416 research outputs found
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 , the
difference in chemical potential between the bulk undersaturated
and saturated liquid divided by 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
Steady-state nucleation rate and flux of composite nucleus at saddle point
The steady-state nucleation rate and flux of composite nucleus at the saddle
point is studied by extending the theory of binary nucleation. The
Fokker-Planck equation that describes the nucleation flux is derived using the
Master equation for the growth of the composite nucleus, which consists of the
core of the final stable phase surrounded by a wetting layer of the
intermediate metastable phase nucleated from a metastable parent phase recently
evaluated by the author [J. Chem. Phys. {\bf 134}, 164508 (2011)]. The
Fokker-Planck equation is similar to that used in the theory of binary
nucleation, but the non-diagonal elements exist in the reaction rate matrix.
First, the general solution for the steady-state nucleation rate and the
direction of nucleation flux is derived. Next, this information is then used to
study the nucleation of composite nucleus at the saddle point. The dependence
of steady-state nucleation rate as well as the direction of nucleation flux on
the reaction rate in addition to the free-energy surface is studied using a
model free-energy surface. The direction of nucleation current deviates from
the steepest-descent direction of the free-energy surface. The results show the
importance of two reaction rate constants: one from the metastable environment
to the intermediate metastable phase and the other from the metastable
intermediate phase to the stable new phase. On the other hand, the gradient of
the potential or the Kramers crossover function (the commitment or
splitting probability) is relatively insensitive to reaction rates or
free-energy surface.Comment: 12 pages, 6 figures, to be published in Journal of Chemical Physic
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
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
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
Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level
Background:
Mycobacterium avium subsp. paratuberculosis (MAP), the causative bacterium of Johne’s disease in dairy cattle, is widespread in the Canadian dairy industry and has significant economic and animal welfare implications. An understanding of the population dynamics of MAP can be used to identify introduction events, improve control efforts and target transmission pathways, although this requires an adequate understanding of MAP diversity and distribution between herds and across the country. Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions. The objective of this study was to evaluate the diversity of bovine MAP isolates in Canadian dairy herds using WGS and then determine if VNTR typing can distinguish truly related and unrelated isolates.<p></p>
Results:
Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from seven Canadian provinces, with the dominant type including over 80% of MAP isolates. VNTR typing of 527 MAP isolates identified 12 types, including “bison type” isolates, from seven different herds. At a national level, MAP isolates differed from each other by 1–2 to 239–240 SNPs, regardless of whether they belonged to the same or different VNTR types. A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd.<p></p>
Conclusions:
The presence of multiple MAP subtypes in Canada suggests multiple introductions into the country including what has now become one dominant type, an important finding for Johne’s disease control. VNTR typing often failed to identify closely and distantly related isolates, limiting the applicability of using this typing scheme to study the molecular epidemiology of MAP at a national and herd-level.<p></p>
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
Demonstration of the effect of stirring on nucleation from experiments on the International Space Station using the ISS-EML facility
The effect of fluid flow on crystal nucleation in supercooled liquids is not
well understood. The variable density and temperature gradients in the liquid
make it difficult to study this under terrestrial gravity conditions.
Nucleation experiments were therefore made in a microgravity environment using
the Electromagnetic Levitation facility on the International Space Station on a
bulk glass-forming Zr57Cu15.4Ni12.6Al10Nb5 (Vit106), as well as Cu50Zr50 and
the quasicrystal-forming Ti39.5Zr39.5Ni21 liquids. The maximum supercooling
temperatures for each alloy were measured as a function of controlled stirring
by applying various combinations of radio frequency positioner and heater
voltages to the water-cooled copper coils. The flow patterns were simulated
from the known parameters for the coil and the levitated samples. The maximum
nucleation temperatures increased systematically with increased fluid flow in
the liquids for Vit106, but stayed nearly unchanged for the other two. These
results are consistent with the predictions from the coupled-flux model for
nucleation.Comment: 21 pages, 2 figure
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