More Like this

1. Surface diffusion of a glassy discotic organic semiconductor and the surface mobility gradient of molecular glasses

   https://doi.org/10.1063/5.0079890  

   Li, Yuhui; Bishop, Camille; Cui, Kai; Schmidt, J. R.; Ediger, M. D.; Yu, Lian (March 2022, The Journal of Chemical Physics)

   Surface diffusion has been measured in the glass of an organic semiconductor, MTDATA, using the method of surface grating decay. The decay rate was measured as a function of temperature and grating wavelength, and the results indicate that the decay mechanism is viscous flow at high temperatures and surface diffusion at low temperatures. Surface diffusion in MTDATA is enhanced by 4 orders of magnitude relative to bulk diffusion when compared at the glass transition temperature T g . The result on MTDATA has been analyzed along with the results on other molecular glasses without extensive hydrogen bonds. In total, these systems cover a wide range of molecular geometries from rod-like to quasi-spherical to discotic and their surface diffusion coefficients vary by 9 orders of magnitude. We find that the variation is well explained by the existence of a steep surface mobility gradient and the anchoring of surface molecules at different depths. Quantitative analysis of these results supports a recently proposed double-exponential form for the mobility gradient: log  D( T, z) = log  D v ( T) + [log  D 0 − log  D v ( T)]exp(− z/ξ), where D( T, z) is the depth-dependent diffusion coefficient, D v ( T) is the bulk diffusion coefficient, D 0 ≈ 10 −8  m 2 /s, and ξ ≈ 1.5 nm. Assuming representative bulk diffusion coefficients for these fragile glass formers, the model reproduces the presently known surface diffusion rates within 0.6 decade. Our result provides a general way to predict the surface diffusion rates in molecular glasses. 

   more » « less
2. Empirical and Theoretical Analysis of Particle Diffusion in Mucus

   https://doi.org/10.3389/fphy.2021.594306  

   Cobarrubia, Antonio; Tall, Jarod; Crispin-Smith, Austin; Luque, Antoni (November 2021, Frontiers in Physics)

   Mucus is a complex fluid that coats multiple organs in animals. Various physicochemical properties can alter the diffusion of microscopic particles in mucus, impacting drug delivery, virus infection, and disease development. The simultaneous effect of these physicochemical properties in particle diffusion, however, remains elusive. Here, we analyzed 106 published experiments to identify the most dominant factors controlling particle diffusion in mucus. The effective diffusion—defined using a one-second sampling time window across experiments—spanned seven orders of magnitude, from 10 –5 to 10 2  μm 2 /s. Univariate and multivariate statistical analyses identified the anomalous exponent (the logarithmic slope of the mean-squared displacement) as the strongest predictor of effective diffusion, revealing an exponential relationship that explained 89 % of the variance. A theoretical scaling analysis revealed that a stronger correlation of the anomalous exponent over the generalized diffusion constant occurs for sampling times two orders of magnitude larger than the characteristic molecular (or local) displacement time. This result predicts that at these timescales, the molecular properties controlling the anomalous exponent, like particle–mucus unbinding times or the particle to mesh size ratio, would be the most relevant physicochemical factors involved in passive microrheology of particles in mucus. Our findings contrast with the fact that only one-third of the studies measured the anomalous exponent, and most experiments did not report the associated molecular properties predicted to dominate the motion of particles in mucus. The theoretical foundation of our work can be extrapolated to other systems, providing a guide to identify dominant molecular mechanisms regulating the mobility of particles in mucus and other polymeric fluids. 

   more » « less
3. The nanocaterpillar's random walk: diffusion with ligand–receptor contacts

   https://doi.org/10.1039/D1SM01544C  

   Marbach, Sophie; Zheng, Jeana Aojie; Holmes-Cerfon, Miranda (April 2022, Soft Matter)

   Particles with ligand–receptor contacts bind and unbind fluctuating “legs” to surfaces, whose fluctuations cause the particle to diffuse. Quantifying the diffusion of such “nanoscale caterpillars” is a challenge, since binding events often occur on very short time and length scales. Here we derive an analytical formula, validated by simulations, for the long time translational diffusion coefficient of an overdamped nanocaterpillar, under a range of modeling assumptions. We demonstrate that the effective diffusion coefficient, which depends on the microscopic parameters governing the legs, can be orders of magnitude smaller than the background diffusion coefficient. Furthermore it varies rapidly with temperature, and reproduces the striking variations seen in existing data and our own measurements of the diffusion of DNA-coated colloids. Our model gives insight into the mechanism of motion, and allows us to ask: when does a nanocaterpillar prefer to move by sliding, where one leg is always linked to the surface, and when does it prefer to move by hopping, which requires all legs to unbind simultaneously? We compare a range of systems (viruses, molecular motors, white blood cells, protein cargos in the nuclear pore complex, bacteria such as Escherichia coli , and DNA-coated colloids) and present guidelines to control the mode of motion for materials design. 

   more » « less
4. Nitrification in a Subterranean Estuary: An Ex Situ and In Situ Method Comparison Determines Nitrate Is Available for Discharge

   https://doi.org/10.1029/2023JG007876  

   Wilson, Stephanie_J; Song, Bongkeun; Anderson, Iris_C; Tobias, Craig_R (June 2024, Journal of Geophysical Research: Biogeosciences)

   Abstract Subterranean estuaries (STEs) form in the subsurface where fresh groundwater and seawater meet and mix. Subterranean estuaries support a variety of biogeochemical processes including those transforming nitrogen (N). Groundwater is often enriched with dissolved inorganic nitrogen (DIN), and transformations in the STE determine the fate of that DIN, which may be discharged to coastal waters. Nitrification oxidizes ammonium (NH₄⁺) to nitrate, making DIN available for N removal via denitrification. We measured nitrification at an STE, in Virginia, USA using in situ and ex situ methods including conservative mixing models informed by in situ geochemical profiles, an in situ experiment with¹⁵NH₄⁺tracer injection, and ex situ sediment slurry incubations with¹⁵NH₄⁺tracer addition. All methods indicated nitrification in the STE, but the ex situ sediment slurries revealed higher rates than both the in situ tracr experiment and mixing model estimations. Nitrification rates ranged 55.0–183.16 μmol N m⁻² d⁻¹based on mixing models, 94.2–225 μmol N m⁻² d⁻¹in the in situ tracer experiment, and 36.6–109 μmol N m⁻² d⁻¹slurry incubations. The in situ tracer experiment revealed higher rates and spatial variation not captured by the other methods. The geochemical complexity of the STE makes it difficult to replicate in situ conditions with incubations and calculations based on chemical profiles integrate over longer timescales, therefore, in situ approaches may best quantify transformation rates. Our data suggest that STE nitrification produces NO₃⁻, altering the DIN pool discharged to overlying water via submarine groundwater discharge. 

   more » « less
5. Using LAMMPS to shed light on Haven’s ratio: Calculation of Haven’s ratio in alkali silicate glasses using molecular dynamics

   https://doi.org/10.3389/fmats.2023.1123213  

   Salrin, Tyler C.; Johnson, Logan; White, Seth; Kilpatrick, Gregory; Weber, Ethan; Bragatto, Caio (February 2023, Frontiers in Materials)

   Haven and Verkerk studied the diffusion of ions in ionic conductive glasses with and without an external electric field to better understand the mechanisms behind ionic conductivity. In their work, they introduced the concept now known as Haven’s ratio (H R ), which is defined as the ratio of the tracer diffusion coefficient (D self ) of ions to the diffusion coefficient from steady-state ionic conductivity (D σ ), calculated by the Nernst–Einstein equation. D σ can be challenging to obtain experimentally because the number of charge carriers has to be implied, a subject still under discussion in the literature. Molecular dynamics (MD) allows for direct measurement of the mean squared displacement ( r 2 ) of diffusing cations, which can be used to calculate D, avoiding the definition of a charge carrier. Using MD, the authors have calculated the r 2 of three alkali ions (Li, Na, and K) at different temperatures and concentrations in silicate glass, with and without the influence of an electric field. Results found for H R generally fell close to 0.6 at lower concentrations (x = 0.1) and close to 0.3 at higher concentrations (x = 0.2 and 0.3), comparable to the literature, implying that the electric field introduces new mechanisms for the diffusion of ions and that MD can be a powerful tool to study ionic diffusion in glasses under external electric fields. 

   more » « less