Scaling properties of critical bubble of homogeneous nucleation in stretched fluid of square-gradient density-functional model with triple-parabolic free energy

The square-gradient density-functional model with triple-parabolic free energy is used to study homogeneous bubble nucleation in a stretched liquid to check the scaling rule for the work of formation of the critical bubble as a function of scaled undersaturation $\Delta\mu/\Delta\mu_{\rm spin}$, the difference in chemical potential $\Delta\mu$ between the bulk undersaturated and saturated liquid divided by $\Delta\mu_{\rm spin}$ between the liquid spinodal and saturated liquid. In contrast to our study, a similar density-functional study for a Lennard-Jones liquid by Shen and Debenedetti [J. Chem. Phys. {\bf 114}, 4149 (2001)] found that not only the work of formation but other various quantities related to the critical bubble show the scaling rule, however, we found virtually no scaling relationships in our model near the coexistence. Although some quantities show almost perfect scaling relations near the spinodal, the work of formation divided by the value deduced from the classical nucleation theory shows no scaling in this model even though it correctly vanishes at the spinodal. Furthermore, the critical bubble does not show any anomaly near the spinodal as predicted many years ago. In particular, our model does not show diverging interfacial width at the spinodal, which is due to the fact that compressibility remains finite until the spinodal is reached in our parabolic models.Comment: 10 pages, 10 figures, Journal of Chemical Physics accepted for publicatio

Direct numerical simulation of homogeneous nucleation and growth in a phase-field model using cell dynamics method

Homogeneous nucleation and growth in a simplest two-dimensional phase field model is numerically studied using the cell dynamics method. Whole process from nucleation to growth is simulated and is shown to follow closely the Kolmogorov-Johnson-Mehl-Avrami (KJMA) scenario of phase transformation. Specifically the time evolution of the volume fraction of new stable phase is found to follow closely the KJMA formula. By fitting the KJMA formula directly to the simulation data, not only the Avrami exponent but the magnitude of nucleation rate and, in particular, of incubation time are quantitatively studied. The modified Avrami plot is also used to verify the derived KJMA parameters. It is found that the Avrami exponent is close to the ideal theoretical value m=3. The temperature dependence of nucleation rate follows the activation-type behavior expected from the classical nucleation theory. On the other hand, the temperature dependence of incubation time does not follow the exponential activation-type behavior. Rather the incubation time is inversely proportional to the temperature predicted from the theory of Shneidman and Weinberg [J. Non-Cryst. Solids {\bf 160}, 89 (1993)]. A need to restrict thermal noise in simulation to deduce correct Avrami exponent is also discussed.Comment: 9 pages, 8 figures, Journal of Chemical Physics to be publishe

Major shifts in nutrient and phytoplankton dynamics in the North Pacific Subtropical Gyre over the last 5000 years revealed by high-resolution proteinaceous deep-sea coral δ\u3csup\u3e15\u3c/sup\u3eN and δ\u3csup\u3e13\u3c/sup\u3eC records

The North Pacific Subtropical Gyre (NPSG) is the largest continuous ecosystem on Earth and is a critical component of global oceanic biogeochemical cycling and carbon sequestration. We report here multi-millennial-scale, sub-decadal-resolution records of bulk stable nitrogen (δ15N) and carbon (δ13C) isotope records from proteinaceous deep-sea corals. Data from three Kulamanamana haumeaae specimens from the main Hawaiian Islands extend the coral-based time-series back ∼5000 yrs for the NPSG and bypass constraints of low resolution sediment cores in this oligotrophic ocean region. We interpret these records in terms of shifting biogeochemical cycles and plankton community structure, with a main goal of placing the extraordinarily rapid ecosystem biogeochemical changes documented by recent coral records during the Anthropocene in a context of broader Late-Holocene variability. During intervals where new data overlaps with previous records, there is strong correspondence in isotope values, indicating that this older data represents a direct extension of Anthropocene records. These results reveal multiple large isotopic shifts in both δ15N and δ13C values similar to or larger in magnitude to those reported in the last 150 yrs. This shows that large fluctuations in the isotopic composition of export production in this region are not unique to the recent past, but have occurred multiple times through the Mid- to Late-Holocene. However, these earlier isotopic shifts occurred over much longer time intervals (∼millennial vs. decadal timescales). Further, the δ15N data confirm that the extremely low present day δ15N values recorded by deep sea corals (∼8‰) are unprecedented for the NPSG, at least within the past five millennia. Together these records reveal centennial to millennial-scale oscillations in NPSG biogeochemical cycles. Further, these data also suggest a number of independent biogeochemical regimes during which δ15N and δ13C trends were synchronous (similar to recent coral records) or distinctly decoupled. We propose that phytoplankton species composition and nutrient source changes are the dominant mechanisms controlling the coupling and de-coupling of δ15N and δ13C values, likely primarily influenced by changing oceanographic conditions (e.g., stratification vs. entrainment). The decoupling observed in the past further suggests that oceanographic forcing and ecosystem responses controlling δ15N and δ13C values of export production have been substantially different earlier in the Holocene compared to mechanisms controlling the present day system

Crystallization Mechanism of Hard Sphere Glasses

In supercooled liquids, vitrification generally suppresses crystallization. Yet some glasses can still crystallize despite the arrest of diffusive motion. This ill-understood process may limit the stability of glasses, but its microscopic mechanism is not yet known. Here we present extensive computer simulations addressing the crystallization of monodisperse hard-sphere glasses at constant volume (as in a colloid experiment). Multiple crystalline patches appear without particles having to diffuse more than one diameter. As these patches grow, the mobility in neighbouring areas is enhanced, creating dynamic heterogeneity with positive feedback. The future crystallization pattern cannot be predicted from the coordinates alone: crystallization proceeds by a sequence of stochastic micro-nucleation events, correlated in space by emergent dynamic heterogeneity.Comment: 4 pages 4 figures Accepted for publication in Phys. Rev. Lett., April 201

Carbon and nitrogen isotope fractionation of amino acids in an avian marine predator, the gentoo penguin (Pygoscelis papua)

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 5 (2015): 1278–1290, doi:10.1002/ece3.1437.Compound-specific stable isotope analysis (CSIA) of amino acids (AA) has rapidly become a powerful tool in studies of food web architecture, resource use, and biogeochemical cycling. However, applications to avian ecology have been limited because no controlled studies have examined the patterns in AA isotope fractionation in birds. We conducted a controlled CSIA feeding experiment on an avian species, the gentoo penguin (Pygoscelis papua), to examine patterns in individual AA carbon and nitrogen stable isotope fractionation between diet (D) and consumer (C) (Δ13CC-D and Δ15NC-D, respectively). We found that essential AA δ13C values and source AA δ15N values in feathers showed minimal trophic fractionation between diet and consumer, providing independent but complimentary archival proxies for primary producers and nitrogen sources respectively, at the base of food webs supporting penguins. Variations in nonessential AA Δ13CC-D values reflected differences in macromolecule sources used for biosynthesis (e.g., protein vs. lipids) and provided a metric to assess resource utilization. The avian-specific nitrogen trophic discrimination factor (TDFGlu-Phe = 3.5 ± 0.4‰) that we calculated from the difference in trophic fractionation (Δ15NC-D) of glutamic acid and phenylalanine was significantly lower than the conventional literature value of 7.6‰. Trophic positions of five species of wild penguins calculated using a multi-TDFGlu-Phe equation with the avian-specific TDFGlu-Phe value from our experiment provided estimates that were more ecologically realistic than estimates using a single TDFGlu-Phe of 7.6‰ from the previous literature. Our results provide a quantitative, mechanistic framework for the use of CSIA in nonlethal, archival feathers to study the movement and foraging ecology of avian consumers.This research was funded by National Science Foundation Office of Polar Programs [grants ANT-0125098, ANT-0739575] and the 2013 Antarctic Science Bursaries

Calibrating amino acid δ\u3csup\u3e13\u3c/sup\u3eC and δ\u3csup\u3e15\u3c/sup\u3eN offsets between polyp and protein skeleton to develop proteinaceous deep-sea corals as paleoceanographic archives.

Compound-specific stable isotopes of amino acids (CSI-AA) from proteinaceous deep-sea coral skeletons have the potential to improve paleoreconstructions of plankton community composition, and our understanding of the trophic dynamics and biogeochemical cycling of sinking organic matter in the Ocean. However, the assumption that the molecular isotopic values preserved in protein skeletal material reflect those of the living coral polyps has never been directly investigated in proteinaceous deep-sea corals. We examined CSI-AA from three genera of proteinaceous deep-sea corals from three oceanographically distinct regions of the North Pacific: Primnoa from the Gulf of Alaska, Isidella from the Central California Margin, and Kulamanamana from the North Pacific Subtropical Gyre. We found minimal offsets in the δ13C values of both essential and non-essential AAs, and in the δ15N values of source AAs, between paired samples of polyp tissue and protein skeleton. Using an essential AA δ13C fingerprinting approach, we show that estimates of the relative contribution of eukaryotic microalgae and prokaryotic cyanobacteria to the sinking organic matter supporting deep-sea corals are the same when calculated from polyp tissue or recently deposited skeletal tissue. The δ15N values of trophic AAs in skeletal tissue, on the other hand, were consistently 3–4‰ lower than polyp tissue for all three genera. We hypothesize that this offset reflects a partitioning of nitrogen flux through isotopic branch points in the synthesis of polyp (fast turnover tissue) and skeleton (slow, unidirectional incorporation). This offset indicates an underestimation, albeit correctable, of approximately half a trophic position from gorgonin protein-based deep-sea coral skeleton. Together, our observations open the door for applying many of the rapidly evolving CSI-AA based tools developed for metabolically active tissues in modern systems to archival coral tissues in a paleoceanographic context

Amino acid isotope discrimination factors for a carnivore: physiological insights from leopard sharks and their diet

Stable isotopes are important ecological tools, because the carbon and nitrogen isotopic composition of consumer tissue reflects the diet. Measurements of isotopes of individual amino acids can disentangle the effects of consumer physiology from spatiotemporal variation in dietary isotopic values. However, this approach requires knowledge of assimilation patterns of dietary amino acids. We reared leopard sharks (Triakis semifasciata) on diets of squid (Loligo opalescens; 1250 days; control sharks) or squid then tilapia (Oreochromis sp.; switched at 565 days; experimental sharks) to evaluate consumer-diet discrimination factors for amino acids in muscle tissue. We found that control sharks exhibited lower nitrogen isotope discrimination factors (∆15N) than most previous consumer studies, potentially because of urea recycling. Control sharks also had large carbon isotope discrimination factors (∆13C) for three essential amino acids, suggesting microbial contributions or fractionation upon assimilation. Compared to controls, experimental sharks exhibited higher ∆13C values for four amino acids and ∆15N values for seven amino acids, corresponding with differences between diets in δ13C and δ15N values. This suggests that not all amino acids in experimental sharks had reached steady state, contrary to the conclusion of a bulk isotope study of these sharks. Our results imply that (1) the magnitude of a shift in dietary δ13C and δ15N values temporarily influences the appearance of discrimination factors; (2) slow turnover of amino acid isotopes in elasmobranch muscle precludes inferences about seasonal dietary changes; (3) elasmobranch discrimination factors for amino acids may be affected by urea recycling and microbial contributions of amino acids

Homogeneous nucleation of colloidal melts under the influence of shearing fields

We study the effect of shear flow on homogeneous crystal nucleation, using Brownian Dynamics simulations in combination with an umbrella sampling like technique. The symmetry breaking due to shear results in anisotropic radial distribution functions. The homogeneous shear rate suppresses crystal nucleation and leads to an increase of the size of the critical nucleus. These observations can be described by a simple, phenomenological extension of classical nucleation theory. In addition, we find that nuclei have a preferential orientation with respect to the direction of shear. On average the longest dimension of a nucleus is along the vorticity direction, while the shortest dimension is preferably perpendicular to that and slightly tilted with respect to the gradient direction.Comment: 10 pages, 8 figures, Submitted to J. Phys.: Condens. Matte

Simulation of fluid-solid coexistence in finite volumes: A method to study the properties of wall-attached crystalline nuclei

The Asakura-Oosawa model for colloid-polymer mixtures is studied by Monte Carlo simulations at densities inside the two-phase coexistence region of fluid and solid. Choosing a geometry where the system is confined between two flat walls, and a wall-colloid potential that leads to incomplete wetting of the crystal at the wall, conditions can be created where a single nanoscopic wall-attached crystalline cluster coexists with fluid in the remainder of the simulation box. Following related ideas that have been useful to study heterogeneous nucleation of liquid droplets at the vapor-liquid coexistence, we estimate the contact angles from observations of the crystalline clusters in thermal equilibrium. We find fair agreement with a prediction based on Young's equation, using estimates of interface and wall tension from the study of flat surfaces. It is shown that the pressure versus density curve of the finite system exhibits a loop, but the pressure maximum signifies the "droplet evaporation-condensation" transition and thus has nothing in common with a van der Waals-like loop. Preparing systems where the packing fraction is deep inside the two-phase coexistence region, the system spontaneously forms a "slab state", with two wall-attached crystalline domains separated by (flat) interfaces from liquid in full equilibrium with the crystal in between; analysis of such states allows a precise estimation of the bulk equilibrium properties at phase coexistence