheric by an ultrasonic-assisted diffusion bonding (U-DB) at only an ultrasonic vibration of10 min. During U-DB, brittle cracks were formed in the interfacial oxide layers due to high strain rate induced by ultrasonic action. Zn diffused into Al alloy through the brittle cracks in oxide layers via “subcutaneous diffusion,” forming a Zn–Al eutectoid diffusion region between the Al alloy and oxide layer. The oxide fragments irregularly migrated to the center of the joint due to Kirkendall effect and ultrasonic action, finally dispersed in the bonded metal. The bonded metal finally transformed as a full Zn–Al eutectoid phase after consuming interlayer. The shear strength of the Zn–Al eutectoid joint reached 82.6 MPa. The Zn–Al mutual diffusion coefficient of U-DB at 360 °C was ∼0.6 μm2/s, which was about 20 times higher than the thermal diffusion coefficient under same temperature condition. Additionally, the mechanism of ultrasonic-assisted diffusion based on the strain-driven diffusion mode was discussed in detail.

Effect of polyelectrolyte (PAA) on the dynamics of weakly charged microemulsion droplets in acidic medium

We use the dynamic light scattering technique (DLS) to study the dynamic behavior of complex constituted by weakly charged microemulsion in the presence of polyelectrolyte. We investigated the impact of adding oppositely charged polyacid (PAA), which is a pH-dependent polyelectrolyte, on the dynamics of charged microemulsion nanodroplets in an acidic medium at pH = 4.5 when the polyacrylic acid are partially charged. In a diluted regime, two diffusive relaxation modes are seen when adding (upon addition) the polyacrylic acid PAA to the microemulsion nanodroplets due to collective diffusion and self-diffusion fluctuations. In the concentrated regime, we observed three diffusive relaxation modes when charged microemulsion nanodroplets complexed with oppositely charged polyacrylic acid. We attribute the two first relaxation modes to the collective diffusion (fluctuation of concentration) and self-diffusion of the microemulsion nanodroplets. The third mode which is a slower relaxation mode; we attribute this relaxation process to the motion of the network formed by the polyacid PAA and microemulsion nanodroplets, or “breathing mode” of the network.

Fast diffusion kinetics improves electron transfer regime selectivity to boost peroxymonosulfate activation

Electron transfer process (ETP) is barely influenced by half-life and migration distance in peroxymonosulfate (PMS) activation because it directly extracts electrons from pollutants for oxidation. However, the enhanced ETP selectivity is still challenging due to the poor mass transfer of PMS and pollutant. In this work, 2D porous N-doped carbon (PNC) with high reactant diffusion kinetics and multiple diffusion modes was designed to induce the interlayer confinement for efficient PMS activation with elevated ETP selectivity. Taking tetrabromobisphenol A as target pollutant, the confined PNC/PMS system achieved significantly enhanced PMS activation performance with the selectivity of ETP up to 97.8%. The vertical mass transfer of reactants into the inner interlayer space of the catalysts was proved to be promoted by the construction of molecule tunnels according to a diffusion model. Density functional theory calculations indicated that the subsequently triggered interlayer confinement facilitated the co-adsorption of PMS/pollutant on the interlayer surface and narrowed the energy gap of charge migration, resulting in enhanced PMS activation performance and ETP selectivity. Benefiting from the almost 100 % ETP selectivity, the confined PNC/PMS system exhibited substantially increased PMS utilization efficiency, admirable anti-interference ability towards various water matrices as well as long-term stability in a continuous-flow reactor. This work provides a new protocol for efficient and selective PMS activation by interlayer confinement in water remediation.

Transient motion classification and segment analysis of diffusive trajectories of G proteins and coupled-receptors in a living cell

The molecular movement in single particle tracking (SPT) experiments shows a crucial role of diffusion in many biological processes such as signaling, cellular organization, transport mechanisms, and more. The SPT analysis detects not only classical Brownian motion but diffusion with other features. These include directed diffusion and confined motion. The behavior remains a challenging problem for several reasons. Due to the action of many physical processes, random trajectories of cellular molecules are segmented in different diffusive modes. Often their study requires sophisticated algorithms for the analysis of statistical properties. In this paper we consider the segment analysis for trajectories of G proteins and coupled-receptors in living cells. Their movement is often transient and switches among free diffusion, confined diffusion, directed diffusion, and immobility. Moreover, the confined segments can have both Gaussian and non-Gaussian statistics. The types of alternation of diffusive modes along the trajectories of G proteins and coupled-receptors are analyzed.

Holographic interferometric vibration measurement based on photorefractive crystal in diffusion mode

A dynamic holographic vibration measurement system based on a photorefractive crystal of BSO in diffuse mode without the need for an external electric field, which allows for simultaneous measurement of in-plane and out-of-plane high-frequency vibrations, is studied theoretically and experimentally in this work. By adjusting the polarization state of the reference beam, the system introduces a necessary additional phase shift of π/2 to achieve highly sensitive and linear demodulation of small phase-to-intensity vibration signals. Both theoretical analysis and experimental results confirm the system's practicality and safety, demonstrating its ability to accurately detect vibrations without the risks associated with high-voltage drift mode operation. Furthermore, some factors that affect measurement sensitivity were analyzed. The results of measuring in-plane and out-of-plane vibrations showcase the system's superior performance in measuring submicron magnitude vibrations at the MHz level.

Adsorption of Bichromate and Arsenate Anions by a Sorbent Based on Bentonite Clay Modified with Polyhydroxocations of Iron and Aluminum by the "Co-Precipitation" Method.

The physicochemical properties of natural bentonite and its sorbents were studied. It has been established the modification of natural bentonites using polyhydroxoxides of iron (III) (mod.1_Fe_5-c) and aluminum (III) (mod.1_Al_5-c) by the "co-precipitation" method led to changes in their chemical composition, structure, and sorption properties. It was shown that modified sorbents based on natural bentonite are finely porous (nanostructured) objects with a predominance of pores of 1.5-8.0 nm in size. The modification of bentonite with iron (III) and aluminum compounds by the "co-precipitation" method also leads to an increase in the sorption capacity of the obtained sorbents with respect to bichromate and arsenate anions. A kinetic analysis showed that, at the initial stage, the sorption process was controlled by an external diffusion factor, that is, the diffusion of the sorbent from the solution to the liquid film on the surface of the sorbent. The sorption process then began to proceed in a mixed diffusion mode when it limited both the external diffusion factor and the intra-diffusion factor (diffusion of the sorbent to the active centers through the system of pores and capillaries). To clarify the contribution of the chemical stage to the rate of adsorption of bichromate and arsenate anions by the sorbents under study, kinetic curves were processed using equations of chemical kinetics (pseudo-first-order, pseudo-second-order, and Elovich models). It was found that the adsorption of the studied anions by the modified sorbents based on natural bentonite was best described by a pseudo-second-order kinetic model. The high value of the correlation coefficient for the Elovich model (R2 > 0.9) allows us to conclude that there are structural disorders in the porous system of the studied sorbents, and their surfaces can be considered heterogeneous. Considering that heterogeneous processes occur on the surface of the sorbent, it is natural that all surface properties (structure, chemical composition of the surface layer, etc.) play an important role in anion adsorption.

Acoustic response of patchy-saturated porous media: Coupling Biot's poroelasticity equations for mono- and biphasic pore fluids.

Patchy saturation is a term used in the seismic prospecting literature to describe the state of a geological formation in which two immiscible pore fluids prevail in mesoscopic-scale clusters. If the pore fluids have contrasting compressibilities, wave-induced fluid pressure diffusion (FPD) processes may induce significant attenuation and velocity dispersion on seismic waves. Biot's monophasic poroelasticity theory is widely used to model the seismic response of rocks containing binary patches of two immiscible pore fluids. Even though effective fluid approximations may help to represent more realistic partially saturated patches using Biot's monophasic equations, the so inferred dissipation may not be representative of actual biphasic FPD phenomena. In this work, Biot's equations for mono- and biphasic fluids are combined to model FPD processes in porous media, comprising fully and partially saturated patches. An analytical solution for one-dimensional layered patchy-saturated media is presented which permits to explain some, as of yet enigmatic, experimentally observed characteristics such as increased seismic attenuation and stiffening effects occurring at low saturations. The results show that the existence of an additional diffusive wave mode within partially saturated patches may render conventional binary and effective fluid approaches incorrect and error prone.