Thermodynamics of bcc metals in phase-field-crystal models

We examine the influence of different forms of the free-energy functionals used in the phase-field-crystal (PFC) model, and compare them with the second-order density-functional theory (DFT) of freezing, by using bcc iron as an example case. We show that there are large differences between the PFC and the DFT and it is difficult to obtain reasonable parameters for existing PFC models directly from the DFT. Therefore, we propose a way of expanding the correlation function in terms of gradients that allows us to incorporate the bulk modulus of the liquid as an additional parameter in the theory. We show that this functional reproduces reasonable values for both bulk and surface properties of bcc iron, and therefore it should be useful in modeling bcc materials. As a further demonstration, we also calculate the grain boundary energy as a function of misorientation for a symmetric tilt boundary close to the melting transition.Peer reviewe

Phase field crystal study of symmetric tilt grain boundaries of iron

We apply the phase field crystal model to study the structure and energy of symmetric tilt grain boundaries of bcc iron in 3D. The parameters for the model are obtained by using a recently developed eight-order fitting scheme [A. Jaatinen et al., (2009)]. The grain boundary free energies we obtain from the model are in good agreement with previous results from molecular dynamics simulations and experiments

Differences in branch characteristics of Scots pine (Pinus sylvestris L.) genetic entries grown at different spacing

• We studied the differences in branch characteristics along the stems of six different genetic entries of 20 year old Scots pines (Pinus sylvestris L.) grown at different spacing (current stand density range 2000–4000 trees ha−1) in central Finland. Furthermore, we studied the phenotypic correlations between yield, wood density traits and branch characteristics. All the genetic entries had Kanerva pine (plus tree S1101) as a father tree, whereas the mother tree represented Finnish plus trees from southern, central and northern Finland. • Spacing affected all yield traits, wood density and living branch characteristics such as relative average branch diameter and relative cumulative branch area (p < 0.05). As a comparison, genetic entry affected height, while origin group (southern, central and northern ones) affected most of the studied traits. Regardless of spacing, the northern origin had, on average, the largest stem diameter and highest wood density, while the central one was the tallest one. Furthermore, average branch diameter along the stem was affected by branch age, origin group and spacing, while average branch angle was affected by branch age and genetic entry (p < 0.05). • In general the average branch size could be decreased especially in lower tree canopy by denser spacing during the early phase of the rotation, but only at the expense of tree growth. Correspondingly differences between origins are mainly related to their differences in stem growth

DDFT calibration and investigation of an anisotropic phase-field crystal model

The anisotropic phase-field crystal model recently proposed and used by Prieler et al. [J. Phys.: Condens. Matter 21, 464110 (2009)] is derived from microscopic density functional theory for anisotropic particles with fixed orientation. Further its morphology diagram is explored. In particular we investigated the influence of anisotropy and undercooling on the process of nucleation and microstructure formation from atomic to the microscale. To that end numerical simulations were performed varying those dimensionless parameters which represent anisotropy and undercooling in our anisotropic phase-field crystal (APFC) model. The results from these numerical simulations are summarized in terms of a morphology diagram of the stable state phase. These stable phases are also investigated with respect to their kinetics and characteristic morphological features.Comment: It contain 13 pages and total of 7 figure

Ectodysplasin has a dual role in ectodermal organogenesis: inhibition of Bmp activity and induction of Shh expression.

Ectodermal organogenesis is regulated by inductive and reciprocal signalling cascades that involve multiple signal molecules in several conserved families. Ectodysplasin-A (Eda), a tumour necrosis factor-like signalling molecule, and its receptor Edar are required for the development of a number of ectodermal organs in vertebrates. In mice, lack of Eda leads to failure in primary hair placode formation and missing or abnormally shaped teeth, whereas mice overexpressing Eda are characterized by enlarged hair placodes and supernumerary teeth and mammary glands. Here, we report two signalling outcomes of the Eda pathway: suppression of bone morphogenetic protein (Bmp) activity and upregulation of sonic hedgehog (Shh) signalling. Recombinant Eda counteracted Bmp4 activity in developing teeth and, importantly, inhibition of BMP activity by exogenous noggin partially restored primary hair placode formation in Eda-deficient skin in vitro, indicating that suppression of Bmp activity was compromised in the absence of Eda. The downstream effects of the Eda pathway are likely to be mediated by transcription factor nuclear factor-kappaB (NF-kappaB), but the transcriptional targets of Edar have remained unknown. Using a quantitative approach, we show in cultured embryonic skin that Eda induced the expression of two Bmp inhibitors, Ccn2/Ctgf (CCN family protein 2/connective tissue growth factor) and follistatin. Moreover, our data indicate that Shh is a likely transcriptional target of Edar, but, unlike noggin, recombinant Shh was unable to rescue primary hair placode formation in Eda-deficient skin explants

Bcc crystal-fluid interfacial free energy in Yukawa systems

We determine the orientation-resolved interfacial free energy between a body-centered-cubic (bcc) crystal and the coexisting fluid for a many-particle system interacting via a Yukawa pair potential. For two different screening strengths, we compare results from molecular dynamics computer simulations, density functional theory, and a phase-field-crystal approach. Simulations predict an almost orientationally isotropic interfacial free energy of 0.12k B T/a 2 (with k B T denoting the thermal energy and a the mean interparticle spacing), which is independent of the screening strength. This value is in reasonable agreement with our Ramakrishnan-Yussouff density functional calculations, while a high-order fitted phase-field-crystal approach gives about 2−3 times higher interfacial free energies for the Yukawa system. Both field theory approaches also give a considerable anisotropy of the interfacial free energy. Our result implies that, in the Yukawa system, bcc crystal-fluid free energies are a factor of about 3 smaller than face-centered-cubic crystal-fluid free energies.Peer reviewe

Properties of pattern formation and selection processes in nonequilibrium systems with external fluctuations

We extend the phase field crystal method for nonequilibrium patterning to stochastic systems with external source where transient dynamics is essential. It was shown that at short time scales the system manifests pattern selection processes. These processes are studied by means of the structure function dynamics analysis. Nonequilibrium pattern-forming transitions are analyzed by means of numerical simulations.Comment: 15 poages, 8 figure

Soil methane sink capacity response to a long-term wildfire chronosequence in Northern Sweden

Boreal forests occupy nearly one fifth of the terrestrial land surface and are recognised as globally important regulators of carbon (C) cycling and greenhouse gas emissions. Carbon sequestration processes in these forests include assimilation of CO2 into biomass and subsequently into soil organic matter, and soil microbial oxidation of methane (CH4). In this study we explored how ecosystem retrogression, which drives vegetation change, regulates the important process of soil CH4 oxidation in boreal forests. We measured soil CH4 oxidation processes on a group of 30 forested islands in northern Sweden differing greatly in fire history, and collectively representing a retrogressive chronosequence, spanning 5000 years. Across these islands the build-up of soil organic matter was observed to increase with time since fire disturbance, with a significant correlation between greater humus depth and increased net soil CH4 oxidation rates. We suggest that this increase in net CH4 oxidation rates, in the absence of disturbance, results as deeper humus stores accumulate and provide niches for methanotrophs to thrive. By using this gradient we have discovered important regulatory controls on the stability of soil CH4 oxidation processes that could not have not been explored through shorter-term experiments. Our findings indicate that in the absence of human interventions such as fire suppression, and with increased wildfire frequency, the globally important boreal CH4 sink could be diminished