Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Channel-length dependence of particle diffusivity in confinement.

ABSTRACT: Understanding the diffusive behavior of particles and large molecules in channels is of fundamental importance in biological and synthetic systems, such as channel proteins, nanopores, and nanofluidics. Although theoretical and numerical modelings have suggested some solutions, these models have not been fully supported with direct experimental measurements. Here, we demonstrate that experimental diffusion coefficients of particles in finite open-ended channels are always higher than the prediction based on the conventional theoretical model of infinitely long channels. By combining microfluidic experiments, numerical simulations, and analytical modeling, we show that diffusion coefficients are dependent not only on the radius ratio but also on the channel length, the boundary conditions of the neighboring reservoirs, and the compressibility of the medium.

SUBMITTER: Tottori S

PROVIDER: S-EPMC8151877 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Channel-length dependence of particle diffusivity in confinement.

Tottori Soichiro S Misiunas Karolis K Tshitoyan Vahe V Keyser Ulrich F UF

Soft matter 20210501 20

Understanding the diffusive behavior of particles and large molecules in channels is of fundamental importance in biological and synthetic systems, such as channel proteins, nanopores, and nanofluidics. Although theoretical and numerical modelings have suggested some solutions, these models have not been fully supported with direct experimental measurements. Here, we demonstrate that experimental diffusion coefficients of particles in finite open-ended channels are always higher than the predict ...[more]

PMID: 34037064

Similar Datasets

Kirkwood diffusivity of long semiflexible chains in nanochannel confinement.

Project description:We compute the axial diffusivity of asymptotically long semiflexible polymers confined in square channels. Our calculations employ the Kirkwood approximation of the mobility tensor by combining computational fluid dynamics (CFD) calculations of the hydrodynamic tensor in channel confinement with pruned-enriched Rosenbluth method (PERM) simulations of a discrete wormlike chain model. Three key results emerge from our study. First, for the classic de Gennes regime, we confirm that Brochard and de Gennes' blob theory correctly predicts the scaling of the axial diffusivity, contrary to the conclusions of previous analyses. Second, for the extended de Gennes regime, we show that a modified blob theory, which has been used to incorporate the effect of local stiffness on DNA diffusion in nanoslits, explains the deviation from the prediction of classic blob theory for diffusion in nanochannels. Third, we provide a calculation similar to the modified blob theory to explain the relative insensitivity of the diffusivity to channel size for channels between the extended de Gennes regime and the Odijk regime, which is the most relevant regime for experiments and technological applications of DNA confinement in nanochannels. Our results are not only relevant to the dynamics of confined semiflexible polymers such as DNA, but also reveal interesting analogies between confinement in channels and slits.

| S-EPMC4494130 | biostudies-literature

Revisiting blob theory for DNA diffusivity in slitlike confinement.

Project description:Blob theory has been widely applied to describe polymer conformations and dynamics in nanoconfinement. In slit confinement, blob theory predicts a scaling exponent of 2/3 for polymer diffusivity as a function of slit height, yet a large body of experimental studies using DNA produce a scaling exponent significantly less than 2/3. In this work, we develop a theory that predicts that this discrepancy occurs because the segment correlation function for a semiflexible chain such as DNA does not follow the Flory exponent for length scales smaller than the persistence length. We show that these short length scale effects contribute significantly to the scaling for the DNA diffusivity, but do not appreciably affect the scalings for static properties. Our theory is fully supported by Monte Carlo simulations, quantitative agreement with DNA experiments, and the results reconcile this outstanding problem for confined polymers.

| S-EPMC3670611 | biostudies-literature

Fast and precise inference on diffusivity in interacting particle systems.

Project description:Particle systems made up of interacting agents is a popular model used in a vast array of applications, not the least in biology where the agents can represent everything from single cells to animals in a herd. Usually, the particles are assumed to undergo some type of random movements, and a popular way to model this is by using Brownian motion. The magnitude of random motion is often quantified using mean squared displacement, which provides a simple estimate of the diffusion coefficient. However, this method often fails when data is sparse or interactions between agents frequent. In order to address this, we derive a conjugate relationship in the diffusion term for large interacting particle systems undergoing isotropic diffusion, giving us an efficient inference method. The method accurately accounts for emerging effects such as anomalous diffusion stemming from mechanical interactions. We apply our method to an agent-based model with a large number of interacting particles, and the results are contrasted with a naive mean square displacement-based approach. We find a significant improvement in performance when using the higher-order method over the naive approach. This method can be applied to any system where agents undergo Brownian motion and will lead to improved estimates of diffusion coefficients compared to existing methods.

| S-EPMC10060353 | biostudies-literature

Confinement suppresses instabilities in particle-laden droplets.

Project description:Tiny concentrations of suspended particles may alter the behavior of an evaporating droplet remarkably, leading to partially viscous and partially elastic dynamical characteristics. This, in turn, may lead to some striking mechanical instabilities, such as buckling and rupture. Here, we report certain non-trivial implications of the consequent morpho-dynamics (macro to nano scales), when such an evaporating droplet is encapsulated in a confined environment. Compared to unconfined scenario, we report non-intuitive suppression of rupturing beyond a critical confinement. We attribute this to confinement-induced dramatic alteration in the evaporating flux, leading to distinctive spatio-temporal characteristics of the internal flow leading to preferential particle transport and subsequent morphological transitions. We present a regime map quantifying buckling-non buckling pathways. These results may turn out to be of profound importance towards achieving desired morphological features of a colloidal droplet, by aptly tuning the confinement space, initial particle concentration, as well as the initial droplet volume.

| S-EPMC5550431 | biostudies-literature

Size-dependence of carbon nanotube confinement in catalysis.

Project description:An increasing number of studies have demonstrated that confinement within carbon nanotubes (CNTs) provides an effective approach for the modulation of catalysis. It was generally predicted that confinement became stronger with a decreasing diameter of CNTs. However, our present study here overturns the previous expectation: the influence on catalysis is not monotonic. Instead, it exhibits a volcano relationship with CNT diameter. Taking Pt catalyzing O2 conversion and Re catalyzing N2 conversion as probes using density functional theory, we show that only within tubes with an i.d. of ∼1 nm can the activity of metal clusters be enhanced to its maximum. Furthermore, confinement only enhances the catalytic activity of metals with strong intrinsic binding with reactants, whereas it is suppressed for those with weak binding. These findings shed further light on the fundamental effects of confinement on catalysis, and could guide more rational design of confined catalysts.

| S-EPMC5458720 | biostudies-literature

Thickness Dependence of the Diffusivity and Solubility of Cyclohexane in Nanoscale Bitumen Films.

Project description:Diffusivity and solubility of cyclohexane in nanoscale bitumen films coated on hydrophilic substrates at ambient conditions were studied using a gravimetric analyzer. Three substrates were used, and they are as follows: sample A, monodisperse spherical glass beads; sample B, polydisperse spherical glass beads mixed with polydisperse irregular-shape kaolin clay particles; and sample C, irregular-shape residual solids generated from a solvent extraction process of an oil sand ore. All of the above samples had a mean diameter of 150 μm. Diffusion coefficients were determined based upon the initial rates of cyclohexane absorption when bitumen-coated samples at various amounts (thicknesses) were exposed to a carrier gas with cyclohexane vapors at two levels of relative saturations (RSs), and they were found to be in the range of 10-18 to 10-16 m2/s. A double-first-order kinetics model fits well to the absorption data, suggesting that there exists a concentration gradient of polar (or nonpolar) bitumen molecules in the nanoscale films. This is because the hydrophilic substrates attract the relatively polar fraction of bitumen molecules to the region close to the substrates and the nonpolar fraction resides in the region near the free surface. As a result, the measured diffusion coefficients exhibited positive thickness dependence when the thickness of the bitumen films was at the nanoscale. The molecules near the substrates tended to diffuse slower than those in the free surface region. However, diffusivity was insensitive to the cyclohexane RS. On the other hand, the measured solubility of cyclohexane in the nanoscale bitumen films exhibited no thickness dependence but strong cyclohexane RS dependence. These results suggest that solubility is not affected by the inhomogeneous distribution of bitumen molecules in the nanoscale films and that it follows more or less Henry's law.

| S-EPMC6921648 | biostudies-literature

Particle Diffusivity and Free-Energy Profiles in Hydrogels from Time-Resolved Penetration Data.

Project description:A combined experimental and theoretical method to simultaneously determine diffusivity and free-energy profiles of particles that penetrate into inhomogeneous hydrogel systems is presented. As the only input, arbitrarily normalized concentration profiles from fluorescence intensity data of labeled tracer particles for different penetration times are needed. The method is applied to dextran molecules of varying size that penetrate into hydrogels of polyethylene-glycol chains with different lengths that are covalently cross-linked by hyperbranched polyglycerol hubs. Extracted dextran bulk diffusivities agree well with fluorescence correlation spectroscopy data obtained separately. Empirical scaling laws for dextran diffusivities and free energies inside the hydrogel are identified as a function of the dextran mass. An elastic free-volume model that includes dextran as well as polyethylene-glycol linker flexibility quantitively describes the repulsive dextran-hydrogel interaction free energy, which is of steric origin, and furthermore suggests that the hydrogel mesh-size distribution is rather broad and particle penetration is dominated by large hydrogel pores. Particle penetration into hydrogels for steric particle-hydrogel interactions is thus suggested to be governed by an elastic size-filtering mechanism that involves the tail of the hydrogel pore-size distribution.

| S-EPMC7896003 | biostudies-literature

Harmonic dependence of thermal magnetic particle imaging.

Project description:Advances in instrumentation and tracer materials are still required to enable sensitive, accurate, and localized in situ 3D temperature monitoring by magnetic particle imaging (MPI). We have developed a high-resolution magnetic particle imaging instrument and implemented a low-noise multi-harmonic lock-in detection method to observe and quantify temperature variations in iron oxide nanoparticle tracers using the harmonic ratio method for determining temperature. Using isolated harmonics for MPI and temperature imaging revealed an apparent dependence of imaging resolution on harmonic number. Thus, we present experimental and simulation studies to quantify the imaging resolution dependence on temperature and harmonic number, and directly validate the fundamental origin of MPI imaging resolution on harmonic number based on the concept of a harmonic point-spread-function.

| S-EPMC10516919 | biostudies-literature

Temperature dependence of DNA persistence length.

Project description:We have determined the temperature dependence of DNA persistence length, a, using two different methods. The first approach was based on measuring the j-factors of short DNA fragments at various temperatures. Fitting the measured j-factors by the theoretical equation allowed us to obtain the values of a for temperatures between 5°C and 42°C. The second approach was based on measuring the equilibrium distribution of the linking number between the strands of circular DNA at different temperatures. The major contribution into the distribution variance comes from the fluctuations of DNA writhe in the nicked circular molecules which are specified by the value of a. The computation-based analysis of the measured variances was used to obtain the values of a for temperatures up to 60°C. We found a good agreement between the results obtained by these two methods. Our data show that DNA persistence length strongly depends on temperature and accounting for this dependence is important in quantitative comparison between experimental results obtained at different temperatures.

| S-EPMC3045604 | biostudies-literature

How Segmental Dynamics and Mesh Confinement Determine the Selective Diffusivity of Molecules in Cross-Linked Dense Polymer Networks.

Project description:The diffusion of molecules ("penetrants") of variable size, shape, and chemistry through dense cross-linked polymer networks is a fundamental scientific problem broadly relevant in materials, polymer, physical, and biological chemistry. Relevant applications include separation membranes, barrier materials, drug delivery, and nanofiltration. A major open question is the relationship between transport, thermodynamic state, and penetrant and polymer chemical structure. Here we combine experiment, simulation, and theory to unravel these competing effects on penetrant transport in rubbery and supercooled polymer permanent networks over a wide range of cross-link densities, size ratios, and temperatures. The crucial importance of the coupling of local penetrant hopping to polymer structural relaxation and the secondary importance of mesh confinement effects are established. Network cross-links strongly slow down nm-scale polymer relaxation, which greatly retards the activated penetrant diffusion. The demonstrated good agreement between experiment, simulation, and theory provides strong support for the size ratio (penetrant diameter to the polymer Kuhn length) as a key variable and the usefulness of coarse-grained simulation and theoretical models that average over Angstrom scale structure. The developed theory provides an understanding of the physical processes underlying the behaviors observed in experiment and simulation and suggests new strategies for enhancing selective polymer membrane design.

| S-EPMC10037493 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data