Diffusive Motion Research Articles

Ribosome hyper-swivel head domain motions are required for translocation and resetting.

Translocation of messenger RNA (mRNA) and transfer RNA (tRNA) substrates through the ribosome during protein synthesis, an exemplar of directional molecular movement in biology, entails a complex interplay of conformational, compositional, and chemical changes. The molecular determinants of early translocation steps have been investigated rigorously. However, the elements enabling the ribosome to complete translocation and reset for subsequent protein synthesis reactions remain poorly understood. Here, we have combined molecular simulations with single-molecule fluorescence resonance energy transfer imaging to gain insights into the rate-limiting events of the translocation mechanism.1 We find that diffusive motions of the ribosomal small subunit head domain to hyper-swivelled positions, governed by universally conserved rRNA, can maneuver the mRNA and tRNAs to their fully translocated positions. Subsequent engagement of peptidyl-tRNA and disengagement of deacyl-tRNA from mRNA, within their respective small subunit binding sites, facilitate the ribosome resetting mechanism after translocation has occurred to enable protein synthesis to resume.1Nishima, et al., Nucleic Acids Research, Volume 50, 8302-8320, 2022.

Tunable and optimal interlayer spacing of 2D VS2 with high response and fast recovery for NO2 detection

Due to the restricted interlayer spacing, the large active regions between the interlayers of most two-dimensional (2D) materials are difficult to be utilized efficiently, which greatly limits their performance for gas sensing. Herein, a novel NO2 sensor based on expanded VS2 (abbreviated as VS2-E) is reported by regulating the interlayer spacing to 11.6 Å (VS2-E3). Compared with VS2-N (natural interlayer spacing of 5.8 Å), VS2-E1 (10.0 Å) and VS2-E2 (10.2 Å), the increased interlayer spacing of the VS2-E3 significantly improved its NO2 sensing performance. With a high response (∼2.77–10 ppm NO2), rapid response/recovery speed (∼10/10 s), low detection limits (distinct response to 200 ppb NO2), and good stability at 100 °C, the sensor based on VS2-E3 demonstrates excellent NO2 sensing qualities. In addition, the interlayer sensing mechanism is explained by simulating the diffusion movement of NO2 between different spacing VS2 interlayers. Enlarging the interlayer space boosts the interaction of VS2 and NO2, increases the diffusion coefficient of NO2 and accelerates their desorption between interlayers, thereby evidently enhancing the response intensity and the recovery speed. These results suggest that VS2-E3 has promising prospect in the realm of low-concentration and rapid NO2 detection.

Achieving exceptional high-temperature resistant Al matrix composites via two-dimensional BN pinning grain rotation

Aiming to develop a new generation of lightweight, high-strength, and heat-resistant structural materials, BNNSs/Al composites were fabricated based on powder metallurgy process. TEM results demonstrated that BNNSs were mainly distributed at grain boundaries, forming BNNSs-AlN-Al transition interface during the sintering process. The Al grains of BNNSs/Al composites maintained stable at temperatures up to 573 K and achieved unprecedented high-temperature tensile strength of about 329 ± 6 MPa. The experimental and simulation results revealed that the reduction of tensile strength of Al matrix at high temperature was due to the decrease of grain boundary stability, which led to grain rotation and stress concentration near grain boundary. However, BNNSs with unique two-dimensional morphology can effectively suppress grain boundary diffusion and grain boundary motion, which retarded the softening of Al grains. More importantly, the strongly bonded BNNSs-AlN-Al transition interface can enhance drag effect of BNNSs, which effectively limits the grain rotation during the high-temperature deformation and stimulates the coordinated intragranular plastic deformation of Al grains. Thus, the BNNSs/Al composite maintained a high level of deformability and efficient load transfer even at 573 K. Our findings provide a promising route to extending the application of Al matrix composites in the field of high-temperature structures.

Localized transverse flow measurement with dynamic light scattering line-scan OCT.

A novel decorrelation-based approach for measuring localized transverse flow velocity using line-scan (LS) optical coherence tomography (OCT) is proposed. The new approach allows for separation of the flow velocity component along the line-illumination direction of the imaging beam from other orthogonal velocity components, from particle diffusion motion, and from noise-induced distortion in the OCT signal's temporal autocorrelation. The new method was verified by imaging flow in a glass capillary and a microfluidic device and mapping the spatial distribution of the flow velocity within the beam's illumination plane. This method can be extended in the future to map the three-dimensional flow velocity fields for both ex-vivo and in-vivo applications.

Mexican jumping beans exhibit diffusive motion.

Organisms across many lengthscales generate specific strategies for motion that are crucial to their survival. Here, we detail the motion of a nontraditional organism, the Mexican jumping bean, where a larva encapsulated within a seed blindly moves the seed in search of shade. Using image analysis techniques, we quantitatively describe the motion of these objects as active particles. From this experimental data, we build a computational simulation that quantitatively captures the motion of these beans. And we further evaluate the effectiveness of using the observed diffusive strategy to find shade, suggesting that the random walk is an advantageous strategy for survival.

Incoherent Neutron Scattering and Terahertz Time-Domain Spectroscopy on Protein and Hydration Water

Incoherent inelastic and quasi-elastic neutron scattering (INS) and terahertz time-domain spectroscopy (THz-TDS) are spectroscopy methods that directly detect molecular dynamics, with an overlap in the measured energy regions of each method. Due to the different characteristics of their probes (i.e., neutron and light), the information obtained and the sample conditions suitable for each method differ. In this review, we introduce the differences in the quantum beam properties of the two methods and their associated advantages and disadvantages in molecular spectroscopy. Neutrons are scattered via interaction with nuclei; one characteristic of neutron scattering is a large incoherent scattering cross-section of a hydrogen atom. INS records the auto-correlation functions of atomic positions. By using the difference in neutron scattering cross-sections of isotopes in multi-component systems, some molecules can be selectively observed. In contrast, THz-TDS observes the cross-correlation function of dipole moments. In water-containing biomolecular samples, the absorption of water molecules is particularly large. While INS requires large-scale experimental facilities, such as accelerators and nuclear reactors, THz-TDS can be performed at the laboratory level. In the analysis of water molecule dynamics, INS is primarily sensitive to translational diffusion motion, while THz-TDS observes rotational motion in the spectrum. The two techniques are complementary in many respects, and a combination of the two is very useful in analyzing the dynamics of biomolecules and hydration water.

Unidirectional motion of C60-based nanovehicles using hybrid substrates with temperature gradient

With the synthesis of nanocar structures the idea of transporting energy and payloads on the surface became closer to reality. To eliminate the concern of diffusive surface motion of nanocars, in this study, we evaluate the motion of C60 and C60-based nanovehicles on graphene and hexagonal boron-nitride (BN) surfaces using molecular dynamics simulations and potential energy analysis. Utilizing the graphene-hBN hybrid substrate, it has been indicated that C60 is more stable on boron-nitride impurity regions in the hybrid substrate and an energy barrier restricts the motion to the boron-nitride impurity. Increasing the temperature causes the molecule to overcome the energy barrier frequently. A nanoroad of boron-nitride with graphene sideways is designed to confine the surface motion of C60 and nanovehicles at 300 K. As expected, the motion of all surface molecules is limited to the boron-nitride nanoroads. Although the motion is restricted to the boron-nitride nanoroad, the diffusive motion is still noticeable in lateral directions. To obtain the unidirectional motion for C60 and nanocars on the surface, a temperature gradient is applied to the surface. The unidirectional transport to the nanoroad regions with a lower temperature occurs in a short period of time due to the lower energies of molecules on the colder parts.

CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos

BackgroundUnderstanding gene transcription and mRNA-protein (mRNP) dynamics in single cells in a multicellular organism has been challenging. The catalytically dead CRISPR-Cas13 (dCas13) system has been used to visualize RNAs in live cells without genetic manipulation. We optimize this system to track developmentally expressed mRNAs in zebrafish embryos and to understand features of endogenous transcription kinetics and mRNP export.ResultsWe report that zygotic microinjection of purified CRISPR-dCas13-fluorescent proteins and modified guide RNAs allows single- and dual-color tracking of developmentally expressed mRNAs in zebrafish embryos from zygotic genome activation (ZGA) until early segmentation period without genetic manipulation. Using this approach, we uncover non-synchronized de novo transcription between inter-alleles, synchronized post-mitotic re-activation in pairs of alleles, and transcriptional memory as an extrinsic noise that potentially contributes to synchronized post-mitotic re-activation. We also reveal rapid dCas13-engaged mRNP movement in the nucleus with a corralled and diffusive motion, but a wide varying range of rate-limiting mRNP export, which can be shortened by Alyref and Nxf1 overexpression.ConclusionsThis optimized dCas13-based toolkit enables robust spatial-temporal tracking of endogenous mRNAs and uncovers features of transcription and mRNP motion, providing a powerful toolkit for endogenous RNA visualization in a multicellular developmental organism.

Local electronic structure of dilute hydrogen in β−Ga2O3 probed by muons

The local electronic structure of muons (Mu) as dilute pseudo-hydrogen in single-crystalline $\beta$-Ga$_2$O$_3$ has been studied by the muon spin rotation/relaxation ($\mu$SR). High-precision measurements over a long time range of $\sim$25 $\mu$s have clearly identified two distinct Mu states: a quasi-static Mu (Mu$_1$) and fast-moving Mu (Mu$_2$). By comparing this result with predictions from the recently established ambipolarity model, these two states are respectively attributed to the relaxed-excited states associated with the donor ($E^{+/0}$) and acceptor ($E^{-/0}$) levels predicted by density functional theory (DFT) calculations for the interstitial H. Furthermore, the local electronic structure of Mu$_1$ is found to be an OMu-bonded state with three-coordinated oxygen. The structure is almost identical with the thermal equilibrium state of H, and it is found to function as an electron donor. The other Mu$_2$ is considered to be in the hydride state (Mu$^-$) from the ambipolarity model, suggesting that it is in fast diffusion motion through the short-lived neutral state due to the charge exchange reaction with conduction electrons (Mu$^0+e^-\rightleftarrows$Mu$^-$).

Activation energy on three-dimensional Casson nanofluid motion via stretching sheet: Implementation of Buongiorno’s model

In this work, the statistical (“Numerical”) modelling of activation energy and chemical reaction on non-Newtonian liquid motion via stretching sheet (SS) were performed, analysed statistically, employing the shooting technique. The convective boundary conditions are considered on Casson liquid (“non-Newtonian”) motion with couple stress SS. The behaviour of thermophoresis diffusion and Brownian motion via a special effect of non-linear thermal radiation are assuming in temperature equation for liquid motion. This analysis highly governing nonlinear system of D. Es of velocity, temperature, concentration and activation are simulated via iterative scheme encoded with MATLAB programming language. The geometric model is described bvp 4th order of R-K-F (“Range-Kutta-Fehlberg”) scheme. We found that, 35% of heat transfer rate produces in motion of couple stress Casson nanofluid and the activation energy released 28% of mass transfer rate at stretching surface. A comparative result of linear and nonlinear SS presented via various dimensionless parameters on graphs and tables.

Charmed Galaxies

The quest for finding the origins of cosmic rays has been going on for many decades. Cosmic rays as charged particles react to cosmic magnetic fields and typically travel in diffusive motion through the Universe. Their imprint on Earth therefore holds little information on their origin, and finding the sources of cosmic rays is a major challenge. The question of their origins has been a leading questions in physics and astrophysics in the past decades. To solve this riddle, a multimessenger approach is used, including cosmic-ray interaction products in the searches, specifically gamma-rays and neutrinos produced in the resulting particle showers. In this multimessenger picture, the detection of high-energy neutrinos from the cosmos by IceCube - as a unique tracer of cosmic rays - is an important piece of the puzzle. First evidence for neutrino emission from the active galaxies TXS0506+056 and NGC1068 indicates that a significant fraction comes from such sources. In this paper, the intriguing fact that gamma-rays seem to be absorbed in these sources discussed. The possibility of neutrinos being produced in regions of high photon or gas densities, together with the possibility of in the future revealing neutrinos from the decay of charmed particles, will be investigated, possibly opening a window to Charmed Galaxies.

Modeling the dynamics of fine dust fraction in the surface layer of the atmosphere

We investigated the operating conditions of excavator equipment, leading to unsteady dynamics of dust far from the pollution source. Wind transport of dust takes into account the non-uniform vertical wind profile. Diffusion movement is also determined by the inhomogeneous coefficient of turbulent diffusion with a nonmonotonic dependence on height. The Earth’s surface is given by a digital elevation model, which allows calculations for a specific area with complex topography. Vertical inhomogeneities of wind and turbulence significantly change the nature of the spatial distributions of dust particles. Our approach makes it possible to determine changes in the disperse composition of particles with distance from the dust source.

Impact of pseudoplastic and dilatants behavior of Reiner-Philippoff nanofluid on peristaltic motion with heat and mass transfer analysis in a tapered channel

<abstract> <p>The main goal of this article is to investigate the effects of pseudoplastic, and dilatants behavior of non-Newtonian based nanofluid on peristaltic motion in an asymmetric tapered channel. Buongiorno's nanofluid model is considered for the study to investigate the heat and mass transfer analysis. The Reiner-Philippoff fluid model is considered to depict the non-Newtonian characteristics of the fluid. The Reiner Philippoff fluid model is the most challenging model among other non-Newtonian fluid models in such a way that shear stress and velocity gradient are non-linearly proportional to each other in this model. This model also represents the implicit relation between stress and deformation rate. The governing equations are based on the dispersion model for nanofluid which incorporates the effects of thermophoretic and Brownian diffusions. The governing equations are simplified in the account of the small Reynolds number and long wavelength assumptions. The solution of the equations is retrieved numerically by the help of built in ND-Solve function of MATHEMATICA software. The sound effects of Reiner-Philippoff based nanofluid on the behavior of velocity and temperature profiles of the fluid, streamlines, pressure gradient fields, and concentration of the nanoparticles are discussed thoroughly. The interesting behavior of Reiner-Philippoff fluid for two limiting shear stress cases when shear stress parameter is very small and very large, for which Reiner-Philippoff fluid behaves like a Newtonian fluid, is also verified. It is observed that fluid flow changes its properties from dilatants fluid to Newtonian and from Newtonian to pseudoplastic fluid by varying the Reiner-Philippoff fluid parameter. According to the findings, the temperature graphs rise against higher thermophoretic diffusion and Brownian motion parameters and falls with higher Prandtl number. Further, the impacts of all the significant parameters are investigated briefly by mathematically as well as graphically.</p> </abstract>

Squeezed Darcy-Forchheimer Casson nanofluid flow between horizontal plates under the effect of inclined magnetic field.

This article explores the properties of heat and mass transport for MHD Casson nanofluid flow between two horizontal plates by considering the Darcy-Forchheimer medium. The effects of a uniform inclined magnetic field are discussed numerically. A Darcy-Forchheimer medium is considered in the x-direction between two plates. The features of Brownian diffusive motion, porosity, friction, viscous dissipation, chemical reaction, and thermophoresis are also considered. The governing equations of the model are a system of partial differential equations. This system is converted into non-linear ordinary differential equations using suitable similarity functions. The numerical shooting technique is used to solve the attained boundary value problem. This numerical technique is endowed with the Runge-Kutta order four method and the Newton method. Graphs and tables depict different significant effects. It is observed that the effect of a magnetic field is inversely related to the fluid flow. Moreover, the porosity factor (λ) and the magnetic inclination (γ) are inversely related to the surface drag force (Cf) and the Nusselt number (Nu).

Pattern formation and collective effects during the process of the motion of magnetic nanomotors in narrow channels.

Magnetic motors can transform the energy of an external magnetic field into the kinetic energy of their motion. When moving collectively in a microchannel, the motors interact not only with each other but also with the channel walls, which leads to a wide variety of motion modes. In our work, the collective motion of magnetic Fe3O4 nanomotors in different fluids in a microchannel in a non-uniform magnetic field is studied. During the process of their motion, the nanomotors induce flow of the surrounding liquid and move together with the liquid convective flow. Due to the liquid deceleration at the channel wall, the velocity of the motors depends on the channel height. In the case of a magnetic field gradient increasing in the direction of the nanomotors' motion, the propagating front, separating the region occupied by the nanomotors, becomes unstable. By contrast, the diffusive motion of the nanomotors in the liquid prevents the development of perturbations on the front. Overall, the velocity of the nanomotors' motion and their spatial distribution were found to vary versus the channel height, magnetic field, concentration of nanomotors in the suspension, and the viscosity of the liquid.

Random Walks and Sticky Surfaces: Single-Molecule Measurements of Solute Diffusion in Ethanol/Water-Filled Anodic Alumina Nanopores

Nanoporous anodic aluminum oxide (AAO) membranes are now being explored for use in advanced chemical separations, including in the dehydration of biofuels such as ethanol. Optimization of membrane performance requires an in-depth understanding of how solvent mixtures and solutes behave under nanoconfinement. In this work, the diffusion of rhodamine B (RhB) dye through 10 and 20 nm AAO nanopores filled with a series of ethanol/water mixtures (0–33% water) is explored by fluorescence correlation spectroscopy (FCS). RhB was found to diffuse through the pores by two distinct mechanisms with mean diffusion coefficients, Df and Ds, reflecting fast and slow diffusive motions, respectively, with values that differ by nearly 2 orders of magnitude. Both Df and Ds increased with pore size and were significantly smaller than Db, the RhB diffusion coefficient in bulk liquid. Mean Df values follow a composition-dependent trend that closely mimics the viscosity dependence of Db. Additional slowing of fast RhB diffusion is attributed to both hydrodynamic drag and electrostatic interactions with the nanopore surface. The mean Ds values exhibit a different trend with increasing water content, revealing an increase in Ds and a decrease in the contributions of slow diffusion to the observed dynamics. The fluorescence time transient data used in the analysis show that the slow diffusion process is strongly hindered and likely involves frequent adsorption of RhB to the pore surfaces. These results provide new insights into the detailed molecular-level mechanisms of mass transport in nanoporous AAO membranes.

Aging resistance of polyurethane/graphene oxide composite modified asphalt: performance evaluation and molecular dynamics simulation

ABSTRACT To evaluate the effect of polymers and nanomaterials on asphalt after thermo-oxidative aging, the aging resistance of thermoplastic polyurethane modified asphalt (PU-MA), polyurethane/graphene oxide composite modified asphalt (PU/GO-MA) were discussed through experiments and molecular dynamics (MD) simulations. The molecular composition and self-healing ability of aged asphalt were investigated. Base asphalt and virgin asphalt were used as control. The aging experiments of base asphalt, PU-MA and asphalt modified with PU and different content of GO composites were carried out by rolling thin-film oven test. The differential scanning calorimeter, thermal gravimetric analyzer, viscous flow deformation, bending beam rheometer and Fourier transform infrared spectrometer tests were carried out. The molecules and cracks models of asphalt were simulated by MD. The parameters such as mean square displacement, fractional free volume, dipole moment and viscosity were calculated. The results show that PU/GO can affect the transformation among components, increase the melting temperature of asphalt, improve the migration ability of asphalt molecules, enhance the self-healing diffusion movement of asphalt molecules and reduce the energy and viscosity of aged asphalt. In brief, nano and chemical synergistic modification has effects on the properties of asphalt after aging.

Cross electromagnetic nanofluid flow examination with infinite shear rate viscosity and melting heat through Skan-Falkner wedge

Abstract This demonstration of study focalizes the melting transport and inclined magnetizing effect of cross fluid with infinite shear rate viscosity along the Skan-Falkner wedge. Transport of energy analysis is brought through the melting process and velocity distribution is numerically achieved under the influence of the inclined magnetic dipole effect. Moreover, this study brings out the numerical effect of the process of thermophoresis diffusion and Brownian motion. The infinite shear rate of viscosity model of cross fluid reveals the set of partial differential equations (PDEs). Similarity transformation of variables converts the PDEs system into nonlinear ordinary differential equations (ODEs). Furthermore, a numerical bvp4c process is imposed on these resultant ODEs for the pursuit of a numerical solution. From the debate, it is concluded that melting process cases boost the velocity of fluid and velocity ratio parameter. The augmentation of the minimum value of energy needed to activate or energize the molecules or atoms to activate the chemical reaction boosts the concentricity.

The interplay of active and passive mechanisms in slow axonal transport

A combination of intermittent active movement of transient aggregates and a paused state that intervenes between periods of active transport has been proposed to underlie the slow, directed transport of soluble proteins in axons. A component of passive diffusion in the axoplasm may also contribute to slow axonal transport, although quantitative estimates of the relative contributions of diffusive and active movement in the slow transport of a soluble protein, and in particular how they might vary across developmental stages, are lacking. Here, we propose and study a model for slow axonal transport, addressing data from bleach recovery measurements on a small, soluble, protein, choline acetyltransferase, in thin axons of the lateral chordotonal (lch5) sensory neurons of Drosophila. Choline acetyltransferase is mainly present in soluble form in the axon and catalyzes the acetylation of choline at the synapse. It does not form particulate structures in axons and moves at rates characteristic of slow component b (≈ 1–10 mm/day or 0.01–0.1 μm/s). Using our model, which incorporates active transport with paused and/or diffusive states, we predict bleach recovery, transport rates, and cargo trajectories obtained through kymographs, comparing these with experimental observations at different developmental stages. We show that changes in the diffusive fraction of cargo during these developmental stages dominate bleach recovery and that a combination of active motion with a paused state alone cannot reproduce the data. We compared predictions of the model with results from photoactivation experiments. The importance of the diffusive state in reproducing the bleach recovery signal in the slow axonal transport of small soluble proteins is our central result.

Hydrogen induced structural phase transformation in ScNiSn-based intermetallic hydride characterized by experimental and computational studies

Understanding an interrelation between the structure, chemical composition and hydrogenation properties of intermetallic hydrides is crucial for the improvement of their hydrogen storage performance. Ability to form the hydrides and to tune the thermodynamics and kinetics of their interaction with hydrogen is related to their chemical composition. Some features of the metal–hydrogen interactions remain however poorly studied, including chemistry of Sc-containing hydrides. ZrNiAl-type ScNiSn-based intermetallic hydride has been probed in the present work using a broad range of experimental techniques including Synchrotron and Neutron Powder Diffraction, 119Sn Möessbauer Spectroscopy, hydrogenation at pressures reaching several kbar H2 and hydrogen Thermal Desorption Spectroscopy studies. Computational DFT calculations have been furthermore performed. This allowed to establish the mechanism of the phase-structural transformation and electronic structure changes causing a unique contraction of the metal lattice of intermetallic alloy and the formation of the ...H-Ni-H-Ni… chains in the structure with H atoms carrying a partial negative charge. Such hydrogen absorption accompanied by a formation of a covalent Ni-H bonding and causing an unusual behavior contracts to the conventionally observed bonding mechanism of hydrogen in metals as based on the metallic bonding frequently accompanied by a jumping diffusion movement of the inserted H atoms – in contrast to the directional Metal-Hydrogen bonding observed in the present work. At high applied pressures ScNiSnH0.83 orthorhombic TiNiSi type hydride is formed with H atoms filling Sc3Ni tetrahedra. Finally, this study shows that scandium closely resembles the behavior of the heavy rare earth metal holmium.