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Journal of the Mechanical Behavior of... Jan 2024Hydrogels are a promising class of material in biomedical and industrial applications, where both the mechanical and diffusion properties play an important role. The...
Hydrogels are a promising class of material in biomedical and industrial applications, where both the mechanical and diffusion properties play an important role. The wide range of polymers that can be used and the different production methods allows these properties to be specifically tuned to a high degree for their application. Producing tough hydrogels with high stiffness has been a long-standing challenge that has recently been addressed by mineralisation methods. Those methods modify the hydrogel into one with a supporting mineral microstructure that is highly heterogeneous. This work investigates methods to determine the macroscopic diffusion behaviour of heterogeneous gels by a homogenisation method implemented in a finite element framework. This is applied to two recently developed materials by calcifying poly-dimethyl-acrylamide (PDMA) and polyacrylamide hydrogels (PAAm). The former has porous, spherical inclusions obstructing diffusion, while the latter has spherical pores enabling it. For both gels the unobstructed volume can be used as the primary parameter to tune the diffusivity. In PDMA the porosity of the obstructions is shown by multiscale analysis to give a strong, non-linear dependence of the diffusivity on the solute molecule radius. The framework is extended to other materials and comparisons are made to experimental works from the literature.
Topics: Hydrogels; Polymers; Calcification, Physiologic; Porosity; Diffusion
PubMed: 37988844
DOI: 10.1016/j.jmbbm.2023.106244 -
Journal of the American Chemical Society Aug 2022
Editorial Summary of the Comment and Responses on "Following Molecular Mobility during Chemical Reactions: No Evidence for Active Propulsion" and "Molecular Diffusivity of Click Reaction Components: The Diffusion Enhancement Question".
Topics: Diffusion
PubMed: 35919984
DOI: 10.1021/jacs.2c05873 -
Journal of Biomedical Optics Jul 2021Diffuse light is ubiquitous in biomedical optics and imaging. Understanding the process of migration of an initial photon population entering tissue to a completely...
SIGNIFICANCE
Diffuse light is ubiquitous in biomedical optics and imaging. Understanding the process of migration of an initial photon population entering tissue to a completely randomized, diffusely scattered population provides valuable insight to the interpretation and design of optical measurements.
AIM
The goal of this perspective is to present a brief, unifying analytical framework to describe how properties of light transition from an initial state to a distributed state as light diffusion occurs.
APPROACH
First, measurement parameters of light are introduced, and Monte Carlo simulations along with a simple analytical expression are used to explore how these individual parameters might exhibit diffusive behavior. Second, techniques to perform optical measurements are considered, highlighting how various measurement parameters can be leveraged to subsample photon populations.
RESULTS
Simulation results reinforce the fact that light undergoes a transition from a non-diffuse population to one that is first subdiffuse and then fully diffuse. Myriad experimental methods exist to isolate subpopulations of photons, which can be broadly categorized as source- and/or detector-encoded techniques, as well as methods of tagging the tissue of interest.
CONCLUSIONS
Characteristic properties of light progressing to diffusion can be described by some form of Gaussian distribution that grows in space, time, angle, wavelength, polarization, and coherence. In some cases, these features can be approximated by simpler exponential behavior. Experimental methods to subsample features of the photon distribution can be achieved or theoretical methods can be used to better interpret the data with this framework.
Topics: Computer Simulation; Diffusion; Monte Carlo Method; Optics and Photonics; Photons
PubMed: 34216136
DOI: 10.1117/1.JBO.26.7.070601 -
Journal of Colloid and Interface Science Mar 2022The boundary layer holds the key to solve the puzzle of the unusual stability of the nanobubbles in solution. The quantitative determination on its mechanical and...
HYPOTHESIS
The boundary layer holds the key to solve the puzzle of the unusual stability of the nanobubbles in solution. The quantitative determination on its mechanical and structural properties has not been achieved due to its diffusive and dynamic nature, lack of distinctive interfaces, and difficult differentiation from bulk background. Therefore, it is necessary to investigate this boundary using more sensitive interface analysis technologies to effectively differentiate the water molecules at the interface from those in the bulk.
EXPERIMENTS
An in-situ and non-deconstructive method, solvent relaxation nuclear magnetic resonance, was used to investigate the boundary layer on bulk nanobubbles, where the relaxation rate of the water in the layer and its thickness were measured by solvent relaxation NMR and the ratio between the water molecules at the bubble interfaces and those in the bulk and the corresponding boundary layer thickness were determined.
FINDINGS
The spin-spin relaxation time for the water in the layer (∼10ms) is found to be two orders of magnitude lower than that of the free water (∼10ms). As the first attempt, the determined boundary layer thickness is around 35-45 nm and 17.0 %-8.7 % of the effective gaseous size of the nanobubbles, which increases with the decrease of the bubble diameter. As a result, a quantitative measurement model for bubble boundary layer has been established in order to better understand the interfacial properties and stabilization mechanism for bulk nanobubbles.
Topics: Diffusion; Gases; Magnetic Resonance Spectroscopy; Solvents; Water
PubMed: 34839918
DOI: 10.1016/j.jcis.2021.11.072 -
Biophysical Journal Jun 2021From nutrient uptake to chemoreception to synaptic transmission, many systems in cell biology depend on molecules diffusing and binding to membrane receptors....
From nutrient uptake to chemoreception to synaptic transmission, many systems in cell biology depend on molecules diffusing and binding to membrane receptors. Mathematical analysis of such systems often neglects the fact that receptors process molecules at finite kinetic rates. A key example is the celebrated formula of Berg and Purcell for the rate that cell surface receptors capture extracellular molecules. Indeed, this influential result is only valid if receptors transport molecules through the cell wall at a rate much faster than molecules arrive at receptors. From a mathematical perspective, ignoring receptor kinetics is convenient because it makes the diffusing molecules independent. In contrast, including receptor kinetics introduces correlations between the diffusing molecules because, for example, bound receptors may be temporarily blocked from binding additional molecules. In this work, we present a modeling framework for coupling bulk diffusion to surface receptors with finite kinetic rates. The framework uses boundary homogenization to couple the diffusion equation to nonlinear ordinary differential equations on the boundary. We use this framework to derive an explicit formula for the cellular uptake rate and show that the analysis of Berg and Purcell significantly overestimates uptake in some typical biophysical scenarios. We confirm our analysis by numerical simulations of a many-particle stochastic system.
Topics: Diffusion; Kinetics; Ligands; Models, Biological; Receptors, Cell Surface
PubMed: 33794148
DOI: 10.1016/j.bpj.2021.03.021 -
The Journal of Chemical Physics Jan 2023We develop a multiscale simulation model for diffusion of solutes through porous triblock copolymer membranes. The approach combines two techniques: self-consistent...
We develop a multiscale simulation model for diffusion of solutes through porous triblock copolymer membranes. The approach combines two techniques: self-consistent field theory (SCFT) to predict the structure of the self-assembled, solvated membrane and on-lattice kinetic Monte Carlo (kMC) simulations to model diffusion of solutes. Solvation is simulated in SCFT by constraining the glassy membrane matrix while relaxing the brush-like membrane pore coating against the solvent. The kMC simulations capture the resulting solute spatial distribution and concentration-dependent local diffusivity in the polymer-coated pores; we parameterize the latter using particle-based simulations. We apply our approach to simulate solute diffusion through nonequilibrium morphologies of a model triblock copolymer, and we correlate diffusivity with structural descriptors of the morphologies. We also compare the model's predictions to alternative approaches based on simple lattice random walks and find our multiscale model to be more robust and systematic to parameterize. Our multiscale modeling approach is general and can be readily extended in the future to other chemistries, morphologies, and models for the local solute diffusivity and interactions with the membrane.
Topics: Polymers; Solutions; Solvents; Diffusion; Computer Simulation
PubMed: 36641407
DOI: 10.1063/5.0127570 -
ACS Macro Letters Feb 2022The laser light scattering experiments were performed to explore the role of dextran (size (): 2.6, 6.9, and 17.0 nm) in compacting the plasmids (pBS: 2.9 kbps;...
The laser light scattering experiments were performed to explore the role of dextran (size (): 2.6, 6.9, and 17.0 nm) in compacting the plasmids (pBS: 2.9 kbps; pCMV-Tag2B: 4.3 kbps; and pET28a: 5.3 kbps) in vitro in the volume fraction (ϕ) range 0.01 to 0.15 of the macromolecular crowder. Two compaction regimes were observed in terms of the radius of gyration () for plasmid-dextran combinations, wherein the plasmid diffusivity is governed by normal diffusion and subdiffusion, respectively. Generalized scaling, ∼ ϕ, where represents the conformational geometry of plasmids, is reported. The plasmid conformation depends on the crowder's size, with larger conformational changes observed in the presence of smaller crowders. The second virial coefficient () and translational diffusion coefficient () indicate that entropically driven depletion of crowders, excluded volume, and interplasmid repulsive interactions govern plasmids' conformational changes, validated herein from the scaling of with molecular weight.
Topics: DNA; Dextrans; Diffusion; Molecular Conformation; Plasmids
PubMed: 35574767
DOI: 10.1021/acsmacrolett.1c00593 -
Nature Communications Jun 2023Semiconductor excitations can hybridize with cavity photons to form exciton-polaritons (EPs) with remarkable properties, including light-like energy flow combined with...
Semiconductor excitations can hybridize with cavity photons to form exciton-polaritons (EPs) with remarkable properties, including light-like energy flow combined with matter-like interactions. To fully harness these properties, EPs must retain ballistic, coherent transport despite matter-mediated interactions with lattice phonons. Here we develop a nonlinear momentum-resolved optical approach that directly images EPs in real space on femtosecond scales in a range of polaritonic architectures. We focus our analysis on EP propagation in layered halide perovskite microcavities. We reveal that EP-phonon interactions lead to a large renormalization of EP velocities at high excitonic fractions at room temperature. Despite these strong EP-phonon interactions, ballistic transport is maintained for up to half-exciton EPs, in agreement with quantum simulations of dynamic disorder shielding through light-matter hybridization. Above 50% excitonic character, rapid decoherence leads to diffusive transport. Our work provides a general framework to precisely balance EP coherence, velocity, and nonlinear interactions.
Topics: Diagnostic Imaging; Diffusion; Hybridization, Genetic; Motion; Phonons
PubMed: 37391396
DOI: 10.1038/s41467-023-39550-x -
The Journal of Physical Chemistry. B May 2022We demonstrate a novel application of the time-temperature superposition (TTS) principle to predict solute diffusivity in glassy polymers using atomistic molecular...
We demonstrate a novel application of the time-temperature superposition (TTS) principle to predict solute diffusivity in glassy polymers using atomistic molecular dynamics simulations. Our TTS approach incorporates the Debye-Waller factor ⟨⟩, a measure of solute caging, along with concepts from thermodynamic scaling methods, allowing us to balance contributions to the dynamics from temperature and ⟨⟩ using adjustable parameters. Our approach rescales the solute mean-squared displacement curves at several temperatures into a master curve that approximates the diffusive dynamics at a reference temperature, effectively extending the simulation time scale from nanoseconds to seconds and beyond. With a set of "universal" parameters, this TTS approach predicts with reasonable accuracy in a broad range of polymer/solute systems. Using TTS greatly reduces the computational cost compared to standard MD simulations. Thus, our method offers a means to rapidly and routinely provide order-of-magnitude estimates of using simulations.
Topics: Diffusion; Molecular Dynamics Simulation; Polymers; Solutions; Temperature
PubMed: 35583328
DOI: 10.1021/acs.jpcb.2c00057 -
ACS Nano Jul 2022Colocalization of cascade enzymes is broadly discussed as a phenomenon that can boost the cascade reaction throughput, although a direct experimental verification is...
Colocalization of cascade enzymes is broadly discussed as a phenomenon that can boost the cascade reaction throughput, although a direct experimental verification is often challenging. This is mainly due to difficulties in establishing proper size regimes and in the analytical quantification of colocalization effect with adequate experimental systems and simulations. In this study, by taking advantage of reversible DNA-directed colocalization of enzymes on microspheres, we established a cascade system that can be used to directly evaluate the colocalization effect with exactly the same experimental settings except for the state of enzyme dispersion. In the regime of highly dilute microspheres of particular sizes, the colocalized cascade shows enhanced activity compared with the freely diffusing cascade, as evidenced by a shortened lag phase in the time-course production. Reaction-diffusion modeling reveals that the enhancement can be ascribed to the initial accumulation of intermediate substrate around the colocalized enzymes and is found to be carrier-size-dependent. This work demonstrates the dependence of the colocalization effect of enzyme cascades on an interplay of nano- and microscales, lending theoretical support to the rational design of highly efficient multienzyme catalysts.
Topics: Kinetics; Diffusion; DNA; Catalysis; Enzymes
PubMed: 35549238
DOI: 10.1021/acsnano.2c00475